A New Notosuchian from the Late Cretaceous of Brazil and the Phylogeny of Advanced Notosuchians

PubMed Central

Pol, Diego; Nascimento, Paulo M.; Carvalho, Alberto B.; Riccomini, Claudio; Pires-Domingues, Ricardo A.; Zaher, Hussam

2014-01-01

A new notosuchian crocodyliform from the Late Cretaceous Bauru Group found in the southeastern State of São Paulo (Brazil) is described here. The new taxon, Caipirasuchus stenognathus, is referred as a new species of the recently erected genus Caipirasuchus within the clade Sphagesauridae based on a phylogenetic analysis of basal mesoeucrocodylians. Caipirasuchus stenognathus is represented by an almost complete skull and lower jaw that has autapomorphic characters that distinguish it from other species of Sphagesauridae. These autapomorphies include: maxilla forming part of the orbital margin (absence of lacrimal-jugal contact), nasal with smooth depressions on the posterior region close to the contact with the maxilla and lacrimal, postorbital with posterior palpebral facet that extends posteriorly underneath the ear-flap groove, and a distinct anterior process of the medial flange of the retroarticular process. Additionally, the new taxon lacks autapomorphic features described in other sphagesaurids. The phylogenetic analysis results in a monophyletic genus Caipirasuchus, that is the sister group of a clade fomed by Sphagesaurus huenei, Caryonosuchus pricei, and Armadillosuchus arrudai. Sphagesaurids also include a basal clade formed by Adamantinasuchus navae and Yacarerani boliviensis. Other notosuchian taxa, such as Mariliasuchus amarali, Labidiosuchus amicum, Notosuchus terrestris, and Morrinhosuchus luziae are successive sister taxa of Sphagesauridae, forming a clade of advanced notosuchians that are restricted to the Late Cretaceous of South America. These results contrast with most previous phylogenetic hypotheses of the group that depicted some members of Sphagesauridae as more closely related to baurusuchids, or found Asian (e.g., Chimaerasuchus) or African (Malawisuchus, Pakasuchus) forms nested within advanced notosuchians that are, according to our analysis, endemic of the Late Cretaceous of South America. PMID:24695105

Persistent genetic signatures of colonization in Brachionus manjavacas rotifers in the Iberian Peninsula.

PubMed

Gómez, Africa; Montero-Pau, Javier; Lunt, David H; Serra, Manuel; Campillo, Sergi

2007-08-01

Recent phylogeographical assessments have consistently shown that continental zooplankton display high levels of population subdivision, despite the high dispersal capacity of their diapausing propagules. As such, there is an apparent paradox between observed cosmopolitanism in the zooplankton that is associated with long-distance dispersal, and strong phylogeographical structures at a regional scale. Such population dynamics, far from migration-drift equilibrium, have been shown in the rotifer species complex Brachionus plicatilis, a group of over a dozen species inhabiting salt lakes and coastal lagoons worldwide. Here we present the mitochondrial DNA phylogeography of one of these species, Brachionus manjavacas, in the Iberian Peninsula, where it often co-occurs with the morphologically similar species B. plicatilis sensu stricto. We obtained sequences from 233 individuals from diapausing eggs and clonal cultures from 16 lakes in the Iberian Peninsula, and a Tunisian lake. Two strongly supported deep mitochondrial DNA clades were found (A and B). Phylogenetic and nested clade analysis showed that clade A has a strong phylogeographical structure, with a strong similarity of phylogeographical patterns between B. manjavacas clade A and B. plicatilis s.s. These include (i) signatures of allopatric fragmentation between central and southern populations, and (ii) range expansions in the Iberian Peninsula, both likely to have occurred during the Pleistocene. We find evidence for a glacial refugium in the Guadiana basin. Clades A and B co-occurred in several of these lakes because of range expansion and secondary contact between both clades. The co-occurrence between B. plicatilis s.s. and B. manjavacas is not recent, and both species might have experienced similar environmental challenges during the Pleistocene. The strong correlation of genetic and geographical distance found suggests that historical events can lead to such correlation, mirroring the effects of 'isolation by distance' in equilibrium populations.

Evolutionary response to the Qinghai-Tibetan Plateau uplift: phylogeny and biogeography of Ammopiptanthus and tribe Thermopsideae (Fabaceae)

PubMed Central

Su, Zhi-Hao

2017-01-01

Previous works resolved diverse phylogenetic positions for genera of the Fabaceae tribe Thermopsideae, without a thoroughly biogeography study. Based on sequence data from nuclear ITS and four cpDNA regions (matK, rbcL, trnH-psbA, trnL-trnF) mainly sourced from GenBank, the phylogeny of tribe Thermopsideae was inferred. Our analyses support the genera of Thermopsideae, with the exclusion of Pickeringia, being merged into a monophyletic Sophoreae. Genera of Sophoreae were assigned into the Thermopsoid clade and Sophoroid clade. Monophyly of Anagyris, Baptisia and Piptanthus were supported in the Thermopsoid clade. However, the genera Thermopsis and Sophora were resolved to be polyphyly, which require comprehensive taxonomic revisions. Interestingly, Ammopiptanthus, consisting of A. mongolicus and A. nanus, nested within the Sophoroid clade, with Salweenia as its sister. Ammopiptanthus and Salweenia have a disjunct distribution in the deserts of northwestern China and the Hengduan Mountains, respectively. Divergence age was estimated based on the ITS phylogenetic analysis. Emergence of the common ancestor of Ammopiptanthus and Salweenia, divergence between these two genera and the split of Ammopiptanthus species occurred at approximately 26.96 Ma, 4.74 Ma and 2.04 Ma, respectively, which may be in response to the second, third and fourth main uplifts of the Qinghai-Tibetan Plateau, respectively. PMID:28785518

In defence of model-based inference in phylogeography

PubMed Central

Beaumont, Mark A.; Nielsen, Rasmus; Robert, Christian; Hey, Jody; Gaggiotti, Oscar; Knowles, Lacey; Estoup, Arnaud; Panchal, Mahesh; Corander, Jukka; Hickerson, Mike; Sisson, Scott A.; Fagundes, Nelson; Chikhi, Lounès; Beerli, Peter; Vitalis, Renaud; Cornuet, Jean-Marie; Huelsenbeck, John; Foll, Matthieu; Yang, Ziheng; Rousset, Francois; Balding, David; Excoffier, Laurent

2017-01-01

Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model-based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model-based inference in population genetics. PMID:29284924

Evolution of the chordate body plan: New insights from phylogenetic analyses of deuterostome phyla

PubMed Central

Cameron, Chris B.; Garey, James R.; Swalla, Billie J.

2000-01-01

The deuterostome phyla include Echinodermata, Hemichordata, and Chordata. Chordata is composed of three subphyla, Vertebrata, Cephalochordata (Branchiostoma), and Urochordata (Tunicata). Careful analysis of a new 18S rDNA data set indicates that deuterostomes are composed of two major clades: chordates and echinoderms + hemichordates. This analysis strongly supports the monophyly of each of the four major deuterostome taxa: Vertebrata + Cephalochordata, Urochordata, Hemichordata, and Echinodermata. Hemichordates include two distinct classes, the enteropneust worms and the colonial pterobranchs. Most previous hypotheses of deuterostome origins have assumed that the morphology of extant colonial pterobranchs resembles the ancestral deuterostome. We present a molecular phylogenetic analysis of hemichordates that challenges this long-held view. We used 18S rRNA to infer evolutionary relationships of the hemichordate classes Pterobranchia and Enteropneusta. Our data show that pterobranchs may be derived within enteropneust worms rather than being a sister clade to the enteropneusts. The nesting of the pterobranchs within the enteropneusts dramatically alters our view of the evolution of the chordate body plan and suggests that the ancestral deuterostome more closely resembled a mobile worm-like enteropneust than a sessile colonial pterobranch. PMID:10781046

Systematics, biogeography, and character evolution of the legume tribe Fabeae with special focus on the middle-Atlantic island lineages

PubMed Central

2012-01-01

Background Tribe Fabeae comprises about 380 legume species, including some of the most ancient and important crops like lentil, pea, and broad bean. Breeding efforts in legume crops rely on a detailed knowledge of closest wild relatives and geographic origin. Relationships within the tribe, however, are incompletely known and previous molecular results conflicted with the traditional morphology-based classification. Here we analyse the systematics, biogeography, and character evolution in the tribe based on plastid and nuclear DNA sequences. Results Phylogenetic analyses including c. 70% of the species in the tribe show that the genera Vicia and Lathyrus in their current circumscription are not monophyletic: Pisum and Vavilovia are nested in Lathyrus, the genus Lens is nested in Vicia. A small, well-supported clade including Vicia hirsuta, V. sylvatica, and some Mediterranean endemics, is the sister group to all remaining species in the tribe. Fabeae originated in the East Mediterranean region in the Miocene (23–16 million years ago (Ma)) and spread at least 39 times into Eurasia, seven times to the Americas, twice to tropical Africa and four times to Macaronesia. Broad bean (V. faba) and its sister V. paucijuga originated in Asia and might be sister to V. oroboides. Lentil (Lens culinaris ssp. culinaris) is of Mediterranean origin and together with eight very close relatives forms a clade that is nested in the core Vicia, where it evolved c. 14 Ma. The Pisum clade is nested in Lathyrus in a grade with the Mediterranean L. gloeosperma, L. neurolobus, and L. nissolia. The extinct Azorean endemic V. dennesiana belongs in section Cracca and is nested among Mediterranean species. According to our ancestral character state reconstruction results, ancestors of Fabeae had a basic chromosome number of 2n=14, an annual life form, and evenly hairy, dorsiventrally compressed styles. Conclusions Fabeae evolved in the Eastern Mediterranean in the middle Miocene and spread from there across Eurasia, into Tropical Africa, and at least seven times to the Americas. The middle-Atlantic islands were colonized four times but apparently did not serve as stepping-stones for Atlantic crossings. Long-distance dispersal events are relatively common in Fabeae (seven per ten million years). Current generic and infrageneric circumscriptions in Fabeae do not reflect monophyletic groups and should be revised. Suggestions for generic level delimitation are offered. PMID:23267563

Systematics, biogeography, and character evolution of the legume tribe Fabeae with special focus on the middle-Atlantic island lineages.

PubMed

Schaefer, Hanno; Hechenleitner, Paulina; Santos-Guerra, Arnoldo; Menezes de Sequeira, Miguel; Pennington, R Toby; Kenicer, Gregory; Carine, Mark A

2012-12-25

Tribe Fabeae comprises about 380 legume species, including some of the most ancient and important crops like lentil, pea, and broad bean. Breeding efforts in legume crops rely on a detailed knowledge of closest wild relatives and geographic origin. Relationships within the tribe, however, are incompletely known and previous molecular results conflicted with the traditional morphology-based classification. Here we analyse the systematics, biogeography, and character evolution in the tribe based on plastid and nuclear DNA sequences. Phylogenetic analyses including c. 70% of the species in the tribe show that the genera Vicia and Lathyrus in their current circumscription are not monophyletic: Pisum and Vavilovia are nested in Lathyrus, the genus Lens is nested in Vicia. A small, well-supported clade including Vicia hirsuta, V. sylvatica, and some Mediterranean endemics, is the sister group to all remaining species in the tribe. Fabeae originated in the East Mediterranean region in the Miocene (23-16 million years ago (Ma)) and spread at least 39 times into Eurasia, seven times to the Americas, twice to tropical Africa and four times to Macaronesia. Broad bean (V. faba) and its sister V. paucijuga originated in Asia and might be sister to V. oroboides. Lentil (Lens culinaris ssp. culinaris) is of Mediterranean origin and together with eight very close relatives forms a clade that is nested in the core Vicia, where it evolved c. 14 Ma. The Pisum clade is nested in Lathyrus in a grade with the Mediterranean L. gloeosperma, L. neurolobus, and L. nissolia. The extinct Azorean endemic V. dennesiana belongs in section Cracca and is nested among Mediterranean species. According to our ancestral character state reconstruction results, ancestors of Fabeae had a basic chromosome number of 2n=14, an annual life form, and evenly hairy, dorsiventrally compressed styles. Fabeae evolved in the Eastern Mediterranean in the middle Miocene and spread from there across Eurasia, into Tropical Africa, and at least seven times to the Americas. The middle-Atlantic islands were colonized four times but apparently did not serve as stepping-stones for Atlantic crossings. Long-distance dispersal events are relatively common in Fabeae (seven per ten million years). Current generic and infrageneric circumscriptions in Fabeae do not reflect monophyletic groups and should be revised. Suggestions for generic level delimitation are offered.

Molecular phylogeny of the spider family Sparassidae with focus on the genus Eusparassus and notes on the RTA-clade and 'Laterigradae'.

PubMed

Moradmand, Majid; Schönhofer, Axel L; Jäger, Peter

2014-05-01

The phylogeny of the spider family Sparassidae is comprehensively investigated using four molecular markers (mitochondrial COI and 16S; nuclear H3 and 28S). Sparassidae was recovered as monophyletic and as most basal group within the RTA-clade. The higher-level clade Dionycha was not but monophyly of RTA-clade was supported. No affiliation of Sparassidae to other members of the 'Laterigradae' (Philodromidae, Selenopidae and Thomisidae) was observed, and the crab-like posture of this group assumed a result of convergent evolution. Only Philodromidae and Selenopidae were found members of a supported clade, but together with Salticidae and Corinnidae, while Thomisidae was nested within the higher Lycosoidea. Within Sparassidae monophyly of the subfamilies Heteropodinae sensu stricto, Palystinae and Deleninae was recovered. Sparianthinae was supported as the most basal clade within Sparassidae. Sparassinae and the genus Olios were found each to be polyphyletic. Eusparassinae was not recovered monophyletic, with the two original genera Eusparassus and Pseudomicrommata in separate clades and only the latter clustered with most other assumed Eusparassinae, here termed the "African clade". Further focus was on the monophyletic genus Eusparassus and its proposed species groups, of which the dufouri-, walckenaeri- and doriae-group were confirmed as monophyletic with the two latter groups more closely related. According to molecular clock analyses, the divergence time of Sparassidae and Eusparassus was estimated with 186 and 70 million years ago respectively. Copyright © 2014 Elsevier Inc. All rights reserved.

A Radical Solution: The Phylogeny of the Nudibranch Family Fionidae

PubMed Central

Cella, Kristen; Ekimova, Irina; Chichvarkhin, Anton; Schepetov, Dimitry; Gosliner, Terrence M.

2016-01-01

Tergipedidae represents a diverse and successful group of aeolid nudibranchs, with approximately 200 species distributed throughout most marine ecosystems and spanning all biogeographical regions of the oceans. However, the systematics of this family remains poorly understood since no modern phylogenetic study has been undertaken to support any of the proposed classifications. The present study is the first molecular phylogeny of Tergipedidae based on partial sequences of two mitochondrial (COI and 16S) genes and one nuclear gene (H3). Maximum likelihood, maximum parsimony and Bayesian analysis were conducted in order to elucidate the systematics of this family. Our results do not recover the traditional Tergipedidae as monophyletic, since it belongs to a larger clade that includes the families Eubranchidae, Fionidae and Calmidae. This newly recovered clade is here referred to as Fionidae, the oldest name for this taxon. In addition, the present molecular phylogeny does not recover the traditional systematic relationships at a generic level, and therefore, systematic changes are required. We recognize the following clades within Fionidae: Calma, Cuthona, Cuthonella, Eubranchus, Fiona, Murmania, Tenellia, Tergipes, Tergiposacca gen. nov., Rubramoena gen. nov. and Abronica gen. nov. The type species of Tergiposacca, T. longicerata nov. sp. is described. The other two new genera have a previously described species as their type species. Most of these taxa, with the exceptions of Eubranchus, Tergipes and Fiona are composed of radically different constituent species from their traditional membership, but appear to be supported by morphological synapomorphies as well as molecular data. Aenigmastyletus, Catriona, Phestilla, Tenellia and Trinchesia are nested within other clades and, thus are here considered as synonyms of the larger clades. The phylogenetic position and validity of Myja, Guyvalvoria, Leostyletus and Subcuthona still need to be tested in future studies when material becomes available. PMID:27977703

Comparative genomics and transcriptomics of sexual development in a nematode-associated strain of Fusarium neocosmosporiellum

USDA-ARS?s Scientific Manuscript database

Fusarium neocosmosporiellum (formerly Neocosmospora vasinfecta) is a ubiquitous saprobic fungus that has been isolated from plants, fungi, nematodes, dung and soil. This homothallic species is nested in a clade within the F. solani species complex near a lineage of fusaria farmed by ambrosia beetles...

The phylogenetic relationships of basal archosauromorphs, with an emphasis on the systematics of proterosuchian archosauriforms

PubMed Central

2016-01-01

The early evolution of archosauromorphs during the Permo-Triassic constitutes an excellent empirical case study to shed light on evolutionary radiations in deep time and the timing and processes of recovery of terrestrial faunas after a mass extinction. However, macroevolutionary studies of early archosauromorphs are currently limited by poor knowledge of their phylogenetic relationships. In particular, one of the main early archosauromorph groups that need an exhaustive phylogenetic study is “Proterosuchia,” which as historically conceived includes members of both Proterosuchidae and Erythrosuchidae. A new data matrix composed of 96 separate taxa (several of them not included in a quantitative phylogenetic analysis before) and 600 osteological characters was assembled and analysed to generate a comprehensive higher-level phylogenetic hypothesis of basal archosauromorphs and shed light on the species-level interrelationships of taxa historically identified as proterosuchian archosauriforms. The results of the analysis using maximum parsimony include a polyphyletic “Prolacertiformes” and “Protorosauria,” in which the Permian Aenigmastropheus and Protorosaurus are the most basal archosauromorphs. The enigmatic choristoderans are either found as the sister-taxa of all other lepidosauromorphs or archosauromorphs, but consistently placed within Sauria. Prolacertids, rhynchosaurs, allokotosaurians and tanystropheids are the major successive sister clades of Archosauriformes. The Early Triassic Tasmaniosaurus is recovered as the sister-taxon of Archosauriformes. Proterosuchidae is unambiguosly restricted to five species that occur immediately after and before the Permo-Triassic boundary, thus implying that they are a short-lived “disaster” clade. Erythrosuchidae is composed of eight nominal species that occur during the Early and Middle Triassic. “Proterosuchia” is polyphyletic, in which erythrosuchids are more closely related to Euparkeria and more crownward archosauriforms than to proterosuchids, and several species are found widespread along the archosauromorph tree, some being nested within Archosauria (e.g., “Chasmatosaurus ultimus,” Youngosuchus). Doswelliids and proterochampsids are recovered as more closely related to each other than to other archosauromorphs, forming a large clade (Proterochampsia) of semi-aquatic to aquatic forms that includes the bizarre genus Vancleavea. Euparkeria is one of the sister-taxa of the clade composed of proterochampsians and archosaurs. The putative Indian archosaur Yarasuchus is recovered in a polytomy with Euparkeria and more crownward archosauriforms, and as more closely related to the Russian Dongusuchus than to other species. Phytosaurs are recovered as the sister-taxa of all other pseudosuchians, thus being nested within Archosauria. PMID:27162705

Two new species of the genus Candida in the Zygoascus clade, Candida lundiana sp. nov. and Candida suthepensis sp. nov., isolated from raw honey in Thailand.

PubMed

Saksinchai, Sujinan; Suzuki, Motofumi; Lumyong, Saisamorn; Ohkuma, Moriya; Chantawannakul, Panuwan

2012-03-01

During a survey of yeasts associated with raw honey collected in Thailand, two strains of the Zygoascus clade were isolated from the Asian cavity-nesting honeybee Apis cerana and the stingless bee Homotrigona fimbriata. Phylogeny based on 26S rDNA D1/D2 sequences placed these yeasts as members of a clade including Candida bituminiphila, Candida patagonica and Candida polysorbophila. The strains of the two novel species, CBS 12271(T) and CBS 12270(T), respectively, could be unquestionably distinguished from their relatives by rDNA sequences and other taxonomic characteristics. Therefore, the novel anamorphic species, Candida lundiana sp. nov. (type strain CBS 12271(T) = JCM 16823(T)) and Candida suthepensis sp. nov. (type strain CBS 12270(T) = JCM 16822(T)) are described.

CNL Disease Resistance Genes in Soybean and Their Evolutionary Divergence

PubMed Central

Nepal, Madhav P; Benson, Benjamin V

2015-01-01

Disease resistance genes (R-genes) encode proteins involved in detecting pathogen attack and activating downstream defense molecules. Recent availability of soybean genome sequences makes it possible to examine the diversity of gene families including disease-resistant genes. The objectives of this study were to identify coiled-coil NBS-LRR (= CNL) R-genes in soybean, infer their evolutionary relationships, and assess structural as well as functional divergence of the R-genes. Profile hidden Markov models were used for sequence identification and model-based maximum likelihood was used for phylogenetic analysis, and variation in chromosomal positioning, gene clustering, and functional divergence were assessed. We identified 188 soybean CNL genes nested into four clades consistent to their orthologs in Arabidopsis. Gene clustering analysis revealed the presence of 41 gene clusters located on 13 different chromosomes. Analyses of the Ks-values and chromosomal positioning suggest duplication events occurring at varying timescales, and an extrapericentromeric positioning may have facilitated their rapid evolution. Each of the four CNL clades exhibited distinct patterns of gene expression. Phylogenetic analysis further supported the extrapericentromeric positioning effect on the divergence and retention of the CNL genes. The results are important for understanding the diversity and divergence of CNL genes in soybean, which would have implication in soybean crop improvement in future. PMID:25922568

CNL Disease Resistance Genes in Soybean and Their Evolutionary Divergence.

PubMed

Nepal, Madhav P; Benson, Benjamin V

2015-01-01

Disease resistance genes (R-genes) encode proteins involved in detecting pathogen attack and activating downstream defense molecules. Recent availability of soybean genome sequences makes it possible to examine the diversity of gene families including disease-resistant genes. The objectives of this study were to identify coiled-coil NBS-LRR (= CNL) R-genes in soybean, infer their evolutionary relationships, and assess structural as well as functional divergence of the R-genes. Profile hidden Markov models were used for sequence identification and model-based maximum likelihood was used for phylogenetic analysis, and variation in chromosomal positioning, gene clustering, and functional divergence were assessed. We identified 188 soybean CNL genes nested into four clades consistent to their orthologs in Arabidopsis. Gene clustering analysis revealed the presence of 41 gene clusters located on 13 different chromosomes. Analyses of the K s-values and chromosomal positioning suggest duplication events occurring at varying timescales, and an extrapericentromeric positioning may have facilitated their rapid evolution. Each of the four CNL clades exhibited distinct patterns of gene expression. Phylogenetic analysis further supported the extrapericentromeric positioning effect on the divergence and retention of the CNL genes. The results are important for understanding the diversity and divergence of CNL genes in soybean, which would have implication in soybean crop improvement in future.

On the use of haplotype phylogeny to detect disease susceptibility loci

PubMed Central

Bardel, Claire; Danjean, Vincent; Hugot, Jean-Pierre; Darlu, Pierre; Génin, Emmanuelle

2005-01-01

Background The cladistic approach proposed by Templeton has been presented as promising for the study of the genetic factors involved in common diseases. This approach allows the joint study of multiple markers within a gene by considering haplotypes and grouping them in nested clades. The idea is to search for clades with an excess of cases as compared to the whole sample and to identify the mutations defining these clades as potential candidate disease susceptibility sites. However, the performance of this approach for the study of the genetic factors involved in complex diseases has never been studied. Results In this paper, we propose a new method to perform such a cladistic analysis and we estimate its power through simulations. We show that under models where the susceptibility to the disease is caused by a single genetic variant, the cladistic test is neither really more powerful to detect an association nor really more efficient to localize the susceptibility site than an individual SNP testing. However, when two interacting sites are responsible for the disease, the cladistic analysis greatly improves the probability to find the two susceptibility sites. The impact of the linkage disequilibrium and of the tree characteristics on the efficiency of the cladistic analysis are also discussed. An application on a real data set concerning the CARD15 gene and Crohn disease shows that the method can successfully identify the three variant sites that are involved in the disease susceptibility. Conclusion The use of phylogenies to group haplotypes is especially interesting to pinpoint the sites that are likely to be involved in disease susceptibility among the different markers identified within a gene. PMID:15904492

Phylogeny and biogeography of the genus Stevia (Asteraceae: Eupatorieae): an example of diversification in the Asteraceae in the new world.

PubMed

Soejima, Akiko; Tanabe, Akifumi S; Takayama, Izumi; Kawahara, Takayuki; Watanabe, Kuniaki; Nakazawa, Miyuki; Mishima, Misako; Yahara, Tetsukazu

2017-11-01

The genus Stevia comprises approximately 200 species, which are distributed in North and South America, and are representative of the species diversity of the Asteraceae in the New World. We reconstructed the phylogenetic relationships using sequences of ITS and cpDNA and estimated the divergence times of the major clade of this genus. Our results suggested that Stevia originated in Mexico 7.0-7.3 million years ago (Mya). Two large clades, one with shrub species and another with herb species, were separated at about 6.6 Mya. The phylogenetic reconstruction suggested that an ancestor of Stevia was a small shrub in temperate pine-oak forests and the evolutionary change from a shrub state to a herb state occurred only once. A Brazilian clade was nested in a Mexican herb clade, and its origin was estimated to be 5.2 Mya, suggesting that the migration from North America to South America occurred after the formation of the Isthmus of Panama. The species diversity in Mexico appears to reflect the habitat diversity within the temperate pine-oak forest zone. The presence of many conspecific diploid-polyploid clades in the phylogenetic tree reflects the high frequency of polyploidization among the perennial Stevia species.

Developmental and Ultrastructural Characterization and Phylogenetic Analysis of Trypanosoma herthameyeri n. sp. of Brazilian Leptodactilydae Frogs.

PubMed

Attias, Márcia; Sato, Lyslaine H; Ferreira, Robson C; Takata, Carmen S A; Campaner, Marta; Camargo, Erney P; Teixeira, Marta M G; de Souza, Wanderley

2016-09-01

We described the phylogenetic affiliation, development in cultures and ultrastructural features of a trypanosome of Leptodacylus chaquensis from the Pantanal biome of Brazil. In the inferred phylogeny, this trypanosome nested into the Anura clade of the basal Aquatic clade of Trypanosoma, but was separate from all known species within this clade. This finding enabled us to describe it as Trypanosoma herthameyeri n. sp., which also infects other Leptodacylus species from the Pantanal and Caatinga biomes. Trypanosoma herthameyeri multiplies as small rounded forms clumped together and evolving into multiple-fission forms and rosettes of epimastigotes released as long forms with long flagella; scarce trypomastigotes and glove-like forms are common in stationary-phase cultures. For the first time, a trypanosome from an amphibian was observed by field emission scanning electron microscopy, revealing a cytostome opening, well-developed flagellar lamella, and many grooves in pumpkin-like forms. Transmission electron microscopy showed highly developed Golgi complexes, relaxed catenation of KDNA, and a rich set of spongiome tubules in a regular parallel arrangement to the flagellar pocket as confirmed by electron tomography. Considering the basal position in the phylogenetic tree, developmental and ultrastructural data of T. herthameyeri are valuable for evolutionary studies of trypanosome architecture and cell biology. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

Testing the monophyly of Aesculus L. and Billia Peyr., woody genera of tribe Hippocastaneae of the Sapindaceae.

PubMed

Harris, A J; Fu, Chengxin; Xiang, Qiu-Yun Jenny; Holland, LaRinda; Wen, Jun

2016-09-01

Hippocastaneae is a well-supported clade in Sapindaceae that comprises 15+ species; 12+ in Aesculus, two in Billia, and one in Handeliodendron Rehder. The monophyly of Aesculus and Billia were widely assumed, but a recent molecular phylogenetic study of Sapindanceae used seven species of Aesculus and one each of Billia and Handeliodendron and showed that Billia and Handeliodendron were nested within Aesculus. Here, we tested the hypothesis that Aesculus and Billia are mutually monophyletic using phylogenetic analyses of seven molecular markers and 31 accessions of Hippocastaneae representing 14 species. We performed phylogenetic analyses using a dataset of concatenated genes as well as with coalescent method for constructing a species tree from individual gene trees. The analysis of seven concatenated markers and the species tree strongly supported the mutual monophyly of Aesculus and Billia. We also recovered support for the traditional arrangement of genera within Hippocastaneae: Aesculus and Billia comprising a clade that is sister to Handeliodendron. However, the relationships among the genera remain incompletely resolved. Copyright © 2016 Elsevier Inc. All rights reserved.

Phylogeny of the Ampelocissus-Vitis clade in Vitaceae supports the New World origin of the grape genus.

PubMed

Liu, Xiu-Qun; Ickert-Bond, Stefanie M; Nie, Ze-Long; Zhou, Zhuo; Chen, Long-Qing; Wen, Jun

2016-02-01

The grapes and the close allies in Vitaceae are of great agronomic and economic importance. Our previous studies showed that the grape genus Vitis was closely related to three tropical genera, which formed the Ampelocissus-Vitis clade (including Vitis, Ampelocissus, Nothocissus and Pterisanthes). Yet the phylogenetic relationships of the four genera within this clade remain poorly resolved. Furthermore, the geographic origin of Vitis is still controversial, because the sampling of the close relatives of Vitis was too limited in the previous studies. This study reconstructs the phylogenetic relationships within the clade, and hypothesizes the origin of Vitis in a broader phylogenetic framework, using five plastid and two nuclear markers. The Ampelocissus-Vitis clade is supported to be composed of five main lineages. Vitis includes two described subgenera each as a monophyletic group. Ampelocissus is paraphyletic. The New World Ampelocissus does not form a clade and shows a complex phylogenetic relationship, with A. acapulcensis and A. javalensis forming a clade, and A. erdvendbergiana sister to Vitis. The majority of the Asian Ampelocissus species form a clade, within which Pterisanthes is nested. Pterisanthes is polyphyletic, suggesting that the lamellate inflorescence characteristic of the genus represents convergence. Nothocissus is sister to the clade of Asian Ampelocissus and Pterisanthes. The African Ampelocissus forms a clade with several Asian species. Based on the Bayesian dating and both the RASP and Lagrange analyses, Vitis is inferred to have originated in the New World during the late Eocene (39.4Ma, 95% HPD: 32.6-48.6Ma), then migrated to Eurasia in the late Eocene (37.3Ma, 95% HPD: 30.9-45.1Ma). The North Atlantic land bridges (NALB) are hypothesized to be the most plausible route for the Vitis migration from the New World to Eurasia, while intercontinental long distance dispersal (LDD) cannot be eliminated as a likely mechanism. Copyright © 2015 Elsevier Inc. All rights reserved.

The origin of Chubutolithes Ihering, ichnofossils from the Eocene and Oligocene of Chubut Province, Argentina.

USGS Publications Warehouse

Brown, T.M.; Ratcliffe, B.C.

1988-01-01

The distinctive trace fossil Chubutolithes gaimanensis n. ichnosp. occurs in Casamayoran (early Eocene) and Colhuehaupian (late Oligocene) alluvial rocks of the Sarmiento Formation in eastern Chubut Province, Argentina. Though known for nearly 70 years, its origin has remained obscure. Examination of new specimens and comparisons with modern analogs demonstrate that specimens of Chubutolithes represent the fossil nests of a mud-dauber (Hymenoptera: Sphecidae). Virtually identical nests are constructed today by mud-daubers in areas as disparate as southern Santa Cruz Province, Argentina, and Nebraska, confirming that quite similar trace fossils can be produced by several different taxa in a higher taxonomic clade. No satisfactory ethological term exists for trace fossils that, like Chubutolithes, were constructed by organisms above, rather than within, a substrate or medium. The new term aedificichnia is proposed. Chubutolithes occurs in alluvial paleosols and is associated with a large terrestrial ichnofauna. These trace fossils include the nests of scarab beetles, compound nests of social insects, and burrows of earthworms. -Authors

Prevalence of severe fever with thrombocytopenia syndrome virus in black goats (Capra hircus coreanae) in the Republic of Korea.

PubMed

Kang, Jun-Gu; Cho, Yoon-Kyoung; Jo, Yong-Sun; Chae, Jeong-Byoung; Oh, Sung-Suck; Kim, Kye-Hyung; Ko, Mee-Kyung; Yi, Jongyoun; Choi, Kyoung-Seong; Yu, Do-Hyeon; Kim, Hyeon-Cheol; Park, Jinho; Park, Bae-Keun; Choi, Chang-Yong; Jung, Young-Hun; Chae, Joon-Seok

2018-04-26

Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne pathogen in China, Japan, and the Republic of Korea (ROK). The aim of this study was to investigate the prevalence of SFTSV antigens and anti-SFTSV antibodies in black goats (Capra hircus coreanae) throughout the ROK. Sera were collected from 737 black goats in nine provinces in the ROK. Eighteen of 737 (2.4%) goat sera were positive for SFTSV on one-step reverse transcription nested polymerase chain reaction. The amplified 346-bp S segments of SFTSV sequences were classified into three genotypes (BG1, BG2, and BG3), and were included in the Japanese clade rather than the Chinese clade, based on phylogenetic analysis. Forty-three of 624 (6.9%) serum samples were seropositive for anti-SFTSV antibodies on enzyme-linked immunosorbent assay analysis. This study is the first to examine the molecular prevalence of SFTSV in goats and the first to perform serological detection of anti-SFTSV antibodies in livestock in the ROK. Moreover, the results indicate that SFTSV is widely distributed in goats and that additional monitoring for SFTSV is needed in livestock in the ROK. Copyright © 2018 Elsevier GmbH. All rights reserved.

Host-ant specificity of endangered large blue butterflies (Phengaris spp., Lepidoptera: Lycaenidae) in Japan.

PubMed

Ueda, Shouhei; Komatsu, Takashi; Itino, Takao; Arai, Ryusuke; Sakamoto, Hironori

2016-11-03

Large blue butterflies, Phengaris (Maculinea), are an important focus of endangered-species conservation in Eurasia. Later-instar Phengaris caterpillars live in Myrmica ant nests and exploit the ant colony's resources, and they are specialized to specific host-ant species. For example, local extinction of P. arion in the U. K. is thought to have been due to the replacement of its host-ant species with a less-suitable congener, as a result of changes in habitat. In Japan, Myrmica kotokui hosts P. teleius and P. arionides caterpillars. We recently showed, however, that the morphological species M. kotokui actually comprises four genetic clades. Therefore, to determine to which group of ants the hosts of these two Japanese Phengaris species belong, we used mitochondrial COI-barcoding of M. kotokui specimens from colonies in the habitats of P. teleius and P. arionides to identify the ant clade actually parasitized by the caterpillars of each species. We found that these two butterfly species parasitize different ant clades within M. kotokui.

Molecular phylogeography and cryptic speciation in the mosses, Mielichhoferia elongata and M. mielichhoferiana (Bryaceae).

PubMed

Shaw, A J

2000-05-01

Nucleotide sequence variation in the ITS1-5.8S-ITS2 region of nuclear ribosomal DNA (nrDNA) from 70 populations of Mielichhoferia elongata and M. mielichhoferiana, plus two outgroup species, was analysed using maximum parsimony and maximum likelihood methods. High levels of nucleotide substitution and numerous insertion-deletion events were detected within and between the two species. M. elongata is monophyletic with regard to nrDNA variation, but M. mielichhoferiana is paraphyletic. (M. elongata is nested within it.) A clade within M. mielichhoferiana provides evidence of vicariance, with North American and Scandinavian sister groups of populations. Two major clades are resolved in M. elongata by sequence data that are completely congruent with previous isozyme work. One clade includes populations from both North America and Europe whereas the other is strictly North American. These two clades, resolved by multiple independent loci, clearly represent cryptic species within the morphologically uniform M. elongata. Certain geographical areas, most notably southwestern Colorado in Ouray and San Juan Counties, harbour diverse populations of M. elongata with distinct phylogenetic and phylogeographical histories. Morphologically indistinguishable but phylogenetically distant populations were detected a few metres apart at one site. In contrast, all populations collected over hundreds of kilometres in California belong to a single clade. Arctic North American populations belong to a clade that includes disjunct populations in Alaska, northern Ellesmere Island, and the northeastern USA, but not subarctic Swedish populations, which are more closely related to plants from the Rocky Mountains. Morphological uniformity belies complex infraspecific phylogenetic patterns within M. elongata and M. mielichhoferiana.

Molecular systematics and biogeography of the amphibious genus Littorella (Plantaginaceae).

PubMed

Hoggard, Ronald K; Kores, Paul J; Molvray, Mia; Hoggard, Gloria D; Broughton, David A

2003-03-01

Littorella (Plantaginaceae) is a disjunct, amphibious genus represented by three closely related species. Littorella uniflora occurs in Europe including Iceland and the Azores, L. americana is found in temperate North America, and L. australis grows in temperate South America. Littorella has been recognized in numerous floristic treatments, but its status as a genus has recently been questioned. Rahn (Botanical Journal of the Linnean Society 120: 145-198, 1996) proposed a new phylogeny for Plantaginaceae based on morphological, embryological, and chemical data in which he reduced Littorella to a subgenus of Plantago. This article compares the phylogeny proposed by Rahn to one based on DNA sequence data from the internal transcribed spacer (ITS) region. In our analysis, Littorella forms a strongly supported monophyletic clade sister to Plantago and its recognition at the generic rank appears warranted. Littorella australis is sister to L. americana, and this clade is sister to the European L. uniflora. This more distant relationship between L. uniflora and L. americana provides support for maintaining both taxa at the specific rank and suggests a European origin for Littorella. Our studies also indicate that the monotypic genus Bougueria is deeply nested within Plantago and that its inclusion within Plantago as proposed by Rahn appears justified.

Kupeantha (Coffeeae, Rubiaceae), a new genus from Cameroon and Equatorial Guinea.

PubMed

Cheek, Martin; Alvarez-Aguirre, Maria G; Grall, Aurélie; Sonké, Bonaventure; Howes, Melanie-Jayne R; Larridon, Isabel

2018-01-01

Two new coffee relatives (tribe Coffeeae, Rubiaceae), discovered during botanical expeditions to Cameroon, are examined for generic placement, and the placement of three previously known species (Argocoffeopsis fosimondi, A. spathulata and Calycosiphonia pentamera) is reinvestigated using plastid sequence (accD-psa1, rpl16, trnL-F) and morphological data. Seed biochemistry of the new species and pollen micromorphology (only one of the two species) are also studied. Based on the plastid sequence data, the new taxa are nested in a well-supported monophyletic group that includes Argocoffeopsis and Calycosiphonia. Within this clade, three well-supported subclades are recovered that are morphologically easy to diagnose: (1) Calycosiphonia (excluding C. pentamera), (2) Argocoffeopsis (excluding A. fosimondi and A. spathulata), and (3) a clade including the above excluded species, in addition to the new species. Based on the results, Kupeantha, a new genus of five species, is described, including two new Critically Endangered taxa from the Highlands of Cameroon: Kupeantha ebo and K. kupensis. Phytochemical analysis of Kupeantha seeds reveals compounds assigned as hydroxycinnamic acid derivatives, amino acids and ent-kaurane diterpenoids; caffeine was not detected. Kupeantha is the first new genus described in tribe Coffeeae in 40 years.

Population structure and history of a phenotypically variable teiid lizard (Ameiva chrysolaema) from Hispaniola: the influence of a geologically complex island.

PubMed

Gifford, Matthew E; Powell, Robert; Larson, Allan; Gutberlet, Ronald L

2004-09-01

Ameiva chrysolaema is distributed across the island of Hispaniola in the West Indies. The species is restricted to dry lowlands between major mountain ranges and along the southern and eastern coasts. Phylogenetic and phylogeographic analyses of mtDNA sequence variation from 14 sampling localities identify at least three independent evolutionary lineages, separated from one another by major mountain ranges. Nested clade phylogeographic analysis (NCPA) suggests a complex history of population fragmentation, consistent with geological evidence of seawater incursions into the Azua and Enriquillo basins during the Pliocene/Pleistocene (approximately 1.6 mya). Significantly negative Fu's F(S) values and parameters of mismatch distributions suggest that formerly fragmented populations have recently expanded their ranges. Significantly large average population clade distances (APCD) for two sampling localities in the Azua basin suggest secondary contact at these localities of previously separated populations. The distribution of haplotypes among polymorphic populations of A. chrysolaema suggests that variation in dorsal pattern represents a polymorphism within evolutionary lineages. Ameiva leberi is ecologically indistinguishable from and syntopic with A. chrysolaema. Genetic data suggest that A. leberi is a junior synonym of A. chrysolaema.

Phylogenetic relationships of the downy mildews (Peronosporales) and related groups based on nuclear large subunit ribosomal DNA sequences.

PubMed

Riethmüller, A; Voglmayr, H; Göker, M; Weiß, M; Oberwinkler, F

2002-01-01

In order to investigate phylogenetic relationships of the Peronosporomycetes (Oomycetes), nuclear large subunit ribosomal DNA sequences containing the D1 and D2 region were analyzed of 92 species belonging to the orders Peronosporales, Pythiales, Leptomitales, Rhipidiales, Saprolegniales and Sclerosporales. The data were analyzed applying methods of neighbor-joining as well as maximum parsimony, both statistically supported using the bootstrap method. The results confirm the major division between the Pythiales and Peronosporales on the one hand and the Saprolegniales, Leptomitales, and Rhipidiales on the other. The Sclerosporales were shown to be polyphyletic; while Sclerosporaceae are nested within the Peronosporaceae, the Verrucalvaceae are merged within the Saprolegniales. Within the Peronosporomycetidae, Pythiales as well as Peronosporales as currently defined are polyphyletic. The well supported Albugo clade appears to be the most basal lineage, followed by a Pythium-Lagenidium clade. The third, highly supported clade comprises the Peronosporaceae together with Sclerospora, Phytophthora, and Peronophythora. Peronophythora is placed within Phytophthora, indicating that both genera should be merged. Bremiella seems to be polyphyletic within the genus Plasmopara, suggesting a transfer to Plasmopara. The species of Peronospora do not appear as a monophyletic group. Peronospora species growing on Brassicaceae form a highly supported clade.

Origins, evolution, and diversification of cleptoparasitic lineages in long-tongued bees.

PubMed

Litman, Jessica R; Praz, Christophe J; Danforth, Bryan N; Griswold, Terry L; Cardinal, Sophie

2013-10-01

The evolution of parasitic behavior may catalyze the exploitation of new ecological niches yet also binds the fate of a parasite to that of its host. It is thus not clear whether evolutionary transitions from free-living organism to parasite lead to increased or decreased rates of diversification. We explore the evolution of brood parasitism in long-tongued bees and find decreased rates of diversification in eight of 10 brood parasitic clades. We propose a pathway for the evolution of brood parasitic strategy and find that a strategy in which a closed host nest cell is parasitized and the host offspring is killed by the adult parasite represents an obligate first step in the appearance of a brood parasitic lineage; this ultimately evolves into a strategy in which an open host cell is parasitized and the host offspring is killed by a specialized larval instar. The transition to parasitizing open nest cells expanded the range of potential hosts for brood parasitic bees and played a fundamental role in the patterns of diversification seen in brood parasitic clades. We address the prevalence of brood parasitic lineages in certain families of bees and examine the evolution of brood parasitism in other groups of organisms. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Sebacinales are associates of the leafy liverwort Lophozia excisa in the southern maritime Antarctic.

PubMed

Newsham, Kevin K; Bridge, Paul D

2010-06-01

The leafy liverwort Lophozia excisa, which is colonised by basidiomycete fungi in other biomes and which evidence suggests may be colonised by mycorrhizal fungi in Antarctica, was sampled from Léonie Island in the southern maritime Antarctic (67 degrees 36' S, 68 degrees 21' W). Microscopic examination of plants indicated that fungal hyphae colonised 78% of the rhizoids of the liverwort, apparently by entering the tips of rhizoids prior to growing into their bases, where they formed hyphal coils. Extensive colonisation of stem medullary cells by hyphae was also observed. DNA was extracted from surface-sterilised liverwort tissues and sequenced following nested PCR, using the primer set ITS1F/TW14, followed by a second round of amplification using the ITSSeb3/TW13 primer set. Neighbour-joining analyses showed that the sequences obtained nested in Sebacinales clade B as a 100% supported sister group to Sebacinales sequences from the leafy liverworts Lophozia sudetica, L. incisa and Calypogeia muelleriana sampled from Europe. Direct PCR using the fungal specific primer set ITS1F/ITS4 similarly identified fungi belonging to Sebacinales clade B as the principal colonists of L. excisa tissues. These observations indicate the presence of a second mycothallus in Antarctica and support the previous suggestion that the Sebacinales has a wide geographical distribution.

A Phylogeographic Assessment of the Malagasy Giant Chameleons (Furcifer verrucosus and Furcifer oustaleti)

PubMed Central

Raxworthy, Christopher J.

2016-01-01

The Malagasy giant chameleons (Furcifer oustaleti and Furcifer verrucosus) are sister species that are both broadly distributed in Madagascar, and also endemic to the island. These species are also morphologically similar and, because of this, have been frequently misidentified in the field. Previous studies have suggested that cryptic species are nested within this chameleon group, and two subspecies have been described in F. verrucosus. In this study, we utilized a phylogeographic approach to assess genetic diversification within these chameleons. This was accomplished by (1) identifying clades within each species supported by both mitochondrial and nuclear DNA, (2) assessing divergence times between clades, and (3) testing for niche divergence or conservatism. We found that both F. oustaleti and F. verrucosus could be readily identified based on genetic data, and within each species, there are two well-supported clades. However, divergence times are not contemporary and spatial patterns are not congruent. Diversification within F. verrucosus occurred during the Plio-Pleistocene, and there is evidence for niche divergence between a southwestern and southeastern clade, in a region of Madagascar that shows no obvious landscape barriers to dispersal. Diversification in F. oustaleti occurred earlier in the Pliocene or Miocene, and niche conservatism is supported with two genetically distinct clades separated at the Sofia River in northwestern Madagascar. Divergence within F. verrucosus is most consistent with patterns expected from ecologically mediated speciation, whereas divergence in F. oustaleti most strongly matches the patterns expected from the riverine barrier hypothesis. PMID:27257819

Two new species of the Liolaemuselongatus-kriegi complex (Iguania, Liolaemidae) from Andean highlands of southern Chile.

PubMed

Troncoso-Palacios, Jaime; Díaz, Hugo A; Esquerré, Damien; Urra, Felix A

2015-01-01

The elongatus-kriegi complex is one of the most diverse clades of the Liolaemus (sensu stricto) subgenus of lizards. There are currently 29 species recognized in this group distributed between Chile and Argentina. Based on molecular evidence, there seem to be five main clades nested within this complex: the elongatus, leopardinus, kriegi, petrophilus and punmahuida clades. Liolaemusbuergeri and Liolaemuskriegi, both of the kriegi clade, were believed to inhabit the surroundings of the Laja Lagoon, in the Biobío Region of Chile. Moreover, this Chilean population of Liolaemuskriegi was recently recognized as an undescribed taxon called "Liolaemus sp. A" based on molecular phylogenetics. In this work, we studied these two populations of the Laja Lagoon and provided the morphological diagnosis to describe them as two new species: Liolaemusscorialis sp. n. and Liolaemuszabalai sp. n., previously considered Liolaemusbuergeri and "Liolaemuskriegi/Liolaemus sp. A" respectively. Additionally, we identified another population of Liolaemusscorialis in the vicinity of La Mula Lagoon in the Araucanía Region of Chile. Liolaemusscorialis differs from almost all of the species of the elongatus-kriegi complex by its considerably smaller size. Nevertheless, without molecular data we cannot assign it to any particular subclade. Liolaemuszabalai belongs to the kriegi clade based on published molecular phylogenies. Finally, we provide some natural history data on both species and we document for the first time the presence of Liolaemusneuquensis in Chile from a museum specimen from La Mula Lagoon.

Population genetic analysis of Mountain Plover using mitochondrial DNA sequence data

USGS Publications Warehouse

Oyler-McCance, S.J.; St. John, J.; Knopf, F.L.; Quinn, T.W.

2005-01-01

Mountain Plover (Charadrius montanus) distribution and abundance have been reduced drastically in the past 30 years and the conversion of shortgrass prairie to agriculture has caused breeding populations to become geographically isolated. This, coupled with the fact that Mountain Plovers are thought to show fidelity to breeding grounds, leads to the prediction that the isolated breeding populations would be genetically distinct. This pattern, if observed, would have important management implications for a species at risk of extinction. Our study examined genetic variation at two mitochondrial regions for 20–30 individuals from each of four breeding sites. We found no evidence of significant population differentiation in the data from the control region or the ATPase 6/8 region. Nested-clade analysis revealed no relationship between haplotype phylogeny, and geography among the 47 control region haplotypes. In the ATPase 6/8 region, however, one of the two clades provided information suggesting that, historically, there has been continuous range expansion. Analysis of mismatch distributions and Tajima's D suggest that the Mountain Plover underwent a population expansion, following the Pleistocene glacial period. To explain the lack of detectable genetic differentiation among populations, despite their geographic isolation and fidelity to breeding locations, we speculate that there is sufficient female-mediated gene flow to homogenize gene pools among populations. Such gene flow might ensue if pair bonds are formed in mixed flocks on wintering grounds rather than on the summer breeding grounds.

Mitochondrial and nuclear DNA sequences support a Cretaceous origin of Columbiformes and a dispersal-driven radiation in the Paleocene .

PubMed

Pereira, Sergio L; Johnson, Kevin P; Clayton, Dale H; Baker, Allan J

2007-08-01

Phylogenetic relationships among genera of pigeons and doves (Aves, Columbiformes) have not been fully resolved because of limited sampling of taxa and characters in previous studies. We therefore sequenced multiple nuclear and mitochondrial DNA genes totaling over 9000 bp from 33 of 41 genera plus 8 outgroup taxa, and, together with sequences from 5 other pigeon genera retrieved from GenBank, recovered a strong phylogenetic hypothesis for the Columbiformes. Three major clades were recovered with the combined data set, comprising the basally branching New World pigeons and allies (clade A) that are sister to Neotropical ground doves (clade B), and the Afro-Eurasian and Australasian taxa (clade C). None of these clades supports the monophyly of current families and subfamilies. The extinct, flightless dodo and solitaires (Raphidae) were embedded within pigeons and doves (Columbidae) in clade C, and monophyly of the subfamily Columbinae was refuted because the remaining subfamilies were nested within it. Divergence times estimated using a Bayesian framework suggest that Columbiformes diverged from outgroups such as Apodiformes and Caprimulgiformes in the Cretaceous before the mass extinction that marks the end of this period. Bayesian and maximum likelihood inferences of ancestral areas, accounting for phylogenetic uncertainty and divergence times, respectively, favor an ancient origin of Columbiformes in the Neotropical portion of what was then Gondwana. The radiation of modern genera of Columbiformes started in the Early Eocene to the Middle Miocene, as previously estimated for other avian groups such as ratites, tinamous, galliform birds, penguins, shorebirds, parrots, passerine birds, and toucans. Multiple dispersals of more derived Columbiformes between Australasian and Afro-Eurasian regions are required to explain current distributions.

Patterns of diversification in the discus fishes (Symphysodon spp. Cichlidae) of the Amazon basin.

PubMed

Farias, Izeni Pires; Hrbek, Tomas

2008-10-01

We carried out a phylogeograhic and population genetic analysis of fishes of the taxonomically contentious genus Symphysodon from the Amazon basin in order to test hypotheses of relationships among taxonomic units, and potential processes driving diversification within this genus. We sampled 334 individuals of the genus Symphysodon from 24 localities that span the complete geographic distribution of this genus. The sampling scheme included all known phenotypic groups, species and subspecies. Analyses were based on 474 bp of the mitochondrial control region and 1443 bp of the exon 3 of RAG1 gene. We observed 102 mtDNA haplotypes defined by 89 segregating sites, and 5 nuDNA alleles defined by three segregating sites. Maximum-likelihood, Bayesian-inference and statistical parsimony analyses revealed three well defined monophyletic groups. These clades corresponded to the 'green' and 'blue' groups of Symphysodon aequifasciatus, and to a previously morphologically unrecognized clade from the Xingu River drainage. These three clades were nested within a paraphyletic assemblage consisting of the 'brown' group of S. aequifasciatus and of both described subspecies of S. discus, the 'Heckel' and the 'abacaxi' discus. Nuclear allele sharing was observed among groups, but there were significant differences in frequencies. We inferred several processes including past fragmentation among groups, and restricted gene flow with isolation by distance within the paraphyletic 'brown+Heckel+abacaxi' groups, and suggest that differences among the 'blue', 'Heckel' and 'brown' groups are potentially maintained by differences in water chemistry preferences. We further inferred colonization of the western Amazon basin by an ancestor of the 'green' clade. The 'green' group was the only group with a pattern of haplotype distribution consistent of a demographic expansion, and the divergence of this clade from other groups of discus was consistent with recent geologic evidence on the breach of the Purus Arch which separates western Amazon from eastern Amazon. We further hypothesized that the differentiation of the 'Xingu' clade could be due to vicariance events resulting from Pleistocene sea level, and thus Amazon River level fluctuations. We discuss the bearings of our results on the current taxonomy of this group, and on the biological reality of the different forms, subspecies and species of Symphysodon concluding that we are probably observing a process of diversification, and therefore taxonomy will remain contentious.

How do obligate parasites evolve? A multi-gene phylogenetic analysis of downy mildews.

PubMed

Göker, Markus; Voglmayr, Hermann; Riethmüller, Alexandra; Oberwinkler, Franz

2007-02-01

Plant parasitism has independently evolved as a nutrition strategy in both true fungi and Oomycetes (stramenopiles). A large number of species within phytopathogenic Oomycetes, the so-called downy mildews, are defined as obligate biotrophs since they have not, to date, been cultured on any artificial medium. Other genera like Phytophthora and Pythium can in general be cultured on standard or non-standard agar media. Within all three groups there are many important plant pathogens responsible for severe economic losses as well as damage to natural ecosystems. Although they are important model systems to elucidate the evolution of obligate parasites, the phylogenetic relationships between these genera have not been clearly resolved. Based on the most comprehensive sampling of downy mildew genera to date and a representative sample of Phytophthora subgroups, we inferred the phylogenetic relationships from a multi-gene dataset containing both coding and non-coding nuclear and mitochondrial loci. Phylogenetic analyses were conducted under several optimality criteria and the results were largely consistent between all the methods applied. Strong support is achieved for monophyly of a clade comprising both the genus Phytophthora and the obligate biotrophic species. The facultatively parasitic genus Phytophthora is shown to be at least partly paraphyletic. Monophyly of a cluster nested within Phytophthora containing all obligate parasites is strongly supported. Within the obligate biotrophic downy mildews, four morphologically or ecologically well-defined subgroups receive statistical support: (1) A cluster containing all species with brownish-violet conidiosporangia, i.e., the genera Peronospora and Pseudoperonospora; (2) a clade comprising the genera with vesicular to pyriform haustoria (Basidiophora, Benua, Bremia, Paraperonospora, Plasmopara, Plasmoverna, Protobremia); (3) a group containing species included in Hyaloperonospora and Perofascia which almost exclusively infect Brassicaceae; (4) a clade including the grass parasites Viennotia oplismeni and Graminivora graminicola. Phylogenetic relationships between these four clades are not clearly resolved, and neither is the position of Sclerospora graminicola within the downy mildews. Character analysis indicates an evolutionary scenario of gradually increasing adaptation to plant parasitism in Peronosporales and that at least the most important of these adaptive steps occurred only once, including major host shifts within downy mildews.

Recent volcanism and mitochondrial DNA structuring in the lizard Gallotia atlantica from the island of Lanzarote.

PubMed

Bloor, P; Kemp, S J; Brown, R P

2008-02-01

The phylogeography of the lacertid lizard Gallotia atlantica from the small volcanic island of Lanzarote (Canary Islands) was analysed based on 1075 bp of mitochondrial DNA (mtDNA) sequence (partial cytochrome b and ND2) for 157 individuals from 27 sites (including three sites from neighbouring islets). Levels of sequence divergence were generally low, with the most distant haplotypes separated by only 14 mutational steps. MtDNA divergence appears to coincide with formation of the middle Pleistocene lowland that united formerly separate ancient islands to form the current island of Lanzarote, allowing rejection of a two-island model of phylogeographical structure. There was evidence of large-scale population expansion after island unification, consistent with the colonization of new areas. A nested clade phylogeographical analysis (NCPA) revealed significant phylogeographical structuring. Two-step and higher-level clades each had disjunct distributions, being found to the east and west of a common area with a north-south orientation that extends between coasts in the centre-east of the island (El Jable). Other clades were almost entirely restricted to the El Jable region alone. Bayesian Markov chain Monte Carlo analyses were used to separate ongoing gene flow from historical associations. These supported the NCPA by indicating recent (75,000-150,000 years ago) east-west vicariance across the El Jable region. Lava flows covered El Jable and other parts of the central lowland at this time and likely led to population extinctions and temporary dispersal barriers, although present-day evidence suggests some populations would have survived in small refugia. Expansion of the latter appears to explain the presence of a clade located between the eastern and western components of the disjunct clades. Direct relationships between mtDNA lineages and morphology were not found, although one of two morphological forms on the island has a disjunct distribution that is broadly concordant with east-west components of the phylogeographical pattern. This work demonstrates how recent volcanic activity can cause population fragmentation and thus shape genetic diversity on microgeographical scales.

[Isolation and identification of cow-origin Cryptosporidium isolates in Hefei].

PubMed

Sun, Tao; Liu, Wei; Wang, Ju-Hua; Xue, Xiu-Heng; Zhao, Chang-Cheng; Li, Pei-Ying

2011-12-01

To isolate cow-origin Cryptosporidium in Hefei, and identify its species. 285 dairy cattle fecal samples collected from a farm in Hefei were examined by using floating saturated solution of sucrose and modified acid-fast staining. Cryptosporidium oocysts were isolated and purified from positive fecal samples. Genetic DNA was extracted to be the template. According to the sequence of 18S rRNA gene and HSP70 gene from Cryptosporidium sp., the primers were designed and synthesized. The PCR products were amplified by PCR and nested-PCR. The nested PCR products were cloned and sequenced. Homology searches and phylogenic tree construction were done by DNAStar software. Five fecal samples were positive by morphological methods with an infection rate of 1.8% (5/285). Oocysts from the 5 positive fecal samples were elliptical or ovoid detected by using floating saturated solution of sucrose and modified acid-fast staining with the size of 7.37 microm x 6.13 microm and 7.58 microm x 6.20 microm, and a shape index of 1.20 and 1.22, respectively. Nested-PCR resulted in a 18S rRNA and HSP70 gene fragments with approximately 250 bp and 325 bp, respectively. The five isolates showed a high level of nucleic acid identity with sequence data of the 18S rRNA gene of Cryptosporidium andersoni (DQ989573), and they were clustered in the same clade. The highest HSP70 gene sequence identity was found among the five isolates and other reported C. andersoni isolates (AY954892 and DQ989576), and they were placed into the same clade. The cow-origin Cryptosporidium isolates derived from Hefei is Cryptosporidium andersoni.

Phylogeny, biogeography and ecological diversification of Sarcocornia (Salicornioideae, Amaranthaceae)

PubMed Central

Steffen, Simone; Ball, Peter; Mucina, Ladislav; Kadereit, Gudrun

2015-01-01

Background and Aims Sarcocornia comprises about 28 species of perennial succulent halophytes distributed worldwide, mainly in saline environments of warm-temperate and subtropical regions. The genus is characterized by strongly reduced leaves and flowers, which cause taxonomic difficulties; however, species in the genus show high diversity in growth form, with a mat-forming habit found in coastal salt marshes of all continents. Sarcocornia forms a monophyletic lineage with Salicornia whose species are all annual, yet the relationship between the two genera is poorly understood. This study is aimed at clarifying the phylogenetic relationship between Sarcocornia and Salicornia, interpreting biogeographical and ecological patterns in Sarcocornia, and gaining insights into putative parallel evolution of habit as an adaptation to environmental factors. Methods A comprehensively sampled and dated phylogeny of Sarcocornia is presented based on nuclear ribosomal DNA (external transcribed spacer) and chloroplast DNA (atpB-rbcL, rpl32-trnL) sequences; representative samples of Salicornia were also included in the analyses. To infer biogeographical patterns, an ancestral area reconstruction was conducted. Key Results The Sarcocornia/Salicornia lineage arose during the Mid-Miocene from Eurasian ancestors and diversified into four subclades: the Salicornia clade, the American Sarcocornia clade, the Eurasian Sarcocornia clade and the South African/Australian Sarcocornia clade. Sarcocornia is supported as paraphyletic, with Salicornia nested within Sarcocornia being sister to the American/Eurasian Sarcocornia clade. The American and the South African/Australian Sarcocornia clade as well as the Salicornia clade were reconstructed to be of Eurasian origin. The prostrate, mat-forming habit arose multiple times in Sarcocornia. Conclusions Sarcocornia diversified in salt-laden environments worldwide, repeatedly evolving superficially similar prostrate, mat-forming habits that seem advantageous in stressed environments with prolonged flooding, high tidal movement and frost. Some of these prostrate-habit types might be considered as ecotypes (e.g. S. pacifica or S. pillansii) while others represent good ecospecies (e.g. S. perennis, S. decumbens, S. capensis), hence representing different stages of speciation. PMID:25617410

A Monograph of Conostegia (Melastomataceae, Miconieae).

PubMed

Kriebel, Ricardo

2016-01-01

A recent molecular phylogenetic analysis identified a clade containing all species of Conostegia, but that also included species of Clidemia and Miconia nested inside. A taxonomic revision of a more broadly circumscribed Conostegia is presented here. In total, 77 species of Conostegia are recognized. One species from Ecuador, Conostegia ortizae is described as new. Twenty-nine new combinations are proposed for the species of Clidemia and Miconia that fall inside Conostegia. Two new names are proposed for the two species for which the epithet was previously occupied in Conostegia. An infrageneric classification of Conostegia is proposed recognizing three sections based on the results of the molecular phylogeny. This taxonomic revision includes ample documentation of the anatomy and morphology of most species in the genus, taxonomic descriptions, a dichotomous key, and distribution maps for all species.

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications.

PubMed

Tank, David C; Eastman, Jonathan M; Pennell, Matthew W; Soltis, Pamela S; Soltis, Douglas E; Hinchliff, Cody E; Brown, Joseph W; Sessa, Emily B; Harmon, Luke J

2015-07-01

Our growing understanding of the plant tree of life provides a novel opportunity to uncover the major drivers of angiosperm diversity. Using a time-calibrated phylogeny, we characterized hot and cold spots of lineage diversification across the angiosperm tree of life by modeling evolutionary diversification using stepwise AIC (MEDUSA). We also tested the whole-genome duplication (WGD) radiation lag-time model, which postulates that increases in diversification tend to lag behind established WGD events. Diversification rates have been incredibly heterogeneous throughout the evolutionary history of angiosperms and reveal a pattern of 'nested radiations' - increases in net diversification nested within other radiations. This pattern in turn generates a negative relationship between clade age and diversity across both families and orders. We suggest that stochastically changing diversification rates across the phylogeny explain these patterns. Finally, we demonstrate significant statistical support for the WGD radiation lag-time model. Across angiosperms, nested shifts in diversification led to an overall increasing rate of net diversification and declining relative extinction rates through time. These diversification shifts are only rarely perfectly associated with WGD events, but commonly follow them after a lag period. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Two new species of the Liolaemus elongatus-kriegi complex (Iguania, Liolaemidae) from Andean highlands of southern Chile

PubMed Central

Troncoso-Palacios, Jaime; Díaz, Hugo A.; Esquerré, Damien; Urra, Felix A.

2015-01-01

Abstract The elongatus-kriegi complex is one of the most diverse clades of the Liolaemus (sensu stricto) subgenus of lizards. There are currently 29 species recognized in this group distributed between Chile and Argentina. Based on molecular evidence, there seem to be five main clades nested within this complex: the elongatus, leopardinus, kriegi, petrophilus and punmahuida clades. Liolaemus buergeri and Liolaemus kriegi, both of the kriegi clade, were believed to inhabit the surroundings of the Laja Lagoon, in the Biobío Region of Chile. Moreover, this Chilean population of Liolaemus kriegi was recently recognized as an undescribed taxon called “Liolaemus sp. A” based on molecular phylogenetics. In this work, we studied these two populations of the Laja Lagoon and provided the morphological diagnosis to describe them as two new species: Liolaemus scorialis sp. n. and Liolaemus zabalai sp. n., previously considered Liolaemus buergeri and “Liolaemus kriegi/Liolaemus sp. A” respectively. Additionally, we identified another population of Liolaemus scorialis in the vicinity of La Mula Lagoon in the Araucanía Region of Chile. Liolaemus scorialis differs from almost all of the species of the elongatus-kriegi complex by its considerably smaller size. Nevertheless, without molecular data we cannot assign it to any particular subclade. Liolaemus zabalai belongs to the kriegi clade based on published molecular phylogenies. Finally, we provide some natural history data on both species and we document for the first time the presence of Liolaemus neuquensis in Chile from a museum specimen from La Mula Lagoon. PMID:25987873

Population differentiation in the red-legged kittiwake (Rissa brevirostris) as revealed by mitochondrial DNA

USGS Publications Warehouse

Patirana, A.; Hatcher, S.A.; Friesen, Vicki L.

2002-01-01

Population decline in red-legged kittiwakes (Rissa brevirostris) over recent decades has necessitated the collection of information on the distribution of genetic variation within and among colonies for implementation of suitable management policies. Here we present a preliminary study of the extent of genetic structuring and gene flow among the three principal breeding locations of red-legged kittiwakes using the hypervariable Domain I of the mitochondrial control region. Genetic variation was high relative to other species of seabirds, and was similar among locations. Analysis of molecular variance indicated that population genetic structure was statistically significant, and nested clade analysis suggested that kittiwakes breeding on Bering Island maybe genetically isolated from those elsewhere. However, phylogeographic structure was weak. Although this analysis involved only a single locus and a small number of samples, it suggests that red-legged kittiwakes probably constitute a single evolutionary significant unit; the possibility that they constitute two management units requires further investigation.

Host species and developmental stage, but not host social structure, affects bacterial community structure in socially polymorphic bees.

PubMed

McFrederick, Quinn S; Wcislo, William T; Hout, Michael C; Mueller, Ulrich G

2014-05-01

Social transmission and host developmental stage are thought to profoundly affect the structure of bacterial communities associated with honey bees and bumble bees, but these ideas have not been explored in other bee species. The halictid bees Megalopta centralis and M. genalis exhibit intrapopulation social polymorphism, which we exploit to test whether bacterial communities differ by host social structure, developmental stage, or host species. We collected social and solitary Megalopta nests and sampled bees and nest contents from all stages of host development. To survey these bacterial communities, we used 16S rRNA gene 454 pyrosequencing. We found no effect of social structure, but found differences by host species and developmental stage. Wolbachia prevalence differed between the two host species. Bacterial communities associated with different developmental stages appeared to be driven by environmentally acquired bacteria. A Lactobacillus kunkeei clade bacterium that is consistently associated with other bee species was dominant in pollen provisions and larval samples, but less abundant in mature larvae and pupae. Foraging adults appeared to often reacquire L. kunkeei clade bacteria, likely while foraging at flowers. Environmental transmission appears to be more important than social transmission for Megalopta bees at the cusp between social and solitary behavior. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Do brooding and polygamy behaviors exist on Cretaceous oviraptoroid dinosaurs of China: a paleobiological perspective

NASA Astrophysics Data System (ADS)

Yang, T.-R.; Cheng, Y.-N.; Yang, K.-M.

2012-04-01

Brooding, parental care, and polygamy represent three different stages in bird's reproduction. The oringin of these behaviors is still in debate. Several samples excavated from China strengthen the phylogenetic relationship between birds and dinosaurs, for example, feathered dinosaurs, paired-eggs in pelvic region of an oviraptorid dinosaur, and small theropod fossils. Previous studies in past two decades, including an oviraptor sitting on a clutch and comparison of the ratio of clutch-volume to adult-body-size between Aves and Mesozoic dinosaurs, proposed that these behaviors had appeared on some Cretaceous theropods (e.g., oviraptor and troodon). These researches also indicate the possibility of endothermy and male care first. In conclusion, this reproduction strategy might support females having more remnant energy to build a larger clutch contributed eggs from multiple females, and brooded by males only. From our cluster analysis through paleoecological perspectives, the eggs in Cretaceous oviraptor's nest should not be corporately laid by multiple females. In morphological observation, the fossilized clutches from Ganzhou, Jiangxi, Mainland China, are 2-layered interbeded with matrix of reddish-brown siltstone or clays. The inner-layer eggs are hampered from directly contacting with adult dinosaurs body. Furthermore, the blunt ends of the eggs point to the center, and incline away forming a mound-shape nest, which is completely different from those of precocial and male-caring megapode. The ornamentation of eggshell surface and microstructures from thin sections of eggs from oviraptors and ostrich (Struthioniformes) are totally different. Comparison of thickness in different part of oviraptor's egg also reveal possible physiological structure in the egg and ecological behaviors. The detailed comparison implies that the Mesozoic oviraptoroid dinosaurs hold absolutely different incubation and caring behaviors from extant birds. We propose an alternative hypothesis herein suggesting that the paternal care and brooding behaviors not originated from Mesozoic clade of dinosaurs, which didn't brood their clutch and show polygamy behaviors, either. The oviraptors dinosaurs adults laid pair eggs each time, arrange them toroidally, buried them in a substrate, and then superpose another layer of eggs. Oviraptoroid dinosaurs probably guard their exquisite nests without caring and egg-rotation behaviors, just alike to extant crocodilians which belong to the same clade of Archosaur Reptiles.

The relationships within the Chaitophorinae and Drepanosiphinae (Hemiptera, Aphididae) inferred from molecular-based phylogeny and comprehensive morphological data

PubMed Central

Wieczorek, Karina; Lachowska-Cierlik, Dorota; Kajtoch, Łukasz; Kanturski, Mariusz

2017-01-01

The Chaitophorinae is a bionomically diverse Holarctic subfamily of Aphididae. The current classification includes two tribes: the Chaitophorini associated with deciduous trees and shrubs, and Siphini that feed on monocotyledonous plants. We present the first phylogenetic hypothesis for the subfamily, based on molecular and morphological datasets. Molecular analyses were based on the mitochondrial gene cytochrome oxidase subunit I (COI) and the nuclear gene elongation factor-1α (EF-1α). Phylogenetic inferences were obtained individually on each of genes and joined alignments using Bayesian inference (BI) and Maximum likelihood (ML). In phylogenetic trees reconstructed on the basis of nuclear and mitochondrial genes as well as a morphological dataset, the monophyly of Siphini and the genus Chaitophorus was supported. Periphyllus forms independent lineages from Chaitophorus and Siphini. Within this genus two clades comprising European and Asiatic species, respectively, were indicated. Concerning relationships within the subfamily, EF-1α and joined COI and EF-1α genes analysis strongly supports the hypothesis that Chaitophorini do not form a monophyletic clade. Periphyllus is a sister group to a clade containing Chaitophorus and Siphini. The Asiatic unit of Periphyllus also includes Trichaitophorus koyaensis. The analysis of morphological dataset under equally weighted parsimony also supports the view that Chaitophorini is an artificial taxon, as Lambersaphis pruinosae and Pseudopterocomma hughi, both traditionally included in the Chaitophorini, formed independent lineages. COI analyses support consistent groups within the subfamily, but relationships between groups are poorly resolved. These analyses were extended to include the species of closely related and phylogenetically unstudied subfamily Drepanosiphinae, which produced congruent results. Genera Drepanosiphum and Depanaphis are monophyletic and sister. The position of Yamatocallis tokyoensis differs in the molecular and morphological analyses, i.e. it is either an independent lineage (EF-1α, COI, joined COI and EF-1α genes) or is nested inside this unit (morphology). Our data also support separation of Chaitophorinae from Drepanosiphinae. PMID:28288166

DNA hybridization evidence for the Australasian affinity of the American marsupial Dromiciops australis.

PubMed Central

Kirsch, J A; Dickerman, A W; Reig, O A; Springer, M S

1991-01-01

DNA hybridization was used to compare representatives of the major groups of marsupials and a eutherian outgroup. Because of the large genetic distances separating marsupial families, trees were calculated from normalized percentages of hybridization; thermal-melting statistics, however, gave identical topologies for the well-supported clades. The most notable results were the association of the only extant microbiotheriid, Dromiciops australis, an American marsupial, with the Australasian Diprotodontia, and of both together with the Dasyuridae. Estimates of the rate of divergence among marsupial genomes suggest that the Dromiciops-Diprotodontia split occurred approximately 50 million years ago, well after the establishment of the major clades of marsupials but before deep oceanic barriers prohibited dispersal among Australia, Antarctica, and South America. Because Dromiciops is nested within an Australasian group, it seems likely that dispersal from Australia accounts for its present distribution. Images PMID:1961710

Tree ferns: monophyletic groups and their relationships as revealed by four protein-coding plastid loci.

PubMed

Korall, Petra; Pryer, Kathleen M; Metzgar, Jordan S; Schneider, Harald; Conant, David S

2006-06-01

Tree ferns are a well-established clade within leptosporangiate ferns. Most of the 600 species (in seven families and 13 genera) are arborescent, but considerable morphological variability exists, spanning the giant scaly tree ferns (Cyatheaceae), the low, erect plants (Plagiogyriaceae), and the diminutive endemics of the Guayana Highlands (Hymenophyllopsidaceae). In this study, we investigate phylogenetic relationships within tree ferns based on analyses of four protein-coding, plastid loci (atpA, atpB, rbcL, and rps4). Our results reveal four well-supported clades, with genera of Dicksoniaceae (sensu ) interspersed among them: (A) (Loxomataceae, (Culcita, Plagiogyriaceae)), (B) (Calochlaena, (Dicksonia, Lophosoriaceae)), (C) Cibotium, and (D) Cyatheaceae, with Hymenophyllopsidaceae nested within. How these four groups are related to one other, to Thyrsopteris, or to Metaxyaceae is weakly supported. Our results show that Dicksoniaceae and Cyatheaceae, as currently recognised, are not monophyletic and new circumscriptions for these families are needed.

Male fighting and "territoriality" within colonies of the ant Cardiocondyla venustula.

PubMed

Frohschammer, Sabine; Heinze, Jürgen

2009-01-01

The ant genus Cardiocondyla is characterized by a bizarre male polymorphism with wingless fighter males and winged disperser males. Winged males have been lost convergently in several clades, and in at least one of them, wingless males have evolved mutual tolerance. To better understand the evolutionary pathways of reproductive tactics, we investigated Cardiocondyla venustula, a species, which in a phylogenetic analysis clusters with species with fighting and species with mutually tolerant, wingless males. Wingless males of C. venustula use their strong mandibles to kill freshly eclosed rival males and also engage in short fights with other adult males, but in addition show a novel behavior hitherto not reported from social insect males: they spread out in the natal nest and defend "territories" against other males. Ant males therefore show a much larger variety of reproductive tactics than previously assumed.

Male fighting and ``territoriality'' within colonies of the ant Cardiocondyla venustula

NASA Astrophysics Data System (ADS)

Frohschammer, Sabine; Heinze, Jürgen

2009-01-01

The ant genus Cardiocondyla is characterized by a bizarre male polymorphism with wingless fighter males and winged disperser males. Winged males have been lost convergently in several clades, and in at least one of them, wingless males have evolved mutual tolerance. To better understand the evolutionary pathways of reproductive tactics, we investigated Cardiocondyla venustula, a species, which in a phylogenetic analysis clusters with species with fighting and species with mutually tolerant, wingless males. Wingless males of C. venustula use their strong mandibles to kill freshly eclosed rival males and also engage in short fights with other adult males, but in addition show a novel behavior hitherto not reported from social insect males: they spread out in the natal nest and defend “territories” against other males. Ant males therefore show a much larger variety of reproductive tactics than previously assumed.

A Monograph of Conostegia (Melastomataceae, Miconieae)

PubMed Central

Kriebel, Ricardo

2016-01-01

Abstract A recent molecular phylogenetic analysis identified a clade containing all species of Conostegia, but that also included species of Clidemia and Miconia nested inside. A taxonomic revision of a more broadly circumscribed Conostegia is presented here. In total, 77 species of Conostegia are recognized. One species from Ecuador, Conostegia ortizae is described as new. Twenty-nine new combinations are proposed for the species of Clidemia and Miconia that fall inside Conostegia. Two new names are proposed for the two species for which the epithet was previously occupied in Conostegia. An infrageneric classification of Conostegia is proposed recognizing three sections based on the results of the molecular phylogeny. This taxonomic revision includes ample documentation of the anatomy and morphology of most species in the genus, taxonomic descriptions, a dichotomous key, and distribution maps for all species. PMID:27536193

Traditional taxonomic groupings mask evolutionary history: a molecular phylogeny and new classification of the chromodorid nudibranchs.

PubMed

Johnson, Rebecca Fay; Gosliner, Terrence M

2012-01-01

Chromodorid nudibranchs (16 genera, 300+ species) are beautiful, brightly colored sea slugs found primarily in tropical coral reef habitats and subtropical coastal waters. The chromodorids are the most speciose family of opisthobranchs and one of the most diverse heterobranch clades. Chromodorids have the potential to be a model group with which to study diversification, color pattern evolution, are important source organisms in natural products chemistry and represent a stunning and widely compelling example of marine biodiversity. Here, we present the most complete molecular phylogeny of the chromodorid nudibranchs to date, with a broad sample of 244 specimens (142 new), representing 157 (106 new) chromodorid species, four actinocylcid species and four additional dorid species utilizing two mitochondrial markers (16s and COI). We confirmed the monophyly of the Chromodorididae and its sister group relationship with the Actinocyclidae. We were also able to, for the first time, test generic monophyly by including more than one member of all 14 of the non-monotypic chromodorid genera. Every one of these 14 traditional chromodorid genera are either non-monophyletic, or render another genus paraphyletic. Additionally, both the monotypic genera Verconia and Diversidoris are nested within clades. Based on data shown here, there are three individual species and five clades limited to the eastern Pacific and Atlantic Oceans (or just one of these ocean regions), while the majority of chromodorid clades and species are strictly Indo-Pacific in distribution. We present a new classification of the chromodorid nudibranchs. We use molecular data to untangle evolutionary relationships and retain a historical connection to traditional systematics by using generic names attached to type species as clade names.

Molecular phylogeny of extant Holothuroidea (Echinodermata).

PubMed

Miller, Allison K; Kerr, Alexander M; Paulay, Gustav; Reich, Mike; Wilson, Nerida G; Carvajal, Jose I; Rouse, Greg W

2017-06-01

Sea cucumbers (Holothuroidea) are a morphologically diverse, ecologically important, and economically valued clade of echinoderms; however, the understanding of the overall systematics of the group remains controversial. Here, we present a phylogeny of extant Holothuroidea assessed with maximum parsimony, maximum likelihood, and Bayesian approaches using approximately 4.3kb of mt- (COI, 16S, 12S) and nDNA (H3, 18S, 28S) sequences from 82 holothuroid terminals representing 23 of the 27 widely-accepted family-ranked taxa. Currently five holothuroid taxa of ordinal rank are accepted. We find that three of the five orders are non-monophyletic, and we revise the taxonomy of the groups accordingly. Apodida is sister to the rest of Holothuroidea, here considered Actinopoda. Within Actinopoda, Elasipodida in part is sister to the remaining Actinopoda. This latter clade, comprising holothuroids with respiratory trees, is now called Pneumonophora. The traditional Aspidochirotida is paraphyletic, with representatives from three orders (Molpadida, Dendrochirotida, and Elasipodida in part) nested within. Therefore, we discontinue the use of Aspidochirotida and instead erect Holothuriida as the sister group to the remaining Pneumonophora, here termed Neoholothuriida. We found four well-supported major clades in Neoholothuriida: Dendrochirotida, Molpadida and two new clades, Synallactida and Persiculida. The mapping of traditionally-used morphological characters in holothuroid systematics onto the phylogeny revealed marked homoplasy in most characters demonstrating that further taxonomic revision of Holothuroidea is required. Two time-tree analyses, one based on calibrations for uncontroversial crown group dates for Eleutherozoa, Echinozoa and Holothuroidea and another using these calibrations plus four more from within Holothuroidea, showed major discrepancies, suggesting that fossils of Holothuroidea may need reassessment in terms of placing these forms with existing crown clades. Copyright © 2017 Elsevier Inc. All rights reserved.

The evolutionary history of Mimosa (Leguminosae): toward a phylogeny of the sensitive plants.

PubMed

Simon, Marcelo F; Grether, Rosaura; de Queiroz, Luciano P; Särkinen, Tiina E; Dutra, Valquíria F; Hughes, Colin E

2011-07-01

Large genera provide remarkable opportunities to investigate patterns of morphological evolution and historical biogeography in plants. A molecular phylogeny of the species-rich and morphologically and ecologically diverse genus Mimosa was generated to evaluate its infrageneric classification, reconstruct the evolution of a set of morphological characters, and establish the relationships of Old World species to the rest of the genus. We used trnD-trnT plastid sequences for 259 species of Mimosa (ca. 50% of the total) to reconstruct the phylogeny of the genus. Six morphological characters (petiolar nectary, inflorescence type, number of stamens, number of petals, pollen type, and seismonasty) were optimized onto the molecular tree. Mimosa was recovered as a monophyletic clade nested within the Piptadenia group and includes the former members of Schrankia, corroborating transfer of that genus to Mimosa. Although we found good support for several infrageneric groups, only one section (Mimadenia) was recovered as monophyletic. All but one of the morphological characters analyzed showed high levels of homoplasy. High levels of geographic structure were found, with species from the same area tending to group together in the phylogeny. Old World species of Mimosa form a monophyletic clade deeply nested within New World groups, indicating recent (6-10 Ma) long-distance dispersal. Although based on a single plastid region, our results establish a preliminary phylogenetic framework for Mimosa that can be used to infer patterns of morphological evolution and relationships and which provides pointers toward a revised infrageneric classification.

Comparative genomics identifies distinct lineages of S. Enteritidis from Queensland, Australia.

PubMed

Graham, Rikki M A; Hiley, Lester; Rathnayake, Irani U; Jennison, Amy V

2018-01-01

Salmonella enterica is a major cause of gastroenteritis and foodborne illness in Australia where notification rates in the state of Queensland are the highest in the country. S. Enteritidis is among the five most common serotypes reported in Queensland and it is a priority for epidemiological surveillance due to concerns regarding its emergence in Australia. Using whole genome sequencing, we have analysed the genomic epidemiology of 217 S. Enteritidis isolates from Queensland, and observed that they fall into three distinct clades, which we have differentiated as Clades A, B and C. Phage types and MLST sequence types differed between the clades and comparative genomic analysis has shown that each has a unique profile of prophage and genomic islands. Several of the phage regions present in the S. Enteritidis reference strain P125109 were absent in Clades A and C, and these clades also had difference in the presence of pathogenicity islands, containing complete SPI-6 and SPI-19 regions, while P125109 does not. Antimicrobial resistance markers were found in 39 isolates, all but one of which belonged to Clade B. Phylogenetic analysis of the Queensland isolates in the context of 170 international strains showed that Queensland Clade B isolates group together with the previously identified global clade, while the other two clades are distinct and appear largely restricted to Australia. Locally sourced environmental isolates included in this analysis all belonged to Clades A and C, which is consistent with the theory that these clades are a source of locally acquired infection, while Clade B isolates are mostly travel related.

Evolutionary assembly of the conifer fauna: distinguishing ancient from recent associations in bark beetles.

PubMed

Sequeira, A S; Normark, B B; Farrell, B D

2000-12-07

Several shifts from ancestral conifer feeding to angiosperm feeding have been implicated in the unparalleled diversification of beetle species. The single largest angiosperm-feeding beetle clade occurs in the weevils, and comprises the family Curculionidae and relatives. Most authorities confidently place the bark beetles (Scolytidae) within this radiation of angiosperm feeders. However, some clues indicate that the association between conifers and some scolytids, particularly in the tribe Tomicini, is a very ancient one. For instance, several fragments of Gondwanaland (South America, New Caledonia, Australia and New Guinea) harbour endemic Tomicini specialized on members of the formerly widespread and abundant conifer family Araucariaceae. As a first step towards resolving this seeming paradox, we present a phylogenetic analysis of the beetle family Scolytidae with particularly intensive sampling of conifer-feeding Tomicini and allies. We sequenced and analysed elongation factor 1alpha and nuclear rDNAs 18S and 28S for 45 taxa, using members of the weevil family Cossoninae as an out-group. Our results indicate that conifer feeding is the ancestral host association of scolytids, and that the most basal lineages of scolytids feed on Aramucaria. If scolytids are indeed nested within a great angiosperm-feeding clade, as many authorities have held, then a reversion to conifer feeding in ancestral scolytids appears to have occurred in the Mesozoic, when Araucaria still formed a major component of the woody flora.

Oligocene Termite Nests with In Situ Fungus Gardens from the Rukwa Rift Basin, Tanzania, Support a Paleogene African Origin for Insect Agriculture

PubMed Central

Roberts, Eric M.; Todd, Christopher N.; Aanen, Duur K.; Nobre, Tânia; Hilbert-Wolf, Hannah L.; O’Connor, Patrick M.; Tapanila, Leif; Mtelela, Cassy; Stevens, Nancy J.

2016-01-01

Based on molecular dating, the origin of insect agriculture is hypothesized to have taken place independently in three clades of fungus-farming insects: the termites, ants or ambrosia beetles during the Paleogene (66–24 Ma). Yet, definitive fossil evidence of fungus-growing behavior has been elusive, with no unequivocal records prior to the late Miocene (7–10 Ma). Here we report fossil evidence of insect agriculture in the form of fossil fungus gardens, preserved within 25 Ma termite nests from southwestern Tanzania. Using these well-dated fossil fungus gardens, we have recalibrated molecular divergence estimates for the origins of termite agriculture to around 31 Ma, lending support to hypotheses suggesting an African Paleogene origin for termite-fungus symbiosis; perhaps coinciding with rift initiation and changes in the African landscape. PMID:27333288

Macroevolutionary assembly of ant/plant symbioses: Pseudomyrmex ants and their ant-housing plants in the Neotropics

PubMed Central

Chomicki, Guillaume; Ward, Philip S.; Renner, Susanne S.

2015-01-01

Symbioses include some of the clearest cases of coevolution, but their origin, loss or reassembly with different partners can rarely be inferred. Here we use ant/plant symbioses involving three plant clades to investigate the evolution of symbioses. We generated phylogenies for the big-eyed arboreal ants (Pseudomyrmecinae), including 72% of their 286 species, as well as for five of their plant host groups, in each case sampling more than 61% of the species. We show that the ant-housing Vachellia (Mimosoideae) clade and its ants co-diversified for the past 5 Ma, with some species additionally colonized by younger plant-nesting ant species, some parasitic. An apparent co-radiation of ants and Tachigali (Caesalpinioideae) was followed by waves of colonization by the same ant clade, and subsequent occupation by a younger ant group. Wide crown and stem age differences between the ant-housing genus Triplaris (Polygonaceae) and its obligate ant inhabitants, and stochastic trait mapping, indicate that its domatium evolved earlier than the ants now occupying it, suggesting previous symbioses that dissolved. Parasitic ant species evolved from generalists, not from mutualists, and are younger than the mutualistic systems they parasitize. Our study illuminates the macroevolutionary assembly of ant/plant symbioses, which has been highly dynamic, even in very specialized systems. PMID:26582029

The mitochondrial phylogeography and intraspecific taxonomy of the Steppe Racerunner, Eremias arguta (Pallas) (Lacertidae: Sauria, Reptilia), reflects biogeographic patterns in Middle Asia.

PubMed

Poyarkov, Nikolay A; Orlova, Valentina F; Chirikova, Marina A

2014-12-15

Steppe racerunner, Eremias (Eremias) arguta, is one of the most widespread species of the Asian racerunners (genus Eremias). Several subspecies were traditionally recognized however, morphological variability is so high that delimitation of these subspecies was always problematic. Here we present a phylogenetic hypothesis for this species based on cytochrome b sequences (55 samples from 35 populations, 900 bp partial sequences), infer it biogeography and the revise its subspecific structure. Six major phylogenetic lineages were revealed. The southernmost populations (E. a. uzbekistanica) from Uzbekistan form a clade together with the Issyk-Kul Lake subspecies (E. a. darevskii) based on both molecular and morphological evidence. Within more northern populations, there is a split between populations from Northern Caucasus, Europe and Western Kazakhstan (E. a. deserti) and Central and Eastern Kazakhstan populations (E. a. arguta). Transcaucasian (E. a. transcaucasica) steppe racerunners are grouped with Middle Asian populations. Finally, the easternmost samples, assigned to "E. a. potanini" are nested within the E. a. arguta clade. Populations from the Ili River Valley form a separate lineage sister to the clade joining all other E. arguta lineages and might represent a yet undescribed taxon. Species distribution in relation to historical biogeography of Middle Asia is discussed. 

Phylogeny and genetic diversity of Bridgeoporus nobilissimus inferred using mitochondrial and nuclear rDNA sequences

USGS Publications Warehouse

Redberg, G.L.; Hibbett, D.S.; Ammirati, J.F.; Rodriguez, R.J.

2003-01-01

The genetic diversity and phylogeny of Bridgeoporus nobilissimus have been analyzed. DNA was extracted from spores collected from individual fruiting bodies representing six geographically distinct populations in Oregon and Washington. Spore samples collected contained low levels of bacteria, yeast and a filamentous fungal species. Using taxon-specific PCR primers, it was possible to discriminate among rDNA from bacteria, yeast, a filamentous associate and B. nobilissimus. Nuclear rDNA internal transcribed spacer (ITS) region sequences of B. nobilissimus were compared among individuals representing six populations and were found to have less than 2% variation. These sequences also were used to design dual and nested PCR primers for B. nobilissimus-specific amplification. Mitochondrial small-subunit rDNA sequences were used in a phylogenetic analysis that placed B. nobilissimus in the hymenochaetoid clade, where it was associated with Oxyporus and Schizopora.

Going to extremes: contrasting rates of diversification in a recent radiation of new world passerine birds.

PubMed

Barker, F Keith; Burns, Kevin J; Klicka, John; Lanyon, Scott M; Lovette, Irby J

2013-03-01

Recent analyses suggest that a few major shifts in diversification rate may be enough to explain most of the disparity in diversity among vertebrate lineages. At least one significant increase in diversification rate appears to have occurred within the birds; however, several nested lineages within birds have been identified as hyperdiverse by different studies. A clade containing the finches and relatives (within the avian order Passeriformes), including a large radiation endemic to the New World that comprises ~8% of all bird species, may be the true driver of this rate increase. Understanding the patterns and processes of diversification of this diverse lineage may go a long way toward explaining the apparently rapid diversification rates of both passerines and of birds as a whole. We present the first multilocus phylogenetic analyses of this endemic New World radiation of finch relatives that include sampling of all recognized genera, a relaxed molecular clock analysis of its divergence history, and an analysis of its broad-scale diversification patterns. These analyses recovered 5 major lineages traditionally recognized as avian families, but identified an additional 10 relatively ancient lineages worthy of recognition at the family level. Time-calibrated diversification analyses suggested that at least 3 of the 15 family-level lineages were significantly species poor given the entire group's background diversification rate, whereas at least one-the tanagers of family Thraupidae-appeared significantly more diverse. Lack of an age-diversity relationship within this clade suggests that, due to rapid initial speciation, it may have experienced density-dependent ecological limits on its overall diversity.

Cranial base evolution within the hominin clade

PubMed Central

Nevell, L; Wood, B

2008-01-01

The base of the cranium (i.e. the basioccipital, the sphenoid and the temporal bones) is of particular interest because it undergoes significant morphological change within the hominin clade, and because basicranial morphology features in several hominin species diagnoses. We use a parsimony analysis of published cranial and dental data to predict the cranial base morphology expected in the hypothetical last common ancestor of the Pan–Homo clade. We also predict the primitive condition of the cranial base for the hominin clade, and document the evolution of the cranial base within the major subclades within the hominin clade. This analysis suggests that cranial base morphology has continued to evolve in the hominin clade, both before and after the emergence of the genus Homo. PMID:18380865

Convergent evolution of embryonic growth and development in the eastern fence lizard (Sceloporus undulatus).

PubMed

Oufieroi, Christopher E; Angilletta, Michael J

2006-05-01

Theory predicts that cold environments will select for strategies that enhance the growth of ectotherms, such as early emergence from nests and more efficient use of resources. We used a common garden experiment to detect parallel clines in rates of embryonic growth and development by eastern fence lizards (Sceloporus undulatus). Using realistic thermal conditions, we measured growth efficiencies and incubation periods of lizards from five populations representing two distinct clades. In both clades, embryos from cold environments (Indiana, New Jersey, and Virginia) grew more efficiently and hatched earlier than embryos from warm environments (Florida and South Carolina). Because eggs from cold environments were larger than eggs from warm environments, we experimentally miniaturized eggs from one population (Virginia) to determine whether rapid growth and development were caused by a greater maternal investment. Embryos in miniaturized eggs grew as efficiently and incubated for the same duration as embryos in unmanipulated eggs. Taken together, our results suggest countergradient variation has evolved at least twice in S. undulatus.

Classification of Cowpox Viruses into Several Distinct Clades and Identification of a Novel Lineage

PubMed Central

Franke, Annika; Pfaff, Florian; Jenckel, Maria; Hoffmann, Bernd; Höper, Dirk; Antwerpen, Markus; Meyer, Hermann; Beer, Martin; Hoffmann, Donata

2017-01-01

Cowpox virus (CPXV) was considered as uniform species within the genus Orthopoxvirus (OPV). Previous phylogenetic analysis indicated that CPXV is polyphyletic and isolates may cluster into different clades with two of these clades showing genetic similarities to either variola (VARV) or vaccinia viruses (VACV). Further analyses were initiated to assess both the genetic diversity and the evolutionary background of circulating CPXVs. Here we report the full-length sequences of 20 CPXV strains isolated from different animal species and humans in Germany. A phylogenetic analysis of altogether 83 full-length OPV genomes confirmed the polyphyletic character of the species CPXV and suggested at least four different clades. The German isolates from this study mainly clustered into two CPXV-like clades, and VARV- and VACV-like strains were not observed. A single strain, isolated from a cotton-top tamarin, clustered distantly from all other CPXVs and might represent a novel and unique evolutionary lineage. The classification of CPXV strains into clades roughly followed their geographic origin, with the highest clade diversity so far observed for Germany. Furthermore, we found evidence for recombination between OPV clades without significant disruption of the observed clustering. In conclusion, this analysis markedly expands the number of available CPXV full-length sequences and confirms the co-circulation of several CPXV clades in Germany, and provides the first data about a new evolutionary CPXV lineage. PMID:28604604

Evolutionary Divergence of Aggregatibacter actinomycetemcomitans

PubMed Central

Kittichotirat, W.; Bumgarner, R.E.; Chen, C.

2016-01-01

Gram-negative facultative Aggregatibacter actinomycetemcomitans is an oral pathogen associated with periodontitis. The genetic heterogeneity among A. actinomycetemcomitans strains has been long recognized. This study provides a comprehensive genomic analysis of A. actinomycetemcomitans and the closely related nonpathogenic Aggregatibacter aphrophilus. Whole genome sequencing by Illumina MiSeq platform was performed for 31 A. actinomycetemcomitans and 2 A. aphrophilus strains. Sequence similarity analysis shows a total of 3,220 unique genes across the 2 species, where 1,550 are core genes present in all genomes and 1,670 are variable genes (accessory genes) missing in at least 1 genome. Phylogenetic analysis based on 397 concatenated core genes distinguished A. aphrophilus and A. actinomycetemcomitans. The latter was in turn divided into 5 clades: clade b (serotype b), clade c (serotype c), clade e/f (serotypes e and f), clade a/d (serotypes a and d), and clade e′ (serotype e strains). Accessory genes accounted for 14.1% to 23.2% of the A. actinomycetemcomitans genomes, with a majority belonging to the category of poorly characterized by Cluster of Orthologous Groups classification. These accessory genes were often organized into genomic islands (n = 387) with base composition biases, suggesting their acquisitions via horizontal gene transfer. There was a greater degree of similarity in gene content and genomic islands among strains within clades than between clades. Strains of clade e′ isolated from human were found to be missing the genomic island that carries genes encoding cytolethal distending toxins. Taken together, the results suggest a pattern of sequential divergence, starting from the separation of A. aphrophilus and A. actinomycetemcomitans through gain and loss of genes and ending with the divergence of the latter species into distinct clades and serotypes. With differing constellations of genes, the A. actinomycetemcomitans clades may have evolved distinct adaptation strategies to the human oral cavity. PMID:26420795

High diversity and rapid diversification in the head louse, Pediculus humanus (Pediculidae: Phthiraptera)

PubMed Central

Ashfaq, Muhammad; Prosser, Sean; Nasir, Saima; Masood, Mariyam; Ratnasingham, Sujeevan; Hebert, Paul D. N.

2015-01-01

The study analyzes sequence variation of two mitochondrial genes (COI, cytb) in Pediculus humanus from three countries (Egypt, Pakistan, South Africa) that have received little prior attention, and integrates these results with prior data. Analysis indicates a maximum K2P distance of 10.3% among 960 COI sequences and 13.8% among 479 cytb sequences. Three analytical methods (BIN, PTP, ABGD) reveal five concordant OTUs for COI and cytb. Neighbor-Joining analysis of the COI sequences confirm five clusters; three corresponding to previously recognized mitochondrial clades A, B, C and two new clades, “D” and “E”, showing 2.3% and 2.8% divergence from their nearest neighbors (NN). Cytb data corroborate five clusters showing that clades “D” and “E” are both 4.6% divergent from their respective NN clades. Phylogenetic analysis supports the monophyly of all clusters recovered by NJ analysis. Divergence time estimates suggest that the earliest split of P. humanus clades occured slightly more than one million years ago (MYa) and the latest about 0.3 MYa. Sequence divergences in COI and cytb among the five clades of P. humanus are 10X those in their human host, a difference that likely reflects both rate acceleration and the acquisition of lice clades from several archaic hominid lineages. PMID:26373806

Phylogeny and classification of the East Asian Amitostigma alliance (Orchidaceae: Orchideae) based on six DNA markers.

PubMed

Tang, Ying; Yukawa, Tomohisa; Bateman, Richard M; Jiang, Hong; Peng, Hua

2015-05-26

Tribe Orchideae dominates the orchid flora of the temperate Northern Hemisphere but its representatives in East Asia had been subject to less intensive phylogenetic study than those in Eurasia and North America. Although this situation was improved recently by the molecular phylogenetic study of Jin et al., comparatively few species were analyzed from the species-rich and taxonomically controversial East Asian Amitostigma alliance. Here, we present a framework nrITS tree of 235 accessions of Orchideae plus an in-depth analysis of 110 representative accessions, encompassing most widely recognized species within the alliance, to elucidate their relationships. We used parsimony, likelihood and Bayesian approaches to generate trees from data for two nuclear (nrITS, low-copy Xdh) and four chloroplast (matK, psbA-trnH, trnL-F, trnS-trnG) markers. Nuclear and plastid data were analyzed separately due to a few hard incongruences that most likely reflect chloroplast capture. Our results suggest key phylogenetic placements for Sirindhornia and Brachycorythis, and confirm previous assertions that the Amitostigma alliance is monophyletic and sister to the Eurasian plus European clades of subtribe Orchidinae. Seven robust clades are evident within the alliance, but none corresponds precisely with any of the traditional genera; the smaller and more morphologically distinct genera Tsaiorchis, Hemipilia, Neottianthe and Hemipiliopsis are monophyletic but each is nested within a polyphyletic plexus of species attributed to either Ponerorchis or the most plesiomorphic genus, Amitostigma. Two early-divergent clades that escaped analysis by Jin et al. undermine their attempt to circumscribe an expanded monophyletic genus Ponerorchis. We provide a new framework on the complex phylogenetic relationships between Amitostigma and other genera traditionally included in its alliance; based on which, we combine the entire Amitostigma alliance into a morphologically and molecularly circumscribed Amitostigma sensu latissimo that also contains seven molecularly circumscribed sections. Our molecular trees imply unusually high levels of morphological homoplasy, but these will need to be quantified via a future group-wide review of the alliance based on living plants if morphology is to be fully integrated into our classification.

Multigene Molecular Phylogeny and Biogeographic Diversification of the Earth Tongue Fungi in the Genera Cudonia and Spathularia (Rhytismatales, Ascomycota)

PubMed Central

Ge, Zai-Wei; Yang, Zhu L.; Pfister, Donald H.; Carbone, Matteo; Bau, Tolgor; Smith, Matthew E.

2014-01-01

The family Cudoniaceae (Rhytismatales, Ascomycota) was erected to accommodate the “earth tongue fungi” in the genera Cudonia and Spathularia. There have been no recent taxonomic studies of these genera, and the evolutionary relationships within and among these fungi are largely unknown. Here we explore the molecular phylogenetic relationships within Cudonia and Spathularia using maximum likelihood and Bayesian inference analyses based on 111 collections from across the Northern Hemisphere. Phylogenies based on the combined data from ITS, nrLSU, rpb2 and tef-1α sequences support the monophyly of three main clades, the /flavida, /velutipes, and /cudonia clades. The genus Cudonia and the family Cudoniaceae are supported as monophyletic groups, while the genus Spathularia is not monophyletic. Although Cudoniaceae is monophyletic, our analyses agree with previous studies that this family is nested within the Rhytismataceae. Our phylogenetic analyses circumscribes 32 species-level clades, including the putative recognition of 23 undescribed phylogenetic species. Our molecular phylogeny also revealed an unexpectedly high species diversity of Cudonia and Spathularia in eastern Asia, with 16 (out of 21) species-level clades of Cudonia and 8 (out of 11) species-level clades of Spathularia. We estimate that the divergence time of the Cudoniaceae was in the Paleogene approximately 28 Million years ago (Mya) and that the ancestral area for this group of fungi was in Eastern Asia based on the current data. We hypothesize that the large-scale geological and climatic events in Oligocene (e.g. the global cooling and the uplift of the Tibetan plateau) may have triggered evolutionary radiations in this group of fungi in East Asia. This work provides a foundation for future studies on the phylogeny, diversity, and evolution of Cudonia and Spathularia and highlights the need for more molecular studies on collections from Europe and North America. PMID:25084276

Molecular phylogenetics of the Ronnbergia Alliance (Bromeliaceae, Bromelioideae) and insights into their morphological evolution.

PubMed

Aguirre-Santoro, Julián; Michelangeli, Fabián A; Stevenson, Dennis W

2016-07-01

The tank-epiphytic clade of berry-fruited bromeliads, also known as the Core Bromelioideae, represents a remarkable event of adaptive radiation within the Bromeliaceae; however, the details of this radiation have been difficult to study because this lineage is plagued with generic delimitation problems. In this study, we used a phylogenetic approach to investigate a well supported, albeit poorly understood, lineage nested within the Core Bromelioideae, here called the "Ronnbergia Alliance". In order to assess the monophyly and phylogenetic relationships of this group, we used three plastid and three nuclear DNA sequence markers combined with a broad sampling across three taxonomic groups and allied species of Aechmea expected to comprise the Ronnbergia Alliance. We combined the datasets to produce a well-supported and resolved phylogenetic hypothesis. Our main results indicated that the Ronnbergia Alliance was a well-supported monophyletic group, sister to the remaining Core Bromelioideae, and it was composed by species of the polyphyletic genera Aechmea, Hohenbergia and Ronnbergia. We identified two major internal lineages with high geographic structure within the Ronnbergia Alliance. The first of these lineages, called the Pacific Clade, contained species of Aechmea and Ronnbergia that occur exclusively from southern Central America to northwestern South America. The second clade, called the Atlantic Clade, contained species of Aechmea, Hohenbergia and Ronnbergia mostly limited to the Atlantic Forest and the Caribbean. We also explored the diagnostic and evolutionary importance of 13 selected characters using ancestral character reconstructions on the phylogenetic hypothesis. We found that the combination of tubular corollas apically spreading and unappendaged ovules had diagnostic value for the Ronnbergia Alliance, whereas flower size, length of the corolla tube, and petal pigmentation and apex were important characters to differentiate the Pacific and Atlantic clades. This study opens new perspectives for future taxonomic reorganizations and provides a framework for evolutionary and biogeographic studies. Copyright © 2016 Elsevier Inc. All rights reserved.

Molecular phylogenetics and biogeography of the mint tribe Elsholtzieae (Nepetoideae, Lamiaceae), with an emphasis on its diversification in East Asia.

PubMed

Li, Pan; Qi, Zhe-Chen; Liu, Lu-Xian; Ohi-Toma, Tetsuo; Lee, Joongku; Hsieh, Tsung-Hsin; Fu, Cheng-Xin; Cameron, Kenneth M; Qiu, Ying-Xiong

2017-05-17

Elsholtzia and its allied genera such as Collinsonia and Perilla (tribe Elsholtzieae, Lamiaceae) are an ecologically and economically important plant group consisting of ~71 species, with most species distributed in East and Southeast Asia, and several species in North America. Their phylogeny and historical biogeography resulting in a distant intercontinental disjunction are poorly understood. Here we use two nuclear (ETS, ITS) and five chloroplast (rbcL, matK, trnL-F, ycf1, ycf1-rps15) fragments to reconstruct the phylogeny, biogeographic history, and patterns of diversification of Elsholtzieae. The tribe Elsholtzieae is monophyletic and divided into five clades. The woody Elsholtzia species are nested within herbaceous ones and are inferred to have evolved from herbaceous ancestors. Molecular dating shows that the five major clades were established during the Eocene period, but most of the modern diversity did not originate until the Miocene. The divergence between the New World Collinsonia and the Old World Mosla-Keiskea-Perilla clade was dated to the mid-Miocene. Ancestral area reconstructions suggest that the tribe originated in East Asia, and then dispersed to Southeast Asia and North America. Overall, our findings highlight the important roles of the uplifts of the Qinghai-Tibetan Plateau (QTP) and climate changes from Middle Miocene onwards in promoting species diversification of Elsholtzieae.

Domestication of a Mesoamerican cultivated fruit tree, Spondias purpurea.

PubMed

Miller, Allison; Schaal, Barbara

2005-09-06

Contemporary patterns of genetic variation in crops reflect historical processes associated with domestication, such as the geographic origin(s) of cultivated populations. Although significant progress has been made in identifying several global centers of domestication, few studies have addressed the issue of multiple origins of cultivated plant populations from different geographic regions within a domestication center. This study investigates the domestication history of jocote (Spondias purpurea), a Mesoamerican cultivated fruit tree. Sequences of the chloroplast spacer trnG-trnS were obtained for cultivated and wild S. purpurea trees, two sympatric taxa (Spondias mombin var. mombin and Spondias radlkoferi), and two outgroups (S. mombin var. globosa and Spondias testudinus). A phylogeographic approach was used and statistically significant associations of clades and geographical location were tested with a nested clade analysis. The sequences confirm that wild populations of S. purpurea are the likely progenitors of cultivated jocote trees. This study provides phylogeographic evidence of multiple domestications of this Mesoamerican cultivated fruit tree. Haplotypes detected in S. purpurea trees form two clusters, each of which includes alleles recovered in both cultivated and wild populations from distinct geographic regions. Cultivated S. purpurea populations have fewer unique trnG-trnS alleles than wild populations; however, five haplotypes were absent in the wild. The presence of unique alleles in cultivation may reflect contemporary extinction of the tropical dry forests of Mesoamerica. These data indicate that some agricultural habitats may be functioning as reservoirs of genetic variation in S. purpurea.

Earliest example of a giant monitor lizard (Varanus, Varanidae, Squamata).

PubMed

Conrad, Jack L; Balcarcel, Ana M; Mehling, Carl M

2012-01-01

Varanidae is a clade of tiny (<20 mm pre-caudal length [PCL]) to giant (>600 mm PCL) lizards first appearing in the Cretaceous. True monitor lizards (Varanus) are known from diagnostic remains beginning in the early Miocene (Varanus rusingensis), although extremely fragmentary remains have been suggested as indicating earlier Varanus. The paleobiogeographic history of Varanus and timing for origin of its gigantism remain uncertain. A new Varanus from the Mytilini Formation (Turolian, Miocene) of Samos, Greece is described. The holotype consists of a partial skull roof, right side of a braincase, partial posterior mandible, fragment of clavicle, and parts of six vertebrae. A cladistic analysis including 83 taxa coded for 5733 molecular and 489 morphological characters (71 previously unincluded) demonstrates that the new fossil is a nested member of an otherwise exclusively East Asian Varanus clade. The new species is the earliest-known giant (>600 mm PCL) terrestrial lizard. Importantly, this species co-existed with a diverse continental mammalian fauna. The new monitor is larger (longer) than 99% of known fossil and living lizards. Varanus includes, by far, the largest limbed squamates today. The only extant non-snake squamates that approach monitors in maximum size are the glass-snake Pseudopus and the worm-lizard Amphisbaena. Mosasauroids were larger, but exclusively marine, and occurred only during the Late Cretaceous. Large, extant, non-Varanus, lizards are limbless and/or largely isolated from mammalian competitors. By contrast, our new Varanus achieved gigantism in a continental environment populated by diverse eutherian mammal competitors.

Domestication of a Mesoamerican cultivated fruit tree, Spondias purpurea

PubMed Central

Miller, Allison; Schaal, Barbara

2005-01-01

Contemporary patterns of genetic variation in crops reflect historical processes associated with domestication, such as the geographic origin(s) of cultivated populations. Although significant progress has been made in identifying several global centers of domestication, few studies have addressed the issue of multiple origins of cultivated plant populations from different geographic regions within a domestication center. This study investigates the domestication history of jocote (Spondias purpurea), a Mesoamerican cultivated fruit tree. Sequences of the chloroplast spacer trnG–trnS were obtained for cultivated and wild S. purpurea trees, two sympatric taxa (Spondias mombin var. mombin and Spondias radlkoferi), and two outgroups (S. mombin var. globosa and Spondias testudinus). A phylogeographic approach was used and statistically significant associations of clades and geographical location were tested with a nested clade analysis. The sequences confirm that wild populations of S. purpurea are the likely progenitors of cultivated jocote trees. This study provides phylogeographic evidence of multiple domestications of this Mesoamerican cultivated fruit tree. Haplotypes detected in S. purpurea trees form two clusters, each of which includes alleles recovered in both cultivated and wild populations from distinct geographic regions. Cultivated S. purpurea populations have fewer unique trnG–trnS alleles than wild populations; however, five haplotypes were absent in the wild. The presence of unique alleles in cultivation may reflect contemporary extinction of the tropical dry forests of Mesoamerica. These data indicate that some agricultural habitats may be functioning as reservoirs of genetic variation in S. purpurea. PMID:16126899

Genetic Diversity of Crimean Congo Hemorrhagic Fever Virus Strains from Iran

PubMed Central

Chinikar, Sadegh; Bouzari, Saeid; Shokrgozar, Mohammad Ali; Mostafavi, Ehsan; Jalali, Tahmineh; Khakifirouz, Sahar; Nowotny, Norbert; Fooks, Anthony R.; Shah-Hosseini, Nariman

2016-01-01

Background: Crimean Congo hemorrhagic fever virus (CCHFV) is a member of the Bunyaviridae family and Nairovirus genus. It has a negative-sense, single stranded RNA genome approximately 19.2 kb, containing the Small, Medium, and Large segments. CCHFVs are relatively divergent in their genome sequence and grouped in seven distinct clades based on S-segment sequence analysis and six clades based on M-segment sequences. Our aim was to obtain new insights into the molecular epidemiology of CCHFV in Iran. Methods: We analyzed partial and complete nucleotide sequences of the S and M segments derived from 50 Iranian patients. The extracted RNA was amplified using one-step RT-PCR and then sequenced. The sequences were analyzed using Mega5 software. Results: Phylogenetic analysis of partial S segment sequences demonstrated that clade IV-(Asia 1), clade IV-(Asia 2) and clade V-(Europe) accounted for 80 %, 4 % and 14 % of the circulating genomic variants of CCHFV in Iran respectively. However, one of the Iranian strains (Iran-Kerman/22) was associated with none of other sequences and formed a new clade (VII). The phylogenetic analysis of complete S-segment nucleotide sequences from selected Iranian CCHFV strains complemented with representative strains from GenBank revealed similar topology as partial sequences with eight major clusters. A partial M segment phylogeny positioned the Iranian strains in either association with clade III (Asia-Africa) or clade V (Europe). Conclusion: The phylogenetic analysis revealed subtle links between distant geographic locations, which we propose might originate either from international livestock trade or from long-distance carriage of CCHFV by infected ticks via bird migration. PMID:27308271

Diversity and Evolution of Disease Resistance Genes in Barley (Hordeum vulgare L.)

PubMed Central

Andersen, Ethan J.; Ali, Shaukat; Reese, R. Neil; Yen, Yang; Neupane, Surendra; Nepal, Madhav P.

2016-01-01

Plant disease resistance genes (R-genes) play a critical role in the defense response to pathogens. Barley is one of the most important cereal crops, having a genome recently made available, for which the diversity and evolution of R-genes are not well understood. The main objectives of this research were to conduct a genome-wide identification of barley Coiled-coil, Nucleotide-binding site, Leucine-rich repeat (CNL) genes and elucidate their evolutionary history. We employed a Hidden Markov Model using 52 Arabidopsis thaliana CNL reference sequences and analyzed for phylogenetic relationships, structural variation, and gene clustering. We identified 175 barley CNL genes nested into three clades, showing (a) evidence of an expansion of the CNL-C clade, primarily due to tandem duplications; (b) very few members of clade CNL-A and CNL-B; and (c) a complete absence of clade CNL-D. Our results also showed that several of the previously identified mildew locus A (MLA) genes may be allelic variants of two barley CNL genes, MLOC_66581 and MLOC_10425, which respond to powdery mildew. Approximately 23% of the barley CNL genes formed 15 gene clusters located in the extra-pericentromeric regions on six of the seven chromosomes; more than half of the clustered genes were located on chromosomes 1H and 7H. Higher average numbers of exons and multiple splice variants in barley relative to those in Arabidopsis and rice may have contributed to a diversification of the CNL-C members. These results will help us understand the evolution of R-genes with potential implications for developing durable resistance in barley cultivars. PMID:27168720

Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes

PubMed Central

Saarela, Jeffery M.; Wysocki, William P.; Barrett, Craig F.; Soreng, Robert J.; Davis, Jerrold I.; Clark, Lynn G.; Kelchner, Scot A.; Pires, J. Chris; Edger, Patrick P.; Mayfield, Dustin R.; Duvall, Melvin R.

2015-01-01

Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some ‘early-diverging’ tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae–Meliceae and Ampelodesmeae–Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae–Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae–Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae–Loliinae clade. PMID:25940204

The inclusion of downy mildews in a multi-locus-dataset and its reanalysis reveals a high degree of paraphyly in Phytophthora.

PubMed

Runge, Fabian; Telle, Sabine; Ploch, Sebastian; Savory, Elizabeth; Day, Brad; Sharma, Rahul; Thines, Marco

2011-12-01

Pathogens belonging to the Oomycota, a group of heterokont, fungal-like organisms, are amongst the most notorious pathogens in agriculture. In particular, the obligate biotrophic downy mildews and the hemibiotrophic members of the genus Phytophthora are responsible for a huge variety of destructive diseases, including sudden oak death caused by P. ramorum, potato late blight caused by P. infestans, cucurbit downy mildew caused by Pseudoperonospora cubensis, and grape downy mildew caused by Plasmopara viticola. About 800 species of downy mildews and roughly 100 species of Phytophthora are currently accepted, and recent studies have revealed that these groups are closely related. However, the degree to which Phytophthora is paraphyletic and where exactly the downy mildews insert into this genus in relation to other clades could not be inferred with certainty to date. Here we present a molecular phylogeny encompassing all clades of Phytophthora as represented in a multi-locus dataset and two representatives of the monophyletic downy mildews from divergent genera. Our results demonstrate that Phytophthora is at least six times paraphyletic with respect to the downy mildews. The downy mildew representatives are consistently nested within clade 4 (contains Phytophthora palmivora), which is placed sister to clade 1 (contains Phytophthora infestans). This finding would either necessitate placing all downy mildews and Phytopthora species in a single genus, either under the oldest generic name Peronospora or by conservation the later name Phytophthora, or the description of at least six new genera within Phytophthora. The complications of both options are discussed, and it is concluded that the latter is preferable, as it warrants fewer name changes and is more practical.

Molecular characterization of avipoxviruses circulating in Mozambique, 2016-2018.

PubMed

Mapaco, Lourenço P; Lacerda, Zeiss; Monjane, Iolanda V A; Sussuro, Afonso; Viljoen, Gerrit J; Cattoli, Giovanni; Dundon, William G; Achá, Sara J

2018-05-08

Samples from 45 chickens, two turkeys, one peacock and one quail with symptoms of fowlpox were collected in Mozambique between November 2016 and January 2018. Phylogenetic analysis revealed that the samples contained avipoxviruses belonging to both clade A1 and clade A2. In addition, all of the Clade A1 viruses were positive by PCR for the integration of reticuloendotheliosis virus, while the clade A2 avipoxvirus samples were negative. This study confirms the circulation of clade A1 avipoxviruses in Mozambique in addition to identifying clade A2 for the first time in the country.

A 12-year molecular survey of clinical herpes simplex virus type 2 isolates demonstrates the circulation of clade A and B strains in Germany.

PubMed

Schmidt-Chanasit, Jonas; Bialonski, Alexandra; Heinemann, Patrick; Ulrich, Rainer G; Günther, Stephan; Rabenau, Holger F; Doerr, Hans Wilhelm

2010-07-01

Recently two different herpes simplex virus type 2 (HSV-2) clades (A and B) were described on DNA sequence data of the glycoprotein E (gE), G (gG) and I (gI) genes. To type the circulating HSV-2 wild-type strains in Germany by a novel approach and to monitor potential changes in the molecular epidemiology between 1997 and 2008. A total of 64 clinical HSV-2 isolates were analyzed by a novel approach using the DNA sequences of the complete open reading frames of glycoprotein B (gB) and gG. Recombination analysis of the gB and gG gene sequences was performed to reveal intragenic recombinants. Based on the phylogenetic analysis of the gB coding DNA sequence 8 of 64 (12%) isolates were classified as clade A strains and 56 of 64 (88%) isolates were classified as clade B strains. Analysis of the gG coding DNA sequence classified 4 (6%) isolates as clade A strains and 60 (94%) isolates as clade B strains. In comparison, the 8 isolates classified as clade A strains using the gB sequence data were classified as clade B strains when using the gG coding DNA sequence, suggesting intergenic recombination events. Intragenic recombination events were not detected. The first molecular survey of clinical HSV-2 isolates from Germany demonstrated the circulation of clade A and B strains and of intergenic recombinants over a period of 12 years. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Evidence that clade A and clade B head lice live in sympatry and recombine in Algeria.

PubMed

Boutellis, A; Bitam, I; Fekir, K; Mana, N; Raoult, D

2015-03-01

Pediculus humanus L. (Psocodea: Pediculidae) can be characterized into three deeply divergent lineages (clades) based on mitochondrial DNA. Clade A consists of both head lice and clothing lice and is distributed worldwide. Clade B consists of head lice only and is mainly found in North and Central America, and in western Europe and Australia. Clade C, which consists only of head lice, is found in Ethiopia, Nepal and Senegal. Twenty-six head lice collected from pupils at different elementary schools in two localities in Algiers (Algeria) were analysed using molecular methods for genotyping lice (cytochrome b and the multi-spacer typing (MST) method. For the first time, we found clade B head lice in Africa living in sympatry with clade A head lice. The phylogenetic analysis of the concatenated sequences of these populations of head lice showed that clade A and clade B head lice had recombined, suggesting that interbreeding occurs when lice live in sympatry. © 2014 The Royal Entomological Society.

Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis

PubMed Central

Malmstrom, Rex R; Rodrigue, Sébastien; Huang, Katherine H; Kelly, Libusha; Kern, Suzanne E; Thompson, Anne; Roggensack, Sara; Berube, Paul M; Henn, Matthew R; Chisholm, Sallie W

2013-01-01

Prochlorococcus is the numerically dominant photosynthetic organism throughout much of the world's oceans, yet little is known about the ecology and genetic diversity of populations inhabiting tropical waters. To help close this gap, we examined natural Prochlorococcus communities in the tropical Pacific Ocean using a single-cell whole-genome amplification and sequencing. Analysis of the gene content of just 10 single cells from these waters added 394 new genes to the Prochlorococcus pan-genome—that is, genes never before seen in a Prochlorococcus cell. Analysis of marker genes, including the ribosomal internal transcribed sequence, from dozens of individual cells revealed several representatives from two uncultivated clades of Prochlorococcus previously identified as HNLC1 and HNLC2. While the HNLC clades can dominate Prochlorococcus communities under certain conditions, their overall geographic distribution was highly restricted compared with other clades of Prochlorococcus. In the Atlantic and Pacific oceans, these clades were only found in warm waters with low Fe and high inorganic P levels. Genomic analysis suggests that at least one of these clades thrives in low Fe environments by scavenging organic-bound Fe, a process previously unknown in Prochlorococcus. Furthermore, the capacity to utilize organic-bound Fe appears to have been acquired horizontally and may be exchanged among other clades of Prochlorococcus. Finally, one of the single Prochlorococcus cells sequenced contained a partial genome of what appears to be a prophage integrated into the genome. PMID:22895163

Comparative analysis of 16S rRNA and amoA genes from archaea selected with organic and inorganic amendments in enrichment culture.

PubMed

Xu, Mouzhong; Schnorr, Jon; Keibler, Brandon; Simon, Holly M

2012-04-01

We took advantage of a plant-root enrichment culture system to characterize mesophilic soil archaea selected through the use of organic and inorganic amendments. Comparative analysis of 16S rRNA and amoA genes indicated that specific archaeal clades were selected under different conditions. Three amoA sequence clades were identified, while for a fourth group, identified by 16S rRNA gene analysis alone and referred to as the "root" clade, we detected no corresponding amoA gene. The amoA-containing archaea were present in media with either organic or inorganic amendments, whereas archaea representing the root clade were present only when organic amendment was used. Analysis of amoA gene abundance and expression, together with nitrification-coupled growth assays, indicated potential growth by autotrophic ammonia oxidation for members of two group 1.1b clades. Increased abundance of one of these clades, however, also occurred upon the addition of organic amendment. Finally, although amoA-containing group 1.1a archaea were present in enrichments, we detected neither expression of amoA genes nor evidence for nitrification-coupled growth of these organisms. These data support a model of a diverse metabolic community in mesophilic soil archaea that is just beginning to be characterized.

Relationships among genera of the Saccharomycotina from multigene sequence analysis

USDA-ARS?s Scientific Manuscript database

Most known species of the subphylum Saccharomycotina (budding ascomycetous yeasts) have now been placed in phylogenetically defined clades following multigene sequence analysis. Terminal clades, which are usually well supported from bootstrap analysis, are viewed as phylogenetically circumscribed ge...

Genetic recombination events between sympatric Clade A and Clade C lice in Africa.

PubMed

Veracx, Aurélie; Boutellis, Amina; Raoult, Didier

2013-09-01

Human head and body lice have been classified into three phylogenetic clades (Clades A, B, and C) based on mitochondrial DNA. Based on nuclear markers (the 18S rRNA gene and the PM2 spacer), two genotypes of Clade A head and body lice, including one that is specifically African (Clade A2), have been described. In this study, we sequenced the PM2 spacer of Clade C head lice from Ethiopia and compared these sequences with sequences from previous works. Trees were drawn, and an analysis of genetic diversity based on the cytochrome b gene and the PM2 spacer was performed for African and non-African lice. In the tree drawn based on the PM2 spacer, the African and non-African lice formed separate clusters. However, Clade C lice from Ethiopia were placed within the African Clade A subcluster (Clade A2). This result suggests that recombination events have occurred between Clade A2 lice and Clade C lice, reflecting the sympatric nature of African lice. Finally, the PM2 spacer and cytochrome b gene sequences of human lice revealed a higher level of genetic diversity in Africa than in other regions.

Molecular and Phenotypic Evaluation of Lichtheimia corymbifera (Formerly Absidia corymbifera) Complex Isolates Associated with Human Mucormycosis: Rehabilitation of L. ramosa▿

PubMed Central

Garcia-Hermoso, Dea; Hoinard, Damien; Gantier, Jean-Charles; Grenouillet, Frédéric; Dromer, Françoise; Dannaoui, Eric

2009-01-01

Thirty-eight isolates (including 28 isolates from patients) morphologically identified as Lichtheimia corymbifera (formerly Absidia corymbifera) were studied by sequence analysis (analysis of the internal transcribed spacer [ITS] region of the ribosomal DNA, the D1-D2 region of 28S, and a portion of the elongation factor 1α [EF-1α] gene). Phenotypic characteristics, including morphology, antifungal susceptibility, and carbohydrate assimilation, were also determined. Analysis of the three loci uncovered two well-delimited clades. The maximum sequence similarity values between isolates from both clades were 66, 95, and 93% for the ITS, 28S, and EF-1α loci, respectively, with differences in the lengths of the ITS sequences being detected (763 to 770 bp for isolates of clade 1 versus 841 to 865 bp for isolates of clade 2). Morphologically, the shapes and the sizes of the sporangiospores were significantly different among the isolates from both clades. On the basis of the molecular and morphological data, we considered isolates of clade 2 to belong to a different species named Lichtheimia ramosa because reference strains CBS 269.65 and CBS 270.65 (which initially belonged to Absidia ramosa) clustered within this clade. As neotype A. corymbifera strain CBS 429.75 belongs to clade 1, the name L. corymbifera was conserved for clade 1 isolates. Of note, the amphotericin B MICs were significantly lower for L. ramosa than for L. corymbifera (P < 0.005) but were always ≤0.5 μg/ml for both species. Among the isolates tested, the assimilation of melezitose was positive for 67% of the L. ramosa isolates and negative for all L. corymbifera isolates. In conclusion, this study reveals that two Lichtheimia species are commonly associated with mucormycosis in humans. PMID:19759217

Infection Dynamics of Coexisting Beta- and Gammaproteobacteria in the Nested Endosymbiotic System of Mealybugs▿

PubMed Central

Kono, Marie; Koga, Ryuichi; Shimada, Masakazu; Fukatsu, Takema

2008-01-01

We investigated the infection dynamics of endosymbiotic bacteria in the developmental course of the mealybugs Planococcus kraunhiae and Pseudococcus comstocki. Molecular phylogenetic analyses identified a betaproteobacterium and a gammaproteobacterium from each of the mealybug species. The former bacterium was related to the β-endosymbionts of other mealybugs, i.e., “Candidatus Tremblaya princeps,” and formed a compact clade in the Betaproteobacteria. Meanwhile, the latter bacterium was related to the γ-endosymbionts of other mealybugs but belonged to distinct clades in the Gammaproteobacteria. Whole-mount in situ hybridization confirmed the peculiar nested formation in the endosymbiotic system of the mealybugs: the β-endosymbiont cells were present in the cytoplasm of the bacteriocytes, and the γ-endosymbiont cells were located in the β-endosymbiont cells. In nymphal and female development, a large oval bacteriome consisting of a number of bacteriocytes was present in the abdomen, wherein the endosymbionts were harbored. In male development, strikingly, the bacteriome progressively degenerated in prepupae and pupae and became almost unrecognizable in adult males. In the degeneration process, the γ-endosymbionts disappeared more rapidly than the β-endosymbionts did. Quantitative PCR analyses revealed that (i) the population dynamics of the endosymbionts in female development reflected the reproductive activity of the insects, (ii) the population dynamics of the endosymbionts were strikingly different between female development and male development, (iii) the endosymbiont populations drastically decreased in male development, and (iv) the γ-endosymbiont populations decreased more rapidly than the β-endosymbiont populations in male development. Possible mechanisms underlying the uncoupled regulation of the β- and γ-endosymbiont populations are discussed in relation to the establishment and evolution of this unique prokaryote-prokaryote endosymbiotic system. PMID:18469124

A multigene phylogeny of Olpidium and its implications for early fungal evolution

PubMed Central

2011-01-01

Background From a common ancestor with animals, the earliest fungi inherited flagellated zoospores for dispersal in water. Terrestrial fungi lost all flagellated stages and reproduce instead with nonmotile spores. Olpidium virulentus (= Olpidium brassicae), a unicellular fungus parasitizing vascular plant root cells, seemed anomalous. Although Olpidium produces zoospores, in previous phylogenetic studies it appeared nested among the terrestrial fungi. Its position was based mainly on ribosomal gene sequences and was not strongly supported. Our goal in this study was to use amino acid sequences from four genes to reconstruct the branching order of the early-diverging fungi with particular emphasis on the position of Olpidium. Results We concatenated sequences from the Ef-2, RPB1, RPB2 and actin loci for maximum likelihood and Bayesian analyses. In the resulting trees, Olpidium virulentus, O. bornovanus and non-flagellated terrestrial fungi formed a strongly supported clade. Topology tests rejected monophyly of the Olpidium species with any other clades of flagellated fungi. Placing Olpidium at the base of terrestrial fungi was also rejected. Within the terrestrial fungi, Olpidium formed a monophyletic group with the taxa traditionally classified in the phylum Zygomycota. Within Zygomycota, Mucoromycotina was robustly monophyletic. Although without bootstrap support, Monoblepharidomycetes, a small class of zoosporic fungi, diverged from the basal node in Fungi. The zoosporic phylum Blastocladiomycota appeared as the sister group to the terrestrial fungi plus Olpidium. Conclusions This study provides strong support for Olpidium as the closest living flagellated relative of the terrestrial fungi. Appearing nested among hyphal fungi, Olpidium's unicellular thallus may have been derived from ancestral hyphae. Early in their evolution, terrestrial hyphal fungi may have reproduced with zoospores. PMID:22085768

Polyphyly of Asian Tree Toads, Genus Pedostibes Günther, 1876 (Anura: Bufonidae), and the Description of a New Genus from Southeast Asia

PubMed Central

Grismer, L. Lee; Zachariah, Anil; Brown, Rafe M.

2016-01-01

The Asian Tree Toad genus Pedostibes, as currently understood, exhibits a conspicuously disjunct distribution, posing several immediate questions relating to the biogeography and taxonomy of this poorly known group. The type species, P. tuberculosus and P. kempi, are known only from India, whereas P. hosii, P. rugosus, and P. everetti are restricted to Southeast Asia. Several studies have shown that these allopatric groups are polyphyletic, with the Indian Pedostibes embedded within a primarily South Asian clade of toads, containing the genera Adenomus, Xanthophryne, and Duttaphrynus. Southeast Asian Pedostibes on the other hand, are nested within a Southeast Asian clade, which is the sister lineage to the Southeast Asian river toad genus Phrynoidis. We demonstrate that Indian and Southeast Asian Pedostibes are not only allopatric and polyphyletic, but also exhibit significant differences in morphology and reproductive mode, indicating that the Southeast Asian species’ are not congeneric with the true Pedostibes of India. As a taxonomic solution, we describe a new genus, Rentapia gen. nov. to accommodate the Southeast Asian species. PMID:26788854

Footprints in the sand: independent reduction of subdigital lamellae in the Namib-Kalahari burrowing geckos.

PubMed

Lamb, Trip; Bauer, Aaron M

2006-04-07

Many desert organisms exhibit convergence, and certain physical factors such as windblown sands have generated remarkably similar ecomorphs across divergent lineages. The burrowing geckos Colopus, Chondrodactylus and Palmatogecko occupy dune ecosystems in the Namib and Kalahari deserts of southwest Africa. Considered closely related, they share several putative synapomorphies, including reduced subdigital pads (toe pads) and spinose digital scales. Though recognized as part of Africa's ecologically diverse Pachydactylus Group, the burrowing geckos' precise phylogenetic affinities remain elusive. Convergent pedal modification provides a tenable alternative explaining the geckos' derived terrestriality and adaptation to Namib and Kalahari sands. We generated a molecular phylogeny for the Pachydactylus Group to examine evolutionary relationships among the burrowing geckos and infer historical patterns of pedal character change. Bayesian and parsimony analyses revealed all three burrowing genera to be deeply nested within Pachydactylus, each genus belonging to a separate clade. Strong support for these distinct clades indicates ecomorphological adaptations for burrowing have evolved independently three times in the southern Pachydactylus Group. We argue that the physical properties of Namib and Kalahari sands played a principal role in selecting for pedal similarity.

Microsatellite markers identify three lineages of Phytophthora ramorum in US nurseries, yet single lineages in US forest and European nursery populations.

PubMed

Ivors, K; Garbelotto, M; Vries, I D E; Ruyter-Spira, C; Te Hekkert, B; Rosenzweig, N; Bonants, P

2006-05-01

Analysis of 12 polymorphic simple sequence repeats identified in the genome sequence of Phytophthora ramorum, causal agent of 'sudden oak death', revealed genotypic diversity to be significantly higher in nurseries (91% of total) than in forests (18% of total). Our analysis identified only two closely related genotypes in US forests, while the genetic structure of populations from European nurseries was of intermediate complexity, including multiple, closely related genotypes. Multilocus analysis determined populations in US forests reproduce clonally and are likely descendants of a single introduced individual. The 151 isolates analysed clustered in three clades. US forest and European nursery isolates clustered into two distinct clades, while one isolate from a US nursery belonged to a third novel clade. The combined microsatellite, sequencing and morphological analyses suggest the three clades represent distinct evolutionary lineages. All three clades were identified in some US nurseries, emphasizing the role of commercial plant trade in the movement of this pathogen.

Sorodiplophrys stercorea: Another Novel Lineage of Sorocarpic Multicellularity.

PubMed

Tice, Alexander K; Silberman, Jeffrey D; Walthall, Austin C; Le, Khoa N D; Spiegel, Frederick W; Brown, Matthew W

2016-09-01

Sorodiplophrys stercorea is a sorocarpic organism that utilizes filose pseudopodia for locomotion and absorptive nutrition. It has traditionally been considered to be a member of the Labyrinthulae based on its morphology. Its closest relatives were thought to be species in the taxon Diplophrys. Since the genus Diplophrys has been shown to be paraphyletic and S. stercorea has pseudopodia similar to some members of Rhizaria, we examined its relationship with other eukaryotes. We obtained four isolates from the dung of cow and horse, brought each into monoeukaryotic culture, and sequenced their SSU rRNA gene for phylogenetic analysis. All our isolates were shown to form a monophyletic group in the Labyrinthulae, nested in the Amphifiloidea clade. Our results demonstrate that Sorodiplophrys is more closely related to species of the genus Amphifila than to Diplophrys and represents an additional independent origin of sorocarpic multicellularity among eukaryotes. This study represents the first confirmed sorocarpic lifestyle in the Stramenopiles. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

Evidence for the possible involvement of Selenomonas ruminantium in rumen fiber digestion.

PubMed

Sawanon, Suriya; Koike, Satoshi; Kobayashi, Yasuo

2011-12-01

Selenomonas ruminantium strains were isolated from sheep rumen, and their significance for fiber digestion was evaluated. Based on the phylogenetic classification, two clades of S. ruminantium (clades I and II) were proposed. Clade II is newly found, as it comprised only new isolates that were phylogenetically distant from the type strain, while all of the known isolates were grouped in the major clade I. More than half of clade I isolates displayed CMCase activity with no relation to the degree of bacterial adherence to fibers. Although none of the isolates digested fiber in monoculture, they stimulated fiber digestion when co-cultured with Fibrobacter succinogenes, and there was an enhancement of propionate production. The extent of such synergy depended on the clade, with higher digestion observed by co-culture of clade I isolates with F. succinogenes than by co-culture with clade II isolates. Quantitative PCR analysis showed that bacterial abundance in the rumen was higher for clade I than for clade II. These results suggest that S. ruminantium, in particular the major clade I, is involved in rumen fiber digestion by cooperating with F. succinogenes. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Phylogeny of Annelida (Lophotrochozoa): total-evidence analysis of morphology and six genes

PubMed Central

Zrzavý, Jan; Říha, Pavel; Piálek, Lubomír; Janouškovec, Jan

2009-01-01

Background Annelida is one of the major protostome phyla, whose deep phylogeny is very poorly understood. Recent molecular phylogenies show that Annelida may include groups once considered separate phyla (Pogonophora, Echiurida, and Sipunculida) and that Clitellata are derived polychaetes. SThe "total-evidence" analyses combining morphological and molecular characters have been published for a few annelid taxa. No attempt has yet been made to analyse simultaneously morphological and molecular information concerning the Annelida as a whole. Results Phylogenetic relationships within Annelida were analysed on the basis of 93 morphological characters and sequences of six genes (18S, 28S, and 16S rRNA, EF1α, H3, COI), altogether, 87 terminals of all annelid "families" and 3,903 informative characters, by Bayesian and maximum-parsimony methods. The analysis of the combined dataset yields the following scheme of relationships: Phyllodocida and Eunicida are monophyletic groups, together probably forming monophyletic Aciculata (incl. Orbiniidae and Parergodrilidae that form a sister group of the Eunicida). The traditional "Scolecida" and "Canalipalpata" are both polyphyletic, forming instead two clades: one including Cirratuliformia and the "sabelloid-spionoid clade" (incl. Sternaspis, Sabellidae-Serpulidae, Sabellariidae, Spionida s.str.), the other ("terebelloid-capitelloid clade") including Terebelliformia, Arenicolidae-Maldanidae, and Capitellidae-Echiurida. The Clitellata and "clitellate-like polychaetes" (Aeolosomatidae, Potamodrilidae, Hrabeiella) form a monophyletic group. The position of the remaining annelid groups is uncertain – the most problematic taxa are the Opheliidae-Scalibregmatidae clade, the Amphinomida-Aberranta clade, Apistobranchus, Chaetopteridae, Myzostomida, the Sipunculida-Dinophilidae clade, and the "core Archiannelida" (= Protodrilidae, Nerillidae, Polygordiidae, Saccocirridae). Conclusion The combined ("total-evidence") phylogenetic analysis provides a modified view of annelid evolution, with several higher-level taxa, i.e. Phyllodocida, Eunicida, orbinioid-parergodrilid clade (OPC), Cirratuliformia, sabelloid-spionoid clade (SSC), terebelloid-capitelloid clade (TCC), and "Clitellatomorpha". Two unorthodox clades, the "core Archiannelida" and Sipunculida-Dinophilidae, are proposed. Although the deep-level evolutionary relationships of Annelida remain poorly understood, we propose the monophyly of the Aciculata, sister-group relationships between the Eunicida and OPC, between the Cirratuliformia and SSC, and possibly also between the "Clitellatomorpha" and Oweniidae-Pogonophora clades. PMID:19660115

Deep-Time Convergence in Rove Beetle Symbionts of Army Ants.

PubMed

Maruyama, Munetoshi; Parker, Joseph

2017-03-20

Recent adaptive radiations provide striking examples of convergence [1-4], but the predictability of evolution over much deeper timescales is controversial, with a scarcity of ancient clades exhibiting repetitive patterns of phenotypic evolution [5, 6]. Army ants are ecologically dominant arthropod predators of the world's tropics, with large nomadic colonies housing diverse communities of socially parasitic myrmecophiles [7]. Remarkable among these are many species of rove beetle (Staphylinidae) that exhibit ant-mimicking "myrmecoid" body forms and are behaviorally accepted into their aggressive hosts' societies: emigrating with colonies and inhabiting temporary nest bivouacs, grooming and feeding with workers, but also consuming the brood [8-11]. Here, we demonstrate that myrmecoid rove beetles are strongly polyphyletic, with this adaptive morphological and behavioral syndrome having evolved at least 12 times during the evolution of a single staphylinid subfamily, Aleocharinae. Each independent myrmecoid clade is restricted to one zoogeographic region and highly host specific on a single army ant genus. Dating estimates reveal that myrmecoid clades are separated by substantial phylogenetic distances-as much as 105 million years. All such groups arose in parallel during the Cenozoic, when army ants diversified into modern genera [12] and rose to ecological dominance [13, 14]. This work uncovers a rare example of an ancient system of complex morphological and behavioral convergence, with replicate beetle lineages following a predictable phenotypic trajectory during their parasitic adaptation to host colonies. Copyright © 2017 Elsevier Ltd. All rights reserved.

The corbiculate bees arose from New World oil-collecting bees: implications for the origin of pollen baskets.

PubMed

Martins, Aline C; Melo, Gabriel A R; Renner, Susanne S

2014-11-01

The economically most important group of bees is the "corbiculates", or pollen basket bees, some 890 species of honeybees (Apis), bumblebees (Bombus), stingless bees (Meliponini), and orchid bees (Euglossini). Molecular studies have indicated that the corbiculates are closest to the New World genera Centris, with 230 species, and Epicharis, with 35, albeit without resolving the precise relationships. Instead of concave baskets, these bees have hairy hind legs on which they transport pollen mixed with floral oil, collected with setae on the anterior and middle legs. We sampled two-thirds of all Epicharis, a third of all Centris, and representatives of the four lineages of corbiculates for four nuclear gene regions, obtaining a well-supported phylogeny that has the corbiculate bees nested inside the Centris/Epicharis clade. Fossil-calibrated molecular clocks, combined with a biogeographic reconstruction incorporating insights from the fossil record, indicate that the corbiculate clade arose in the New World and diverged from Centris 84 (72-95)mya. The ancestral state preceding corbiculae thus was a hairy hind leg, perhaps adapted for oil transport as in Epicharis and Centris bees. Its replacement by glabrous, concave baskets represents a key innovation, allowing efficient transport of plant resins and large pollen/nectar loads and freeing the corbiculate clade from dependence on oil-offering flowers. The transformation could have involved a novel function of Ubx, the gene known to change hairy into smooth pollen baskets in Apis and Bombus. Copyright © 2014 Elsevier Inc. All rights reserved.

Phenology and productivity of C3 and C4 grasslands in Hawaii.

PubMed

Pau, Stephanie; Still, Christopher J

2014-01-01

Grasslands account for a large proportion of global terrestrial productivity and play a critical role in carbon and water cycling. Within grasslands, photosynthetic pathway is an important functional trait yielding different rates of productivity along environmental gradients. Recently, C3-C4 sorting along spatial environmental gradients has been reassessed by controlling for confounding traits in phylogenetically structured comparisons. C3 and C4 grasses should sort along temporal environmental gradients as well, resulting in differing phenologies and growing season lengths. Here we use 10 years of satellite data (NDVI) to examine the phenology and greenness (as a proxy for productivity) of C3 and C4 grass habitats, which reflect differences in both environment and plant physiology. We perform phylogenetically structured comparisons based on 3,595 digitized herbarium collections of 152 grass species across the Hawaiian Islands. Our results show that the clade identity of grasses captures differences in their habitats better than photosynthetic pathway. Growing season length (GSL) and associated productivity (GSP) were not significantly different when considering photosynthetic type alone, but were indeed different when considering photosynthetic type nested within clade. The relationship between GSL and GSP differed most strongly between C3 clade habitats, and not between C3-C4 habitats. Our results suggest that accounting for the interaction between phylogeny and photosynthetic pathway can help improve predictions of productivity, as commonly used C3-C4 classifications are very broad and appear to mask important diversity in grassland ecosystem functions.

Characterization of bacterial community associated to biofilms of corroded oil pipelines from the southeast of Mexico.

PubMed

Neria-González, Isabel; Wang, En Tao; Ramírez, Florina; Romero, Juan M; Hernández-Rodríguez, César

2006-06-01

Microbial communities associated to biofilms promote corrosion of oil pipelines. The community structure of bacteria in the biofilm formed in oil pipelines is the basic knowledge to understand the complexity and mechanisms of metal corrosion. To assess bacterial diversity, biofilm samples were obtained from X52 steel coupons corroded after 40 days of exposure to normal operation and flow conditions. The biofilm samples were directly used to extract metagenomic DNA, which was used as template to amplify 16S ribosomal gene by PCR. The PCR products of 16S ribosomal gene were also employed as template for sulfate-reducing bacteria (SRB) specific nested-PCR and both PCR products were utilized for the construction of gene libraries. The V3 region of the 16S rRNA gene was also amplified to analyse the bacterial diversity by analysis of denaturing gradient gel electrophoresis (DGGE). Ribosomal library and DGGE profiles exhibited limited bacterial diversity, basically including Citrobacter spp., Enterobacter spp. and Halanaerobium spp. while Desulfovibrio alaskensis and a novel clade within the genus Desulfonatronovibrio were detected from the nested PCR library. The biofilm samples were also taken for the isolation of SRB. Desulfovibrio alaskensis and Desulfovibrio capillatus, as well as some strains related to Citrobacter were isolated. SRB consists in a very small proportion of the community and Desulfovibrio spp. were the relatively abundant groups among the SRB. This is the first study directly exploring bacterial diversity in corrosive biofilms associated to steel pipelines subjected to normal operation conditions.

Novel reassortant clade 2.3.4.4 avian influenza A (H5N8) virus in a grey heron in South Korea in 2017.

PubMed

Woo, Chanjin; Kwon, Jung-Hoon; Lee, Dong-Hun; Kim, Youngsik; Lee, Kwanghee; Jo, Seong-Deok; Son, Ki Dong; Oem, Jae-Ku; Wang, Seung-Jun; Kim, Yongkwan; Shin, Jeonghwa; Song, Chang-Seon; Jheong, Weonhwa; Jeong, Jipseol

2017-12-01

We report the identification of a novel reassortant clade 2.3.4.4 H5N8 virus from a dead grey heron in Korea in 2017. Outbreaks of clade 2.3.4.4 H5 HPAIVs have been reported worldwide, and they have evolved into multiple genotypes among wild birds. Phylogenetic analysis indicated that this virus likely originated from Qinghai Lake and Western Siberia and further evolved through reassortment with Eurasian LPAI during the 2016 fall migration of wild birds. Enhanced surveillance and comparative genetic analysis will help to monitor the further evolution and dissemination of clade 2.3.4.4 HPAIVs.

Molecular detection and genetic diversity of Babesia gibsoni in dogs in India.

PubMed

Singh, M N; Raina, O K; Sankar, M; Rialch, Ajayta; Tigga, M N; Kumar, G Ravi; Banerjee, P S

2016-07-01

Babesia gibsoni is a tick borne intraerythrocytic protozoan parasite causing piroplasmosis in dogs and has been predominantly reported in Asian countries, including Japan, Korea, Taiwan, Malaysia, Bangladesh and India. The present communication is the first evidence on the genetic diversity of B. gibsoni of dogs in India. Blood samples were collected from 164 dogs in north and northeast states of India and 13 dogs (7.9%) were found positive for B. gibsoni infection by microscopic examination of blood smears. Molecular confirmation of these microscopic positive cases for B. gibsoni was carried out by 18S rRNA nested-PCR, followed by sequencing. Nested-PCR for the 18S rRNA gene was also carried out on microscopically B. gibsoni negative samples that detected a higher percentage of dogs (28.6%) infected with B. gibsoni. Genetic diversity in B. gibsoni in India was determined by studying B. gibsoni thrombospondin-related adhesive protein (BgTRAP) gene fragments (855bp) in 19 isolates from four north and northeast states of India. Phylogenetic analysis of the BgTRAP gene revealed that B. gibsoni parasite in India and Bangladesh formed a distinct cluster away from other Asian B. gibsoni isolates available from Japan, Taiwan and Korea. In addition, tandem repeat analysis of the BgTRAP gene clearly showed considerable genetic variation among Indian isolates that was shared by B. gibsoni isolates of Bangladesh. These results suggested that B. gibsoni parasites in a different genetic clade are endemic in dogs in India and Bangladesh. Further studies are required for better understanding of the genetic diversity of B. gibsoni prevalent in India and in its neighbouring countries. Copyright © 2016 Elsevier B.V. All rights reserved.

Dispersal, habitat differences, and comparative phylogeography of Southeast Asian seahorses (Syngnathidae: Hippocampus).

PubMed

Lourie, S A; Green, D M; Vincent, A C J

2005-04-01

Four distinct phylogeographical patterns across Southeast Asia were observed for four species of seahorse (genus Hippocampus) with differing ecologies. For all species, genetic differentiation (based on cytochrome b sequence comparisons) was significantly associated with sample site (Phi(ST) = 0.190-0.810, P < 0.0001) and with geographical distance (Mantel's r = 0.37-0.59, P < 0.019). Geographic locations of genetic breaks were inconsistent across species in 7/10 comparisons, although some similarities across species were also observed. The two shallow-water species (Hippocampus barbouri and Hippocampus kuda) have colonized the Sunda Shelf to a lesser degree than the two deeper-water species (Hippocampus spinosissimus and Hippocampus trimaculatus). In all species the presence of geographically restricted haplotypes in the Philippines could indicate past population fragmentation and/or long-distance colonization. A nested clade analysis (NCA) revealed that long-distance colonization and/or fragmentation were likely the dominant forces that structure populations of the two shallow-water species, whereas range expansion and restricted dispersal with isolation by distance were proportionally more important in the history of the two deeper-water species. H. trimaculatus has the most widespread haplotypes [average clade distance (D(c)) of nonsingleton haplotypes = 1169 km], indicating potentially high dispersal capabilities, whereas H. barbouri has the least widespread haplotypes (average D(c) = 67 km) indicating potentially lower dispersal capabilities. Pleistocene separation of marine basins and postglacial flooding of the Sunda Shelf are extrinsic factors likely to have contributed to the phylogeographical structure observed, whereas differences among the species appear to reflect their individual ecologies.

Earliest Example of a Giant Monitor Lizard (Varanus, Varanidae, Squamata)

PubMed Central

Conrad, Jack L.; Balcarcel, Ana M.; Mehling, Carl M.

2012-01-01

Background Varanidae is a clade of tiny (<20 mm pre-caudal length [PCL]) to giant (>600 mm PCL) lizards first appearing in the Cretaceous. True monitor lizards (Varanus) are known from diagnostic remains beginning in the early Miocene (Varanus rusingensis), although extremely fragmentary remains have been suggested as indicating earlier Varanus. The paleobiogeographic history of Varanus and timing for origin of its gigantism remain uncertain. Methodology/Principal Findings A new Varanus from the Mytilini Formation (Turolian, Miocene) of Samos, Greece is described. The holotype consists of a partial skull roof, right side of a braincase, partial posterior mandible, fragment of clavicle, and parts of six vertebrae. A cladistic analysis including 83 taxa coded for 5733 molecular and 489 morphological characters (71 previously unincluded) demonstrates that the new fossil is a nested member of an otherwise exclusively East Asian Varanus clade. The new species is the earliest-known giant (>600 mm PCL) terrestrial lizard. Importantly, this species co-existed with a diverse continental mammalian fauna. Conclusions/Significance The new monitor is larger (longer) than 99% of known fossil and living lizards. Varanus includes, by far, the largest limbed squamates today. The only extant non-snake squamates that approach monitors in maximum size are the glass-snake Pseudopus and the worm-lizard Amphisbaena. Mosasauroids were larger, but exclusively marine, and occurred only during the Late Cretaceous. Large, extant, non-Varanus, lizards are limbless and/or largely isolated from mammalian competitors. By contrast, our new Varanus achieved gigantism in a continental environment populated by diverse eutherian mammal competitors. PMID:22900001

Acremonium phylogenetic overview and revision of Gliomastix, Sarocladium, and Trichothecium.

PubMed

Summerbell, R C; Gueidan, C; Schroers, H-J; de Hoog, G S; Starink, M; Rosete, Y Arocha; Guarro, J; Scott, J A

2011-01-01

Over 200 new sequences are generated for members of the genus Acremonium and related taxa including ribosomal small subunit sequences (SSU) for phylogenetic analysis and large subunit (LSU) sequences for phylogeny and DNA-based identification. Phylogenetic analysis reveals that within the Hypocreales, there are two major clusters containing multiple Acremonium species. One clade contains Acremonium sclerotigenum, the genus Emericellopsis, and the genus Geosmithia as prominent elements. The second clade contains the genera Gliomastixsensu stricto and Bionectria. In addition, there are numerous smaller clades plus two multi-species clades, one containing Acremonium strictum and the type species of the genus Sarocladium, and, as seen in the combined SSU/LSU analysis, one associated subclade containing Acremonium breve and related species plus Acremonium curvulum and related species. This sequence information allows the revision of three genera. Gliomastix is revived for five species, G. murorum, G. polychroma, G. tumulicola, G. roseogrisea, and G. masseei. Sarocladium is extended to include all members of the phylogenetically distinct A. strictum clade including the medically important A. kiliense and the protective maize endophyte A. zeae. Also included in Sarocladium are members of the phylogenetically delimited Acremonium bacillisporum clade, closely linked to the A. strictum clade. The genus Trichothecium is revised following the principles of unitary nomenclature based on the oldest valid anamorph or teleomorph name, and new combinations are made in Trichothecium for the tightly interrelated Acremonium crotocinigenum, Spicellum roseum, and teleomorph Leucosphaerinaindica. Outside the Hypocreales, numerous Acremonium-like species fall into the Plectosphaerellaceae, and A. atrogriseum falls into the Cephalothecaceae.

Short Report: Comparison of Oral Infectious Dose of West Nile Virus Isolates Representing Three Distinct Genotypes in Culex quinquefasciatus

PubMed Central

Vanlandingham, Dana L.; McGee, Charles E.; Klingler, Kimberly A.; Galbraith, Sareen E.; Barrett, Alan D. T.; Higgs, Stephen

2009-01-01

Phylogenetic analysis of West Nile virus in North America has identified replacement of the originally introduced clade, Eastern United States (NY99), by the North American clade. In addition, the transient emergence of other clades and genetic variants has also been observed. In this study, we investigated the potential role of the mosquito in the selection of these clades and genetic variants. We determined the relative susceptibility of Culex quinquefasciatus to infection with isolates from the Eastern U.S. clade, the North American clade, and the Southeast coastal Texas clade. Although significant differences were observed in 50% oral infectious dose values between the Eastern U.S. and two attenuated North American genetic variants compared with the North American and Southeast coastal Texas clade viruses, these differences did not correlate with persistence of the genotype in nature. These results indicate that selection of these viral genotypes was independent of viral oral infectivity in the mosquito. PMID:19052310

DISCRIMINATION 28S RIBOSOMAL GENE OF TREMATODE CERCARIAE IN SNAILS FROM CHIANG MAI PROVINCE, THAILAND.

PubMed

Wongsawad, Chalobol; Wongsawad, Pheravut; Sukontason, Kom; Phalee, Anawat; Noikong-Phalee, Waraporn; Chai, Jong Yil

2016-03-01

Trematode cercariae are commonly found in many freshwater gastropods. These cercariae can serve to identify the occurrence of such trematodes as Centrocestus formosanus, Haplorchis taichui, Haplorchoides sp, and Stellantchasmus falcatus, which are important parasites in Chiang Mai Province, Thailand. As the species of these cercariae cannot be identified accurately based on morphology, this study employed sequencing of a fragment of 28S ribosomal DNA and phylogenetic analysis to identify the trematode cercariae found in freshwater gastropods in Chiang Mai Province. Eight types of trematode cercariae were identified, namely, distome cercaria (grouped with Philophthalmus spp clade), echinostome cercaria (grouped with Echinostoma spp clade), furcocercous cercaria (grouped with Posthodiplostomum sp/Alaria taxideae/Hysteromorpha triloba clade), monostome cercaria (grouped with Catatropis indicus clade), parapleurolophocercous cercaria (grouped with Haplorchoides sp clade), pleurolophocercous cercaria (grouped with Centrocestusformosanus clade), transversotrema cercaria (grouped with Transversotrema spp clade), and xiphidiocercaria (grouped with Prosthodendrium spp clade). These results provide important information that can be used for identifying these parasites in epidemiological surveys.

Comparative Chloroplast Genomics of Gossypium Species: Insights Into Repeat Sequence Variations and Phylogeny

PubMed Central

Wu, Ying; Liu, Fang; Yang, Dai-Gang; Li, Wei; Zhou, Xiao-Jian; Pei, Xiao-Yu; Liu, Yan-Gai; He, Kun-Lun; Zhang, Wen-Sheng; Ren, Zhong-Ying; Zhou, Ke-Hai; Ma, Xiong-Feng; Li, Zhong-Hu

2018-01-01

Cotton is one of the most economically important fiber crop plants worldwide. The genus Gossypium contains a single allotetraploid group (AD) and eight diploid genome groups (A–G and K). However, the evolution of repeat sequences in the chloroplast genomes and the phylogenetic relationships of Gossypium species are unclear. Thus, we determined the variations in the repeat sequences and the evolutionary relationships of 40 cotton chloroplast genomes, which represented the most diverse in the genus, including five newly sequenced diploid species, i.e., G. nandewarense (C1-n), G. armourianum (D2-1), G. lobatum (D7), G. trilobum (D8), and G. schwendimanii (D11), and an important semi-wild race of upland cotton, G. hirsutum race latifolium (AD1). The genome structure, gene order, and GC content of cotton species were similar to those of other higher plant plastid genomes. In total, 2860 long sequence repeats (>10 bp in length) were identified, where the F-genome species had the largest number of repeats (G. longicalyx F1: 108) and E-genome species had the lowest (G. stocksii E1: 53). Large-scale repeat sequences possibly enrich the genetic information and maintain genome stability in cotton species. We also identified 10 divergence hotspot regions, i.e., rpl33-rps18, psbZ-trnG (GCC), rps4-trnT (UGU), trnL (UAG)-rpl32, trnE (UUC)-trnT (GGU), atpE, ndhI, rps2, ycf1, and ndhF, which could be useful molecular genetic markers for future population genetics and phylogenetic studies. Site-specific selection analysis showed that some of the coding sites of 10 chloroplast genes (atpB, atpE, rps2, rps3, petB, petD, ccsA, cemA, ycf1, and rbcL) were under protein sequence evolution. Phylogenetic analysis based on the whole plastomes suggested that the Gossypium species grouped into six previously identified genetic clades. Interestingly, all 13 D-genome species clustered into a strong monophyletic clade. Unexpectedly, the cotton species with C, G, and K-genomes were admixed and nested in a large clade, which could have been due to their recent radiation, incomplete lineage sorting, and introgression hybridization among different cotton lineages. In conclusion, the results of this study provide new insights into the evolution of repeat sequences in chloroplast genomes and interspecific relationships in the genus Gossypium. PMID:29619041

Characterization of cross-clade monoclonal antibodies against H5N1 highly pathogenic avian influenza virus and their application to the antigenic analysis of diverse H5 subtype viruses.

PubMed

Gronsang, Dulyatad; Bui, Anh N; Trinh, Dai Q; Bui, Vuong N; Nguyen, Khong V; Can, Minh X; Omatsu, Tsutomu; Mizutani, Tetsuya; Nagai, Makoto; Katayama, Yukie; Thampaisarn, Rapeewan; Ogawa, Haruko; Imai, Kunitoshi

2017-08-01

H5N1 highly pathogenic avian influenza viruses (HPAIVs) are a threat to both animal and public health and require specific and rapid detection for prompt disease control. We produced three neutralizing anti-hemagglutinin (HA) monoclonal antibodies (mAbs) using two clades (2.2 and 2.5) of the H5N1 HPAIV isolated in Japan. Blocking immunofluorescence tests showed that each mAb recognized different epitopes; 3B5.1 and 3B5.2 mAbs against the clade 2.5 virus showed cross-clade reactivity to all 26 strains from clades 1, 2.2, 2.3.2.1, 2.3.2.1a, b, c and 2.3.4, suggesting that the epitope(s) recognized are conserved. Conversely, the 1G5 mAb against the clade 2.2 virus showed reactivity to only clades 1, 2.3.4 and 2.5 strains. An analysis of escape mutants, and some clades of the H5N1 viruses recognized by 3B5.1 and 3B5.2 mAbs, suggested that the mAbs bind to an epitope, including amino acid residues at position 162 in the HA1 protein (R162 and K162). Unexpectedly, however, when five Eurasian-origin H5 low-pathogenic AIV (LPAIV) strains with R162 were examined (EA-nonGsGD clade) as well as two American-origin strains (Am-nonGsGD clade), the mAb recognized only EA-nonGsGD clade strains. The R162 and K162 residues in the HA1 protein were highly conserved among 36 of the 43 H5N1 clades reported, including clades 2.3.2.1a and 2.3.2.1c that are currently circulating in Asia, Africa and Europe. The amino acid residues (158-PTIKRSYNNTNQE-170) in the HA1 protein are probably an epitope responsible for the cross-clade reactivity of the mAbs, considering the epitopes reported elsewhere. The 3B5.1 and 3B5.2 mAbs may be useful for the specific detection of H5N1 HPAIVs circulating in the field.

Enhanced virulence of clade 2.3.2.1 highly pathogenic avian influenza A(H5N1) viruses in ferrets

USDA-ARS?s Scientific Manuscript database

Sporadic avian to human transmission of highly pathogenic avian influenza (HPAI) A (H5N1) viruses necessitates the analysis of currently circulating and evolving clades to assess their potential risk. Following the spread and sustained circulation of clade 2 viruses across multiple continents, num...

A functional genomic analysis of Arabidopsis thaliana PP2C clade D

USDA-ARS?s Scientific Manuscript database

In the reference dicot plant Arabidopsis thaliana, the PP2C family of P-protein phosphatases includes the products of 80 genes that have been separated into 10 multi-protein clades plus six singletons. Clade D includes the products of nine genes distributed among 3 chromosomes (PPD1, At3g12620; PPD2...

Taxonomic evaluation of species in the Streptomyces hirsutus clade using multi-locus sequence analysis and proposals to reclassify several species in this clade

USDA-ARS?s Scientific Manuscript database

Previous phylogenetic analyses of species of Streptomyces based on 16S rRNA gene sequences resulted in a statistically well-supported clade (100% bootstrap value) containing 8 species that exhibited very similar gross morphology in producing open looped (Retinaculum-Apertum) to spiral (Spira) chains...

Fusarium solani is responsible for mass mortalities in nests of loggerhead sea turtle, Caretta caretta, in Boavista, Cape Verde.

PubMed

Sarmiento-Ramírez, Jullie M; Abella, Elena; Martín, María P; Tellería, María T; López-Jurado, Luis F; Marco, Adolfo; Diéguez-Uribeondo, Javier

2010-11-01

The fungus Fusarium solani (Mart.) Saccardo (1881) was found to be the cause of infections in the eggs of the sea turtle species Caretta caretta in Boavista Island, Cape Verde. Egg shells with early and severe symptoms of infection, as well as diseased embryos were sampled from infected nests. Twenty-five isolates with similar morphological characteristics were obtained. Their ITS rRNA gene sequences were similar to the GenBank sequences corresponding to F. solani and their maximum identity ranged from 95% to 100%. Phylogenetic parsimony and Bayesian analyses of these isolates showed that they belong to a single F. solani clade and that they are distributed in two subclades named A and C (the latter containing 23 out of 25). A representative isolate of subclade C was used in challenge inoculation experiments to test Koch postulates. Mortality rates were c. 83.3% in challenged eggs and 8.3% in the control. Inoculated challenged eggs exhibited the same symptoms as infected eggs found in the field. Thus, this work demonstrates that a group of strains of F. solani are responsible for the symptoms observed on turtle-nesting beaches, and that they represent a risk for the survival of this endangered species. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Development of a molecular approach to describe the composition of Trichoderma communities.

PubMed

Meincke, Remo; Weinert, Nicole; Radl, Viviane; Schloter, Michael; Smalla, Kornelia; Berg, Gabriele

2010-01-01

Trichoderma and its teleomorphic stage Hypocrea play a key role for ecosystem functioning in terrestrial habitats. However, little is known about the ecology of the fungus. In this study we developed a novel Trichoderma-specific primer pair for diversity analysis. Based on a broad range master alignment, specific Trichoderma primers (ITSTrF/ITSTrR) were designed that comprise an approximate 650bp fragment of the internal transcribed spacer region from all taxonomic clades of the genus Trichoderma. This amplicon is suitable for identification with TrichoKey and TrichoBLAST. Moreover, this primer system was successfully applied to study the Trichoderma communities in the rhizosphere of different potato genotypes grown at two field sites in Germany. Cloning and sequencing confirmed the specificity of the primer and revealed a site-dependent Trichoderma composition. Based on the new primer system a semi-nested approach was used to generate amplicons suitable for denaturing gradient gel electrophoresis (DGGE) analysis and applied to analyse Trichoderma communities in the rhizosphere of potatoes. High field heterogeneity of Trichoderma communities was revealed by both DGGE. Furthermore, qPCR showed significantly different Trichoderma copy numbers between the sites. Copyright 2009 Elsevier B.V. All rights reserved.

Acremonium phylogenetic overview and revision of Gliomastix, Sarocladium, and Trichothecium

PubMed Central

Summerbell, R.C.; Gueidan, C.; Schroers, H-J.; de Hoog, G.S.; Starink, M.; Rosete, Y. Arocha; Guarro, J.; Scott, J.A.

2011-01-01

Over 200 new sequences are generated for members of the genus Acremonium and related taxa including ribosomal small subunit sequences (SSU) for phylogenetic analysis and large subunit (LSU) sequences for phylogeny and DNA-based identification. Phylogenetic analysis reveals that within the Hypocreales, there are two major clusters containing multiple Acremonium species. One clade contains Acremonium sclerotigenum, the genus Emericellopsis, and the genus Geosmithia as prominent elements. The second clade contains the genera Gliomastix sensu stricto and Bionectria. In addition, there are numerous smaller clades plus two multi-species clades, one containing Acremonium strictum and the type species of the genus Sarocladium, and, as seen in the combined SSU/LSU analysis, one associated subclade containing Acremonium breve and related species plus Acremonium curvulum and related species. This sequence information allows the revision of three genera. Gliomastix is revived for five species, G. murorum, G. polychroma, G. tumulicola, G. roseogrisea, and G. masseei. Sarocladium is extended to include all members of the phylogenetically distinct A. strictum clade including the medically important A. kiliense and the protective maize endophyte A. zeae. Also included in Sarocladium are members of the phylogenetically delimited Acremonium bacillisporum clade, closely linked to the A. strictum clade. The genus Trichothecium is revised following the principles of unitary nomenclature based on the oldest valid anamorph or teleomorph name, and new combinations are made in Trichothecium for the tightly interrelated Acremonium crotocinigenum, Spicellum roseum, and teleomorph Leucosphaerina indica. Outside the Hypocreales, numerous Acremonium-like species fall into the Plectosphaerellaceae, and A. atrogriseum falls into the Cephalothecaceae. PMID:21523192

Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes.

PubMed

Saarela, Jeffery M; Wysocki, William P; Barrett, Craig F; Soreng, Robert J; Davis, Jerrold I; Clark, Lynn G; Kelchner, Scot A; Pires, J Chris; Edger, Patrick P; Mayfield, Dustin R; Duvall, Melvin R

2015-05-04

Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae-Loliinae clade. Published by Oxford University Press on behalf of the Annals of Botany Company.

A family-level Tree of Life for bivalves based on a Sanger-sequencing approach.

PubMed

Combosch, David J; Collins, Timothy M; Glover, Emily A; Graf, Daniel L; Harper, Elizabeth M; Healy, John M; Kawauchi, Gisele Y; Lemer, Sarah; McIntyre, Erin; Strong, Ellen E; Taylor, John D; Zardus, John D; Mikkelsen, Paula M; Giribet, Gonzalo; Bieler, Rüdiger

2017-02-01

The systematics of the molluscan class Bivalvia are explored using a 5-gene Sanger-based approach including the largest taxon sampling to date, encompassing 219 ingroup species spanning 93 (or 82%) of the 113 currently accepted bivalve families. This study was designed to populate the bivalve Tree of Life at the family level and to place many genera into a clear phylogenetic context, but also pointing to several major clades where taxonomic work is sorely needed. Despite not recovering monophyly of Bivalvia or Protobranchia-as in most previous Sanger-based approaches to bivalve phylogeny-our study provides increased resolution in many higher-level clades, and supports the monophyly of Autobranchia, Pteriomorphia, Heteroconchia, Palaeoheterodonta, Heterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata, Imparidentia, and Neoheterodontei, in addition to many other lower clades. However, deep nodes within some of these clades, especially Pteriomorphia and Imparidentia, could not be resolved with confidence. In addition, many families are not supported, and several are supported as non-monophyletic, including Malletiidae, Nuculanidae, Yoldiidae, Malleidae, Pteriidae, Arcidae, Propeamussiidae, Iridinidae, Carditidae, Myochamidae, Lyonsiidae, Pandoridae, Montacutidae, Galeommatidae, Tellinidae, Semelidae, Psammobiidae, Donacidae, Mactridae, and Cyrenidae; Veneridae is paraphyletic with respect to Chamidae, although this result appears to be an artifact. The denser sampling however allowed testing specific placement of species, showing, for example, that the unusual Australian Plebidonax deltoides is not a member of Donacidae and instead nests within Psammobiidae, suggesting that major revision of Tellinoidea may be required. We also showed that Cleidothaerus is sister group to the cementing member of Myochamidae, suggesting that Cleidothaeridae may not be a valid family and that cementation in Cleidothaerus and Myochama may have had a single origin. These results highlight the need for an integrative approach including as many genera as possible, and that the monophyly and relationships of many families require detailed reassessment. NGS approaches may be able to resolve the most recalcitrant nodes in the near future. Copyright © 2016 Elsevier Inc. All rights reserved.

Origin and Dispersal History of Two Colonial Ascidian Clades in the Botryllus schlosseri Species Complex.

PubMed

Nydam, Marie L; Giesbrecht, Kirsten B; Stephenson, Emily E

2017-01-01

Human-induced global warming and species introductions are rapidly altering the composition and functioning of Earth's marine ecosystems. Ascidians (Phylum Chordata, Subphylum Tunicata, Class Ascidiacea) are likely to play an increasingly greater role in marine communities. The colonial ascidian B. schlosseri is a cryptic species complex comprising five genetically divergent clades (A-E). Clade A is a global species, and Clade E has so far been identified in European waters only. Using the largest mitochondrial cytochrome oxidase I datasets yet assembled, we determine the origin and dispersal history of these species. Nucleotide diversity and Approximate Bayesian Computation analyses support a Pacific origin for Clade A, with two likely dispersal scenarios that both show the northwestern Atlantic populations establishing early in the history of the species. Both Discrete Phylogeographic Analysis and Approximate Bayesian Computation support an origin of Clade E on the French side of the English Channel. An unsampled lineage evolved from the French lineage, which reflects the conclusion from the median joining network that not all Clade E lineages have been sampled. This unsampled lineage gave rise to the haplotypes on the English side of the English Channel, which were the ancestors to the Mediterranean and Bay of Biscay populations. Clade E has a wider geographic range than previously thought, and shows evidence of recent range expansion. Both Clade A and Clade E should be considered widespread species: Clade A globally and Clade E within Europe.

Spatio-Temporal History of HIV-1 CRF35_AD in Afghanistan and Iran.

PubMed

Eybpoosh, Sana; Bahrampour, Abbas; Karamouzian, Mohammad; Azadmanesh, Kayhan; Jahanbakhsh, Fatemeh; Mostafavi, Ehsan; Zolala, Farzaneh; Haghdoost, Ali Akbar

2016-01-01

HIV-1 Circulating Recombinant Form 35_AD (CRF35_AD) has an important position in the epidemiological profile of Afghanistan and Iran. Despite the presence of this clade in Afghanistan and Iran for over a decade, our understanding of its origin and dissemination patterns is limited. In this study, we performed a Bayesian phylogeographic analysis to reconstruct the spatio-temporal dispersion pattern of this clade using eligible CRF35_AD gag and pol sequences available in the Los Alamos HIV database (432 sequences available from Iran, 16 sequences available from Afghanistan, and a single CRF35_AD-like pol sequence available from USA). Bayesian Markov Chain Monte Carlo algorithm was implemented in BEAST v1.8.1. Between-country dispersion rates were tested with Bayesian stochastic search variable selection method and were considered significant where Bayes factor values were greater than three. The findings suggested that CRF35_AD sequences were genetically similar to parental sequences from Kenya and Uganda, and to a set of subtype A1 sequences available from Afghan refugees living in Pakistan. Our results also showed that across all phylogenies, Afghan and Iranian CRF35_AD sequences formed a monophyletic cluster (posterior clade credibility> 0.7). The divergence date of this cluster was estimated to be between 1990 and 1992. Within this cluster, a bidirectional dispersion of the virus was observed across Afghanistan and Iran. We could not clearly identify if Afghanistan or Iran first established or received this epidemic, as the root location of this cluster could not be robustly estimated. Three CRF35_AD sequences from Afghan refugees living in Pakistan nested among Afghan and Iranian CRF35_AD branches. However, the CRF35_AD-like sequence available from USA diverged independently from Kenyan subtype A1 sequences, suggesting it not to be a true CRF35_AD lineage. Potential factors contributing to viral exchange between Afghanistan and Iran could be injection drug networks and mass migration of Afghan refugees and labours to Iran, which calls for extensive preventive efforts.

Spatio-Temporal History of HIV-1 CRF35_AD in Afghanistan and Iran

PubMed Central

Eybpoosh, Sana; Bahrampour, Abbas; Karamouzian, Mohammad; Azadmanesh, Kayhan; Jahanbakhsh, Fatemeh; Mostafavi, Ehsan; Zolala, Farzaneh; Haghdoost, Ali Akbar

2016-01-01

HIV-1 Circulating Recombinant Form 35_AD (CRF35_AD) has an important position in the epidemiological profile of Afghanistan and Iran. Despite the presence of this clade in Afghanistan and Iran for over a decade, our understanding of its origin and dissemination patterns is limited. In this study, we performed a Bayesian phylogeographic analysis to reconstruct the spatio-temporal dispersion pattern of this clade using eligible CRF35_AD gag and pol sequences available in the Los Alamos HIV database (432 sequences available from Iran, 16 sequences available from Afghanistan, and a single CRF35_AD-like pol sequence available from USA). Bayesian Markov Chain Monte Carlo algorithm was implemented in BEAST v1.8.1. Between-country dispersion rates were tested with Bayesian stochastic search variable selection method and were considered significant where Bayes factor values were greater than three. The findings suggested that CRF35_AD sequences were genetically similar to parental sequences from Kenya and Uganda, and to a set of subtype A1 sequences available from Afghan refugees living in Pakistan. Our results also showed that across all phylogenies, Afghan and Iranian CRF35_AD sequences formed a monophyletic cluster (posterior clade credibility> 0.7). The divergence date of this cluster was estimated to be between 1990 and 1992. Within this cluster, a bidirectional dispersion of the virus was observed across Afghanistan and Iran. We could not clearly identify if Afghanistan or Iran first established or received this epidemic, as the root location of this cluster could not be robustly estimated. Three CRF35_AD sequences from Afghan refugees living in Pakistan nested among Afghan and Iranian CRF35_AD branches. However, the CRF35_AD-like sequence available from USA diverged independently from Kenyan subtype A1 sequences, suggesting it not to be a true CRF35_AD lineage. Potential factors contributing to viral exchange between Afghanistan and Iran could be injection drug networks and mass migration of Afghan refugees and labours to Iran, which calls for extensive preventive efforts. PMID:27280293

Identification and screening of rare actinomycetes isolated from Neesia altissima Bl.

NASA Astrophysics Data System (ADS)

Pratiwi, R. H.; Hidayat, I.; Hanafi, M.; Mangunwardoyo, W.

2017-07-01

Actinomycetes is the main source of antibiotics and endophytic actinomycetes from medicinal plants has considerable potential as like the host. The aim of this research is to identify rare actinomycetes isolated from Neesia altissima and to screen their antagonistic activity against diarrhea-causing bacteria in order to find new potential secondary metabolites. Samples of N. altissima were collected from mount Halimun-Salak National Park. Endophytic actinomycetes were isolated from roots of N. altissima by surface sterilization method. Screening of antagonistic activity was conducted against five diarrhea-causing bacteria such as Bacillus cereus ATCC 10876, Escherichia coli ATCC 25922, Salmonella typhimurium ATCC 25241, Shigella flexneri ATCC 12022, and Staphylococcus aureus ATCC 25923 by using diffusion disc methods. The endophytic actinomycete showed in vitro antibacterial activity against four diarrhea-causing bacteria, except the B. cereus ATCC 10876. The phylogenetic tree generated from 16S rRNA sequence showed that sequence of endophytic actinomycetes isolates nested in the clade belonging to the genus Nonomuraea. Sequence of UICC B-94 formed a monophyletic clade with N. jabiensis strain A4036 and N. rubra strain AC 615. Therefore, it is named as Nonomuraea sp. strain UICC B-94.

Paragonimus & paragonimiasis in India

PubMed Central

Singh, T. Shantikumar; Sugiyama, Hiromu; Rangsiruji, Achariya

2012-01-01

Ever since the discovery of the first indigenous case in 1981, paragonimiasis has gained recognition as a significant food borne parasitic zoonosis in India. The data available on the occurrence of paragonimiasis, until today, may be just the tip of an iceberg as the study areas covered were restricted to Northeast Indian States. Nevertheless, the results of research on paragonimiasis in India have revealed valuable information in epidemiology, life cycle, pathobiology and speciation of Indian Paragonimus. Potamiscus manipurensis, Alcomon superciliosum and Maydelliathelphusa lugubris were identified as the crab hosts of Paragonimus. Paragonimus miyazakii manipurinus n. sub sp., P. hueit’ungensis, P. skrjabini, P. heterotremus, P. compactus, and P. westermani have been described from India. P. heterotremus was found as the causative agent of human paragonimiasis. Ingestion of undercooked crabs and raw crab extract was the major mode of infection. Pulmonary paragonimiasis was the commonest clinical manifestation while pleural effusion and subcutaneous nodules were the common extra-pulmonary forms. Clinico-radiological features of pulmonary paragonimiasis simulated pulmonary tuberculosis. Intradermal test, ELISA and Dot-immunogold filtration assay (DIGFA) were used for diagnosis and epidemiological survey of paragonimiasis. Phylogenitically, Indian Paragonimus species, although nested within the respective clade were distantly related to others within the clade. PMID:22960885

Evolution of foraging behaviour: Deep intra-generic genetic divergence between territorial and non-territorial southern African patellid limpets.

PubMed

Mmonwa, Kolobe L; Teske, Peter R; McQuaid, Christopher D; Barker, Nigel P

2017-12-01

Southern Africa is a biodiversity hotspot of patellid limpets, with three genera (Helcion, Cymbula and Scutellastra) identified and described in the region. Scutellastra is the most diverse and most frequently studied of these and, along with Cymbula, includes species with territorial and non-territorial foraging behaviours. We used three mitochondrial markers (12S rRNA, 16S rRNA and COI) and one nuclear marker (ATPSβ intron) to assess evolutionary relationships among species of Cymbula and Scutellastra with these two foraging behaviours and to identify which foraging mode is the more ancient. Maximum Likelihood and Bayesian Inference phylogenetic analyses revealed that the species sharing a foraging type are monophyletic in both genera. Territoriality is a derived character, as the clades with this foraging type are nested within a tree that otherwise comprises non-territorial taxa. These include Helcion, which was recovered as sister to the Cymbula/Scutellastra clade, and the next basal genus, Patella, which is ancestral to all southern African patellogastropods. Deep genetic divergence between the two foraging traits reflects strong adaptive effects of resource partitioning in the evolution of southern African patellid limpets. Copyright © 2017 Elsevier Inc. All rights reserved.

Footprints in the sand: independent reduction of subdigital lamellae in the Namib–Kalahari burrowing geckos

PubMed Central

Lamb, Trip; Bauer, Aaron M

2005-01-01

Many desert organisms exhibit convergence, and certain physical factors such as windblown sands have generated remarkably similar ecomorphs across divergent lineages. The burrowing geckos Colopus, Chondrodactylus and Palmatogecko occupy dune ecosystems in the Namib and Kalahari deserts of southwest Africa. Considered closely related, they share several putative synapomorphies, including reduced subdigital pads (toe pads) and spinose digital scales. Though recognized as part of Africa's ecologically diverse Pachydactylus Group, the burrowing geckos' precise phylogenetic affinities remain elusive. Convergent pedal modification provides a tenable alternative explaining the geckos' derived terrestriality and adaptation to Namib and Kalahari sands. We generated a molecular phylogeny for the Pachydactylus Group to examine evolutionary relationships among the burrowing geckos and infer historical patterns of pedal character change. Bayesian and parsimony analyses revealed all three burrowing genera to be deeply nested within Pachydactylus, each genus belonging to a separate clade. Strong support for these distinct clades indicates ecomorphological adaptations for burrowing have evolved independently three times in the southern Pachydactylus Group. We argue that the physical properties of Namib and Kalahari sands played a principal role in selecting for pedal similarity. PMID:16618680

Tightly congruent bursts of lineage and phenotypic diversification identified in a continental ant radiation.

PubMed

Price, Shauna L; Etienne, Rampal S; Powell, Scott

2016-04-01

Adaptive diversification is thought to be shaped by ecological opportunity. A prediction of this ecological process of diversification is that it should result in congruent bursts of lineage and phenotypic diversification, but few studies have found this expected association. Here, we study the relationship between rates of lineage diversification and body size evolution in the turtle ants, a diverse Neotropical clade. Using a near complete, time-calibrated phylogeny we investigated lineage diversification dynamics and body size disparity through model fitting analyses and estimation of per-lineage rates of cladogenesis and phenotypic evolution. We identify an exceptionally high degree of congruence between the high rates of lineage and body size diversification in a young clade undergoing renewed diversification in the ecologically distinct Chacoan biogeographical region of South America. It is likely that the region presented turtle ants with novel ecological opportunity, which facilitated a nested burst of diversification and phenotypic evolution within the group. Our results provide a compelling quantitative example of tight congruence between rates of lineage and phenotypic diversification, meeting the key predicted pattern of adaptive diversification shaped by ecological opportunity. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Nocturnality in synapsids predates the origin of mammals by over 100 million years

PubMed Central

Angielczyk, K. D.; Schmitz, L.

2014-01-01

Nocturnality is widespread among extant mammals and often considered the ancestral behavioural pattern for all mammals. However, mammals are nested within a larger clade, Synapsida, and non-mammalian synapsids comprise a rich phylogenetic, morphological and ecological diversity. Even though non-mammalian synapsids potentially could elucidate the early evolution of diel activity patterns and enrich the understanding of synapsid palaeobiology, data on their diel activity are currently unavailable. Using scleral ring and orbit dimensions, we demonstrate that nocturnal activity was not an innovation unique to mammals but a character that appeared much earlier in synapsid history, possibly several times independently. The 24 Carboniferous to Jurassic non-mammalian synapsid species in our sample featured eye morphologies consistent with all major diel activity patterns, with examples of nocturnality as old as the Late Carboniferous (ca 300 Ma). Carnivores such as Sphenacodon ferox and Dimetrodon milleri, but also the herbivorous cynodont Tritylodon longaevus were likely nocturnal, whereas most of the anomodont herbivores are reconstructed as diurnal. Recognizing the complexity of diel activity patterns in non-mammalian synapsids is an important step towards a more nuanced picture of the evolutionary history of behaviour in the synapsid clade. PMID:25186003

Influence of sexual selection and feeding functional morphology on diversification rate of parrotfishes (Scaridae).

PubMed

Kazancioglu, Erem; Near, Thomas J; Hanel, Reinhold; Wainwright, Peter C

2009-10-07

Scaridae (parrotfishes) is a prominent clade of 96 species that shape coral reef communities worldwide through their actions as grazing herbivores. Phylogenetically nested within Labridae, the profound ecological impact and high species richness of parrotfishes suggest that their diversification and ecological success may be linked. Here, we ask whether parrotfish evolution is characterized by a significant burst of lineage diversification and whether parrotfish diversity is shaped more strongly by sexual selection or modifications of the feeding mechanism. We first examined scarid diversification within the greater context of labrid diversity. We used a supermatrix approach for 252 species to propose the most extensive phylogenetic hypothesis of Labridae to date, and time-calibrated the phylogeny with fossil and biogeographical data. Using divergence date estimates, we find that several parrotfish clades exhibit the highest diversification rates among all labrid lineages. Furthermore, we pinpoint a rate shift at the shared ancestor of Scarus and Chlorurus, a scarid subclade characterized by territorial behaviour and strong sexual dichromatism, suggesting that sexual selection was a major factor in parrotfish diversification. Modifications of the pharyngeal and oral jaws that happened earlier in parrotfish evolution may have contributed to this diversity by establishing parrotfishes as uniquely capable reef herbivores.

Molecular phylogeny of the lionfish genera Dendrochirus and Pterois (Scorpaenidae, Pteroinae) based on mitochondrial DNA sequences.

PubMed

Kochzius, Marc; Söller, Rainer; Khalaf, Maroof A; Blohm, Dietmar

2003-09-01

This study investigates the molecular phylogeny of seven lionfishes of the genera Dendrochirus and Pterois. MP, ML, and NJ phylogenetic analysis based on 964 bp of partial mitochondrial DNA sequences (cytochrome b and 16S rDNA) revealed two main clades: (1) "Pterois" clade (Pterois miles and Pterois volitans), and (2) "Pteropterus-Dendrochirus" clade (remainder of the sampled species). The position of Dendrochirus brachypterus either basal to the main clades or in the "Pteropterus-Dendrochirus" clade cannot be resolved. However, the molecular phylogeny did not support the current separation of the genera Pterois and Dendrochirus. The siblings P. miles and P. volitans are clearly separated and our results support the proposed allopatric or parapatric distribution in the Indian and Pacific Ocean. However, the present analysis cannot reveal if P. miles and P. volitans are separate species or two populations of a single species, because the observed separation in different clades can be either explained by speciation or lineage sorting. Molecular clock estimates for the siblings P. miles and P. volitans suggest a divergence time of 2.4-8.3 mya, which coincide with geological events that created vicariance between populations of the Indian and Pacific Ocean.

Whole-Genome Phylogenetic Analysis of Influenza B/Phuket/3073/2013-Like Viruses and Unique Reassortants Detected in Malaysia between 2012 and 2014

PubMed Central

Tan, Joon Ling; Chan, Kok Gan; Kamarulzaman, Adeeba; Chan, Yoke Fun; Sam, I-Ching; Tee, Kok Keng

2017-01-01

Reassortment of genetic segments between and within influenza B lineages (Victoria and Yamagata) has been shown to generate novel reassortants with unique genetic characteristics. Based on hemagglutinin (HA) and neuraminidase (NA) genes, recent surveillance study has identified reassortment properties in B/Phuket/3073/2013-like virus, which is currently used in the WHO-recommended influenza vaccine. To understand the potential reassortment patterns for all gene segments, four B/Phuket/3073/2013-like viruses and two unique reassortants (one each from Yamagata and Victoria) detected in Malaysia from 2012–2014 were subjected to whole-genome sequencing. Each gene was phylogenetically classified into lineages, clades and sub-clades. Three B/Phuket/3073/2013-like viruses from Yamagata lineage were found to be intra-clade reassortants, possessing PA and NA genes derived from Stockholm/12-like sub-clade, while the remaining genes from Wisconsin/01-like sub-clade (both sub-clades were within Yamagata Clade 3/Yam-3). However, the other B/Phuket/3073/2013-like virus had NS gene that derived from Stockholm/12-like sub-clade instead of Wisconsin/01-like sub-clade. One inter-clade reassortant had Yamagata Clade 2/Yam-2-derived HA and NP, and its remaining genes were Yam-3-derived. Within Victoria Clade 1/Vic-1 in Victoria lineage, one virus had intra-clade reassortment properties: HA and PB2 from Vic-1B sub-clade, MP and NS from a unique sub-clade “Vic-1C”, and the remaining genes from Vic-1A sub-clade. Although random reassortment event may generate unique reassortants, detailed phylogenetic classification of gene segments showed possible genetic linkage between PA and NA genes in B/Phuket/3073/2013-like viruses, which requires further investigation. Understanding on reassortment patterns in influenza B evolution may contribute to future vaccine design. PMID:28129386

Mitochondrial and nuclear DNA analysis revealed a cryptic species and genetic introgression in Littorina sitkana (Mollusca, Gastropoda).

PubMed

Azuma, Noriko; Yamazaki, Tomoyasu; Chiba, Susumu

2011-12-01

We investigated mitochondrial and nuclear DNA genotypes in nominal Littorina sitkana samples from 2 localities in Eastern Hokkaido, northern Japan. Our results indicated the existence of cryptic species. In the analysis of partial mitochondrial Cytchrome b gene sequences, haplotypes of L. sitkana samples were monophyletic in a phylogenetic tree with orthologous sequences from other Littorina species, but were apparently separated in 2 clades. One included typical L. sitkana (CBa clade) samples, which formed a clade with an allopatric species, L. horikawai. The other, CBb, was independent from CBa and L. horikawai. Haplotypes of the mitochondrial 16S rRNA gene also separated into 2 clades. We additionally examined intron sequence of the heat shock cognate 70 (HSC70) nuclear gene and identified 17 haplotypes. These were also separated into 2 clades, HSCa and HSCb. Among the examined Hokkaido samples, 60% of individuals were heterozygotes. However, each heterozygote consisted of haplotypes from the same clade, HSCa or HSCb, and no admixture of HSCa and HSCb haplotypes was observed. These results indicate reproductive isolation between the 2 clades. Among the genotyped Hokkaido samples, 93% of individuals had CBa + HSCa or CBb + HSCb genotypes, and 7% had CBb + HSCa genotypes. The discrepancy between the mtDNA and nuclear DNA haplotypes in a few individuals may have been caused by genetic introgression due to past hybridization.

Beringian origins and cryptic speciation events in the fly agaric (Amanita muscaria).

PubMed

Geml, J; Laursen, G A; O'neill, K; Nusbaum, H C; Taylor, D L

2006-01-01

Amanita muscaria sensu lato has a wide geographic distribution, occurring in Europe, Asia, Africa, Australia, New Zealand, and North, Central and South America. Previous phylogenetic work by others indicates three geographic clades (i.e. 'Eurasian', 'Eurasian-alpine' and 'North American' groups) within A. muscaria. However, the historical dispersal patterns of A. muscaria remained unclear. In our project, we collected specimens from arctic, boreal and humid temperate regions in Alaska, and generated DNA sequence data from the protein-coding beta-tubulin gene and the internal transcribed spacer (ITS) and large subunit (LSU) regions of the ribosomal DNA repeat. Homologous sequences from additional A. muscaria isolates were downloaded from GenBank. We conducted phylogenetic and nested clade analyses (NCA) to reveal the phylogeographic history of the species complex. Although phylogenetic analyses confirmed the existence of the three above-mentioned clades, representatives of all three groups were found to occur sympatrically in Alaska, suggesting that they represent cryptic phylogenetic species with partially overlapping geographic distributions rather than being allopatric populations. All phylogenetic species share at least two morphological varieties with other species, suggesting ancestral polymorphism in pileus and wart colour pre-dating their speciations. The ancestral population of A. muscaria likely evolved in the Siberian-Beringian region and underwent fragmentation as inferred from NCA and the coalescent analyses. The data suggest that these populations later evolved into species, expanded their range in North America and Eurasia. In addition to range expansions, populations of all three species remained in Beringia and adapted to the cooling climate.

Evolutionary history of the Afro-Madagascan Ixora species (Rubiaceae): species diversification and distribution of key morphological traits inferred from dated molecular phylogenetic trees

PubMed Central

Tosh, J.; Dessein, S.; Buerki, S.; Groeninckx, I.; Mouly, A.; Bremer, B.; Smets, E. F.; De Block, P.

2013-01-01

Background and Aims Previous work on the pantropical genus Ixora has revealed an Afro-Madagascan clade, but as yet no study has focused in detail on the evolutionary history and morphological trends in this group. Here the evolutionary history of Afro-Madagascan Ixora spp. (a clade of approx. 80 taxa) is investigated and the phylogenetic trees compared with several key morphological traits in taxa occurring in Madagascar. Methods Phylogenetic relationships of Afro-Madagascan Ixora are assessed using sequence data from four plastid regions (petD, rps16, rpoB-trnC and trnL-trnF) and nuclear ribosomal external transcribed spacer (ETS) and internal transcribed spacer (ITS) regions. The phylogenetic distribution of key morphological characters is assessed. Bayesian inference (implemented in BEAST) is used to estimate the temporal origin of Ixora based on fossil evidence. Key Results Two separate lineages of Madagascan taxa are recovered, one of which is nested in a group of East African taxa. Divergence in Ixora is estimated to have commenced during the mid Miocene, with extensive cladogenesis occurring in the Afro-Madagascan clade during the Pliocene onwards. Conclusions Both lineages of Madagascan Ixora exhibit morphological innovations that are rare throughout the rest of the genus, including a trend towards pauciflorous inflorescences and a trend towards extreme corolla tube length, suggesting that the same ecological and selective pressures are acting upon taxa from both Madagascan lineages. Novel ecological opportunities resulting from climate-induced habitat fragmentation and corolla tube length diversification are likely to have facilitated species radiation on Madagascar. PMID:24142919

Molecular phylogeny supports the paraphyletic nature of the genus Trogoderma (Coleoptera: Dermestidae) collected in the Australasian ecozone.

PubMed

Castalanelli, M A; Baker, A M; Munyard, K A; Grimm, M; Groth, D M

2012-02-01

To date, a molecular phylogenetic approach has not been used to investigate the evolutionary structure of Trogoderma and closely related genera. Using two mitochondrial genes, Cytochrome Oxidase I and Cytochrome B, and the nuclear gene, 18S, the reported polyphyletic positioning of Trogoderma was examined. Paraphyly in Trogoderma was observed, with one Australian Trogoderma species reconciled as sister to all Dermestidae and the Anthrenocerus genus deeply nested within the Australian Trogoderma clade. In addition, time to most recent common ancestor for a number of Dermestidae was calculated. Based on these estimations, the Dermestidae origin exceeded 175 million years, placing the origins of this family in Pangaea.

CR1 clade of non-LTR retrotransposons from Maculinea butterflies (Lepidoptera: Lycaenidae): evidence for recent horizontal transmission

PubMed Central

Novikova, Olga; Śliwińska, Ewa; Fet, Victor; Settele, Josef; Blinov, Alexander; Woyciechowski, Michal

2007-01-01

Background Non-long terminal repeat (non-LTR) retrotransposons are mobile genetic elements that propagate themselves by reverse transcription of an RNA intermediate. Non-LTR retrotransposons are known to evolve mainly via vertical transmission and random loss. Horizontal transmission is believed to be a very rare event in non-LTR retrotransposons. Our knowledge of distribution and diversity of insect non-LTR retrotransposons is limited to a few species – mainly model organisms such as dipteran genera Drosophila, Anopheles, and Aedes. However, diversity of non-LTR retroelements in arthropods seems to be much richer. The present study extends the analysis of non-LTR retroelements to CR1 clade from four butterfly species of genus Maculinea (Lepidoptera: Lycaenidae). The lycaenid genus Maculinea, the object of interest for evolutionary biologists and also a model group for European biodiversity studies, possesses a unique, specialized myrmecophilous lifestyle at larval stage. Their caterpillars, after three weeks of phytophagous life on specific food plants drop to the ground where they are adopted to the ant nest by Myrmica foraging workers. Results We found that the genome of Maculinea butterflies contains multiple CR1 lineages of non-LTR retrotransposons, including those from MacCR1A, MacCR1B and T1Q families. A comparative analysis of RT nucleotide sequences demonstrated an extremely high similarity among elements both in interspecific and intraspecific comparisons. CR1A-like elements were found only in family Lycaenidae. In contrast, MacCR1B lineage clones were extremely similar to CR1B non-LTR retrotransposons from Bombycidae moths: silkworm Bombyx mori and Oberthueria caeca. Conclusion The degree of coding sequence similarity of the studied elements, their discontinuous distribution, and results of divergence-versus-age analysis make it highly unlikely that these sequences diverged at the same time as their host taxa. The only reasonable alternative explanation is horizontal transfer. In addition, phylogenetic markers for population analysis of Maculinea could be developed based on the described non-LTR retrotransposons. PMID:17588269

Polyphyletic origin of MERS coronaviruses and isolation of a novel clade A strain from dromedary camels in the United Arab Emirates

PubMed Central

Lau, Susanna K P; Wernery, Renate; Wong, Emily Y M; Joseph, Sunitha; Tsang, Alan K L; Patteril, Nissy Annie Georgy; Elizabeth, Shyna K; Chan, Kwok-Hung; Muhammed, Rubeena; Kinne, Jöerg; Yuen, Kwok-Yung; Wernery, Ulrich; Woo, Patrick C Y

2016-01-01

Little is known regarding the molecular epidemiology of Middle East respiratory syndrome coronavirus (MERS-CoV) circulating in dromedaries outside Saudi Arabia. To address this knowledge gap, we sequenced 10 complete genomes of MERS-CoVs isolated from 2 live and 8 dead dromedaries from different regions in the United Arab Emirates (UAE). Phylogenetic analysis revealed one novel clade A strain, the first detected in the UAE, and nine clade B strains. Strain D998/15 had a distinct phylogenetic position within clade A, being more closely related to the dromedary isolate NRCE-HKU205 from Egypt than to the human isolates EMC/2012 and Jordan-N3/2012. A comparison of predicted protein sequences also demonstrated the existence of two clade A lineages with unique amino acid substitutions, A1 (EMC/2012 and Jordan-N3/2012) and A2 (D998/15 and NRCE-HKU205), circulating in humans and camels, respectively. The nine clade B isolates belong to three distinct lineages: B1, B3 and B5. Two B3 strains, D1271/15 and D1189.1/15, showed evidence of recombination between lineages B4 and B5 in ORF1ab. Molecular clock analysis dated the time of the most recent common ancestor (tMRCA) of clade A to March 2011 and that of clade B to November 2011. Our data support a polyphyletic origin of MERS-CoV in dromedaries and the co-circulation of diverse MERS-CoVs including recombinant strains in the UAE. PMID:27999424

A Comprehensive Analysis of RALF Proteins in Green Plants Suggests There Are Two Distinct Functional Groups

PubMed Central

Campbell, Liam; Turner, Simon R.

2017-01-01

Rapid Alkalinization Factors (RALFs) are small, cysteine-rich peptides known to be involved in various aspects of plant development and growth. Although RALF peptides have been identified within many species, a single wide-ranging phylogenetic analysis of the family across the plant kingdom has not yet been undertaken. Here, we identified RALF proteins from 51 plant species that represent a variety of land plant lineages. The inferred evolutionary history of the 795 identified RALFs suggests that the family has diverged into four major clades. We found that much of the variation across the family exists within the mature peptide region, suggesting clade-specific functional diversification. Clades I, II, and III contain the features that have been identified as important for RALF activity, including the RRXL cleavage site and the YISY motif required for receptor binding. In contrast, members of clades IV that represent a third of the total dataset, is highly diverged and lacks these features that are typical of RALFs. Members of clade IV also exhibit distinct expression patterns and physico-chemical properties. These differences suggest a functional divergence of clades and consequently, we propose that the peptides within clade IV are not true RALFs, but are more accurately described as RALF-related peptides. Expansion of this RALF–related clade in the Brassicaceae is responsible for the large number of RALF genes that have been previously described in Arabidopsis thaliana. Future experimental work will help to establish the nature of the relationship between the true RALFs and the RALF-related peptides, and whether they function in a similar manner. PMID:28174582

First comprehensive phylogenetic analysis of the genus Erysiphe (Erysiphales, Erysiphaceae) I. The Microsphaera lineage.

PubMed

Takamatsu, Susumu; Ito Arakawa, Hanako; Shiroya, Yoshiaki; Kiss, Levente; Heluta, Vasyl

2015-01-01

The genus Erysiphe (including powdery mildew fungi only known as anamorph, Pseudoidium) is the largest genus in the Erysiphaceae and contains more than 50% of all species in this family. Little is known about the phylogenetic structure of this genus. We conducted a comprehensive phylogenetic analysis of the Microsphaera-lineage, a monophyletic group including species of sects. Microsphaera and Erysiphe, using 401 sequences of nuc ITS1-5.8S-ITS2 and the 28S rDNA regions. This analysis gave many small clades delimited by the host plant genus or family. We identified two deep branches, albeit with moderate bootstrap supports, that divided the 401 sequences into three large groups. In addition, we identified four large clades consisting of homogeneous sequences of powdery mildews from a wide range of host plants beyond family level, namely, the E. aquilegiae clade, the E. alphitoides clade, the E. quercicola clade, and the E. trifoliorum s. lat. clade. Isolates from herbaceous plants were mostly situated in the E. aquilegiae clade and in Group III that was located at the most derived position of the Microsphaera-lineage. On the other hand, the basal part of the Microsphaera-lineage was occupied by isolates from woody plants except for E. glycines that was used as an outgroup taxon. This supports our previous hypothesis that tree-parasitic powdery mildews are phylogenetically primitive in the Erysiphaceae in general, and host-shift from trees to herbs occurred many times independently during the evolution of powdery mildews. Molecular clock analyses suggested that the divergence of the Microsphaera-lineage began ca. 20 million years ago in the Miocene Epoch of the Neogene Period. © 2015 by The Mycological Society of America.

Multivariate analysis of early and late nest sites of Abert's Towhees

Treesearch

Deborah M. Finch

1985-01-01

Seasonal variation in nest site selection by the Abert's towhee (Pipilo aberti) was studied in honey mesquite (Prosopis glandulosa) habitat along the lower Colorado River from March to July, 1981. Stepwise discriminant function analysis identified nest vegetation type, nest direction, and nest height as the three most important variables that characterized the...

The critically endangered forest owlet Heteroglaux blewitti is nested within the currently recognized Athene clade: A century-old debate addressed.

PubMed

Koparde, Pankaj; Mehta, Prachi; Reddy, Sushma; Ramakrishnan, Uma; Mukherjee, Shomita; Robin, V V

2018-01-01

Range-restricted species generally have specific niche requirements and may often have unique evolutionary histories. Unfortunately, many of these species severely lack basic research, resulting in poor conservation strategies. The phylogenetic relationship of the Critically Endangered Forest Owlet Heteroglaux blewitti has been the subject of a century-old debate. The current classifications based on non-phylogenetic comparisons of morphology place the small owls of Asia into three genera, namely, Athene, Glaucidium, and Heteroglaux. Based on morphological and anatomical data, H. blewitti has been alternatively hypothesized to belong within Athene, Glaucidium, or its own monotypic genus Heteroglaux. To test these competing hypotheses, we sequenced six loci (~4300 bp data) and performed phylogenetic analyses of owlets. Mitochondrial and nuclear trees were not congruent in their placement of H. blewitti. However, both mitochondrial and nuclear combined datasets showed strong statistical support with high maximum likelihood bootstrap (>/ = 90) and Bayesian posterior probability values (>/ = 0.98) for H. blewitti being nested in the currently recognized Athene group, but not sister to Indian A. brama. The divergence of H. blewitti from its sister taxa was between 4.3 and 5.7 Ma coinciding with a period of drastic climatic changes in the Indian subcontinent. This study presented the first genetic analysis of H. blewitti, a Critically Endangered species, and addressed the long debate on the relationships of the Athene-Heteroglaux-Glaucidium complex. We recommend further studies with more data and complete taxon sampling to understand the biogeography of Indian Athene species.

The critically endangered forest owlet Heteroglaux blewitti is nested within the currently recognized Athene clade: A century-old debate addressed

PubMed Central

Mehta, Prachi; Reddy, Sushma; Ramakrishnan, Uma

2018-01-01

Range-restricted species generally have specific niche requirements and may often have unique evolutionary histories. Unfortunately, many of these species severely lack basic research, resulting in poor conservation strategies. The phylogenetic relationship of the Critically Endangered Forest Owlet Heteroglaux blewitti has been the subject of a century-old debate. The current classifications based on non-phylogenetic comparisons of morphology place the small owls of Asia into three genera, namely, Athene, Glaucidium, and Heteroglaux. Based on morphological and anatomical data, H. blewitti has been alternatively hypothesized to belong within Athene, Glaucidium, or its own monotypic genus Heteroglaux. To test these competing hypotheses, we sequenced six loci (~4300 bp data) and performed phylogenetic analyses of owlets. Mitochondrial and nuclear trees were not congruent in their placement of H. blewitti. However, both mitochondrial and nuclear combined datasets showed strong statistical support with high maximum likelihood bootstrap (>/ = 90) and Bayesian posterior probability values (>/ = 0.98) for H. blewitti being nested in the currently recognized Athene group, but not sister to Indian A. brama. The divergence of H. blewitti from its sister taxa was between 4.3 and 5.7 Ma coinciding with a period of drastic climatic changes in the Indian subcontinent. This study presented the first genetic analysis of H. blewitti, a Critically Endangered species, and addressed the long debate on the relationships of the Athene-Heteroglaux-Glaucidium complex. We recommend further studies with more data and complete taxon sampling to understand the biogeography of Indian Athene species. PMID:29401484

Molecular epidemiology and evolutionary analysis of dengue virus type 2, circulating in Delhi, India.

PubMed

Sharma, Pankaj; Mittal, Veena; Chhabra, Mala; Kumari, Roop; Singh, Priyanka; Venkatesh, Srinivas

2016-12-01

Dengue virus type 2 (DENV-2) has been associated with severe dengue outbreaks in many countries including India. Its predominance was recorded nearly after a decade in the capital city, Delhi in 2013. The present study characterizes DENV-2 circulated during 2013-2014. Analysis based on envelope (E) gene showed the presence of two clades (I and II) of DENV-2, within the Cosmopolitan genotype. Analysis of time of most recent common ancestor revealed the existence of clade I for more than a decade (95 % HPD 13-16 years) however, clade II showed comparatively recent emergence (95 % HPD 5-13 years). Presence of different clades is of high significance as this may result in increased virus transmission and major outbreaks. Further, the presence of a unique amino acid substitution, Q325H was also observed in an isolate; 14/D2/Del/2013 (KT717981). This substitution falls in immune epitope (epitope id: 150268) and may have important role in host immune response.

Phylogeny of the Celastreae (Celastraceae) and the relationships of Catha edulis (qat) inferred from morphological characters and nuclear and plastid genes.

PubMed

Simmons, Mark P; Cappa, Jennifer J; Archer, Robert H; Ford, Andrew J; Eichstedt, Dedra; Clevinger, Curtis C

2008-08-01

The phylogeny of Celastraceae tribe Celastreae, which includes about 350 species of trees and shrubs in 15 genera, was inferred in a simultaneous analysis of morphological characters together with nuclear (ITS and 26S rDNA) and plastid (matK, trnL-F) genes. A strong correlation was found between the geography of the species sampled and their inferred relationships. Species of Maytenus and Gymnosporia from different regions were resolved as polyphyletic groups. Maytenus was resolved in three lineages (New World, African, and Austral-Pacific), while Gymnosporia was resolved in two lineages (New World and Old World). Putterlickia was resolved as nested within the Old World Gymnosporia. Catha edulis (qat, khat) was resolved as sister to the clade of Allocassine, Cassine, Lauridia, and Maurocenia. Gymnosporia cassinoides, which is reportedly chewed as a stimulant in the Canary Islands, was resolved as a derived member of Gymnosporia and is more closely related to Lydenburgia and Putterlickia than it is to Catha. Therefore, all eight of these genera are candidates for containing cathinone- and/or cathine-related alkaloids.

Molecular-based estimate of species number, phylogenetic relationships and divergence times for the genus Stenotaenia (Chilopoda, Geophilomorpha) in the Italian region

PubMed Central

Del Latte, Laura; Bortolin, Francesca; Rota-Stabelli, Omar; Fusco, Giuseppe; Bonato, Lucio

2015-01-01

Abstract Stenotaenia is one of the largest and most widespread genera of geophilid centipedes in the Western Palearctic, with a very uniform morphology and about fifteen species provisionally recognized. For a better understanding of Stenotaenia species-level taxonomy, we have explored the possibility of using molecular data. As a preliminary assay, we sampled twelve populations, mainly from the Italian region, and analyzed partial sequences of the two genes COI and 28S. We employed a DNA-barcoding approach, complemented by a phylogenetic analysis coupled with divergence time estimation. Assuming a barcoding gap of 10–16% K2P pairwise distances, we found evidence for the presence of at least six Stenotaenia species in the Italian region, which started diverging about 50 million years ago, only partially matching with previously recognized species. We found that small-sized oligopodous species belong to a single clade that originated about 33 million years ago, and obtained some preliminary evidence of the related genus Tuoba being nested within Stenotaenia. PMID:26257533

Mitochondrial DNA phylogeography of lake cisco (Coregonus artedi): evidence supporting extensive secondary contacts between two glacial races.

PubMed

Turgeon, J; Bernatchez, L

2001-04-01

The comparative molecular phylogeography of regional fish fauna has revealed the wide distribution of young clades in freshwater fishes of formerly glaciated areas as well as interspecific incongruences in their refugial origins and recolonization routes. In this study, we employed single-strand conformation polymorphism (SSCP) and sequence analyses to describe mitochondrial DNA (mtDNA) polymorphism among 27 populations of the lake cisco (Coregonus artedi) from its entire range of distribution in order to evaluate the hypothesis of dual glacial refuges proposed by Bernatchez & Dodson against the traditional view that this species is solely of Mississippian origin. Results indicate that this taxon is composed of two closely related groups that are widely distributed and intermixed over most of the sampled range. The estimated level of divergence (0.48%), the contrast in the geographical distribution of each group, as well as the general distribution of C. artedi in North America together support the hypothesis that one group dispersed from a Mississippian refuge via the proglacial lakes, while the other is of Atlantic origin and also took advantages of earlier dispersal routes towards eastern Hudson Bay drainages. However, the signal of past range fragmentation revealed by a nested clade analysis was weak, and did not allow to formally exclude the hypothesis of a single Mississippian origin for both lineages. Comparisons with the phylogeographic patterns of other Nearctic freshwater fishes suggest that the salinity tolerance and thermal sensitivity of lake cisco may have been determinant for its extensive postglacial dispersal. The presence or co-occurrence of sympatric or allopatric eco/morphotypes were not found to be necessarily associated with the presence of both haplotype groups.

Phylogenetic Analyses of Meloidogyne Small Subunit rDNA.

PubMed

De Ley, Irma Tandingan; De Ley, Paul; Vierstraete, Andy; Karssen, Gerrit; Moens, Maurice; Vanfleteren, Jacques

2002-12-01

Phylogenies were inferred from nearly complete small subunit (SSU) 18S rDNA sequences of 12 species of Meloidogyne and 4 outgroup taxa (Globodera pallida, Nacobbus abberans, Subanguina radicicola, and Zygotylenchus guevarai). Alignments were generated manually from a secondary structure model, and computationally using ClustalX and Treealign. Trees were constructed using distance, parsimony, and likelihood algorithms in PAUP* 4.0b4a. Obtained tree topologies were stable across algorithms and alignments, supporting 3 clades: clade I = [M. incognita (M. javanica, M. arenaria)]; clade II = M. duytsi and M. maritima in an unresolved trichotomy with (M. hapla, M. microtyla); and clade III = (M. exigua (M. graminicola, M. chitwoodi)). Monophyly of [(clade I, clade II) clade III] was given maximal bootstrap support (mbs). M. artiellia was always a sister taxon to this joint clade, while M. ichinohei was consistently placed with mbs as a basal taxon within the genus. Affinities with the outgroup taxa remain unclear, although G. pallida and S. radicicola were never placed as closest relatives of Meloidogyne. Our results show that SSU sequence data are useful in addressing deeper phylogeny within Meloidogyne, and that both M. ichinohei and M. artiellia are credible outgroups for phylogenetic analysis of speciations among the major species.

Phylogenetic Analyses of Meloidogyne Small Subunit rDNA

PubMed Central

De Ley, Irma Tandingan; De Ley, Paul; Vierstraete, Andy; Karssen, Gerrit; Moens, Maurice; Vanfleteren, Jacques

2002-01-01

Phylogenies were inferred from nearly complete small subunit (SSU) 18S rDNA sequences of 12 species of Meloidogyne and 4 outgroup taxa (Globodera pallida, Nacobbus abberans, Subanguina radicicola, and Zygotylenchus guevarai). Alignments were generated manually from a secondary structure model, and computationally using ClustalX and Treealign. Trees were constructed using distance, parsimony, and likelihood algorithms in PAUP* 4.0b4a. Obtained tree topologies were stable across algorithms and alignments, supporting 3 clades: clade I = [M. incognita (M. javanica, M. arenaria)]; clade II = M. duytsi and M. maritima in an unresolved trichotomy with (M. hapla, M. microtyla); and clade III = (M. exigua (M. graminicola, M. chitwoodi)). Monophyly of [(clade I, clade II) clade III] was given maximal bootstrap support (mbs). M. artiellia was always a sister taxon to this joint clade, while M. ichinohei was consistently placed with mbs as a basal taxon within the genus. Affinities with the outgroup taxa remain unclear, although G. pallida and S. radicicola were never placed as closest relatives of Meloidogyne. Our results show that SSU sequence data are useful in addressing deeper phylogeny within Meloidogyne, and that both M. ichinohei and M. artiellia are credible outgroups for phylogenetic analysis of speciations among the major species. PMID:19265950

A Phylogenetic Analysis of the Genus Fragaria (Strawberry) Using Intron-Containing Sequence from the ADH-1 Gene

PubMed Central

DiMeglio, Laura M.; Yu, Hongrun; Davis, Thomas M.

2014-01-01

The genus Fragaria encompasses species at ploidy levels ranging from diploid to decaploid. The cultivated strawberry, Fragaria×ananassa, and its two immediate progenitors, F. chiloensis and F. virginiana, are octoploids. To elucidate the ancestries of these octoploid species, we performed a phylogenetic analysis using intron-containing sequences of the nuclear ADH-1 gene from 39 germplasm accessions representing nineteen Fragaria species and one outgroup species, Dasiphora fruticosa. All trees from Maximum Parsimony and Maximum Likelihood analyses showed two major clades, Clade A and Clade B. Each of the sampled octoploids contributed alleles to both major clades. All octoploid-derived alleles in Clade A clustered with alleles of diploid F. vesca, with the exception of one octoploid allele that clustered with the alleles of diploid F. mandshurica. All octoploid-derived alleles in clade B clustered with the alleles of only one diploid species, F. iinumae. When gaps encoded as binary characters were included in the Maximum Parsimony analysis, tree resolution was improved with the addition of six nodes, and the bootstrap support was generally higher, rising above the 50% threshold for an additional nine branches. These results, coupled with the congruence of the sequence data and the coded gap data, validate and encourage the employment of sequence sets containing gaps for phylogenetic analysis. Our phylogenetic conclusions, based upon sequence data from the ADH-1 gene located on F. vesca linkage group II, complement and generally agree with those obtained from analyses of protein-encoding genes GBSSI-2 and DHAR located on F. vesca linkage groups V and VII, respectively, but differ from a previous study that utilized rDNA sequences and did not detect the ancestral role of F. iinumae. PMID:25078607

Trachyrhizium urniformis n. g., n. sp., a Novel Marine Filose Thecate Amoeba Related to a Cercozoan Environmental Clade (Novel Clade 4).

PubMed

Shiratori, Takashi; Ishida, Ken-Ichiro

2016-11-01

A novel cercozoan filose thecate amoeba, Trachyrhizium urniformis n. g., n. sp., was isolated from a marine sediment sample collected at Agenashiku Island, Okinawa, Japan. We performed light and electron microscopic observations, and a molecular phylogenetic analysis using the small subunit ribosomal RNA gene of the isolate. Cells of T. urniformis are spherical in shape and are covered by a thin theca possessing a wide rounded aperture. Branching and occasionally anastomosing filopodia with small granules emerge from the aperture. The granules are transported in the filopodia bidirectionally. Transmission electron microscopy showed that cells of T. urniformis possess nucleus with permanently condensed chromatin, Golgi apparatuses, microbodies, mitochondria with tubular cristae, and extrusomes. Several morphological and ultrastructural features of T. urniformis (the presence of thecae and nucleus with permanently condensed chromatin) show similarities with those of Thecofilosea. In a phylogenetic analysis, T. urniformis included in Thecofilosea with weak statistical supports and formed a clade with two sequences that constitutes a cercozoan environmental clade, novel clade 4. On the basis of morphological and ultrastructural information and the results of the phylogenetic analysis, we propose T. urniformis as a new member of class Thecofilosea. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

Comparative genomic and functional analysis reveal conservation of plant growth promoting traits in Paenibacillus polymyxa and its closely related species

PubMed Central

Xie, Jianbo; Shi, Haowen; Du, Zhenglin; Wang, Tianshu; Liu, Xiaomeng; Chen, Sanfeng

2016-01-01

Paenibacillus polymyxa has widely been studied as a model of plant-growth promoting rhizobacteria (PGPR). Here, the genome sequences of 9 P. polymyxa strains, together with 26 other sequenced Paenibacillus spp., were comparatively studied. Phylogenetic analysis of the concatenated 244 single-copy core genes suggests that the 9 P. polymyxa strains and 5 other Paenibacillus spp., isolated from diverse geographic regions and ecological niches, formed a closely related clade (here it is called Poly-clade). Analysis of single nucleotide polymorphisms (SNPs) reveals local diversification of the 14 Poly-clade genomes. SNPs were not evenly distributed throughout the 14 genomes and the regions with high SNP density contain the genes related to secondary metabolism, including genes coding for polyketide. Recombination played an important role in the genetic diversity of this clade, although the rate of recombination was clearly lower than mutation. Some genes relevant to plant-growth promoting traits, i.e. phosphate solubilization and IAA production, are well conserved, while some genes relevant to nitrogen fixation and antibiotics synthesis are evolved with diversity in this Poly-clade. This study reveals that both P. polymyxa and its closely related species have plant growth promoting traits and they have great potential uses in agriculture and horticulture as PGPR. PMID:26856413

Comparative transcriptome analysis of Sogatella furcifera (Horváth) exposed to different insecticides.

PubMed

Zhou, Cao; Yang, Hong; Wang, Zhao; Long, Gui-Yun; Jin, Dao-Chao

2018-06-08

White-backed planthopper, Sogatella furcifera (Horváth) (Hemiptera: Delphacidae), one of the main agricultural insect pests in China, is resistant to a wide variety of insecticides. We used transcriptome analysis to compare the expression patterns of resistance- and stress-response genes in S. furcifera subjected to imidacloprid, deltamethrin, and triazophos stress, to determine the molecular mechanisms of resistance to these insecticides. A comparative analysis of gene expression under imidacloprid, deltamethrin, and triazophos stress revealed 1,123, 841, and 316 upregulated unigenes, respectively, compared to the control. These upregulated genes included seven P450s (two CYP2 clade, three CYP3 clade, and two CYP4 clade), one GST, one ABC transporter (ABCF), and seven Hsps (one 90 and six Hsp70s) under imidacloprid stress; one P450 (CYP3 clade), two ABC transporters (one ABCF and one ABCD), and one Hsp (Hsp90) under deltamethrin stress; one P450 (CYP3 clade) and one ABC transporter (ABCF) under triazophos stress. In addition, 80 genes were commonly upregulated in response to the three insecticide treatments, including laminin, larval cuticle protein, and fasciclin, which are associated with epidermal formation. These results provide a valuable resource for the molecular characterisation of insecticide action in S. furcifera, especially the molecular characteristics of insecticide cross resistance.

The evolutionary dynamics of highly pathogenic avian influenza H5N1 in south-central Vietnam reveals multiple clades evolving from Chinese and Cambodian viruses.

PubMed

Nguyen, Tinh Huu; Than, Van Thai; Thanh, Hien Dang; Nguyen, Van Quang; Nguyen, Kim Hue; Nguyen, Duc Tan; Park, Jong-Hwa; Chung, In Sik; Jeong, Dae Gwin; Chang, Kyu-Tae; Oh, Tae Kwang; Kim, Wonyong

2015-10-01

In Vietnam, highly pathogenic avian influenza (HPAI), such as that caused by H5N1 viruses, is the most highly contagious infectious disease that has been affecting domestic poultry in recent years. Vietnam might be an evolutionary hotspot and a potential source of globally pandemic strains. However, few studies have reported viruses circulating in the south-central region of Vietnam. In the present study, 47 H5N1-positive samples were collected from both vaccinated and unvaccinated poultry farms in the South Central Coast region of Vietnam during 2013-2014, and their genetic diversity was analyzed. A common sequence motif for HPAI virus was identified at HA-cleavage sites in all samples: either RERRRKR/G (clades 2.3.2.1c and 2.3.2.1a) or REGRRKKR/G (clade 1.1.2). Phylogenetic analysis of HA genes identified three clades of HPAI H5N1: 1.1.2 (n=1), 2.3.2.1a (n=1), and 2.3.2.1c (n=45). The phylogenetic analysis indicated that these Vietnamese clades may have evolved from Chinese and Cambodian virus clades isolated in 2012-2013 but are less closely related to the clades detected from the Tyva Republic, Bulgaria, Mongolia, Japan, and Korea in 2009-2011. Detection of the coexistence of virus clades 2.3.2.1 and the very virulent 1.1.2 in the south-central regions suggests their local importance and highlights concerns regarding their spread, both northwards and southwards, as well as the potential for reassortment. The obtained data highlight the importance of regular identification of viral evolution and the development and use of region-specific vaccines. Copyright © 2015 Elsevier Ltd. All rights reserved.

Soft-tissue anatomy of the extant hominoids: a review and phylogenetic analysis.

PubMed

Gibbs, S; Collard, M; Wood, B

2002-01-01

This paper reports the results of a literature search for information about the soft-tissue anatomy of the extant non-human hominoid genera, Pan, Gorilla, Pongo and Hylobates, together with the results of a phylogenetic analysis of these data plus comparable data for Homo. Information on the four extant non-human hominoid genera was located for 240 out of the 1783 soft-tissue structures listed in the Nomina Anatomica. Numerically these data are biased so that information about some systems (e.g. muscles) and some regions (e.g. the forelimb) are over-represented, whereas other systems and regions (e.g. the veins and the lymphatics of the vascular system, the head region) are either under-represented or not represented at all. Screening to ensure that the data were suitable for use in a phylogenetic analysis reduced the number of eligible soft-tissue structures to 171. These data, together with comparable data for modern humans, were converted into discontinuous character states suitable for phylogenetic analysis and then used to construct a taxon-by-character matrix. This matrix was used in two tests of the hypothesis that soft-tissue characters can be relied upon to reconstruct hominoid phylogenetic relationships. In the first, parsimony analysis was used to identify cladograms requiring the smallest number of character state changes. In the second, the phylogenetic bootstrap was used to determine the confidence intervals of the most parsimonious clades. The parsimony analysis yielded a single most parsimonious cladogram that matched the molecular cladogram. Similarly the bootstrap analysis yielded clades that were compatible with the molecular cladogram; a (Homo, Pan) clade was supported by 95% of the replicates, and a (Gorilla, Pan, Homo) clade by 96%. These are the first hominoid morphological data to provide statistically significant support for the clades favoured by the molecular evidence.

Genetic Identification of Rickettsial Isolates from Fatal Cases of Brazilian Spotted Fever and Comparison with Rickettsia rickettsii Isolates from the American Continents

PubMed Central

Santos, Fabiana C. P.; Ogrzewalska, Maria; Nascimento, Elvira M. M.; Colombo, Silvia; Marcili, Arlei; Angerami, Rodrigo N.

2014-01-01

Fifteen bacterial isolates from spotted fever group rickettsiosis in Brazil were genetically identified as Rickettsia rickettsii. In a phylogenetic analysis with other R. rickettsii isolates from GenBank, the Central/South American isolates showed low polymorphism and formed a clade distinct from two North American clades, with the North American clades having greater in-branch polymorphism. PMID:25078908

Genetic and Morphological Differentiation of the Indo-West Pacific Intertidal Barnacle Chthamalus malayensis

PubMed Central

Tsang, Ling Ming; Wu, Tsz Huen; Shih, Hsi-Te; Williams, Gray A.; Chu, Ka Hou; Chan, Benny K.K.

2012-01-01

Chthamalus malayensis is a common intertidal acorn barnacle widely distributed in the Indo-West Pacific. Analysis of sequences of mitochondrial cytochrome c oxidase subunit I reveals four genetically differentiated clades with almost allopatric distribution in this region. The four clades exhibit morphological differences in arthropodal characters, including the number of conical spines and number of setules of the basal guard setae on the cirri. These characters are, however, highly variable within each clade; such that the absolute range of the number of conical spines and setules overlaps between clades, and therefore, these are not diagnostic characters for taxonomic identification. The geographic distribution of the four clades displays a strong relationship between surface temperatures of the sea and ocean-current realms. The Indo-Malay (IM) clade is widespread in the tropical, equatorial region, including the Indian Ocean, Malay Peninsula, and North Borneo. The South China (SC) and Taiwan (TW) clades are found in tropical to subtropical regions, with the former distributed along the coasts of southern China, Vietnam, Thailand, and the western Philippines under the influence of the South China Warm Current. The TW clade is endemic to Taiwan, while the Christmas Island (CI) clade is confined to CI. There was weak or no population subdivision observed within these clades, suggesting high gene flow within the range of the clades. The clades demonstrate clear signatures of recent demographic expansion that predated the Last Glacial Maximum (LGM), but they have maintained a relatively stable effective population in the past 100,000 years. The persistence of intertidal fauna through the LGM may, therefore, be a common biogeographic pattern. The lack of genetic subdivision in the IM clade across the Indian and Pacific Oceans may be attributed to recent expansion of ranges and the fact that a mutation-drift equilibrium has not been reached, or the relaxed habitat requirements of C. malayensis that facilitates high concurrent gene flow. Further studies are needed to determine between these alternative hypotheses. PMID:22523127

Phylogenetic Clades 6 and 8 of Enterohemorrhagic Escherichia coli O157:H7 With Particular stx Subtypes are More Frequently Found in Isolates From Hemolytic Uremic Syndrome Patients Than From Asymptomatic Carriers

PubMed Central

Iyoda, Sunao; Manning, Shannon D.; Seto, Kazuko; Kimata, Keiko; Isobe, Junko; Etoh, Yoshiki; Ichihara, Sachiko; Migita, Yuji; Ogata, Kikuyo; Honda, Mikiko; Kubota, Tsutomu; Kawano, Kimiko; Matsumoto, Kazutoshi; Kudaka, Jun; Asai, Norio; Yabata, Junko; Tominaga, Kiyoshi; Terajima, Jun; Morita-Ishihara, Tomoko; Izumiya, Hidemasa; Ogura, Yoshitoshi; Saitoh, Takehito; Iguchi, Atsushi; Kobayashi, Hideki; Hara-Kudo, Yukiko; Ohnishi, Makoto; Arai, Reiko; Kawase, Masao; Asano, Yukiko; Asoshima, Nanami; Chiba, Kazuki; Furukawa, Ichiro; Kuroki, Toshiro; Hamada, Madoka; Harada, Seiya; Hatakeyama, Takashi; Hirochi, Takashi; Sakamoto, Yumiko; Hiroi, Midori; Takashi, Kanda; Horikawa, Kazumi; Iwabuchi, Kaori; Kameyama, Mitsuhiro; Kasahara, Hitomi; Kawanishi, Shinya; Kikuchi, Koji; Ueno, Hiroyuki; Kitahashi, Tomoko; Kojima, Yuka; Konishi, Noriko; Obata, Hiromi; Kai, Akemi; Kono, Tomomi; Kurazono, Takayuki; Matsumoto, Masakado; Matsumoto, Yuko; Nagai, Yuhki; Naitoh, Hideki; Nakajima, Hiroshi; Nakamura, Hiromi; Nakane, Kunihiko; Nishi, Keiko; Saitoh, Etsuko; Satoh, Hiroaki; Takamura, Mitsuteru; Shiraki, Yutaka; Tanabe, Junichi; Tanaka, Keiko; Tokoi, Yuki; Yatsuyanagi, Jun

2014-01-01

Background  Enterohemorrhagic Escherichia coli (EHEC) O157:H7 infection causes severe diseases such as bloody diarrhea and hemolytic uremic syndrome (HUS). Although EHEC O157:H7 strains have exhibited high genetic variability, their abilities to cause human diseases have not been fully examined. Methods  Clade typing and stx subtyping of EHEC O157:H7 strains, which were isolated in Japan during 1999–2011 from 269 HUS patients and 387 asymptomatic carriers (ACs) and showed distinct pulsed-field gel electrophoresis patterns, were performed to determine relationships between specific lineages and clinical presentation. Results  Clades 6 and 8 strains were more frequently found among the isolates from HUS cases than those from ACs (P = .00062 for clade 6, P < .0001 for clade 8). All clade 6 strains isolated from HUS patients harbored stx2a and/or stx2c, whereas all clade 8 strains harbored either stx2a or stx2a/stx2c. However, clade 7 strains were predominantly found among the AC isolates but less frequently found among the HUS isolates, suggesting a significant association between clade 7 and AC (P < .0001). Logistic regression analysis revealed that 0–9 year old age is a significant predictor of the association between clade 8 and HUS. We also found an intact norV gene, which encodes for a nitric oxide reductase that inhibits Shiga toxin activity under anaerobic condition, in all clades 1–3 isolates but not in clades 4–8 isolates. Conclusions  Early detection of EHEC O157:H7 strains that belonged to clades 6/8 and harbored specific stx subtypes may be important for defining the risk of disease progression in EHEC-infected 0- to 9-year-old children. PMID:25734131

Evolutionary Diversification of Insect Innexins

PubMed Central

Hughes, Austin L.

2014-01-01

Abstract Phylogenetic analysis of insect innexins supported the hypothesis that six major clades of insect innexins arose by gene duplication prior to the origin of the endopterygote insects. Within one of the six clades (the Zpg Clade), two independent gene duplication events were inferred to have occurred in the lineage of Drosophila , after the most recent common ancestor of the dipteran families Culicidae and Drosophilidae. The relationships among this clades were poorly resolved, except for a sister relationship between ShakB and Ogre. Gene expression data from FlyAtlas supported the hypothesis that the latter gene duplication events gave rise to functional differentiation, with Zpg showing a high level of expression in ovary, and Inx5 and Inx6 showing a high level of expression in testis. Because unduplicated members of this clade in Bombyx mori and Anopheles gambiae showed high levels of expression in both ovary and tests, the expression patterns of the Drosophila members of this clade provide evidence of subdivision of an ancestral gene function after gene duplication. PMID:25502029

Morphological rates of angiosperm seed size evolution.

PubMed

Sims, Hallie J

2013-05-01

The evolution of seed size among angiosperms reflects their ecological diversification in a complex fitness landscape of life-history strategies. The lineages that have evolved seeds beyond the upper and lower boundaries that defined nonflowering seed plants since the Paleozoic are more dispersed across the angiosperm phylogeny than would be expected under a neutral model of phenotypic evolution. Morphological rates of seed size evolution estimated for 40 clades based on 17,375 species ranged from 0.001 (Garryales) to 0.207 (Malvales). Comparative phylogenetic analysis indicated that morphological rates are not associated with the clade's seed size but are negatively correlated with the clade's position in the overall distribution of angiosperm seed sizes; clades with seed sizes closer to the angiosperm mean had significantly higher morphological rates than clades with extremely small or extremely large seeds. Likewise, per-clade taxonomic diversification rates are not associated with the seed size of the clade but with where the clade falls within the angiosperm seed size distribution. These results suggest that evolutionary rates (morphological and taxonomic) are elevated in densely occupied regions of the seed morphospace relative to lineages whose ecophenotypic innovations have moved them toward the edges. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Townsend, Ted M.; Larson, Allan; Louis, Edward

Squamate reptiles serve as model systems for evolutionary studies of a variety of morphological and behavioral traits, and phylogeny is crucial to many generalizations derived from such studies. Specifically, the traditional dichotomy between Iguania and Scleroglossa has been correlated with major evolutionary shifts within Squamata. We present a molecular phylogenetic study of squamates using DNA sequence data from the nuclear genes RAG-1 and c-mos and the mitochondrial ND2 region, sampling all major clades and most major subclades. Monophyly of Iguania, Anguimorpha, and almost all currently recognized squamate families is strongly supported. However, monophyly is rejected for Scleroglossa, Varanoidea, and severalmore » other higher taxa, and Iguania is highly nested within Squamata. Limblessness evolved independently in snakes, dibamids, and amphisbaenians, suggesting widespread morphological convergence or parallelism in limbless, burrowing forms. Amphisbaenians are the sister group of lacertids, and snakes are grouped with iguanians and anguimorphs. Dibamids diverged early in squamate evolutionary history. Xantusiidae is the sister taxon of Cordylidae. Studies of functional tongue morphology and feeding mode have found significant differences between Scleroglossa and Iguania, and our finding of a nonmonophyletic Scleroglossa and a highly nested Iguania suggest that similar states evolved separately in Sphenodon and Iguania, and that jaw prehension is the ancestral feeding mode in squamates.« less

Temporal variability of coastal Planctomycetes clades at Kabeltonne station, North Sea.

PubMed

Pizzetti, Ilaria; Fuchs, Bernhard M; Gerdts, Gunnar; Wichels, Antje; Wiltshire, Karen H; Amann, Rudolf

2011-07-01

Members of the bacterial phylum Planctomycetes are reported in marine water samples worldwide, but quantitative information is scarce. Here we investigated the phylogenetic diversity, abundance, and distribution of Planctomycetes in surface waters off the German North Sea island Helgoland during different seasons by 16S rRNA gene analysis and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). Generally Planctomycetes are more abundant in samples collected in summer and autumn than in samples collected in winter and spring. Statistical analysis revealed that Planctomycetes abundance was correlated to the Centrales diatom bloom in spring 2007. The analysis of size-fractionated seawater samples and of macroaggregates showed that ~90% of the Planctomycetes reside in the >3-μm size fraction. Comparative sequence analysis of 184 almost full-length 16S rRNA genes revealed three dominant clades. The clades, named Planctomyces-related group A, uncultured Planctomycetes group B, and Pirellula-related group D, were monitored by CARD-FISH using newly developed oligonucleotide probes. All three clades showed recurrent abundance patterns during two annual sampling campaigns. Uncultured Planctomycetes group B was most abundant in autumn samples, while Planctomyces-related group A was present in high numbers only during late autumn and winter. The levels of Pirellula-related group D were more constant throughout the year, with elevated counts in summer. Our analyses suggest that the seasonal succession of the Planctomycetes is correlated with algal blooms. We hypothesize that the niche partitioning of the different clades might be caused by their algal substrates.

Phylogenetic relationships of Semaphore geckos (Squamata: Sphaerodactylidae: Pristurus) with an assessment of the taxonomy of Pristurus rupestris.

PubMed

Badiane, Arnaud; Garcia-Porta, Joan; Červenka, Jan; Kratochvíl, Lukáš; Sindaco, Roberto; Robinson, Michael D; Morales, Hernan; Mazuch, Tomáš; Price, Thomas; Amat, Fèlix; Shobrak, Mohammed Y; Wilms, Thomas; Simó-Riudalbas, Marc; Ahmadzadeh, Faraham; Papenfuss, Theodore J; Cluchier, Alexandre; Viglione, Julien; Carranza, Salvador

2014-07-09

A molecular phylogeny of the sphaerodactylid geckos of the genus Pristurus is inferred based on an alignment of 1845 base pairs (bp) of concatenated mitochondrial (12S) and nuclear (acm4, cmos, rag1 and rag2) genes for 80 individuals, representing 18 of the 23-26 species, and the three subspecies of P. rupestris. The results indicate that P. rupestris is polyphyletic and includes two highly divergent clades: the eastern clade, found in coastal Iran and throughout the Hajar Mountain range in northern Oman and eastern UAE; and the western clade, distributed from central coastal Oman, through Yemen, Saudi Arabia and north to southern Jordan. Inferred haplotype networks for the four nuclear genes show that the eastern and western clades of "P. rupestris" are highly differentiated and do not share any alleles. Moreover, although the two clades are differentiated by a morphological multivariate analysis, no one character or set of characters was found to be diagnostic. Based on the molecular analysis of specimens from the type locality of P. rupestris rupestris, the name P. rupestris is applied to the eastern clade. The name that should apply to the western clade cannot be clarified until morphological and genetic data for "P. rupestris" is available from the vicinity of Bosaso, Somalia, and therefore we refer to it as Pristurus sp. 1. The phylogenetic tree of Pristurus supports the hypothesis that P. celerrimus is sister to all the other species in the analyses and that the Socotra Archipelago was independently colonized a minimum of two times.

The earliest known titanosauriform sauropod dinosaur and the evolution of Brachiosauridae

PubMed Central

Moine, Olivier

2017-01-01

Brachiosauridae is a clade of titanosauriform sauropod dinosaurs that includes the well-known Late Jurassic taxa Brachiosaurus and Giraffatitan. However, there is disagreement over the brachiosaurid affinities of most other taxa, and little consensus regarding the clade’s composition or inter-relationships. An unnamed partial sauropod skeleton was collected from middle–late Oxfordian (early Late Jurassic) deposits in Damparis, in the Jura department of eastern France, in 1934. Since its brief description in 1943, this specimen has been informally known in the literature as the ‘Damparis sauropod’ and ‘French Bothriospondylus’, and has been considered a brachiosaurid by most authors. If correctly identified, this would make the specimen the earliest known titanosauriform. Coupled with its relatively complete nature and the rarity of Oxfordian sauropod remains in general, this is an important specimen for understanding the early evolution of Titanosauriformes. Full preparation and description of this specimen, known from teeth, vertebrae and most of the appendicular skeleton of a single individual, recognises it as a distinct taxon: Vouivria damparisensis gen. et sp. nov. Phylogenetic analysis of a data matrix comprising 77 taxa (including all putative brachiosaurids) scored for 416 characters recovers a fairly well resolved Brachiosauridae. Vouivria is a basal brachiosaurid, confirming its status as the stratigraphically oldest known titanosauriform. Brachiosauridae consists of a paraphyletic array of Late Jurassic forms, with Europasaurus, Vouivria and Brachiosaurus recovered as successively more nested genera that lie outside of a clade comprising (Giraffatitan + Sonorasaurus) + (Lusotitan + (Cedarosaurus + Venenosaurus)). Abydosaurus forms an unresolved polytomy with the latter five taxa. The Early Cretaceous South American sauropod Padillasaurus was previously regarded as a brachiosaurid, but is here placed within Somphospondyli. A recent study contended that a number of characters used in a previous iteration of this data matrix are ‘biologically related’, and thus should be excluded from phylogenetic analysis. We demonstrate that almost all of these characters show variation between taxa, and implementation of sensitivity analyses, in which these characters are excluded, has no effect on tree topology or resolution. We argue that where there is morphological variation, this should be captured, rather than ignored. Unambiguous brachiosaurid remains are known only from the USA, western Europe and Africa, and the clade spanned the Late Jurassic through to the late Albian/early Cenomanian, with the last known occurrences all from the USA. Regardless of whether their absence from the Cretaceous of Europe, as well as other regions entirely, reflects regional extinctions and genuine absences, or sampling artefacts, brachiosaurids appear to have become globally extinct by the earliest Late Cretaceous. PMID:28480136

Spathaspora boniae sp. nov., a D-xylose-fermenting species in the Candida albicans/Lodderomyces clade.

PubMed

Morais, Camila G; Batista, Thiago M; Kominek, Jacek; Borelli, Beatriz M; Furtado, Carolina; Moreira, Rennan G; Franco, Gloria R; Rosa, Luiz H; Fonseca, César; Hittinger, Chris T; Lachance, Marc-André; Rosa, Carlos A

2017-10-01

Two yeast isolates producing asci-containing elongate ascospores with curved ends typical of the genus Spathaspora were isolated from rotting wood samples collected in an Atlantic rainforest ecosystem in Brazil. Phylogenetic analysis of the LSU rRNA gene D1/D2 domain sequences demonstrated that the strains represent a new species and placed it next to Candida blackwellae, in a clade that also contains Candida albicans and Candida dubliniensis. Other sequences of the ribosomal gene cluster supported same placementin the same clade, and a phylogenomic analysis placed this new species in an early emerging position relative to the larger C. albicans/Lodderomyces clade. One interpretation is that the genus Spathaspora is, in fact, paraphyletic. In conformity with this view, we propose the novel species Spathaspora boniae sp. nov. to accommodate the isolates. The type strain of Spathaspora boniae sp. nov. is UFMG-CM-Y306 T (=CBS 13262 T ). The MycoBank number is MB 821297. A detailed analysis of xylose metabolism was conducted for the new species.

Evolution of larval life mode of Oecophoridae (Lepidoptera: Gelechioidea) inferred from molecular phylogeny.

PubMed

Kim, Sora; Kaila, Lauri; Lee, Seunghwan

2016-08-01

Phylogenetic relationships within family Oecophoridae have been poorly understood. Consequently the subfamily and genus level classifications with this family problematic. A comprehensive phylogenetic analysis of Oecophoridae, the concealer moths, was performed based on analysis of 4444 base pairs of mitochondrial COI, nuclear ribosomal RNA genes (18S and 28S) and nuclear protein coding genes (IDH, MDH, Rps5, EF1a and wingless) for 82 taxa. Data were analyzed using maximum likelihood (ML), parsimony (MP) and Bayesian (BP) phylogenetic frameworks. Phylogenetic analyses indicated that (i) genera Casmara, Tyrolimnas and Pseudodoxia did not belong to Oecophoridae, suggesting that Oecophoridae s. authors was not monophyletic; (ii) other oecophorids comprising two subfamilies, Pleurotinae and Oecophorinae, were nested within the same clade, and (iii) Martyringa, Acryptolechia and Periacmini were clustered with core Xyloryctidae. They appeared to be sister lineage with core Oecophoridae. BayesTraits were implemented to explore the ancestral character states to infer historical microhabitat patterns and sheltering strategy of larvae. Reconstruction of ancestral microhabitat of oecophorids indicated that oecophorids might have evolved from dried plant feeders and further convergently specialized. The ancestral larva sheltering strategy of oecophorids might have used a silk tube by making itself, shifting from mining leaves. Copyright © 2016 Elsevier Inc. All rights reserved.

Unnoticed in the tropics: phylogenomic resolution of the poorly known arachnid order Ricinulei (Arachnida)

PubMed Central

Fernández, Rosa; Giribet, Gonzalo

2015-01-01

Ricinulei are among the most obscure and cryptic arachnid orders, constituting a micro-diverse group with extreme endemism. The 76 extant species described to date are grouped in three genera: Ricinoides, from tropical Western and Central Africa, and the two Neotropical genera Cryptocellus and Pseudocellus. Until now, a single molecular phylogeny of Ricinulei has been published, recovering the African Ricinoides as the sister group of the American Pseudocellus and providing evidence for the diversification of the order pre-dating the fragmentation of Gondwana. Here, we present, to our knowledge, the first phylogenomic study of this neglected arachnid order based on data from five transcriptomes obtained from the five major mitochondrial lineages of Ricinulei. Our results, based on up to more than 2000 genes, strongly support a clade containing Pseudocellus and Cryptocellus, constituting the American group of Ricinulei, with the African Ricinoides nesting outside. Our dating of the diversification of the African and American clades using a 76 gene data matrix with 90% gene occupancy indicates that this arachnid lineage was distributed in the South American, North American and African plates of Gondwana and that its diversification is concordant with a biogeographic scenario (both for pattern and tempo) of Gondwanan vicariance. PMID:26543583

The last diadectomorph sheds light on Late Palaeozoic tetrapod biogeography.

PubMed

Liu, Jun; Bever, G S

2015-05-01

Diadectomorpha is a clade of Late Palaeozoic vertebrates widely recognized as the sister group of crown-group Amniota and the first tetrapod lineage to evolve high-fibre herbivory. Despite their evolutionary importance, diadectomorphs are restricted stratigraphically and geographically, with all records being from the Upper Carboniferous and Lower Permian of North America and Germany. We describe a new diadectomorph, Alveusdectes fenestralis, based on a partial skull from the Upper Permian of China. The new species exhibits the derived mechanism for herbivory and is recovered phylogenetically as a deeply nested diadectid. Approximately 16 Myr younger than any other diadectomorph, Alveusdectes is the product of at least a 46 Myr ghost lineage. How much of this time was probably spent in Russia and/or central Asia will remain unclear until a specimen is described that subdivides this cryptic history, but the lineage assuredly crossed this region before entering the relatively isolated continent of North China. The discovery of Alveusdectes raises important questions regarding diadectomorph extinction dynamics including what, if any, ecological factors limited the diversity of this group in eastern Pangea. It also suggests that increased sampling in Asia will likely significantly affect our views of clade and faunal insularity leading up to the Permo-Triassic extinction. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

The last diadectomorph sheds light on Late Palaeozoic tetrapod biogeography

PubMed Central

Liu, Jun; Bever, G. S.

2015-01-01

Diadectomorpha is a clade of Late Palaeozoic vertebrates widely recognized as the sister group of crown-group Amniota and the first tetrapod lineage to evolve high-fibre herbivory. Despite their evolutionary importance, diadectomorphs are restricted stratigraphically and geographically, with all records being from the Upper Carboniferous and Lower Permian of North America and Germany. We describe a new diadectomorph, Alveusdectes fenestralis, based on a partial skull from the Upper Permian of China. The new species exhibits the derived mechanism for herbivory and is recovered phylogenetically as a deeply nested diadectid. Approximately 16 Myr younger than any other diadectomorph, Alveusdectes is the product of at least a 46 Myr ghost lineage. How much of this time was probably spent in Russia and/or central Asia will remain unclear until a specimen is described that subdivides this cryptic history, but the lineage assuredly crossed this region before entering the relatively isolated continent of North China. The discovery of Alveusdectes raises important questions regarding diadectomorph extinction dynamics including what, if any, ecological factors limited the diversity of this group in eastern Pangea. It also suggests that increased sampling in Asia will likely significantly affect our views of clade and faunal insularity leading up to the Permo-Triassic extinction. PMID:25948572

Nocturnality in synapsids predates the origin of mammals by over 100 million years.

PubMed

Angielczyk, K D; Schmitz, L

2014-10-22

Nocturnality is widespread among extant mammals and often considered the ancestral behavioural pattern for all mammals. However, mammals are nested within a larger clade, Synapsida, and non-mammalian synapsids comprise a rich phylogenetic, morphological and ecological diversity. Even though non-mammalian synapsids potentially could elucidate the early evolution of diel activity patterns and enrich the understanding of synapsid palaeobiology, data on their diel activity are currently unavailable. Using scleral ring and orbit dimensions, we demonstrate that nocturnal activity was not an innovation unique to mammals but a character that appeared much earlier in synapsid history, possibly several times independently. The 24 Carboniferous to Jurassic non-mammalian synapsid species in our sample featured eye morphologies consistent with all major diel activity patterns, with examples of nocturnality as old as the Late Carboniferous (ca 300 Ma). Carnivores such as Sphenacodon ferox and Dimetrodon milleri, but also the herbivorous cynodont Tritylodon longaevus were likely nocturnal, whereas most of the anomodont herbivores are reconstructed as diurnal. Recognizing the complexity of diel activity patterns in non-mammalian synapsids is an important step towards a more nuanced picture of the evolutionary history of behaviour in the synapsid clade. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Races of the Celery Pathogen Fusarium oxysporum f. sp. apii Are Polyphyletic.

PubMed

Epstein, Lynn; Kaur, Sukhwinder; Chang, Peter L; Carrasquilla-Garcia, Noelia; Lyu, Guiyun; Cook, Douglas R; Subbarao, Krishna V; O'Donnell, Kerry

2017-04-01

Fusarium oxysporum species complex (FOSC) isolates were obtained from celery with symptoms of Fusarium yellows between 1993 and 2013 primarily in California. Virulence tests and a two-gene dataset from 174 isolates indicated that virulent isolates collected before 2013 were a highly clonal population of F. oxysporum f. sp. apii race 2. In 2013, new highly virulent clonal isolates, designated race 4, were discovered in production fields in Camarillo, California. Long-read Illumina data were used to analyze 16 isolates: six race 2, one of each from races 1, 3, and 4, and seven genetically diverse FOSC that were isolated from symptomatic celery but are nonpathogenic on this host. Analyses of a 10-gene dataset comprising 38 kb indicated that F. oxysporum f. sp. apii is polyphyletic; race 2 is nested within clade 3, whereas the evolutionary origins of races 1, 3, and 4 are within clade 2. Based on 6,898 single nucleotide polymorphisms from the core FOSC genome, race 3 and the new highly virulent race 4 are highly similar with Nei's Da = 0.0019, suggesting that F. oxysporum f. sp. apii race 4 evolved from race 3. Next generation sequences were used to develop PCR primers that allow rapid diagnosis of races 2 and 4 in planta.

Genomic Evaluation of Thermoanaerobacter spp. for the Construction of Designer Co-Cultures to Improve Lignocellulosic Biofuel Production

PubMed Central

Verbeke, Tobin J.; Zhang, Xiangli; Henrissat, Bernard; Spicer, Vic; Rydzak, Thomas; Krokhin, Oleg V.; Fristensky, Brian; Levin, David B.; Sparling, Richard

2013-01-01

The microbial production of ethanol from lignocellulosic biomass is a multi-component process that involves biomass hydrolysis, carbohydrate transport and utilization, and finally, the production of ethanol. Strains of the genus Thermoanaerobacter have been studied for decades due to their innate abilities to produce comparatively high ethanol yields from hemicellulose constituent sugars. However, their inability to hydrolyze cellulose, limits their usefulness in lignocellulosic biofuel production. As such, co-culturing Thermoanaerobacter spp. with cellulolytic organisms is a plausible approach to improving lignocellulose conversion efficiencies and yields of biofuels. To evaluate native lignocellulosic ethanol production capacities relative to competing fermentative end-products, comparative genomic analysis of 11 sequenced Thermoanaerobacter strains, including a de novo genome, Thermoanaerobacter thermohydrosulfuricus WC1, was conducted. Analysis was specifically focused on the genomic potential for each strain to address all aspects of ethanol production mentioned through a consolidated bioprocessing approach. Whole genome functional annotation analysis identified three distinct clades within the genus. The genomes of Clade 1 strains encode the fewest extracellular carbohydrate active enzymes and also show the least diversity in terms of lignocellulose relevant carbohydrate utilization pathways. However, these same strains reportedly are capable of directing a higher proportion of their total carbon flux towards ethanol, rather than non-biofuel end-products, than other Thermoanaerobacter strains. Strains in Clade 2 show the greatest diversity in terms of lignocellulose hydrolysis and utilization, but proportionately produce more non-ethanol end-products than Clade 1 strains. Strains in Clade 3, in which T. thermohydrosulfuricus WC1 is included, show mid-range potential for lignocellulose hydrolysis and utilization, but also exhibit extensive divergence from both Clade 1 and Clade 2 strains in terms of cellular energetics. The potential implications regarding strain selection and suitability for industrial ethanol production through a consolidated bioprocessing co-culturing approach are examined throughout the manuscript. PMID:23555660

Chloroplast DNA Structural Variation, Phylogeny, and Age of Divergence among Diploid Cotton Species.

PubMed

Chen, Zhiwen; Feng, Kun; Grover, Corrinne E; Li, Pengbo; Liu, Fang; Wang, Yumei; Xu, Qin; Shang, Mingzhao; Zhou, Zhongli; Cai, Xiaoyan; Wang, Xingxing; Wendel, Jonathan F; Wang, Kunbo; Hua, Jinping

2016-01-01

The cotton genus (Gossypium spp.) contains 8 monophyletic diploid genome groups (A, B, C, D, E, F, G, K) and a single allotetraploid clade (AD). To gain insight into the phylogeny of Gossypium and molecular evolution of the chloroplast genome in this group, we performed a comparative analysis of 19 Gossypium chloroplast genomes, six reported here for the first time. Nucleotide distance in non-coding regions was about three times that of coding regions. As expected, distances were smaller within than among genome groups. Phylogenetic topologies based on nucleotide and indel data support for the resolution of the 8 genome groups into 6 clades. Phylogenetic analysis of indel distribution among the 19 genomes demonstrates contrasting evolutionary dynamics in different clades, with a parallel genome downsizing in two genome groups and a biased accumulation of insertions in the clade containing the cultivated cottons leading to large (for Gossypium) chloroplast genomes. Divergence time estimates derived from the cpDNA sequence suggest that the major diploid clades had diverged approximately 10 to 11 million years ago. The complete nucleotide sequences of 6 cpDNA genomes are provided, offering a resource for cytonuclear studies in Gossypium.

Chloroplast DNA Structural Variation, Phylogeny, and Age of Divergence among Diploid Cotton Species

PubMed Central

Li, Pengbo; Liu, Fang; Wang, Yumei; Xu, Qin; Shang, Mingzhao; Zhou, Zhongli; Cai, Xiaoyan; Wang, Xingxing; Wendel, Jonathan F.; Wang, Kunbo

2016-01-01

The cotton genus (Gossypium spp.) contains 8 monophyletic diploid genome groups (A, B, C, D, E, F, G, K) and a single allotetraploid clade (AD). To gain insight into the phylogeny of Gossypium and molecular evolution of the chloroplast genome in this group, we performed a comparative analysis of 19 Gossypium chloroplast genomes, six reported here for the first time. Nucleotide distance in non-coding regions was about three times that of coding regions. As expected, distances were smaller within than among genome groups. Phylogenetic topologies based on nucleotide and indel data support for the resolution of the 8 genome groups into 6 clades. Phylogenetic analysis of indel distribution among the 19 genomes demonstrates contrasting evolutionary dynamics in different clades, with a parallel genome downsizing in two genome groups and a biased accumulation of insertions in the clade containing the cultivated cottons leading to large (for Gossypium) chloroplast genomes. Divergence time estimates derived from the cpDNA sequence suggest that the major diploid clades had diverged approximately 10 to 11 million years ago. The complete nucleotide sequences of 6 cpDNA genomes are provided, offering a resource for cytonuclear studies in Gossypium. PMID:27309527

Multilocus sequence typing and virulence analysis of Haemophilus parasuis strains isolated in five provinces of China.

PubMed

Wang, Liyan; Ma, Lina; Liu, Yongan; Gao, Pengcheng; Li, Youquan; Li, Xuerui; Liu, Yongsheng

2016-10-01

Haemophilus parasuis is the etiological agent of Glässers disease, which causes high morbidity and mortality in swine herds. Although H. parasuis strains can be classified into 15 serovars with the Kielstein-Rapp-Gabrielson serotyping scheme, a large number of isolates cannot be classified and have been designated 'nontypeable' strains. In this study, multilocus sequence typing (MLST) of H. parasuis was used to analyze 48 H. parasuis field strains isolated in China and two strains from Australia. Twenty-six new alleles and 29 new sequence types (STs) were detected, enriching the H. parasuis MLST databases. A BURST analysis indicated that H. parasuis lacks stable population structure and is highly heterogeneous, and that there is no association between STs and geographic area. When an UPGMA dendrogram was constructed, two major clades, clade A and clade B, were defined. Animal experiments, in which guinea pigs were challenged intraperitoneally with the bacterial isolates, supported the hypothesis that the H. parasuis STs in clade A are generally avirulent or weakly virulent, whereas the STs in clade B tend to be virulent. Copyright © 2016 Elsevier B.V. All rights reserved.

Characterization of humoral responses to soluble trimeric HIV gp140 from a clade A Ugandan field isolate

PubMed Central

2013-01-01

Trimeric soluble forms of HIV gp140 envelope glycoproteins represent one of the closest molecular structures compared to native spikes present on intact virus particles. Trimeric soluble gp140 have been generated by several groups and such molecules have been shown to induce antibodies with neutralizing activity against homologous and heterologous viruses. In the present study, we generated a recombinant trimeric soluble gp140, derived from a previously identified Ugandan A-clade HIV field isolate (gp14094UG018). Antibodies elicited in immunized rabbits show a broad binding pattern to HIV envelopes of different clades. An epitope mapping analysis reveals that, on average, the binding is mostly focused on the C1, C2, V3, V5 and C5 regions. Immune sera show neutralization activity to Tier 1 isolates of different clades, demonstrating cross clade neutralizing activity which needs to be further broadened by possible structural modifications of the clade A gp14094UG018. Our results provide a rationale for the design and evaluation of immunogens and the clade A gp14094UG018 shows promising characteristics for potential involvement in an effective HIV vaccine with broad activity. PMID:23835244

Characterization of humoral responses to soluble trimeric HIV gp140 from a clade A Ugandan field isolate.

PubMed

Visciano, Maria Luisa; Tagliamonte, Maria; Stewart-Jones, Guillaume; Heyndrickx, Leo; Vanham, Guido; Jansson, Marianne; Fomsgaard, Anders; Grevstad, Berit; Ramaswamy, Meghna; Buonaguro, Franco M; Tornesello, Maria Lina; Biswas, Priscilla; Scarlatti, Gabriella; Buonaguro, Luigi

2013-07-08

Trimeric soluble forms of HIV gp140 envelope glycoproteins represent one of the closest molecular structures compared to native spikes present on intact virus particles. Trimeric soluble gp140 have been generated by several groups and such molecules have been shown to induce antibodies with neutralizing activity against homologous and heterologous viruses. In the present study, we generated a recombinant trimeric soluble gp140, derived from a previously identified Ugandan A-clade HIV field isolate (gp14094UG018). Antibodies elicited in immunized rabbits show a broad binding pattern to HIV envelopes of different clades. An epitope mapping analysis reveals that, on average, the binding is mostly focused on the C1, C2, V3, V5 and C5 regions. Immune sera show neutralization activity to Tier 1 isolates of different clades, demonstrating cross clade neutralizing activity which needs to be further broadened by possible structural modifications of the clade A gp14094UG018. Our results provide a rationale for the design and evaluation of immunogens and the clade A gp14094UG018 shows promising characteristics for potential involvement in an effective HIV vaccine with broad activity.

Genetic diversification and demographic history of the cactophilic pseudoscorpion Dinocheirus arizonensis from the Sonoran Desert

PubMed Central

Pfeiler, Edward; Bitler, Ben G.; Castrezana, Sergio; Matzkin, Luciano M.; Markow, Therese A.

2009-01-01

Sequence data from a segment of the mitochondrial cytochrome c oxidase subunit I (COI) gene were used to examine phylogenetic relationships, estimate gene flow and infer demographic history of the cactophilic chernetid pseudoscorpion, Dinocheirus arizonensis (Banks, 1901), from the Sonoran Desert. Phylogenetic trees resolved two clades of D. arizonensis, one from mainland Sonora, Mexico and southern Arizona (clade I) and the other from the Baja California peninsula and southern Arizona (clade II). The two clades were separated by a mean genetic distance (d) of ~2.6%. Hierarchical analysis of molecular variance indicated highly significant population structuring in D. arizonensis (overall ΦST = 0.860; P < 0.0001), with 80% of the genetic variation distributed among the two clades. Most pairwise comparisons of ΦST among populations within each clade, however, were not significant. The results suggest that phoretic dispersal on vagile cactophilic insects such as the neriid cactus fly Odontoloxozus longicornis (Coquillett, 1904) provides sufficient gene flow to offset the accumulation of unique haplotypes within each clade of the non-vagile pseudoscorpion. Preliminary results on dispersal capability of O. longicornis were consistent with this conclusion. Tests designed to reconstruct demographic history from sequence data indicated that both clades of D. arizonensis, as well as O. longicornis, have experienced historical population expansions. Potential barriers to gene flow that may have led to genetic isolation and diversification in clades I and II of Dinocheirus arizonensis are discussed. PMID:19166949

Genetic identification of rickettsial isolates from fatal cases of Brazilian spotted fever and comparison with Rickettsia rickettsii isolates from the American continents.

PubMed

Labruna, Marcelo B; Santos, Fabiana C P; Ogrzewalska, Maria; Nascimento, Elvira M M; Colombo, Silvia; Marcili, Arlei; Angerami, Rodrigo N

2014-10-01

Fifteen bacterial isolates from spotted fever group rickettsiosis in Brazil were genetically identified as Rickettsia rickettsii. In a phylogenetic analysis with other R. rickettsii isolates from GenBank, the Central/South American isolates showed low polymorphism and formed a clade distinct from two North American clades, with the North American clades having greater in-branch polymorphism. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Phylodynamics of HIV-1 subtype F1 in Angola, Brazil and Romania.

PubMed

Bello, Gonzalo; Afonso, Joana Morais; Morgado, Mariza G

2012-07-01

The HIV-1 subtype F1 is exceptionally prevalent in Angola, Brazil and Romania. The epidemiological context in which the spread of HIV occurred was highly variable from one country to another, mainly due to the existence of a long-term civil war in Angola and the contamination of a large number of children in Romania. Here we apply phylogenetic and Bayesian coalescent-based methods to reconstruct the phylodynamic patterns of HIV-1 subtype F1 in such different epidemiological settings. The phylogenetic analyses of HIV-1 subtype F1 pol sequences sampled worldwide confirmed that most sequences from Angola, Brazil and Romania segregated in country-specific monophyletic groups, while most subtype F1 sequences from Romanian children branched as a monophyletic sub-cluster (Romania-CH) nested within sequences from adults. The inferred time of the most recent common ancestor of the different subtype F1 clades were as follow: Angola=1983 (1978-1989), Brazil=1977 (1972-1981), Romania adults=1980 (1973-1987), and Romania-CH=1985 (1978-1989). All subtype F1 clades showed a demographic history best explained by a model of logistic population growth. Although the expansion phase of subtype F1 epidemic in Angola (mid 1980s to early 2000s) overlaps with the civil war period (1975-2002), the mean estimated growth rate of the Angolan F1 clade (0.49 year(-1)) was not exceptionally high, but quite similar to that estimated for the Brazilian (0.69 year(-1)) and Romanian adult (0.36 year(-1)) subtype F1 clades. The Romania-CH subtype F1 lineage, by contrast, displayed a short and explosive dissemination phase, with a median growth rate (2.47 year(-1)) much higher than that estimated for adult populations. This result supports the idea that the AIDS epidemic that affected the Romanian children was mainly caused by the spread of the HIV through highly efficient parenteral transmission networks, unlike adult populations where HIV is predominantly transmitted through sexual route. Copyright © 2012 Elsevier B.V. All rights reserved.

Nest site characteristics of three coexisting Accipiter hawks in northeastern Oregon

USGS Publications Warehouse

Moore, K.R.; Henny, C.J.

1983-01-01

Habitat data were evaluated at 34 Goshawk (Accipiter gentilis), 31 Cooper's Hawk (A. cooperii), and 15 Sharp-shinned Hawk (A. striatus) nest sites in coniferous forests of northeastern Oregon. Crown volume profiles indicate a strong similarity in vegetative structure at nest sites of cooperii and striatus; both commonly nest in younger successional stands than gentilis. Habitat separation of nest sites among the three species was illustrated using a stepwise discriminant analysis; 88% of all gentilis sites were correctly classified. Interspecific overlap in nest site habitat was further demonstrated using a canonical analysis of habitat variables. Nest site habitat space of gentilis is distinct and is less variable in structure than that of the other species. Cooperii preferred nesting sites with norhern aspects, whereas striatus and gentilis showed no preference. The use of mistletoe (Arceuthobium sp.) growth by cooperii for nest platforms (64% of all nests) may explain its preference for Douglas fir (Pseudotsuga menziesii) as a nesting tree. Douglas fir is most commonly parasitized by mistletoe.

Comparative Analysis and Distribution of Omega-3 lcPUFA Biosynthesis Genes in Marine Molluscs

PubMed Central

Surm, Joachim M.; Prentis, Peter J.; Pavasovic, Ana

2015-01-01

Recent research has identified marine molluscs as an excellent source of omega-3 long-chain polyunsaturated fatty acids (lcPUFAs), based on their potential for endogenous synthesis of lcPUFAs. In this study we generated a representative list of fatty acyl desaturase (Fad) and elongation of very long-chain fatty acid (Elovl) genes from major orders of Phylum Mollusca, through the interrogation of transcriptome and genome sequences, and various publicly available databases. We have identified novel and uncharacterised Fad and Elovl sequences in the following species: Anadara trapezia, Nerita albicilla, Nerita melanotragus, Crassostrea gigas, Lottia gigantea, Aplysia californica, Loligo pealeii and Chlamys farreri. Based on alignments of translated protein sequences of Fad and Elovl genes, the haeme binding motif and histidine boxes of Fad proteins, and the histidine box and seventeen important amino acids in Elovl proteins, were highly conserved. Phylogenetic analysis of aligned reference sequences was used to reconstruct the evolutionary relationships for Fad and Elovl genes separately. Multiple, well resolved clades for both the Fad and Elovl sequences were observed, suggesting that repeated rounds of gene duplication best explain the distribution of Fad and Elovl proteins across the major orders of molluscs. For Elovl sequences, one clade contained the functionally characterised Elovl5 proteins, while another clade contained proteins hypothesised to have Elovl4 function. Additional well resolved clades consisted only of uncharacterised Elovl sequences. One clade from the Fad phylogeny contained only uncharacterised proteins, while the other clade contained functionally characterised delta-5 desaturase proteins. The discovery of an uncharacterised Fad clade is particularly interesting as these divergent proteins may have novel functions. Overall, this paper presents a number of novel Fad and Elovl genes suggesting that many mollusc groups possess most of the required enzymes for the synthesis of lcPUFAs. PMID:26308548

Clade perseverance from Mesozoic to present: a multidisciplinary approach to interpretation of pattern and process.

PubMed

Barnes, David K A

2002-10-01

Two clades of marine bryozoans, cyclostomes and cheilostomes, exemplify the benefits of applying a multidisciplinary approach to the interpretation of long-term evolutionary patterns. The cyclostome bryozoans were dominant in the Mesozoic; since that era, they have decreased in absolute terms and the cheilostomes have come to exceed them in both abundance and diversity. Many studies of living assemblages of the encrusting members of these two clades indicate that cheilostomes are superior space competitors, but paleontological studies suggest that competition between the two taxa has not been escalating over geological time. Both clades occur throughout the world's oceans and seas, and recent work in the geographical extremes has shown that the relative success of the clades varies markedly from place to place. In this study, the importance of differential patterns of recruitment and cumulative space occupation in the two clades was evaluated over four years and in two environments, one temperate and one polar. In both of these environments, peaks of recruitment and space occupation by the two clades were out of phase. The different strategies and outcomes of spatial competition are examined, largely using data from the literature. Only recently has it been realized that tied outcomes of competition are stable alternative results and not simply transitory phases. Many competitive encounters involving cyclostomes result in ties, implying that their strategy is based on persistence rather than dominance. When different indices and models are used to analyze competition data from the two clades, the interpretation varies markedly with methodology. The differences in patterns of recruitment, space occupation, and spatial competition have influenced both our understanding of how the two clades have persisted alongside each other and our perception of cheilostome superiority. Analysis of fluid dynamics has shown that small differences in the mechanical structure of typical members of each clade lead to fundamental differences in water movement. For animals that rely on water motion for transport of nutritional and excretory elements (suspension feeders), small changes in current velocity and direction can have a major impact. Preliminary chemical analysis of the excurrent stream leaving cheilostome colonies has shown it to be laden with excretory products, which can interfere and mix with a neighbor's feeding currents. Clearly, spatial competition involves more than a simple mechanical "showdown."

The Origin of Large-Bodied Shrimp that Dominate Modern Global Aquaculture

PubMed Central

Wilkins, Blake; Bracken-Grissom, Heather D.; Chan, Tin-Yam; O’Leary, Maureen A.

2016-01-01

Several shrimp species from the clade Penaeidae are farmed industrially for human consumption, and this farming has turned shrimp into the largest seafood commodity in the world. The species that are in demand for farming are an anomaly within their clade because they grow to much larger sizes than other members of Penaeidae. Here we trace the evolutionary history of the anomalous farmed shrimp using combined data phylogenetic analysis of living and fossil species. We show that exquisitely preserved fossils of †Antrimpos speciosus from the Late Jurassic Solnhofen limestone belong to the same clade as the species that dominate modern farming, dating the origin of this clade to at least 145 mya. This finding contradicts a much younger Late Cretaceous age (ca. 95 mya) previously estimated for this clade using molecular clocks. The species in the farmed shrimp clade defy a widespread tendency, by reaching relatively large body sizes despite their warm water lifestyles. Small body sizes have been shown to be physiologically favored in warm aquatic environments because satisfying oxygen demands is difficult for large organisms breathing in warm water. Our analysis shows that large-bodied, farmed shrimp have more gills than their smaller-bodied shallow-water relatives, suggesting that extra gills may have been key to the clade’s ability to meet oxygen demands at a large size. Our combined data phylogenetic tree also suggests that, during penaeid evolution, the adoption of mangrove forests as habitats for young shrimp occurred multiple times independently. PMID:27415002

Phylogeny of Kinorhyncha Based on Morphology and Two Molecular Loci

PubMed Central

Sørensen, Martin V.; Dal Zotto, Matteo; Rho, Hyun Soo; Herranz, Maria; Sánchez, Nuria; Pardos, Fernando; Yamasaki, Hiroshi

2015-01-01

The phylogeny of Kinorhyncha was analyzed using morphology and the molecular loci 18S rRNA and 28S rRNA. The different datasets were analyzed separately and in combination, using maximum likelihood and Bayesian Inference. Bayesian inference of molecular sequence data in combination with morphology supported the division of Kinorhyncha into two major clades: Cyclorhagida comb. nov. and Allomalorhagida nom. nov. The latter clade represents a new kinorhynch class, and accommodates Dracoderes, Franciscideres, a yet undescribed genus which is closely related with Franciscideres, and the traditional homalorhagid genera. Homalorhagid monophyly was not supported by any analyses with molecular sequence data included. Analysis of the combined molecular and morphological data furthermore supported a cyclorhagid clade which included all traditional cyclorhagid taxa, except Dracoderes that no longer should be considered a cyclorhagid genus. Accordingly, Cyclorhagida is divided into three main lineages: Echinoderidae, Campyloderidae, and a large clade, ‘Kentrorhagata’, which except for species of Campyloderes, includes all species with a midterminal spine present in adult individuals. Maximum likelihood analysis of the combined datasets produced a rather unresolved tree that was not regarded in the following discussion. Results of the analyses with only molecular sequence data included were incongruent at different points. However, common for all analyses was the support of several major clades, i.e., Campyloderidae, Kentrorhagata, Echinoderidae, Dracoderidae, Pycnophyidae, and a clade with Paracentrophyes + New Genus and Franciscideres (in those analyses where the latter was included). All molecular analyses including 18S rRNA sequence data furthermore supported monophyly of Allomalorhagida. Cyclorhagid monophyly was only supported in analyses of combined 18S rRNA and 28S rRNA (both ML and BI), and only in a restricted dataset where taxa with incomplete information from 28S rRNA had been omitted. Analysis of the morphological data produced results that were similar with those from the combined molecular and morphological analysis. E.g., the morphological data also supported exclusion of Dracoderes from Cyclorhagida. The main differences between the morphological analysis and analyses based on the combined datasets include: 1) Homalorhagida appears as monophyletic in the morphological tree only, 2) the morphological analyses position Franciscideres and the new genus within Cyclorhagida near Zelinkaderidae and Cateriidae, whereas analyses including molecular data place the two genera inside Allomalorhagida, and 3) species of Campyloderes appear in a basal trichotomy within Kentrorhagata in the morphological tree, whereas analysis of the combined datasets places species of Campyloderes as a sister clade to Echinoderidae and Kentrorhagata. PMID:26200115

Highly Pathogenic Avian Influenza H5N1 Clade 2.3.2.1c Virus in Lebanon, 2016.

PubMed

El Romeh, Ali; Zecchin, Bianca; Fusaro, Alice; Ibrahim, Elias; El Bazzal, Bassel; El Hage, Jeanne; Milani, Adelaide; Zamperin, Gianpiero; Monne, Isabella

2017-06-01

We report the phylogenetic analysis of the first outbreak of H5N1 highly pathogenic avian influenza virus detected in Lebanon from poultry in April 2016. Our whole-genome sequencing analysis revealed that the Lebanese H5N1 virus belongs to genetic clade 2.3.2.1c and clusters with viruses from Europe and West Africa.

A DNA fingerprinting procedure for ultra high-throughput genetic analysis of insects.

PubMed

Schlipalius, D I; Waldron, J; Carroll, B J; Collins, P J; Ebert, P R

2001-12-01

Existing procedures for the generation of polymorphic DNA markers are not optimal for insect studies in which the organisms are often tiny and background molecular information is often non-existent. We have used a new high throughput DNA marker generation protocol called randomly amplified DNA fingerprints (RAF) to analyse the genetic variability in three separate strains of the stored grain pest, Rhyzopertha dominica. This protocol is quick, robust and reliable even though it requires minimal sample preparation, minute amounts of DNA and no prior molecular analysis of the organism. Arbitrarily selected oligonucleotide primers routinely produced approximately 50 scoreable polymorphic DNA markers, between individuals of three independent field isolates of R. dominica. Multivariate cluster analysis using forty-nine arbitrarily selected polymorphisms generated from a single primer reliably separated individuals into three clades corresponding to their geographical origin. The resulting clades were quite distinct, with an average genetic difference of 37.5 +/- 6.0% between clades and of 21.0 +/- 7.1% between individuals within clades. As a prelude to future gene mapping efforts, we have also assessed the performance of RAF under conditions commonly used in gene mapping. In this analysis, fingerprints from pooled DNA samples accurately and reproducibly reflected RAF profiles obtained from individual DNA samples that had been combined to create the bulked samples.

Soft-tissue anatomy of the extant hominoids: a review and phylogenetic analysis

PubMed Central

Gibbs, S; Collard, M; Wood, B

2002-01-01

This paper reports the results of a literature search for information about the soft-tissue anatomy of the extant non-human hominoid genera, Pan, Gorilla, Pongo and Hylobates, together with the results of a phylogenetic analysis of these data plus comparable data for Homo. Information on the four extant non-human hominoid genera was located for 240 out of the 1783 soft-tissue structures listed in the Nomina Anatomica. Numerically these data are biased so that information about some systems (e.g. muscles) and some regions (e.g. the forelimb) are over-represented, whereas other systems and regions (e.g. the veins and the lymphatics of the vascular system, the head region) are either under-represented or not represented at all. Screening to ensure that the data were suitable for use in a phylogenetic analysis reduced the number of eligible soft-tissue structures to 171. These data, together with comparable data for modern humans, were converted into discontinuous character states suitable for phylogenetic analysis and then used to construct a taxon-by-character matrix. This matrix was used in two tests of the hypothesis that soft-tissue characters can be relied upon to reconstruct hominoid phylogenetic relationships. In the first, parsimony analysis was used to identify cladograms requiring the smallest number of character state changes. In the second, the phylogenetic bootstrap was used to determine the confidence intervals of the most parsimonious clades. The parsimony analysis yielded a single most parsimonious cladogram that matched the molecular cladogram. Similarly the bootstrap analysis yielded clades that were compatible with the molecular cladogram; a (Homo, Pan) clade was supported by 95% of the replicates, and a (Gorilla, Pan, Homo) clade by 96%. These are the first hominoid morphological data to provide statistically significant support for the clades favoured by the molecular evidence. PMID:11833653

Phylogenetic estimation and morphological evolution of Arundinarieae (Bambusoideae: Poaceae) based on plastome phylogenomic analysis.

PubMed

Attigala, Lakshmi; Wysocki, William P; Duvall, Melvin R; Clark, Lynn G

2016-08-01

We explored phylogenetic relationships among the twelve lineages of the temperate woody bamboo clade (tribe Arundinarieae) based on plastid genome (plastome) sequence data. A representative sample of 28 taxa was used and maximum parsimony, maximum likelihood and Bayesian inference analyses were conducted to estimate the Arundinarieae phylogeny. All the previously recognized clades of Arundinarieae were supported, with Ampelocalamus calcareus (Clade XI) as sister to the rest of the temperate woody bamboos. Well supported sister relationships between Bergbambos tessellata (Clade I) and Thamnocalamus spathiflorus (Clade VII) and between Kuruna (Clade XII) and Chimonocalmus (Clade III) were revealed by the current study. The plastome topology was tested by taxon removal experiments and alternative hypothesis testing and the results supported the current plastome phylogeny as robust. Neighbor-net analyses showed few phylogenetic signal conflicts, but suggested some potentially complex relationships among these taxa. Analyses of morphological character evolution of rhizomes and reproductive structures revealed that pachymorph rhizomes were most likely the ancestral state in Arundinarieae. In contrast leptomorph rhizomes either evolved once with reversions to the pachymorph condition or multiple times in Arundinarieae. Further, pseudospikelets evolved independently at least twice in the Arundinarieae, but the ancestral state is ambiguous. Copyright © 2016 Elsevier Inc. All rights reserved.

Systematics of marine brown alga Sargassum from Thailand: A preliminary study based on morphological data and nuclear ribosomal internal transcribed spacer 2 (ITS2) sequences

NASA Astrophysics Data System (ADS)

Kantachumpoo, Attachai; Uwai, Shinya; Noiraksar, Thidarat; Komatsu, Teruhisa

2015-06-01

The marine brown algal genus Sargassum has been investigated extensively based on genetic information. In this report, we performed the first comparative study of morphological and molecular data among common species of Sargassum found in Thailand and explored the phylogenetic diversity within the genus. Our results revealed an incongruent pattern for species classification in Thai Sargassum. Morphologically, our Sargassum specimens were distinguishable and represented 8 species, namely, S. aquifolium (Turner) C.Agardh, Sargassum baccularia (Mertens) C. Agardh, S. cinereum J. Agardh, S. ilicifolium (Turner) C.Agardh, S. oligocystum Montagne, S. plagiophyllum C. Agardh, S. polycystum C. Agardh and S. swartzii (Turuner) C. Agardh. In contrast, using three different methods, phylogenetic analysis of nuclear ribosomal internal transcribed spacer 2 (ITS2) revealed six distinct clades, including S. baccularia/ S. oligosyntum clade, S. aquifolium/ S. swartzii clade, S. cinereum clade, S. aquifolium/ S. ilicifolium clade, S. polycystum clade, and S. plagiophyllum clade, which was suggestive of a phenotypic plasticity species complex. Our molecular data also confirmed the paraphyletic relationship in the section Binderianae and suggested that this section requires reassessment. Overall, further studies are required to increase our understanding of the taxonomy, phylogenetic relationships and species boundaries among Sargassum species in Thailand.

First Report of a Fatal Case Associated with EV-D68 Infection in Hong Kong and Emergence of an Interclade Recombinant in China Revealed by Genome Analysis.

PubMed

Yip, Cyril C Y; Lo, Janice Y C; Sridhar, Siddharth; Lung, David C; Luk, Shik; Chan, Kwok-Hung; Chan, Jasper F W; Cheng, Vincent C C; Woo, Patrick C Y; Yuen, Kwok-Yung; Lau, Susanna K P

2017-05-16

A fatal case associated with enterovirus D68 (EV-D68) infection affecting a 10-year-old boy was reported in Hong Kong in 2014. To examine if a new strain has emerged in Hong Kong, we sequenced the partial genome of the EV-D68 strain identified from the fatal case and the complete VP1, and partial 5'UTR and 2C sequences of nine additional EV-D68 strains isolated from patients in Hong Kong. Sequence analysis indicated that a cluster of strains including the previously recognized A2 strains should belong to a separate clade, clade D, which is further divided into subclades D1 and D2. Among the 10 EV-D68 strains, 7 (including the fatal case) belonged to the previously described, newly emerged subclade B3, 2 belonged to subclade B1, and 1 belonged to subclade D1. Three EV-D68 strains, each from subclades B1, B3, and D1, were selected for complete genome sequencing and recombination analysis. While no evidence of recombination was noted among local strains, interclade recombination was identified in subclade D2 strains detected in mainland China in 2008 with VP2 acquired from clade A. This study supports the reclassification of subclade A2 into clade D1, and demonstrates interclade recombination between clades A and D2 in EV-D68 strains from China.

Trading Capsule for Increased Cytotoxin Production: Contribution to Virulence of a Newly Emerged Clade of emm89 Streptococcus pyogenes.

PubMed

Zhu, Luchang; Olsen, Randall J; Nasser, Waleed; de la Riva Morales, Ivan; Musser, James M

2015-10-06

Strains of emm89 Streptococcus pyogenes have become one of the major causes of invasive infections worldwide in the last 10 years. We recently sequenced the genome of 1,125 emm89 strains and identified three major phylogenetic groups, designated clade 1, clade 2, and the epidemic clade 3. Epidemic clade 3 strains, which now cause the great majority of infections, have two distinct genetic features compared to clade 1 and clade 2 strains. First, all clade 3 organisms have a variant 3 nga promoter region pattern, which is associated with increased production of secreted cytolytic toxins SPN (S. pyogenes NADase) and SLO (streptolysin O). Second, all clade 3 strains lack the hasABC locus mediating hyaluronic acid capsule synthesis, whereas this locus is intact in clade 1 and clade 2 strains. We constructed isogenic mutant strains that produce different levels of SPN and SLO toxins and capsule (none, low, or high). Here we report that emm89 strains with elevated toxin production are significantly more virulent than low-toxin producers. Importantly, we also show that capsule production is dispensable for virulence in strains that already produce high levels of SPN and SLO. Our results provide new understanding about the molecular mechanisms contributing to the rapid emergence and molecular pathogenesis of epidemic clade 3 emm89 S. pyogenes. S. pyogenes (group A streptococcus [GAS]) causes pharyngitis ("strep throat"), necrotizing fasciitis, and other human infections. Serious infections caused by emm89 S. pyogenes strains have recently increased in frequency in many countries. Based on whole-genome sequence analysis of 1,125 strains recovered from patients on two continents, we discovered that a new emm89 clone, termed clade 3, has two distinct genetic features compared to its predecessors: (i) absence of the genes encoding antiphagocytic hyaluronic acid capsule virulence factor and (ii) increased production of the secreted cytolytic toxins SPN and SLO. emm89 S. pyogenes strains with the clade 3 phenotype (absence of capsule and high expression of SPN and SLO) are highly virulent in mice. These findings provide new understanding of how new virulent clones emerge and cause severe infections worldwide. This newfound knowledge of S. pyogenes virulence can be used to help understand future epidemics and conduct new translational research. Copyright © 2015 Zhu et al.

Stabilities of ant nests and their adjacent soils

NASA Astrophysics Data System (ADS)

Echezona, B. C.; Igwe, C. A.

2012-10-01

Nests habour ants and termites and protect them from harsh environmental conditions. The structural stabilities of nests were studied to ascertain their relative vulnerability to environmental stresses. Arboreal-ant nests were pried from different trees, while epigeous-termite nests were excavated from soil surface within the sample area. Soils without any visible sign of ant or termite activity were also sampled 6 m away from the nests as control. Laboratory analysis result showed that irrespective of the tree hosts, the aggregate stabilities of the ant nests were lower than those of the ground termite, with nests formed on Cola nitida significantly showing lower aggregate stability (19.7%) than other antnest structures. Clay dispersion ratio, moisture content, water stable aggregate class <0.25mm and sand mass were each negatively correlated with aggregate stability, while water stable aggregate class1.00-0.50 mm gave a positive correlation. Nest structures were dominated more by water stable aggregate class >2.00 mm but path analysis demonstrated that water stable aggregate class <0.25 mm contributed most to the higher aggregate stability of the termite nest than the other nest. Nest aggregates had greater structural stability compared to the control soil. The higher structural stability of termite nests over other nest and soil was considered a better adaptive mechanism against body desiccation.

Prevalence of Tobacco mosaic virus in Iran and Evolutionary Analyses of the Coat Protein Gene

PubMed Central

Alishiri, Athar; Rakhshandehroo, Farshad; Zamanizadeh, Hamid-Reza; Palukaitis, Peter

2013-01-01

The incidence and distribution of Tobacco mosaic virus (TMV) and related tobamoviruses was determined using an enzyme-linked immunosorbent assay on 1,926 symptomatic horticultural crops and 107 asymptomatic weed samples collected from 78 highly infected fields in the major horticultural crop-producing areas in 17 provinces throughout Iran. The results were confirmed by host range studies and reverse transcription-polymerase chain reaction. The overall incidence of infection by these viruses in symptomatic plants was 11.3%. The coat protein (CP) gene sequences of a number of isolates were determined and disclosed to be a high identity (up to 100%) among the Iranian isolates. Phylogenetic analysis of all known TMV CP genes showed three clades on the basis of nucleotide sequences with all Iranian isolates distinctly clustered in clade II. Analysis using the complete CP amino acid sequence showed one clade with two subgroups, IA and IB, with Iranian isolates in both subgroups. The nucleotide diversity within each sub-group was very low, but higher between the two clades. No correlation was found between genetic distance and geographical origin or host species of isolation. Statistical analyses suggested a negative selection and demonstrated the occurrence of gene flow from the isolates in other clades to the Iranian population. PMID:25288953

Testing Evolutionary Hypotheses in the Classroom with MacClade Software.

ERIC Educational Resources Information Center

Codella, Sylvio G.

2002-01-01

Introduces MacClade which is a Macintosh-based software package that uses the techniques of cladistic analysis to explore evolutionary patterns. Describes a novel and effective exercise that allows undergraduate biology majors to test a hypothesis about behavioral evolution in insects. (Contains 13 references.) (Author/YDS)

Construction patterns of birds' nests provide insight into nest-building behaviours.

PubMed

Biddle, Lucia; Goodman, Adrian M; Deeming, D Charles

2017-01-01

Previous studies have suggested that birds and mammals select materials needed for nest building based on their thermal or structural properties, although the amounts or properties of the materials used have been recorded for only a very small number of species. Some of the behaviours underlying the construction of nests can be indirectly determined by careful deconstruction of the structure and measurement of the biomechanical properties of the materials used. Here we examined this idea in an investigation of Bullfinch ( Pyrrhula pyrrhula ) nests as a model for open-nesting songbird species that construct a "twig" nest, and tested the hypothesis that materials in different parts of nests serve different functions. The quantities of materials present in the nest base, sides and cup were recorded before structural analysis. Structural analysis showed that the base of the outer nests were composed of significantly thicker, stronger and more rigid materials compared to the side walls, which in turn were significantly thicker, stronger and more rigid than materials used in the cup. These results suggest that the placement of particular materials in nests may not be random, but further work is required to determine if the final structure of a nest accurately reflects the construction process.

Community structures and population dynamics of "Candidatus Accumulibacter" in activated sludges of wastewater treatment plants using ppk1 as phylogenetic marker.

PubMed

Zeng, Wei; Zhang, Limin; Fan, Pengchao; Guo, Jingjing; Peng, Yongzhen

2018-05-01

Candidatus Accumulibacter has been identified as dominant polyphosphate-accumulating organisms (PAOs) in enhanced biological phosphorus (P) removal (EBPR) from wastewater. This study revealed the relevance of community structure, abundance and seasonal population dynamics of Candidatus Accumulibacter to process operation of wastewater treatment plants (WWTPs) in China using ppk1 gene as phylogenetic marker. All sludge samples had properties of denitrifying P removal using nitrate as an electron acceptor. Accumulibacter abundance in the anaerobic-anoxic-oxic (A 2 O) process was the highest (26% of total bacteria), and higher in winter than in summer with a better EBPR performance. Type-II was the dominant Accumulibacter in all processes, and type-I accounted for a small proportion of total Accumulibacter. The abundance of Clade-IIC as the most dominant clade reached 2.59×10 9 cells/g MLSS and accounted for 87.3% of total Accumulibacter. Clade IIC mainly contributed to denitrifying P removal. Clades IIA, IIC and IID were found in all processes, while clade-IIF was only found in oxidation ditch process through phylogenetic analysis. High proportion of clade IID to total Accumulibacter led to poor performance of aerobic P-uptake in inverted A 2 O process. Therefore, Accumulibacter clades in WWTPs were diverse, and EBPR performance was closely related to the clade-level community structures and abundances of Accumulibacter. Copyright © 2017. Published by Elsevier B.V.

A New Saurolophine Dinosaur from the Latest Cretaceous of Far Eastern Russia

PubMed Central

Godefroit, Pascal; Bolotsky, Yuri L.; Lauters, Pascaline

2012-01-01

Background Four main dinosaur sites have been investigated in latest Cretaceous deposits from the Amur/Heilongjiang Region: Jiayin and Wulaga in China (Yuliangze Formation), Blagoveschensk and Kundur in Russia (Udurchukan Formation). More than 90% of the bones discovered in these localities belong to hollow-crested lambeosaurine saurolophids, but flat-headed saurolophines are also represented: Kerberosaurus manakini at Blagoveschensk and Wulagasaurus dongi at Wulaga. Methodology/Principal Findings Herein we describe a new saurolophine dinosaur, Kundurosaurus nagornyi gen. et sp. nov., from the Udurchukan Formation (Maastrichtian) of Kundur, represented by disarticulated cranial and postcranial material. This new taxon is diagnosed by four autapomorphies. Conclusions/Significance A phylogenetic analysis of saurolophines indicates that Kundurosaurus nagornyi is nested within a rather robust clade including Edmontosaurus spp., Saurolophus spp., and Prosaurolophus maximus, possibly as a sister-taxon for Kerberosaurus manakini also from the Udurchukan Formation of Far Eastern Russia. The high diversity and mosaic distribution of Maastrichtian hadrosaurid faunas in the Amur-Heilongjiang region are the result of a complex palaeogeographical history and imply that many independent hadrosaurid lineages dispersed without any problem between western America and eastern Asia at the end of the Cretaceous. PMID:22666331

Phylogeographic History and Gene Flow Among Giant Galápagos Tortoises on Southern Isabela Island

PubMed Central

Ciofi, Claudio; Wilson, Gregory A.; Beheregaray, Luciano B.; Marquez, Cruz; Gibbs, James P.; Tapia, Washington; Snell, Howard L.; Caccone, Adalgisa; Powell, Jeffrey R.

2006-01-01

Volcanic islands represent excellent models with which to study the effect of vicariance on colonization and dispersal, particularly when the evolution of genetic diversity mirrors the sequence of geological events that led to island formation. Phylogeographic inference, however, can be particularly challenging for recent dispersal events within islands, where the antagonistic effects of land bridge formation and vicariance can affect movements of organisms with limited dispersal ability. We investigated levels of genetic divergence and recovered signatures of dispersal events for 631 Galápagos giant tortoises across the volcanoes of Sierra Negra and Cerro Azul on the island of Isabela. These volcanoes are among the most recent formations in the Galápagos (<0.7 million years), and previous studies based on genetic and morphological data could not recover a consistent pattern of lineage sorting. We integrated nested clade analysis of mitochondrial DNA control region sequences, to infer historical patterns of colonization, and a novel Bayesian multilocus genotyping method for recovering evidence of recent migration across volcanoes using eleven microsatellite loci. These genetic studies illuminate taxonomic distinctions as well as provide guidance to possible repatriation programs aimed at countering the rapid population declines of these spectacular animals. PMID:16387883

Molecular characterization of avian malaria in the spotless starling (Sturnus unicolor).

PubMed

Muriel, Jaime; Graves, Jeff A; Gil, Diego; Magallanes, S; Salaberria, Concepción; Casal-López, Miriam; Marzal, Alfonso

2018-03-01

We studied the prevalence and genetic diversity of malaria parasites in the poorly investigated spotless starling (Sturnus unicolor) breeding in central Spain, aiming to describe the phylogenetic relationships among them and with other haemosporidians infecting the genus Sturnus. A total of 180 nestlings and 180 adult individuals from four different breeding seasons were screened for haemosporidian parasites using a nested PCR approach for the genera Plasmodium and Haemoproteus. Although the malaria prevalence ranged between years, the overall prevalence was 6.94%. Adults had a higher prevalence than chicks: 12.77 vs. 1.11%, respectively. We molecularly characterized avian malaria isolated in peripheral blood samples taken from malaria-infected individuals. Sequence analyses revealed four unique Plasmodium lineages of avian malaria (STURUNI01, STURUNI02, SYAT05, SGS1) in our spotless starling population. The phylogenetic analysis showed a well-supported clade comprised by STURUNI01, STURUNI02, and SYAT05. The most common lineage (SYAT05) has been previously found in 26 other avian host species, including populations of spotless starling in Portugal. Because this sedentary species is widely distributed throughout the Iberian Peninsula, we suggest that the local transmission of these lineages might place migratory birds at infection risk.

Phylogeographic history and gene flow among giant Galápagos tortoises on southern Isabela Island.

PubMed

Ciofi, Claudio; Wilson, Gregory A; Beheregaray, Luciano B; Marquez, Cruz; Gibbs, James P; Tapia, Washington; Snell, Howard L; Caccone, Adalgisa; Powell, Jeffrey R

2006-03-01

Volcanic islands represent excellent models with which to study the effect of vicariance on colonization and dispersal, particularly when the evolution of genetic diversity mirrors the sequence of geological events that led to island formation. Phylogeographic inference, however, can be particularly challenging for recent dispersal events within islands, where the antagonistic effects of land bridge formation and vicariance can affect movements of organisms with limited dispersal ability. We investigated levels of genetic divergence and recovered signatures of dispersal events for 631 Galápagos giant tortoises across the volcanoes of Sierra Negra and Cerro Azul on the island of Isabela. These volcanoes are among the most recent formations in the Galápagos (<0.7 million years), and previous studies based on genetic and morphological data could not recover a consistent pattern of lineage sorting. We integrated nested clade analysis of mitochondrial DNA control region sequences, to infer historical patterns of colonization, and a novel Bayesian multilocus genotyping method for recovering evidence of recent migration across volcanoes using eleven microsatellite loci. These genetic studies illuminate taxonomic distinctions as well as provide guidance to possible repatriation programs aimed at countering the rapid population declines of these spectacular animals.

Histology and affinity of anaspids, and the early evolution of the vertebrate dermal skeleton

PubMed Central

Keating, Joseph N.; Donoghue, Philip C. J.

2016-01-01

The assembly of the gnathostome bodyplan constitutes a formative episode in vertebrate evolutionary history, an interval in which the mineralized skeleton and its canonical suite of cell and tissue types originated. Fossil jawless fishes, assigned to the gnathostome stem-lineage, provide an unparalleled insight into the origin and evolution of the skeleton, hindered only by uncertainty over the phylogenetic position and evolutionary significance of key clades. Chief among these are the jawless anaspids, whose skeletal composition, a rich source of phylogenetic information, is poorly characterized. Here we survey the histology of representatives spanning anaspid diversity and infer their generalized skeletal architecture. The anaspid dermal skeleton is composed of odontodes comprising spheritic dentine and enameloid, overlying a basal layer of acellular parallel fibre bone containing an extensive shallow canal network. A recoded and revised phylogenetic analysis using equal and implied weights parsimony resolves anaspids as monophyletic, nested among stem-gnathostomes. Our results suggest the anaspid dermal skeleton is a degenerate derivative of a histologically more complex ancestral vertebrate skeleton, rather than reflecting primitive simplicity. Hypotheses that anaspids are ancestral skeletonizing lampreys, or a derived lineage of jawless vertebrates with paired fins, are rejected. PMID:26962140

Evolutionary history of Stratiomyidae (Insecta: Diptera): the molecular phylogeny of a diverse family of flies.

PubMed

Brammer, Colin A; von Dohlen, Carol D

2007-05-01

Stratiomyidae is a cosmopolitan family of Brachycera (Diptera) that contains over 2800 species. This study focused on the relationships of members of the subfamily Clitellariinae, which has had a complicated taxonomic history. To investigate the monophyly of the Clitellariinae, the relationships of its genera, and the ages of Stratiomyidae lineages, representatives for all 12 subfamilies of Stratiomyidae, totaling 68 taxa, were included in a phylogenetic reconstruction. A Xylomyidae representative, Solva sp., was used as an outgroup. Sequences of EF-1alpha and 28S rRNA genes were analyzed under maximum parsimony with bootstrapping, and Bayesian methods to recover the best estimate of phylogeny. A chronogram with estimated dates for all nodes in the phylogeny was generated with the program, r8s, and divergence dates and confidence intervals were further explored with the program, multidivtime. All subfamilies of Stratiomyidae with more than one representative were found to be monophyletic, except for Stratiomyinae and Clitellariinae. Clitellariinae were distributed among five separate clades in the phylogeny, and Raphiocerinae were nested within Stratiomyinae. Dating analysis suggested an early Cretaceous origin for the common ancestor of extant Stratiomyidae, and a radiation of several major Stratiomyidae lineages in the Late Cretaceous.

Phylogenetic Diversity, Distribution, and Cophylogeny of Giant Bacteria (Epulopiscium) with their Surgeonfish Hosts in the Red Sea

PubMed Central

Miyake, Sou; Ngugi, David K.; Stingl, Ulrich

2016-01-01

Epulopiscium is a group of giant bacteria found in high abundance in intestinal tracts of herbivorous surgeonfish. Despite their peculiarly large cell size (can be up to 600 μm), extreme polyploidy (some with over 100,000 genome copies per cell) and viviparity (whereby mother cells produce live offspring), details about their diversity, distribution or their role in the host gut are lacking. Previous studies have highlighted the existence of morphologically distinct Epulopiscium cell types (defined as morphotypes A to J) in some surgeonfish genera, but the corresponding genetic diversity and distribution among other surgeonfishes remain mostly unknown. Therefore, we investigated the phylogenetic diversity of Epulopiscium, distribution and co-occurrence in multiple hosts. Here, we identified eleven new phylogenetic clades, six of which were also morphologically characterized. Three of these novel clades were phylogenetically and morphologically similar to cigar-shaped type A1 cells, found in a wide range of surgeonfishes including Acanthurus nigrofuscus, while three were similar to smaller, rod-shaped type E that has not been phylogenetically classified thus far. Our results also confirmed that biogeography appears to have relatively little influence on Epulopiscium diversity, as clades found in the Great Barrier Reef and Hawaii were also recovered from the Red Sea. Although multiple symbiont clades inhabited a given species of host surgeonfish and multiple host species possessed a given symbiont clade, statistical analysis of host and symbiont phylogenies indicated significant cophylogeny, which in turn suggests co-evolutionary relationships. A cluster analysis of Epulopiscium sequences from previously published amplicon sequencing dataset revealed a similar pattern, where specific clades were consistently found in high abundance amongst closely related surgeonfishes. Differences in abundance may indicate specialization of clades to certain gut environments reflected by inferred differences in the host diets. Overall, our analysis identified a large phylogenetic diversity of Epulopiscium (up to 10% sequence divergence of 16S rRNA genes), which lets us hypothesize that there are multiple species that are spread across guts of different host species. PMID:27014209

Insights into the phylogeny of Northern Hemisphere Armillaria: Neighbor-net and Bayesian analyses of translation elongation factor 1-α gene sequences.

PubMed

Klopfenstein, Ned B; Stewart, Jane E; Ota, Yuko; Hanna, John W; Richardson, Bryce A; Ross-Davis, Amy L; Elías-Román, Rubén D; Korhonen, Kari; Keča, Nenad; Iturritxa, Eugenia; Alvarado-Rosales, Dionicio; Solheim, Halvor; Brazee, Nicholas J; Łakomy, Piotr; Cleary, Michelle R; Hasegawa, Eri; Kikuchi, Taisei; Garza-Ocañas, Fortunato; Tsopelas, Panaghiotis; Rigling, Daniel; Prospero, Simone; Tsykun, Tetyana; Bérubé, Jean A; Stefani, Franck O P; Jafarpour, Saeideh; Antonín, Vladimír; Tomšovský, Michal; McDonald, Geral I; Woodward, Stephen; Kim, Mee-Sook

2017-01-01

Armillaria possesses several intriguing characteristics that have inspired wide interest in understanding phylogenetic relationships within and among species of this genus. Nuclear ribosomal DNA sequence-based analyses of Armillaria provide only limited information for phylogenetic studies among widely divergent taxa. More recent studies have shown that translation elongation factor 1-α (tef1) sequences are highly informative for phylogenetic analysis of Armillaria species within diverse global regions. This study used Neighbor-net and coalescence-based Bayesian analyses to examine phylogenetic relationships of newly determined and existing tef1 sequences derived from diverse Armillaria species from across the Northern Hemisphere, with Southern Hemisphere Armillaria species included for reference. Based on the Bayesian analysis of tef1 sequences, Armillaria species from the Northern Hemisphere are generally contained within the following four superclades, which are named according to the specific epithet of the most frequently cited species within the superclade: (i) Socialis/Tabescens (exannulate) superclade including Eurasian A. ectypa, North American A. socialis (A. tabescens), and Eurasian A. socialis (A. tabescens) clades; (ii) Mellea superclade including undescribed annulate North American Armillaria sp. (Mexico) and four separate clades of A. mellea (Europe and Iran, eastern Asia, and two groups from North America); (iii) Gallica superclade including Armillaria Nag E (Japan), multiple clades of A. gallica (Asia and Europe), A. calvescens (eastern North America), A. cepistipes (North America), A. altimontana (western USA), A. nabsnona (North America and Japan), and at least two A. gallica clades (North America); and (iv) Solidipes/Ostoyae superclade including two A. solidipes/ostoyae clades (North America), A. gemina (eastern USA), A. solidipes/ostoyae (Eurasia), A. cepistipes (Europe and Japan), A. sinapina (North America and Japan), and A. borealis (Eurasia) clade 2. Of note is that A. borealis (Eurasia) clade 1 appears basal to the Solidipes/Ostoyae and Gallica superclades. The Neighbor-net analysis showed similar phylogenetic relationships. This study further demonstrates the utility of tef1 for global phylogenetic studies of Armillaria species and provides critical insights into multiple taxonomic issues that warrant further study.

Occurrence and Identification of Phytophthora spp. Pathogenic to Pear Fruit in Irrigation Water in the Wenatchee River Valley of Washington State.

PubMed

Yamak, F; Peever, T L; Grove, G G; Boal, R J

2002-11-01

ABSTRACT Seven hundred forty-nine isolates of Phytophthora spp. were obtained from irrigation canals in eastern Washington State during the 1992 to 1995 and 1999 growing seasons. Isolates were retrieved using pear baiting techniques. All isolates were pathogenic to pear and were present in irrigation water beginning early in fruit development. Over the course of the 5 year study, 10 and 5% of isolates were identified as P. cactorum and P. citricola, respectively, using morphological criteria. The remaining isolates could not be identified using morphological criteria. Colony morphology of these isolates was characterized during all years of the study. In 1999, more detailed studies utilizing polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis of entire internal transcribed spacer (ITS) regions (ITS1, 5.8S, and ITS2) of ribosomal DNA for 180 isolates, and sequence analysis of ITS2 for 50 isolates, were used to investigate genetic variation and phylogenetic relationships among isolates. Isolates were divided into 12 groups based on their growth type on corn meal agar. Restriction digestion of the entire ITS region with three enzymes revealed 11 restriction digestion patterns among 180 isolates. PCR-RFLP and sequence data were obtained for 12 reference Phytophthora spp. (two species in each of Waterhouse's six morphological groups). Phylogenetic analysis of ITS2 regions revealed nine clades, each with strong bootstrap support. Molecular analyses revealed 23 isolates that were in the P. gonapodyides clade, 9 in the P. parasitica clade, 1 in the P. cactorum clade, 7 in the P. citricola/capsici clade, and 4 in the P. cambivora/pseudotsugae clade. The three isolates comprising clade 5 were significantly distinct from all other Phytophthora spp. in the databases and may represent a new Phytophthora sp. Colony morphology was not consistently correlated to PCR-RFLP pattern or ITS2 phylogeny, suggesting that the former criterion is insufficient for species identification. The results of this study indicate that at least nine phylogenetically distinct taxa of Phytophthora pathogenic to pear are present in irrigation water in North Central Washington.

A systematic analysis of Heliotropium, Tournefortia, and allied taxa of the Heliotropiaceae (Boraginales) based on ITS1 sequences and morphological data.

PubMed

Diane, Nadja; Förther, Harald; Hilger, Hartmut H

2002-02-01

The relationships of Heliotropium, Tournefortia, Schleidenia, Ixorhea, and Ceballosia of the Heliotropiaceae (Boraginaceae in the traditional sense, Boraginales) are investigated using molecular data (ITS1). These genera form a monophyletic group. Five clades can be distinguished on the basis of molecular data, morphological traits, and distribution. In their current circumscription, Tournefortia is polyphyletic and Heliotropium is paraphyletic. Tournefortia section Cyphocyema is the sister group to all other ingroup taxa. Heliotropium section Orthostachys including Schleidenia sensu lato is the well supported sister group of a clade comprising the other species of Heliotropium sensu stricto (s.s.), Tournefortia section Tournefortia, and Ceballosia. Heliotropium s.s. forms two clades: one clade includes all species of the Old World and represents the only monophylum of Heliotropium s.s. The other clade consists of all Heliotropium s.s. species of the New World but also includes Tournefortia section Tournefortia and Ceballosia. The results suggest that taxonomic changes are inevitable.

Description of Teunomyces gen. nov. for the Candida kruisii clade, Suhomyces gen. nov. for the Candida tanzawaensis clade and Suhomyces kilbournensis sp. nov.

PubMed

Kurtzman, Cletus P; Robnett, Christie J; Blackwell, Meredith

2016-08-01

DNA sequence analysis has shown that species of the Candida kruisii clade and species of the C. tanzawaensis clade represent phylogenetically circumscribed genera, which are described as Teunomyces gen. nov., type species T kruisii, and Suhomyces gen. nov., type species S tanzawaensis Many of the species are distributed worldwide and they are often isolated from fungus-feeding insects and their habitats. Included is the description of S. kilbournensis (type strain NRRL Y-17864, CBS 14276), a species found almost exclusively on maize kernels (Zea mays) in IL, USA. Published by Oxford University Press on behalf of FEMS 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Origin and Evolution of the Kiwifruit Canker Pandemic

PubMed Central

Li, Li; Liu, Yifei; Li, Dawei; Pan, Hui; Zhong, Caihong; Rikkerink, Erik H.A.; Templeton, Matthew D.; Straub, Christina; Colombi, Elena

2017-01-01

Recurring epidemics of kiwifruit (Actinidia spp.) bleeding canker disease are caused by Pseudomonas syringae pv. actinidiae (Psa). In order to strengthen understanding of population structure, phylogeography, and evolutionary dynamics, we isolated Pseudomonas from cultivated and wild kiwifruit across six provinces in China. Based on the analysis of 80 sequenced Psa genomes, we show that China is the origin of the pandemic lineage but that strain diversity in China is confined to just a single clade. In contrast, Korea and Japan harbor strains from multiple clades. Distinct independent transmission events marked introduction of the pandemic lineage into New Zealand, Chile, Europe, Korea, and Japan. Despite high similarity within the core genome and minimal impact of within-clade recombination, we observed extensive variation even within the single clade from which the global pandemic arose. PMID:28369338

Description of Groenewaldozyma gen. nov. for placement of Candida auringiensis, Candida salmanticensis and Candida tartarivorans.

PubMed

Kurtzman, Cletus P

2016-07-01

DNA sequence analyses have demonstrated that species of the polyphyletic anamorphic ascomycete genus Candida may be members of described teleomorphic genera, members of the Candida tropicalis clade upon which the genus Candida is circumscribed, or members of isolated clades that represent undescribed genera. From phylogenetic analysis of gene sequences from nuclear large subunit rRNA, mitochondrial small subunit rRNA and cytochrome oxidase II, Candida auringiensis (NRRL Y-17674(T), CBS 6913(T)), Candida salmanticensis (NRRL Y-17090(T), CBS 5121(T)), and Candida tartarivorans (NRRL Y-27291(T), CBS 7955(T)) were shown to be members of an isolated clade and are proposed for reclassification in the genus Groenewaldozyma gen. nov. (MycoBank MB 815817). Neighbouring taxa include species of the Wickerhamiella clade and Candida blankii.

Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes.

PubMed

Shoguchi, Eiichi; Beedessee, Girish; Tada, Ipputa; Hisata, Kanako; Kawashima, Takeshi; Takeuchi, Takeshi; Arakaki, Nana; Fujie, Manabu; Koyanagi, Ryo; Roy, Michael C; Kawachi, Masanobu; Hidaka, Michio; Satoh, Noriyuki; Shinzato, Chuya

2018-06-14

The marine dinoflagellate, Symbiodinium, is a well-known photosynthetic partner for coral and other diverse, non-photosynthetic hosts in subtropical and tropical shallows, where it comprises an essential component of marine ecosystems. Using molecular phylogenetics, the genus Symbiodinium has been classified into nine major clades, A-I, and one of the reported differences among phenotypes is their capacity to synthesize mycosporine-like amino acids (MAAs), which absorb UV radiation. However, the genetic basis for this difference in synthetic capacity is unknown. To understand genetics underlying Symbiodinium diversity, we report two draft genomes, one from clade A, presumed to have been the earliest branching clade, and the other from clade C, in the terminal branch. The nuclear genome of Symbiodinium clade A (SymA) has more gene families than that of clade C, with larger numbers of organelle-related genes, including mitochondrial transcription terminal factor (mTERF) and Rubisco. While clade C (SymC) has fewer gene families, it displays specific expansions of repeat domain-containing genes, such as leucine-rich repeats (LRRs) and retrovirus-related dUTPases. Interestingly, the SymA genome encodes a gene cluster for MAA biosynthesis, potentially transferred from an endosymbiotic red alga (probably of bacterial origin), while SymC has completely lost these genes. Our analysis demonstrates that SymC appears to have evolved by losing gene families, such as the MAA biosynthesis gene cluster. In contrast to the conservation of genes related to photosynthetic ability, the terminal clade has suffered more gene family losses than other clades, suggesting a possible adaptation to symbiosis. Overall, this study implies that Symbiodinium ecology drives acquisition and loss of gene families.

Phylogenetic analysis of Euthyneura (Gastropoda) by means of the 16S rRNA gene: use of a 'fast' gene for 'higher-level' phylogenies

PubMed Central

Thollesson, M.

1999-01-01

The phylogeny of Euthyneura is analysed by using DNA sequences of the mitochondrial 16S rRNA gene. Despite the common notion that this gene is too variable to provide useful information at high taxonomic levels, such as in the present study, bootstrap proportions are high for several clades in the study. This indicates that there is a useful amount of variation despite the noise due to multiple substitutions. The analyses furthermore indicate that (i) Gymnosomata (represented by Clione) is not a part of Euthyneura, but Clione forms a clade with the caenogastropods; (ii) Acteon is the sister group to the remaining euthyneuran taxa in the study; (iii) the nudibranch taxa form two clades, one comprising Dendronotoidea, Arminoidea and Aeolidoidea (together Cladobranchia) with Notaspidea (represented by Berthella) as sister group, while the fourth nudibranch taxon, Doridoidea, forms a separate clade; (iv) Cephalaspidea s.s. and Anaspidea form clades that are each other's sister groups (together Pleurocoela). Finally, there is no clade present in the analyses corresponding to the taxon Opisthobranchia in the traditional sense, and the use of this name is probably better abandoned altogether.

The assembly of ant-farmed gardens: mutualism specialization following host broadening

PubMed Central

Janda, Milan

2017-01-01

Ant-gardens (AGs) are ant/plant mutualisms in which ants farm epiphytes in return for nest space and food rewards. They occur in the Neotropics and Australasia, but not in Africa, and their evolutionary assembly remains unclear. We here use phylogenetic frameworks for important AG lineages in Australasia, namely the ant genus Philidris and domatium-bearing ferns (Lecanopteris) and flowering plants in the Apocynaceae (Hoya and Dischidia) and Rubiaceae (Myrmecodia, Hydnophytum, Anthorrhiza, Myrmephytum and Squamellaria). Our analyses revealed that in these clades, diaspore dispersal by ants evolved at least 13 times, five times in the Late Miocene and Pliocene in Australasia and seven times during the Pliocene in Southeast Asia, after Philidris ants had arrived there, with subsequent dispersal between these two areas. A uniquely specialized AG system evolved in Fiji at the onset of the Quaternary. The farming in the same AG of epiphytes that do not offer nest spaces suggests that a broadening of the ants' plant host spectrum drove the evolution of additional domatium-bearing AG-epiphytes by selecting on pre-adapted morphological traits. Consistent with this, we found a statistical correlation between the evolution of diaspore dispersal by ants and domatia in all three lineages. Our study highlights how host broadening by a symbiont has led to new farming mutualisms. PMID:28298344

Model of the best-of-N nest-site selection process in honeybees.

PubMed

Reina, Andreagiovanni; Marshall, James A R; Trianni, Vito; Bose, Thomas

2017-05-01

The ability of a honeybee swarm to select the best nest site plays a fundamental role in determining the future colony's fitness. To date, the nest-site selection process has mostly been modeled and theoretically analyzed for the case of binary decisions. However, when the number of alternative nests is larger than two, the decision-process dynamics qualitatively change. In this work, we extend previous analyses of a value-sensitive decision-making mechanism to a decision process among N nests. First, we present the decision-making dynamics in the symmetric case of N equal-quality nests. Then, we generalize our findings to a best-of-N decision scenario with one superior nest and N-1 inferior nests, previously studied empirically in bees and ants. Whereas previous binary models highlighted the crucial role of inhibitory stop-signaling, the key parameter in our new analysis is the relative time invested by swarm members in individual discovery and in signaling behaviors. Our new analysis reveals conflicting pressures on this ratio in symmetric and best-of-N decisions, which could be solved through a time-dependent signaling strategy. Additionally, our analysis suggests how ecological factors determining the density of suitable nest sites may have led to selective pressures for an optimal stable signaling ratio.

Model of the best-of-N nest-site selection process in honeybees

NASA Astrophysics Data System (ADS)

Reina, Andreagiovanni; Marshall, James A. R.; Trianni, Vito; Bose, Thomas

2017-05-01

The ability of a honeybee swarm to select the best nest site plays a fundamental role in determining the future colony's fitness. To date, the nest-site selection process has mostly been modeled and theoretically analyzed for the case of binary decisions. However, when the number of alternative nests is larger than two, the decision-process dynamics qualitatively change. In this work, we extend previous analyses of a value-sensitive decision-making mechanism to a decision process among N nests. First, we present the decision-making dynamics in the symmetric case of N equal-quality nests. Then, we generalize our findings to a best-of-N decision scenario with one superior nest and N -1 inferior nests, previously studied empirically in bees and ants. Whereas previous binary models highlighted the crucial role of inhibitory stop-signaling, the key parameter in our new analysis is the relative time invested by swarm members in individual discovery and in signaling behaviors. Our new analysis reveals conflicting pressures on this ratio in symmetric and best-of-N decisions, which could be solved through a time-dependent signaling strategy. Additionally, our analysis suggests how ecological factors determining the density of suitable nest sites may have led to selective pressures for an optimal stable signaling ratio.

Phylogenetics and biogeography of a spectacular Old World radiation of butterflies: the subtribe Mycalesina (Lepidoptera: Nymphalidae: Satyrini)

PubMed Central

2010-01-01

Background Butterflies of the subtribe Mycalesina (Nymphalidae: Satyrinae) are important model organisms in ecology and evolution. This group has radiated spectacularly in the Old World tropics and presents an exciting opportunity to better understand processes of invertebrate rapid radiations. However, the generic-level taxonomy of the subtribe has been in a constant state of flux, and relationships among genera are unknown. There are six currently recognized genera in the group. Mycalesis, Lohora and Nirvanopsis are found in the Oriental region, the first of which is the most speciose genus among mycalesines, and extends into the Australasian region. Hallelesis and Bicyclus are found in mainland Africa, while Heteropsis is primarily Madagascan, with a few species in Africa. We infer the phylogeny of the group with data from three genes (total of 3139 bp) and use these data to reconstruct events in the biogeographic history of the group. Results The results indicate that the group Mycalesina radiated rapidly around the Oligocene-Miocene boundary. Basal relationships are unresolved, but we recover six well-supported clades. Some species of Mycalesis are nested within a primarily Madagascan clade of Heteropsis, while Nirvanopsis is nested within Lohora. The phylogeny suggests that the group had its origin either in Asia or Africa, and diversified through dispersals between the two regions, during the late Oligocene and early Miocene. The current dataset tentatively suggests that the Madagascan fauna comprises two independent radiations. The Australasian radiation shares a common ancestor derived from Asia. We discuss factors that are likely to have played a key role in the diversification of the group. Conclusions We propose a significantly revised classification scheme for Mycalesina. We conclude that the group originated and radiated from an ancestor that was found either in Asia or Africa, with dispersals between the two regions and to Australasia. Our phylogeny paves the way for further comparative studies on this group that will help us understand the processes underlying diversification in rapid radiations of invertebrates. PMID:20537168

Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat preferences.

PubMed

Söllinger, Andrea; Schwab, Clarissa; Weinmaier, Thomas; Loy, Alexander; Tveit, Alexander T; Schleper, Christa; Urich, Tim

2016-01-01

Methanogenic Thermoplasmata of the novel order Methanomassiliicoccales were recently discovered in human and animal gastro-intestinal tracts (GITs). However, their distribution in other methanogenic environments has not been addressed systematically. Here, we surveyed Methanomassiliicoccales presence in wetland soils, a globally important source of methane emissions to the atmosphere, and in the GITs of different animals by PCR targeting their 16S rRNA and methyl:coenzyme M reductase (α-subunit) genes. We detected Methanomassiliicoccales in all 16 peat soils investigated, indicating their wide distribution in these habitats. Additionally, we detected their genes in various animal faeces. Methanomassiliicoccales were subdivided in two broad phylogenetic clades designated 'environmental' and 'GIT' clades based on differential, although non-exclusive, habitat preferences of their members. A well-supported cluster within the environmental clade comprised more than 80% of all wetland 16S rRNA gene sequences. Metagenome assembly from bovine rumen fluid enrichments resulted in two almost complete genomes of both Methanomassiliicoccales clades. Comparative genomics revealed that members of the environmental clade contain larger genomes and a higher number of genes encoding anti-oxidative enzymes than animal GIT clade representatives. This study highlights the wide distribution of Methanomassiliicoccales in wetlands, which suggests that they contribute to methane emissions from these climate-relevant ecosystems. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Genome rearrangement shapes Prochlorococcus ecological adaptation.

PubMed

Yan, Wei; Wei, Shuzhen; Wang, Qiong; Xiao, Xilin; Zeng, Qinglu; Jiao, Nianzhi; Zhang, Rui

2018-06-18

Prochlorococcus is the most abundant and smallest known free-living photosynthetic microorganism and is a key player in marine ecosystems and biogeochemical cycles. Prochlorococcus can be broadly divided into high-light-adapted (HL) and low-light-adapted (LL) clades. In this study, we isolated two low-light-adapted I (LLI) strains from the western Pacific Ocean and obtained their genomic data. We reconstructed Prochlorococcus evolution based on genome rearrangement. Our results showed that genome rearrangement might have played an important role in Prochlorococcus evolution. We also found that the Prochlorococcus clades with streamlined genomes maintained relatively high synteny throughout most of their genomes, and several regions served as rearrangement hotspots. Backbone analysis showed that different clades shared a conserved backbone but also had clade-specific regions, and the genes in these regions were associated with ecological adaptations. Importance Prochlorococcus , the most abundant and smallest known free-living photosynthetic microorganism, play a key role in marine ecosystems and biogeochemical cycles. The Prochlorococcus genome evolution is a fundamental question related to how Prochlorococcus clades adapted to different ecological niches. Recent studies revealed that the gene gain and loss is crucial to the clade differentiation. The significance of our research is that we interpreted the Prochlorococcus genome evolution from the perspective of genome structure, and associated the genome rearrangement with the Prochlorococcus clade differentiation and subsequent ecological adaptation. Copyright © 2018 Yan et al.

Phylogeographical analysis of a cold-temperate freshwater fish, the Amur sleeper (Perccottus glenii) in the Amur and Liaohe River basins of Northeast Asia.

PubMed

Xu, Wang; Yin, Wei; Chen, Anhui; Li, Jiao; Lei, Guangchun; Fu, Cuizhang

2014-10-01

The Amur sleeper Perccottus glenii (Perciformes, Gobioidei, Odontobutidae) is well known as an invasive fish in the river basins of Eastern and Central Europe, but its genetic background is unavailable across its native habitats in northeast Asia. In this study, we used the mitochondrial cytochrome b gene by sampling 19 populations of P. glenii across its native distributional areas of Liaohe and Amur River basins to explore its evolutionary history. Phylogenetic analyses identified three major clades within P. glenii, among which Clade A and Clade B were co-distributed in the Liaohe and Amur River basins, and Clade C was restricted to the latter. Molecular dating showed that the splits of Clades A, B and C have happened in the late Early-early Middle Pleistocene and the most recent common ancestors of these clades have been presented in the late Middle-early Late Pleistocene. The P. glenii showed very high levels of genetic structure among populations (ΦST = 0.801), probably due to the characters of its life histories with very limited dispersal ability. The admixture of different clades in some populations of P. glenii probably reflects historical secondary contact. These findings indicate that Pleistocene climatic oscillation and river capture were major determinants for genetic variations and evolutionary history of the P. glenii.

Phylogeny, evolutionary trends and classification of the Spathelia–Ptaeroxylon clade: morphological and molecular insights

PubMed Central

Appelhans, M. S.; Smets, E.; Razafimandimbison, S. G.; Haevermans, T.; van Marle, E. J.; Couloux, A.; Rabarison, H.; Randrianarivelojosia, M.; Keßler, P. J. A.

2011-01-01

Background and Aims The Spathelia–Ptaeroxylon clade is a group of morphologically diverse plants that have been classified together as a result of molecular phylogenetic studies. The clade is currently included in Rutaceae and recognized at a subfamilial level (Spathelioideae) despite the fact that most of its genera have traditionally been associated with other families and that there are no obvious morphological synapomorphies for the clade. The aim of the present study is to construct phylogenetic trees for the Spathelia–Ptaeroxylon clade and to investigate anatomical characters in order to decide whether it should be kept in Rutaceae or recognized at the familial level. Anatomical characters were plotted on a cladogram to help explain character evolution within the group. Moreover, phylogenetic relationships and generic limits within the clade are also addressed. Methods A species-level phylogenetic analysis of the Spathelia–Ptaeroxylon clade based on five plastid DNA regions (rbcL, atpB, trnL–trnF, rps16 and psbA–trnH) was conducted using Bayesian, maximum parsimony and maximum likelihood methods. Leaf and seed anatomical characters of all genera were (re)investigated by light and scanning electron microscopy. Key Results With the exception of Spathelia, all genera of the Spathelila–Ptaeroxylon clade are monophyletic. The typical leaf and seed anatomical characters of Rutaceae were found. Further, the presence of oil cells in the leaves provides a possible synapomorphy for the clade. Conclusions The Spathelia–Ptaeroxylon clade is well placed in Rutaceae and it is reasonable to unite the genera into one subfamily (Spathelioideae). We propose a new tribal classification of Spathelioideae. A narrow circumscription of Spathelia is established to make the genus monophyletic, and Sohnreyia is resurrected to accommodate the South American species of Spathelia. The most recent common ancestor of Spathelioideae probably had leaves with secretory cavities and oil cells, haplostemonous flowers with appendaged staminal filaments, and a tracheidal tegmen. PMID:21610209

Phylogeny, evolutionary trends and classification of the Spathelia-Ptaeroxylon clade: morphological and molecular insights.

PubMed

Appelhans, M S; Smets, E; Razafimandimbison, S G; Haevermans, T; van Marle, E J; Couloux, A; Rabarison, H; Randrianarivelojosia, M; Kessler, P J A

2011-06-01

The Spathelia-Ptaeroxylon clade is a group of morphologically diverse plants that have been classified together as a result of molecular phylogenetic studies. The clade is currently included in Rutaceae and recognized at a subfamilial level (Spathelioideae) despite the fact that most of its genera have traditionally been associated with other families and that there are no obvious morphological synapomorphies for the clade. The aim of the present study is to construct phylogenetic trees for the Spathelia-Ptaeroxylon clade and to investigate anatomical characters in order to decide whether it should be kept in Rutaceae or recognized at the familial level. Anatomical characters were plotted on a cladogram to help explain character evolution within the group. Moreover, phylogenetic relationships and generic limits within the clade are also addressed. A species-level phylogenetic analysis of the Spathelia-Ptaeroxylon clade based on five plastid DNA regions (rbcL, atpB, trnL-trnF, rps16 and psbA-trnH) was conducted using Bayesian, maximum parsimony and maximum likelihood methods. Leaf and seed anatomical characters of all genera were (re)investigated by light and scanning electron microscopy. With the exception of Spathelia, all genera of the Spathelila-Ptaeroxylon clade are monophyletic. The typical leaf and seed anatomical characters of Rutaceae were found. Further, the presence of oil cells in the leaves provides a possible synapomorphy for the clade. The Spathelia-Ptaeroxylon clade is well placed in Rutaceae and it is reasonable to unite the genera into one subfamily (Spathelioideae). We propose a new tribal classification of Spathelioideae. A narrow circumscription of Spathelia is established to make the genus monophyletic, and Sohnreyia is resurrected to accommodate the South American species of Spathelia. The most recent common ancestor of Spathelioideae probably had leaves with secretory cavities and oil cells, haplostemonous flowers with appendaged staminal filaments, and a tracheidal tegmen.

Why do leafcutter bees cut leaves? New insights into the early evolution of bees.

PubMed

Litman, Jessica R; Danforth, Bryan N; Eardley, Connal D; Praz, Christophe J

2011-12-07

Stark contrasts in clade species diversity are reported across the tree of life and are especially conspicuous when observed in closely related lineages. The explanation for such disparity has often been attributed to the evolution of key innovations that facilitate colonization of new ecological niches. The factors underlying diversification in bees remain poorly explored. Bees are thought to have originated from apoid wasps during the Mid-Cretaceous, a period that coincides with the appearance of angiosperm eudicot pollen grains in the fossil record. The reliance of bees on angiosperm pollen and their fundamental role as angiosperm pollinators have contributed to the idea that both groups may have undergone simultaneous radiations. We demonstrate that one key innovation--the inclusion of foreign material in nest construction--underlies both a massive range expansion and a significant increase in the rate of diversification within the second largest bee family, Megachilidae. Basal clades within the family are restricted to deserts and exhibit plesiomorphic features rarely observed among modern bees, but prevalent among apoid wasps. Our results suggest that early bees inherited a suite of behavioural traits that acted as powerful evolutionary constraints. While the transition to pollen as a larval food source opened an enormous ecological niche for the early bees, the exploitation of this niche and the subsequent diversification of bees only became possible after bees had evolved adaptations to overcome these constraints.

Construction patterns of birds’ nests provide insight into nest-building behaviours

PubMed Central

Goodman, Adrian M.

2017-01-01

Previous studies have suggested that birds and mammals select materials needed for nest building based on their thermal or structural properties, although the amounts or properties of the materials used have been recorded for only a very small number of species. Some of the behaviours underlying the construction of nests can be indirectly determined by careful deconstruction of the structure and measurement of the biomechanical properties of the materials used. Here we examined this idea in an investigation of Bullfinch (Pyrrhula pyrrhula) nests as a model for open-nesting songbird species that construct a “twig” nest, and tested the hypothesis that materials in different parts of nests serve different functions. The quantities of materials present in the nest base, sides and cup were recorded before structural analysis. Structural analysis showed that the base of the outer nests were composed of significantly thicker, stronger and more rigid materials compared to the side walls, which in turn were significantly thicker, stronger and more rigid than materials used in the cup. These results suggest that the placement of particular materials in nests may not be random, but further work is required to determine if the final structure of a nest accurately reflects the construction process. PMID:28265501

Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity.

PubMed

Krishnan, Arunkumar; Iyer, Lakshminarayan M; Holland, Stephen J; Boehm, Thomas; Aravind, L

2018-04-03

AID/APOBEC deaminases (AADs) convert cytidine to uridine in single-stranded nucleic acids. They are involved in numerous mutagenic processes, including those underpinning vertebrate innate and adaptive immunity. Using a multipronged sequence analysis strategy, we uncover several AADs across metazoa, dictyosteliida, and algae, including multiple previously unreported vertebrate clades, and versions from urochordates, nematodes, echinoderms, arthropods, lophotrochozoans, cnidarians, and porifera. Evolutionary analysis suggests a fundamental division of AADs early in metazoan evolution into secreted deaminases (SNADs) and classical AADs, followed by diversification into several clades driven by rapid-sequence evolution, gene loss, lineage-specific expansions, and lateral transfer to various algae. Most vertebrate AADs, including AID and APOBECs1-3, diversified in the vertebrates, whereas the APOBEC4-like clade has a deeper origin in metazoa. Positional entropy analysis suggests that several AAD clades are diversifying rapidly, especially in the positions predicted to interact with the nucleic acid target motif, and with potential viral inhibitors. Further, several AADs have evolved neomorphic metal-binding inserts, especially within loops predicted to interact with the target nucleic acid. We also observe polymorphisms, driven by alternative splicing, gene loss, and possibly intergenic recombination between paralogs. We propose that biological conflicts of AADs with viruses and genomic retroelements are drivers of rapid AAD evolution, suggesting a widespread presence of mutagenesis-based immune-defense systems. Deaminases like AID represent versions "institutionalized" from the broader array of AADs pitted in such arms races for mutagenesis of self-DNA, and similar recruitment might have independently occurred elsewhere in metazoa. Copyright © 2018 the Author(s). Published by PNAS.

The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes

PubMed Central

Danchin, Etienne G.J.; Perfus-Barbeoch, Laetitia; Rancurel, Corinne; Thorpe, Peter; Da Rocha, Martine; Bajew, Simon; Neilson, Roy; Sokolova (Guzeeva), Elena; Da Silva, Corinne; Guy, Julie; Labadie, Karine; Esmenjaud, Daniel; Helder, Johannes; Jones, John T.

2017-01-01

Nematodes have evolved the ability to parasitize plants on at least four independent occasions, with plant parasites present in Clades 1, 2, 10 and 12 of the phylum. In the case of Clades 10 and 12, horizontal gene transfer of plant cell wall degrading enzymes from bacteria and fungi has been implicated in the evolution of plant parasitism. We have used ribonucleic acid sequencing (RNAseq) to generate reference transcriptomes for two economically important nematode species, Xiphinema index and Longidorus elongatus, representative of two genera within the early-branching Clade 2 of the phylum Nematoda. We used a transcriptome-wide analysis to identify putative horizontal gene transfer events. This represents the first in-depth transcriptome analysis from any plant-parasitic nematode of this clade. For each species, we assembled ~30 million Illumina reads into a reference transcriptome. We identified 62 and 104 transcripts, from X. index and L. elongatus, respectively, that were putatively acquired via horizontal gene transfer. By cross-referencing horizontal gene transfer prediction with a phylum-wide analysis of Pfam domains, we identified Clade 2-specific events. Of these, a GH12 cellulase from X. index was analysed phylogenetically and biochemically, revealing a likely bacterial origin and canonical enzymatic function. Horizontal gene transfer was previously shown to be a phenomenon that has contributed to the evolution of plant parasitism among nematodes. Our findings underline the importance and the extensiveness of this phenomenon in the evolution of plant-parasitic life styles in this speciose and widespread animal phylum. PMID:29065523

The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes.

PubMed

Danchin, Etienne G J; Perfus-Barbeoch, Laetitia; Rancurel, Corinne; Thorpe, Peter; Da Rocha, Martine; Bajew, Simon; Neilson, Roy; Guzeeva, Elena Sokolova; Da Silva, Corinne; Guy, Julie; Labadie, Karine; Esmenjaud, Daniel; Helder, Johannes; Jones, John T; den Akker, Sebastian Eves-van

2017-10-23

Nematodes have evolved the ability to parasitize plants on at least four independent occasions, with plant parasites present in Clades 1, 2, 10 and 12 of the phylum. In the case of Clades 10 and 12, horizontal gene transfer of plant cell wall degrading enzymes from bacteria and fungi has been implicated in the evolution of plant parasitism. We have used ribonucleic acid sequencing (RNAseq) to generate reference transcriptomes for two economically important nematode species, Xiphinema index and Longidorus elongatus , representative of two genera within the early-branching Clade 2 of the phylum Nematoda. We used a transcriptome-wide analysis to identify putative horizontal gene transfer events. This represents the first in-depth transcriptome analysis from any plant-parasitic nematode of this clade. For each species, we assembled ~30 million Illumina reads into a reference transcriptome. We identified 62 and 104 transcripts, from X. index and L. elongatus , respectively, that were putatively acquired via horizontal gene transfer. By cross-referencing horizontal gene transfer prediction with a phylum-wide analysis of Pfam domains, we identified Clade 2-specific events. Of these, a GH12 cellulase from X. index was analysed phylogenetically and biochemically, revealing a likely bacterial origin and canonical enzymatic function. Horizontal gene transfer was previously shown to be a phenomenon that has contributed to the evolution of plant parasitism among nematodes. Our findings underline the importance and the extensiveness of this phenomenon in the evolution of plant-parasitic life styles in this speciose and widespread animal phylum.

The alveolate translation initiation factor 4E family reveals a custom toolkit for translational control in core dinoflagellates.

PubMed

Jones, Grant D; Williams, Ernest P; Place, Allen R; Jagus, Rosemary; Bachvaroff, Tsvetan R

2015-02-10

Dinoflagellates are eukaryotes with unusual cell biology and appear to rely on translational rather than transcriptional control of gene expression. The eukaryotic translation initiation factor 4E (eIF4E) plays an important role in regulating gene expression because eIF4E binding to the mRNA cap is a control point for translation. eIF4E is part of an extended, eukaryote-specific family with different members having specific functions, based on studies of model organisms. Dinoflagellate eIF4E diversity could provide a mechanism for dinoflagellates to regulate gene expression in a post-transcriptional manner. Accordingly, eIF4E family members from eleven core dinoflagellate transcriptomes were surveyed to determine the diversity and phylogeny of the eIF4E family in dinoflagellates and related lineages including apicomplexans, ciliates and heterokonts. The survey uncovered eight to fifteen (on average eleven) different eIF4E family members in each core dinoflagellate species. The eIF4E family members from heterokonts and dinoflagellates segregated into three clades, suggesting at least three eIF4E cognates were present in their common ancestor. However, these three clades are distinct from the three previously described eIF4E classes, reflecting diverse approaches to a central eukaryotic function. Heterokonts contain four clades, ciliates two and apicomplexans only a single recognizable eIF4E clade. In the core dinoflagellates, the three clades were further divided into nine sub-clades based on the phylogenetic analysis and species representation. Six of the sub-clades included at least one member from all eleven core dinoflagellate species, suggesting duplication in their shared ancestor. Conservation within sub-clades varied, suggesting different selection pressures. Phylogenetic analysis of eIF4E in core dinoflagellates revealed complex layering of duplication and conservation when compared to other eukaryotes. Our results suggest that the diverse eIF4E family in core dinoflagellates may provide a toolkit to enable selective translation as a strategy for controlling gene expression in these enigmatic eukaryotes.

Molecular systematics of Serrasalmidae: Deciphering the identities of piranha species and unraveling their evolutionary histories

USGS Publications Warehouse

Freeman, B.; Nico, L.G.; Osentoski, M.; Jelks, H.L.; Collins, T.M.

2007-01-01

Piranhas and their relatives have proven to be a challenging group from a systematic perspective, with difficulties in identification of species, linking of juveniles to adults, diagnosis of genera, and recognition of higher-level clades. In this study we add new molecular data consisting of three mitochondrial regions for museum vouchered and photo-documented representatives of the Serrasalmidae. These are combined with existing serrasalmid sequences in GenBank to address species and higher-level questions within the piranhas using parsimony and Bayesian methods. We found robust support for the monophyly of Serrasalmus manueli, but not for Serrasalmus gouldingi when GenBank specimens identified as S. gouldingi were included in the analysis. "Serrasalmus gouldingi" sequences in GenBank may, however, be misidentified. Linking of juveniles to adults of the same species was greatly facilitated by the addition of sequence data. Based on our sampling and identifications, our data robustly reject the monophyly of the genera Serrasalmus and Pristobrycon. We found evidence for a well-supported clade comprised of Serrasalmus, Pygocentrus, and Pristobrycon (in part). This clade was robustly supported in separate and combined analyses of gene regions, and was also supported by a unique molecular character, the loss of a tandem repeat in the control region. Analysis of specimens and a literature review suggest this clade is also characterized by the presence of a pre-anal spine and ectopterygoid teeth. A persistent polytomy at the base of this clade was dated using an independent calibration as 1.8 million years old, corresponding to the beginning of the Pleistocene Epoch, and suggesting an origin for this clade more recent than dates cited in the recent literature. The sister group to this clade is also robustly supported, and consists of Catoprion, Pygopristis, and Pristobrycon striolatus. If the term piranha is to refer to a monophyletic clade, it should be restricted to Serrasalmus, Pygocentrus, and Pristobrycon (in part), or expanded to include these taxa plus Pygopristis, Catoprion, and Pristobrycon striolatus. Copyright ?? 2007 Magnolia Press.

Clades reach highest morphological disparity early in their evolution

PubMed Central

Hughes, Martin; Gerber, Sylvain; Wills, Matthew Albion

2013-01-01

There are few putative macroevolutionary trends or rules that withstand scrutiny. Here, we test and verify the purported tendency for animal clades to reach their maximum morphological variety relatively early in their evolutionary histories (early high disparity). We present a meta-analysis of 98 metazoan clades radiating throughout the Phanerozoic. The disparity profiles of groups through time are summarized in terms of their center of gravity (CG), with values above and below 0.50 indicating top- and bottom-heaviness, respectively. Clades that terminate at one of the “big five” mass extinction events tend to have truncated trajectories, with a significantly top-heavy CG distribution overall. The remaining 63 clades show the opposite tendency, with a significantly bottom-heavy mean CG (relatively early high disparity). Resampling tests are used to identify groups with a CG significantly above or below 0.50; clades not terminating at a mass extinction are three times more likely to be significantly bottom-heavy than top-heavy. Overall, there is no clear temporal trend in disparity profile shapes from the Cambrian to the Recent, and early high disparity is the predominant pattern throughout the Phanerozoic. Our results do not allow us to distinguish between ecological and developmental explanations for this phenomenon. To the extent that ecology has a role, however, the paucity of bottom-heavy clades radiating in the immediate wake of mass extinctions suggests that early high disparity more probably results from the evolution of key apomorphies at the base of clades rather than from physical drivers or catastrophic ecospace clearing. PMID:23884651

Genetic variation of wheat streak mosaic virus in the United States Pacific Northwest.

PubMed

Robinson, Megan D; Murray, Timothy D

2013-01-01

Wheat streak mosaic virus (WSMV), the cause of wheat streak mosaic, is a widespread and damaging pathogen of wheat. WSMV is not a chronic problem of annual wheat in the United States Pacific Northwest but could negatively affect the establishment of perennial wheat, which is being developed as an alternative to annual wheat to prevent soil erosion. Fifty local isolates of WSMV were collected from 2008 to 2010 near Lewiston, ID, Pullman, WA, and the United States Department of Agriculture Central Ferry Research Station, near Pomeroy, WA to determine the amount of genetic variation present in the region. The coat protein gene from each isolate was sequenced and the data subjected to four different methods of phylogenetic analyses. Two well-supported clades of WSMV were identified. Isolates in clade I share sequence similarity with isolates from Central Europe; this is the first report of isolates from Central Europe being reported in the United States. Isolates in clade II are similar to isolates originating from Australia, Argentina, and the American Pacific Northwest. Nine isolates showed evidence of recombination and the same two well-supported clades were observed when recombinant isolates were omitted from the analysis. More polymorphic sites, parsimony informative sites, and increased diversity were observed in clade II than clade I, suggesting more recent establishment of the virus in the latter. The observed diversity within both clades could make breeding for durable disease resistance in perennial wheat difficult if there is a differential response of WSMV resistance genes to isolates from different clades.

Culture and hybridization experiments on an ulva clade including the Qingdao strain blooming in the yellow sea.

PubMed

Hiraoka, Masanori; Ichihara, Kensuke; Zhu, Wenrong; Ma, Jiahai; Shimada, Satoshi

2011-05-05

In the summer of 2008, immediately prior to the Beijing Olympics, a massive green tide of the genus Ulva covered the Qingdao coast of the Yellow Sea in China. Based on molecular analyses using the nuclear encoded rDNA internal transcribed spacer (ITS) region, the Qingdao strains dominating the green tide were reported to be included in a single phylogenetic clade, currently regarded as a single species. On the other hand, our detailed phylogenetic analyses of the clade, using a higher resolution DNA marker, suggested that two genetically separate entities could be included within the clade. However, speciation within the Ulva clade has not yet been examined. We examined the occurrence of an intricate speciation within the clade, including the Qingdao strains, via combined studies of culture, hybridization and phylogenetic analysis. The two entities separated by our phylogenetic analyses of the clade were simply distinguished as U. linza and U. prolifera morphologically by the absence or presence of branches in cultured thalli. The inclusion of sexual strains and several asexual strains were found in each taxon. Hybridizations among the sexual strains also supported the separation by a partial gamete incompatibility. The sexually reproducing Qingdao strains crossed with U. prolifera without any reproductive boundary, but a complete reproductive isolation to U. linza occurred by gamete incompatibility. The results demonstrate that the U. prolifera group includes two types of sexual strains distinguishable by crossing affinity to U. linza. Species identification within the Ulva clade requires high resolution DNA markers and/or hybridization experiments and is not possible by reliance on the ITS markers alone.

Phylogeography of Australia's king brown snake (Pseudechis australis) reveals Pliocene divergence and Pleistocene dispersal of a top predator.

PubMed

Kuch, Ulrich; Keogh, J Scott; Weigel, John; Smith, Laurie A; Mebs, Dietrich

2005-03-01

King brown snakes or mulga snakes (Pseudechis australis) are the largest and among the most dangerous and wide-ranging venomous snakes in Australia and New Guinea. They occur in diverse habitats, are important predators, and exhibit considerable morphological variation. We infer the relationships and historical biogeography of P. australis based on phylogenetic analysis of 1,249 base pairs from the mitochondrial cytochrome b, NADH dehydrogenase subunit 4 and three adjacent tRNA genes using Bayesian, maximum-likelihood, and maximum-parsimony methods. All methods reveal deep phylogenetic structure with four strongly supported clades comprising snakes from New Guinea (I), localities all over Australia (II), the Kimberleys of Western Australia (III), and north-central Australia (IV), suggesting a much more ancient radiation than previously believed. This conclusion is robust to different molecular clock estimations indicating divergence in Pliocene or Late Miocene, after landbridge dispersal to New Guinea had occurred. While members of clades I, III and IV are medium-sized, slender snakes, those of clade II attain large sizes and a robust build, rendering them top predators in their ecosystems. Genetic differentiation within clade II is low and haplotype distribution largely incongruent with geography or colour morphs, suggesting Pleistocene dispersal and recent ecomorph evolution. Significant haplotype diversity exists in clades III and IV, implying that clade IV comprises two species. Members of clade II are broadly sympatric with members of both northern Australian clades. Thus, our data support the recognition of at least five species from within P. australis (auct.) under various criteria. We discuss biogeographical, ecological and medical implications of our findings.

Phylogeography of Australia's king brown snake (Pseudechis australis) reveals Pliocene divergence and Pleistocene dispersal of a top predator

NASA Astrophysics Data System (ADS)

Kuch, Ulrich; Keogh, J. Scott; Weigel, John; Smith, Laurie A.; Mebs, Dietrich

2005-03-01

King brown snakes or mulga snakes (Pseudechis australis) are the largest and among the most dangerous and wide-ranging venomous snakes in Australia and New Guinea. They occur in diverse habitats, are important predators, and exhibit considerable morphological variation. We infer the relationships and historical biogeography of P. australis based on phylogenetic analysis of 1,249 base pairs from the mitochondrial cytochrome b, NADH dehydrogenase subunit 4 and three adjacent tRNA genes using Bayesian, maximum-likelihood, and maximum-parsimony methods. All methods reveal deep phylogenetic structure with four strongly supported clades comprising snakes from New Guinea (I), localities all over Australia (II), the Kimberleys of Western Australia (III), and north-central Australia (IV), suggesting a much more ancient radiation than previously believed. This conclusion is robust to different molecular clock estimations indicating divergence in Pliocene or Late Miocene, after landbridge dispersal to New Guinea had occurred. While members of clades I, III and IV are medium-sized, slender snakes, those of clade II attain large sizes and a robust build, rendering them top predators in their ecosystems. Genetic differentiation within clade II is low and haplotype distribution largely incongruent with geography or colour morphs, suggesting Pleistocene dispersal and recent ecomorph evolution. Significant haplotype diversity exists in clades III and IV, implying that clade IV comprises two species. Members of clade II are broadly sympatric with members of both northern Australian clades. Thus, our data support the recognition of at least five species from within P. australis (auct.) under various criteria. We discuss biogeographical, ecological and medical implications of our findings.

A Single Early Introduction of HIV-1 Subtype B into Central America Accounts for Most Current Cases

PubMed Central

Murillo, Wendy; Veras, Nazle; Prosperi, Mattia; de Rivera, Ivette Lorenzana; Paz-Bailey, Gabriela; Morales-Miranda, Sonia; Juarez, Sandra I.; Yang, Chunfu; DeVos, Joshua; Marín, José Pablo; Mild, Mattias; Albert, Jan

2013-01-01

Human immunodeficiency virus type 1 (HIV-1) variants show considerable geographical separation across the world, but there is limited information from Central America. We provide the first detailed investigation of the genetic diversity and molecular epidemiology of HIV-1 in six Central American countries. Phylogenetic analysis was performed on 625 HIV-1 pol gene sequences collected between 2002 and 2010 in Honduras, El Salvador, Nicaragua, Costa Rica, Panama, and Belize. Published sequences from neighboring countries (n = 57) and the rest of the world (n = 740) were included as controls. Maximum likelihood methods were used to explore phylogenetic relationships. Bayesian coalescence-based methods were used to time HIV-1 introductions. Nearly all (98.9%) Central American sequences were of subtype B. Phylogenetic analysis revealed that 437 (70%) sequences clustered within five significantly supported monophyletic clades formed essentially by Central American sequences. One clade contained 386 (62%) sequences from all six countries; the other four clades were smaller and more country specific, suggesting discrete subepidemics. The existence of one large well-supported Central American clade provides evidence that a single introduction of HIV-1 subtype B in Central America accounts for most current cases. An introduction during the early phase of the HIV-1 pandemic may explain its epidemiological success. Moreover, the smaller clades suggest a subsequent regional spread related to specific transmission networks within each country. PMID:23616665

Redescription and molecular diagnosis of Hepatozoon theileri (Laveran, 1905) (Apicomplexa: Adeleorina: Hepatozoidae), infecting Amietia quecketti (Anura: Pyxicephalidae).

PubMed

Netherlands, Edward C; Cook, Courtney A; Smit, Nico J; du Preez, Louis H

2014-08-01

Blood smears prepared from the peripheral blood of 20 wild caught Amietia quecketti (Boulenger) from the North-West University Botanical Gardens, North West Province, South Africa, were examined for the presence of haemogregarines. A haemogregarine species comparative in morphology, host and geographical locality to that of Haemogregarina theileri Laveran, 1905 was detected. The original description of H. theileri was based solely on frog peripheral blood gamont stages. Later, further parasite stages, including trophozoites and merogonic liver stages, were recorded in a related Amietia sp. from equatorial Africa. This species was originally classified as a member of the genus Haemogregarina Danilewsky, 1885, but due to the close life cycle and morphological resemblance to those of Hepatozoon species, H. theileri was later transferred from Haemogregarina to Hepatozoon Miller, 1908. In the present study, meront and merozoite stages not described before, along with previously observed trophozoite, immature and mature gamont stages, are described from the peripheral blood of hosts. In addition, comparative phylogenetic analysis of the partial 18S rDNA sequence of Hepatozoon theileri to those of other haemogregarine species, including those of species of Hepatozoon and a Haemogregarina, support the taxonomic transfer of H. theileri to Hepatozoon, nesting H. theileri within a clade comprising species parasitising other amphibians. This is the first molecular and phylogenetic analysis of an African anuran species of Hepatozoon.

Molecular phylogenetic, morphological, and mycotoxin data support reidentification of the Quorn mycoprotein fungus as Fusarium venenatum.

PubMed

O'Donnell, K; Cigelnik, E; Casper, H H

1998-02-01

Molecular phylogenetic, morphological, and mycotoxin data were obtained in order to investigate the relationships and identity of the Quorn mycoprotein fungus within Fusarium and to examine Quorn strains and commercial Quorn food products for trichothecene mycotoxins. Phylogenetic analyses of aligned DNA sequences obtained via the polymerase chain reaction from the nuclear 28S ribosomal DNA, nuclear ribosomal internal transcribed spacer region, and beta-tubulin gene exons and introns indicate that the Quorn fungus is Fusarium venenatum, rather than F. graminearum as previously reported. All of the Quorn strains examined were morphologically degenerate aconidial colonial mutants except for NRRL 25139, which produced chlamydospores in recurved terminal chains together with mostly 5-septate sporodochial conidia on doliform monophialides diagnostic of F. venenatum. Bootstrap and decay analyses provide strong support for a monophyletic lineage containing F. venenatum and several other type A trichothecene-producing species, while reference strains of F. graminearum were nested in a separate clade of species that produce type B trichothecenes and/or zearalenone. Analysis of mycotoxins from rice cultures inoculated with Quorn strain NRRL 25416 revealed that four type A trichothecenes are produced, but at low levels relative to strain NRRL 22198 of F. venenatum. No trichothecene mycotoxins, however, were detected from the analysis of three commercial Quorn products marketed for human consumption in England.

Using survival analysis of artificial and Real Brewer's sparrow (Spizella breweri breweri) nests to model site level and nest site factors associated with nest success in the South Okanagan region of Canada

Treesearch

Pam Krannitz Kym Welstead

2005-01-01

Predation is the predominant cause of nest failure for the Brewer's Sparrow (Spizella breweri breweri), a provincially red-listed shrub-steppe species that has experienced significant declines throughout most of its range. We monitored Brewer’s Sparrow nests and conducted an artificial nest experiment, in the South Okanagan Valley,...

Effects of industrial and investigator disturbance on Arctic-nesting geese

USGS Publications Warehouse

Meixell, Brandt W.; Flint, Paul L.

2017-01-01

Oil and gas development on the Arctic Coastal Plain (ACP) of Alaska, USA may have effects on Arctic-nesting birds. To estimate effects of industrial activity and investigator disturbance on avian productivity, we monitored nests of greater white-fronted geese (Anser albifrons) with digital cameras and periodic nest visits during 2013–2014 at 2 sites on the ACP. A disturbed site was adjacent to human-made infrastructure and industrial clean-up activities initiated at the onset of the study and a control site was >2 km from sources of industrial disturbance. We assessed variation in estimates of incubation constancy, nest survival, and predator behavior relative to site, year, and distance from industrial activity using nest photographs obtained at 1-minute intervals. We compared analysis of hourly nest survival informed by intensive monitoring with cameras to analysis of daily nest survival informed by traditional nest visit data obtained at intervals of 5–7 days to assess how method and time scale of sampling affect ecological inference. Geese in both sites exhibited high levels of nest attendance and initiated incubation breaks less than once per day. Observer-caused incubation breaks associated with nest visits ( = 37.8 min) were longer than other types of incubation breaks ( = 8.7 min), demonstrating a differential response by nesting geese to direct human encroachment versus indirect vehicular and aircraft traffic. During both years, geese were absent from nests more frequently in the disturbed ( = 0.9 breaks/day) than control ( = 0.6 breaks/day) site, and this break frequency was slightly higher for nests closer to industrial activity. In the year with high rates of depredation, nest survival was positively related to distance from industrial activity and abandoned infrastructure, consistent with predictions of industry-caused effects. This relationship, however, was not evident in the year with reduced predation pressure, likely because of annual variation in arctic fox (Vulpes lagopus) behavior. Analysis of nest survival probability informed by camera data allowed for detection of detailed patterns of variation that were not supported when using only visit data for the same nests. Observer visits were responsible for reductions of 7–35% in nest survival probability, highlighting the importance of minimizing, and controlling for, observer effects in studies of avian productivity. Indirect vehicular and aircraft disturbance posed less risk to nest survival than direct encroachment by observers at nest sites. Therefore, effects of industrial activities on avian productivity in the Arctic can be minimized through practices that limit direct encounters with nests. 

A phylogeny of Cichlidogyrus spp. (Monogenea, Dactylogyridea) clarifies a host-switch between fish families and reveals an adaptive component to attachment organ morphology of this parasite genus.

PubMed

Messu Mandeng, Françoise D; Bilong Bilong, Charles F; Pariselle, Antoine; Vanhove, Maarten P M; Bitja Nyom, Arnold R; Agnèse, Jean-François

2015-11-10

Parasite switches to new host species are of fundamental scientific interest and may be considered an important speciation mechanism. For numerous monogenean fish parasites, infecting different hosts is associated with morphological adaptations, in particular of the attachment organ (haptor). However, haptoral morphology in Cichlidogyrus spp. (Monogenea, Dactylogyridea), parasites of African cichlids, has been mainly linked to phylogenetic rather than to host constraints. Here we determined the position of Cichlidogyrus amieti, a parasite of species of Aphyosemion (Cyprinodontiformes, Nothobranchiidae) in the phylogeny of its congeners in order to infer its origin and assess the morphological changes associated with host-switching events. The DNA of specimens of C. amieti isolated from Aphyosemion cameronense in Cameroon was sequenced and analyzed together with that of Cichlidogyrus spp. from cichlid hosts. In order to highlight the influence of the lateral transfer of C. amieti on the haptoral sclerotised parts we performed a Principal Component Analysis (PCA) to compare the attachment organ structure of C. amieti to that of congeners infecting cichlids. Cichlidogyrus amieti was found to be nested within a strongly supported clade of species described from Hemichromis spp. (i.e. C. longicirrus and C. dracolemma). This clade is located at a derived position of the tree, suggesting that C. amieti transferred from cichlids to Cyprinodontiformes and not inversely. The morphological similarity between features of their copulatory organs suggested that C. amieti shares a recent ancestor with C. dracolemma. It also indicates that in this case, these organs do not seem subjected to strong divergent selection pressure. On the other hand, there are substantial differences in haptoral morphology between C. amieti and all of its closely related congeners described from Hemichromis spp.. Our study provides new evidence supporting the hypothesis of the adaptive nature of haptor morphology. It demonstrates this adaptive component for the first time within Cichlidogyrus, the attachment organs of which were usually considered to be mainly phylogenetically constrained.

Flightless Notaris (Coleoptera: Curculionidae: Brachycerinae: Erirhinini) in Southwest China: monophyly, mtDNA phylogeography and evolution of habitat associations.

PubMed

Grebennikov, Vasily V; Kolov, Sergey V

2016-04-26

This paper reports the recent discovery of flightless populations of weevils of the genus Notaris in Yunnan and Sichuan provinces of China. Specimens were found in the middle or high altitude mountains (2440-4195 m), by either sifting leaf litter in the deciduous forest and among alpine Rhododendron shrubs, or by turning rocks in the alpine zone. These finds extend southwards the Asian range of this Holarctic genus and report its highest altitudinal records. DNA barcodes of 127 specimens were phylogenetically analysed, of them 42 are those of newly discovered Notaris from Southwest China. The genera Notaris and Tournotaris consistently formed a clade, with Tournotaris nested inside Notaris in Maximum Parsimony (MP) and Maximum Likelihood (ML) analysis. The newly discovered flightless Notaris from Southwest China were either monophyletic (MP) or paraphyletic with respect to volant Holarctic N. aethiops (ML); the latter placement being likely an artefact. A strict linear molecular clock approach suggests a pre-Pliocene separation of Notaris populations in Southwest China. Habitat associations of these high-altitude flightless Notaris contrast sharply with that of the predominantly volant lowland riparian Notaris and other Erirhinini. We hypothesis that evolution of habitat selection in Notaris went from lowland riparian, to high altitude (via uplift of the Tibetan Plateau and adjacent regions of Central Asia), and then to forest leaf litter (via subsequent erosions of isolated mountains such as Emei Shan in Sichuan losing the alpine zone and forcing Notaris into the forest floor). Taxonomic uncertainty of Asian Notaris is addressed and remains unresolved due to uninformative morphology and conflicting DNA signal. Identities of two obscure and likely closely related species, Notaroides brevirostris and Notaris kozlovi from nearby SE Qinghai and NW Sichuan, respectively, are discussed and illustrated. Pending further research, all reported flightless Notaris from Yunnan and Sichuan are hypothesised to form a clade, for which the available name N. kozlovi is used. Habitus and genitalia of Notaris specimens from the newly detected populations are illustrated.

Multilevel Dynamic Generalized Structured Component Analysis for Brain Connectivity Analysis in Functional Neuroimaging Data.

PubMed

Jung, Kwanghee; Takane, Yoshio; Hwang, Heungsun; Woodward, Todd S

2016-06-01

We extend dynamic generalized structured component analysis (GSCA) to enhance its data-analytic capability in structural equation modeling of multi-subject time series data. Time series data of multiple subjects are typically hierarchically structured, where time points are nested within subjects who are in turn nested within a group. The proposed approach, named multilevel dynamic GSCA, accommodates the nested structure in time series data. Explicitly taking the nested structure into account, the proposed method allows investigating subject-wise variability of the loadings and path coefficients by looking at the variance estimates of the corresponding random effects, as well as fixed loadings between observed and latent variables and fixed path coefficients between latent variables. We demonstrate the effectiveness of the proposed approach by applying the method to the multi-subject functional neuroimaging data for brain connectivity analysis, where time series data-level measurements are nested within subjects.

Human papillomavirus detection and typing using a nested-PCR-RFLP assay.

PubMed

Coser, Janaina; Boeira, Thaís da Rocha; Fonseca, André Salvador Kazantzi; Ikuta, Nilo; Lunge, Vagner Ricardo

2011-01-01

It is clinically important to detect and type human papillomavirus (HPV) in a sensitive and specific manner. Development of a nested-polymerase chain reaction-restriction fragment length polymorphism (nested-PCR-RFLP) assay to detect and type HPV based on the analysis of L1 gene. Analysis of published DNA sequence of mucosal HPV types to select sequences of new primers. Design of an original nested-PCR assay using the new primers pair selected and classical MY09/11 primers. HPV detection and typing in cervical samples using the nested-PCR-RFLP assay. The nested-PCR-RFLP assay detected and typed HPV in cervical samples. Of the total of 128 clinical samples submitted to simple PCR and nested-PCR for detection of HPV, 37 (28.9%) were positive for the virus by both methods and 25 samples were positive only by nested-PCR (67.5% increase in detection rate compared with single PCR). All HPV positive samples were effectively typed by RFLP assay. The method of nested-PCR proved to be an effective diagnostic tool for HPV detection and typing.

Language Nests and Language Acquisition: An Empirical Analysis

ERIC Educational Resources Information Center

Okura, Eve K.

2017-01-01

This dissertation presents the findings from interviews conducted with language nest workers, teachers, language nest coordinators, administrators of language revitalization programs, principals and directors of language immersion schools that work in close proximity with language nests, and linguists involved in language revitalization efforts.…

Pitfalls in applying mitochondrial markers onto the scolytid species Pityogenes chalcographus

Treesearch

Wolfgang Arthofer; Dimitrios N. Avtzis; Markus Riegler; Wolfgang J. Miller; Christian Stauffer

2007-01-01

Pityogenes chalcographus is one of the major pests in Eurasian spruce stands. Crossing experiments performed in the mid-1970s suggested race differentiation, and mtDNA analysis of P. chalcographus gave evidence that today’s populations are divided into several clades. The genetic distance between clades favours a model of...

Nested Neural Networks

NASA Technical Reports Server (NTRS)

Baram, Yoram

1992-01-01

Report presents analysis of nested neural networks, consisting of interconnected subnetworks. Analysis based on simplified mathematical models more appropriate for artificial electronic neural networks, partly applicable to biological neural networks. Nested structure allows for retrieval of individual subpatterns. Requires fewer wires and connection devices than fully connected networks, and allows for local reconstruction of damaged subnetworks without rewiring entire network.

Protein evolution in two co-occurring types of Symbiodinium: an exploration into the genetic basis of thermal tolerance in Symbiodinium clade D

PubMed Central

2012-01-01

Background The symbiosis between reef-building corals and photosynthetic dinoflagellates (Symbiodinium) is an integral part of the coral reef ecosystem, as corals are dependent on Symbiodinium for the majority of their energy needs. However, this partnership is increasingly at risk due to changing climatic conditions. It is thought that functional diversity within Symbiodinium may allow some corals to rapidly adapt to different environments by changing the type of Symbiodinium with which they partner; however, very little is known about the molecular basis of the functional differences among symbiont groups. One group of Symbiodinium that is hypothesized to be important for the future of reefs is clade D, which, in general, seems to provide the coral holobiont (i.e., coral host and associated symbiont community) with elevated thermal tolerance. Using high-throughput sequencing data from field-collected corals we assembled, de novo, draft transcriptomes for Symbiodinium clades C and D. We then explore the functional basis of thermal tolerance in clade D by comparing rates of coding sequence evolution among the four clades of Symbiodinium most commonly found in reef-building corals (A-D). Results We are able to highlight a number of genes and functional categories as candidates for involvement in the increased thermal tolerance of clade D. These include a fatty acid desaturase, molecular chaperones and proteins involved in photosynthesis and the thylakoid membrane. We also demonstrate that clades C and D co-occur within most of the sampled colonies of Acropora hyacinthus, suggesting widespread potential for this coral species to acclimatize to changing thermal conditions via ‘shuffling’ the proportions of these two clades from within their current symbiont communities. Conclusions Transcriptome-wide analysis confirms that the four main Symbiodinium clades found within corals exhibit extensive evolutionary divergence (18.5-27.3% avg. pairwise nucleotide difference). Despite these evolutionary distinctions, many corals appear to host multiple clades simultaneously, which may allow for rapid acclimatization to changing environmental conditions. This study provides a first step toward understanding the molecular basis of functional differences between Symbiodinium clades by highlighting a number of genes with signatures consistent with positive selection along the thermally tolerant clade D lineage. PMID:23145489

Toward a comprehensive phylogenetic reconstruction of the evolutionary history of mitogen-activated protein kinases in the plant kingdom.

PubMed

Janitza, Philipp; Ullrich, Kristian Karsten; Quint, Marcel

2012-01-01

The mitogen-activated protein kinase (MAPK) pathway is a three-tier signaling cascade that transmits cellular information from the plasma membrane to the cytoplasm where it triggers downstream responses. The MAPKs represent the last step in this cascade and are activated when both tyrosine and threonine residues in a conserved TxY motif are phosphorylated by MAPK kinases, which in turn are themselves activated by phosphorylation by MAPK kinase kinases. To understand the molecular evolution of MAPKs in the plant kingdom, we systematically conducted a Hidden-Markov-Model based screen to identify MAPKs in 13 completely sequenced plant genomes. In this analysis, we included green algae, bryophytes, lycophytes, and several mono- and eudicotyledonous species covering >800 million years of evolution. The phylogenetic relationships of the 204 identified MAPKs based on Bayesian inference facilitated the retraction of the sequence of emergence of the four major clades that are characterized by the presence of a TDY or TEY-A/TEY-B/TEY-C type kinase activation loop. We present evidence that after the split of TDY- and TEY-type MAPKs, initially the TEY-C clade emerged. This was followed by the TEY-B clade in early land plants until the TEY-A clade finally emerged in flowering plants. In addition to these well characterized clades, we identified another highly conserved clade of 45 MAPK-likes, members of which were previously described as Mak-homologous kinases. In agreement with their essential functions, molecular population genetic analysis of MAPK genes in Arabidopsis thaliana accessions reveal that purifying selection drove the evolution of the MAPK family, implying strong functional constraints on MAPK genes. Closely related MAPKs most likely subfunctionalized, a process in which differential transcriptional regulation of duplicates may be involved.

Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics.

PubMed

Flury, Pascale; Aellen, Nora; Ruffner, Beat; Péchy-Tarr, Maria; Fataar, Shakira; Metla, Zane; Dominguez-Ferreras, Ana; Bloemberg, Guido; Frey, Joachim; Goesmann, Alexander; Raaijmakers, Jos M; Duffy, Brion; Höfte, Monica; Blom, Jochen; Smits, Theo H M; Keel, Christoph; Maurhofer, Monika

2016-10-01

Bacteria of the genus Pseudomonas occupy diverse environments. The Pseudomonas fluorescens group is particularly well-known for its plant-beneficial properties including pathogen suppression. Recent observations that some strains of this group also cause lethal infections in insect larvae, however, point to a more versatile ecology of these bacteria. We show that 26 P. fluorescens group strains, isolated from three continents and covering three phylogenetically distinct sub-clades, exhibited different activities toward lepidopteran larvae, ranging from lethal to avirulent. All strains of sub-clade 1, which includes Pseudomonas chlororaphis and Pseudomonas protegens, were highly insecticidal regardless of their origin (animals, plants). Comparative genomics revealed that strains in this sub-clade possess specific traits allowing a switch between plant- and insect-associated lifestyles. We identified 90 genes unique to all highly insecticidal strains (sub-clade 1) and 117 genes common to all strains of sub-clade 1 and present in some moderately insecticidal strains of sub-clade 3. Mutational analysis of selected genes revealed the importance of chitinase C and phospholipase C in insect pathogenicity. The study provides insight into the genetic basis and phylogenetic distribution of traits defining insecticidal activity in plant-beneficial pseudomonads. Strains with potent dual activity against plant pathogens and herbivorous insects have great potential for use in integrated pest management for crops.

Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics

PubMed Central

Flury, Pascale; Aellen, Nora; Ruffner, Beat; Péchy-Tarr, Maria; Fataar, Shakira; Metla, Zane; Dominguez-Ferreras, Ana; Bloemberg, Guido; Frey, Joachim; Goesmann, Alexander; Raaijmakers, Jos M; Duffy, Brion; Höfte, Monica; Blom, Jochen; Smits, Theo H M; Keel, Christoph; Maurhofer, Monika

2016-01-01

Bacteria of the genus Pseudomonas occupy diverse environments. The Pseudomonas fluorescens group is particularly well-known for its plant-beneficial properties including pathogen suppression. Recent observations that some strains of this group also cause lethal infections in insect larvae, however, point to a more versatile ecology of these bacteria. We show that 26 P. fluorescens group strains, isolated from three continents and covering three phylogenetically distinct sub-clades, exhibited different activities toward lepidopteran larvae, ranging from lethal to avirulent. All strains of sub-clade 1, which includes Pseudomonas chlororaphis and Pseudomonas protegens, were highly insecticidal regardless of their origin (animals, plants). Comparative genomics revealed that strains in this sub-clade possess specific traits allowing a switch between plant- and insect-associated lifestyles. We identified 90 genes unique to all highly insecticidal strains (sub-clade 1) and 117 genes common to all strains of sub-clade 1 and present in some moderately insecticidal strains of sub-clade 3. Mutational analysis of selected genes revealed the importance of chitinase C and phospholipase C in insect pathogenicity. The study provides insight into the genetic basis and phylogenetic distribution of traits defining insecticidal activity in plant-beneficial pseudomonads. Strains with potent dual activity against plant pathogens and herbivorous insects have great potential for use in integrated pest management for crops. PMID:26894448

Congopain genes diverged to become specific to Savannah, Forest and Kilifi subgroups of Trypanosoma congolense, and are valuable for diagnosis, genotyping and phylogenetic inferences.

PubMed

Rodrigues, Adriana C; Ortiz, Paola A; Costa-Martins, André G; Neves, Luis; Garcia, Herakles A; Alves, João M P; Camargo, Erney P; Alfieri, Silvia C; Gibson, Wendy; Teixeira, Marta M G

2014-04-01

Trypanosoma congolense is the most important agent of nagana, a wasting livestock trypanosomosis in sub-Saharan Africa. This species is a complex of three subgroups (Savannah, Forest and Kilifi) that differ in virulence, pathogenicity, drug resistance, vectors, and geographical distribution. Congopain, the major Cathepsin L-like cysteine protease (CP2) of T. congolense, has been extensively investigated as a pathogenic factor and target for drugs and vaccines, but knowledge about this enzyme is mostly restricted to the reference strain IL3000, which belongs to the Savannah subgroup. In this work we compared sequences of congopain genes from IL3000 genome database and isolates of the three subgroups of T. congolense. Results demonstrated that the congopain genes diverged into three subclades consistent with the three subgroups within T. congolense. Laboratory and field isolates of Savannah exhibited a highly polymorphic repertoire both inter- and intra-isolates: sequences sharing the archetypical catalytic triad clustered into SAV1-SAV3 groups, whereas polymorphic sequences that, in general, exhibited unusual catalytic triad (variants) assigned to SAV4 or not assigned to any group. Congopain homologous genes from Forest and Kilifi isolates showed, respectively, moderate and limited diversity. In the phylogenetic tree based on congopain and homologues, Savannah was closer to Forest than to Kilifi. All T. congolense subgroup nested into a single clade, which together with the sister clade formed by homologues from Trypanosoma simiae and Trypanosoma godfreyi formed a clade supporting the subgenus Nannomonas. A single PCR targeting congopain sequences was developed for the diagnosis of T. congolense isolates of the three subgroups. Our findings demonstrated that congopain genes are valuable targets for the diagnosis, genotyping, and phylogenetic and taxonomic inferences among T. congolense isolates and other members of the subgenus Nannomonas. Copyright © 2014 Elsevier B.V. All rights reserved.

Impact of the terrestrial-aquatic transition on disparity and rates of evolution in the carnivoran skull.

PubMed

Jones, Katrina E; Smaers, Jeroen B; Goswami, Anjali

2015-02-04

Which factors influence the distribution patterns of morphological diversity among clades? The adaptive radiation model predicts that a clade entering new ecological niche will experience high rates of evolution early in its history, followed by a gradual slowing. Here we measure disparity and rates of evolution in Carnivora, specifically focusing on the terrestrial-aquatic transition in Pinnipedia. We analyze fissiped (mostly terrestrial, arboreal, and semi-arboreal, but also including the semi-aquatic otter) and pinniped (secondarily aquatic) carnivorans as a case study of an extreme ecological transition. We used 3D geometric morphometrics to quantify cranial shape in 151 carnivoran specimens (64 fissiped, 87 pinniped) and five exceptionally-preserved fossil pinnipeds, including the stem-pinniped Enaliarctos emlongi. Range-based and variance-based disparity measures were compared between pinnipeds and fissipeds. To distinguish between evolutionary modes, a Brownian motion model was compared to selective regime shifts associated with the terrestrial-aquatic transition and at the base of Pinnipedia. Further, evolutionary patterns were estimated on individual branches using both Ornstein-Uhlenbeck and Independent Evolution models, to examine the origin of pinniped diversity. Pinnipeds exhibit greater cranial disparity than fissipeds, even though they are less taxonomically diverse and, as a clade nested within fissipeds, phylogenetically younger. Despite this, there is no increase in the rate of morphological evolution at the base of Pinnipedia, as would be predicted by an adaptive radiation model, and a Brownian motion model of evolution is supported. Instead basal pinnipeds populated new areas of morphospace via low to moderate rates of evolution in new directions, followed by later bursts within the crown-group, potentially associated with ecological diversification within the marine realm. The transition to an aquatic habitat in carnivorans resulted in a shift in cranial morphology without an increase in rate in the stem lineage, contra to the adaptive radiation model. Instead these data suggest a release from evolutionary constraint model, followed by aquatic diversifications within crown families.

Genetic and Pathogenic Variability of Fusarium oxysporum f. sp. cepae Isolated from Onion and Welsh Onion in Japan.

PubMed

Sasaki, Kazunori; Nakahara, Katsuya; Tanaka, Shuhei; Shigyo, Masayoshi; Ito, Shin-ichi

2015-04-01

Fusarium oxysporum f. sp. cepae causes Fusarium basal rot in onion (common onion) and Fusarium wilt in Welsh onion. Although these diseases have been detected in various areas in Japan, knowledge about the genetic and pathogenic variability of F. oxysporum f. sp. cepae is very limited. In this study, F. oxysporum f. sp. cepae was isolated from onion and Welsh onion grown in 12 locations in Japan, and a total of 55 F. oxysporum f. sp. cepae isolates (27 from onion and 28 from Welsh onion) were characterized based on their rDNA intergenic spacer (IGS) and translation elongation factor-1α (EF-1α) nucleotide sequences, vegetative compatibility groups (VCGs), and the presence of the SIX (secreted in xylem) homologs. Phylogenetic analysis of IGS sequences showed that these isolates were grouped into eight clades (A to H), and 20 onion isolates belonging to clade H were monophyletic and assigned to the same VCG. All the IGS-clade H isolates possessed homologs of SIX3, SIX5, and SIX7. The SIX3 homolog was located on a 4 Mb-sized chromosome in the IGS-clade H isolates. Pathogenicity tests using onion seedlings showed that all the isolates with high virulence were in the IGS-clade H. These results suggest that F. oxysporum f. sp. cepae isolates belonging to the IGS-clade H are genetically and pathogenically different from those belonging to the other IGS clades.

Diversification and biogeography of the Neotropical caviomorph lineage Octodontoidea (Rodentia: Hystricognathi).

PubMed

Upham, Nathan S; Patterson, Bruce D

2012-05-01

The rodent superfamily Octodontoidea comprises 6 families, 38 genera, and 193 living species of spiny rats, tuco-tucos, degus, hutias, and their relatives. All are endemic to the Neotropical Region where they represent roughly three-quarters of extant caviomorphs. Although caviomorph monophyly is well established and phylogenetic hypotheses exist for several families, understanding of octodontoid relationships is clouded by sparse taxon sampling and single-gene analyses. We examined sequence variation in one mitochondrial (12S rRNA) and three nuclear genes (vWF, GHR, and RAG1) across all caviomorph families (including 47 octodontoid species), all phiomorph families, and the sole remaining hystricognath family, using the gundi (Ctenodactylus) and springhaas (Pedetes) as outgroups. Our analyses support the monophyly of Phiomorpha, Caviomorpha, and the caviomorph superfamilies Cavioidea (Dasyproctidae, Cuniculidae, and Caviidae, the latter including Hydrochoerus), Erethizontoidea, Chinchilloidea (including Dinomyidae), and Octodontoidea. Cavioids and erethizontoids are strongly supported as sisters, whereas chinchilloids appear to be sister to octodontoids. Among octodontoids, Abrocomidae is consistently recovered as the basal element, sister to a pair of strongly supported clades; one includes Octodontidae and Ctenomyidae as reciprocally monophyletic lineages, whereas the other includes taxa currently allocated to Echimyidae, Capromyidae and Myocastoridae. Capromys appears near the base of this clade, in keeping with current classification, but Myocastor is nested securely inside a clade of Echimyidae that also contains eumysopines, echimyines and dactylomyines. Another, more weakly supported clade of Echimyidae contains fossorial and scansorial taxa from the Chaco-Cerrado-Caatinga and the Atlantic Forest. Biogeographic analyses robustly recover the Patagonia-Southern Andes complex as ancestral for the Octodontoidea, with three component lineages emerging by the Oligocene-Miocene boundary (∼23Ma): (1) stem abrocomids in the Central and Southern Andes; (2) a lineage leading to octodontids plus ctenomyids in Patagonia, later dispersing into the Chaco-Cerrado-Caatinga; and (3) a lineage leading to echimyids, capromyids, and myocastorids that subsequently radiated in more mesic biomes, including Amazonia, Atlantic Forest, and the Antilles. This reconstruction refutes earlier ideas that the diverse, generalized, mainly lowland family Echimyidae, which appears early in the fossil record, gave rise to the Andean lineages of octodontoids-instead, the reverse derivation appears to be true. We recommend formal synonymy of Myocastoridae with Echimyidae but defer a similar treatment of Capromyidae until additional hutia taxa and sequences can be analyzed. Copyright © 2012 Elsevier Inc. All rights reserved.

A multiscale analysis of nest predation on Least Bell's Vireos (Vireo bellii pusillus)

USGS Publications Warehouse

Kus, Barbara E.; Peterson, Bonnie L.; Deutschman, Douglas H.

2008-01-01

We examined variables influencing nest predation on the endangered Least Bell's Vireo (Vireo bellii pusillus) at three spatial scales to determine what nest-site, habitat, or landscape characteristics affect the likelihood of nest predation and to determine the spatial distribution of predation risk and the variables influencing it. We used MARK to calculate daily survival rates of Least Bell's Vireo nests and applied an information-theoretic approach to evaluate support for logistic regression models of the effect of habitat variables on predation risk. Analysis of data for 195 nests collected during 1999 and 2000 at the San Luis Rey River and Pilgrim Creek in southern California revealed no effect of fine-scale factors, including nest height, supporting plant species, and three measures of nest concealment, on the likelihood of predation. At the intermediate scale, distances to the riparian-habitat edge and to internal gaps in the canopy were unrelated to nest survival. Surrounding land-use type was a poor predictor of predation risk, with the exception of proximity to golf course–park habitat and wetland. Nests within 400 m of golf course–park were only 20% as likely to avoid predation as nests >400 m from this habitat, and nests near wetland were more than twice as likely to survive as nests distant from wetland. Spatially, predation appeared to be random throughout the site, with localized clustering evident in the vicinity of golf course–park and wetland. Our results suggest that the landscape may be the most appropriate scale at which to manage nest predation in this system.

Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1).

PubMed

Saarela, Jeffery M; Bull, Roger D; Paradis, Michel J; Ebata, Sharon N; Paul M Peterson; Soreng, Robert J; Paszko, Beata

2017-01-01

Circumscriptions of and relationships among many genera and suprageneric taxa of the diverse grass tribe Poeae remain controversial. In an attempt to clarify these, we conducted phylogenetic analyses of >2400 new DNA sequences from two nuclear ribosomal regions (ITS, including internal transcribed spacers 1 and 2 and the 5.8S gene, and the 3'-end of the external transcribed spacer (ETS)) and five plastid regions ( matK , trnL-trnF , atpF-atpH , psbK-psbI , psbA-rps19-trnH ), and of more than 1000 new and previously published ITS sequences, focused particularly on Poeae chloroplast group 1 and including broad and increased species sampling compared to previous studies. Deep branches in the combined plastid and combined ITS+ETS trees are generally well resolved, the trees are congruent in most aspects, branch support across the trees is stronger than in trees based on only ITS and fewer plastid regions, and there is evidence of conflict between data partitions in some taxa. In plastid trees, a strongly supported clade corresponds to Poeae chloroplast group 1 and includes Agrostidinae p.p., Anthoxanthinae, Aveninae s.str., Brizinae, Koeleriinae (sometimes included in Aveninae s.l.), Phalaridinae and Torreyochloinae. In the ITS+ETS tree, a supported clade includes these same tribes as well as Sesleriinae and Scolochloinae. Aveninae s.str. and Sesleriinae are sister taxa and form a clade with Koeleriinae in the ITS+ETS tree whereas Aveninae s.str. and Koeleriinae form a clade and Sesleriinae is part of Poeae chloroplast group 2 in the plastid tree. All species of Trisetum are part of Koeleriinae, but the genus is polyphyletic. Koeleriinae is divided into two major subclades: one comprises Avellinia , Gaudinia , Koeleria , Rostraria , Trisetaria and Trisetum subg. Trisetum, and the other Calamagrostis / Deyeuxia p.p. (multiple species from Mexico to South America), Peyritschia , Leptophyllochloa , Sphenopholis , Trisetopsis and Trisetum subg. Deschampsioidea. Graphephorum , Trisetum cernuum , T. irazuense and T. macbridei fall in different clades of Koeleriinae in plastid vs. nuclear ribosomal trees, and are likely of hybrid origin. ITS and matK trees identify a third lineage of Koeleriinae corresponding to Trisetum subsect. Sibirica, and affinities of Lagurus ovatus with respect to Aveninae s.str. and Koeleriinae are incongruent in nuclear ribosomal and plastid trees, supporting recognition of Lagurus in its own subtribe. A large clade comprises taxa of Agrostidinae, Brizinae and Calothecinae, but neither Agrostidinae nor Calothecinae are monophyletic as currently circumscribed and affinities of Brizinae differ in plastid and nuclear ribosomal trees. Within this clade, one newly identified lineage comprises Calamagrostis coarctata , Dichelachne , Echinopogon (Agrostidinae p.p.) and Relchela (Calothecinae p.p.), and another comprises Chascolytrum (Calothecinae p.p.) and Deyeuxia effusa (Agrostidinae p.p.). Within Agrostidinae p.p., the type species of Deyeuxia and Calamagrostis s.str. are closely related, supporting classification of Deyeuxia as a synonym of Calamagrostis s.str. Furthermore, the two species of Ammophila are not sister taxa and are nested among different groups of Calamagrostis s.str., supporting their classification in Calamagrostis . Agrostis , Lachnagrostis and Polypogon form a clade and species of each are variously intermixed in plastid and nuclear ribosomal trees. Additionally, all but one species from South America classified in Deyeuxia sect. Stylagrostis resolve in Holcinae p.p. ( Deschampsia ). The current phylogenetic results support recognition of the latter species in Deschampsia , and we also demonstrate Scribneria is part of this clade. Moreover, Holcinae is not monophyletic in its current circumscription because Deschampsia does not form a clade with Holcus and Vahlodea , which are sister taxa. The results support recognition of Deschampsia in its own subtribe Aristaveninae. Substantial further changes to the classification of these grasses will be needed to produce generic circumscriptions consistent with phylogenetic evidence. The following 15 new combinations are made: Calamagrostis × calammophila, C. breviligulata , C. breviligulata subsp. champlainensis, C. × don-hensonii, Deschampsia aurea , D. bolanderi , D. chrysantha , D. chrysantha var. phalaroides, D. eminens , D. eminens var. fulva, D. eminens var. inclusa, D. hackelii , D. ovata , and D. ovata var. nivalis. D. podophora ; the new name Deschampsia parodiana is proposed; the new subtribe Lagurinae is described; and a second-step lectotype is designated for the name Deyeuxia phalaroides .

Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1)

PubMed Central

Saarela, Jeffery M.; Bull, Roger D.; Paradis, Michel J.; Ebata, Sharon N.; Paul M. Peterson; Soreng, Robert J.; Paszko, Beata

2017-01-01

Abstract Circumscriptions of and relationships among many genera and suprageneric taxa of the diverse grass tribe Poeae remain controversial. In an attempt to clarify these, we conducted phylogenetic analyses of >2400 new DNA sequences from two nuclear ribosomal regions (ITS, including internal transcribed spacers 1 and 2 and the 5.8S gene, and the 3’-end of the external transcribed spacer (ETS)) and five plastid regions (matK, trnL–trnF, atpF–atpH, psbK–psbI, psbA–rps19–trnH), and of more than 1000 new and previously published ITS sequences, focused particularly on Poeae chloroplast group 1 and including broad and increased species sampling compared to previous studies. Deep branches in the combined plastid and combined ITS+ETS trees are generally well resolved, the trees are congruent in most aspects, branch support across the trees is stronger than in trees based on only ITS and fewer plastid regions, and there is evidence of conflict between data partitions in some taxa. In plastid trees, a strongly supported clade corresponds to Poeae chloroplast group 1 and includes Agrostidinae p.p., Anthoxanthinae, Aveninae s.str., Brizinae, Koeleriinae (sometimes included in Aveninae s.l.), Phalaridinae and Torreyochloinae. In the ITS+ETS tree, a supported clade includes these same tribes as well as Sesleriinae and Scolochloinae. Aveninae s.str. and Sesleriinae are sister taxa and form a clade with Koeleriinae in the ITS+ETS tree whereas Aveninae s.str. and Koeleriinae form a clade and Sesleriinae is part of Poeae chloroplast group 2 in the plastid tree. All species of Trisetum are part of Koeleriinae, but the genus is polyphyletic. Koeleriinae is divided into two major subclades: one comprises Avellinia, Gaudinia, Koeleria, Rostraria, Trisetaria and Trisetum subg. Trisetum, and the other Calamagrostis/Deyeuxia p.p. (multiple species from Mexico to South America), Peyritschia, Leptophyllochloa, Sphenopholis, Trisetopsis and Trisetum subg. Deschampsioidea. Graphephorum, Trisetum cernuum, T. irazuense and T. macbridei fall in different clades of Koeleriinae in plastid vs. nuclear ribosomal trees, and are likely of hybrid origin. ITS and matK trees identify a third lineage of Koeleriinae corresponding to Trisetum subsect. Sibirica, and affinities of Lagurus ovatus with respect to Aveninae s.str. and Koeleriinae are incongruent in nuclear ribosomal and plastid trees, supporting recognition of Lagurus in its own subtribe. A large clade comprises taxa of Agrostidinae, Brizinae and Calothecinae, but neither Agrostidinae nor Calothecinae are monophyletic as currently circumscribed and affinities of Brizinae differ in plastid and nuclear ribosomal trees. Within this clade, one newly identified lineage comprises Calamagrostis coarctata, Dichelachne, Echinopogon (Agrostidinae p.p.) and Relchela (Calothecinae p.p.), and another comprises Chascolytrum (Calothecinae p.p.) and Deyeuxia effusa (Agrostidinae p.p.). Within Agrostidinae p.p., the type species of Deyeuxia and Calamagrostis s.str. are closely related, supporting classification of Deyeuxia as a synonym of Calamagrostis s.str. Furthermore, the two species of Ammophila are not sister taxa and are nested among different groups of Calamagrostis s.str., supporting their classification in Calamagrostis. Agrostis, Lachnagrostis and Polypogon form a clade and species of each are variously intermixed in plastid and nuclear ribosomal trees. Additionally, all but one species from South America classified in Deyeuxia sect. Stylagrostis resolve in Holcinae p.p. (Deschampsia). The current phylogenetic results support recognition of the latter species in Deschampsia, and we also demonstrate Scribneria is part of this clade. Moreover, Holcinae is not monophyletic in its current circumscription because Deschampsia does not form a clade with Holcus and Vahlodea, which are sister taxa. The results support recognition of Deschampsia in its own subtribe Aristaveninae. Substantial further changes to the classification of these grasses will be needed to produce generic circumscriptions consistent with phylogenetic evidence. The following 15 new combinations are made: Calamagrostis × calammophila, C. breviligulata, C. breviligulata subsp. champlainensis, C. × don-hensonii, Deschampsia aurea, D. bolanderi, D. chrysantha, D. chrysantha var. phalaroides, D. eminens, D. eminens var. fulva, D. eminens var. inclusa, D. hackelii, D. ovata, and D. ovata var. nivalis. D. podophora; the new name Deschampsia parodiana is proposed; the new subtribe Lagurinae is described; and a second-step lectotype is designated for the name Deyeuxia phalaroides. PMID:29114171

Molecular Phylogenetic Analysis of a Geographically and Temporally Matched Set of Candida albicans Isolates from Humans and Nonmigratory Wildlife in Central Illinois ▿

PubMed Central

Wrobel, Lauren; Whittington, Julia K.; Pujol, Claude; Oh, Soon-Hwan; Ruiz, Marilyn O.; Pfaller, Michael A.; Diekema, Daniel J.; Soll, David R.; Hoyer, Lois L.

2008-01-01

This study explored whether wildlife species serve as the reservoir for human Candida albicans strains in a given geographic area. C. albicans isolates were collected from nonmigratory wildlife admitted to the University of Illinois Wildlife Medical Clinic. A geographically and temporally matched set of C. albicans oral isolates was collected from healthy human volunteers. Multilocus sequence typing was used to assign strains to genetic clades. Clade 1 isolates, particularly diploid sequence type 69 (DST 69), were most common in humans. Clade 1 strains were less frequently recovered from wildlife, while clade 8 strains, particularly DST 90, were overrepresented in the wildlife collection. All instances where a wildlife and human isolate shared the same DST occurred within clade 1. Clade distributions between human and wildlife isolates were significantly different, demonstrating population isolation between the groups. These differences may indicate limited strain transfer between groups or differential selection of C. albicans isolates in humans and wildlife. Wildlife strains had an amphotericin B MIC significantly lower than that of human isolates; strains with increased susceptibility were from several clades. C. albicans isolates were collected from domestic animals to provide comparisons with human and wildlife data sets. C. albicans isolation from canine and feline oral and anal swabs was infrequent; companion animal isolates were closely related to clade 1 human isolates. Collectively, the data suggest a greater likelihood of C. albicans transfer from humans to animals than from animals to humans. The nontransient human population may maintain the connection between geography and the C. albicans genetic groups recovered from humans. PMID:18621922

Combining high-throughput sequencing and targeted loci data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae).

PubMed

Fonseca, Luiz Henrique M; Lohmann, Lúcia G

2018-06-01

Combining high-throughput sequencing data with amplicon sequences allows the reconstruction of robust phylogenies based on comprehensive sampling of characters and taxa. Here, we combine Next Generation Sequencing (NGS) and Sanger sequencing data to infer the phylogeny of the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae), a diverse lineage of Neotropical plants, using Maximum Likelihood and Bayesian approaches. We used NGS to obtain complete or nearly-complete plastomes of members of this clade, leading to a final dataset with 54 individuals, representing 44 members of ingroup and 10 outgroups. In addition, we obtained Sanger sequences of two plastid markers (ndhF and rpl32-trnL) for 44 individuals (43 ingroup and 1 outgroup) and the nuclear PepC for 64 individuals (63 ingroup and 1 outgroup). Our final dataset includes 87 individuals of members of the "Adenocalymma-Neojobertia" clade, representing 66 species (ca. 90% of the diversity), plus 11 outgroups. Plastid and nuclear datasets recovered congruent topologies and were combined. The combined analysis recovered a monophyletic "Adenocalymma-Neojobertia" clade and a paraphyletic Adenocalymma that also contained a monophyletic Neojobertia plus Pleonotoma albiflora. Relationships are strongly supported in all analyses, with most lineages within the "Adenocalymma-Neojobertia" clade receiving maximum posterior probabilities. Ancestral character state reconstructions using Bayesian approaches identified six morphological synapomorphies of clades namely, prophyll type, petiole and petiolule articulation, tendril ramification, inflorescence ramification, calyx shape, and fruit wings. Other characters such as habit, calyx cupular trichomes, corolla color, and corolla shape evolved multiple times. These characters are putatively related with the clade diversification and can be further explored in diversification studies. Copyright © 2018 Elsevier Inc. All rights reserved.

The Search for Therapeutic Bacteriophages Uncovers One New Subfamily and Two New Genera of Pseudomonas-Infecting Myoviridae

PubMed Central

Henry, Marine; Bobay, Louis-Marie; Chevallereau, Anne; Saussereau, Emilie; Ceyssens, Pieter-Jan; Debarbieux, Laurent

2015-01-01

In a previous study, six virulent bacteriophages PAK_P1, PAK_P2, PAK_P3, PAK_P4, PAK_P5 and CHA_P1 were evaluated for their in vivo efficacy in treating Pseudomonas aeruginosa infections using a mouse model of lung infection. Here, we show that their genomes are closely related to five other Pseudomonas phages and allow a subdivision into two clades, PAK_P1-like and KPP10-like viruses, based on differences in genome size, %GC and genomic contents, as well as number of tRNAs. These two clades are well delineated, with a mean of 86% and 92% of proteins considered homologous within individual clades, and 25% proteins considered homologous between the two clades. By ESI-MS/MS analysis we determined that their virions are composed of at least 25 different proteins and electron microscopy revealed a morphology identical to the hallmark Salmonella phage Felix O1. A search for additional bacteriophage homologs, using profiles of protein families defined from the analysis of the 11 genomes, identified 10 additional candidates infecting hosts from different species. By carrying out a phylogenetic analysis using these 21 genomes we were able to define a new subfamily of viruses, the Felixounavirinae within the Myoviridae family. The new Felixounavirinae subfamily includes three genera: Felixounalikevirus, PAK_P1likevirus and KPP10likevirus. Sequencing genomes of bacteriophages with therapeutic potential increases the quantity of genomic data on closely related bacteriophages, leading to establishment of new taxonomic clades and the development of strategies for analyzing viral genomes as presented in this article. PMID:25629728

Genetic evolution of H5 highly pathogenic avian influenza virus in domestic poultry in Vietnam between 2011 and 2013.

PubMed

Lee, Eun-Kyoung; Kang, Hyun-Mi; Kim, Kwang-Il; Choi, Jun-Gu; To, Thanh Long; Nguyen, Tho Dang; Song, Byung-Min; Jeong, Jipseol; Choi, Kang-Seuk; Kim, Ji-Ye; Lee, Hee-Soo; Lee, Youn-Jeong; Kim, Jae-Hong

2015-04-01

In spite of highly pathogenic avian influenza H5N1 vaccination campaigns for domestic poultry, H5N1 viruses continue to circulate in Vietnam. To estimate the prevalence of avian influenza virus in Vietnam, surveillance was conducted between November 2011 and February 2013. Genetic analysis of 312 highly pathogenic avian influenza H5 viruses isolated from poultry in Vietnam was conducted and possible genetic relationships with strains from neighboring countries were investigated. As previously reported, phylogenetic analysis of the avian influenza virus revealed two H5N1 HPAI clades that were circulating in Vietnam. Clade 1.1, related to Cambodian strains, was predominant in the southern provinces, while clade 2.3.2.1 viruses were predominant in the northern and central provinces. Sequence analysis revealed evidence of active genetic evolution. In the gene constellation of clade 2.3.2.1, genotypes A, B, and B(II) existed during the 2011/2012 winter season. In June 2012, new genotype C emerged by reassortment between genotype A and genotype B(II), and this genotype was predominant in 2013 in the northern and central provinces. Interestingly, enzootic Vietnamese clade 2.3.2.1C H5 virus subsequently reassorted with N2, which originated from wild birds, to generate H5N2 highly pathogenic avian influenza, which was isolated from duck in the northeast region. This investigation indicated that H5N1 outbreaks persist in Vietnam and cause genetic reassortment with circulating viruses. It is necessary to strengthen active influenza surveillance to eradicate highly pathogenic avian influenza viruses and sever the link between highly pathogenic avian influenza and other circulating influenza viruses. © 2015 Poultry Science Association Inc.

Soil attributes drive nest-site selection by the campo miner Geositta poeciloptera.

PubMed

Meireles, Ricardo Camargos de; Teixeira, João Paulo Gusmão; Solar, Ricardo; Vasconcelos, Bruno Nery F; Fernandes, Raphael B A; Lopes, Leonardo Esteves

2018-01-01

Substrate type is a key-factor in nest-site selection and nest architecture of burrowing birds. However, little is known about which factors drive nest-site selection for these species, especially in the tropics. We studied the influence of soil attributes on nest-site selection by the campo miner Geositta poeciloptera, an open grassland bird that builds its nests within soil cavities. For all nests found, we measured the depth of the nest cavity and the resistance of the soil to penetration, and identified the soil horizon in which the nest was located. In soil banks with nests, we collected soil samples for granulometric analysis around each nest cavity, while in soil banks without nests we collected these samples at random points. From 43 nests found, 86% were located in the deeper soil horizons (C-horizon), and only 14% in the shallower horizons (B-horizon). Granulometric analysis showed that the C-horizons possessed a high similar granulometric composition, with high silt and low clay contents. These characteristics are associated with a low degree of structural development of the soil, which makes it easier to excavate. Contrarily, soil resistance to penetration does not seem to be an important criterion for nest site selection, although nests in more resistant the soils tend to have shallower nest cavities. Among the soil banks analyzed, 40% of those without cavities possessed a larger proportion of B-horizon relative to the C-horizon, and their texture was more clayey. On the other hand, almost all soil banks containing nest cavities had a larger C-horizon and a silty texture, indicating that soil attributes drive nest-site selection by G. poeciloptera. Thus, we conclude that the patchy distribution of G. poeciloptera can attributed to the infrequent natural exposure of the C-horizon in the tropical region, where well developed, deep and permeable soils are more common.

Soil attributes drive nest-site selection by the campo miner Geositta poeciloptera

PubMed Central

Teixeira, João Paulo Gusmão; Solar, Ricardo; Vasconcelos, Bruno Nery F.; Fernandes, Raphael B. A.; Lopes, Leonardo Esteves

2018-01-01

Substrate type is a key-factor in nest-site selection and nest architecture of burrowing birds. However, little is known about which factors drive nest-site selection for these species, especially in the tropics. We studied the influence of soil attributes on nest-site selection by the campo miner Geositta poeciloptera, an open grassland bird that builds its nests within soil cavities. For all nests found, we measured the depth of the nest cavity and the resistance of the soil to penetration, and identified the soil horizon in which the nest was located. In soil banks with nests, we collected soil samples for granulometric analysis around each nest cavity, while in soil banks without nests we collected these samples at random points. From 43 nests found, 86% were located in the deeper soil horizons (C-horizon), and only 14% in the shallower horizons (B-horizon). Granulometric analysis showed that the C-horizons possessed a high similar granulometric composition, with high silt and low clay contents. These characteristics are associated with a low degree of structural development of the soil, which makes it easier to excavate. Contrarily, soil resistance to penetration does not seem to be an important criterion for nest site selection, although nests in more resistant the soils tend to have shallower nest cavities. Among the soil banks analyzed, 40% of those without cavities possessed a larger proportion of B-horizon relative to the C-horizon, and their texture was more clayey. On the other hand, almost all soil banks containing nest cavities had a larger C-horizon and a silty texture, indicating that soil attributes drive nest-site selection by G. poeciloptera. Thus, we conclude that the patchy distribution of G. poeciloptera can attributed to the infrequent natural exposure of the C-horizon in the tropical region, where well developed, deep and permeable soils are more common. PMID:29381768

Major clades of Agaricales: a multilocus phylogenetic overview.

Treesearch

P. Brandon Matheny; Judd M. Curtis; Valerie Hofstetter; M. Catherine Aime; Jean-Marc Moncalvo; Zai-Wei Ge; Zhu-Liang Yang; Joseph F. Ammirati; Timothy J. Baroni; Neale L. Bougher; Karen W. Lodge Hughes; Richard W. Kerrigan; Michelle T. Seidl; Aanen; Matthew Duur K. DeNitis; Graciela M. Daniele; Dennis E. Desjardin; Bradley R. Kropp; Lorelei L. Norvell; Andrew Parker; Else C. Vellinga; Rytas Vilgalys; David S. Hibbett

2006-01-01

An overview of the phylogeny of the Agaricales is presented based on a multilocus analysis of a six-gene region supermatrix. Bayesian analyses of 5611 nucleotide characters of rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S ribosomal RNA genes recovered six major clades, which are recognized informally and labeled the Agaricoid, Tricholomatoid, Marasmioid, Pluteoid,...

Seasonal variations in the composition of the essential oils of Lavandula angustifolia (Lamiacae).

PubMed

Lakusić, Branislava; Lakusić, Dmitar; Ristić, Mihailo; Marcetić, Mirjana; Slavkovska, Violeta

2014-06-01

Seasonal variations in the composition of the essential oils obtained from the same individual (of the same genotype) of Lavandula angustifolia cultivated in Belgrade were determined by GC and GC/MS. The main constituents were 1,8-cineole (7.1-48.4%), linalool (0.1-38.7%), bomeol (10.9-27.7%), beta-phellandrene (0.5-21.2%) and camphor (1.5-15.8%). Cluster analysis showed that the 21 samples collected each month during the vegetation cycle were separable into three main clades with different compositions of essential oils. In the shoots with flowers, inflorescences and fruits of clade I, linalool is dominant, in the young leaves before flowering and old leaves of clade II, 1,8-cineole is dominant. In the young and incompletely developed leaves of clade III, beta-phellandrene is dominant. The composition of the essential oils of lavender depended on the plant part and the stage of development.

Hyperdiversity of Genes Encoding Integral Light-Harvesting Proteins in the Dinoflagellate Symbiodinium sp

PubMed Central

Boldt, Lynda; Yellowlees, David; Leggat, William

2012-01-01

The superfamily of light-harvesting complex (LHC) proteins is comprised of proteins with diverse functions in light-harvesting and photoprotection. LHC proteins bind chlorophyll (Chl) and carotenoids and include a family of LHCs that bind Chl a and c. Dinophytes (dinoflagellates) are predominantly Chl c binding algal taxa, bind peridinin or fucoxanthin as the primary carotenoid, and can possess a number of LHC subfamilies. Here we report 11 LHC sequences for the chlorophyll a-chlorophyll c 2-peridinin protein complex (acpPC) subfamily isolated from Symbiodinium sp. C3, an ecologically important peridinin binding dinoflagellate taxa. Phylogenetic analysis of these proteins suggests the acpPC subfamily forms at least three clades within the Chl a/c binding LHC family; Clade 1 clusters with rhodophyte, cryptophyte and peridinin binding dinoflagellate sequences, Clade 2 with peridinin binding dinoflagellate sequences only and Clades 3 with heterokontophytes, fucoxanthin and peridinin binding dinoflagellate sequences. PMID:23112815

Enhanced virulence of clade 2.3.2.1 highly pathogenic avian influenza A H5N1 viruses in ferrets.

PubMed

Pearce, Melissa B; Pappas, Claudia; Gustin, Kortney M; Davis, C Todd; Pantin-Jackwood, Mary J; Swayne, David E; Maines, Taronna R; Belser, Jessica A; Tumpey, Terrence M

2017-02-01

Sporadic avian to human transmission of highly pathogenic avian influenza (HPAI) A(H5N1) viruses necessitates the analysis of currently circulating and evolving clades to assess their potential risk. Following the spread and sustained circulation of clade 2 viruses across multiple continents, numerous subclades and genotypes have been described. To better understand the pathogenesis associated with the continued diversification of clade 2A(H5N1) influenza viruses, we investigated the relative virulence of eleven human and poultry isolates collected from 2006 to 2013 by determining their ability to cause disease in the ferret model. Numerous clade 2 viruses, including a clade 2.2 avian isolate, a 2.2.2.1 human isolate, and two 2.2.1 human isolates, were found to be of low virulence in the ferret model, though lethality was detected following infection with one 2.2.1 human isolate. In contrast, three of six clade 2.3.2.1 avian isolates tested led to severe disease and death among infected ferrets. Clade 2.3.2.1b and 2.3.2.1c isolates, but not 2.3.2.1a isolates, were associated with ferret lethality. All A(H5N1) viruses replicated efficiently in the respiratory tract of ferrets regardless of their virulence and lethality. However, lethal isolates were characterized by systemic viral dissemination, including detection in the brain and enhanced histopathology in lung tissues. The finding of disparate virulence phenotypes between clade 2A(H5N1) viruses, notably differences between subclades of 2.3.2.1 viruses, suggests there are distinct molecular determinants present within the established subclades, the identification of which will assist in molecular-based surveillance and public health efforts against A(H5N1) viruses. Published by Elsevier Inc.

Enhanced virulence of clade 2.3.2.1 highly pathogenic avian influenza A H5N1 viruses in ferrets

PubMed Central

Pearce, Melissa B.; Pappas, Claudia; Gustin, Kortney M.; Davis, C. Todd; Pantin-Jackwood, Mary J.; Swayne, David E.; Maines, Taronna R.; Belser, Jessica A.; Tumpey, Terrence M.

2017-01-01

Sporadic avian to human transmission of highly pathogenic avian influenza (HPAI) A(H5N1) viruses necessitates the analysis of currently circulating and evolving clades to assess their potential risk. Following the spread and sustained circulation of clade 2 viruses across multiple continents, numerous subclades and genotypes have been described. To better understand the pathogenesis associated with the continued diversification of clade 2 A(H5N1) influenza viruses, we investigated the relative virulence of eleven human and poultry isolates collected from 2006 to 2013 by determining their ability to cause disease in the ferret model. Numerous clade 2 viruses, including a clade 2.2 avian isolate, a 2.2.2.1 human isolate, and two 2.2.1 human isolates, were found to be of low virulence in the ferret model, though lethality was detected following infection with one 2.2.1 human isolate. In contrast, three of six clade 2.3.2.1 avian isolates tested led to severe disease and death among infected ferrets. Clade 2.3.2.1b and 2.3.2.1c isolates, but not 2.3.2.1a isolates, were associated with ferret lethality. All A(H5N1) viruses replicated efficiently in the respiratory tract of ferrets regardless of their virulence and lethality. However, lethal isolates were characterized by systemic viral dissemination, including detection in the brain and enhanced histopathology in lung tissues. The finding of disparate virulence phenotypes between clade 2 A(H5N1) viruses, notably differences between subclades of 2.3.2.1 viruses, suggests there are distinct molecular determinants present within the established subclades, the identification of which will assist in molecular-based surveillance and public health efforts against A(H5N1) viruses. PMID:28038412

Molecular phylogeography of the Andean alpine plant, Gunnera magellanica

NASA Astrophysics Data System (ADS)

Shimizu, M.; Fujii, N.; Ito, M.; Asakawa, T.; Nishida, H.; Suyama, C.; Ueda, K.

2015-12-01

To clarify the evolutionary history of Gunnera magellanica (Gunneraceae), an alpine plant of the Andes mountains, we performed molecular phylogeographic analyses based on the sequences of an internal transcribed spacer (ITS) of nuclear ribosomal DNA and four non-coding regions (trnH-psbA, trnL-trnF, atpB-rbcL, rpl16 intron) of chloroplast DNA. We investigated 3, 4, 4 and 11 populations in, Ecuador, Bolivia, Argentina, and Chile, respectively, and detected six ITS genotypes (Types A-F) in G. magellanica. Five genotypes (Types A-E) were observed in the northern Andes population (Ecuador and Bolivia); only one ITS genotype (Type F) was observed in the southern Andes population (Chile and Argentina). Phylogenetic analyses showed that the ITS genotypes of the northern and southern Andes populations form different clades with high bootstrap probability. Furthermore, network analysis, analysis of molecular variance, and spatial analysis of molecular variance showed that there were two major clusters (the northern and southern Andes populations) in this species. Furthermore, in chloroplast DNA analysis, three major clades (northern Andes, Chillan, and southern Andes) were inferred from phylogenetic analyses using four non-coding regions, a finding that was supported by the above three types of analysis. The Chillan clade is the northernmost population in the southern Andes populations. With the exception of the Chillan clade (Chillan population), results of nuclear DNA and chloroplast DNA analyses were consistent. Both markers showed that the northern and southern Andes populations of G. magellanica were genetically different from each other. This type of clear phylogeographical structure was supported by PERMUT analysis according to Pons & Petit (1995, 1996). Moreover, based on our preliminary estimation that is based on the ITS sequences, the northern and southern Andes clades diverged ~0.63-3 million years ago, during a period of upheaval in the Andes. This suggests that the populations of G. magellanica that were distributed along the Andes have been divided into the two local populations of the northern and southern Andes during the uplift of the Andes.

Vigna (Leguminosae) sensu lato: the names and identities of the American segregate genera.

PubMed

Delgado-Salinas, Alfonso; Thulin, Mats; Pasquet, Rémy; Weeden, Norm; Lavin, Matt

2011-10-01

The legume genus Vigna and close relatives have highly elaborated floral morphologies that involve the coiling, bending, and intricate connection of flower parts. Banners, levers, platforms, and pumps have evolved that attract pollinators and then manipulate their movement. Given this three-dimensional floral complexity, the taxonomy of Vigna and relatives has been confounded by the study of mostly two-dimensional museum specimens. A molecular phylogenetic analysis was undertaken in the effort to resolve long-standing taxonomic questions centered on floral morphology. The phylogenetic analysis included cpDNA trnK and nuclear ribosomal ITS/5.8S (ITS) sequence variation. The American species were comprehensively sampled and outgroups included Old World relatives. The trnK and ITS data analyses concurred in resolving six well-supported clades of American Vigna that are most closely related to other American genera: Dolichopsis, Macroptilium, Mysanthus, Oryxis, Oxyrhynchus, Phaseolus, Ramirezella, and Strophostyles. These 14 American clades ranked here as genera are resolved as sister to a clade comprising the mainly Old World species of Vigna. American Vigna clades were reassigned to the genera Ancistrotropis, Cochliasanthus, Condylostylis, Leptospron, Sigmoidotropis, and the newly described Helicotropis. Vigna sensu stricto in the Americas now includes relatively few and mostly pantropical species. Elaborate floral asymmetries are readily used to apomorphically diagnose nearly all of the American genera. The age estimates of the extant diversification of the American and its Old World sister clade are approximately coeval at ca. 6-7 million yr, which belies much greater floral variation in the Americas.

Genetic analysis of Aedes albopictus (Diptera, Culicidae) reveals a deep divergence in the original regions.

PubMed

Ruiling, Zhang; Tongkai, Liu; Zhendong, Huang; Guifen, Zhuang; Dezhen, Ma; Zhong, Zhang

2018-05-02

Aedes albopictus has been described as one of the 100 worst invasive species in the world. This mosquito originated from southeastern Asia and currently has a widespread presence in every continent except Antarctica. The rapid global expansion of Ae. albopictus has increased public health concerns about arbovirus-related disease threats. Adaptation, adaption to novel areas is a biological challenge for invasive species, and the underlying processes can be studied at the molecular level. In this study, genetic analysis was performed using mitochondrial gene NADH dehydrogenase subunit 5 (ND5), based on both native and invasive populations. Altogether, 38 haplotypes were detected with H1 being the dominant and widely distributed in 21 countries. Both phylogenetic and network analyses supported the existence of five clades, with only clade I being involved in the subsequent global spread of Asian tiger mosquito. The other four clades (II, III, IV and V) were restricted to their original regions, which could be ancestral populations that had diverged from clade I in the early stages of evolution. Neutrality tests suggested that most of the populations had experienced recent expansion. Analysis of molecular variance and the population-pair statistic F ST revealed that most populations lacked genetic structure, while high variability was detected within populations. Multiple and independent human-mediated introductions may explain the present results. Copyright © 2018 Elsevier B.V. All rights reserved.

Computational analysis of antibody dynamics identifies recent HIV-1 infection.

PubMed

Seaton, Kelly E; Vandergrift, Nathan A; Deal, Aaron W; Rountree, Wes; Bainbridge, John; Grebe, Eduard; Anderson, David A; Sawant, Sheetal; Shen, Xiaoying; Yates, Nicole L; Denny, Thomas N; Liao, Hua-Xin; Haynes, Barton F; Robb, Merlin L; Parkin, Neil; Santos, Breno R; Garrett, Nigel; Price, Matthew A; Naniche, Denise; Duerr, Ann C; Keating, Sheila; Hampton, Dylan; Facente, Shelley; Marson, Kara; Welte, Alex; Pilcher, Christopher D; Cohen, Myron S; Tomaras, Georgia D

2017-12-21

Accurate HIV-1 incidence estimation is critical to the success of HIV-1 prevention strategies. Current assays are limited by high false recent rates (FRRs) in certain populations and a short mean duration of recent infection (MDRI). Dynamic early HIV-1 antibody response kinetics were harnessed to identify biomarkers for improved incidence assays. We conducted retrospective analyses on circulating antibodies from known recent and longstanding infections and evaluated binding and avidity measurements of Env and non-Env antigens and multiple antibody forms (i.e., IgG, IgA, IgG3, IgG4, dIgA, and IgM) in a diverse panel of 164 HIV-1-infected participants (clades A, B, C). Discriminant function analysis identified an optimal set of measurements that were subsequently evaluated in a 324-specimen blinded biomarker validation panel. These biomarkers included clade C gp140 IgG3, transmitted/founder clade C gp140 IgG4 avidity, clade B gp140 IgG4 avidity, and gp41 immunodominant region IgG avidity. MDRI was estimated at 215 day or alternatively, 267 days. FRRs in untreated and treated subjects were 5.0% and 3.6%, respectively. Thus, computational analysis of dynamic HIV-1 antibody isotype and antigen interactions during infection enabled design of a promising HIV-1 recency assay for improved cross-sectional incidence estimation.

Computational analysis of antibody dynamics identifies recent HIV-1 infection

PubMed Central

Seaton, Kelly E.; Vandergrift, Nathan A.; Deal, Aaron W.; Rountree, Wes; Anderson, David A.; Sawant, Sheetal; Shen, Xiaoying; Yates, Nicole L.; Denny, Thomas N.; Haynes, Barton F.; Robb, Merlin L.; Parkin, Neil; Santos, Breno R.; Price, Matthew A.; Naniche, Denise; Duerr, Ann C.; Hampton, Dylan; Facente, Shelley; Marson, Kara; Welte, Alex; Pilcher, Christopher D.; Cohen, Myron S.

2017-01-01

Accurate HIV-1 incidence estimation is critical to the success of HIV-1 prevention strategies. Current assays are limited by high false recent rates (FRRs) in certain populations and a short mean duration of recent infection (MDRI). Dynamic early HIV-1 antibody response kinetics were harnessed to identify biomarkers for improved incidence assays. We conducted retrospective analyses on circulating antibodies from known recent and longstanding infections and evaluated binding and avidity measurements of Env and non-Env antigens and multiple antibody forms (i.e., IgG, IgA, IgG3, IgG4, dIgA, and IgM) in a diverse panel of 164 HIV-1–infected participants (clades A, B, C). Discriminant function analysis identified an optimal set of measurements that were subsequently evaluated in a 324-specimen blinded biomarker validation panel. These biomarkers included clade C gp140 IgG3, transmitted/founder clade C gp140 IgG4 avidity, clade B gp140 IgG4 avidity, and gp41 immunodominant region IgG avidity. MDRI was estimated at 215 day or alternatively, 267 days. FRRs in untreated and treated subjects were 5.0% and 3.6%, respectively. Thus, computational analysis of dynamic HIV-1 antibody isotype and antigen interactions during infection enabled design of a promising HIV-1 recency assay for improved cross-sectional incidence estimation. PMID:29263306

Molecular systematics and global phylogeography of angel sharks (genus Squatina).

PubMed

Stelbrink, Björn; von Rintelen, Thomas; Cliff, Geremy; Kriwet, Jürgen

2010-02-01

Angel sharks of the genus Squatina represent a group comprising 22 extant benthic species inhabiting continental shelves and upper slopes. In the present study, a comprehensive phylogenetic reconstruction of 17 Squatina species based on two mitochondrial markers (COI and 16S rRNA) is provided. The phylogenetic reconstructions are used to test biogeographic patterns. In addition, a molecular clock analysis is conducted to estimate divergence times of the emerged clades. All analyses show Squatina to be monophyletic. Four geographic clades are recognized, of which the Europe-North Africa-Asia clade is probably a result of the Tethys Sea closure. A second sister group relationship emerged in the analyses, including S. californica (eastern North Pacific) and S. dumeril (western North Atlantic), probably related to the rise of the Panamanian isthmus. The molecular clock analysis show that both lineage divergences coincide with the estimated time of these two geological events. Copyright (c) 2009. Published by Elsevier Inc.

Nest marking behavior and chemical composition of olfactory cues involved in nest recognition in Megachile rotundata.

PubMed

Guédot, Christelle; Buckner, James S; Hagen, Marcia M; Bosch, Jordi; Kemp, William P; Pitts-Singer, Theresa L

2013-08-01

In-nest observations of the solitary bee, Megachile rotundata (F.), revealed that nesting females apply olfactory cues to nests for nest recognition. On their way in and out of the nest, females drag the abdomen along the entire length of the nest, and sometimes deposit fluid droplets from the tip of the abdomen. The removal of bee-marked sections of the nest resulted in hesitation and searching behavior by females, indicating the loss of olfactory cues used for nest recognition. Chemical analysis of female cuticles and the deposits inside marked nesting tubes revealed the presence of hydrocarbons, wax esters, fatty aldehydes, and fatty alcohol acetate esters. Chemical compositions were similar across tube samples, but proportionally different from cuticular extracts. These findings reveal the importance of lipids as chemical signals for nest recognition and suggest that the nest-marking cues are derived from a source in addition to, or other than, the female cuticle.

Characterization of Clade 7.2 H5 Avian Influenza Viruses That Continue To Circulate in Chickens in China

PubMed Central

Liu, Liling; Zeng, Xianying; Chen, Pucheng; Deng, Guohua; Li, Yanbing; Shi, Jianzhong; Gu, Chunyang; Kong, Huihui; Suzuki, Yasuo; Jiang, Yongping; Tian, Guobin

2016-01-01

ABSTRACT The H5N1 avian influenza viruses emerged in Southeast Asia in the late 20th century and have evolved into multiple phylogenetic clades based on their hemagglutinin (HA)-encoding genes. The clade 7.2 viruses were first detected in chickens in northern China in 2006, and vaccines specifically targeted to the clade were developed and have been used in poultry in China since 2006. During routine surveillance and disease diagnosis, we isolated seven H5 viruses between 2011 and 2014 that bear the clade 7.2 HA genes. Here, we performed extensive studies to understand how the clade 7.2 H5 viruses have evolved in chickens in China. Full genome sequence analysis revealed that the seven viruses formed two subtypes (four H5N1 viruses and three H5N2 viruses) and four genotypes by deriving genes from other influenza viruses. All of the viruses had antigenically drifted from the clade 7.2 viruses that were isolated in 2006. Pathogenicity studies of four viruses, one from each genotype, revealed that all of the viruses are highly pathogenic in chickens, but none of them could replicate in ducks. The four viruses exclusively bound to avian-type receptors and replicated only in the turbinates and/or lungs of mice; none of them were lethal to mice at a dosage of 106 50% egg infective doses (EID50). Our study indicates that although the clade 7.2 viruses have not been eradicated from poultry through vaccination, they have not become more dangerous to other animals (e.g., ducks and mice) and humans. IMPORTANCE Animal influenza viruses can acquire the ability to infect and kill humans. The H5N1 viruses have been a concern in recent decades because of their clear pandemic potential. We sorted H5N1 influenza viruses into different phylogenetic clades based on their HA genes. The clade 7.2 viruses were detected in chickens in several provinces of northern China in 2006. Vaccines for these viruses were subsequently developed and have been used ever since to control infection of poultry. Here, we analyzed the genetic and biologic properties of seven clade 7.2 viruses that were isolated from chickens between 2011 and 2014. We found that after nearly 9 years of circulation in chickens, the clade 7.2 viruses still exclusively bind to avian-type receptors and are of low pathogenicity to mice, suggesting that these H5 viruses pose a low risk to human public health. PMID:27558424

Characterization of Clade 7.2 H5 Avian Influenza Viruses That Continue To Circulate in Chickens in China.

PubMed

Liu, Liling; Zeng, Xianying; Chen, Pucheng; Deng, Guohua; Li, Yanbing; Shi, Jianzhong; Gu, Chunyang; Kong, Huihui; Suzuki, Yasuo; Jiang, Yongping; Tian, Guobin; Chen, Hualan

2016-11-01

The H5N1 avian influenza viruses emerged in Southeast Asia in the late 20th century and have evolved into multiple phylogenetic clades based on their hemagglutinin (HA)-encoding genes. The clade 7.2 viruses were first detected in chickens in northern China in 2006, and vaccines specifically targeted to the clade were developed and have been used in poultry in China since 2006. During routine surveillance and disease diagnosis, we isolated seven H5 viruses between 2011 and 2014 that bear the clade 7.2 HA genes. Here, we performed extensive studies to understand how the clade 7.2 H5 viruses have evolved in chickens in China. Full genome sequence analysis revealed that the seven viruses formed two subtypes (four H5N1 viruses and three H5N2 viruses) and four genotypes by deriving genes from other influenza viruses. All of the viruses had antigenically drifted from the clade 7.2 viruses that were isolated in 2006. Pathogenicity studies of four viruses, one from each genotype, revealed that all of the viruses are highly pathogenic in chickens, but none of them could replicate in ducks. The four viruses exclusively bound to avian-type receptors and replicated only in the turbinates and/or lungs of mice; none of them were lethal to mice at a dosage of 10 6 50% egg infective doses (EID 50 ). Our study indicates that although the clade 7.2 viruses have not been eradicated from poultry through vaccination, they have not become more dangerous to other animals (e.g., ducks and mice) and humans. Animal influenza viruses can acquire the ability to infect and kill humans. The H5N1 viruses have been a concern in recent decades because of their clear pandemic potential. We sorted H5N1 influenza viruses into different phylogenetic clades based on their HA genes. The clade 7.2 viruses were detected in chickens in several provinces of northern China in 2006. Vaccines for these viruses were subsequently developed and have been used ever since to control infection of poultry. Here, we analyzed the genetic and biologic properties of seven clade 7.2 viruses that were isolated from chickens between 2011 and 2014. We found that after nearly 9 years of circulation in chickens, the clade 7.2 viruses still exclusively bind to avian-type receptors and are of low pathogenicity to mice, suggesting that these H5 viruses pose a low risk to human public health. Copyright © 2016 Liu et al.

A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland.

PubMed

Raven, Kathy E; Reuter, Sandra; Reynolds, Rosy; Brodrick, Hayley J; Russell, Julie E; Török, M Estée; Parkhill, Julian; Peacock, Sharon J

2016-10-01

Vancomycin-resistant Enterococcus faecium (VREfm) is an important cause of healthcare-associated infections worldwide. We undertook whole-genome sequencing (WGS) of 495 E. faecium bloodstream isolates from 2001-2011 in the United Kingdom and Ireland (UK&I) and 11 E. faecium isolates from a reference collection. Comparison between WGS and multilocus sequence typing (MLST) identified major discrepancies for 17% of isolates, with multiple instances of the same sequence type (ST) being located in genetically distant positions in the WGS tree. This confirms that WGS is superior to MLST for evolutionary analyses and is more accurate than current typing methods used during outbreak investigations. E. faecium has been categorized as belonging to three clades (Clades A1, hospital-associated; A2, animal-associated; and B, community-associated). Phylogenetic analysis of our isolates replicated the distinction between Clade A (97% of isolates) and Clade B but did not support the subdivision of Clade A into Clade A1 and A2. Phylogeographic analyses revealed that Clade A had been introduced multiple times into each hospital referral network or country, indicating frequent movement of E. faecium between regions that rarely share hospital patients. Numerous genetic clusters contained highly related vanA-positive and -negative E. faecium, which implies that control of vancomycin-resistant enterococci (VRE) in hospitals also requires consideration of vancomycin-susceptible E. faecium Our findings reveal the evolution and dissemination of hospital-associated E. faecium in the UK&I and provide evidence for WGS as an instrument for infection control. © 2016 Raven et al.; Published by Cold Spring Harbor Laboratory Press.

A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland

PubMed Central

Raven, Kathy E.; Reuter, Sandra; Reynolds, Rosy; Brodrick, Hayley J.; Russell, Julie E.; Török, M. Estée; Parkhill, Julian; Peacock, Sharon J.

2016-01-01

Vancomycin-resistant Enterococcus faecium (VREfm) is an important cause of healthcare-associated infections worldwide. We undertook whole-genome sequencing (WGS) of 495 E. faecium bloodstream isolates from 2001–2011 in the United Kingdom and Ireland (UK&I) and 11 E. faecium isolates from a reference collection. Comparison between WGS and multilocus sequence typing (MLST) identified major discrepancies for 17% of isolates, with multiple instances of the same sequence type (ST) being located in genetically distant positions in the WGS tree. This confirms that WGS is superior to MLST for evolutionary analyses and is more accurate than current typing methods used during outbreak investigations. E. faecium has been categorized as belonging to three clades (Clades A1, hospital-associated; A2, animal-associated; and B, community-associated). Phylogenetic analysis of our isolates replicated the distinction between Clade A (97% of isolates) and Clade B but did not support the subdivision of Clade A into Clade A1 and A2. Phylogeographic analyses revealed that Clade A had been introduced multiple times into each hospital referral network or country, indicating frequent movement of E. faecium between regions that rarely share hospital patients. Numerous genetic clusters contained highly related vanA-positive and -negative E. faecium, which implies that control of vancomycin-resistant enterococci (VRE) in hospitals also requires consideration of vancomycin-susceptible E. faecium. Our findings reveal the evolution and dissemination of hospital-associated E. faecium in the UK&I and provide evidence for WGS as an instrument for infection control. PMID:27527616

A new slider turtle (Testudines: Emydidae: Deirochelyinae: Trachemys) from the late Hemphillian (late Miocene/early Pliocene) of eastern Tennessee and the evolution of the deirochelyines

PubMed Central

2018-01-01

Trachemys (Testudines: Emydidae) represents one of the most well-known turtle genera today. The evolution of Trachemys, while being heavily documented with fossil representatives, is not well understood. Numerous fossils from the late Hemphillian Gray Fossil Site (GFS) in northeastern Tennessee help to elucidate its evolution. The fossil Trachemys at the GFS represent a new species. The new taxon, Trachemys haugrudi, is described, and currently represents the most thoroughly described fossil emydid species known. A phylogenetic analysis, including 31 species, focusing on the subfamily Deirochelyinae is performed that includes the new fossil species, along with numerous other modern and fossil deirochelyine species, representing the first phylogenetic analysis published that includes several fossil deirochelyines. The phylogenetic analysis, utilizing morphological evidence, provides monophyletic clades of all modern deirochelyines, including Chrysemys, Deirochelys, Pseudemys, Malaclemys, Graptemys, and Trachemys. A strict consensus tree finds the recently described fossil species Graptemys kerneri to be part of a clade of Graptemys + Malaclemys. Three fossil taxa, including one previously referred to Pseudemys (Pseudemys caelata) and two to Deirochelys (Deirochelys carri and Deirochelys floridana) are found to form a clade with modern Deirochelys reticularia reticularia, with D. floridana sister to the other members of the clade. Chrysemys is found to be part of a basal polytomy with Deirochelys in relation to other deirochelyine taxa. Two fossil taxa previously referred to Chrysemys (Chrysemys timida and Chrysemys williamsi) form a paraphyly with the modern Chrysemys picta picta and Deirochelys, and may be referable to distinct genera. Additionally, fossil taxa previously attributed to Trachemys (Trachemys hillii, Trachemys idahoensis, Trachemys inflata, and Trachemys platymarginata) and T. haugrudi are found to form a clade separate from clades of northern and southern Trachemys species, potentially suggesting a distinct lineage of Trachemys with no modern survivors. Hypotheses of phylogenetic relationships mostly agree between the present study and previous ones, although the inclusion of fossil taxa provides further clues to the evolution of parts of the Deirochelyinae. The inclusion of more fossil taxa and characters may help resolve the placement of some taxa, and further elucidate the evolution of these New World turtles. PMID:29456887

Evaluation of hsp65 Nested PCR-Restriction Analysis (PRA) for Diagnosing Tuberculosis in a High Burden Country

PubMed Central

Macente, Sara; Fujimura Leite, Clarice Queico; Santos, Adolfo Carlos Barreto; Siqueira, Vera Lúcia Dias; Machado, Luzia Neri Cosmo; Marcondes, Nadir Rodrigues; Hirata, Mario Hiroyuki; Hirata, Rosário Dominguez Crespo

2013-01-01

Current study evaluated the hsp65 Nested PCR Restriction Fragment Length Polymorphism Analysis (hsp65 Nested PCR-PRA) to detect and identify Mycobacterium tuberculosis complex directly in clinical samples for a rapid and specific diagnosis of tuberculosis (TB). hsp65 Nested PCR-PRA was applied directly to 218 clinical samples obtained from 127 patients suspected of TB or another mycobacterial infection from July 2009 to July 2010. The hsp65 Nested PCR-PRA showed 100% sensitivity and 95.0 and 93.1% specificity in comparison with culture and microscopy (acid fast bacillus smear), respectively. hsp65 Nested PCR-PRA was shown to be a fast and reliable assay for diagnosing TB, which may contribute towards a fast diagnosis that could help the selection of appropriate chemotherapeutic and early epidemiological management of the cases which are of paramount importance in a high TB burden country. PMID:24260739

Chemical Communication and Reproduction Partitioning in Social Wasps.

PubMed

Dani, Francesca Romana; Turillazzi, Stefano

2018-05-22

Social wasps encompass species displaying diverse social organization regarding colony cycle, nest foundation, caste differences (from none to significant dimorphism) and number of reproductive queens. Current phylogenetic data suggests that sociality occured independently in the subfamily Stenogastrinae and in the Polistinae+Vespinae clade. In most species, including those with the simplest social organization, colony reproduction is monopolised by a single or few females. Since their nest mates can also develop ovaries and lay eggs, dominant females must somehow inhibit them from reproducing. Physical interactions in the form of open aggression or, usually, ritualised dominance by the fertile females contribute to fertility inhibition in several species, but it is unlikely to function in large colonies. In the latter case, reproduction within the colony is likely to be regulated through pheromones. Relatively little is known about these semiochemicals. Studies on all the three social wasp subfamilies, revealed that cuticular hydrocarbon components differ in abundance between egg-laying and not egg-laying females and that their composition depends on fertility status. In several species, females have been reported to manifestly react towards females with activated ovaries, but there is little evidence to support the hypothesis that fertile individuals are either recognized through their CHC composition, or that over-represented CHC constituents can inhibit fertility. Moreover, very little information exists on the possibility that exocrine glands release fertility signals or chemicals inhibiting fertility.

Mealybugs with distinct endosymbiotic systems living on the same host plant.

PubMed

Koga, Ryuichi; Nikoh, Naruo; Matsuura, Yu; Meng, Xian-Ying; Fukatsu, Takema

2013-01-01

Mealybugs (Homoptera: Coccoidea: Pseudococcidae) possess a large bacteriome consisting of a number of bacteriocytes whose cytoplasm is populated by endosymbiotic bacteria. In many mealybugs of the subfamily Pseudococcinae, a peculiar endosymbiotic configuration has been identified: within the bacteriocytes, the primary betaproteobacterial endosymbiont Tremblaya princeps endocellularly harbor secondary gammaproteobacterial endosymbionts in a nested manner. Meanwhile, some mealybugs of the subfamily Phenacoccinae are associated only with a betaproteobacterial endosymbiont, designated as Tremblaya phenacola, which constitutes a distinct sister clade of T. princeps. However, cytological configuration of the endosymbiotic system in the phenacoccine mealybugs has not been established. Here, we investigated the endosymbiotic systems of the azalea mealybugs Crisicoccus azaleae (Pseudococcinae) and Phenacoccus azaleae (Phenacoccinae) living on the same host plants. Crisicoccus azaleae possessed a nested endosymbiotic system with T. princeps within the bacteriocyte cytoplasm and itself endocellularly harboring gammaproteobacterial cells, whereas P. azaleae exhibited a simple endosymbiotic system in which T. phenacola cells are localized within the bacteriocytes without additional gammaproteobacterial associates. Considering that these mealybugs live on the identical plant phloem sap, these different endosymbiotic consortia likely play similar biological roles for their host insects. The findings presented here should be helpful for future functional and comparative genomics toward elucidating evolutionary pathways of mealybugs and their endosymbionts. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Historical and contemporary population genetic connectivity of the European short-snouted seahorse Hippocampus hippocampus and implications for management.

PubMed

Woodall, L C; Koldewey, H J; Shaw, P W

2011-06-01

This first genetic study of Hippocampus hippocampus covers the species' entire geographic range and employs two mtDNA markers (control region and cytochrome b) to establish patterns of population structuring. A total of 255 specimens from 21 locations were used to obtain 89 concatenated haplotypes. The common haplotype was present in all but one population, however, most haplotypes were unique. The haplotype network had a star-like construction, suggesting expansion from a bottleneck event. F(ST) and AMOVA revealed population subdivision into three geographic regions (English Channel + Bay of Biscay, Mediterranean Sea + Atlantic Ocean Iberian coast + Macaronesian Islands, and West Africa) with barriers to gene flow indentified at Cape Finisterre and the Cape Verde frontal zone. Neutrality tests and nested clade analysis suggest a complex demographic history, with both historic events and contemporary processes shaping patterns of genetic differentiation. The genetic population subdivision detected in this study indicates that H. hippocampus should be managed as three separate units. This is especially pertinent as H. hippocampus populations within the West African region are the only ones known to be specifically targeted for exploitation. © 2011 The Authors. Journal of Fish Biology © 2011 The Fisheries Society of the British Isles.

DIM SUM: demography and individual migration simulated using a Markov chain.

PubMed

Brown, Jeremy M; Savidge, Kevin; McTavish, Emily Jane B

2011-03-01

An increasing number of studies seek to infer demographic history, often jointly with genetic relationships. Despite numerous analytical methods for such data, few simulations have investigated the methods' power and robustness, especially when underlying assumptions have been violated. DIM SUM (Demography and Individual Migration Simulated Using a Markov chain) is a stand-alone Java program for the simulation of population demography and individual migration while recording ancestor-descendant relationships. It does not employ coalescent assumptions or discrete population boundaries. It is extremely flexible, allowing the user to specify border positions, reactions of organisms to borders, local and global carrying capacities, individual dispersal kernels, rates of reproduction and strategies for sampling individuals. Spatial variables may be specified using image files (e.g., as exported from gis software) and may vary through time. In combination with software for genetic marker simulation, DIM SUM will be useful for testing phylogeographic (e.g., nested clade phylogeographic analysis, coalescent-based tests and continuous-landscape frameworks) and landscape-genetic methods, specifically regarding violations of coalescent assumptions. It can also be used to explore the qualitative features of proposed demographic scenarios (e.g. regarding biological invasions) and as a pedagogical tool. DIM SUM (with user's manual) can be downloaded from http://code.google.com/p/bio-dimsum. © 2010 Blackwell Publishing Ltd.

Spillover of Newcastle disease viruses from poultry to wild birds in Guangdong province, southern China.

PubMed

Xiang, Bin; Han, Lujie; Gao, Pei; You, Renrong; Wang, Fumin; Xiao, Jiajie; Liao, Ming; Kang, Yinfeng; Ren, Tao

2017-11-01

Despite intensive vaccination programs in many countries, including China, Newcastle disease has been reported sporadically and is still a significant threat to the poultry industry in China. Newcastle disease virus (NDV) is infectious for at least 250 bird species, but the role of wild birds in virus epidemiology remains largely unknown. Fourteen NDV isolates were obtained from 2040 samples collected from wild birds or the environment in Guangdong province, southern China, from 2013 to 2015. The isolation rate was the highest in the period of wintering and lowest during the periods of spring migration, nesting, and postnesting. A maximum clade credibility phylogenetic analysis revealed that at least four genotypes circulate in southern China: three class II genotypes (II, VI, and IX) and one class I (1b). We also demonstrated that most isolates from wild birds were highly similar to isolates from poultry, and two isolates were linked to viruses from wild birds in northern China. These data suggested that wild birds could disseminate NDV and poultry-derived viruses may spillover to wild birds. Accordingly, vaccine development and poultry management strategies should be considered to prevent future NDV outbreaks, particularly given the strength of the poultry industry in developing countries, such as China. Copyright © 2017 Elsevier B.V. All rights reserved.

Evolutionary History and Conservation Status of Cave Crayfishes Along the Cumberland Plateau

NASA Astrophysics Data System (ADS)

Buhay, J. E.; Crandall, K. A.

2005-05-01

Obligate cave-dwelling crayfish species are found only in southeastern United States, Mexico, and Cuba. Most species are considered to be endangered because of surface pollution threats to groundwater and small geographic distributions. There are currently three subterranean species of the genus Orconectes found along the Cumberland Plateau, a worldwide hotspot of cave biodiversity. The objectives of my dissertation research are to: 1) delineate species' boundaries using molecular genetic data in a phylogenetic framework, 2) examine evolutionary history of each species using Nested Clade Analysis, and 3) assess conservation status of each species using measures of effective population size and genetic diversity. This research project has uncovered a new species of cave crayfish along the border of Tennessee and Kentucky, an area previously thought to have "intergrades" between two subspecies of O. australis. It appears that Cambarus gentryi, a surface-dwelling burrowing species, is the closest living ancestor to the cave Orconectes assemblage on the Plateau. The origin appears to be Eastern Kentucky, with range expansions occuring southward down the Plateau. Although controversial, these cave species exhibit high levels of genetic diversity, especially in comparison to surface-dwellers. Conservation efforts should focus on protecting `high-traffic' areas to maintain gene flow and prevent isolation.

Nuclear Genetic Analysis of the Red Fox Across its Trans-Pacific Range.

PubMed

Sacks, Benjamin N; Lounsberry, Zachary T; Statham, Mark J

2018-06-27

The red fox (Vulpes vulpes) occurs on multiple continents in diverse habitats, making it an informative system for evolutionary genomic research. However, its phylogeography remains unclear. Previously, mitochondrial DNA and small numbers of nuclear loci provided discordant views. Both markers indicated deep divergence (~ 0.5 million years [MY]) between Eurasian and southern North American populations but differed in the apparent continental affinity of Alaskan red foxes, implying some degree of gene exchange during secondary contact (~0.1 MY). We assayed >173000 nuclear genomic sites in 52 red foxes, along with 2 Rueppell's foxes (Vulpes rueppellii) and a gray wolf (Canis lupus) using the Illumina CanineHD BeadChip. We obtained 5107 single nucleotide polymorphisms (SNPs) in the foxes. Consistent with the Afro-Eurasian origins of red foxes, genetic diversity was higher in Eurasian than North American samples. Phylogenetic trees indicated that Alaskan and southern North American red foxes formed a monophyletic group nested within the Eurasian clade. However, admixture models suggested Alaskan red foxes contained up to 40% Eurasian ancestry. We hypothesize that North American red foxes either hybridized with Eurasian foxes in Beringia at the start of the last glaciation or merged with a Beringian population after the last glaciation. Future work is needed to test between these scenarios and assess speciation.

A molecular phylogeny of Raddia and its allies within the tribe Olyreae (Poaceae, Bambusoideae) based on noncoding plastid and nuclear spacers.

PubMed

Oliveira, Reyjane P; Clark, Lynn G; Schnadelbach, Alessandra S; Monteiro, Silvana H N; Borba, Eduardo L; Longhi-Wagner, Hilda M; van den Berg, Cassio

2014-09-01

The plastid spacer trnD-trnT and the nuclear ribosomal internal transcribed spacer (ITS) were sequenced for 37 samples of herbaceous bamboos (Poaceae: Olyreae), including all Raddia species and allied genera, as well as two members of the woody bamboos (tribes Bambuseae and Arundinarieae), in order to examine their relationships. The sequences were analyzed using maximum parsimony and Bayesian inference. Both the individual and combined analyses of ITS and trnD-trnT supported Olyreae as a monophyletic group. All species of Raddia also formed a well-supported monophyletic group, and combined datasets allowed us to outline some relationships within this group. Individual analyses indicated incongruence regarding the sister group of Raddia, with ITS data weakly indicating Raddiella malmeana whereas trnD-trnT data supported Sucrea maculata in this position. However, the combined analysis supported Sucrea as sister to Raddia, although the monophyly of Sucrea is not well supported. Parodiolyra is paraphyletic to Raddiella in all analyses; Olyra is also paraphyletic, with species of Lithachne, Arberella and Cryptochloa nested within it. Eremitis and Pariana appeared as an isolated clade within Olyreae, and the position of the New Guinean Buergersiochloa remains uncertain within this tribe. Copyright © 2014 Elsevier Inc. All rights reserved.

Origin, radiation, dispersion and allopatric hybridization in the chub Leuciscus cephalus.

PubMed

Durand, J D; Unlü, E; Doadrio, I; Pipoyan, S; Templeton, A R

2000-08-22

The phylogenetic relationships of 492 chub (Leuciscus cephalus) belonging to 89 populations across the species' range were assessed using 600 base pairs of cytochrome b. Furthermore, nine species belonging to the L. cephalus complex were also analysed (over the whole cytochrome b) in order to test potential allopatric hybridization with L. cephalus sensu stricto (i.e. the chub). Our results show that the chub includes four highly divergent lineages descending from a quick radiation that took place three million years ago. The geographical distribution of these lineages and results of the nested clade analysis indicated that the chub may have originated from Mesopotamia. Chub radiation probably occurred during an important vicariant event such as the isolation of numerous Turkish river systems, a consequence of the uplift of the Anatolian Plateau (formerly covered by a broad inland lake). Dispersion of these lineages arose from the changes in the European hydrographic network and, thus, the chub and endemic species of the L. cephalus complex met by secondary contacts. Our results show several patterns of introgression, from Leuciscus lepidus fully introgressed by chub mitochondrial DNA to Leuciscus borysthenicus where no introgression at all was detected. We assume that these hybridization events might constitute an important evolutionary process for the settlement of the chub in new environments in the Mediterranean area.

Origin, radiation, dispersion and allopatric hybridization in the chub Leuciscus cephalus.

PubMed Central

Durand, J D; Unlü, E; Doadrio, I; Pipoyan, S; Templeton, A R

2000-01-01

The phylogenetic relationships of 492 chub (Leuciscus cephalus) belonging to 89 populations across the species' range were assessed using 600 base pairs of cytochrome b. Furthermore, nine species belonging to the L. cephalus complex were also analysed (over the whole cytochrome b) in order to test potential allopatric hybridization with L. cephalus sensu stricto (i.e. the chub). Our results show that the chub includes four highly divergent lineages descending from a quick radiation that took place three million years ago. The geographical distribution of these lineages and results of the nested clade analysis indicated that the chub may have originated from Mesopotamia. Chub radiation probably occurred during an important vicariant event such as the isolation of numerous Turkish river systems, a consequence of the uplift of the Anatolian Plateau (formerly covered by a broad inland lake). Dispersion of these lineages arose from the changes in the European hydrographic network and, thus, the chub and endemic species of the L. cephalus complex met by secondary contacts. Our results show several patterns of introgression, from Leuciscus lepidus fully introgressed by chub mitochondrial DNA to Leuciscus borysthenicus where no introgression at all was detected. We assume that these hybridization events might constitute an important evolutionary process for the settlement of the chub in new environments in the Mediterranean area. PMID:11467433

The effects of ant nests on soil fertility and plant performance: a meta-analysis.

PubMed

Farji-Brener, Alejandro G; Werenkraut, Victoria

2017-07-01

Ants are recognized as one of the major sources of soil disturbance world-wide. However, this view is largely based on isolated studies and qualitative reviews. Here, for the first time, we quantitatively determined whether ant nests affect soil fertility and plant performance, and identified the possible sources of variation of these effects. Using Bayesian mixed-models meta-analysis, we tested the hypotheses that ant effects on soil fertility and plant performance depend on the substrate sampled, ant feeding type, latitude, habitat and the plant response variable measured. Ant nests showed higher nutrient and cation content than adjacent non-nest soil samples, but similar pH. Nutrient content was higher in ant refuse materials than in nest soils. The fertilizer effect of ant nests was also higher in dry habitats than in grasslands or savannas. Cation content was higher in nests of plant-feeding ants than in nests of omnivorous species, and lower in nests from agro-ecosystems than in nests from any other habitat. Plants showed higher green/root biomass and fitness on ant nests soils than in adjacent, non-nest sites; but plant density and diversity were unaffected by the presence of ant nests. Root growth was particularly higher in refuse materials than in ant nest soils, in leaf-cutting ant nests and in deserts habitats. Our results confirm the major role of ant nests in influencing soil fertility and vegetation patterns and provide information about the factors that mediate these effects. First, ant nests improve soil fertility mainly through the accumulation of refuse materials. Thus, different refuse dump locations (external or in underground nest chambers) could benefit different vegetation life-forms. Second, ant nests could increase plant diversity at larger spatial scales only if the identity of favoured plants changes along environmental gradients (i.e. enhancing β-diversity). Third, ant species that feed on plants play a relevant role fertilizing soils, which may balance their known influence as primary consumers. Fourth, the effects of ant nests as fertility islands are larger in arid lands, possibly because fertility is intrinsically lower in these habitats. Overall, this study provide novel and quantitative evidence confirming that ant nests are key soil modifiers, emphasizing their role as ecological engineers. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

How Many Parasites Species a Frog Might Have? Determinants of Parasite Diversity in South American Anurans

PubMed Central

Campião, Karla Magalhães; Ribas, Augusto Cesar de Aquino; Morais, Drausio Honorio; da Silva, Reinaldo José; Tavares, Luiz Eduardo Roland

2015-01-01

There is an increasing interest in unveiling the dynamics of parasite infection. Understanding the interaction patterns, and determinants of host-parasite association contributes to filling knowledge gaps in both community and disease ecology. Despite being targeted as a relevant group for conservation efforts, determinants of the association of amphibians and their parasites in broad scales are poorly understood. Here we describe parasite biodiversity in South American amphibians, testing the influence of host body size and geographic range in helminth parasites species richness (PSR). We also test whether parasite diversity is related to hosts’ phylogenetic diversity. Results showed that nematodes are the most common anuran parasites. Host-parasite network has a nested pattern, with specialist helminth taxa generally associated with hosts that harbour the richest parasite faunas. Host size is positively correlated with helminth fauna richness, but we found no support for the association of host geographic range and PSR. These results remained consistent after correcting for uneven study effort and hosts’ phylogenic correlation. However, we found no association between host and parasite diversity, indicating that more diversified anuran clades not necessarily support higher parasite diversity. Overall, considering both the structure and the determinants of PRS in anurans, we conclude that specialist parasites are more likely to be associated with large anurans, which are the ones harbouring higher PSR, and that the lack of association of PSR with hosts’ clade diversification suggests it is strongly influenced by ecological and contemporary constrains. PMID:26473593

Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?

PubMed

Pimentel, Manuel; Escudero, Marcial; Sahuquillo, Elvira; Minaya, Miguel Ángel; Catalán, Pilar

2017-01-01

The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding ( ndhF , matk ) and three non-coding ( trnH-psbA , trnT-L and trnL-F ), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome number n  = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae.

Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?

PubMed Central

Escudero, Marcial; Sahuquillo, Elvira; Minaya, Miguel Ángel; Catalán, Pilar

2017-01-01

The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding (ndhF, matk) and three non-coding (trnH-psbA, trnT-L and trnL-F), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome number n = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae. PMID:28951814

How Many Parasites Species a Frog Might Have? Determinants of Parasite Diversity in South American Anurans.

PubMed

Campião, Karla Magalhães; Ribas, Augusto Cesar de Aquino; Morais, Drausio Honorio; da Silva, Reinaldo José; Tavares, Luiz Eduardo Roland

2015-01-01

There is an increasing interest in unveiling the dynamics of parasite infection. Understanding the interaction patterns, and determinants of host-parasite association contributes to filling knowledge gaps in both community and disease ecology. Despite being targeted as a relevant group for conservation efforts, determinants of the association of amphibians and their parasites in broad scales are poorly understood. Here we describe parasite biodiversity in South American amphibians, testing the influence of host body size and geographic range in helminth parasites species richness (PSR). We also test whether parasite diversity is related to hosts' phylogenetic diversity. Results showed that nematodes are the most common anuran parasites. Host-parasite network has a nested pattern, with specialist helminth taxa generally associated with hosts that harbour the richest parasite faunas. Host size is positively correlated with helminth fauna richness, but we found no support for the association of host geographic range and PSR. These results remained consistent after correcting for uneven study effort and hosts' phylogenic correlation. However, we found no association between host and parasite diversity, indicating that more diversified anuran clades not necessarily support higher parasite diversity. Overall, considering both the structure and the determinants of PRS in anurans, we conclude that specialist parasites are more likely to be associated with large anurans, which are the ones harbouring higher PSR, and that the lack of association of PSR with hosts' clade diversification suggests it is strongly influenced by ecological and contemporary constrains.

The nest-concealment hypothesis: New insights from a comparative analysis

USGS Publications Warehouse

Borgmann, Kathi L.; Conway, Courtney J.

2015-01-01

Selection of a breeding site is critical for many animals, especially for birds whose offspring are stationary during development. Thus, birds are often assumed to prefer concealed nest sites. However, 74% of studies (n = 106) that have evaluated this relationship for open-cup nesting songbirds in North America failed to support the nest-concealment hypothesis. We conducted a comparative analysis to identify factors that contribute to variation in the ability of researchers to find support for the nest-concealment hypothesis. We found that some of the discrepancy among studies can be explained by interspecific differences in morphological and extrinsic factors that affect nest predation. Moreover, methods that investigators used to estimate concealment affected whether studies found support for the nest-concealment hypothesis; 33% of the studies that used quantitative estimates found support for the nest-concealment hypothesis whereas only 10% of the studies that used qualitative estimates found support. The timing of measurements also explained some of the ambiguity; studies that provided little information regarding the timing of their foliage density estimates were less likely to support the nest-concealment hypothesis. Species with more conspicuous male plumage were less likely to support the nest-concealment hypothesis when we analyzed studies that used visual estimates. Whereas species with more conspicuous female plumage were more likely to support the nest-concealment hypothesis when we analyzed studies that used quantitative measures. Our results demonstrate that support for the nest-concealment hypothesis has been equivocal, but that some of the ambiguity can be explained by morphological traits and methods used to measure concealment.

Development of a species-diagnostic marker and its application for population genetics studies of the stingless bee Trigona collina in Thailand.

PubMed

Theeraapisakkun, M; Klinbunga, S; Sittipraneed, S

2010-05-18

A molecular maker for authenticating species origin of the stingless bee (Trigona collina) was developed. Initially, amplified fragment length polymorphism analysis was made of 11 stingless bee species using 64 primer combinations. A 316-bp band found only in T. collina was cloned and sequenced. A primer pair (CUTc1-F/R) was designed and tested for species-specificity in 15 stingless bee species (239 nests). The expected 259-bp fragment was consistently amplified in all T. collina individuals (134/134 nests, 100%). Cross-species amplification was observed in T. pagdeni (43/51 nests; 84.3%), but not in other species. SSCP analysis of CUTc1 unambiguously differentiated T. collina from T. pagdeni. CUTc1 generated three genotypes in Thai T. collina (134 nests). An AA (259/259 bp) genotype was found in all stingless bees from the north (21 nests) and northeast (32 nests), and 23/28 nests from the Central region, whereas a BB (253/253 bp) genotype was observed in most samples from peninsular Thailand (42/53 nests). Heterozygotes exhibiting the AB (253/259 bp) genotype were observed in 5 of 28 nests from Prachuap Khiri Khan located slightly above the Kra ecotone and 11 of 53 nests originated further south of the Kra ecotone. Genotype distribution patterns of CUTc1 clearly indicated intraspecific population differentiation of Thai T. collina.

Highly pathogenic avian influenza H5N1 Clade 2.3.2.1c virus in migratory birds, 2014-2015.

PubMed

Bi, Yuhai; Chen, Jianjun; Zhang, Zhenjie; Li, Mingxin; Cai, Tianlong; Sharshov, Kirill; Susloparov, Ivan; Shestopalov, Alexander; Wong, Gary; He, Yubang; Xing, Zhi; Sun, Jianqing; Liu, Di; Liu, Yingxia; Liu, Lei; Liu, Wenjun; Lei, Fumin; Shi, Weifeng; Gao, George F

2016-08-01

A novel Clade 2.3.2.1c H5N1 reassortant virus caused several outbreaks in wild birds in some regions of China from late 2014 to 2015. Based on the genetic and phylogenetic analyses, the viruses possess a stable gene constellation with a Clade 2.3.2.1c HA, a H9N2-derived PB2 gene and the other six genes of Asian H5N1-origin. The Clade 2.3.2.1c H5N1 reassortants displayed a high genetic relationship to a human H5N1 strain (A/Alberta/01/2014). Further analysis showed that similar viruses have been circulating in wild birds in China, Russia, Dubai (Western Asia), Bulgaria and Romania (Europe), as well as domestic poultry in some regions of Africa. The affected areas include the Central Asian, East Asian-Australasian, West Asian-East African, and Black Sea/Mediterranean flyways. These results show that the novel Clade 2.3.2.1c reassortant viruses are circulating worldwide and may have gained a selective advantage in migratory birds, thus posing a serious threat to wild birds and potentially humans.

Fibroblast growth factor-10 signals development of von Brunn's nests in the exstrophic bladder

PubMed Central

Eastman, Rocky; Leaf, Elizabeth M.; Zhang, Dianzhong; True, Lawrence D.; Sweet, Robert M.; Seidel, Kristy; Siebert, Joseph R.; Grady, Richard; Mitchell, Michael E.

2010-01-01

von Brunn's nests have long been recognized as precursors of benign lesions of the urinary bladder mucosa. We report here that von Brunn's nests are especially prevalent in the exstrophic bladder, a birth defect that predisposes the patient to formation of bladder cancer. Cells of von Brunn's nest were found to coalesce into a stratified, polarized epithelium which surrounds itself with a capsule-like structure rich in types I, III, and IV collagen. Histocytochemical analysis and keratin profiling demonstrated that nested cells exhibited a phenotype similar, but not identical, to that of urothelial cells of transitional epithelium. Immunostaining and in situ hybridization analysis of exstrophic tissue demonstrated that the FGF-10 receptor is synthesized and retained by cells of von Brunn's nest. In contrast, FGF-10 is synthesized and secreted by mesenchymal fibroblasts via a paracrine pathway that targets basal epithelial cells of von Brunn's nests. Small clusters of 10pRp cells, positive for both FGF-10 and its receptor, were observed both proximal to and inside blood vessels in the lamina propria. The collective evidence points to a mechanism where von Brunn's nests develop under the control of the FGF-10 signal transduction system and suggests that 10pRp cells may be the original source of nested cells. PMID:20719973

Preliminary evaluation of a nest usage sensor to detect double nest occupations of laying hens.

PubMed

Zaninelli, Mauro; Costa, Annamaria; Tangorra, Francesco Maria; Rossi, Luciana; Agazzi, Alessandro; Savoini, Giovanni

2015-01-26

Conventional cage systems will be replaced by housing systems that allow hens to move freely. These systems may improve hens' welfare, but they lead to some disadvantages: disease, bone fractures, cannibalism, piling and lower egg production. New selection criteria for existing commercial strains should be identified considering individual data about laying performance and the behavior of hens. Many recording systems have been developed to collect these data. However, the management of double nest occupations remains critical for the correct egg-to-hen assignment. To limit such events, most systems adopt specific trap devices and additional mechanical components. Others, instead, only prevent these occurrences by narrowing the nest, without any detection and management. The aim of this study was to develop and test a nest usage "sensor", based on imaging analysis, that is able to automatically detect a double nest occupation. Results showed that the developed sensor correctly identified the double nest occupation occurrences. Therefore, the imaging analysis resulted in being a useful solution that could simplify the nest construction for this type of recording system, allowing the collection of more precise and accurate data, since double nest occupations would be managed and the normal laying behavior of hens would not be discouraged by the presence of the trap devices.

Preliminary Evaluation of a Nest Usage Sensor to Detect Double Nest Occupations of Laying Hens

PubMed Central

Zaninelli, Mauro; Costa, Annamaria; Tangorra, Francesco Maria; Rossi, Luciana; Agazzi, Alessandro; Savoini, Giovanni

2015-01-01

Conventional cage systems will be replaced by housing systems that allow hens to move freely. These systems may improve hens' welfare, but they lead to some disadvantages: disease, bone fractures, cannibalism, piling and lower egg production. New selection criteria for existing commercial strains should be identified considering individual data about laying performance and the behavior of hens. Many recording systems have been developed to collect these data. However, the management of double nest occupations remains critical for the correct egg-to-hen assignment. To limit such events, most systems adopt specific trap devices and additional mechanical components. Others, instead, only prevent these occurrences by narrowing the nest, without any detection and management. The aim of this study was to develop and test a nest usage “sensor”, based on imaging analysis, that is able to automatically detect a double nest occupation. Results showed that the developed sensor correctly identified the double nest occupation occurrences. Therefore, the imaging analysis resulted in being a useful solution that could simplify the nest construction for this type of recording system, allowing the collection of more precise and accurate data, since double nest occupations would be managed and the normal laying behavior of hens would not be discouraged by the presence of the trap devices. PMID:25629704

Taxonomic changes in Oenothera sections Gaura and Calylophus (Onagraceae).

PubMed

Wagner, Warren L; Krakos, Kyra N; Hoch, Peter C

2013-01-01

The long-recognized genus Gaura was shown recently to be deeply nested within one of two major clades of Oenothera. New molecular data indicate further taxonomic changes are necessary in Oenothera sect. Gaura. We make these changes here, including three new combinations, in advance of the Onagraceae treatment for the Flora of North America. The new phylogenetic studies show that several pairs of taxa treated as subspecies in the most recent revision by Raven and Gregory (1972) had independent origins within sect. Gaura, and are here elevated to species level (Oenothera nealleyi for Gaura suffulta subsp. nealleyi; Oenothera dodgeniana for Gaura neomexicana subsp. neomexicana; and Oenothera podocarpa for Gaura hexandra subsp. gracilis). Also, a nomenclatural problem in Oenothera sect. Calylophus is corrected by adopting the name Oenothera capillifolia Scheele for the species known previously, and nomenclaturally correct, as Calylophus berlandieri Spach. This problem necessitates a new combination Oenothera capillifolia subsp. berlandieri.

Taxonomic changes in Oenothera sections Gaura and Calylophus (Onagraceae)

PubMed Central

Wagner, Warren L.; Krakos, Kyra N.; Hoch, Peter C.

2013-01-01

Abstract The long-recognized genus Gaura was shown recently to be deeply nested within one of two major clades of Oenothera. New molecular data indicate further taxonomic changes are necessary in Oenothera sect. Gaura. We make these changes here, including three new combinations, in advance of the Onagraceae treatment for the Flora of North America. The new phylogenetic studies show that several pairs of taxa treated as subspecies in the most recent revision by Raven and Gregory (1972) had independent origins within sect. Gaura, and are here elevated to species level (Oenothera nealleyi for Gaura suffulta subsp. nealleyi; Oenothera dodgeniana for Gaura neomexicana subsp. neomexicana; and Oenothera podocarpa for Gaura hexandra subsp. gracilis). Also, a nomenclatural problem in Oenothera sect. Calylophus is corrected by adopting the name Oenothera capillifolia Scheele for the species known previously, and nomenclaturally correct, as Calylophus berlandieri Spach. This problem necessitates a new combination Oenothera capillifolia subsp. berlandieri. PMID:24399892

Two new species of Cyrtodactylus (Squamata: Gekkonidae) from the karst forest of Hoa Binh Province, Vietnam.

PubMed

Nguyen, Truong Quang; Le, Minh Duc; Pham, Anh Van; Ngo, Hai Ngoc; Hoang, Chung Van; Ziegler, Thomas

2015-07-13

We describe two new species of the genus Cyrtodactylus on the basis of a new reptile collection from the limestone karst forest of Hoa Binh Province, northwestern Vietnam. Cyrtodactylus otai sp. nov. from Hang Kia-Pa Co Nature Reserve and Cyrtodactylus bobrovi sp. nov. from Ngoc Son-Ngo Luong Nature Reserve can be distinguished from each other and from their congeners by their genetic distinction and morphological differences in number of precloacal pores, femoral scales, ventral scales, lamellae, subcaudals and dorsal tubercle arrangement, as well as in size and color pattern. In phylogenetic analyses, both new species are nested in a clade containing taxa from northwestern and northcentral Vietnam and northern Laos, i.e., C. bichnganae and C. cf. martini from northwestern Vietnam, C. puhuensis from northcentral Vietnam, and C. spelaeus, C. vilaphongi, and C. wayakonei from northern Laos.

Nest-site selection analysis of hooded crane (Grus monacha) in Northeastern China based on a multivariate ensemble model.

PubMed

Jiao, Shengwu; Guo, Yumin; Huettmann, Falk; Lei, Guangchun

2014-07-01

Avian nest-site selection is an important research and management subject. The hooded crane (Grus monacha) is a vulnerable (VU) species according to the IUCN Red List. Here, we present the first long-term Chinese legacy nest data for this species (1993-2010) with publicly available metadata. Further, we provide the first study that reports findings on multivariate nest habitat preference using such long-term field data for this species. Our work was carried out in Northeastern China, where we found and measured 24 nests and 81 randomly selected control plots and their environmental parameters in a vast landscape. We used machine learning (stochastic boosted regression trees) to quantify nest selection. Our analysis further included varclust (R Hmisc) and (TreenNet) to address statistical correlations and two-way interactions. We found that from an initial list of 14 measured field variables, water area (+), water depth (+) and shrub coverage (-) were the main explanatory variables that contributed to hooded crane nest-site selection. Agricultural sites played a smaller role in the selection of these nests. Our results are important for the conservation management of cranes all over East Asia and constitute a defensible and quantitative basis for predictive models.

Multilocus sequence analysis reveals extensive genetic variety within Tenacibaculum spp. associated with ulcers in sea-farmed fish in Norway.

PubMed

Olsen, Anne Berit; Gulla, Snorre; Steinum, Terje; Colquhoun, Duncan J; Nilsen, Hanne K; Duchaud, Eric

2017-06-01

Skin ulcer development in sea-reared salmonids, commonly associated with Tenacibaculum spp., is a significant fish welfare- and economical problem in Norwegian aquaculture. A collection of 89 Tenacibaculum isolates was subjected to multilocus sequence analysis (MLSA). The isolates were retrieved from outbreaks of clinical disease in farms spread along the Norwegian coast line from seven different fish species over a period of 19 years. MLSA analysis reveals considerable genetic diversity, but allows identification of four main clades. One clade encompasses isolates belonging to the species T. dicentrarchi, whereas three clades encompass bacteria that likely represent novel, as yet undescribed species. The study identified T. maritimum in lumpsucker, T. ovolyticum in halibut, and has extended the host and geographic range for T. soleae, isolated from wrasse. The overall lack of clonality and host specificity, with some indication of geographical range restriction argue for local epidemics involving multiple strains. The diversity of Tenacibaculum isolates from fish displaying ulcerative disease may complicate vaccine development. Copyright © 2017 Elsevier B.V. All rights reserved.

Comparing primate crania: The importance of fossils.

PubMed

Fleagle, John G; Gilbert, Christopher C; Baden, Andrea L

2016-10-01

Extant primate crania represent a small subset of primate crania that have existed. The main objective here is to examine how the inclusion of fossil crania changes our understanding of primate cranial diversity relative to analyses of extant primates. We hypothesize that fossil taxa will change the major axes of cranial shape, occupy new areas of morphospace, change the relative diversity of major primate clades, and fill in notable gaps separating major primate taxa/clades. Eighteen 3D landmarks were collected on 157 extant and fossil crania representing 90 genera. Data were subjected to a Generalized Procrustes Analysis then principal components analysis. Relative diversity between clades was assessed using an F-statistic. Fossil taxa do not significantly alter major axes of cranial shape, but they do occupy unique areas of morphospace, change the relative diversity between clades, and fill in notable gaps in primate cranial evolution. Strepsirrhines remain significantly less diverse than anthropoids. Fossil hominins fill the gap in cranial morphospace between extant great apes and modern humans. The morphospace outlined by living primates largely includes that occupied by fossil taxa, suggesting that the cranial diversity of living primates generally encompasses the total diversity that has evolved in this Order. The evolution of the anthropoid cranium was a significant event allowing anthropoids to achieve significantly greater cranial diversity compared to strepsirrhines. Fossil taxa fill in notable gaps within and between clades, highlighting their transitional nature and eliminating the appearance of large morphological distances between extant taxa, particularly in the case of extant hominids. © 2016 Wiley Periodicals, Inc.

A critical evaluation of various methods for the analysis of flow-solid interaction in a nest of thin cylinders subjected to cross flows

NASA Technical Reports Server (NTRS)

Kim, Sang-Wook

1987-01-01

Various experimental, analytical, and numerical analysis methods for flow-solid interaction of a nest of cylinders subjected to cross flows are reviewed. A nest of cylinders subjected to cross flows can be found in numerous engineering applications including the Space Shuttle Maine Engine-Main Injector Assembly (SSME-MIA) and nuclear reactor heat exchangers. Despite its extreme importance in engineering applications, understanding of the flow-solid interaction process is quite limited and design of the tube banks are mostly dependent on experiments and/or experimental correlation equations. For future development of major numerical analysis methods for the flow-solid interaction of a nest of cylinders subjected to cross flow, various turbulence models, nonlinear structural dynamics, and existing laminar flow-solid interaction analysis methods are included.

New Information on the Cranial Anatomy of Acrocanthosaurus atokensis and Its Implications for the Phylogeny of Allosauroidea (Dinosauria: Theropoda)

PubMed Central

Eddy, Drew R.; Clarke, Julia A.

2011-01-01

Background Allosauroidea has a contentious taxonomic and systematic history. Within this group of theropod dinosaurs, considerable debate has surrounded the phylogenetic position of the large-bodied allosauroid Acrocanthosaurus atokensis from the Lower Cretaceous Antlers Formation of North America. Several prior analyses recover Acrocanthosaurus atokensis as sister taxon to the smaller-bodied Allosaurus fragilis known from North America and Europe, and others nest Acrocanthosaurus atokensis within Carcharodontosauridae, a large-bodied group of allosauroids that attained a cosmopolitan distribution during the Early Cretaceous. Methodology/Principal Findings Re-evaluation of a well-preserved skull of Acrocanthosaurus atokensis (NCSM 14345) provides new information regarding the palatal complex and inner surfaces of the skull and mandible. Previously inaccessible internal views and articular surfaces of nearly every element of the skull are described. Twenty-four new morphological characters are identified as variable in Allosauroidea, combined with 153 previously published characters, and evaluated for eighteen terminal taxa. Systematic analysis of this dataset recovers a single most parsimonious topology placing Acrocanthosaurus atokensis as a member of Allosauroidea, in agreement with several recent analyses that nest the taxon well within Carcharodontosauridae. Conclusions/Significance A revised diagnosis of Acrocanthosaurus atokensis finds that the species is distinguished by four primary characters, including: presence of a knob on the lateral surangular shelf; enlarged posterior surangular foramen; supraoccipital protruding as a double-boss posterior to the nuchal crest; and pneumatic recess within the medial surface of the quadrate. Furthermore, the recovered phylogeny more closely agrees with the stratigraphic record than hypotheses that place Acrocanthosaurus atokensis as more closely related to Allosaurus fragilis. Fitch optimization of body size is also more consistent with the placement of Acrocanthosaurus atokensis within a clade of larger carcharodontosaurid taxa than with smaller-bodied taxa near the base of Allosauroidea. This placement of Acrocanthosaurus atokensis supports previous hypotheses of a global carcharodontosaurid radiation during the Early Cretaceous. PMID:21445312

Host range and community structure of avian nest parasites in the genus Philornis (Diptera: Muscidae) on the island of Trinidad.

PubMed

Bulgarella, Mariana; Heimpel, George E

2015-09-01

Parasite host range can be influenced by physiological, behavioral, and ecological factors. Combining data sets on host-parasite associations with phylogenetic information of the hosts and the parasites involved can generate evolutionary hypotheses about the selective forces shaping host range. Here, we analyzed associations between the nest-parasitic flies in the genus Philornis and their host birds on Trinidad. Four of ten Philornis species were only reared from one species of bird. Of the parasite species with more than one host bird species, P. falsificus was the least specific and P. deceptivus the most specific attacking only Passeriformes. Philornis flies in Trinidad thus include both specialists and generalists, with varying degrees of specificity within the generalists. We used three quantities to more formally compare the host range of Philornis flies: the number of bird species attacked by each species of Philornis, a phylogenetically informed host specificity index (Poulin and Mouillot's S TD), and a branch length-based S TD. We then assessed the phylogenetic signal of these measures of host range for 29 bird species. None of these measures showed significant phylogenetic signal, suggesting that clades of Philornis did not differ significantly in their ability to exploit hosts. We also calculated two quantities of parasite species load for the birds - the parasite species richness, and a variant of the S TD index based on nodes rather than on taxonomic levels - and assessed the signal of these measures on the bird phylogeny. We did not find significant phylogenetic signal for the parasite species load or the node-based S TD index. Finally, we calculated the parasite associations for all bird pairs using the Jaccard index and regressed these similarity values against the number of nodes in the phylogeny separating bird pairs. This analysis showed that Philornis on Trinidad tend to feed on closely related bird species more often than expected by chance.

Trypanosoma janseni n. sp. (Trypanosomatida: Trypanosomatidae) isolated from Didelphis aurita (Mammalia: Didelphidae) in the Atlantic Rainforest of Rio de Janeiro, Brazil: integrative taxonomy and phylogeography within the Trypanosoma cruzi clade.

PubMed

Lopes, Camila Madeira Tavares; Menna-Barreto, Rubem Figueiredo Sadok; Pavan, Márcio Galvão; Pereira, Mirian Cláudia De Souza; Roque, André Luiz R

2018-01-01

Didelphis spp. are a South American marsupial species that are among the most ancient hosts for the Trypanosoma spp. We characterise a new species (Trypanosoma janseni n. sp.) isolated from the spleen and liver tissues of Didelphis aurita in the Atlantic Rainforest of Rio de Janeiro, Brazil. The parasites were isolated and a growth curve was performed in NNN and Schneider's media containing 10% foetal bovine serum. Parasite morphology was evaluated via light microscopy on Giemsa-stained culture smears, as well as scanning and transmission electron microscopy. Molecular taxonomy was based on a partial region (737-bp) of the small subunit (18S) ribosomal RNA gene and 708 bp of the nuclear marker, glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) genes. Maximum likelihood and Bayesian inference methods were used to perform a species coalescent analysis and to generate individual and concatenated gene trees. Divergence times among species that belong to the T. cruzi clade were also inferred. In vitro growth curves demonstrated a very short log phase, achieving a maximum growth rate at day 3 followed by a sharp decline. Only epimastigote forms were observed under light and scanning microscopy. Transmission electron microscopy analysis showed structures typical to Trypanosoma spp., except one structure that presented as single-membraned, usually grouped in stacks of three or four. Phylogeography analyses confirmed the distinct species status of T. janseni n. sp. within the T. cruzi clade. Trypanosoma janseni n. sp. clusters with T. wauwau in a well-supported clade, which is exclusive and monophyletic. The separation of the South American T. wauwau + T. janseni coincides with the separation of the Southern Super Continent. This clade is a sister group of the trypanosomes found in Australian marsupials and its discovery sheds light on the initial diversification process based on what we currently know about the T. cruzi clade.

Phylogenetic relationships of Cranichidinae and Prescottiinae (Orchidaceae, Cranichideae) inferred from plastid and nuclear DNA sequences

PubMed Central

Salazar, Gerardo A.; Cabrera, Lidia I.; Madriñán, Santiago; Chase, Mark W.

2009-01-01

Background and Aims Phylogenetic relationships of subtribes Cranichidinae and Prescottiinae, two diverse groups of neotropical terrestrial orchids, are not satisfactorily understood. A previous molecular phylogenetic study supported monophyly for Cranichidinae, but Prescottiinae consisted of two clades not sister to one another. However, that analysis included only 11 species and eight genera of these subtribes. Here, plastid and nuclear DNA sequences are analysed for an enlarged sample of genera and species of Cranichidinae and Prescottiinae with the aim of clarifying their relationships, evaluating the phylogenetic position of the monospecific genera Exalaria, Ocampoa and Pseudocranichis and examining the value of various structural traits as taxonomic markers. Methods Approx. 6000 bp of nucleotide sequences from nuclear ribosomal (ITS) and plastid DNA (rbcL, matK-trnK and trnL-trnF) were analysed with cladistic parsimony and Bayesian inference for 45 species/14 genera of Cranichidinae and Prescottiinae (plus suitable outgroups). The utility of flower orientation, thickenings of velamen cell walls, hamular viscidium and pseudolabellum to mark clades recovered by the molecular analysis was assessed by tracing these characters on the molecular trees. Key Results Spiranthinae, Cranichidinae, paraphyletic Prescottia (with Pseudocranichis embedded), and a group of mainly Andean ‘prescottioid’ genera (the ‘Stenoptera clade’) were strongly supported. Relationships among these clades were unresolved by parsimony but the Bayesian tree provided moderately strong support for the resolution (Spiranthinae–(Stenoptera clade-(Prescottia/Pseudocranichis–Cranichidinae))). Three of the four structural characters mark clades on the molecular trees, but the possession of a pseudolabellum is variable in the polyphyletic Ponthieva. Conclusions No evidence was found for monophyly of Prescottiinae and the reinstatement of Cranichidinae s.l. (including the genera of ‘Prescottiinae’) is favoured. Cranichidinae s.l. are diagnosed by non-resupinate flowers. Lack of support from parsimony for relationships among the major clades of core spiranthids is suggestive of a rapid morphological radiation or a slow rate of molecular evolution. PMID:19136493

Ecological consequences of colony structure in dynamic ant nest networks.

PubMed

Ellis, Samuel; Franks, Daniel W; Robinson, Elva J H

2017-02-01

Access to resources depends on an individual's position within the environment. This is particularly important to animals that invest heavily in nest construction, such as social insects. Many ant species have a polydomous nesting strategy: a single colony inhabits several spatially separated nests, often exchanging resources between the nests. Different nests in a polydomous colony potentially have differential access to resources, but the ecological consequences of this are unclear. In this study, we investigate how nest survival and budding in polydomous wood ant ( Formica lugubris ) colonies are affected by being part of a multi-nest system. Using field data and novel analytical approaches combining survival models with dynamic network analysis, we show that the survival and budding of nests within a polydomous colony are affected by their position in the nest network structure. Specifically, we find that the flow of resources through a nest, which is based on its position within the wider nest network, determines a nest's likelihood of surviving and of founding new nests. Our results highlight how apparently disparate entities in a biological system can be integrated into a functional ecological unit. We also demonstrate how position within a dynamic network structure can have important ecological consequences.

A new giant titanosaur sheds light on body mass evolution among sauropod dinosaurs.

PubMed

Carballido, José L; Pol, Diego; Otero, Alejandro; Cerda, Ignacio A; Salgado, Leonardo; Garrido, Alberto C; Ramezani, Jahandar; Cúneo, Néstor R; Krause, Javier M

2017-08-16

Titanosauria was the most diverse and successful lineage of sauropod dinosaurs. This clade had its major radiation during the middle Early Cretaceous and survived up to the end of that period. Among sauropods, this lineage has the most disparate values of body mass, including the smallest and largest sauropods known. Although recent findings have improved our knowledge on giant titanosaur anatomy, there are still many unknown aspects about their evolution, especially for the most gigantic forms and the evolution of body mass in this clade. Here we describe a new giant titanosaur, which represents the largest species described so far and one of the most complete titanosaurs. Its inclusion in an extended phylogenetic analysis and the optimization of body mass reveals the presence of an endemic clade of giant titanosaurs inhabited Patagonia between the Albian and the Santonian. This clade includes most of the giant species of titanosaurs and represents the major increase in body mass in the history of Titanosauria. © 2017 The Author(s).

Colletotrichum gloeosporioides s.l. associated with Theobroma cacao and other plants in Panama: multilocus phylogenies distinguish host-associated pathogens from asymptomatic endophytes.

PubMed

Rojas, Enith I; Rehner, Stephen A; Samuels, Gary J; Van Bael, Sunshine A; Herre, Edward A; Cannon, Paul; Chen, Rui; Pang, Junfeng; Wang, Ruiwu; Zhang, Yaping; Peng, Yan-Qiong; Sha, Tao

2010-01-01

Colletotrichum interacts with numerous plant species overtly as symptomatic pathogens and cryptically as asymptomatic endophytes. It is not known whether these contrasting ecological modes are optional strategies expressed by individual Colletotrichum species or whether a species' ecology is explicitly pathogenic or endophytic. We explored this question by inferring relationships among 77 C. gloeosporioides s.l. strains isolated from asymptomatic leaves and from anthracnose lesions on leaves and fruits of Theobroma cacao (cacao) and other plants from Panamá. ITS and 5'-tef1 were used to assess diversity and to delineate operational taxonomic units for multilocus phylogenetic analysis. The ITS and 5'-tef1 screens concordantly resolved four strongly supported lineages, clades A-D: Clade A includes the ex type of C. gloeosporioides, clade B includes the ex type ITS sequence of C. boninense, and clades C and D are unidentified. The ITS yielded limited resolution and support within all clades, in particular the C. gloeosporioides clade (A), the focal lineage dealt with in this study. In contrast the 5'-tef1 screen differentiated nine distinctive haplotype subgroups within the C. gloeosporioides clade that were concordant with phylogenetic terminals resolved in a five-locus nuclear phylogeny. Among these were two phylogenetic species associated with symptomatic infections specific to either cacao or mango and five phylogenetic species isolated principally as asymptomatic infections from cacao and other plant hosts. We formally describe two new species, C. tropicale and C. ignotum, that are frequent asymptomatic associates of cacao and other Neotropical plant species, and epitypify C. theobromicola, which is associated with foliar and fruit anthracnose lesions of cacao. Asymptomatic Colletotrichum strains isolated from cacao plants grown in China included six distinct C. gloeosporioides clade taxa, only one of which is known to occur in the Neotropics.

New insights into the intricate taxonomy and phylogeny of the Sylvia curruca complex.

PubMed

Olsson, Urban; Leader, Paul J; Carey, Geoff J; Khan, Aleem Ahmed; Svensson, Lars; Alström, Per

2013-04-01

We use the mitochondrial cytochrome b from 213 individuals and the three nuclear introns BRM 15, myoglobin 2 and ODC 6-7 from a smaller subsample to evaluate the taxonomy of the Lesser Whitethroat Sylvia curruca (Aves, Passeriformes, Sylviidae) complex, which has long been controversial. We sequenced type material of the taxa althaea, blythi, margelanica and minula, and used topotypical material of caucasica, chuancheica, curruca and telengitica. The nuclear introns fail to resolve the complex, but cytochrome b recovers six major clades, revealing genetically identifiable populations corresponding to previously named taxa, and we propose that the names althaea, blythi, curruca, halimodendri, margelanica and minula, respectively, should be used for these. The margelanica clade is suggested to have a more extensive distribution than previously known, including both the taxon telengitica and a population in eastern Mongolia. The taxon minula is found to have a more restricted range than generally believed, only breeding in China. According to the mitochondrial gene tree, there is a basal dichotomy, with the taxa althaea, blythi, halimodendri and margelanica being part of one clade, well separated from a clade containing curruca and minula. Dating analysis suggests that a basal divergence separating curruca and minula from the other four taxa occurred between 4.2 and 7.2 mya; these two then diverged between 2.3 and 4.4 mya. The splits between the althaea, blythi, halimodendri and margelanica lineages is inferred to have occurred later, approximately between 1.0 and 2.5 mya (all 95% HPD). The nucleotide data suggest significant departure from demographic equilibrium in blythi (clade 1a), halimodendri (clade 2a) and minula, whereas tendencies are weaker for other clades. We propose that the names althaea, blythi, curruca, halimodendri, margelanica and minula should be used for the major clades. However, whether these are treated as subspecies or species is largely a matter of species definition and is not resolved by our data. Copyright © 2013 Elsevier Inc. All rights reserved.

Expanding the World of Marine Bacterial and Archaeal Clades

PubMed Central

Yilmaz, Pelin; Yarza, Pablo; Rapp, Josephine Z.; Glöckner, Frank O.

2016-01-01

Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 “clades,” at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as our CTU approach breaks down these randomly lumped clades into smaller objectively calculated subgroups. Finally, all taxa were classified and named following standards compatible with the Bacteriological Code rules, enhancing their digitization, and comparability with future microbial ecological and taxonomy studies. PMID:26779174

Molecular phylogeny of the subgenus Ceratotropis (genus Vigna, Leguminosae) reveals three eco-geographical groups and Late Pliocene-Pleistocene diversification: evidence from four plastid DNA region sequences.

PubMed

Javadi, Firouzeh; Tun, Ye Tun; Kawase, Makoto; Guan, Kaiyun; Yamaguchi, Hirofumi

2011-08-01

The subgenus Ceratotropis in the genus Vigna is widely distributed from the Himalayan highlands to South, Southeast and East Asia. However, the interspecific and geographical relationships of its members are poorly understood. This study investigates the phylogeny and biogeography of the subgenus Ceratotropis using chloroplast DNA sequence data. Sequence data from four intergenic spacer regions (petA-psbJ, psbD-trnT, trnT-trnE and trnT-trnL) of chloroplast DNA, alone and in combination, were analysed using Bayesian and parsimony methods. Divergence times for major clades were estimated with penalized likelihood. Character evolution was examined by means of parsimony optimization and MacClade. Parsimony and Bayesian phylogenetic analyses on the combined data demonstrated well-resolved species relationships in which 18 Vigna species were divided into two major geographical clades: the East Asia-Southeast Asian clade and the Indian subcontinent clade. Within these two clades, three well-supported eco-geographical groups, temperate and subtropical (the East Asia-Southeast Asian clade) and tropical (the Indian subcontinent clade), are recognized. The temperate group consists of V. minima, V. nepalensis and V. angularis. The subtropical group comprises the V. nakashimae-V. riukiuensis-V. minima subgroup and the V. hirtella-V. exilis-V. umbellata subgroup. The tropical group contains two subgroups: the V. trinervia-V. reflexo-pilosa-V. trilobata subgroup and the V. mungo-V. grandiflora subgroup. An evolutionary rate analysis estimated the divergence time between the East Asia-Southeast Asia clade and the Indian subcontinent clade as 3·62 ± 0·3 million years, and that between the temperate and subtropical groups as 2·0 ± 0·2 million years. The findings provide an improved understanding of the interspecific relationships, and ecological and geographical phylogenetic structure of the subgenus Ceratotropis. The quaternary diversification of the subgenus Ceratotropis implicates its geographical dispersal in the south-eastern part of Asia involving adaptation to climatic condition after the collision of the Indian subcontinent with the Asian plate. The phylogenetic results indicate that the epigeal germination is plesiomorphic, and the germination type evolved independently multiple times in this subgenus, implying its limited taxonomic utility.

Symbiodinium diversity among host clionaid sponges from Caribbean and Pacific reefs: Evidence of heteroplasmy and putative host-specific symbiont lineages.

PubMed

Hill, Malcolm; Allenby, Ashley; Ramsby, Blake; Schönberg, Christine; Hill, April

2011-04-01

Among the Porifera, symbiosis with Symbiodinium spp. (i.e., zooxanthellae) is largely restricted to members of the family Clionaidae. We surveyed the diversity of zooxanthellae associated with sponges from the Caribbean and greater Indo-Pacific regions using chloroplast large subunit (cp23S) domain V sequences. We provide the first report of Clade C Symbiodinium harbored by a sponge (Cliona caesia), and the first report of Clade A Symbiodinium from an Indo-Pacific sponge (C. jullieni). Clade A zooxanthellae were also identified in sponges from the Caribbean, which has been reported previously. Sponges that we examined from the Florida Keys all harbored Clade G Symbiodinium as did C. orientalis from the Indo-Pacific, which also supports earlier work with sponges. Two distinct Clade G lineages were identified in our phylogenetic analysis; Symbiodinium extracted from clionaid sponges formed a monophyletic group sister to Symbiodinium found in foraminiferans. Truncated and 'normal' length variants of 23S rDNA sequences were detected simultaneously in all three morphotypes of C. varians providing the first evidence of chloroplast-based heteroplasmy in a sponge. None of the other sponge species examined showed evidence of heteroplasmy. As in previous work, length variation in cp23S domain V sequences was found to correspond in a highly precise manner to finer resolution of phylogenetic topology among Symbiodinium clades. On a global scale, existing data indicate that members of the family Clionaidae that host zooxanthellae can form symbiotic associations with at least four Symbiodinium clades. The majority of sponge hosts appear to harbor only one cladal type of symbiont, but some species can harbor more than one clade of zooxanthellae concurrently. The observed differences in the number of partners harbored by sponges raise important questions about the degree of coevolutionary integration and specificity of these symbioses. Although our sample sizes are small, we propose that one of the Clade G lineages identified in this study is comprised of sponge-specialist zooxanthellae. These zooxanthellae are common in Caribbean sponges, but additional work in other geographic regions is necessary to test this idea. Sponges from the Indo-Pacific region harbor zooxanthellae from Clades A, C, and G, but more sponges from this region should be examined. Copyright © 2011 Elsevier Inc. All rights reserved.

Molecular detection and genetic diversity of Babesia gibsoni in dogs in Bangladesh.

PubMed

Terao, Masashi; Akter, Shirin; Yasin, Md Golam; Nakao, Ryo; Kato, Hirotomo; Alam, Mohammad Zahangir; Katakura, Ken

2015-04-01

Babesia gibsoni is a tick-borne hemoprotozoan parasite of dogs that often causes fever and hemolytic illness. Detection of B. gibsoni has been predominantly reported in Asian countries, including Japan, Korea, Taiwan, Malaysia, Bangladesh and India. The present study shows the first molecular characterization of B. gibsoni detected from dogs in Bangladesh. Blood samples were collected on FTA® Elute cards from 50 stray dogs in Mymensingh District in Bangladesh. DNA eluted from the cards was subjected to nested PCR for the 18S rRNA gene of Babesia species. Approximately 800bp PCR products were detected in 15 of 50 dogs (30%). Based on restriction fragment length polymorphism (RFLP) and direct sequencing of the PCR products, all parasite isolates were identified as B. gibsoni. Furthermore, the BgTRAP (B. gibsoni thrombospondin-related adhesive protein) gene fragments were detected in 13 of 15 18S rRNA gene PCR positive blood samples. Phylogenetic analysis of the BgTRAP gene revealed that B. gibsoni parasites in Bangladesh formed a cluster, which was genetically different from other Asian B. gibsoni isolates. In addition, tandem repeat analysis of the BgTRAP gene clearly showed considerable genetic variation among Bangladeshi isolates. These results suggested that B. gibsoni parasites in a different genetic clade are endemic in dogs in Bangladesh. Further studies are required to elucidate the origin, distribution, vector and pathogenesis of B. gibsoni parasites circulating in dogs in Bangladesh. Copyright © 2015 Elsevier B.V. All rights reserved.

Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea.

PubMed

Ravago-Gotanco, Rachel; de la Cruz, Talna Lorena; Pante, Ma Josefa; Borsa, Philippe

2018-01-01

The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P < 0.001); (2) low frequency of later-generation hybrids; (3) significant association with mitochondrial Clade A and Clade B, respectively; and (4) subtle yet significant body shape differences as inferred from geometric morphometric analysis. The divergence between mitochondrial Clade C and the two other clades was not matched by genetic differences at microsatellite marker loci. The occurrence of discordant mitonuclear combinations (20.5% of the total number of individuals) is thought to result from mitochondrial introgression, consistent with a scenario of demographic, and presumably spatial, post-Pleistocene expansion of populations from northern regions into a secondary contact zone in the South China Sea. Mitonuclear discordance due to introgression obscures phylogenetic relationships for recently-diverged lineages, and cautions against the use of mitochondrial markers alone for species identification within the mottled rabbitfish species complex in the South China Sea region.

Phylogenetic constraints do not explain the rarity of nitrogen-fixing trees in late-successional temperate forests.

PubMed

Menge, Duncan N L; DeNoyer, Jeanne L; Lichstein, Jeremy W

2010-08-06

Symbiotic nitrogen (N)-fixing trees are rare in late-successional temperate forests, even though these forests are often N limited. Two hypotheses could explain this paradox. The 'phylogenetic constraints hypothesis' states that no late-successional tree taxa in temperate forests belong to clades that are predisposed to N fixation. Conversely, the 'selective constraints hypothesis' states that such taxa are present, but N-fixing symbioses would lower their fitness. Here we test the phylogenetic constraints hypothesis. Using U.S. forest inventory data, we derived successional indices related to shade tolerance and stand age for N-fixing trees, non-fixing trees in the 'potentially N-fixing clade' (smallest angiosperm clade that includes all N fixers), and non-fixing trees outside this clade. We then used phylogenetically independent contrasts (PICs) to test for associations between these successional indices and N fixation. Four results stand out from our analysis of U.S. trees. First, N fixers are less shade-tolerant than non-fixers both inside and outside of the potentially N-fixing clade. Second, N fixers tend to occur in younger stands in a given geographical region than non-fixers both inside and outside of the potentially N-fixing clade. Third, the potentially N-fixing clade contains numerous late-successional non-fixers. Fourth, although the N fixation trait is evolutionarily conserved, the successional traits are relatively labile. These results suggest that selective constraints, not phylogenetic constraints, explain the rarity of late-successional N-fixing trees in temperate forests. Because N-fixing trees could overcome N limitation to net primary production if they were abundant, this study helps to understand the maintenance of N limitation in temperate forests, and therefore the capacity of this biome to sequester carbon.

Catastrophic health expenditure: a comparative analysis of empty-nest and non-empty-nest households with seniors in Shandong, China.

PubMed

Yang, Tingting; Chu, Jie; Zhou, Chengchao; Medina, Alexis; Li, Cuicui; Jiang, Shan; Zheng, Wengui; Sun, Liyuan; Liu, Jing

2016-07-05

The aim of this study was to compare the catastrophic health expenditure (CHE) prevalence and its determinants between empty-nest and non-empty-nest elderly households. Shandong province of China. A total of 2761 elderly households are included in the analysis. CHE incidence among elderly households was 44.9%. The CHE incidence of empty-nest singles (59.3%, p=0.000, OR=3.19) and empty-nest couples (52.9%, p=0.000, OR=2.45) are both statistically higher than that of non-empty-nest elderly households (31.4%). An inverse association was observed between CHE incidence and income level in all elderly household types. Factors including 1 or more household elderly members with non-communicable chronic diseases in the past 6 months, 1 or more elderly household members being hospitalised in the past year and lower household income, are significant risk factors for CHE in all 3 household types (p<0.05). Health insurance status was found to be a significant determinant of CHE among empty-nest singles and non-empty-nest households (p<0.05). CHE incidence among elderly households is high in China. Empty-nest households are at higher risk for CHE than non-empty-nest households. Based on these findings, we suggest that special insurance be developed to broaden the coverage of health services and heighten the reimbursement rate for empty-nest elderly in the existing health insurance schemes. Financial and social protection interventions are also essential for identified at-risk subgroups among different types of elderly households. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Catastrophic health expenditure: a comparative analysis of empty-nest and non-empty-nest households with seniors in Shandong, China

PubMed Central

Yang, Tingting; Chu, Jie; Zhou, Chengchao; Medina, Alexis; Li, Cuicui; Jiang, Shan; Zheng, Wengui; Sun, Liyuan; Liu, Jing

2016-01-01

Objective The aim of this study was to compare the catastrophic health expenditure (CHE) prevalence and its determinants between empty-nest and non-empty-nest elderly households. Setting Shandong province of China. Participants A total of 2761 elderly households are included in the analysis. Results CHE incidence among elderly households was 44.9%. The CHE incidence of empty-nest singles (59.3%, p=0.000, OR=3.19) and empty-nest couples (52.9%, p=0.000, OR=2.45) are both statistically higher than that of non-empty-nest elderly households (31.4%). An inverse association was observed between CHE incidence and income level in all elderly household types. Factors including 1 or more household elderly members with non-communicable chronic diseases in the past 6 months, 1 or more elderly household members being hospitalised in the past year and lower household income, are significant risk factors for CHE in all 3 household types (p<0.05). Health insurance status was found to be a significant determinant of CHE among empty-nest singles and non-empty-nest households (p<0.05). Conclusions CHE incidence among elderly households is high in China. Empty-nest households are at higher risk for CHE than non-empty-nest households. Based on these findings, we suggest that special insurance be developed to broaden the coverage of health services and heighten the reimbursement rate for empty-nest elderly in the existing health insurance schemes. Financial and social protection interventions are also essential for identified at-risk subgroups among different types of elderly households. PMID:27381206

Monochromatic X-ray-induced thermal effect on four-reflection “nested” meV-monochromators: dynamical diffraction theory and finite-element analysis

NASA Astrophysics Data System (ADS)

Hu, Ling-Fei; Gao, Li-Dan; Li, Zhen-Jie; Wang, Shan-Feng; Sheng, Wei-Fan; Liu, Peng; Xu, Wei

2015-09-01

The high energy resolution monochromator (HRM) is widely used in inelastic scattering programs to detect phonons with energy resolution, down to the meV level. Although the large amount of heat from insertion devices can be reduced by a high heat-load monochromator, the unbalanced heat load on the inner pair of crystals in a nested HRM can affect its overall performance. Here, a theoretical analysis of the unbalanced heat load using dynamical diffraction theory and finite element analysis is presented. By utilizing the ray-tracing method, the performance of different HRM nesting configurations is simulated. It is suggested that the heat balance ratio, energy resolution, and overall spectral transmission efficiency are the figures of merit for evaluating the performance of nested HRMs. Although the present study is mainly focused on nested HRMs working at 57Fe nuclear resonant energy at 14.4 keV, it is feasible to extend this to other nested HRMs working at different energies.

Selection of anthropogenic features and vegetation characteristics by nesting Common Ravens in the sagebrush ecosystem

USGS Publications Warehouse

Howe, Kristy B.; Coates, Peter S.; Delehanty, David J.

2014-01-01

Common Raven (Corvus corax) numbers and distribution are increasing throughout the sagebrush steppe, influencing avian communities in complex ways. Anthropogenic structures are thought to increase raven populations by providing food and nesting subsidies, which is cause for concern because ravens are important nest predators of sensitive species, including Greater Sage-Grouse (Centrocercus urophasianus). During 2007–2009, we located raven nests in southeastern Idaho and conducted a resource selection analysis. We measured variables at multiple spatial scales for 72 unique nest locations, including landscape-level vegetation characteristics and anthropogenic structures. Using generalized linear mixed models and an information-theoretic approach, we found a 31% decrease in the odds of nesting by ravens for every 1 km increase in distance away from a transmission line. Furthermore, a 100-m increase in distance away from the edge of two different land cover types decreased the odds of nesting by 20%, and an increase in the amount of edge by 1 km within an area of 102.1 ha centered on the nest increased the odds of nesting by 49%. A post hoc analysis revealed that ravens were most likely to nest near edges of adjoining big sagebrush (Artemisia tridentata) and land cover types that were associated with direct human disturbance or fire. These findings contribute to our understanding of raven expansion into rural environments and could be used to make better-informed conservation decisions, especially in the face of increasing renewable energy development.

The use of generalized estimating equations in the analysis of motor vehicle crash data.

PubMed

Hutchings, Caroline B; Knight, Stacey; Reading, James C

2003-01-01

The purpose of this study was to determine if it is necessary to use generalized estimating equations (GEEs) in the analysis of seat belt effectiveness in preventing injuries in motor vehicle crashes. The 1992 Utah crash dataset was used, excluding crash participants where seat belt use was not appropriate (n=93,633). The model used in the 1996 Report to Congress [Report to congress on benefits of safety belts and motorcycle helmets, based on data from the Crash Outcome Data Evaluation System (CODES). National Center for Statistics and Analysis, NHTSA, Washington, DC, February 1996] was analyzed for all occupants with logistic regression, one level of nesting (occupants within crashes), and two levels of nesting (occupants within vehicles within crashes) to compare the use of GEEs with logistic regression. When using one level of nesting compared to logistic regression, 13 of 16 variance estimates changed more than 10%, and eight of 16 parameter estimates changed more than 10%. In addition, three of the independent variables changed from significant to insignificant (alpha=0.05). With the use of two levels of nesting, two of 16 variance estimates and three of 16 parameter estimates changed more than 10% from the variance and parameter estimates in one level of nesting. One of the independent variables changed from insignificant to significant (alpha=0.05) in the two levels of nesting model; therefore, only two of the independent variables changed from significant to insignificant when the logistic regression model was compared to the two levels of nesting model. The odds ratio of seat belt effectiveness in preventing injuries was 12% lower when a one-level nested model was used. Based on these results, we stress the need to use a nested model and GEEs when analyzing motor vehicle crash data.

Mixed-stock analysis reveals the migrations of juvenile hawksbill turtles (Eretmochelys imbricata) in the Caribbean Sea.

PubMed

Bowen, B W; Grant, W S; Hillis-Starr, Z; Shaver, D J; Bjorndal, K A; Bolten, A B; Bass, A L

2007-01-01

Hawksbill turtles (Eretmochelys imbricata) migrate between nesting beaches and feeding habitats that are often associated with tropical reefs, but it is uncertain which nesting colonies supply which feeding habitats. To address this gap in hawksbill biology, we compile previously published and new mitochondrial DNA (mtDNA) haplotype data for 10 nesting colonies (N = 347) in the western Atlantic and compare these profiles to four feeding populations and four previously published feeding samples (N = 626). Nesting colonies differ significantly in mtDNA haplotype frequencies (Phi(ST) = 0.588, P < 0.001), corroborating earlier conclusions of nesting site fidelity and setting the stage for mixed-stock analysis. Feeding aggregations show lower but significant structure (Phi(ST) = 0.089, P < 0.001), indicating that foraging populations are not homogenous across the Caribbean Sea. Bayesian mixed-stock estimates of the origins of juveniles in foraging areas show a highly significant, but shallow, correlation with nesting population size (r = 0.378, P = 0.004), supporting the premise that larger rookeries contribute more juveniles to feeding areas. A significant correlation between the estimated contribution and geographical distance from nesting areas (r = -0.394, P = 0.003) demonstrates the influence of proximity on recruitment to feeding areas. The influence of oceanic currents is illustrated by pelagic stage juveniles stranded in Texas, which are assigned primarily (93%) to the upstream rookery in Yucatan. One juvenile had a haplotype previously identified only in the eastern Atlantic, invoking rare trans-oceanic migrations. The mixed-stock analysis demonstrates that harvests in feeding habitats will impact nesting colonies throughout the region, with the greatest detriment to nearby nesting populations.

Habitat fragmentation reduces nest survival in an Afrotropical bird community in a biodiversity hotspot

USGS Publications Warehouse

Newmark, W.D.; Stanley, T.R.

2011-01-01

Ecologists have long hypothesized that fragmentation of tropical landscapes reduces avian nest success. However, this hypothesis has not been rigorously assessed because of the difficulty of finding large numbers of well-hidden nests in tropical forests. Here we report that in the East Usambara Mountains in Tanzania, which are part of the Eastern Arc Mountains, a global biodiversity hotspot, that daily nest survival rate and nest success for seven of eight common understory bird species that we examined over a single breeding season were significantly lower in fragmented than in continuous forest, with the odds of nest failure for these seven species ranging from 1.9 to 196.8 times higher in fragmented than continuous forest. Cup-shaped nests were particularly vulnerable in fragments. We then examined over six breeding seasons and 14 study sites in a multivariable survival analysis the influence of landscape structure and nest location on daily nest survival for 13 common species representing 1,272 nests and four nest types (plate, cup, dome, and pouch). Across species and nest types, area, distance of nest to edge, and nest height had a dominant influence on daily nest survival, with area being positively related to nest survival and distance of nest to edge and nest height being both positively and negatively associated with daily nest survival. Our results indicate that multiple environmental factors contribute to reduce nest survival within a tropical understory bird community in a fragmented landscape and that maintaining large continuous forest is important for enhancing nest survival for Afrotropical understory birds.

Habitat fragmentation reduces nest survival in an Afrotropical bird community in a biodiversity hotspot.

PubMed

Newmark, William D; Stanley, Thomas R

2011-07-12

Ecologists have long hypothesized that fragmentation of tropical landscapes reduces avian nest success. However, this hypothesis has not been rigorously assessed because of the difficulty of finding large numbers of well-hidden nests in tropical forests. Here we report that in the East Usambara Mountains in Tanzania, which are part of the Eastern Arc Mountains, a global biodiversity hotspot, that daily nest survival rate and nest success for seven of eight common understory bird species that we examined over a single breeding season were significantly lower in fragmented than in continuous forest, with the odds of nest failure for these seven species ranging from 1.9 to 196.8 times higher in fragmented than continuous forest. Cup-shaped nests were particularly vulnerable in fragments. We then examined over six breeding seasons and 14 study sites in a multivariable survival analysis the influence of landscape structure and nest location on daily nest survival for 13 common species representing 1,272 nests and four nest types (plate, cup, dome, and pouch). Across species and nest types, area, distance of nest to edge, and nest height had a dominant influence on daily nest survival, with area being positively related to nest survival and distance of nest to edge and nest height being both positively and negatively associated with daily nest survival. Our results indicate that multiple environmental factors contribute to reduce nest survival within a tropical understory bird community in a fragmented landscape and that maintaining large continuous forest is important for enhancing nest survival for Afrotropical understory birds.

Habitat fragmentation reduces nest survival in an Afrotropical bird community in a biodiversity hotspot

PubMed Central

Newmark, William D.; Stanley, Thomas R.

2011-01-01

Ecologists have long hypothesized that fragmentation of tropical landscapes reduces avian nest success. However, this hypothesis has not been rigorously assessed because of the difficulty of finding large numbers of well-hidden nests in tropical forests. Here we report that in the East Usambara Mountains in Tanzania, which are part of the Eastern Arc Mountains, a global biodiversity hotspot, that daily nest survival rate and nest success for seven of eight common understory bird species that we examined over a single breeding season were significantly lower in fragmented than in continuous forest, with the odds of nest failure for these seven species ranging from 1.9 to 196.8 times higher in fragmented than continuous forest. Cup-shaped nests were particularly vulnerable in fragments. We then examined over six breeding seasons and 14 study sites in a multivariable survival analysis the influence of landscape structure and nest location on daily nest survival for 13 common species representing 1,272 nests and four nest types (plate, cup, dome, and pouch). Across species and nest types, area, distance of nest to edge, and nest height had a dominant influence on daily nest survival, with area being positively related to nest survival and distance of nest to edge and nest height being both positively and negatively associated with daily nest survival. Our results indicate that multiple environmental factors contribute to reduce nest survival within a tropical understory bird community in a fragmented landscape and that maintaining large continuous forest is important for enhancing nest survival for Afrotropical understory birds. PMID:21709237

ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales)

PubMed Central

2008-01-01

Background Within Chlorophyceae the ITS2 secondary structure shows an unbranched helix I, except for the 'Hydrodictyon' and the 'Scenedesmus' clade having a ramified first helix. The latter two are classified within the Sphaeropleales, characterised by directly opposed basal bodies in their flagellar apparatuses (DO-group). Previous studies could not resolve the taxonomic position of the 'Sphaeroplea' clade within the Chlorophyceae without ambiguity and two pivotal questions remain open: (1) Is the DO-group monophyletic and (2) is a branched helix I an apomorphic feature of the DO-group? In the present study we analysed the secondary structure of three newly obtained ITS2 sequences classified within the 'Sphaeroplea' clade and resolved sphaeroplealean relationships by applying different phylogenetic approaches based on a combined sequence-structure alignment. Results The newly obtained ITS2 sequences of Ankyra judayi, Atractomorpha porcata and Sphaeroplea annulina of the 'Sphaeroplea' clade do not show any branching in the secondary structure of their helix I. All applied phylogenetic methods highly support the 'Sphaeroplea' clade as a sister group to the 'core Sphaeropleales'. Thus, the DO-group is monophyletic. Furthermore, based on characteristics in the sequence-structure alignment one is able to distinguish distinct lineages within the green algae. Conclusion In green algae, a branched helix I in the secondary structure of the ITS2 evolves past the 'Sphaeroplea' clade. A branched helix I is an apomorph characteristic within the monophyletic DO-group. Our results corroborate the fundamental relevance of including the secondary structure in sequence analysis and phylogenetics. PMID:18655698

Evaluating trans-tethys migration: an example using acrodont lizard phylogenetics.

PubMed

Macey, J R; Schulte, J A; Larson, A; Ananjeva, N B; Wang, Y; Pethiyagoda, R; Rastegar-Pouyani, N; Papenfuss, T J

2000-06-01

A phylogenetic tree for acrodont lizards (Chamaeleonidae and Agamidae) is established based on 1434 bases (1041 informative) of aligned DNA positions from a 1685-1778 base pair region of the mitochondrial genome. Sequences from three protein-coding genes (ND1, ND2, and COI) are combined with sequences from eight intervening tRNA genes for samples of 70 acrodont taxa and two outgroups. Parsimony analysis of nucleotide sequences identifies eight major clades in the Acrodonta. Most agamid lizards are placed into three distinct clades. One clade is composed of all taxa occurring in Australia and New Guinea; Physignathus cocincinus from Southeast Asia is the sister taxon to the Australia-New Guinea clade. A second clade is composed of taxa occurring from Tibet and the Indian Subcontinent east through South and East Asia. A third clade is composed of taxa occurring from Africa east through Arabia and West Asia to Tibet and the Indian Subcontinent. These three clades contain all agamid lizards except Uromastyx, Leiolepis, and Hydrosaurus, which represent three additional clades of the Agamidae. The Chamaeleonidae forms another clade weakly supported as the sister taxon to the Agamidae. All eight clades of the Acrodonta contain members occurring on land masses derived from Gondwanaland. A hypothesis of agamid lizards rafting with Gondwanan plates is examined statistically. This hypothesis suggests that the African/West Asian clade is of African or Indian origin, and the South Asian clade is either of Indian or Southeast Asian origin. The shortest tree suggests a possible African origin for the former and an Indian origin for the latter, but this result is not statistically robust. The Australia-New Guinea clade rafted with the Australia-New Guinea plate and forms the sister group to a Southeast Asian taxon that occurs on plates that broke from northern Australia-New Guinea. Other acrodont taxa are inferred to be associated with the plates of Afro-Arabia and Madagascar (Chameleonidae), India (Uromastyx), or southeast Asia (Hydrosaurus and Leiolepis). Introduction of different biotic elements to Asia by way of separate Gondwanan plates may be a major theme of Asian biogeography. Three historical events may be responsible for the sharp faunal barrier between Southeast Asia and Australia-New Guinea, known as Wallace's line: (1) primary vicariance caused by plate separations; (2) secondary contact of Southeast Asian plates with Eurasia, leading to dispersal from Eurasia into Southeast Asia, and (3) dispersal of the Indian fauna (after collision of that subcontinent) to Southeast Asia. Acrodont lizards show the first and third of these biogeographic patterns and anguid lizards exhibit the second pattern. Modern faunal diversity may be influenced primarily by historical events such as tectonic collisions and land bridge connections, which are expected to promote episodic turnover of continental faunas by introducing new faunal elements into an area. Repeated tectonic collisions may be one of the most important phenomena promoting continental biodiversity. Phylogenetics is a powerful method for investigating these processes.

Phylogenetic studies favour the unification of Pennisetum, Cenchrus and Odontelytrum (Poaceae): a combined nuclear, plastid and morphological analysis, and nomenclatural combinations in Cenchrus.

PubMed

Chemisquy, M Amelia; Giussani, Liliana M; Scataglini, María A; Kellogg, Elizabeth A; Morrone, Osvaldo

2010-07-01

Twenty-five genera having sterile inflorescence branches were recognized as the bristle clade within the x = 9 Paniceae (Panicoideae). Within the bristle clade, taxonomic circumscription of Cenchrus (20-25 species), Pennisetum (80-140) and the monotypic Odontelytrum is still unclear. Several criteria have been applied to characterize Cenchrus and Pennisetum, but none of these has proved satisfactory as the diagnostic characters, such as fusion of bristles in the inflorescences, show continuous variation. A phylogenetic analysis based on morphological, plastid (trnL-F, ndhF) and nuclear (knotted) data is presented for a representative species sampling of the genera. All analyses were conducted under parsimony, using heuristic searches with TBR branch swapping. Branch support was assessed with parsimony jackknifing. Based on plastid and morphological data, Pennisetum, Cenchrus and Odontelytrum were supported as a monophyletic group: the PCO clade. Only one section of Pennisetum (Brevivalvula) was supported as monophyletic. The position of P. lanatum differed among data partitions, although the combined plastid and morphology and nuclear analyses showed this species to be a member of the PCO clade. The basic chromosome number x = 9 was found to be plesiomorphic, and x = 5, 7, 8, 10 and 17 were derived states. The nuclear phylogenetic analysis revealed a reticulate pattern of relationships among Pennisetum and Cenchrus, suggesting that there are at least three different genomes. Because apomixis can be transferred among species through hybridization, its history most likely reflects crossing relationships, rather than multiple independent appearances. Due to the consistency between the present results and different phylogenetic hypotheses (including morphological, developmental and multilocus approaches), and the high support found for the PCO clade, also including the type species of the three genera, we propose unification of Pennisetum, Cenchrus and Odontelytrum. Species of Pennisetum and Odontelytrum are here transferred into Cenchrus, which has priority. Sixty-six new combinations are made here.

A molecular phylogeny of anseriformes based on mitochondrial DNA analysis.

PubMed

Donne-Goussé, Carole; Laudet, Vincent; Hänni, Catherine

2002-06-01

To study the phylogenetic relationships among Anseriformes, sequences for the complete mitochondrial control region (CR) were determined from 45 waterfowl representing 24 genera, i.e., half of the existing genera. To confirm the results based on CR analysis we also analyzed representative species based on two mitochondrial protein-coding genes, cytochrome b (cytb) and NADH dehydrogenase subunit 2 (ND2). These data allowed us to construct a robust phylogeny of the Anseriformes and to compare it with existing phylogenies based on morphological or molecular data. Chauna and Dendrocygna were identified as early offshoots of the Anseriformes. All the remaining taxa fell into two clades that correspond to the two subfamilies Anatinae and Anserinae. Within Anserinae Branta and Anser cluster together, whereas Coscoroba, Cygnus, and Cereopsis form a relatively weak clade with Cygnus diverging first. Five clades are clearly recognizable among Anatinae: (i) the Anatini with Anas and Lophonetta; (ii) the Aythyini with Aythya and Netta; (iii) the Cairinini with Cairina and Aix; (iv) the Mergini with Mergus, Bucephala, Melanitta, Callonetta, Somateria, and Clangula, and (v) the Tadornini with Tadorna, Chloephaga, and Alopochen. The Tadornini diverged early on from the Anatinae; then the Mergini and a large group that comprises the Anatini, Aythyini, Cairinini, and two isolated genera, Chenonetta and Marmaronetta, diverged. The phylogeny obtained with the control region appears more robust than the one obtained with mitochondrial protein-coding genes such as ND2 and cytb. This suggests that the CR is a powerful tool for bird phylogeny, not only at a small scale (i.e., relationships between species) but also at the family level. Whereas morphological analysis effectively resolved the split between Anatinae and Anserinae and the existence of some of the clades, the precise composition of the clades are different when morphological and molecular data are compared. (c) 2002 Elsevier Science (USA).

Phylogenetic studies favour the unification of Pennisetum, Cenchrus and Odontelytrum (Poaceae): a combined nuclear, plastid and morphological analysis, and nomenclatural combinations in Cenchrus

PubMed Central

Chemisquy, M. Amelia; Giussani, Liliana M.; Scataglini, María A.; Kellogg, Elizabeth A.; Morrone, Osvaldo

2010-01-01

Backgrounds and Aims Twenty-five genera having sterile inflorescence branches were recognized as the bristle clade within the x = 9 Paniceae (Panicoideae). Within the bristle clade, taxonomic circumscription of Cenchrus (20–25 species), Pennisetum (80–140) and the monotypic Odontelytrum is still unclear. Several criteria have been applied to characterize Cenchrus and Pennisetum, but none of these has proved satisfactory as the diagnostic characters, such as fusion of bristles in the inflorescences, show continuous variation. Methods A phylogenetic analysis based on morphological, plastid (trnL-F, ndhF) and nuclear (knotted) data is presented for a representative species sampling of the genera. All analyses were conducted under parsimony, using heuristic searches with TBR branch swapping. Branch support was assessed with parsimony jackknifing. Key Results Based on plastid and morphological data, Pennisetum, Cenchrus and Odontelytrum were supported as a monophyletic group: the PCO clade. Only one section of Pennisetum (Brevivalvula) was supported as monophyletic. The position of P. lanatum differed among data partitions, although the combined plastid and morphology and nuclear analyses showed this species to be a member of the PCO clade. The basic chromosome number x = 9 was found to be plesiomorphic, and x = 5, 7, 8, 10 and 17 were derived states. The nuclear phylogenetic analysis revealed a reticulate pattern of relationships among Pennisetum and Cenchrus, suggesting that there are at least three different genomes. Because apomixis can be transferred among species through hybridization, its history most likely reflects crossing relationships, rather than multiple independent appearances. Conclusions Due to the consistency between the present results and different phylogenetic hypotheses (including morphological, developmental and multilocus approaches), and the high support found for the PCO clade, also including the type species of the three genera, we propose unification of Pennisetum, Cenchrus and Odontelytrum. Species of Pennisetum and Odontelytrum are here transferred into Cenchrus, which has priority. Sixty-six new combinations are made here. PMID:20570830

Decoupled form and function in disparate herbivorous dinosaur clades

NASA Astrophysics Data System (ADS)

Lautenschlager, Stephan; Brassey, Charlotte A.; Button, David J.; Barrett, Paul M.

2016-05-01

Convergent evolution, the acquisition of morphologically similar traits in unrelated taxa due to similar functional demands or environmental factors, is a common phenomenon in the animal kingdom. Consequently, the occurrence of similar form is used routinely to address fundamental questions in morphofunctional research and to infer function in fossils. However, such qualitative assessments can be misleading and it is essential to test form/function relationships quantitatively. The parallel occurrence of a suite of morphologically convergent craniodental characteristics in three herbivorous, phylogenetically disparate dinosaur clades (Sauropodomorpha, Ornithischia, Theropoda) provides an ideal test case. A combination of computational biomechanical models (Finite Element Analysis, Multibody Dynamics Analysis) demonstrate that despite a high degree of morphological similarity between representative taxa (Plateosaurus engelhardti, Stegosaurus stenops, Erlikosaurus andrewsi) from these clades, their biomechanical behaviours are notably different and difficult to predict on the basis of form alone. These functional differences likely reflect dietary specialisations, demonstrating the value of quantitative biomechanical approaches when evaluating form/function relationships in extinct taxa.

Decoupled form and function in disparate herbivorous dinosaur clades.

PubMed

Lautenschlager, Stephan; Brassey, Charlotte A; Button, David J; Barrett, Paul M

2016-05-20

Convergent evolution, the acquisition of morphologically similar traits in unrelated taxa due to similar functional demands or environmental factors, is a common phenomenon in the animal kingdom. Consequently, the occurrence of similar form is used routinely to address fundamental questions in morphofunctional research and to infer function in fossils. However, such qualitative assessments can be misleading and it is essential to test form/function relationships quantitatively. The parallel occurrence of a suite of morphologically convergent craniodental characteristics in three herbivorous, phylogenetically disparate dinosaur clades (Sauropodomorpha, Ornithischia, Theropoda) provides an ideal test case. A combination of computational biomechanical models (Finite Element Analysis, Multibody Dynamics Analysis) demonstrate that despite a high degree of morphological similarity between representative taxa (Plateosaurus engelhardti, Stegosaurus stenops, Erlikosaurus andrewsi) from these clades, their biomechanical behaviours are notably different and difficult to predict on the basis of form alone. These functional differences likely reflect dietary specialisations, demonstrating the value of quantitative biomechanical approaches when evaluating form/function relationships in extinct taxa.

Mountain building triggered late cretaceous North American megaherbivore dinosaur radiation.

PubMed

Gates, Terry A; Prieto-Márquez, Albert; Zanno, Lindsay E

2012-01-01

Prior studies of Mesozoic biodiversity document a diversity peak for dinosaur species in the Campanian stage of the Late Cretaceous, yet have failed to provide explicit causal mechanisms. We provide evidence that a marked increase in North American dinosaur biodiversity can be attributed to dynamic orogenic episodes within the Western Interior Basin (WIB). Detailed fossil occurrences document an association between the shift from Sevier-style, latitudinally arrayed basins to smaller Laramide-style, longitudinally arrayed basins and a well substantiated decreased geographic range/increased taxonomic diversity of megaherbivorous dinosaur species. Dispersal-vicariance analysis demonstrates that the nearly identical biogeographic histories of the megaherbivorous dinosaur clades Ceratopsidae and Hadrosauridae are attributable to rapid diversification events within restricted basins and that isolation events are contemporaneous with known tectonic activity in the region. SymmeTREE analysis indicates that megaherbivorous dinosaur clades exhibited significant variation in diversification rates throughout the Late Cretaceous. Phylogenetic divergence estimates of fossil clades offer a new lower boundary on Laramide surficial deformation that precedes estimates based on sedimentological data alone.

Mountain Building Triggered Late Cretaceous North American Megaherbivore Dinosaur Radiation

PubMed Central

Gates, Terry A.; Prieto-Márquez, Albert; Zanno, Lindsay E.

2012-01-01

Prior studies of Mesozoic biodiversity document a diversity peak for dinosaur species in the Campanian stage of the Late Cretaceous, yet have failed to provide explicit causal mechanisms. We provide evidence that a marked increase in North American dinosaur biodiversity can be attributed to dynamic orogenic episodes within the Western Interior Basin (WIB). Detailed fossil occurrences document an association between the shift from Sevier-style, latitudinally arrayed basins to smaller Laramide-style, longitudinally arrayed basins and a well substantiated decreased geographic range/increased taxonomic diversity of megaherbivorous dinosaur species. Dispersal-vicariance analysis demonstrates that the nearly identical biogeographic histories of the megaherbivorous dinosaur clades Ceratopsidae and Hadrosauridae are attributable to rapid diversification events within restricted basins and that isolation events are contemporaneous with known tectonic activity in the region. SymmeTREE analysis indicates that megaherbivorous dinosaur clades exhibited significant variation in diversification rates throughout the Late Cretaceous. Phylogenetic divergence estimates of fossil clades offer a new lower boundary on Laramide surficial deformation that precedes estimates based on sedimentological data alone. PMID:22876302

Highly pathogenic influenza H5N1 virus of clade 2.3.2.1c in Western Siberia.

PubMed

Marchenko, V Y; Susloparov, I M; Kolosova, N P; Goncharova, N I; Shipovalov, A V; Ilyicheva, T N; Durymanov, A G; Chernyshova, O A; Kozlovskiy, L I; Chernyshova, T V; Pryadkina, E N; Karimova, T V; Mikheev, V N; Ryzhikov, A B

2016-06-01

In the spring of 2015, avian influenza virus surveillance in Western Siberia resulted in isolation of several influenza H5N1 virus strains. The strains were isolated from several wild bird species. Investigation of biological features of those strains demonstrated their high pathogenicity for mammals. Phylogenetic analysis of the HA gene showed that the strains belong to clade 2.3.2.1c.

Sulfurospirillum barnesii sp. nov. and Sulfurospirillum arsenophilum sp. nov., new members of the Sulfurospirillum clade of the ε-Proteobacteria

USGS Publications Warehouse

Stolz, J.F.; Ellis, D.J.; Blum, J.S.; Ahmann, D.; Lovley, D.R.; Oremland, R.S.

1999-01-01

Two strains of dissimilatory arsenate-reducing vibrio-shaped bacteria are assigned to the genus Sulfurospirillum. These two new species, Sulfurospirillum barnesii strain SES-3(T) and Sulfurospirillum arsenophilum strain MIT-13(T), in addition to Sulfurospirillum sp. SM-5, two strains of Sulfurospirillum deleyianum, and Sulfurospirillum arcachonense, form a distinct clade within the ?? subclass of the Proteobacteria based on 16S rRNA analysis.

Towards a molecular taxonomic key of the Aurantioideae subfamily using chloroplastic SNP diagnostic markers of the main clades genotyped by competitive allele-specific PCR.

PubMed

Oueslati, Amel; Ollitrault, Frederique; Baraket, Ghada; Salhi-Hannachi, Amel; Navarro, Luis; Ollitrault, Patrick

2016-08-18

Chloroplast DNA is a primary source of molecular variations for phylogenetic analysis of photosynthetic eukaryotes. However, the sequencing and analysis of multiple chloroplastic regions is difficult to apply to large collections or large samples of natural populations. The objective of our work was to demonstrate that a molecular taxonomic key based on easy, scalable and low-cost genotyping method should be developed from a set of Single Nucleotide Polymorphisms (SNPs) diagnostic of well-established clades. It was applied to the Aurantioideae subfamily, the largest group of the Rutaceae family that includes the cultivated citrus species. The publicly available nucleotide sequences of eight plastid genomic regions were compared for 79 accessions of the Aurantioideae subfamily to search for SNPs revealing taxonomic differentiation at the inter-tribe, inter-subtribe, inter-genus and interspecific levels. Diagnostic SNPs (DSNPs) were found for 46 of the 54 clade levels analysed. Forty DSNPs were selected to develop KASPar markers and their taxonomic value was tested by genotyping 108 accessions of the Aurantioideae subfamily. Twenty-seven markers diagnostic of 24 clades were validated and they displayed a very high rate of transferability in the Aurantioideae subfamily (only 1.2 % of missing data on average). The UPGMA from the validated markers produced a cladistic organisation that was highly coherent with the previous phylogenetic analysis based on the sequence data of the eight plasmid regions. In particular, the monophyletic origin of the "true citrus" genera plus Oxanthera was validated. However, some clarification remains necessary regarding the organisation of the other wild species of the Citreae tribe. We validated the concept that with well-established clades, DSNPs can be selected and efficiently transformed into competitive allele-specific PCR markers (KASPar method) allowing cost-effective highly efficient cladistic analysis in large collections at subfamily level. The robustness of this genotyping method is an additional decisive advantage for network collaborative research. The availability of WGS data for the main "true citrus" species should soon make it possible to develop a set of DSNP markers allowing very fine resolution of this very important horticultural group.

Genomic and Phylogenetic Characterization of Luminous Bacteria Symbiotic with the Deep-Sea Fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae)

PubMed Central

Dunlap, Paul V.; Ast, Jennifer C.

2005-01-01

Bacteria forming light-organ symbiosis with deep-sea chlorophthalmid fishes (Aulopiformes: Chlorophthalmidae) are considered to belong to the species Photobacterium phosphoreum. The identification of these bacteria as P. phosphoreum, however, was based exclusively on phenotypic traits, which may not discriminate between phenetically similar but evolutionarily distinct luminous bacteria. Therefore, to test the species identification of chlorophthalmid symbionts, we carried out a genomotypic (repetitive element palindromic PCR genomic profiling) and phylogenetic analysis on strains isolated from the perirectal light organ of Chlorophthalmus albatrossis. Sequence analysis of the 16S rRNA gene of 10 strains from 5 fish specimens placed these bacteria in a cluster related to but phylogenetically distinct from the type strain of P. phosphoreum, ATCC 11040T, and the type strain of Photobacterium iliopiscarium, ATCC 51760T. Analysis of gyrB resolved the C. albatrossis strains as a strongly supported clade distinct from P. phosphoreum and P. iliopiscarium. Genomic profiling of 109 strains from the 5 C. albatrossis specimens revealed a high level of similarity among strains but allowed identification of genomotypically different types from each fish. Representatives of each type were then analyzed phylogenetically, using sequence of the luxABFE genes. As with gyrB, analysis of luxABFE resolved the C. albatrossis strains as a robustly supported clade distinct from P. phosphoreum. Furthermore, other strains of luminous bacteria reported as P. phosphoreum, i.e., NCIMB 844, from the skin of Merluccius capensis (Merlucciidae), NZ-11D, from the light organ of Nezumia aequalis (Macrouridae), and pjapo.1.1, from the light organ of Physiculus japonicus (Moridae), grouped phylogenetically by gyrB and luxABFE with the C. albatrossis strains, not with ATCC 11040T. These results demonstrate that luminous bacteria symbiotic with C. albatrossis, together with certain other strains of luminous bacteria, form a clade, designated the kishitanii clade, that is related to but evolutionarily distinct from P. phosphoreum. Members of the kishitanii clade may constitute the major or sole bioluminescent symbiont of several families of deep-sea luminous fishes. PMID:15691950

Genomic and phylogenetic characterization of luminous bacteria symbiotic with the deep-sea fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae).

PubMed

Dunlap, Paul V; Ast, Jennifer C

2005-02-01

Bacteria forming light-organ symbiosis with deep-sea chlorophthalmid fishes (Aulopiformes: Chlorophthalmidae) are considered to belong to the species Photobacterium phosphoreum. The identification of these bacteria as P. phosphoreum, however, was based exclusively on phenotypic traits, which may not discriminate between phenetically similar but evolutionarily distinct luminous bacteria. Therefore, to test the species identification of chlorophthalmid symbionts, we carried out a genomotypic (repetitive element palindromic PCR genomic profiling) and phylogenetic analysis on strains isolated from the perirectal light organ of Chlorophthalmus albatrossis. Sequence analysis of the 16S rRNA gene of 10 strains from 5 fish specimens placed these bacteria in a cluster related to but phylogenetically distinct from the type strain of P. phosphoreum, ATCC 11040(T), and the type strain of Photobacterium iliopiscarium, ATCC 51760(T). Analysis of gyrB resolved the C. albatrossis strains as a strongly supported clade distinct from P. phosphoreum and P. iliopiscarium. Genomic profiling of 109 strains from the 5 C. albatrossis specimens revealed a high level of similarity among strains but allowed identification of genomotypically different types from each fish. Representatives of each type were then analyzed phylogenetically, using sequence of the luxABFE genes. As with gyrB, analysis of luxABFE resolved the C. albatrossis strains as a robustly supported clade distinct from P. phosphoreum. Furthermore, other strains of luminous bacteria reported as P. phosphoreum, i.e., NCIMB 844, from the skin of Merluccius capensis (Merlucciidae), NZ-11D, from the light organ of Nezumia aequalis (Macrouridae), and pjapo.1.1, from the light organ of Physiculus japonicus (Moridae), grouped phylogenetically by gyrB and luxABFE with the C. albatrossis strains, not with ATCC 11040(T). These results demonstrate that luminous bacteria symbiotic with C. albatrossis, together with certain other strains of luminous bacteria, form a clade, designated the kishitanii clade, that is related to but evolutionarily distinct from P. phosphoreum. Members of the kishitanii clade may constitute the major or sole bioluminescent symbiont of several families of deep-sea luminous fishes.

Nest-site characteristics of Glyptemys muhlenbergii (Bog Turtle) in New Jersey and Pennsylvania

USGS Publications Warehouse

Zappalorti, Robert T.; Lovich, Jeffrey E.; Farrell, Ray F.; Torocco, Michael E.

2015-01-01

Nest-site selection can affect both the survival and fitness of female turtles and their offspring. In many turtle species, the nest environment determines the thermal regime during incubation, length of incubation period, sex ratio of the hatchlings, and exposure to predators and other forms of mortality for both mothers and their offspring. Between 1974 and 2012, we collected detailed data on habitat variables at 66 Glyptemys muhlenbergii (Bog Turtle) nests in 9 different bogs, fens, and wetland complexes in New Jersey and Pennsylvania. The nests had a mean elevation above the substrate of 8.2 cm, and many were shallow and located in raised tussocks of grass or sedges. Females covered most nests, but we also observed partially or completely uncovered eggs. Some females deposited eggs in communal nests; we found 4 nests with 2 separate clutches, and 2 nests with 3 clutches. Principal component analysis confirmed the importance of cover and vegetation to nest-site selection in this species. Availability of open, shade-free, wet nesting areas is an important habitat requirement for Bog Turtles.

Identification of potent maturation inhibitors against HIV-1 clade C.

PubMed

Timilsina, Uddhav; Ghimire, Dibya; Timalsina, Bivek; Nitz, Theodore J; Wild, Carl T; Freed, Eric O; Gaur, Ritu

2016-06-06

Antiretroviral therapy has led to a profound improvement in the clinical care of HIV-infected patients. However, drug tolerability and the evolution of drug resistance have limited treatment options for many patients. Maturation inhibitors are a new class of antiretroviral agents for treatment of HIV-1. They act by interfering with the maturation of the virus by blocking the last step in Gag processing: the cleavage of the capsid-spacer peptide 1 (CA-SP1) intermediate to mature CA by the viral protease (PR). The first-in-class maturation inhibitor bevirimat (BVM) failed against a subset of HIV-1 isolates in clinical trials due to polymorphisms present in the CA-SP1 region of the Gag protein. Sequence analysis indicated that these polymorphisms are more common in non-clade B strains of HIV-1 such as HIV-1 clade C. Indeed, BVM was found to be ineffective against HIV-1 clade C molecular clones tested in this study. A number of BVM analogs were synthesized by chemical modifications at the C-28 position to improve its activity. The new BVM analogs displayed potent activity against HIV-1 clade B and C and also reduced infectivity of the virus. This study identifies novel and broadly active BVM analogs that may ultimately demonstrate efficacy in the clinic.

Phylogeny-dominant classification of J-proteins in Arabidopsis thaliana and Brassica oleracea.

PubMed

Zhang, Bin; Qiu, Han-Lin; Qu, Dong-Hai; Ruan, Ying; Chen, Dong-Hong

2018-04-05

Hsp40s or DnaJ/J-proteins are evolutionarily conserved in all organisms as co-chaperones of molecular chaperone HSP70s that mainly participate in maintaining cellular protein homeostasis, such as protein folding, assembly, stabilization, and translocation under normal conditions as well as refolding and degradation under environmental stresses. It has been reported that Arabidopsis J-proteins are classified into four classes (types A-D) according to domain organization, but their phylogenetic relationships are unknown. Here, we identified 129 J-proteins in the world-wide popular vegetable Brassica oleracea, a close relative of the model plant Arabidopsis, and also revised the information of Arabidopsis J-proteins based on the latest online bioresources. According to phylogenetic analysis with domain organization and gene structure as references, the J-proteins from Arabidopsis and B. oleracea were classified into 15 main clades (I-XV) separated by a number of undefined small branches with remote relationship. Based on the number of members, they respectively belong to multigene clades, oligo-gene clades, and mono-gene clades. The J-protein genes from different clades may function together or separately to constitute a complicated regulatory network. This study provides a constructive viewpoint for J-protein classification and an informative platform for further functional dissection and resistant genes discovery related to genetic improvement of crop plants.

A New Snake Skull from the Paleocene of Bolivia Sheds Light on the Evolution of Macrostomatans

PubMed Central

Scanferla, Agustín; Zaher, Hussam; Novas, Fernando E.; de Muizon, Christian; Céspedes, Ricardo

2013-01-01

Macrostomatan snakes, one of the most diverse extant clades of squamates, display an impressive arsenal of cranial features to consume a vast array of preys. In the absence of indisputable fossil representatives of this clade with well-preserved skulls, the mode and timing of these extraordinary morphological novelties remain obscure. Here, we report the discovery of Kataria anisodonta n. gen. n. sp., a macrostomatan snake recovered in the Early Palaeocene locality of Tiupampa, Bolivia. The holotype consists of a partial, minute skull that exhibits a combination of booid and caenophidian characters, being the presence of an anisodont dentition and diastema in the maxilla the most distinctive trait. Phylogenetic analysis places Kataria basal to the Caenophidia+Tropidophiidae, and represents along with bolyeriids a distinctive clade of derived macrostomatans. The discovery of Kataria highlights the morphological diversity in the maxilla among derived macrostomatans, demonstrating the relevance of maxillary transformations in the evolution of this clade. Kataria represents the oldest macrostomatan skull recovered, revealing that the diversification of macrostomatans was well under way in early Tertiary times. This record also reinforces the importance of Gondwanan territories in the history of snakes, not only in the origin of the entire group but also in the evolution of ingroup clades. PMID:23469206

Phylogenetic analysis of honey bee behavioral evolution.

PubMed

Raffiudin, Rika; Crozier, Ross H

2007-05-01

DNA sequences from three mitochondrial (rrnL, cox2, nad2) and one nuclear gene (itpr) from all 9 known honey bee species (Apis), a 10th possible species, Apis dorsata binghami, and three outgroup species (Bombus terrestris, Melipona bicolor and Trigona fimbriata) were used to infer Apis phylogenetic relationships using Bayesian analysis. The dwarf honey bees were confirmed as basal, and the giant and cavity-nesting species to be monophyletic. All nodes were strongly supported except that grouping Apis cerana with A. nigrocincta. Two thousand post-burnin trees from the phylogenetic analysis were used in a Bayesian comparative analysis to explore the evolution of dance type, nest structure, comb structure and dance sound within Apis. The ancestral honey bee species was inferred with high support to have nested in the open, and to have more likely than not had a silent vertical waggle dance and a single comb. The common ancestor of the giant and cavity-dwelling bees is strongly inferred to have had a buzzing vertical directional dance. All pairwise combinations of characters showed strong association, but the multiple comparisons problem reduces the ability to infer associations between states between characters. Nevertheless, a buzzing dance is significantly associated with cavity-nesting, several vertical combs, and dancing vertically, a horizontal dance is significantly associated with a nest with a single comb wrapped around the support, and open nesting with a single pendant comb and a silent waggle dance.

[Pollen analysis of the post-emergence residue of Centris tarsata Smith (Hymenoptera: Apidae, Centridini) nests].

PubMed

Dórea, Marcos da C; Dos Santos, Francisco de A R; Lima, Luciene C de L E; Figueroa, Luís E R

2009-01-01

A new treatment protocol was developed to analyze pollen residues found in nests of Centris tarsata Smith harvested from nest-traps. The study area was located in the Canudos Biological Station in the municipality of Canudos (09 masculine56'34'S; 38 masculine59'17'W), in the northeastern micro-region of Bahia State, Brazil. The local vegetation is an open caatinga (deciduous dryland vegetation), the regional climate is semi-arid, the average annual temperature is 24.1 masculineC, and the annual regional rainfall rate is 454 mm. Ten nests of C. tarsata were collected in trap-nests during the first semester of 2004. Pollen analysis from the nests required the development of a new methodology that combined techniques of palynological sediment analysis with the more common pollinic analysis by acetolysis. Microscopic analyses employed optical microscopy techniques. The pollinic spectrum of the samples from C. tarsata indicated the presence of 17 pollen types from seven plant families, which were present in assemblage of five to eleven pollen types, pointed to the plants used by bees to feed on their offspring. The most represented plant families were Leguminosae (49.3%) and Solanaceae (43.2%). The most frequent pollen types in the samples were from Solanum paniculatum (43.8%) and Senna rizzini (32.1%). The protocol developed provides a new tool for diet assessment of Centris and other groups of solitary bees.

Comparing the Effects of Symbiotic Algae (Symbiodinium) Clades C1 and D on Early Growth Stages of Acropora tenuis

PubMed Central

Yuyama, Ikuko; Higuchi, Tomihiko

2014-01-01

Reef-building corals switch endosymbiotic algae of the genus Symbiodinium during their early growth stages and during bleaching events. Clade C Symbiodinium algae are dominant in corals, although other clades — including A and D — have also been commonly detected in juvenile Acroporid corals. Previous studies have been reported that only molecular data of Symbiodinium clade were identified within field corals. In this study, we inoculated aposymbiotic juvenile polyps with cultures of clades C1 and D Symbiodinium algae, and investigated the different effect of these two clades of Symbiodinium on juvenile polyps. Our results showed that clade C1 algae did not grow, while clade D algae grew rapidly during the first 2 months after inoculation. Polyps associated with clade C1 algae exhibited bright green fluorescence across the body and tentacles after inoculation. The growth rate of polyp skeletons was lower in polyps associated with clade C1 algae than those associated with clade D algae. On the other hand, antioxidant activity (catalase) of corals was not significantly different between corals with clade C1 and clade D algae. Our results suggested that clade D Symbiodinium algae easily form symbiotic relationships with corals and that these algae could contribute to coral growth in early symbiosis stages. PMID:24914677

A Simple Method for Estimating Informative Node Age Priors for the Fossil Calibration of Molecular Divergence Time Analyses

PubMed Central

Nowak, Michael D.; Smith, Andrew B.; Simpson, Carl; Zwickl, Derrick J.

2013-01-01

Molecular divergence time analyses often rely on the age of fossil lineages to calibrate node age estimates. Most divergence time analyses are now performed in a Bayesian framework, where fossil calibrations are incorporated as parametric prior probabilities on node ages. It is widely accepted that an ideal parameterization of such node age prior probabilities should be based on a comprehensive analysis of the fossil record of the clade of interest, but there is currently no generally applicable approach for calculating such informative priors. We provide here a simple and easily implemented method that employs fossil data to estimate the likely amount of missing history prior to the oldest fossil occurrence of a clade, which can be used to fit an informative parametric prior probability distribution on a node age. Specifically, our method uses the extant diversity and the stratigraphic distribution of fossil lineages confidently assigned to a clade to fit a branching model of lineage diversification. Conditioning this on a simple model of fossil preservation, we estimate the likely amount of missing history prior to the oldest fossil occurrence of a clade. The likelihood surface of missing history can then be translated into a parametric prior probability distribution on the age of the clade of interest. We show that the method performs well with simulated fossil distribution data, but that the likelihood surface of missing history can at times be too complex for the distribution-fitting algorithm employed by our software tool. An empirical example of the application of our method is performed to estimate echinoid node ages. A simulation-based sensitivity analysis using the echinoid data set shows that node age prior distributions estimated under poor preservation rates are significantly less informative than those estimated under high preservation rates. PMID:23755303

Microevolutionary analyses of Pythium insidiosum isolates of Brazil and Thailand based on exo-1,3-β-glucanase gene.

PubMed

Ribeiro, Tatiana Corrêa; Weiblen, Carla; de Azevedo, Maria Isabel; de Avila Botton, Sônia; Robe, Lizandra Jaqueline; Pereira, Daniela Isabel Brayer; Monteiro, Danieli Urach; Lorensetti, Douglas Miotto; Santurio, Janio Morais

2017-03-01

Pythium insidiosum is an important oomycete due to its ability to infect humans and animals. It causes pythiosis, a disease of difficult treatment that occurs more frequently in humans in Thailand and in horses in Brazil. Since cell-wall components are frequently related to host shifts, we decided here to use sequences from the exo-1,3-β-glucanase gene (exo1), which encodes an immunodominant protein putatively involved in cell wall remodeling, to investigate the microevolutionary relationships of Brazilian and Thai isolates of P. insidiosum. After neutrality ratification, the phylogenetic analyses performed through Maximum parsimony (MP), Neighbor-joining (NJ), Maximum likelihood (ML), and Bayesian analysis (BA) strongly supported Thai isolates being paraphyletic in relation to those from Brazil. The structure recovered by these analyses, as well as by Spatial Analysis of Molecular Variance (SAMOVA), suggests the subdivision of P. insidiosum into three clades or population groups, which are able to explain almost 81% of the variation encountered for exo1. Moreover, the two identified Thai clades were almost as strongly differentiated between each other, as they were from the Brazilian clade, suggesting an ancient Asian subdivision. The derived positioning in the phylogenetic tree, linked to the lower diversity values and the recent expansion signs detected for the Brazilian clade, further support this clade as derived in relation to the Asian populations. Thus, although some patterns presented here are compatible with those recovered with different molecular markers, exo1 was revealed to be a good marker for studying evolution in Pythium, providing robust and strongly supported results with regard to the patterns of origin and diversification of P. insidiosum. Copyright © 2016 Elsevier B.V. All rights reserved.

Brain scaling in mammalian evolution as a consequence of concerted and mosaic changes in numbers of neurons and average neuronal cell size

PubMed Central

Herculano-Houzel, Suzana; Manger, Paul R.; Kaas, Jon H.

2014-01-01

Enough species have now been subject to systematic quantitative analysis of the relationship between the morphology and cellular composition of their brain that patterns begin to emerge and shed light on the evolutionary path that led to mammalian brain diversity. Based on an analysis of the shared and clade-specific characteristics of 41 modern mammalian species in 6 clades, and in light of the phylogenetic relationships among them, here we propose that ancestral mammal brains were composed and scaled in their cellular composition like modern afrotherian and glire brains: with an addition of neurons that is accompanied by a decrease in neuronal density and very little modification in glial cell density, implying a significant increase in average neuronal cell size in larger brains, and the allocation of approximately 2 neurons in the cerebral cortex and 8 neurons in the cerebellum for every neuron allocated to the rest of brain. We also propose that in some clades the scaling of different brain structures has diverged away from the common ancestral layout through clade-specific (or clade-defining) changes in how average neuronal cell mass relates to numbers of neurons in each structure, and how numbers of neurons are differentially allocated to each structure relative to the number of neurons in the rest of brain. Thus, the evolutionary expansion of mammalian brains has involved both concerted and mosaic patterns of scaling across structures. This is, to our knowledge, the first mechanistic model that explains the generation of brains large and small in mammalian evolution, and it opens up new horizons for seeking the cellular pathways and genes involved in brain evolution. PMID:25157220

Mitochondrial DNA markers reveal high genetic diversity and strong genetic differentiation in populations of Dendrolimus kikuchii Matsumura (Lepidoptera: Lasiocampidae).

PubMed

Men, Qiulei; Xue, Guoxi; Mu, Dan; Hu, Qingling; Huang, Minyi

2017-01-01

Dendrolimus kikuchii Matsumura, 1927 is a serious forest pest causing great damage to coniferous trees in China. Despite its economic importance, the population genetics of this pest are poorly known. We used three mitochondrial genes (COI, COII and Cytb) to investigate the genetic diversity and genetic differentiation of 15 populations collected from the main distribution regions of D. kikuchii in China. Populations show high haplotype and nucleotide diversity. Haplotype network and phylogenetic analysis divides the populations into three major clades, the central and southeastern China (CC+SEC) clade, the eastern China (EC) clade, and the southwestern China (SWC) clade. Populations collected from adjacent localities share the same clade, which is consistent with the strong relationship of isolation by distance (r = 0.74824, P = 0.00001). AMOVA analysis indicated that the major portion of this molecular genetic variation is found among the three groups of CC+SEC, EC and SWC (61.26%). Of 105 pairwise FST comparisons, 93 show high genetic differentiation. Populations of Puer (PE), Yangshuo (YS) and Leishan (LS) are separated from other populations by a larger genetic distance. Distributions of pairwise differences obtained with single and combined gene data from the overall populations are multimodal, suggesting these populations had no prior population expansion in southern China. The nonsignificant neutral test on the basis of Tajima' D and Fu's Fs, and the lack of a star-shaped haplotype network together with the multiple haplotypes support this hypothesis. Pleistocene climatic fluctuations, combined with the host specificity to Pinus species, made these regions of south China into a refuge for D. kikuchii. The high level of population genetic structuring is related to their weak flight capacity, their variations of life history and the geographic distance among populations.

SRP-2 is a cross-class inhibitor that participates in postembryonic development of the nematode Caenorhabditis elegans: initial characterization of the clade L serpins.

PubMed

Pak, Stephen C; Kumar, Vasantha; Tsu, Christopher; Luke, Cliff J; Askew, Yuko S; Askew, David J; Mills, David R; Brömme, Dieter; Silverman, Gary A

2004-04-09

High molecular weight serpins are members of a large superfamily of structurally conserved proteins that inactivate target proteinases by a suicide substrate-like mechanism. In vertebrates, different clades of serpins distribute predominantly to either the intracellular or extracellular space. Although much is known about the function, structure, and inhibitory mechanism of circulating serpins such as alpha(1)-antitrypsin (SERPINA1) and antithrombin III (SERPINC1), relatively little is known about the function of the vertebrate intracellular (clade B) serpins. To gain a better understanding of the biology of the intracellular serpins, we initiated a comparative genomics study using Caenorhabditis elegans as a model system. A screen of the C. elegans genomic and cDNA databases revealed nine serpin genes, tandemly arrayed on chromosome V. Although the C. elegans serpins represent a unique clade (L), they share significant functional homology with members of the clade B group of intracellular serpins, since they lack typical N-terminal signal peptides and reside intracellularly. To determine whether nematode serpins function as proteinase inhibitors, one family member, srp-2, was chosen for further characterization. Biochemical analysis of recombinant SRP-2 protein revealed SRP-2 to be a dual cross-class inhibitor of the apoptosis-related serine proteinase, granzyme B, and the lysosomal cysteine proteinases, cathepsins K, L, S, and V. Analysis of temporal and spatial expression indicated that SRP-2 was present during early embryonic development and highly expressed in the intestine and hypoderm of larval and adult worms. Transgenic animals engineered to overexpress SRP-2 were slow growing and/or arrested at the first, second, or third larval stages. These data suggest that perturbations of serpin-proteinase balance are critical for correct postembryonic development in C. elegans.

Comparative Genomic Analysis Indicates that Niche Adaptation of Terrestrial Flavobacteria Is Strongly Linked to Plant Glycan Metabolism

PubMed Central

Kolton, Max; Sela, Noa; Elad, Yigal; Cytryn, Eddie

2013-01-01

Flavobacteria are important members of aquatic and terrestrial bacterial communities, displaying extreme variations in lifestyle, geographical distribution and genome size. They are ubiquitous in soil, but are often strongly enriched in the rhizosphere and phyllosphere of plants. In this study, we compared the genome of a root-associated Flavobacterium that we recently isolated, physiologically characterized and sequenced, to 14 additional Flavobacterium genomes, in order to pinpoint characteristics associated with its high abundance in the rhizosphere. Interestingly, flavobacterial genomes vary in size by approximately two-fold, with terrestrial isolates having predominantly larger genomes than those from aquatic environments. Comparative functional gene analysis revealed that terrestrial and aquatic Flavobacteria generally segregated into two distinct clades. Members of the aquatic clade had a higher ratio of peptide and protein utilization genes, whereas members of the terrestrial clade were characterized by a significantly higher abundance and diversity of genes involved in metabolism of carbohydrates such as xylose, arabinose and pectin. Interestingly, genes encoding glycoside hydrolase (GH) families GH78 and GH106, responsible for rhamnogalacturonan utilization (exclusively associated with terrestrial plant hemicelluloses), were only present in terrestrial clade genomes, suggesting adaptation of the terrestrial strains to plant-related carbohydrate metabolism. The Peptidase/GH ratio of aquatic clade Flavobacteria was significantly higher than that of terrestrial strains (1.7±0.7 and 9.7±4.7, respectively), supporting the concept that this relation can be used to infer Flavobacterium lifestyles. Collectively, our research suggests that terrestrial Flavobacteria are highly adapted to plant carbohydrate metabolism, which appears to be a key to their profusion in plant environments. PMID:24086761

Molecular phylogeny of the Afroedura nivaria (Reptilia: Gekkonidae) species complex in South Africa provides insight on cryptic speciation.

PubMed

Makhubo, Buyisile G; Tolley, Krystal A; Bates, Michael F

2015-01-01

The Afroedura nivaria species complex (A. nivaria, A. karroica, A. amatolica, A. tembulica and A. halli) is a morphologically conservative group of medium-sized flat geckos endemic to South Africa and Lesotho. Species are allopatric, as are some populations within species that are separated by large expanses of unsuitable habitat. Because of this isolation of populations we hypothesised that several cryptic species may be present. To investigate this hypothesis we constructed a molecular phylogeny using multiple markers, and included representatives of other Afroedura species. Bayesian inference and maximum likelihood analyses (439bp 16S, 593bp ND4, 948bp RAG1) strongly supported the genetic distinctiveness of the five described species. However, the A. nivaria species complex as currently described is not monophyletic, as A. karroica was positioned outside a clade containing all other Afroedura species, and A. pondolia (which was presumed to belong to a different species complex) was recovered within the A. nivaria complex. Several distinct clades within A. halli and A. nivaria were also recovered, and the narrowly-distributed A. amatolica consisted of two highly divergent clades. We also conducted a multivariate analysis using 19 morphological characters to investigate whether the clades recovered by the phylogeny were distinct in terms of head, body and limb shape. The analysis showed some variation between clades in terms of locomotor apparatus (forelimbs and feet), head and body dimensions, but overall the morphological differences were minor. This morphological conservatism in the A. nivaria complex may be a result of adaptation to similar microhabitats. Exclusive of A. karroica, the results suggest that there are at least nine species in this complex, of which four are cryptic and undescribed. Copyright © 2014 Elsevier Inc. All rights reserved.

Transitions between Andean and Amazonian centers of endemism in the radiation of some arboreal rodents

PubMed Central

2013-01-01

Background The tropical Andes and Amazon are among the richest regions of endemism for mammals, and each has given rise to extensive in situ radiations. Various animal lineages have radiated ex situ after colonizing one of these regions from the other: Amazonian clades of dendrobatid frogs and passerine birds may have Andean ancestry, and transitions from the Amazon to Andes may be even more common. To examine biogeographic transitions between these regions, we investigated the evolutionary history of three clades of rodents in the family Echimyidae: bamboo rats (Dactylomys-Olallamys-Kannabateomys), spiny tree-rats (Mesomys-Lonchothrix), and brush-tailed rats (Isothrix). Each clade is distributed in both the Andes and Amazonia, and is more diverse in the lowlands. We used two mitochondrial (cyt-b and 12S) and three nuclear (GHR, vWF, and RAG1) markers to reconstruct their phylogenetic relationships. Tree topologies and ancestral geographic ranges were then used to determine whether Andean forms were basal to or derived from lowland radiations. Results Four biogeographic transitions are identified among the generic radiations. The bamboo rat clade unambiguously originated in the Amazon ca. 9 Ma, followed by either one early transition to the Andes (Olallamys) and a later move to the Amazon (Dactylomys), or two later shifts to the Andes (one in each genus). The Andean species of both Dactylomys and Isothrix are sister to their lowland species, raising the possibility that highland forms colonized the Amazon Basin. However, uncertainty in their reconstructed ancestral ranges obscures the origin of these transitions. The lone Andean species of Mesomys is confidently nested within the lowland radiation, thereby indicating an Amazon-to-Andes transition ca. 2 Ma. Conclusions Differences in the timing of these biogeographic transitions do not appear to explain the different polarities of these trees. Instead, even within the radiation of a single family, both Andean and Amazonian centers of endemism appear enriched by lineages that originated in the other region. Our survey of other South American lineages suggests a pattern of reciprocal exchange between these regions—among mammals, birds, amphibians, and insects we found no fewer than 87 transitions between the Andes and Amazon from Miocene-Pleistocene. Because no clear trend emerges between the timing and polarity of transitions, or in their relative frequency, we suggest that reciprocal exchange between tropical highland and lowland faunas in South America has been a continual process since ca. 12 Ma. PMID:24015814

The influence of coyotes on an urban Canada goose population in the Chicago metropolitan area

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, Justin L.; /Ohio State U.

Canada geese (Branta canadensis) have become common in many urban areas, often creating nuisance problems for human residents. The presence of urban geese has raised concerns about the spread of disease, increased erosion, excessive noise, eutrophication of waterways, and general nuisance problems. Goose populations have grown due to an increase in urbanization resulting in an abundance of high quality food (urban grass) and suitable nesting sites, as well as a decrease in some predators. I monitored nest predation in the Chicago suburbs during the 2004 and 2005 nesting seasons using 3 nest monitoring techniques to identify predators: video cameras, plasticinemore » eggs, and sign from nest using a classification tree analysis. Of 58 nests monitored in 2004 and 286 in 2005, only raccoons (Procyon lotor) and coyotes (Canis latrans) were identified as nest predators. Raccoons were responsible for 22-25% of depredated nests, but were rarely capable of depredating nests that were actively defended by a goose. Coyotes were responsible for 75-78% of all Canada goose nest depredation and were documented killing one adult goose and feeding on several others. The coyote is a top-level predator that had increased in many metropolitan areas in recent years. To determine if coyotes were actively hunting geese or eggs during the nesting season, I analyzed coyote habitat selection between nesting and pre-nesting or post-nesting seasons. Coyote home ranges (95% Minimum Convex Polygon) were calculated for 19 coyotes to examine third order habitat selection related to goose nest abundance. A 100 m buffer (buffer habitat) was created and centered on each waterway edge and contained 90% of all nests. Coyotes showed selection for habitats during all seasons. Buffer habitat was the top ranked habitat in both pre-nesting and nesting seasons, but dropped to third ranked in post-nesting season. Habitat selection across seasons was compared using a repeated measures MANOVA. Habitat selection between pre-nesting and nesting seasons (P=0.72) were similar, while between post-nesting and nesting seasons there was a nearly significant difference (P=0.07). The insignificant change in habitat use across seasons suggests that coyotes did not switch habitat use to take advantage of goose nests. Alternatively, the change in ranking of buffer habitat across seasons suggests that coyotes may have switched habitat use to take advantage of goose nests. The results are not clear as large individual variation between coyotes due to differences in habitat availability, and social status interfere with the results of the analysis. Even though I failed to find strong support for coyotes actively hunting goose nests, they nevertheless were the primary nest predator in the area and may influence Canada goose populations. To determine the potential influence of coyotes on the Canada goose population, I created a Canada goose matrix population model that included variables such as coyote predation on adults and nests as well as coyote influence on nest desertion. Using the base population model I calculated the Canada goose population to be increasing with {lambda} = 1.055. The removal of all coyote influence on the goose population would allow {lambda} to increase to 1.214. Nest predation was the most important factor related to coyotes: the removal of coyote nest predation from the model resulted in a population growth rate {lambda} = 1.157. Modeling results suggest coyotes are serving as a limiting factor for the Canada goose population within the Chicago metropolitan area.« less

Whole Genome Characterization, Phylogenetic and Genome Signature Analysis of Human Pandemic H1N1 Virus in Thailand, 2009–2012

PubMed Central

Makkoch, Jarika; Suwannakarn, Kamol; Payungporn, Sunchai; Prachayangprecha, Slinporn; Cheiocharnsin, Thaweesak; Linsuwanon, Piyada; Theamboonlers, Apiradee; Poovorawan, Yong

2012-01-01

Background Three waves of human pandemic influenza occurred in Thailand in 2009–2012. The genome signature features and evolution of pH1N1 need to be characterized to elucidate the aspects responsible for the multiple waves of pandemic. Methodology/Findings Forty whole genome sequences and 584 partial sequences of pH1N1 circulating in Thailand, divided into 1st, 2nd and 3rd wave and post-pandemic were characterized and 77 genome signatures were analyzed. Phylogenetic trees of concatenated whole genome and HA gene sequences were constructed calculating substitution rate and dN/dS of each gene. Phylogenetic analysis showed a distinct pattern of pH1N1 circulation in Thailand, with the first two isolates from May, 2009 belonging to clade 5 while clades 5, 6 and 7 co-circulated during the first wave of pH1N1 pandemic in Thailand. Clade 8 predominated during the second wave and different proportions of the pH1N1 viruses circulating during the third wave and post pandemic period belonged to clades 8, 11.1 and 11.2. The mutation analysis of pH1N1 revealed many adaptive mutations which have become the signature of each clade and may be responsible for the multiple pandemic waves in Thailand, especially with regard to clades 11.1 and 11.2 as evidenced with V731I, G154D of PB1 gene, PA I330V, HA A214T S160G and S202T. The substitution rate of pH1N1 in Thailand ranged from 2.53×10−3±0.02 (M2 genes) to 5.27×10−3±0.03 per site per year (NA gene). Conclusions All results suggested that this virus is still adaptive, maybe to evade the host's immune response and tends to remain in the human host although the dN/dS were under purifying selection in all 8 genes. Due to the gradual evolution of pH1N1 in Thailand, continuous monitoring is essential for evaluation and surveillance to be prepared for and able to control future influenza activities. PMID:23251479

Variability in nest survival rates and implications to nesting studies

USGS Publications Warehouse

Klett, A.T.; Johnson, D.H.

1982-01-01

We used four reasonably large samples (83-213) of Mallard (Anas platyrhynchos) and Blue-winged Teal (A. discors) nests on an interstate highway right-of-way in southcentral North Dakota to evaluate potential biases in hatch-rate estimates. Twelve consecutive, weekly searches for nests were conducted with a cable-chain drag in 1976 and 1977. Nests were revisited at weekly intervals. Four methods were used to estimate hatch rates for the four data sets: the Traditional Method, the Mayfield Method, and two modifications of the Mayfield Method that are sometimes appropriate when daily mortality rates of nests are not constant. Hatch rates and the average age of nests at discovery declined as the interval between searches decreased, suggesting that mortality rates were not constant in our samples. An analysis of variance indicated that daily mortality rates varied with the age of nests in all four samples. Mortality was generally highest during the early laying period, moderately high during the late laying period, and lowest during incubation. We speculate that this relationship of mortality to nest age might be due to the presence of hens at nests or to differences in the vulnerability of nest sites to predation. A modification of the Mayfield Method that accounts for age-related variation in nest mortality was most appropriate for our samples. We suggest methods for conducting nesting studies and estimating nest success for species possessing similar nesting habits.

Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes

PubMed Central

2012-01-01

Background Enterococci are among the leading causes of hospital-acquired infections in the United States and Europe, with Enterococcus faecalis and Enterococcus faecium being the two most common species isolated from enterococcal infections. In the last decade, the proportion of enterococcal infections caused by E. faecium has steadily increased compared to other Enterococcus species. Although the underlying mechanism for the gradual replacement of E. faecalis by E. faecium in the hospital environment is not yet understood, many studies using genotyping and phylogenetic analysis have shown the emergence of a globally dispersed polyclonal subcluster of E. faecium strains in clinical environments. Systematic study of the molecular epidemiology and pathogenesis of E. faecium has been hindered by the lack of closed, complete E. faecium genomes that can be used as references. Results In this study, we report the complete genome sequence of the E. faecium strain TX16, also known as DO, which belongs to multilocus sequence type (ST) 18, and was the first E. faecium strain ever sequenced. Whole genome comparison of the TX16 genome with 21 E. faecium draft genomes confirmed that most clinical, outbreak, and hospital-associated (HA) strains (including STs 16, 17, 18, and 78), in addition to strains of non-hospital origin, group in the same clade (referred to as the HA clade) and are evolutionally considerably more closely related to each other by phylogenetic and gene content similarity analyses than to isolates in the community-associated (CA) clade with approximately a 3–4% average nucleotide sequence difference between the two clades at the core genome level. Our study also revealed that many genomic loci in the TX16 genome are unique to the HA clade. 380 ORFs in TX16 are HA-clade specific and antibiotic resistance genes are enriched in HA-clade strains. Mobile elements such as IS16 and transposons were also found almost exclusively in HA strains, as previously reported. Conclusions Our findings along with other studies show that HA clonal lineages harbor specific genetic elements as well as sequence differences in the core genome which may confer selection advantages over the more heterogeneous CA E. faecium isolates. Which of these differences are important for the success of specific E. faecium lineages in the hospital environment remain(s) to be determined. PMID:22769602

Firewalls in bee nests-survival value of propolis walls of wild Cape honeybee (Apis mellifera capensis).

PubMed

Tribe, Geoff; Tautz, Jürgen; Sternberg, Karin; Cullinan, Jenny

2017-04-01

The Cape bee is endemic to the winter rainfall region of South Africa where fires are an integral part of the ecology of the fynbos (heathland) vegetation. Of the 37 wild nests in pristine Peninsula Sandstone Fynbos in the Cape Point section of Table Mountain National Park that have been analyzed so far, only 22 could be accessed sufficiently to determine the existence of a propolis wall of which 68% had propolis walls which entirely enclosed their openings. The analysis of the 37 wild nests revealed that 78% occurred under boulders or in clefts within rocks, 11% in the ground, 8% in tree cavities, and 3% within shrubs. The analysis of 17 of these nests following a fire within the park revealed that the propolis walls materially protected the nests and retarded the fire with all the colonies surviving. The bees responded to the smoke by imbibing honey and retreating to the furthest recess of their nest cavity. The bees were required to utilize this honey for about 3 weeks after which fire-loving plants appeared and began flowering. Considerable resources were utilized in the construction of the propolis walls, which ranged in thickness from 1.5 to 40 mm (mean 5 mm). Its physical environment determines the nesting behavior of the Cape bee. The prolific use of propolis serves to insulate the nest from extremes of temperature and humidity, restricts entry, camouflages the nest, and acts as an effective fire barrier protecting nests established mostly under rocks in vegetation subjected to periodic fires.

Nest site attributes and temporal patterns of northern flicker nest loss: effects of predation and competition.

PubMed

Fisher, Ryan J; Wiebe, Karen L

2006-04-01

To date, most studies of nest site selection have failed to take into account more than one source of nest loss (or have combined all sources in one analysis) when examining nest site characteristics, leaving us with an incomplete understanding of the potential trade-offs that individuals may face when selecting a nest site. Our objectives were to determine whether northern flickers (Colaptes auratus) may experience a trade-off in nest site selection in response to mammalian nest predation and nest loss to a cavity nest competitor (European starling, Sturnus vulgaris). We also document within-season temporal patterns of these two sources of nest loss with the hypothesis that flickers may also be constrained in the timing of reproduction under both predatory and competitive influence. Mammalian predators frequently depredated flicker nests that were: lower to the ground, less concealed by vegetation around the cavity entrance and at the base of the nest tree, closer to coniferous forest edges and in forest clumps with a high percentage of conifer content. Proximity to coniferous edges or coniferous trees increased the probability of nest predation, but nests near conifers were less likely to be lost to starlings. Flickers may thus face a trade-off in nest site selection with respect to safety from predators or competitors. Models suggested that peaks of nest predation and nest loss to eviction occurred at the same time, although a competing model suggested that the peak of nest loss to starlings occurred 5 days earlier than the peak of mammalian predation. Differences in peaks of mammalian predation and loss to starlings may constrain any adjustment in clutch initiation date by flickers to avoid one source of nest loss.

Clonal Lineages of Erysipelothrix rhusiopathiae Responsible for Acute Swine Erysipelas in Japan Identified by Using Genome-Wide Single-Nucleotide Polymorphism Analysis.

PubMed

Ogawa, Yohsuke; Shiraiwa, Kazumasa; Ogura, Yoshitoshi; Ooka, Tadasuke; Nishikawa, Sayaka; Eguchi, Masahiro; Hayashi, Tetsuya; Shimoji, Yoshihiro

2017-06-01

Erysipelothrix rhusiopathiae causes swine erysipelas, an important infectious disease in the swine industry. In Japan, the incidence of acute swine erysipelas due to E. rhusiopathiae serovar 1a has recently increased markedly. To study the genetic relatedness of the strains from the recent cases, we analyzed 34 E. rhusiopathiae serovar 1a swine isolates collected between 1990 and 2011 and further investigated the possible association of the live Koganei 65-0.15 vaccine strain (serovar 1a) with the increase in cases. Pulsed-field gel electrophoresis analysis revealed no marked variation among the isolates; however, sequencing analysis of a hypervariable region in the surface-protective antigen A gene ( spaA ) revealed that the strains isolated after 2007 exhibited the same spaA genotype and could be differentiated from older strains. Phylogenetic analysis based on genome-wide single-nucleotide polymorphisms (SNPs) revealed that the Japanese strains examined were closely related, showing a relatively small number of SNPs among them. The strains were classified into four major lineages, with Koganei 65-0.15 (lineage III) being phylogenetically separated from the other three lineages. The strains isolated after 2007 and the two older strains constituted one major lineage (lineage IV) with a specific spaA genotype (M203/I257-SpaA), while the recent isolates were further divided into two geographic groups. The remaining older isolates belonged to either lineage I, with the I203/L257-SpaA type, or lineage II, with the I203/I257-SpaA type. These results indicate that the recent increased incidence of acute swine erysipelas in Japan is associated with two sublineages of lineage IV, which have independently evolved in two different geographic regions. IMPORTANCE Using large-scale whole-genome sequence data from Erysipelothrix rhusiopathiae isolates from a wide range of hosts and geographic origins, a recent study clarified the existence of three distinct clades (clades 1, 2, and 3) that are found across multiple continents and host species, representing both livestock and wildlife, and an "intermediate" clade between clade 2 and the dominant clade 3 within the species. In this study, we found that the E. rhusiopathiae Japanese strains examined exhibited remarkably low levels of genetic diversity and confirmed that all of the Japanese and Chinese swine isolates examined in this study belong to clonal lineages within the intermediate clade. We report that spaA genotyping of E. rhusiopathiae strains is a practical alternative to whole-genome sequencing analysis of the E. rhusiopathiae isolates from eastern Asian countries. Copyright © 2017 American Society for Microbiology.

The structure of gallery networks in the nests of termite Cubitermes spp. revealed by X-ray tomography

NASA Astrophysics Data System (ADS)

Perna, Andrea; Jost, Christian; Couturier, Etienne; Valverde, Sergi; Douady, Stéphane; Theraulaz, Guy

2008-09-01

Recent studies have introduced computer tomography (CT) as a tool for the visualisation and characterisation of insect architectures. Here, we use CT to map the three-dimensional networks of galleries inside Cubitermes nests in order to analyse them with tools from graph theory. The structure of these networks indicates that connections inside the nest are rearranged during the whole nest life. The functional analysis reveals that the final network topology represents an excellent compromise between efficient connectivity inside the nest and defence against attacking predators. We further discuss and illustrate the usefulness of CT to disentangle environmental and specific influences on nest architecture.

The evolutionary dynamics of ancient and recent polyploidy in the African semiaquatic species of the legume genus Aeschynomene.

PubMed

Chaintreuil, Clémence; Gully, Djamel; Hervouet, Catherine; Tittabutr, Panlada; Randriambanona, Herizo; Brown, Spencer C; Lewis, Gwilym P; Bourge, Mickaël; Cartieaux, Fabienne; Boursot, Marc; Ramanankierana, Heriniaina; D'Hont, Angélique; Teaumroong, Neung; Giraud, Eric; Arrighi, Jean-François

2016-08-01

The legume genus Aeschynomene is notable in the ability of certain semiaquatic species to develop nitrogen-fixing stem nodules. These species are distributed in two clades. In the first clade, all the species are characterized by the use of a unique Nod-independent symbiotic process. In the second clade, the species use a Nod-dependent symbiotic process and some of them display a profuse stem nodulation as exemplified in the African Aeschynomene afraspera. To facilitate the molecular analysis of the symbiotic characteristics of such legumes, we took an integrated molecular and cytogenetic approach to track occurrences of polyploidy events and to analyze their impact on the evolution of the African species of Aeschynomene. Our results revealed two rounds of polyploidy: a paleopolyploid event predating the African group and two neopolyploid speciations, along with significant chromosomal variations. Hence, we found that A. afraspera (8x) has inherited the contrasted genomic properties and the stem-nodulation habit of its parental lineages (4x). This study reveals a comprehensive picture of African Aeschynomene diversification. It notably evidences a history that is distinct from the diploid Nod-independent clade, providing clues for the identification of the specific determinants of the Nod-dependent and Nod-independent symbiotic processes, and for comparative analysis of stem nodulation. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Defense mutualisms enhance plant diversification

PubMed Central

Weber, Marjorie G.; Agrawal, Anurag A.

2014-01-01

The ability of plants to form mutualistic relationships with animal defenders has long been suspected to influence their evolutionary success, both by decreasing extinction risk and by increasing opportunity for speciation through an expanded realized niche. Nonetheless, the hypothesis that defense mutualisms consistently enhance plant diversification across lineages has not been well tested due to a lack of phenotypic and phylogenetic information. Using a global analysis, we show that the >100 vascular plant families in which species have evolved extrafloral nectaries (EFNs), sugar-secreting organs that recruit arthropod mutualists, have twofold higher diversification rates than families that lack species with EFNs. Zooming in on six distantly related plant clades, trait-dependent diversification models confirmed the tendency for lineages with EFNs to display increased rates of diversification. These results were consistent across methodological approaches. Inference using reversible-jump Markov chain Monte Carlo (MCMC) to model the placement and number of rate shifts revealed that high net diversification rates in EFN clades were driven by an increased number of positive rate shifts following EFN evolution compared with sister clades, suggesting that EFNs may be indirect facilitators of diversification. Our replicated analysis indicates that defense mutualisms put lineages on a path toward increased diversification rates within and between clades, and is concordant with the hypothesis that mutualistic interactions with animals can have an impact on deep macroevolutionary patterns and enhance plant diversity. PMID:25349406

Genome-wide analysis of the Glycerol-3-Phosphate Acyltransferase (GPAT) gene family reveals the evolution and diversification of plant GPATs

PubMed Central

Waschburger, Edgar; Kulcheski, Franceli Rodrigues; Veto, Nicole Moreira; Margis, Rogerio; Margis-Pinheiro, Marcia; Turchetto-Zolet, Andreia Carina

2018-01-01

Abstract sn-Glycerol-3-phosphate 1-O-acyltransferase (GPAT) is an important enzyme that catalyzes the transfer of an acyl group from acyl-CoA or acyl-ACP to the sn-1 or sn-2 position of sn-glycerol-3-phosphate (G3P) to generate lysophosphatidic acids (LPAs). The functional studies of GPAT in plants demonstrated its importance in controlling storage and membrane lipid. Identifying genes encoding GPAT in a variety of plant species is crucial to understand their involvement in different metabolic pathways and physiological functions. Here, we performed genome-wide and evolutionary analyses of GPATs in plants. GPAT genes were identified in all algae and plants studied. The phylogenetic analysis showed that these genes group into three main clades. While clades I (GPAT9) and II (soluble GPAT) include GPATs from algae and plants, clade III (GPAT1-8) includes GPATs specific from plants that are involved in the biosynthesis of cutin or suberin. Gene organization and the expression pattern of GPATs in plants corroborate with clade formation in the phylogeny, suggesting that the evolutionary patterns is reflected in their functionality. Overall, our results provide important insights into the evolution of the plant GPATs and allowed us to explore the evolutionary mechanism underlying the functional diversification among these genes. PMID:29583156

Defense mutualisms enhance plant diversification.

PubMed

Weber, Marjorie G; Agrawal, Anurag A

2014-11-18

The ability of plants to form mutualistic relationships with animal defenders has long been suspected to influence their evolutionary success, both by decreasing extinction risk and by increasing opportunity for speciation through an expanded realized niche. Nonetheless, the hypothesis that defense mutualisms consistently enhance plant diversification across lineages has not been well tested due to a lack of phenotypic and phylogenetic information. Using a global analysis, we show that the >100 vascular plant families in which species have evolved extrafloral nectaries (EFNs), sugar-secreting organs that recruit arthropod mutualists, have twofold higher diversification rates than families that lack species with EFNs. Zooming in on six distantly related plant clades, trait-dependent diversification models confirmed the tendency for lineages with EFNs to display increased rates of diversification. These results were consistent across methodological approaches. Inference using reversible-jump Markov chain Monte Carlo (MCMC) to model the placement and number of rate shifts revealed that high net diversification rates in EFN clades were driven by an increased number of positive rate shifts following EFN evolution compared with sister clades, suggesting that EFNs may be indirect facilitators of diversification. Our replicated analysis indicates that defense mutualisms put lineages on a path toward increased diversification rates within and between clades, and is concordant with the hypothesis that mutualistic interactions with animals can have an impact on deep macroevolutionary patterns and enhance plant diversity.

Lowering sample size in comparative analyses can indicate a correlation where there is none: example from Rensch's rule in primates.

PubMed

Lindenfors, P; Tullberg, B S

2006-07-01

The fact that characters may co-vary in organism groups because of shared ancestry and not always because of functional correlations was the initial rationale for developing phylogenetic comparative methods. Here we point out a case where similarity due to shared ancestry can produce an undesired effect when conducting an independent contrasts analysis. Under special circumstances, using a low sample size will produce results indicating an evolutionary correlation between characters where an analysis of the same pattern utilizing a larger sample size will show that this correlation does not exist. This is the opposite effect of increased sample size to that expected; normally an increased sample size increases the chance of finding a correlation. The situation where the problem occurs is when co-variation between the two continuous characters analysed is clumped in clades; e.g. when some phylogenetically conservative factors affect both characters simultaneously. In such a case, the correlation between the two characters becomes contingent on the number of clades sharing this conservative factor that are included in the analysis, in relation to the number of species contained within these clades. Removing species scattered evenly over the phylogeny will in this case remove the exact variation that diffuses the evolutionary correlation between the two characters - the variation contained within the clades sharing the conservative factor. We exemplify this problem by discussing a parallel in nature where the described problem may be of importance. This concerns the question of the presence or absence of Rensch's rule in primates.

Origin and Possible Genetic Recombination of the Middle East Respiratory Syndrome Coronavirus from the First Imported Case in China: Phylogenetics and Coalescence Analysis.

PubMed

Wang, Yanqun; Liu, Di; Shi, Weifeng; Lu, Roujian; Wang, Wenling; Zhao, Yanjie; Deng, Yao; Zhou, Weimin; Ren, Hongguang; Wu, Jun; Wang, Yu; Wu, Guizhen; Gao, George F; Tan, Wenjie

2015-09-08

The Middle East respiratory syndrome coronavirus (MERS-CoV) causes a severe acute respiratory tract infection with a high fatality rate in humans. Coronaviruses are capable of infecting multiple species and can evolve rapidly through recombination events. Here, we report the complete genomic sequence analysis of a MERS-CoV strain imported to China from South Korea. The imported virus, provisionally named ChinaGD01, belongs to group 3 in clade B in the whole-genome phylogenetic tree and also has a similar tree topology structure in the open reading frame 1a and -b (ORF1ab) gene segment but clusters with group 5 of clade B in the tree constructed using the S gene. Genetic recombination analysis and lineage-specific single-nucleotide polymorphism (SNP) comparison suggest that the imported virus is a recombinant comprising group 3 and group 5 elements. The time-resolved phylogenetic estimation indicates that the recombination event likely occurred in the second half of 2014. Genetic recombination events between group 3 and group 5 of clade B may have implications for the transmissibility of the virus. The recent outbreak of MERS-CoV in South Korea has attracted global media attention due to the speed of spread and onward transmission. Here, we present the complete genome of the first imported MERS-CoV case in China and demonstrate genetic recombination events between group 3 and group 5 of clade B that may have implications for the transmissibility of MERS-CoV. Copyright © 2015 Wang et al.

Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits

PubMed Central

Goudenège, David; Labreuche, Yannick; Krin, Evelyne; Ansquer, Dominique; Mangenot, Sophie; Calteau, Alexandra; Médigue, Claudine; Mazel, Didier; Polz, Martin F; Le Roux, Frédérique

2013-01-01

Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have suggested that pathogenicity is linked to particular lineages. Here, we performed high-throughput sequencing-based comparative genome analysis of 16 V. nigripulchritudo strains to explore the genomic diversity and evolutionary history of pathogen-containing lineages and to identify pathogen-specific genetic elements. Our phylogenetic analysis revealed three pathogen-containing V. nigripulchritudo clades, including two clades previously identified from New Caledonia and one novel clade comprising putatively pathogenic isolates from septicemic shrimp in Madagascar. The similar genetic distance between the three clades indicates that they have diverged from an ancestral population roughly at the same time and recombination analysis indicates that these genomes have, in the past, shared a common gene pool and exchanged genes. As each contemporary lineage is comprised of nearly identical strains, comparative genomics allowed differentiation of genetic elements specific to shrimp pathogenesis of varying severity. Notably, only a large plasmid present in all highly pathogenic (HP) strains encodes a toxin. Although less/non-pathogenic strains contain related plasmids, these are differentiated by a putative toxin locus. Expression of this gene by a non-pathogenic V. nigripulchritudo strain resulted in production of toxic culture supernatant, normally an exclusive feature of HP strains. Thus, this protein, here termed ‘nigritoxin', is implicated to an extent that remains to be precisely determined in the toxicity of V. nigripulchritudo. PMID:23739050

Cross-reactivity of anti-HIV-1 T cell immune responses among the major HIV-1 clades in HIV-1-positive individuals from 4 continents.

PubMed

Coplan, Paul M; Gupta, Swati B; Dubey, Sheri A; Pitisuttithum, Punnee; Nikas, Alex; Mbewe, Bernard; Vardas, Efthyia; Schechter, Mauro; Kallas, Esper G; Freed, Dan C; Fu, Tong-Ming; Mast, Christopher T; Puthavathana, Pilaipan; Kublin, James; Brown Collins, Kelly; Chisi, John; Pendame, Richard; Thaler, Scott J; Gray, Glenda; Mcintyre, James; Straus, Walter L; Condra, Jon H; Mehrotra, Devan V; Guess, Harry A; Emini, Emilio A; Shiver, John W

2005-05-01

The genetic diversity of human immunodeficiency virus type 1 (HIV-1) raises the question of whether vaccines that include a component to elicit antiviral T cell immunity based on a single viral genetic clade could provide cellular immune protection against divergent HIV-1 clades. Therefore, we quantified the cross-clade reactivity, among unvaccinated individuals, of anti-HIV-1 T cell responses to the infecting HIV-1 clade relative to other major circulating clades. Cellular immune responses to HIV-1 clades A, B, and C were compared by standardized interferon- gamma enzyme-linked immunospot assays among 250 unvaccinated individuals, infected with diverse HIV-1 clades, from Brazil, Malawi, South Africa, Thailand, and the United States. Cross-clade reactivity was evaluated by use of the ratio of responses to heterologous versus homologous (infecting) clades of HIV-1. Cellular immune responses were predominantly focused on viral Gag and Nef proteins. Cross-clade reactivity of cellular immune responses to HIV-1 clade A, B, and C proteins was substantial for Nef proteins (ratio, 0.97 [95% confidence interval, 0.89-1.05]) and lower for Gag proteins (ratio, 0.67 [95% confidence interval, 0.62-0.73]). The difference in cross-clade reactivity to Nef and Gag proteins was significant (P<.0001). Cross-clade reactivity of cellular immune responses can be substantial but varies by viral protein.

Genomic analysis of coxsackieviruses A1, A19, A22, enteroviruses 113 and 104: viruses representing two clades with distinct tropism within enterovirus C

PubMed Central

Haq, Saddef; Sameroff, Stephen; Howie, Stephen R. C.; Lipkin, W. Ian

2013-01-01

Coxsackieviruses (CV) A1, CV-A19 and CV-A22 have historically comprised a distinct phylogenetic clade within Enterovirus (EV) C. Several novel serotypes that are genetically similar to these three viruses have been recently discovered and characterized. Here, we report the coding sequence analysis of two genotypes of a previously uncharacterized serotype EV-C113 from Bangladesh and demonstrate that it is most similar to CV-A22 and EV-C116 within the capsid region. We sequenced novel genotypes of CV-A1, CV-A19 and CV-A22 from Bangladesh and observed a high rate of recombination within this group. We also report genomic analysis of the rarely reported EV-C104 circulating in the Gambia in 2009. All available EV-C104 sequences displayed a high degree of similarity within the structural genes but formed two clusters within the non-structural genes. One cluster included the recently reported EV-C117, suggesting an ancestral recombination between these two serotypes. Phylogenetic analysis of all available complete genome sequences indicated the existence of two subgroups within this distinct Enterovirus C clade: one has been exclusively recovered from gastrointestinal samples, while the other cluster has been implicated in respiratory disease. PMID:23761409

Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi.

PubMed

Zhang, Ning; Cai, Guohong; Price, Dana C; Crouch, Jo Anne; Gladieux, Pierre; Hillman, Bradley; Khang, Chang Hyun; LeBrun, Marc-Henri; Lee, Yong-Hwan; Luo, Jing; Qiu, Huan; Veltri, Daniel; Wisecaver, Jennifer H; Zhu, Jie; Bhattacharya, Debashish

2018-04-12

The rice blast fungus Pyricularia oryzae (syn. Magnaporthe oryzae, Magnaporthe grisea), a member of the order Magnaporthales in the class Sordariomycetes, is an important plant pathogen and a model species for studying pathogen infection and plant-fungal interaction. In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis. Our results suggest that the Magnaporthales diverged ca. 31 millon years ago from other Sordariomycetes, with the phytopathogenic blast clade diverging ca. 21 million years ago. Little evidence of inter-phylum horizontal gene transfer (HGT) was detected in Magnaporthales. In contrast, many genes underwent positive selection in this order and the majority of these sequences are clade-specific. The blast clade genomes contain more secretome and avirulence effector genes, which likely play key roles in the interaction between Pyricularia species and their plant hosts. Finally, analysis of transposable elements (TE) showed differing proportions of TE classes among Magnaporthales genomes, suggesting that species-specific patterns may hold clues to the history of host/environmental adaptation in these fungi.

Origin and Possible Genetic Recombination of the Middle East Respiratory Syndrome Coronavirus from the First Imported Case in China: Phylogenetics and Coalescence Analysis

PubMed Central

Wang, Yanqun; Liu, Di; Shi, Weifeng; Lu, Roujian; Wang, Wenling; Zhao, Yanjie; Deng, Yao; Zhou, Weimin; Ren, Hongguang; Wu, Jun; Wang, Yu; Wu, Guizhen

2015-01-01

ABSTRACT The Middle East respiratory syndrome coronavirus (MERS-CoV) causes a severe acute respiratory tract infection with a high fatality rate in humans. Coronaviruses are capable of infecting multiple species and can evolve rapidly through recombination events. Here, we report the complete genomic sequence analysis of a MERS-CoV strain imported to China from South Korea. The imported virus, provisionally named ChinaGD01, belongs to group 3 in clade B in the whole-genome phylogenetic tree and also has a similar tree topology structure in the open reading frame 1a and -b (ORF1ab) gene segment but clusters with group 5 of clade B in the tree constructed using the S gene. Genetic recombination analysis and lineage-specific single-nucleotide polymorphism (SNP) comparison suggest that the imported virus is a recombinant comprising group 3 and group 5 elements. The time-resolved phylogenetic estimation indicates that the recombination event likely occurred in the second half of 2014. Genetic recombination events between group 3 and group 5 of clade B may have implications for the transmissibility of the virus. PMID:26350969

Reintroduction of highly pathogenic avian influenza A/H5N8 virus of clade 2.3.4.4. in Russia.

PubMed

Marchenko, Vasiliy Y; Susloparov, Ivan M; Komissarov, Andrey B; Fadeev, Artem; Goncharova, Nataliya I; Shipovalov, Andrey V; Svyatchenko, Svetlana V; Durymanov, Alexander G; Ilyicheva, Tatyana N; Salchak, Lyudmila K; Svintitskaya, Elena P; Mikheev, Valeriy N; Ryzhikov, Alexander B

2017-05-01

In the spring of 2016, a loss of wild birds was observed during the monitoring of avian influenza virus activity in the Republic of Tyva. That outbreak was caused by influenza H5N8 virus of clade 2.3.4.4. In the fall, viruses of H5N8 clade 2.3.4.4 were propagated in European countries. This paper presents some results of analysis of the virus strains isolated during the spring and fall seasons in 2016 in the Russian Federation. The investigated strains were highly pathogenic for mice, and some of their antigenic and genetic features differed from those of an H5N8 strain that circulated in 2014 in Russia.

Sequential and Simultaneous Immunization of Rabbits with HIV-1 Envelope Glycoprotein SOSIP.664 Trimers from Clades A, B and C

PubMed Central

Klasse, P. J.; Ozorowski, Gabriel; Cupo, Albert; Pugach, Pavel; Ringe, Rajesh P.; Golabek, Michael; van Gils, Marit J.; Guttman, Miklos; Lee, Kelly K.; Wilson, Ian A.; Butera, Salvatore T.; Ward, Andrew B.; Montefiori, David C.; Sanders, Rogier W.; Moore, John P.

2016-01-01

We have investigated the immunogenicity in rabbits of native-like, soluble, recombinant SOSIP.664 trimers based on the env genes of four isolates of human immunodeficiency virus type 1 (HIV-1); specifically BG505 (clade A), B41 (clade B), CZA97 (clade C) and DU422 (clade C). The various trimers were delivered either simultaneously (as a mixture of clade A + B trimers) or sequentially over a 73-week period. Autologous, Tier-2 neutralizing antibody (NAb) responses were generated to the clade A and clade B trimers in the bivalent mixture. When delivered as boosting immunogens to rabbits immunized with the clade A and/or clade B trimers, the clade C trimers also generated autologous Tier-2 NAb responses, the CZA97 trimers doing so more strongly and consistently than the DU422 trimers. The clade C trimers also cross-boosted the pre-existing NAb responses to clade A and B trimers. We observed heterologous Tier-2 NAb responses albeit inconsistently, and with limited overall breath. However, cross-neutralization of the clade A BG505.T332N virus was consistently observed in rabbits immunized only with clade B trimers and then boosted with clade C trimers. The autologous NAbs induced by the BG505, B41 and CZA97 trimers predominantly recognized specific holes in the glycan shields of the cognate virus. The shared location of some of these holes may account for the observed cross-boosting effects and the heterologous neutralization of the BG505.T332N virus. These findings will guide the design of further experiments to determine whether and how multiple Env trimers can together induce more broadly neutralizing antibody responses. PMID:27627672

Nested PCR and RFLP analysis based on the 16S rRNA gene

USDA-ARS?s Scientific Manuscript database

Current phytoplasma detection and identification method is primarily based on nested PCR followed by restriction fragment length polymorphism analysis and gel electrophoresis. This method can potentially detect and differentiate all phytoplasmas including those previously not described. The present ...

Lyme disease with facial nerve palsy: rapid diagnosis using a nested polymerase chain reaction-restriction fragment length polymorphism analysis.

PubMed

Hashimoto, Y; Takahashi, H; Kishiyama, K; Sato, Y; Nakao, M; Miyamoto, K; Iizuka, H

1998-02-01

A 64-year-old woman with Lyme disease and manifesting facial nerve palsy had been bitten by a tick on the left frontal scalp 4 weeks previously. Erythema migrans appeared on the left forehead, accompanied by left facial paralysis. Nested polymerase chain reaction-restriction fragment length polymorphism analysis (nested PCR-RFLP) was performed on DNA extracted from a skin biopsy of the erythema on the left forehead. Borrelia flagellin gene DNA was detected and its RFLP pattern indicated that the organism was B. garinii, Five weeks later, B. garinii was isolated by conventional culture from the erythematous skin lesion, but not from the cerebrospinal fluid. After treatment with ceftriaxone intravenously for 10 days and oral administration of minocycline for 7 days, both the erythema and facial nerve palsy improved significantly. Nested PCR and culture taken after the lesion subsided, using skin samples obtained from a site adjacent to the original biopsy, were both negative. We suggest that nested PCR-RFLP analysis might be useful for the rapid diagnosis of Lyme disease and for evaluating therapy.

Recurrent hybridization and recent origin obscure phylogenetic relationships within the ‘white-headed’ gull (Larus sp.) complex

USGS Publications Warehouse

Sonsthagen, Sarah A.; Wilson, Robert E.; Chesser, Terry; Pons, Jean-Marc; Crochet, Pierre-Andre; Driscoll, Amy; Dove, Carla

2016-01-01

Species complexes that have undergone recent radiations are often characterized by extensive allele sharing due to recent ancestry and (or) introgressive hybridization. This can result in discordant evolutionary histories of genes and heterogeneous genomes, making delineating species limits difficult. Here we examine the phylogenetic relationships among a complex group of birds, the white-headed gulls (Aves: Laridae), which offer a unique window into the speciation process due to their recent evolutionary history and propensity to hybridize. Relationships were examined among 17 species (61 populations) using a multilocus approach, including mitochondrial and nuclear intron DNA sequences and microsatellite genotype information. Analyses of microsatellite and intron data resulted in some species-based groupings, although most species were not represented by a single cluster. Considerable allele and haplotype sharing among white-headed gull species was observed; no locus contained a species-specific clade. Despite this, our multilocus approach provided better resolution among some species than previous studies. Interestingly, most clades appear to correspond to geographic locality: our BEAST analysis recovered strong support for a northern European/Icelandic clade, a southern European/Russian clade, and a western North American/canus clade, with weak evidence for a high latitude clade spanning North America and northwestern Europe. This geographical structuring is concordant with behavioral observations of pervasive hybridization in areas of secondary contact. The extent of allele and haplotype sharing indicates that ecological and sexual selection are likely not strong enough to complete reproductive isolation within several species in the white-headed gull complex. This suggests that just a few genes are driving the speciation process.

Phylogenetics and Gene Structure Dynamics of Polygalacturonase Genes in Aspergillus and Neurospora crassa

PubMed Central

Hong, Jin-Sung; Ryu, Ki-Hyun; Kwon, Soon-Jae; Kim, Jin-Won; Kim, Kwang-Soo; Park, Kyong-Cheul

2013-01-01

Polygalacturonase (PG) gene is a typical gene family present in eukaryotes. Forty-nine PGs were mined from the genomes of Neurospora crassa and five Aspergillus species. The PGs were classified into 3 clades such as clade 1 for rhamno-PGs, clade 2 for exo-PGs and clade 3 for exo- and endo-PGs, which were further grouped into 13 sub-clades based on the polypeptide sequence similarity. In gene structure analysis, a total of 124 introns were present in 44 genes and five genes lacked introns to give an average of 2.5 introns per gene. Intron phase distribution was 64.5% for phase 0, 21.8% for phase 1, and 13.7% for phase 2, respectively. The introns varied in their sequences and their lengths ranged from 20 bp to 424 bp with an average of 65.9 bp, which is approximately half the size of introns in other fungal genes. There were 29 homologous intron blocks and 26 of those were sub-clade specific. Intron losses were counted in 18 introns in which no obvious phase preference for intron loss was observed. Eighteen introns were placed at novel positions, which is considerably higher than those of plant PGs. In an evolutionary sense both intron loss and gain must have taken place for shaping the current PGs in these fungi. Together with the small intron size, low conservation of homologous intron blocks and higher number of novel introns, PGs of fungal species seem to have recently undergone highly dynamic evolution. PMID:25288950

Phylogenetic analysis of the Pacific cutthroat trout (Oncorhynchus clarki ssp.: Salmonidae) based on partial mtDNA ND4 sequences: a closer look at the highly fragmented inland species.

PubMed

Wilson, Wade D; Turner, Thomas F

2009-08-01

The genus Oncorhynchus includes Pacific salmon and trout (anadromous and land-locked) species of the western United States and Mexico. All species and subspecies in this group are threatened, endangered, sensitive, or species of conservation concern in portions of their native ranges. To examine the relationships of the species within Oncorhynchus we sequenced a 768 bp fragment of the protein-encoding ND4 mtDNA region. We included all six recognized subspecies of O. clarki (cutthroat trout), O. gilaegilae (Gila trout) and O. g. apache (Apache trout). Gene trees from likelihood and Bayesian phylogenetic analyses revealed that Salvelinus was the sister group to Oncorhynchus, and as expected based on previous studies, O. clarki was sister to a clade that consisted of O. mykiss plus O. g. gilae and O. g. apache. Within the cutthroat clade (O. clarki), the coastal form O. c. clarki was basal with the Rio Grande cutthroat (O. c. virginalis) most derived. Divergence dating based on a fossil calibration molecular clock showed the oldest clade (mean node age) was O. masou ssp., which diverged roughly 7.6 MYA. Highest probability density intervals for divergence of O. masou overlapped with divergence (6.3 MYA) of Pacific salmon clades ((O. gorbuscha + O. nerka) and (O. tshawytscha + O. kisutch)). The Pacific trout clade ((O. mykiss + O. gilae ssp.) + (O. clarki ssp.)) diverged from the Pacific salmon around 6.3 MYA, with most of the diversification within the O. clarki clade occurring in the last 1 MY.

Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed.

PubMed

Tanaka, Mami; Endo, Shoko; Kotake, Fumihito; Al-Saari, Nurhidayu; Amin, A K M Rohul; Feng, Gao; Mino, Sayaka; Doi, Hidetaka; Ogura, Yoshitoshi; Hayashi, Tetsuya; Suda, Wataru; Hattori, Masahira; Yumoto, Isao; Sawabe, Toko; Sawabe, Tomoo; Araki, Toshiyoshi

2017-01-01

A novel strain Vibrio aphrogenes sp. nov. strain CA-1004T isolated from the surface of seaweed collected on the coast of Mie Prefecture in 1994 [1] was characterized using polyphasic taxonomy including multilocus sequence analysis (MLSA) and a genome based comparison. Both phylogenetic analyses on the basis of 16S rRNA gene sequences and MLSA based on eight protein-coding genes (gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA) showed the strain could be placed in the Rumoiensis clade in the genus Vibrio. Sequence similarities of the 16S rRNA gene and the multilocus genes against the Rumoiensis clade members, V. rumoiensis, V. algivorus, V. casei, and V. litoralis, were low enough to propose V. aphrogenes sp. nov. strain CA-1004T as a separate species. The experimental DNA-DNA hybridization data also revealed that the strain CA-1004T was separate from four known Rumoiensis clade species. The G+C content of the V. aphrogenes strain was determined as 42.1% based on the genome sequence. Major traits of the strain were non-motile, halophilic, fermentative, alginolytic, and gas production. A total of 27 traits (motility, growth temperature range, amylase, alginase and lipase productions, and assimilation of 19 carbon compounds) distinguished the strain from the other species in the Rumoiensis clade. The name V. aphrogenes sp. nov. is proposed for this species in the Rumoiensis clade, with CA-1004T as the type strain (JCM 31643T = DSM 103759T).

Spiny frogs (Paini) illuminate the history of the Himalayan region and Southeast Asia

PubMed Central

Che, Jing; Zhou, Wei-Wei; Hu, Jian-Sheng; Yan, Fang; Papenfuss, Theodore J.; Wake, David B.; Zhang, Ya-Ping

2010-01-01

Asian frogs of the tribe Paini (Anura: Dicroglossidae) range across several first-order tectono-morphological domains of the Cenozoic Indo-Asian collision that include the Tibetan Plateau, the Himalayas, and Indochina. We show how the tectonic events induced by the Indo-Asian collision affected the regional biota and, in turn, how the geological history of the earth can be viewed from a biological perspective. Our analysis of a concatenated dataset comprising four nuclear gene sequences of Paini revealed two main radiations, corresponding to the genera Nanorana (I) and Quasipaa (II). Five distinct clades are recognized: Tibetan plateau clade (I-1), Himalaya clade (I-2), environs of Himalaya–Tibetan plateau clade (I-3), South China clade (II-1), and Indochina clade (II-2). This pattern of relationships highlights the significance of geography in shaping evolutionary history. Building on our molecular dating, ancestral region reconstruction, and distributional patterns, we hypothesize a distinct geographic and climatic transition in Asia beginning in the Oligocene and intensifying in the Miocene; this stimulated rapid diversification of Paini. Vicariance explains species formation among major lineages within Nanorana. Dispersal, in contrast, plays an important role among Quasipaa, with the southern Chinese taxa originating from Indochina. Our results support the tectonic hypothesis that an uplift in the Himalaya–Tibetan plateau region resulting from crustal thickening and lateral extrusion of Indochina occurred synchronously during the transition between Oligocene and Miocene in reaction to the Indo-Asian collision. The phylogenetic history of Paini illuminates critical aspects of the timing of geological events responsible for the current geography of Southeast Asia. PMID:20643945

Identification of seven polyamine oxidase genes in tomato (Solanum lycopersicum L.) and their expression profiles under physiological and various stress conditions.

PubMed

Hao, Yanwei; Huang, Binbin; Jia, Dongyu; Mann, Taylor; Jiang, Xinyi; Qiu, Yuxing; Niitsu, Masaru; Berberich, Thomas; Kusano, Tomonobu; Liu, Taibo

2018-05-15

Polyamines (PAs) are implicated in developmental processes and stress responses of plants. Polyamine oxidases (PAOs), flavin adenine dinucleotide-dependent enzymes that function in PA catabolism, play a critical role. Even though PAO gene families of Arabidopsis and rice have been intensely characterized and their expression in response to developmental and environmental changes has been investigated, little is known about PAOs in tomato (Solanum lycopersicum). We found seven PAO genes in S. lycopersicum and named them SlPAO1∼7. Plant PAOs form four clades in phylogenetic analysis, of which SlPAO1 belongs to clade-I, SlPAO6 and SlPAO7 to clade-III, and the residual four (SlPAO2∼5) to clade-IV, while none belongs to clade-II. All the clade-IV members in tomato also retain the putative peroxisomal-targeting signals in their carboxy termini, suggesting their peroxisome localization. SlPAO1 to SlPAO5 genes consist of 10 exons and 9 introns, while SlPAO6 and SlPAO7 are intronless genes. To address the individual roles of SlPAOs, we analyzed their expression in various tissues and during flowering and fruit development. The expression of SlPAO2∼4 was constitutively high, while that of the other SlPAO members was relatively lower. We further analyzed the expressional changes of SlPAOs upon abiotic stresses, oxidative stresses, phytohormone application, and PA application. Based on the data obtained, we discuss the distinctive roles of SlPAOs. Copyright © 2018 Elsevier GmbH. All rights reserved.

Molecular phylogenetic diversity, multilocus haplotype nomenclature, and in vitro antifungal resistance within the Fusarium solani species complex.

PubMed

O'Donnell, Kerry; Sutton, Deanna A; Fothergill, Annette; McCarthy, Dora; Rinaldi, Michael G; Brandt, Mary E; Zhang, Ning; Geiser, David M

2008-08-01

Members of the species-rich Fusarium solani species complex (FSSC) are responsible for approximately two-thirds all fusarioses of humans and other animals. In addition, many economically important phytopathogenic species are nested within this complex. Due to their increasing clinical relevance and because most of the human pathogenic and plant pathogenic FSSC lack Latin binomials, we have extended the multilocus haplotype nomenclatural system introduced in a previous study (D. C. Chang, G. B. Grant, K. O'Donnell, K. A. Wannemuehler, J. Noble-Wang, C. Y. Rao, L. M. Jacobson, C. S. Crowell, R. S. Sneed, F. M. T. Lewis, J. K. Schaffzin, M. A. Kainer, C. A. Genese, E. C. Alfonso, D. B. Jones, A. Srinivasan, S. K. Fridkin, and B. J. Park, JAMA 296:953-963, 2006) to all 34 species within the medically important FSSC clade 3 to facilitate global epidemiological studies. The typing scheme is based on polymorphisms in portions of the following three genes: the internal transcribed spacer region and domains D1 plus D2 of the nuclear large-subunit rRNA, the translation elongation factor 1 alpha gene (EF-1alpha), and the second largest subunit of RNA polymerase II gene (RPB2). Of the 251 isolates subjected to multilocus DNA sequence typing, 191 sequence types were differentiated, and these were distributed among three strongly supported clades designated 1, 2, and 3. All of the mycosis-associated isolates were restricted to FSSC clade 3, as previously reported (N. Zhang, K. O'Donnell, D. A. Sutton, F. A Nalim, R. C. Summerbell, A. A. Padhye, and D. M. Geiser, J. Clin. Microbiol. 44:2186-2190, 2006), and these represent at least 20 phylogenetically distinct species. Analyses of the combined DNA sequence data by use of two separate phylogenetic methods yielded the most robust hypothesis of evolutionary relationships and genetic diversity within the FSSC to date. The in vitro activities of 10 antifungals tested against 19 isolates representing 18 species that span the breadth of the FSSC phylogeny show that members of this complex are broadly resistant to these drugs.

Lesser prairie-chicken nest site selection, microclimate, and nest survival in association with vegetation response to a grassland restoration program

USGS Publications Warehouse

Boal, Clint W.; Grisham, Blake A.; Haukos, David A.; Zavaleta, Jennifer C.; Dixon, Charles

2014-01-01

Climate models predict that the region of the Great Plains Landscape Conservation Cooperative (GPLCC) will experience increased maximum and minimum temperatures, reduced frequency but greater intensity of precipitation events, and earlier springs. These climate changes along with different landscape management techniques may influence the persistence of the lesser prairie-chicken (Tympanuchus pallidicinctus), a candidate for protection under the Endangered Species Act and a priority species under the GPLCC, in positive or negative ways. The objectives of this study were to conduct (1) a literature review of lesser prairie-chicken nesting phenology and ecology, (2) an analysis of thermal aspects of lesser prairie-chicken nest microclimate data, and (3) an analysis of nest site selection, nest survival, and vegetation response to 10 years of tebuthiuron and/or grazing treatments. We found few reports in the literature containing useful data on the nesting phenology of lesser prairie-chickens; therefore, managers must rely on short-term observations and measurements of parameters that provide some predictive insight into climate impacts on nesting ecology. Our field studies showed that prairie-chickens on nests were able to maintain relatively consistent average nest temperature of 31 °C and nest humidities of 56.8 percent whereas average external temperatures (20.3–35.0 °C) and humidities (35.2–74.9 percent) varied widely throughout the 24 hour (hr) cycle. Grazing and herbicide treatments within our experimental areas were designed to be less intensive than in common practice. We determined nest locations by radio-tagging hen lesser prairie-chickens captured at leks, which are display grounds at which male lesser prairie-chickens aggregate and attempt to attract a female for mating. Because nest locations selected by hen lesser prairie-chicken are strongly associated with the lek at which they were captured, we assessed nesting habitat use on the basis of hens captured at individual leks, and then for all leks pooled. There was no clear pattern of selection for treatment type for nest placement among hens associated with individual leks; however, when hens from all leks were pooled, we found nesting lesser prairie-chickens selected control plots for nesting over plots that were grazed, treated with tebuthiuron, or were both grazed and treated with tebuthiuron. Overall, the probability of a nest surviving the incubation period was 0.57 for this study and did not vary significantly among treatment types. In contrast to nesting preference for untreated habitats, lek use exhibited no noticeable selection of treatment type. Over the 10 years of the habitat management study, there was 91 percent less sand shinnery oak (Quercus havardii) in treated areas than untreated areas. The removal of sand shinnery oak made environmental soil moisture more available for grasses and forbs to germinate and grow. Grasses increased by 149 percent and forbs increased by 257 percent in treated areas as compared to untreated areas throughout the study period. Our combined results, including our habitat selection analysis at the individual lek level, indicated that reduced rates of herbicide and short-duration grazing treatments were not detrimental to nesting lesser prairie-chickens and that populations of lesser prairie-chickens in shrub-dominated ecosystems may benefit from reduced rates of herbicide application and short duration of grazing that results in increased habitat heterogeneity.

Gisekia (Gisekiaceae): phylogenetic relationships, biogeography, and ecophysiology of a poorly known C₄ lineage in the Caryophyllales.

PubMed

Bissinger, Kerstin; Khoshravesh, Roxanne; Kotrade, Jan Peter; Oakley, Jason; Sage, Tammy L; Sage, Rowan F; Hartmann, Heidrun E K; Kadereit, Gudrun

2014-03-01

Gisekiaceae are a monogeneric family of the core Caryophyllales distributed in arid regions of Africa and Asia. The only widespread species of the genus, Gisekia pharnaceoides, performs C4 photosynthesis based on CO2 compensation point measurements. This study investigates the C4 syndrome and its evolution in Gisekia. The infrageneric relationships, distribution and bioclimatic preferences of Gisekia are also investigated. Leaf gas exchange characteristics, activity of Rubisco and major C4 cycle enzymes, and ultrastructural characteristics of mesophyll and bundle sheath cells are studied for Gisekia pharnaceoides. δ(13)C values and leaf anatomy are analyzed for all species. A dated molecular phylogeny of 39 accessions representing all species of Gisekiaceae and 14 representatives of closely related core Caryophyllales families is generated using four cp markers and ITS. The precise current distribution and bioclimatic niche of Gisekia is assessed on the basis of 520 georeferenced specimen localities. All traditionally recognized species of Gisekia are C4 plants with atriplicoid Kranz anatomy. Gisekia pharnaceoides uses the NAD-ME biochemical type. The molecular phylogeny demonstrated two East African clades nested within South African clades, demonstrating migration along the arid areas of eastern Africa during the Late Miocene/Pliocene Epochs. Most traditionally defined species are polyphyletic. Gisekia represents an isolated C4 lineage within core Caryophyllales dating back to the Miocene Epoch and probably spread along the African arid corridor from a South African center of origin. The seven currently recognized species should be treated as one polymorphic species or species complex, Gisekia pharnaceoides agg.

Rediscovery of the enigmatic fungus-farming ant "Mycetosoritis" asper Mayr (Hymenoptera: Formicidae): Implications for taxonomy, phylogeny, and the evolution of agriculture in ants

PubMed Central

Ješovnik, Ana; Vasconcelos, Heraldo L.; Bacci, Mauricio; Schultz, Ted R.

2017-01-01

We report the rediscovery of the exceedingly rarely collected and enigmatic fungus-farming ant species Mycetosoritis asper. Since the description of the type specimen in 1887, only four additional specimens are known to have been added to the world's insect collections. Its biology is entirely unknown and its phylogenetic position within the fungus-farming ants has remained puzzling due to its aberrant morphology. In 2014 we excavated and collected twenty-one colonies of M. asper in the Floresta Nacional de Chapecó in Santa Catarina, Brazil. We describe here for the first time the male and larva of the species and complement the previous descriptions of both the queen and the worker. We describe, also for the first time, M. asper biology, nest architecture, and colony demographics, and identify its fungal cultivar. Molecular phylogenetic analyses indicate that both M. asper and M. clorindae are members of the genus Cyphomyrmex, which we show to be paraphyletic as currently defined. More precisely, M. asper is a member of the Cyphomyrmex strigatus group, which we also show to be paraphyletic with respect to the genus Mycetophylax. Based on these results, and in the interest of taxonomic stability, we transfer the species M. asper, M. clorindae, and all members of the C. strigatus group to the genus Mycetophylax, the oldest available name for this clade. Based on ITS sequence data, Mycetophylax asper practices lower agriculture, cultivating a fungal species that belongs to lower-attine fungal Clade 2, subclade F. PMID:28489860

Veterinary Fusarioses within the United States

PubMed Central

Sutton, Deanna A.; Wiederhold, Nathan; Robert, Vincent A. R. G.; Crous, Pedro W.; Geiser, David M.

2016-01-01

Multilocus DNA sequence data were used to assess the genetic diversity and evolutionary relationships of 67 Fusarium strains from veterinary sources, most of which were from the United States. Molecular phylogenetic analyses revealed that the strains comprised 23 phylogenetically distinct species, all but two of which were previously known to infect humans, distributed among eight species complexes. The majority of the veterinary isolates (47/67 = 70.1%) were nested within the Fusarium solani species complex (FSSC), and these included 8 phylospecies and 33 unique 3-locus sequence types (STs). Three of the FSSC species (Fusarium falciforme, Fusarium keratoplasticum, and Fusarium sp. FSSC 12) accounted for four-fifths of the veterinary strains (38/47) and STs (27/33) within this clade. Most of the F. falciforme strains (12/15) were recovered from equine keratitis infections; however, strains of F. keratoplasticum and Fusarium sp. FSSC 12 were mostly (25/27) isolated from marine vertebrates and invertebrates. Our sampling suggests that the Fusarium incarnatum-equiseti species complex (FIESC), with eight mycoses-associated species, may represent the second most important clade of veterinary relevance within Fusarium. Six of the multilocus STs within the FSSC (3+4-eee, 1-b, 12-a, 12-b, 12-f, and 12-h) and one each within the FIESC (1-a) and the Fusarium oxysporum species complex (ST-33) were widespread geographically, including three STs with transoceanic disjunctions. In conclusion, fusaria associated with veterinary mycoses are phylogenetically diverse and typically can only be identified to the species level using DNA sequence data from portions of one or more informative genes. PMID:27605713

Veterinary Fusarioses within the United States.

PubMed

O'Donnell, Kerry; Sutton, Deanna A; Wiederhold, Nathan; Robert, Vincent A R G; Crous, Pedro W; Geiser, David M

2016-11-01

Multilocus DNA sequence data were used to assess the genetic diversity and evolutionary relationships of 67 Fusarium strains from veterinary sources, most of which were from the United States. Molecular phylogenetic analyses revealed that the strains comprised 23 phylogenetically distinct species, all but two of which were previously known to infect humans, distributed among eight species complexes. The majority of the veterinary isolates (47/67 = 70.1%) were nested within the Fusarium solani species complex (FSSC), and these included 8 phylospecies and 33 unique 3-locus sequence types (STs). Three of the FSSC species (Fusarium falciforme, Fusarium keratoplasticum, and Fusarium sp. FSSC 12) accounted for four-fifths of the veterinary strains (38/47) and STs (27/33) within this clade. Most of the F. falciforme strains (12/15) were recovered from equine keratitis infections; however, strains of F. keratoplasticum and Fusarium sp. FSSC 12 were mostly (25/27) isolated from marine vertebrates and invertebrates. Our sampling suggests that the Fusarium incarnatum-equiseti species complex (FIESC), with eight mycoses-associated species, may represent the second most important clade of veterinary relevance within Fusarium Six of the multilocus STs within the FSSC (3+4-eee, 1-b, 12-a, 12-b, 12-f, and 12-h) and one each within the FIESC (1-a) and the Fusarium oxysporum species complex (ST-33) were widespread geographically, including three STs with transoceanic disjunctions. In conclusion, fusaria associated with veterinary mycoses are phylogenetically diverse and typically can only be identified to the species level using DNA sequence data from portions of one or more informative genes. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species.

PubMed

Nepal, Madhav P; Andersen, Ethan J; Neupane, Surendra; Benson, Benjamin V

2017-09-30

Disease resistance genes (R genes), as part of the plant defense system, have coevolved with corresponding pathogen molecules. The main objectives of this project were to identify non-Toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (nTNL) genes and elucidate their evolutionary divergence across six plant genomes. Using reference sequences from Arabidopsis , we investigated nTNL orthologs in the genomes of common bean, Medicago , soybean, poplar, and rice. We used Hidden Markov Models for sequence identification, performed model-based phylogenetic analyses, visualized chromosomal positioning, inferred gene clustering, and assessed gene expression profiles. We analyzed 908 nTNL R genes in the genomes of the six plant species, and classified them into 12 subgroups based on the presence of coiled-coil (CC), nucleotide binding site (NBS), leucine rich repeat (LRR), resistance to Powdery mildew 8 (RPW8), and BED type zinc finger domains. Traditionally classified CC-NBS-LRR (CNL) genes were nested into four clades (CNL A-D) often with abundant, well-supported homogeneous subclades of Type-II R genes. CNL-D members were absent in rice, indicating a unique R gene retention pattern in the rice genome. Genomes from Arabidopsis , common bean, poplar and soybean had one chromosome without any CNL R genes. Medicago and Arabidopsis had the highest and lowest number of gene clusters, respectively. Gene expression analyses suggested unique patterns of expression for each of the CNL clades. Differential gene expression patterns of the nTNL genes were often found to correlate with number of introns and GC content, suggesting structural and functional divergence.

Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species

PubMed Central

Andersen, Ethan J.; Neupane, Surendra; Benson, Benjamin V.

2017-01-01

Disease resistance genes (R genes), as part of the plant defense system, have coevolved with corresponding pathogen molecules. The main objectives of this project were to identify non-Toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (nTNL) genes and elucidate their evolutionary divergence across six plant genomes. Using reference sequences from Arabidopsis, we investigated nTNL orthologs in the genomes of common bean, Medicago, soybean, poplar, and rice. We used Hidden Markov Models for sequence identification, performed model-based phylogenetic analyses, visualized chromosomal positioning, inferred gene clustering, and assessed gene expression profiles. We analyzed 908 nTNL R genes in the genomes of the six plant species, and classified them into 12 subgroups based on the presence of coiled-coil (CC), nucleotide binding site (NBS), leucine rich repeat (LRR), resistance to Powdery mildew 8 (RPW8), and BED type zinc finger domains. Traditionally classified CC-NBS-LRR (CNL) genes were nested into four clades (CNL A-D) often with abundant, well-supported homogeneous subclades of Type-II R genes. CNL-D members were absent in rice, indicating a unique R gene retention pattern in the rice genome. Genomes from Arabidopsis, common bean, poplar and soybean had one chromosome without any CNL R genes. Medicago and Arabidopsis had the highest and lowest number of gene clusters, respectively. Gene expression analyses suggested unique patterns of expression for each of the CNL clades. Differential gene expression patterns of the nTNL genes were often found to correlate with number of introns and GC content, suggesting structural and functional divergence. PMID:28973974

Phylogeny, biogeography and character evolution in the tribe Desmodieae (Fabaceae: Papilionoideae), with special emphasis on the New Caledonian endemic genera.

PubMed

Jabbour, Florian; Gaudeul, Myriam; Lambourdière, Josie; Ramstein, Guillaume; Hassanin, Alexandre; Labat, Jean-Noël; Sarthou, Corinne

2018-01-01

The nearly cosmopolitan tribe Desmodieae (Fabaceae) includes many important genera for medicine and forage. However, the phylogenetic relationships among the infratribal groups circumscribed using morphological traits are still poorly known. In this study, we used chloroplast (rbcL, psbA-trnH) and nuclear (ITS-1) DNA sequences to investigate the molecular phylogeny and historical biogeography of Desmodieae, and infer ancestral states for several vegetative and reproductive traits. Three groups, corresponding to the Desmodium, Lespedeza, and Phyllodium groups sensu Ohashi were retrieved in the phylogenetic analyses. Conflicts in the topologies inferred from the chloroplast and nuclear datasets were detected. For instance, the Lespedeza clade was sister to the groups Phyllodium+Desmodium based on chloroplast DNA, but nested within the Desmodium group based on ITS-1. Moreover, the New Caledonian endemic genera Arthroclianthus and Nephrodesmus were not monophyletic but together formed a clade, which also included Hanslia and Ohwia based on chloroplast DNA. The hypothetical common ancestor of Desmodieae was dated to the Middle Oligocene (ca. 28.3Ma) and was likely an Asian shrub or tree producing indehiscent loments. Several colonization events towards Oceania, America, and Africa occurred (all less than ca. 17.5Ma), most probably through long distance dispersal. The fruits of Desmodieae repeatedly evolved from indehiscence to dehiscence. We also showed that indehiscent loments allow for more variability in the number of seeds per fruit than indehiscent legumes. Modularity seems here to allow variability in the number of ovules produced in a single ovary. Copyright © 2017 Elsevier Inc. All rights reserved.

Spiralian phylogeny informs the evolution of microscopic lineages.

PubMed

Laumer, Christopher E; Bekkouche, Nicolas; Kerbl, Alexandra; Goetz, Freya; Neves, Ricardo C; Sørensen, Martin V; Kristensen, Reinhardt M; Hejnol, Andreas; Dunn, Casey W; Giribet, Gonzalo; Worsaae, Katrine

2015-08-03

Despite rapid advances in the study of metazoan evolutionary history [1], phylogenomic analyses have so far neglected a number of microscopic lineages that possess a unique combination of characters and are thus informative for our understanding of morphological evolution. Chief among these lineages are the recently described animal groups Micrognathozoa and Loricifera, as well as the two interstitial "Problematica" Diurodrilus and Lobatocerebrum [2]. These genera show a certain resemblance to Annelida in their cuticle and gut [3, 4]; however, both lack primary annelid characters such as segmentation and chaetae [5]. Moreover, they show unique features such as an inverted body-wall musculature or a novel pharyngeal organ. This and their ciliated epidermis have led some to propose relationships with other microscopic spiralians, namely Platyhelminthes, Gastrotricha, and in the case of Diurodrilus, with Micrognathozoa [6, 7]-lineages that are grouped by some analyses into "Platyzoa," a clade whose status remains uncertain [1, 8-11]. Here, we assess the interrelationships among the meiofaunal and macrofaunal members of Spiralia using 402 orthologs mined from genome and transcriptome assemblies of 90 taxa. Lobatocerebrum and Diurodrilus are found to be deeply nested members of Annelida, and unequivocal support is found for Micrognathozoa as the sister group of Rotifera. Analyses using site-heterogeneous substitution models further recover a lophophorate clade and position Loricifera + Priapulida as sister group to the remaining Ecdysozoa. Finally, with several meiofaunal lineages branching off early in the diversification of Spiralia, the emerging concept of a microscopic, acoelomate, direct-developing ancestor of Spiralia is reviewed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Recent developments in the taxonomic affiliation and phylogenetic positioning of fungi: impact in applied microbiology and environmental biotechnology.

PubMed

Voigt, Kerstin; Kirk, Paul M

2011-04-01

The goal of modern taxonomy is to understand the relationships of living organisms in terms of evolutionary descent. Thereby, the relationships between living organisms are understood in terms of nested clades--every time a speciation event takes place, two new clades are produced. Life comprises three domains of living organisms, these are the Bacteria, the Archaea and the Eukaryota. Within the eukaryotic domain, the fungi form a monophyletic group of the eukaryotic crown group and are thus high up in the evolutionary hierarchy of life. Fungus-like organisms possess certain morphological features of fungi, such as the hyphal organization of the Oomycota or the spores and reproductive structures inside a fructification of plasmodiophorids (Plasmodiophoromycota) and slime moulds (Mycetozoa). The first group are algae which secondarily lost their plastids during evolution and contain cellulose in their cell walls. Both osmotrophic phyla, the Oomycota and the Plasmidiophoromycota belong to the Chromista and Rhizaria, respectively, whereas the last group, the cellular and plasmodial slime moulds (Mycetozoa) are phagotrophic amoeboid protists belonging to the Amoebozoa. These fungus-like organisms are not considered further in this review. The Fungi sensu stricto comprise a heterogenous, often inconspicuous group of microorganisms which (1) are primarily heterotrophic with an (2) osmotrophic style of nutrition containing (3) chitin and its derivatives in the cell wall. This review discusses species concepts and current strategies in fungal taxonomy, phylogenetic affiliations of miscellaneous fungus-like groups like the microsporidia, perspectives of fungal nomenclature, and their impact on natural product research.

Effects of spatial disturbance on common loon nest site selection and territory success

USGS Publications Warehouse

McCarthy, K.P.; DeStefano, S.

2011-01-01

The common loon (Gavia immer) breeds during the summer on northern lakes and water bodies that are also often desirable areas for aquatic recreation and human habitation. In northern New England, we assessed how the spatial nature of disturbance affects common loon nest site selection and territory success. We found through classification and regression analysis that distance to and density of disturbance factors can be used to classify observed nest site locations versus random points, suggesting that these factors affect loon nest site selection (model 1: Correct classification = 75%, null = 50%, K = 0.507, P < 0.001; model 2: Correct classification = 78%, null = 50%, K = 0.551, P < 0.001). However, in an exploratory analysis, we were unable to show a relation between spatial disturbance variables and breeding success (P = 0.595, R 2 = 0.436), possibly because breeding success was so low during the breeding seasons of 2007-2008. We suggest that by selecting nest site locations that avoid disturbance factors, loons thereby limit the effect that disturbance will have on their breeding success. Still, disturbance may force loons to use sub-optimal nesting habitat, limiting the available number of territories, and overall productivity. We advise that management efforts focus on limiting disturbance factors to allow breeding pairs access to the best nesting territories, relieving disturbance pressures that may force sub-optimal nest placement. ?? 2011 The Wildlife Society.

Circumscription of the anthracnose pathogens Colletotrichum lindemuthianum and C. nigrum.

PubMed

Liu, Fang; Cai, Lei; Crous, Pedro W; Damm, Ulrike

2013-01-01

The anthracnose pathogen of common bean (Phaseolus vulgaris) is usually identified as Colletotrichum lindemuthianum, while anthracnose of potato (Solanum tuberosum), peppers (Capsicum annuum), tomato (S. lycopersicum) and several other crop plants is often attributed to C. coccodes. In order to study the phylogenetic relationships of these important pathogens, we conducted a multigene analysis (ITS, ACT, TUB2, CHS-1, GAPDH) of strains previously identified as C. lindemuthianum, C. coccodes and other related species, as well as representative species of the major Colletotrichum species complexes. Strains of C. lindemuthianum belonged to a single clade; we selected an authentic specimen as lectotype, and an appropriate specimen and culture from the CBS collection to serve as epitype. Two clades were resolved within C. coccodes s. lat. One clade included the ex-neotype strain of C. coccodes on Solanum, while an epitype was selected for C. nigrum, which represents the oldest name of the second clade, which occurs on Capsicum, Solanum, as well as several other host plants. Furthermore, we recognized C. lycopersici as a synonym of C. nigrum, and C. biologicum as a synonym of C. coccodes.

Formyltetrahydrofolate Synthetase Gene Diversity in the Guts of Higher Termites with Different Diets and Lifestyles ▿ †

PubMed Central

Ottesen, Elizabeth A.; Leadbetter, Jared R.

2011-01-01

In this study, we examine gene diversity for formyl-tetrahydrofolate synthetase (FTHFS), a key enzyme in homoacetogenesis, recovered from the gut microbiota of six species of higher termites. The “higher” termites (family Termitidae), which represent the majority of extant termite species and genera, engage in a broader diversity of feeding and nesting styles than the “lower” termites. Previous studies of termite gut homoacetogenesis have focused on wood-feeding lower termites, from which the preponderance of FTHFS sequences recovered were related to those from acetogenic treponemes. While sequences belonging to this group were present in the guts of all six higher termites examined, treponeme-like FTHFS sequences represented the majority of recovered sequences in only two species (a wood-feeding Nasutitermes sp. and a palm-feeding Microcerotermes sp.). The remaining four termite species analyzed (a Gnathamitermes sp. and two Amitermes spp. that were recovered from subterranean nests with indeterminate feeding strategies and a litter-feeding Rhynchotermes sp.) yielded novel FTHFS clades not observed in lower termites. These termites yielded two distinct clusters of probable purinolytic Firmicutes and a large group of potential homoacetogens related to sequences previously recovered from the guts of omnivorous cockroaches. These findings suggest that the gut environments of different higher termite species may select for different groups of homoacetogens, with some species hosting treponeme-dominated homoacetogen populations similar to those of wood-feeding, lower termites while others host Firmicutes-dominated communities more similar to those of omnivorous cockroaches. PMID:21441328

Reintroduction of H5N1 highly pathogenic avian influenza virus by migratory water birds, causing poultry outbreaks in the 2010-2011 winter season in Japan.

PubMed

Sakoda, Yoshihiro; Ito, Hiroshi; Uchida, Yuko; Okamatsu, Masatoshi; Yamamoto, Naoki; Soda, Kosuke; Nomura, Naoki; Kuribayashi, Saya; Shichinohe, Shintaro; Sunden, Yuji; Umemura, Takashi; Usui, Tatsufumi; Ozaki, Hiroichi; Yamaguchi, Tsuyoshi; Murase, Toshiyuki; Ito, Toshihiro; Saito, Takehiko; Takada, Ayato; Kida, Hiroshi

2012-03-01

H5N1 highly pathogenic avian influenza virus (HPAIV) was reintroduced and caused outbreaks in chickens in the 2010-2011 winter season in Japan, which had been free from highly pathogenic avian influenza (HPAI) since 2007 when HPAI outbreaks occurred and were controlled. On 14 October 2010 at Lake Ohnuma, Wakkanai, the northernmost part of Hokkaido, Japan, H5N1 HPAIVs were isolated from faecal samples of ducks flying from their nesting lakes in Siberia. Since then, in Japan, H5N1 HPAIVs have been isolated from 63 wild birds in 17 prefectures and caused HPAI outbreaks in 24 chicken farms in nine prefectures by the end of March in 2011. Each of these isolates was genetically closely related to the HPAIV isolates at Lake Ohnuma, and those in China, Mongolia, Russia and Korea, belonging to genetic clade 2.3.2.1. In addition, these isolates were genetically classified into three groups, suggesting that the viruses were transmitted by migratory water birds through at least three different routes from their northern territory to Japan. These isolates were antigenic variants, which is consistent with selection in poultry under the immunological pressure induced by vaccination. To prevent the perpetuation of viruses in the lakes where water birds nest in summer in Siberia, prompt eradication of HPAIVs in poultry is urgently needed in Asian countries where HPAI has not been controlled.

Highly pathogenic avian influenza H5N1 clade 2.3.2.1 and clade 2.3.4 viruses do not induce a clade-specific phenotype in mallard ducks

PubMed Central

Crumpton, Jeri Carol; Rubrum, Adam; Phommachanh, Phouvong; Douangngeun, Bounlom; Peiris, Malik; Guan, Yi; Webster, Robert; Webby, Richard

2017-01-01

Among the diverse clades of highly pathogenic avian influenza (HPAI) H5N1 viruses of the goose/Guangdong lineage, only a few have been able to spread across continents: clade 2.2 viruses spread from China to Europe and into Africa in 2005–2006, clade 2.3.2.1 viruses spread from China to Eastern Europe in 2009–2010 and clade 2.3.4.4 viruses of the H5Nx subtype spread from China to Europe and North America in 2014/2015. While the poultry trade and wild-bird migration have been implicated in the spread of HPAI H5N1 viruses, it has been proposed that robust virus-shedding by wild ducks in the absence of overt clinical signs may have contributed to the wider dissemination of the clade 2.2, 2.3.2.1 and 2.3.4.4 viruses. Here we determined the phenotype of two divergent viruses from clade 2.3.2.1, a clade that spread widely, and two divergent viruses from clade 2.3.4, a clade that was constrained to Southeast Asia, in young (ducklings) and adult (juvenile) mallard ducks. We found that the virus-shedding magnitude and duration, transmission pattern and pathogenicity of the viruses in young and adult mallard ducks were largely independent of the virus clade. A clade-specific pattern could only be detected in terms of cumulative virus shedding, which was higher with clade 2.3.2.1 than with clade 2.3.4 viruses in juvenile mallards, but not in ducklings. The ability of clade 2.3.2.1c A/common buzzard/Bulgaria/38 WB/2010-like viruses to spread cross-continentally may, therefore, have been strain-specific or independent of phenotype in wild ducks. PMID:28631606

Spatiotemporal patterns of duck nest density and predation risk: a multi-scale analysis of 18 years and more than 10,000 nests

USGS Publications Warehouse

Ringelman, Kevin M.; Eadie, John M.; Ackerman, Joshua T.; Sih, Andrew; Loughman, Daniel L.; Yarris, Gregory S.; Oldenburger, Shaun L.; McLandress, M. Robert

2017-01-01

Many avian species are behaviorally-plastic in selecting nest sites, and may shift to new locations or habitats following an unsuccessful breeding attempt. If there is predictable spatial variation in predation risk, the process of many individuals using prior experience to adaptively change nest sites may scale up to create shifting patterns of nest density at a population level. We used 18 years of waterfowl nesting data to assess whether there were areas of consistently high or low predation risk, and whether low-risk areas increased, and high-risk areas decreased in nest density the following year. We created kernel density maps of successful and unsuccessful nests in consecutive years and found no correlation in predation risk and no evidence for adaptive shifts, although nest density was correlated between years. We also examined between-year correlations in nest density and nest success at three smaller spatial scales: individual nesting fields (10–28 ha), 16-ha grid cells and 4-ha grid cells. Here, results were similar across all scales: we found no evidence for year-to-year correlation in nest success but found strong evidence that nest density was correlated between years, and areas of high nest success increased in nest density the following year. Prior research in this system has demonstrated that areas of high nest density have higher nest success, and taken together, our results suggest that ducks may adaptively select nest sites based on the local density of conspecifics, rather than the physical location of last year's nest. In unpredictable environments, current cues, such as the presence of active conspecific nests, may be especially useful in selecting nest sites. The cues birds use to select breeding locations and successfully avoid predators deserve continued attention, especially in systems of conservation concern.

Evidence of territoriality and species interactions from spatial point-pattern analyses of subarctic-nesting geese

USGS Publications Warehouse

Reiter, Matthew E.; Andersen, David E.

2013-01-01

Quantifying spatial patterns of bird nests and nest fate provides insights into processes influencing a species’ distribution. At Cape Churchill, Manitoba, Canada, recent declines in breeding Eastern Prairie Population Canada geese (Branta canadensis interior) has coincided with increasing populations of nesting lesser snow geese (Chen caerulescens caerulescens) and Ross’s geese (Chen rossii). We conducted a spatial analysis of point patterns using Canada goose nest locations and nest fate, and lesser snow goose nest locations at two study areas in northern Manitoba with different densities and temporal durations of sympatric nesting Canada and lesser snow geese. Specifically, we assessed (1) whether Canada geese exhibited territoriality and at what scale and nest density; and (2) whether spatial patterns of Canada goose nest fate were associated with the density of nesting lesser snow geese as predicted by the protective-association hypothesis. Between 2001 and 2007, our data suggest that Canada geese were territorial at the scale of nearest neighbors, but were aggregated when considering overall density of conspecifics at slightly broader spatial scales. The spatial distribution of nest fates indicated that lesser snow goose nest proximity and density likely influence Canada goose nest fate. Our analyses of spatial point patterns suggested that continued changes in the distribution and abundance of breeding lesser snow geese on the Hudson Bay Lowlands may have impacts on the reproductive performance of Canada geese, and subsequently the spatial distribution of Canada goose nests.

Intron-loss evolution of hatching enzyme genes in Teleostei

PubMed Central

2010-01-01

Background Hatching enzyme, belonging to the astacin metallo-protease family, digests egg envelope at embryo hatching. Orthologous genes of the enzyme are found in all vertebrate genomes. Recently, we found that exon-intron structures of the genes were conserved among tetrapods, while the genes of teleosts frequently lost their introns. Occurrence of such intron losses in teleostean hatching enzyme genes is an uncommon evolutionary event, as most eukaryotic genes are generally known to be interrupted by introns and the intron insertion sites are conserved from species to species. Here, we report on extensive studies of the exon-intron structures of teleostean hatching enzyme genes for insight into how and why introns were lost during evolution. Results We investigated the evolutionary pathway of intron-losses in hatching enzyme genes of 27 species of Teleostei. Hatching enzyme genes of basal teleosts are of only one type, which conserves the 9-exon-8-intron structure of an assumed ancestor. On the other hand, otocephalans and euteleosts possess two types of hatching enzyme genes, suggesting a gene duplication event in the common ancestor of otocephalans and euteleosts. The duplicated genes were classified into two clades, clades I and II, based on phylogenetic analysis. In otocephalans and euteleosts, clade I genes developed a phylogeny-specific structure, such as an 8-exon-7-intron, 5-exon-4-intron, 4-exon-3-intron or intron-less structure. In contrast to the clade I genes, the structures of clade II genes were relatively stable in their configuration, and were similar to that of the ancestral genes. Expression analyses revealed that hatching enzyme genes were high-expression genes, when compared to that of housekeeping genes. When expression levels were compared between clade I and II genes, clade I genes tends to be expressed more highly than clade II genes. Conclusions Hatching enzyme genes evolved to lose their introns, and the intron-loss events occurred at the specific points of teleostean phylogeny. We propose that the high-expression hatching enzyme genes frequently lost their introns during the evolution of teleosts, while the low-expression genes maintained the exon-intron structure of the ancestral gene. PMID:20796321

Density and Distribution of Xylocopa Nests (Hymenoptera: Apidae) in Caatinga Areas in the Surroundings of Passion Fruit Crops.

PubMed

Martins, C F; de Siqueira, K M M; Kiill, L H P; Sá, I I S; Aguiar, C M L

2014-08-01

Due to their importance as pollinators of many plant species, this study aimed to know the nest density, spatial distribution, and nesting substrates used by Xylocopa species in the Caatinga, a xerophilous vegetation of Northeastern Brazil. Three areas of Caatinga in the surroundings of passion fruit crops were sampled. The bee species found in these areas were Xylocopa grisescens Lepeletier and Xylocopa frontalis (Olivier). All nests were in Commiphora leptophloeos (Burseraceae) trees (n = 113). Phytosociological analysis showed that this tree species presented the highest absolute density (212.5 individuals/ha) and index of importance value (52.7). The distribution pattern of the C. leptophloeos was aggregated. The nests were located in dead and dried branches with an average diameter of 5.3 ± 2.0 cm (n = 43). The mean number of nests/tree was 3.1 ± 2.8 (n = 113). The less disturbed area showed 6.7 nests/ha and 4.2 nests/tree. In the disturbed areas, 0.9 nests/ha and 2.4 to 2.7 nests/tree were observed. The availability of substrate for nesting in the studied areas and its importance as a limiting factor for nesting are discussed.

Nest-niche differentiation in two sympatric columbid species from a Mediterranean Tetraclinis woodland: Considerations for forest management

NASA Astrophysics Data System (ADS)

Hanane, Saâd; Yassin, Mohamed

2017-01-01

Studies of niche partitioning among Columbid species have mainly addressed food habits and foraging activities, while partitioning in relation to nest-niche differentiation has been little studied. Here we investigate whether two sympatric columbid species-Woodpigeon (Columba palumbus) and Turtle dove (Streptopelia turtur)-occupy similar niches. A total of 74 nests were monitored: 37 nests for each species. The study, conducted in June 2016, attempted to determine the factors that may play a role in nest-niche differentiation among the two sympatric columbid species in a Moroccan Thuya (Tetraclinis articulata) forest. We used Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) to test the relevance of nest placement, proximity of food resources, forest edge and human presence variables in the nest distribution of the two species. The results show substantial niche segregation in the T. articulata nest-trees selected by Woodpigeons and Turtle doves, with selection depending primarily on the tree size and nest height. Observed nest-niche partitioning may diminish the potential for competition between these species and enhance opportunities for their coexistence. Management policies and practices aimed at ensuring the presence of mixed-sized class of Thuya trees must be prioritized. We recommend additional studies designed to: (1) reproduce the same experimental approach on other Mediterranean Thuya forests to improve our understanding of the effects of different levels of anthropogenic disturbance on the breeding behaviour of these two game species; (2) better understand the spatio-temporal dynamics of Woodpigeon and Turtle dove coexistence in the region; and (3) better identify the spatio-temporal extent of the effect of forest management on Woodpigeon and Turtle dove site occupancy.

Loneliness and depression among rural empty-nest elderly adults in Liuyang, China: a cross-sectional study

PubMed Central

Wang, Guojun; Hu, Mi; Xiao, Shui-yuan; Zhou, Liang

2017-01-01

Objective To compare loneliness, depressive symptoms and major depressive episodes between empty-nest and not-empty-nest older adults in rural areas of Liuyang city, Hunan, China. Methods A cross-sectional multi-stage random cluster survey was conducted from November 2011 to April 2012 in Liuyang, China. A total of 839 rural older residents aged 60 or above completed the survey (response rate 97.6%). In line with the definition of empty nest, 25 participants who had no children were excluded from the study, while the remaining 814 elderly adults with at least one child were included for analysis. Loneliness and depressive symptoms in rural elderly parents were assessed using the short-form UCLA Loneliness Scale (ULS-6) and the Geriatric Depression Scale (GDS). Major depressive episodes were diagnosed using the Structured Clinical Interview for DSM-IV (SCID-I). Results Significant differences were found between empty-nest and not-empty-nest older adults regarding loneliness (16.19±3.90 vs. 12.87±3.02, Cohen’s d=0.97), depressive symptoms (8.50±6.26 vs. 6.92±5.19, Cohen’s d=0.28) and the prevalence of major depressive episodes (10.1% vs. 4.6%) (all p<0.05). After controlling for demographic characteristics and physical disease, the differences in loneliness, depressive symptoms and major depressive episodes remained significant. Path analysis showed that loneliness mediated the relationship between empty-nest syndrome and depressive symptoms and major depressive episodes. Conclusion Loneliness and depression are more severe among empty-nest than not-empty-nest rural elderly adults. Loneliness was a mediating variable between empty-nest syndrome and depression. PMID:28988166

Multilocus genetics to reconstruct aeromonad evolution

PubMed Central

2012-01-01

Background Aeromonas spp. are versatile bacteria that exhibit a wide variety of lifestyles. In an attempt to improve the understanding of human aeromonosis, we investigated whether clinical isolates displayed specific characteristics in terms of genetic diversity, population structure and mode of evolution among Aeromonas spp. A collection of 195 Aeromonas isolates from human, animal and environmental sources was therefore genotyped using multilocus sequence analysis (MLSA) based on the dnaK, gltA, gyrB, radA, rpoB, tsf and zipA genes. Results The MLSA showed a high level of genetic diversity among the population, and multilocus-based phylogenetic analysis (MLPA) revealed 3 major clades: the A. veronii, A. hydrophila and A. caviae clades, among the eleven clades detected. Lower genetic diversity was observed within the A. caviae clade as well as among clinical isolates compared to environmental isolates. Clonal complexes, each of which included a limited number of strains, mainly corresponded to host-associated subsclusters of strains, i.e., a fish-associated subset within A. salmonicida and 11 human-associated subsets, 9 of which included only disease-associated strains. The population structure was shown to be clonal, with modes of evolution that involved mutations in general and recombination events locally. Recombination was detected in 5 genes in the MLSA scheme and concerned approximately 50% of the STs. Therefore, these recombination events could explain the observed phylogenetic incongruities and low robustness. However, the MLPA globally confirmed the current systematics of the genus Aeromonas. Conclusions Evolution in the genus Aeromonas has resulted in exceptionally high genetic diversity. Emerging from this diversity, subsets of strains appeared to be host adapted and/or “disease specialized” while the A. caviae clade displayed an atypical tempo of evolution among aeromonads. Considering that A. salmonicida has been described as a genetically uniform pathogen that has adapted to fish through evolution from a variable ancestral population, we hypothesize that the population structure of aeromonads described herein suggested an ongoing process of adaptation to specialized niches associated with different degrees of advancement according to clades and clusters. PMID:22545815

Cenozoic biogeography and evolution in direct-developing frogs of Central America (Leptodactylidae: Eleutherodactylus) as inferred from a phylogenetic analysis of nuclear and mitochondrial genes.

PubMed

Crawford, Andrew J; Smith, Eric N

2005-06-01

We report the first phylogenetic analysis of DNA sequence data for the Central American component of the genus Eleutherodactylus (Anura: Leptodactylidae: Eleutherodactylinae), one of the most ubiquitous, diverse, and abundant components of the Neotropical amphibian fauna. We obtained DNA sequence data from 55 specimens representing 45 species. Sampling was focused on Central America, but also included Bolivia, Brazil, Jamaica, and the USA. We sequenced 1460 contiguous base pairs (bp) of the mitochondrial genome containing ND2 and five neighboring tRNA genes, plus 1300 bp of the c-myc nuclear gene. The resulting phylogenetic inferences were broadly concordant between data sets and among analytical methods. The subgenus Craugastor is monophyletic and its initial radiation was potentially rapid and adaptive. Within Craugastor, the earliest splits separate three northern Central American species groups, milesi, augusti, and alfredi, from a clade comprising the rest of Craugastor. Within the latter clade, the rhodopis group as formerly recognized comprises three deeply divergent clades that do not form a monophyletic group; we therefore restrict the content of the rhodopis group to one of two northern clades, and use new names for the other northern (mexicanus group) and one southern clade (bransfordii group). The new rhodopis and bransfordii groups together form the sister taxon to a clade comprising the biporcatus, fitzingeri, mexicanus, and rugulosus groups. We used a Bayesian MCMC approach together with geological and biogeographic assumptions to estimate divergence times from the combined DNA sequence data. Our results corroborated three independent dispersal events for the origins of Central American Eleutherodactylus: (1) an ancestor of Craugastor entered northern Central America from South American in the early Paleocene, (2) an ancestor of the subgenus Syrrhophus entered northern Central America from the Caribbean at the end of the Eocene, and (3) a wave of independent dispersal events from South America coincided with formation of the Isthmus of Panama during the Pliocene. We elevate the subgenus Craugastor to the genus rank.

Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species

PubMed Central

Sawana, Amandeep; Adeolu, Mobolaji; Gupta, Radhey S.

2014-01-01

The genus Burkholderia contains large number of diverse species which include many clinically important organisms, phytopathogens, as well as environmental species. However, currently, there is a paucity of biochemical or molecular characteristics which can reliably distinguish different groups of Burkholderia species. We report here the results of detailed phylogenetic and comparative genomic analyses of 45 sequenced species of the genus Burkholderia. In phylogenetic trees based upon concatenated sequences for 21 conserved proteins as well as 16S rRNA gene sequence based trees, members of the genus Burkholderia grouped into two major clades. Within these main clades a number of smaller clades including those corresponding to the clinically important Burkholderia cepacia complex (BCC) and the Burkholderia pseudomallei groups were also clearly distinguished. Our comparative analysis of protein sequences from Burkholderia spp. has identified 42 highly specific molecular markers in the form of conserved sequence indels (CSIs) that are uniquely found in a number of well-defined groups of Burkholderia spp. Six of these CSIs are specific for a group of Burkholderia spp. (referred to as Clade I in this work) which contains all clinically relevant members of the genus (viz. the BCC and the B. pseudomallei group) as well as the phytopathogenic Burkholderia spp. The second main clade (Clade II), which is composed of environmental Burkholderia species, is also distinguished by 2 identified CSIs that are specific for this group. Additionally, our work has also identified multiple CSIs that serve to clearly demarcate a number of smaller groups of Burkholderia spp. including 3 CSIs that are specific for the B. cepacia complex, 4 CSIs that are uniquely found in the B. pseudomallei group, 5 CSIs that are specific for the phytopathogenic Burkholderia spp. and 22 other CSI that distinguish two groups within Clade II. The described molecular markers provide highly specific means for the demarcation of different groups of Burkholderia spp. and they also offer novel and useful targets for the development of diagnostic assays for the clinically important members of the BCC or the pseudomallei groups. Based upon the results of phylogenetic analyses, the identified CSIs and the pathogenicity profile of Burkholderia species, we are proposing a division of the genus Burkholderia into two genera. In this new proposal, the emended genus Burkholderia will correspond to the Clade I and it will contain only the clinically relevant and phytopathogenic Burkholderia species. All other Burkholderia spp., which are primarily environmental, will be transferred to a new genus Paraburkholderia gen. nov. PMID:25566316

Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades

PubMed Central

Blanga-Kanfi, Shani; Miranda, Hector; Penn, Osnat; Pupko, Tal; DeBry, Ronald W; Huchon, Dorothée

2009-01-01

Background Rodentia is the most diverse order of placental mammals, with extant rodent species representing about half of all placental diversity. In spite of many morphological and molecular studies, the family-level relationships among rodents and the location of the rodent root are still debated. Although various datasets have already been analyzed to solve rodent phylogeny at the family level, these are difficult to combine because they involve different taxa and genes. Results We present here the largest protein-coding dataset used to study rodent relationships. It comprises six nuclear genes, 41 rodent species, and eight outgroups. Our phylogenetic reconstructions strongly support the division of Rodentia into three clades: (1) a "squirrel-related clade", (2) a "mouse-related clade", and (3) Ctenohystrica. Almost all evolutionary relationships within these clades are also highly supported. The primary remaining uncertainty is the position of the root. The application of various models and techniques aimed to remove non-phylogenetic signal was unable to solve the basal rodent trifurcation. Conclusion Sequencing and analyzing a large sequence dataset enabled us to resolve most of the evolutionary relationships among Rodentia. Our findings suggest that the uncertainty regarding the position of the rodent root reflects the rapid rodent radiation that occurred in the Paleocene rather than the presence of conflicting phylogenetic and non-phylogenetic signals in the dataset. PMID:19341461

Phylogenetics, systematics, paleoecology, and evolution of the trilobite genera Paladin and Kaskia from the United States

USGS Publications Warehouse

Brezinski, D.K.

2008-01-01

Late Mississippian and earliest Pennsylvanian trilobite faunas of North America are dominated by the Paladin and Kaskia clades. Phylogenetic analysis of middle Carboniferous species of these clades demonstrates the close ancestral relationship between these groups. The Kaskia clade consists of eight species: K. chesterensis Weller, 1936, K. osagensis (Cisne, 1967), K. longispina (Strong, 1872), K. wilsoni (Walter, 1924), K. genevievensis (Walter, 1924), K. rosei (Cisne, 1967), K. gersnai n. sp., and K. rollinsi n. sp. Kaskia Weller, 1936 ranges from late Osagean to middle Chesterian (early Visean-early Serpukhovian) and is restricted to cyclothemic shelf and nearshore deposits. Species of Kaskia appear to have evolved in areas of shallow water and high environmental stress. The Paladin clade consists of 12 species including previously named species P. morrowensis (Mather, 1915), P. girtyianus Hahn and Hahn, 1970, P. rarus Whittington, 1954, P. helmsensis Whittington, 1954, and P. moorei (Branson, 1937). New species belonging to this clade are Paladin moorefieldensis n. sp., P. pleisiomorphus n. sp., P. imoensis n. sp., P. mangeri n. sp., and P. wapanukaensis n. sp. This group ranges from the early Chesterian to early Morrowan (late Viseanlate Bashkirian). Species of Paladin appear to be confined to outer shelf shelf-edge and off-shelf facies where presumably deeper water environments existed. This is manifested in their paleogeographic distribution, which is paleoenvironmentally controlled. Copyright ?? 2008, The Paleontological Society.

Brachypodium distachyon BdPP2CA6 Interacts with BdPYLs and BdSnRK2 and Positively Regulates Salt Tolerance in Transgenic Arabidopsis

PubMed Central

Zhang, Fan; Wei, Qiuhui; Shi, Jiaochun; Jin, Xia; He, Yuan; Zhang, Yang; Luo, Qingchen; Wang, Yuesheng; Chang, Junli; Yang, Guangxiao; He, Guangyuan

2017-01-01

The phytohormone abscisic acid (ABA) is essential in plant responding to biotic and abiotic stresses. Although ABA signaling model is well established in Arabidopsis, ABA receptor PYL family and clade A PP2C subfamily are not yet characterized in monocot model plant Brachypodium distachyon. In this study, we identified 12 PYLs and 8 clade A PP2Cs from B. distachyon genome and successfully cloned 12 PYLs and 7 clade A PP2Cs. Bioinformatic and expression analyses showed that most of the identified genes respond to several signal molecules and abiotic stresses. Protein–protein interaction analysis revealed that many BdPYLs and BdPP2CAs participate in the classic ABA-PYL-PP2C-SnRK2 signaling pathway. A clade A PP2C, designated BdPP2CA6, interacted with BdPYL11 in the absence of ABA and localized in nucleus. Most clade A PP2C members from Arabidopsis showed negatively regulation in ABA signaling pathway, whereas BdPP2CA6-overexpression transgenic Arabidopsis showed ABA hypersensitive phenotype, resulting in enhanced stomatal closure and salinity tolerance. Our results indicate that BdPP2CA6 positively regulates ABA and stress signal pathway in transgenic Arabidopsis plant seedlings. PMID:28293246

Lineage-Specific Responses of Tooth Shape in Murine Rodents (Murinae, Rodentia) to Late Miocene Dietary Change in the Siwaliks of Pakistan

PubMed Central

Kimura, Yuri; Jacobs, Louis L.; Flynn, Lawrence J.

2013-01-01

Past ecological responses of mammals to climate change are recognized in the fossil record by adaptive significance of morphological variations. To understand the role of dietary behavior on functional adaptations of dental morphology in rodent evolution, we examine evolutionary change of tooth shape in late Miocene Siwalik murine rodents, which experienced a dietary shift toward C4 diets during late Miocene ecological change indicated by carbon isotopic evidence. Geometric morphometric analysis in the outline of upper first molars captures dichotomous lineages of Siwalik murines, in agreement with phylogenetic hypotheses of previous studies (two distinct clades: the Karnimata and Progonomys clades), and indicates lineage-specific functional responses to mechanical properties of their diets. Tooth shapes of the two clades are similar at their sympatric origin but deviate from each other with decreasing overlap through time. Shape change in the Karnimata clade is associated with greater efficiency of propalinal chewing for tough diets than in the Progonomys clade. Larger body mass in Karnimata may be related to exploitation of lower-quality food items, such as grasses, than in smaller-bodied Progonomys. The functional and ecophysiological aspects of Karnimata exploiting C4 grasses are concordant with their isotopic dietary preference relative to Progonomys. Lineage-specific selection was differentially greater in Karnimata, and a faster rate of shape change toward derived Karnimata facilitated inclusion of C4 grasses in the diet. Sympatric speciation in these clades is most plausibly explained by interspecific competition on resource utilization between the two, based on comparisons of our results with the carbon isotope data. Interspecific competition with Karnimata may have suppressed morphological innovation of the Progonomys clade. Pairwise analyses of morphological and carbon isotope data can uncover ecological causes of sympatric speciation and define functional adaptations of teeth to resources. PMID:24155885

Lineage-specific responses of tooth shape in murine rodents (murinae, rodentia) to late Miocene dietary change in the Siwaliks of Pakistan.

PubMed

Kimura, Yuri; Jacobs, Louis L; Flynn, Lawrence J

2013-01-01

Past ecological responses of mammals to climate change are recognized in the fossil record by adaptive significance of morphological variations. To understand the role of dietary behavior on functional adaptations of dental morphology in rodent evolution, we examine evolutionary change of tooth shape in late Miocene Siwalik murine rodents, which experienced a dietary shift toward C4 diets during late Miocene ecological change indicated by carbon isotopic evidence. Geometric morphometric analysis in the outline of upper first molars captures dichotomous lineages of Siwalik murines, in agreement with phylogenetic hypotheses of previous studies (two distinct clades: the Karnimata and Progonomys clades), and indicates lineage-specific functional responses to mechanical properties of their diets. Tooth shapes of the two clades are similar at their sympatric origin but deviate from each other with decreasing overlap through time. Shape change in the Karnimata clade is associated with greater efficiency of propalinal chewing for tough diets than in the Progonomys clade. Larger body mass in Karnimata may be related to exploitation of lower-quality food items, such as grasses, than in smaller-bodied Progonomys. The functional and ecophysiological aspects of Karnimata exploiting C4 grasses are concordant with their isotopic dietary preference relative to Progonomys. Lineage-specific selection was differentially greater in Karnimata, and a faster rate of shape change toward derived Karnimata facilitated inclusion of C4 grasses in the diet. Sympatric speciation in these clades is most plausibly explained by interspecific competition on resource utilization between the two, based on comparisons of our results with the carbon isotope data. Interspecific competition with Karnimata may have suppressed morphological innovation of the Progonomys clade. Pairwise analyses of morphological and carbon isotope data can uncover ecological causes of sympatric speciation and define functional adaptations of teeth to resources.

A New Phylogeographic Pattern of Endemic Bufo bankorensis in Taiwan Island Is Attributed to the Genetic Variation of Populations

PubMed Central

Yu, Teng-Lang; Lin, Hung-Du; Weng, Ching-Feng

2014-01-01

Aim To comprehend the phylogeographic patterns of genetic variation in anurans at Taiwan Island, this study attempted to examine (1) the existence of various geological barriers (Central Mountain Ranges, CMRs); and (2) the genetic variation of Bufo bankorensis using mtDNA sequences among populations located in different regions of Taiwan, characterized by different climates and existing under extreme conditions when compared available sequences of related species B. gargarizans of mainland China. Methodology/Principal Findings Phylogenetic analyses of the dataset with mitochondrial DNA (mtDNA) D-loop gene (348 bp) recovered a close relationship between B. bankorensis and B. gargarizans, identified three distinct lineages. Furthermore, the network of mtDNA D-loop gene (564 bp) amplified (279 individuals, 27 localities) from Taiwan Island indicated three divergent clades within B. bankorensis (Clade W, E and S), corresponding to the geography, thereby verifying the importance of the CMRs and Kaoping River drainage as major biogeographic barriers. Mismatch distribution analysis, neutrality tests and Bayesian skyline plots revealed that a significant population expansion occurred for the total population and Clade W, with horizons dated to approximately 0.08 and 0.07 Mya, respectively. These results suggest that the population expansion of Taiwan Island species B. bankorensis might have resulted from the release of available habitat in post-glacial periods, the genetic variation on mtDNA showing habitat selection, subsequent population dispersal, and co-distribution among clades. Conclusions The multiple origins (different clades) of B. bankorensis mtDNA sequences were first evident in this study. The divergent genetic clades found within B. bankorensis could be independent colonization by previously diverged lineages; inferring B. bankorensis originated from B. gargarizans of mainland China, then dispersal followed by isolation within Taiwan Island. Highly divergent clades between W and E of B. bankorensis, implies that the CMRs serve as a genetic barrier and separated the whole island into the western and eastern phylogroups. PMID:24853679

Time-scale of minor HIV-1 complex circulating recombinant forms from Central and West Africa.

PubMed

Delatorre, Edson; Bello, Gonzalo

2016-11-16

Several HIV-1 circulating recombinant forms with a complex mosaic structure (CRFs_cpx) circulate in central and western African regions. Here we reconstruct the evolutionary history of some of these complex CRFs (09_cpx, 11_cpx, 13_cpx and 45_cpx) and further investigate the dissemination dynamic of the CRF11_cpx clade by using a Bayesian coalescent-based method. The analysis of two HIV-1 datasets comprising 181 pol (36 CRF09_cpx, 116 CRF11_cpx, 20 CRF13_cpx and 9 CRF45_cpx) and 125 env (12 CRF09_cpx, 67 CRF11_cpx, 17 CRF13_cpx and 29 CRF45_cpx) sequences pointed to quite consistent onset dates for CRF09_cpx (~1966: 1958-1979), CRF11_cpx (~1957: 1950-1966) and CRF13_cpx (~1965: 1958-1973) clades; while some divergence was found for the estimated date of origin of CRF45_cpx clade [pol = 1970 (1964-1976); env = 1960 (1952-1969)]. Phylogeographic reconstructions indicate that the HIV-1 CRF11_cpx clade most probably emerged in Cameroon and from there it was first disseminated to the Central Africa Republic and Chad in the early 1970s and to other central and western African countries from the early 1980s onwards. Demographic reconstructions suggest that the CRF11_cpx epidemic grew between 1960 and 1990 with a median exponential growth rate of 0.27 year -1 , and stabilized after. These results reveal that HIV-1 CRFs_cpx clades have been circulating in Central Africa for a period comparable to other much more prevalent HIV-1 group M lineages. Cameroon was probably the epicenter of dissemination of the CRF11_cpx clade that seems to have experienced a long epidemic growth phase before stabilization. The epidemic growth of the CRF11_cpx clade was roughly comparable to other HIV-1 group M lineages circulating in Central Africa.

Genetic Diversity and Geographic Distribution of Genetically Distinct Rabies Viruses in the Philippines

PubMed Central

Saito, Mariko; Oshitani, Hitoshi; Orbina, Jun Ryan C.; Tohma, Kentaro; de Guzman, Alice S.; Kamigaki, Taro; Demetria, Catalino S.; Manalo, Daria L.; Noguchi, Akira; Inoue, Satoshi; Quiambao, Beatriz P.

2013-01-01

Background Rabies continues to be a major public health problem in the Philippines, where 200–300 human cases were reported annually between 2001 and 2011. Understanding the phylogeography of rabies viruses is important for establishing a more effective and feasible control strategy. Methods We performed a molecular analysis of rabies viruses in the Philippines using rabied animal brain samples. The samples were collected from 11 of 17 regions, which covered three island groups (Luzon, Visayas, and Mindanao). Partial nucleoprotein (N) gene sequencing was performed on 57 samples and complete glycoprotein (G) gene sequencing was performed on 235 samples collected between 2004 and 2010. Results The Philippine strains of rabies viruses were included in a distinct phylogenetic cluster, previously named Asian 2b, which appeared to have diverged from the Chinese strain named Asian 2a. The Philippine strains were further divided into three major clades, which were found exclusively in different island groups: clades L, V, and M in Luzon, Visayas, and Mindanao, respectively. Clade L was subdivided into nine subclades (L1–L9) and clade V was subdivided into two subclades (V1 and V2). With a few exceptions, most strains in each subclade were distributed in specific geographic areas. There were also four strains that were divided into two genogroups but were not classified into any of the three major clades, and all four strains were found in the island group of Luzon. Conclusion We detected three major clades and two distinct genogroups of rabies viruses in the Philippines. Our data suggest that viruses of each clade and subclade evolved independently in each area without frequent introduction into other areas. An important implication of these data is that geographically targeted dog vaccination using the island group approach may effectively control rabies in the Philippines. PMID:23593515

Genetic divergence of rabies viruses from bat species of Colorado, USA

USGS Publications Warehouse

Shanker, V.; Orciari, L.A.; De Mattos, C.; Kuzmin, I.V.; Pape, W.J.; O'Shea, T.J.; Rupprecht, C.E.

2005-01-01

Molecular epidemiological studies have linked many cryptic human rabies cases in the United States with exposure to rabies virus (RV) variants associated with insectivorous bats. In Colorado, bats accounted for 98% of all reported animal rabies cases between 1977 and 1996. The genetic divergence of RV was investigated in bat and terrestrial animal specimens that were submitted for rabies diagnosis to the Colorado Department of Public Health and Environment (CDPHE), Colorado, USA. RV isolates from animal specimens across the United States were also included in the analysis. Phylogenetic analyses were performed on partial nucleoprotein (N) gene sequences, which revealed seven principal clades. RV associated with the colonial big brown bat, Eptesicus fuscus, an bats of the genus Myotis were found to segregate into two distinct clades (I and IV). Clade I was harbored by E. fuscus and Myotis species, but was also identified in terrestrial animals such as domestic cats and striped skunks (Mephitis mephitis). Clade IV was divided into subclades IVA, IVB, and IVC; IVA was identified in E. fuscus, and Myotis species bats, and also in a fox; subclades IVB and IVC circulated predominantly in E. fuscus. Clade II was formed by big free-tailed bat (Nyctinomops macrotis) and striped skunk (Mephitis mephitis) samples. Clade III included RVs that are maintained by generally solitary, migratory bats such as the silver-haired bat (Lasionycteris noctivagans) and bats of the genus Lasiurus. Big brown bats were found to harbor this RV variant. None of the Colorado specimens segregated with clades V and VII that harbor RVs associated with terrestrial animals. Different species of bats had the same RV variant, indicating active inter-species rabies transmission. In Colorado, animal rabies occurs principally in bats, and the identification of bat RVs in cat, gray fox Urocyon cinereoargenteus), and striped skunks demonstrated the importance of rabies spillover from bats to domestic and terrestrial wildlife species.

Phylogeny and taxonomy of the North American clade of the Ceratocystis fimbriata complex.

PubMed

Johnson, Jason A; Harrington, Thomas C; Engelbrecht, C J B

2005-01-01

Ceratocystis fimbriata is a widely distributed, plant pathogenic fungus that causes wilts and cankers on many woody hosts. Earlier phylogenetic analyses of DNA sequences revealed three geographic clades within the C. fimbriata complex that are centered respectively in North America, Latin America and Asia. This study looked for cryptic species within the North American clade. The internal transcribed spacer regions (ITS) of the rDNA were sequenced, and phylogenetic analysis indicated that most isolates from the North American clade group into four host-associated lineages, referred to as the aspen, hickory, oak and cherry lineages, which were isolated primarily from wounds or diseased trees of Populus, Carya, Quercus and Prunus, respectively. A single isolate collected from P. serotina in Wisconsin had a unique ITS sequence. Allozyme electromorphs also were highly polymorphic within the North American clade, and the inferred phylogenies from these data were congruent with the ITS-rDNA analyses. In pairing experiments isolates from the aspen, hickory, oak and cherry lineages were interfertile only with other isolates from their respective lineages. Inoculation experiments with isolates of the four host-associated groupings showed strong host specialization by isolates from the aspen and hickory lineages on Populus tremuloides and Carya illinoensis, respectively, but isolates from the oak and cherry lineages did not consistently reveal host specialization. Morphological features distinguish isolates in the North American clade from those of the Latin American clade (including C. fimbriata sensu stricto). Based on the phylogenetic evidence, interfertility, host specialization and morphology, the oak and cherry lineages are recognized as the earlier described C. variospora, the poplar lineage as C. populicola sp. nov., and the hickory lineage as C. caryae sp. nov. A new species associated with the bark beetle Scolytus quadrispinosus on Carya is closely related to C. caryae and is described as C. smalleyi.

Detection and Characterization of Clade 1 Reassortant H5N1 Viruses Isolated from Human Cases in Vietnam during 2013

PubMed Central

Balish, Amanda; Hoang, Anh Nguyen; Gustin, Kortney M.; Nhung, Pham Thi; Jones, Joyce; Thu, Ngoc Nguyen; Davis, William; Ngoc, Thao Nguyen Thi; Jang, Yunho; Sleeman, Katrina; Villanueva, Julie; Kile, James; Gubareva, Larisa V.; Lindstrom, Stephen; Tumpey, Terrence M.; Davis, C. Todd; Long, Nguyen Thanh

2015-01-01

Highly pathogenic avian influenza (HPAI) H5N1 is endemic in Vietnamese poultry and has caused sporadic human infection in Vietnam since 2003. Human infections with HPAI H5N1 are of concern due to a high mortality rate and the potential for the emergence of pandemic viruses with sustained human-to-human transmission. Viruses isolated from humans in southern Vietnam have been classified as clade 1 with a single genome constellation (VN3) since their earliest detection in 2003. This is consistent with detection of this clade/genotype in poultry viruses endemic to the Mekong River Delta and surrounding regions. Comparison of H5N1 viruses detected in humans from southern Vietnamese provinces during 2012 and 2013 revealed the emergence of a 2013 reassortant virus with clade 1.1.2 hemagglutinin (HA) and neuraminidase (NA) surface protein genes but internal genes derived from clade 2.3.2.1a viruses (A/Hubei/1/2010-like; VN12). Closer analysis revealed mutations in multiple genes of this novel genotype (referred to as VN49) previously associated with increased virulence in animal models and other markers of adaptation to mammalian hosts. Despite the changes identified between the 2012 and 2013 genotypes analyzed, their virulence in a ferret model was similar. Antigenically, the 2013 viruses were less cross-reactive with ferret antiserum produced to the clade 1 progenitor virus, A/Vietnam/1203/2004, but reacted with antiserum produced against a new clade 1.1.2 WHO candidate vaccine virus (A/Cambodia/W0526301/2012) with comparable hemagglutination inhibition titers as the homologous antigen. Together, these results indicate changes to both surface and internal protein genes of H5N1 viruses circulating in southern Vietnam compared to 2012 and earlier viruses. PMID:26244768

Firewalls in bee nests—survival value of propolis walls of wild Cape honeybee ( Apis mellifera capensis)

NASA Astrophysics Data System (ADS)

Tribe, Geoff; Tautz, Jürgen; Sternberg, Karin; Cullinan, Jenny

2017-04-01

The Cape bee is endemic to the winter rainfall region of South Africa where fires are an integral part of the ecology of the fynbos (heathland) vegetation. Of the 37 wild nests in pristine Peninsula Sandstone Fynbos in the Cape Point section of Table Mountain National Park that have been analyzed so far, only 22 could be accessed sufficiently to determine the existence of a propolis wall of which 68% had propolis walls which entirely enclosed their openings. The analysis of the 37 wild nests revealed that 78% occurred under boulders or in clefts within rocks, 11% in the ground, 8% in tree cavities, and 3% within shrubs. The analysis of 17 of these nests following a fire within the park revealed that the propolis walls materially protected the nests and retarded the fire with all the colonies surviving. The bees responded to the smoke by imbibing honey and retreating to the furthest recess of their nest cavity. The bees were required to utilize this honey for about 3 weeks after which fire-loving plants appeared and began flowering. Considerable resources were utilized in the construction of the propolis walls, which ranged in thickness from 1.5 to 40 mm (mean 5 mm). Its physical environment determines the nesting behavior of the Cape bee. The prolific use of propolis serves to insulate the nest from extremes of temperature and humidity, restricts entry, camouflages the nest, and acts as an effective fire barrier protecting nests established mostly under rocks in vegetation subjected to periodic fires.

Analysis of the WUSCHEL-RELATED HOMEOBOX gene family in Pinus pinaster: New insights into the gene family evolution.

PubMed

Alvarez, José M; Bueno, Natalia; Cañas, Rafael A; Avila, Concepción; Cánovas, Francisco M; Ordás, Ricardo J

2018-02-01

WUSCHEL-RELATED HOMEOBOX (WOX) genes are key players controlling stem cells in plants and can be divided into three clades according to the time of their appearance during plant evolution. Our knowledge of stem cell function in vascular plants other than angiosperms is limited, they separated from gymnosperms ca 300 million years ago and their patterning during embryogenesis differs significantly. For this reason, we have used the model gymnosperm Pinus pinaster to identify WOX genes and perform a thorough analysis of their gene expression patterns. Using transcriptomic data from a comprehensive range of tissues and stages of development we have shown three major outcomes: that the P. pinaster genome encodes at least fourteen members of the WOX family spanning all the major clades, that the genome of gymnosperms contains a WOX gene with no homologues in angiosperms representing a transitional stage between intermediate- and WUS-clade proteins, and that we can detect discrete WUS and WOX5 transcripts for the first time in a gymnosperm. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Taxonomic revision and phylogenetic analysis of the flightless Mancallinae (Aves, Pan-Alcidae)

PubMed Central

Smith, Neil Adam

2011-01-01

Abstract Although flightless alcids from the Miocene and Pliocene of the eastern Pacific Ocean have been known for over 100 years, there is no detailed evaluation of diversity and systematic placement of these taxa. This is the first combined analysis of morphological and molecular data to include all extant alcids, the recently extinct Great Auk Pinguinus impennis, the mancalline auks, and a large outgroup sampling of 29 additional non-alcid charadriiforms. Based on the systematic placement of Mancallinae outside of crown clade Alcidae, the clade name Pan-Alcidae is proposed to include all known alcids. An extensive review of the Mancallinae fossil record resulted in taxonomic revision of the clade, and identification of three new species. In addition to positing the first hypothesis of inter-relationships between Mancallinae species, phylogenetic results support placement of Mancallinae as the sister taxon to all other Alcidae, indicating that flightlessness evolved at least twice in the alcid lineage. Convergent osteological characteristics of Mancallinae, the flightless Great Auk, and Spheniscidae are summarized, and implications of Mancallinae diversity, radiation, and extinction in the context of paleoclimatic changes are discussed. PMID:21594108

Rapid Classification and Identification of Microcystis aeruginosa Strains Using MALDI-TOF MS and Polygenetic Analysis.

PubMed

Sun, Li-Wei; Jiang, Wen-Jing; Sato, Hiroaki; Kawachi, Masanobu; Lu, Xi-Wu

2016-01-01

Matrix-assisted laser desorption-ionization-time-of-flight mass spectrometry (MALDI-TOF MS) was used to establish a rapid, simple, and accurate method to differentiate among strains of Microcystis aeruginosa, one of the most prevalent types of bloom-forming cyanobacteria. M. aeruginosa NIES-843, for which a complete genome has been sequenced, was used to characterize ribosomal proteins as biomarkers and to optimize conditions for observing ribosomal proteins as major peaks in a given mass spectrum. Thirty-one of 52 ribosomal subunit proteins were detected and identified along the mass spectrum. Fifty-five strains of M. aeruginosa from different habitats were analyzed using MALDI-TOF MS; among these samples, different ribosomal protein types were observed. A polygenetic analysis was performed using an unweighted pair-group method with arithmetic means and different ribosomal protein types to classify the strains into five major clades. Two clades primarily contained toxic strains, and the other three clades contained exclusively non-toxic strains. This is the first study to differentiate cyanobacterial strains using MALDI-TOF MS.

Patterns and processes in the genetic differentiation of the Brachionus calyciflorus complex, a passively dispersing freshwater zooplankton.

PubMed

Xiang, Xian-ling; Xi, Yi-long; Wen, Xin-li; Zhang, Gen; Wang, Jin-xia; Hu, Ke

2011-05-01

Elucidating the evolutionary patterns and processes of extant species is an important objective of any research program that seeks to understand population divergence and, ultimately, speciation. The island-like nature and temporal fluctuation of limnetic habitats create opportunities for genetic differentiation in rotifers through space and time. To gain further understanding of spatio-temporal patterns of genetic differentiation in rotifers other than the well-studied Brachionus plicatilis complex in brackish water, a total of 318 nrDNA ITS sequences from the B. calyciflorus complex in freshwater were analysed using phylogenetic and phylogeographic methods. DNA taxonomy conducted by both the sequence divergence and the GMYC model suggested the occurrence of six potential cryptic species, supported also by reproductive isolation among the tested lineages. The significant genetic differentiation and non-significant correlation between geographic and genetic distances existed in the most abundant cryptic species, BcI-W and Bc-SW. The large proportion of genetic variability for cryptic species Bc-SW was due to differences between sampling localities within seasons, rather than between different seasons. Nested Clade Analysis suggested allopatric or past fragmentation, contiguous range expansion and long-distance colonization possibly coupled with subsequent fragmentation as the probable main forces shaping the present-day phylogeographic structure of the B. calyciflorus species complex. Copyright © 2011 Elsevier Inc. All rights reserved.

Population genetic structure of the point-head flounder, Cleisthenes herzensteini, in the Northwestern Pacific.

PubMed

Xiao, Yongshuang; Zhang, Yan; Yanagimoto, Takashi; Li, Jun; Xiao, Zhizhong; Gao, Tianxiang; Xu, Shihong; Ma, Daoyuan

2011-02-01

Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. To determine the population genetic structure and the demographic and colonization history of Cleisthenes herzensteini in the Northwestern Pacific, one hundred and twenty-one individuals were sampled from six localities along the coastal regions of Japan and the Yellow Sea of China. Mitochondrial DNA variation was analyzed using DNA sequence data from the 5' end of control region. High levels of haplotype diversity (>0.96) were found for all populations, indicating a high level of genetic diversity. No pattern of isolation by distance was detected among the population differentiation throughout the examined range. Analyses of molecular variance (AMOVA) and the conventional population statistic Fst revealed no significant population genetic structure among populations. According to the exact test of differentiation among populations, the null hypothesis that C. herzensteini within the examined range constituted a non-differential mtDNA gene pool was accepted. The demographic history of C. herzensteini was examined using neutrality test and mismatch distribution analyses and results indicated Pleistocene population expansion (about 94-376 kya) in the species, which was consistent with the inference result of nested clade phylogeographical analysis (NCPA) showing contiguous range expansion for C. herzensteini. The lack of phylogeographical structure for the species may reflect a recent range expansion after the glacial maximum and insufficient time to attain migration-drift equilibrium.

Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification.

PubMed

Gupta, Radhey S

2016-07-01

Analyses of genome sequences, by some approaches, suggest that the widespread occurrence of horizontal gene transfers (HGTs) in prokaryotes disguises their evolutionary relationships and have led to questioning of the Darwinian model of evolution for prokaryotes. These inferences are critically examined in the light of comparative genome analysis, characteristic synapomorphies, phylogenetic trees and Darwin's views on examining evolutionary relationships. Genome sequences are enabling discovery of numerous molecular markers (synapomorphies) such as conserved signature indels (CSIs) and conserved signature proteins (CSPs), which are distinctive characteristics of different prokaryotic taxa. Based on these molecular markers, exhibiting high degree of specificity and predictive ability, numerous prokaryotic taxa of different ranks, currently identified based on the 16S rRNA gene trees, can now be reliably demarcated in molecular terms. Within all studied groups, multiple CSIs and CSPs have been identified for successive nested clades providing reliable information regarding their hierarchical relationships and these inferences are not affected by HGTs. These results strongly support Darwin's views on evolution and classification and supplement the current phylogenetic framework based on 16S rRNA in important respects. The identified molecular markers provide important means for developing novel diagnostics, therapeutics and for functional studies providing important insights regarding prokaryotic taxa. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Genetic variability in Melipona quinquefasciata (Hymenoptera, Apidae, Meliponini) from northeastern Brazil determined using the first internal transcribed spacer (ITS1).

PubMed

Pereira, J O P; Freitas, B M; Jorge, D M M; Torres, D C; Soares, C E A; Grangeiro, T B

2009-01-01

Melipona quinquefasciata is a ground-nesting South American stingless bee whose geographic distribution was believed to comprise only the central and southern states of Brazil. We obtained partial sequences (about 500-570 bp) of first internal transcribed spacer (ITS1) nuclear ribosomal DNA from Melipona specimens putatively identified as M. quinquefasciata collected from different localities in northeastern Brazil. To confirm the taxonomic identity of the northeastern samples, specimens from the state of Goiás (Central region of Brazil) were included for comparison. All sequences were deposited in GenBank (accession numbers EU073751-EU073759). The mean nucleotide divergence (excluding sites with insertions/deletions) in the ITS1 sequences was only 1.4%, ranging from 0 to 4.1%. When the sites with insertions/deletions were also taken into account, sequence divergences varied from 0 to 5.3%. In all pairwise comparisons, the ITS1 sequence from the specimens collected in Goiás was most divergent compared to the ITS1 sequences of the bees from the other locations. However, neighbor-joining phylogenetic analysis showed that all ITS1 sequences from northeastern specimens along with the sample of Goiás were resolved in a single clade with a bootstrap support of 100%. The ITS1 sequencing data thus support the occurrence of M. quinquefasciata in northeast Brazil.

Historic cycles of fragmentation and expansion in Parnassius smintheus (papilionidae) inferred using mitochondrial DNA.

PubMed

DeChaine, Eric G; Martini, Andrew P

2004-01-01

Climate oscillations of the Quaternary drove the repeated expansion and contraction of ecosystems. Alpine organisms were probably isolated in sky island refugia during warm interglacials, such as now, and expanded their range by migrating down-slope during glacial periods. We used population genetic and phylogenetic approaches to infer how paleoclimatic events influenced the distribution of genetic variation in the predominantly alpine butterfly Parnassius smintheus. We sequenced a 789 bp region of cytochrome oxidase I for 385 individuals from 20 locations throughout the Rocky Mountains, ranging from southern Colorado to northern Montana. Analyses revealed at lease two centers of diversity in the northern and southern Rocky Mountains and strong population structure. Nested clade analysis suggested that the species experienced repeated cycles of population expansion and fragmentation. The estimated ages of these events, assuming a molecular clock, corresponded with paleoclimatic data on habitat expansion and contraction over the past 400,000 years. We propose that alpine butterflies persisted in an archipelago of isolated sky islands during interglacials and that populations expanded and became more connected during cold glacial periods. An archipelago model implies that the effects of genetic drift and selection varied among populations, depending on their latitude, area, and local environment. Alpine organisms are sensitive indicators of climate change and their history can be used to predict how high-elevation ecosystems might respond to further climate warming.

Evolutionary history and phylogeography of Encelia farinosa (Asteraceae) from the Sonoran, Mojave, and Peninsular Deserts.

PubMed

Fehlberg, Shannon D; Ranker, Tom A

2009-02-01

Pleistocene glaciations have had a profound influence on the genetic structure of plant species throughout the Northern Hemisphere because of range contractions, fragmentations, and expansions. Phylogeographic studies have contributed to our knowledge of this influence in several geographic regions of North America, however, very few phylogeographic studies have examined plant species in the Sonoran, Mojave, and Peninsular deserts. In this study, we used sequence data from the chloroplast DNA psbA-trnH intergenic spacer to obtain information on phylogeographic patterns among 310 individuals from 21 populations of Encelia farinosa ("brittlebush"; Asteraceae) across its range. We applied several population and spatial genetic analyses that allowed us to interpret our data with respect to Pleistocene climate change. These analyses indicate that E. farinosa displays patterns of genetic differentiation and geographic structuring consistent with postglacial range expansion. Populations of E. farinosa are characterized by distinct haplotype lineages significantly associated with geography. Centers of genetic diversity for the species occur in southwestern Arizona, the plains of Sonora, and Baja California Sur, all of which are putative sites of glacial refugia as predicted by analyses of macrofossil and pollen data. Nested clade analysis suggests that genetic structure in E. farinosa has been affected by past fragmentation followed by range expansion. Range expansion in several locations is further supported by significant departures from neutrality for values of Fu's F(S) and Tajima's D, and mismatch analyses.

Concurrent occurrence of human and equine West Nile virus infections in Central Anatolia, Turkey: the first evidence for circulation of lineage 1 viruses.

PubMed

Ozkul, Aykut; Ergunay, Koray; Koysuren, Aydan; Alkan, Feray; Arsava, Ethem M; Tezcan, Seda; Emekdas, Gurol; Hacioglu, Sabri; Turan, Mahur; Us, Durdal

2013-07-01

West Nile fever is an important zoonotic infection caused by West Nile virus (WNV), a member of the Flaviviridae. Previous serological data from Turkey suggest widespread WNV circulation. This report includes cases of human and equine WNV infections occurring concurrently, and manifesting as central nervous system infections, in two neighboring provinces of Central Anatolia, Turkey. A partial phylogenetic analysis of the causative virus is given for the first time. The cases were reported in February (horses) and March (human). Symptoms of the disease were similar in the two species, characterized by neurological manifestations suggesting meningoencephalitis. Real-time/nested PCRs and commercial immunoassays and a plaque reduction neutralization assay were employed for the detection of viral RNA and specific antibodies, respectively. WNV RNAs were detected in buffy coat (horses) and cerebrospinal fluid (human) samples. Partial nucleotide sequences of the E-gene coding region revealed that the strains are closely related to viruses of lineage 1, clade 1a. Accompanying equine serosurveillance demonstrated WNV-specific antibodies in 31.6% of the samples. This is the first report of acute WNV infections caused by lineage 1 strains from Turkey, in concordance with previous reports from some European and North African countries. Copyright © 2013 International Society for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Fire and ice: volcanic and glacial impacts on the phylogeography of the New Zealand forest fern Asplenium hookerianum.

PubMed

Shepherd, Lara D; Perrie, Leon R; Brownsey, Patrick J

2007-11-01

In the Southern Hemisphere there has been little phylogeographical investigation of forest refugia sites during the last glacial. Hooker's spleenwort, Asplenium hookerianum, is a fern that is found throughout New Zealand. It is strongly associated with forest and is a proxy for the survival of woody vegetation during the last glacial maximum. DNA sequence data from the chloroplast trnL-trnF locus were obtained from 242 samples, including c. 10 individuals from each of 21 focal populations. Most populations contained multiple, and in many cases unique, haplotypes, including those neighbouring formerly glaciated areas, while the predominant inference from nested clade analysis was restricted gene flow with isolation by distance. These results suggest that A. hookerianum survived the last glacial maximum in widespread populations of sufficient size to retain the observed phylogeography, and therefore that the sheltering woody vegetation must have been similarly abundant. This is consistent with palynological interpretations for the survival in New Zealand of thermophilous forest species at considerably smaller distances from the ice sheets than recorded for the Northern Hemisphere. Eastern and central North Island populations of A. hookerianum were characterized by a different subset of haplotypes to populations from the remainder of the country. A similar east-west phylogeographical pattern has been detected in a diverse array of taxa, and has previously been attributed to recurrent vulcanism in the central North Island.

Savanna chimpanzee (Pan troglodytes verus) nesting ecology at Bagnomba (Kedougou, Senegal).

PubMed

Badji, L; Ndiaye, P I; Lindshield, S M; Ba, C T; Pruetz, J D

2018-05-01

We studied the nesting behavior of the critically endangered West African chimpanzee (Pan troglodytes verus). We assumed that the nesting data stemmed from a single, unhabituated community at the Bagnomba hill site in the savanna-woodlands of southeastern Senegal. The aim of this study was to examine chimpanzees' nesting habits in terms of the tree species utilized and sleeping nest heights. We recorded a total of 550 chimpanzee nests at Bagnomba between January 2015 and December 2015. The chimpanzees here made nests in particular tree species more often than others. The majority of nests (63%) were in two tree species: Diospyros mespiliformis and Pterocarpus erinaceus. The average height of nesting trees was 10.54 m (SD 3.91, range, 0.0-29.0 m) and average nest height was 7.90 m (SD 3.62, range, 0.0-25.0 m). The result of a linear regression analysis (r = 0.7874; n = 550; p < 0.05) is consistent with a preference for nesting at a particular height. Bagnomba chimpanzees rarely made ground nests (0.36% of nests), but the presence of any ground nesting was unexpected, given that at least one leopard (Panthera pardus) also occupied the hill. This knowledge will enable stakeholders involved in the protection of chimpanzees specifically and of biodiversity in general to better understand chimpanzee ecology and inform a conservation action plan in Senegal where the survival of this species is threatened.

The nest growth of the neotropical mound-building termite, Cornitermes cumulans: a micromorphological analysis.

PubMed

Cosarinsky, Marcela I

2011-01-01

The nests of Cornitermes cumulans K. (Isoptera: Termitidae), a very common termite in South American grasslands, display notable morphological transformations during the development of the colony. Young colonies inhabit small subterranean nests that develop into large, conspicuous, epigean mounds, inhabited by very populous colonies. Those macromorphological transformations are accompanied by micromorphological changes occurring gradually in the nest walls. The micromorphological changes during nest development described in the present study expand on previous macromorphological descriptions by explaining the re-organization of the soil components during nest growth. In subterranean nests, walls are composed of piles of lensshaped aggregates of soil material, each one surrounded by a thin organic coating. As the nest grows, mound walls are constructed by disassembling this first lenticular structure and rearranging the materials in a new fabric, where sand grains are loosely distributed among soil microaggregates of organic matter and clay. This is also a temporary construction, because the walls of large nests are composed of a porous mass of sands densely cemented with organic matter and clay in the mound, and a compact mass of the same components in the floor.

Benefits from living together? Clades whose species use similar habitats may persist as a result of eco-evolutionary feedbacks.

PubMed

Prinzing, Andreas; Ozinga, Wim A; Brändle, Martin; Courty, Pierre-Emmanuel; Hennion, Françoise; Labandeira, Conrad; Parisod, Christian; Pihain, Mickael; Bartish, Igor V

2017-01-01

Contents 66 I. 67 II. 68 III. 69 IV. 70 V. 73 VI. 75 VII. 77 78 References 78 SUMMARY: Recent decades have seen declines of entire plant clades while other clades persist despite changing environments. We suggest that one reason why some clades persist is that species within these clades use similar habitats, because such similarity may increase the degree of co-occurrence of species within clades. Traditionally, co-occurrence among clade members has been suggested to be disadvantageous because of increased competition and enemy pressure. Here, we hypothesize that increased co-occurrence among clade members promotes mutualist exchange, niche expansion or hybridization, thereby helping species avoid population decline from environmental change. We review the literature and analyse published data for hundreds of plant clades (genera) within a well-studied region and find major differences in the degree to which species within clades occupy similar habitats. We tentatively show that, in clades for which species occupy similar habitats, species tend to exhibit increased co-occurrence, mutualism, niche expansion, and hybridization - and rarely decline. Consistently, throughout the geological past, clades whose species occupied similar habitats often persisted through long time-spans. Overall, for many plant species, the occupation of similar habitats among fellow clade members apparently reduced their vulnerability to environmental change. Future research should identify when and how this previously unrecognized eco-evolutionary feedback operates. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Neofunctionalization of a duplicate hatching enzyme gene during the evolution of teleost fishes.

PubMed

Sano, Kaori; Kawaguchi, Mari; Watanabe, Satoshi; Yasumasu, Shigeki

2014-10-19

Duplication and subsequent neofunctionalization of the teleostean hatching enzyme gene occurred in the common ancestor of Euteleostei and Otocephala, producing two genes belonging to different phylogenetic clades (clade I and II). In euteleosts, the clade I enzyme inherited the activity of the ancestral enzyme of swelling the egg envelope by cleavage of the N-terminal region of egg envelope proteins. The clade II enzyme gained two specific cleavage sites, N-ZPd and mid-ZPd but lost the ancestral activity. Thus, euteleostean clade II enzymes assumed a new function; solubilization of the egg envelope by the cooperative action with clade I enzyme. However, in Otocephala, the clade II gene was lost during evolution. Consequently, in a late group of Otocephala, only the clade I enzyme is present to swell the egg envelope. We evaluated the egg envelope digestion properties of clade I and II enzymes in Gonorynchiformes, an early diverging group of Otocephala, using milkfish, and compared their digestion with those of other fishes. Finally, we propose a hypothesis of the neofunctionalization process. The milkfish clade II enzyme cleaved N-ZPd but not mid-ZPd, and did not cause solubilization of the egg envelope. We conclude that neofunctionalization is incomplete in the otocephalan clade II enzymes. Comparison of clade I and clade II enzyme characteristics implies that the specificity of the clade II enzymes gradually changed during evolution after the duplication event, and that a change in substrate was required for the addition of the mid-ZPd site and loss of activity at the N-terminal region. We infer the process of neofunctionalization of the clade II enzyme after duplication of the gene. The ancestral clade II gene gained N-ZPd cleavage activity in the common ancestral lineage of the Euteleostei and Otocephala. Subsequently, acquisition of cleavage activity at the mid-ZPd site and loss of cleavage activity in the N-terminal region occurred during the evolution of Euteleostei, but not of Otocephala. The clade II enzyme provides an example of the development of a neofunctional gene for which the substrate, the egg envelope protein, has adapted to a gradual change in the specificity of the corresponding enzyme.

Age-specific productivity and nest site characteristics of Cooper's hawks (Accipiter cooperii)

USGS Publications Warehouse

Moore, K.R.; Henny, C.J.

1984-01-01

Nesting Cooper's Hawks (Accipiter cooperii) were studied in northeastern Oregon. Second-year (SY) males did not breed, but 22 percent of the breeding females were SY's. Mean clutch size (P = 0.012) and mean number of young fledged per pair that laid eggs (P < 0.10) were lower for SY females than for adult (after second year [ASY}) females; however, an equal percentage of the eggs (excluding a collected sample egg) yielded fledged young for each age class. Stepwise discriminant analysis suggested differences in structural characteristics of the nest site habitat for ASY and SY females, i.e., SY female nest sites were associated with younger successional stages than ASY female nest sites. Nests of both age groups were built in trees with high crown volume, but ASY females utilized mistletoe (Arceuthobium sp.) for nest structures more frequently (P < 0.01) than SY females.

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chai, Juanjuan; Kora, Guruprasad; Ahn, Tae-Hyuk

2014-10-09

To supply some background, phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathways and biological processes, has not been systematically characterized. Many clades in the prokaryotic tree of life have now been covered by sequenced genomes in GenBank. This enables a large-scale functional phylogenomics study of many computationally inferred cellular functions across all sequenced prokaryotes. Our results show a total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accuratemore » comparison. The functional profile of a genome was represented by the biological process Gene Ontology (GO) terms in its annotation. The GO term enrichment analysis differentiated the functional profiles between selected archaeal taxa. 706 prokaryotic metabolic pathways were inferred from these genomes using Pathway Tools and MetaCyc. The consistency between the distribution of metabolic pathways in the genomes and the phylogenetic tree of the genomes was measured using parsimony scores and retention indices. The ancestral functional profiles at the internal nodes of the phylogenetic tree were reconstructed to track the gains and losses of metabolic pathways in evolutionary history. In conclusion, our functional phylogenomics analysis shows divergent functional profiles of taxa and clades. Such function-phylogeny correlation stems from a set of clade-specific cellular functions with low parsimony scores. On the other hand, many cellular functions are sparsely dispersed across many clades with high parsimony scores. These different types of cellular functions have distinct evolutionary patterns reconstructed from the prokaryotic tree.« less

Analysis of Ecological Distribution and Genomic Content from a Clade of Bacteroidetes Endemic to Sulfidic Environments

NASA Astrophysics Data System (ADS)

Zhou, K.; Sylvan, J. B.; Hallam, S. J.

2017-12-01

The Bacteroidetes are a ubiquitous phylum of bacteria found in a wide variety of habitats. Marine Bacteroidetes are known to utilize complex carbohydrates and have a potentially important role in the global carbon cycle through processing these compounds, which are not digestible by many other microbes. Some members of the phylum are known to perform denitrification and are facultative anaerobes, but Bacteroidetes are not known to participate in sulfur redox cycling. Recently, it was shown that a clade of uncultured Bacteroidetes, including the VC2.1_Bac22 group, appears to be endemic to sulfidic environments, including hydrothermal vent sulfide chimneys, sediments and marine water column oxygen minimum zones (OMZs). This clade, dubbed the Sulfiphilic Bacteroidetes, is not detected in 16S rRNA amplicon studies from non-sulfidic environments. To test the hypothesis that the Sulphiphilic Bacteroidetes are involved in sulfur redox chemistry, we updated our meta-analysis of the clade using 16s rRNA sequences from public databases and employed single-cell genomics to survey their genomic potential using 19 single amplified genomes (SAGs) isolated from the seasonally anoxic Saanich Inlet, a seasonally hypoxic basin in British Columbia. Initial analysis of these SAGs indicates the Sulphiphilic Bacteroidetes may perform sulfur redox reactions using a three gene psrABC operon encoding the polysulfide reductase enzyme complex with a thiosulfate sulfurtransferase (rhodanese), which putatively uses cyanide to convert thiosulfate to sulfite, just upstream. Interestingly, this is the same configuration as discovered recently in some Marine Group A bacteria. Further aspects of the Sulphiphilic Bacteroidetes' genomic potential will be presented in light of their presence in sulfidic environments.

Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

PubMed Central

Matus, José Tomás; Aquea, Felipe; Arce-Johnson, Patricio

2008-01-01

Background The MYB superfamily constitutes the most abundant group of transcription factors described in plants. Members control processes such as epidermal cell differentiation, stomatal aperture, flavonoid synthesis, cold and drought tolerance and pathogen resistance. No genome-wide characterization of this family has been conducted in a woody species such as grapevine. In addition, previous analysis of the recently released grape genome sequence suggested expansion events of several gene families involved in wine quality. Results We describe and classify 108 members of the grape R2R3 MYB gene subfamily in terms of their genomic gene structures and similarity to their putative Arabidopsis thaliana orthologues. Seven gene models were derived and analyzed in terms of gene expression and their DNA binding domain structures. Despite low overall sequence homology in the C-terminus of all proteins, even in those with similar functions across Arabidopsis and Vitis, highly conserved motif sequences and exon lengths were found. The grape epidermal cell fate clade is expanded when compared with the Arabidopsis and rice MYB subfamilies. Two anthocyanin MYBA related clusters were identified in chromosomes 2 and 14, one of which includes the previously described grape colour locus. Tannin related loci were also detected with eight candidate homologues in chromosomes 4, 9 and 11. Conclusion This genome wide transcription factor analysis in Vitis suggests that clade-specific grape R2R3 MYB genes are expanded while other MYB genes could be well conserved compared to Arabidopsis. MYB gene abundance, homology and orientation within particular loci also suggests that expanded MYB clades conferring quality attributes of grapes and wines, such as colour and astringency, could possess redundant, overlapping and cooperative functions. PMID:18647406

Evolutionary genomics revealed interkingdom distribution of Tcn1-like chromodomain-containing Gypsy LTR retrotransposons among fungi and plants.

PubMed

Novikova, Olga; Smyshlyaev, Georgiy; Blinov, Alexander

2010-04-08

Chromodomain-containing Gypsy LTR retrotransposons or chromoviruses are widely distributed among eukaryotes and have been found in plants, fungi and vertebrates. The previous comprehensive survey of chromoviruses from mosses (Bryophyta) suggested that genomes of non-seed plants contain the clade which is closely related to the retrotransposons from fungi. The origin, distribution and evolutionary history of this clade remained unclear mainly due to the absence of information concerning the diversity and distribution of LTR retrotransposons in other groups of non-seed plants as well as in fungal genomes. In present study we preformed in silico analysis of chromodomain-containing LTR retrotransposons in 25 diverse fungi and a number of plant species including spikemoss Selaginella moellendorffii (Lycopodiophyta) coupled with an experimental survey of chromodomain-containing Gypsy LTR retrotransposons from diverse non-seed vascular plants (lycophytes, ferns, and horsetails). Our mining of Gypsy LTR retrotransposons in genomic sequences allowed identification of numerous families which have not been described previously in fungi. Two new well-supported clades, Galahad and Mordred, as well as several other previously unknown lineages of chromodomain-containing Gypsy LTR retrotransposons were described based on the results of PCR-mediated survey of LTR retrotransposon fragments from ferns, horsetails and lycophytes. It appeared that one of the clades, namely Tcn1 clade, was present in basidiomycetes and non-seed plants including mosses (Bryophyta) and lycophytes (genus Selaginella). The interkingdom distribution is not typical for chromodomain-containing LTR retrotransposons clades which are usually very specific for a particular taxonomic group. Tcn1-like LTR retrotransposons from fungi and non-seed plants demonstrated high similarity to each other which can be explained by strong selective constraints and the 'retained' genes theory or by horizontal transmission.

Decoupled evolution of floral traits and climatic preferences in a clade of Neotropical Gesneriaceae.

PubMed

Serrano-Serrano, Martha Liliana; Perret, Mathieu; Guignard, Maïté; Chautems, Alain; Silvestro, Daniele; Salamin, Nicolas

2015-11-10

Major factors influencing the phenotypic diversity of a lineage can be recognized by characterizing the extent and mode of trait evolution between related species. Here, we compared the evolutionary dynamics of traits associated with floral morphology and climatic preferences in a clade composed of the genera Codonanthopsis, Codonanthe and Nematanthus (Gesneriaceae). To test the mode and specific components that lead to phenotypic diversity in this group, we performed a Bayesian phylogenetic analysis of combined nuclear and plastid DNA sequences and modeled the evolution of quantitative traits related to flower shape and size and to climatic preferences. We propose an alternative approach to display graphically the complex dynamics of trait evolution along a phylogenetic tree using a wide range of evolutionary scenarios. Our results demonstrated heterogeneous trait evolution. Floral shapes displaced into separate regimes selected by the different pollinator types (hummingbirds versus insects), while floral size underwent a clade-specific evolution. Rates of evolution were higher for the clade that is hummingbird pollinated and experienced flower resupination, compared with species pollinated by bees, suggesting a relevant role of plant-pollinator interactions in lowland rainforest. The evolution of temperature preferences is best explained by a model with distinct selective regimes between the Brazilian Atlantic Forest and the other biomes, whereas differentiation along the precipitation axis was characterized by higher rates, compared with temperature, and no regime or clade-specific patterns. Our study shows different selective regimes and clade-specific patterns in the evolution of morphological and climatic components during the diversification of Neotropical species. Our new graphical visualization tool allows the representation of trait trajectories under parameter-rich models, thus contributing to a better understanding of complex evolutionary dynamics.

A novel homodimeric geranyl diphosphate synthase from the orchid Phalaenopsis bellina lacking a DD(X)2-4D motif.

PubMed

Hsiao, Yu-Yun; Jeng, Mei-Fen; Tsai, Wen-Chieh; Chuang, Yu-Chen; Li, Chia-Ying; Wu, Tian-Shung; Kuoh, Chang-Sheng; Chen, Wen-Huei; Chen, Hong-Hwa

2008-09-01

Geranyl diphosphate (GDP) is the precursor of monoterpenes, which are the major floral scent compounds in Phalaenopsis bellina. The cDNA of P. bellina GDP synthase (PbGDPS) was cloned, and its sequence corresponds to the second Asp-rich motif (SARM), but not to any aspartate-rich (Asp-rich) motif. The recombinant PbGDPS enzyme exhibits dual prenyltransferase activity, producing both GDP and farnesyl diphosphate (FDP), and a yeast two-hybrid assay and gel filtration revealed that PbGDPS was able to form a homodimer. Spatial and temporal expression analyses showed that the expression of PbGDPS was flower specific, and that maximal PbGDPS expression was concomitant with maximal emission of monoterpenes on day 5 post-anthesis. Homology modelling of PbGDPS indicated that the Glu-rich motif might provide a binding site for Mg(2+) and catalyze the formation of prenyl products in a similar way to SARM. Replacement of the key Glu residues with alanine totally abolished enzyme activity, whereas their mutation to Asp resulted in a mutant with two-thirds of the activity of the wild-type protein. Phylogenetic analysis indicated that plant GDPS proteins formed four clades: members of both GDPS-a and GDPS-b clades contain Asp-rich motifs, and function as homodimers. In contrast, proteins in the GDPS-c and GDPS-d clades do not contain Asp-rich motifs, but although members of the GDPS-c clade function as heterodimers, PbGDPS, which is more closely related to the GDPS-c clade proteins than to GDPS-a and GDPS-b proteins, and is currently the sole member of the GDPS-d clade, functions as a homodimer.

Phylogenetic Constraints Do Not Explain the Rarity of Nitrogen-Fixing Trees in Late-Successional Temperate Forests

PubMed Central

Menge, Duncan N. L.; DeNoyer, Jeanne L.; Lichstein, Jeremy W.

2010-01-01

Background Symbiotic nitrogen (N)-fixing trees are rare in late-successional temperate forests, even though these forests are often N limited. Two hypotheses could explain this paradox. The ‘phylogenetic constraints hypothesis’ states that no late-successional tree taxa in temperate forests belong to clades that are predisposed to N fixation. Conversely, the ‘selective constraints hypothesis’ states that such taxa are present, but N-fixing symbioses would lower their fitness. Here we test the phylogenetic constraints hypothesis. Methodology/Principal Findings Using U.S. forest inventory data, we derived successional indices related to shade tolerance and stand age for N-fixing trees, non-fixing trees in the ‘potentially N-fixing clade’ (smallest angiosperm clade that includes all N fixers), and non-fixing trees outside this clade. We then used phylogenetically independent contrasts (PICs) to test for associations between these successional indices and N fixation. Four results stand out from our analysis of U.S. trees. First, N fixers are less shade-tolerant than non-fixers both inside and outside of the potentially N-fixing clade. Second, N fixers tend to occur in younger stands in a given geographical region than non-fixers both inside and outside of the potentially N-fixing clade. Third, the potentially N-fixing clade contains numerous late-successional non-fixers. Fourth, although the N fixation trait is evolutionarily conserved, the successional traits are relatively labile. Conclusions/Significance These results suggest that selective constraints, not phylogenetic constraints, explain the rarity of late-successional N-fixing trees in temperate forests. Because N-fixing trees could overcome N limitation to net primary production if they were abundant, this study helps to understand the maintenance of N limitation in temperate forests, and therefore the capacity of this biome to sequester carbon. PMID:20700466

High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences

PubMed Central

Vergin, Kevin L; Beszteri, Bánk; Monier, Adam; Cameron Thrash, J; Temperton, Ben; Treusch, Alexander H; Kilpert, Fabian; Worden, Alexandra Z; Giovannoni, Stephen J

2013-01-01

Advances in next-generation sequencing technologies are providing longer nucleotide sequence reads that contain more information about phylogenetic relationships. We sought to use this information to understand the evolution and ecology of bacterioplankton at our long-term study site in the Western Sargasso Sea. A bioinformatics pipeline called PhyloAssigner was developed to align pyrosequencing reads to a reference multiple sequence alignment of 16S ribosomal RNA (rRNA) genes and assign them phylogenetic positions in a reference tree using a maximum likelihood algorithm. Here, we used this pipeline to investigate the ecologically important SAR11 clade of Alphaproteobacteria. A combined set of 2.7 million pyrosequencing reads from the 16S rRNA V1–V2 regions, representing 9 years at the Bermuda Atlantic Time-series Study (BATS) site, was quality checked and parsed into a comprehensive bacterial tree, yielding 929 036 Alphaproteobacteria reads. Phylogenetic structure within the SAR11 clade was linked to seasonally recurring spatiotemporal patterns. This analysis resolved four new SAR11 ecotypes in addition to five others that had been described previously at BATS. The data support a conclusion reached previously that the SAR11 clade diversified by subdivision of niche space in the ocean water column, but the new data reveal a more complex pattern in which deep branches of the clade diversified repeatedly across depth strata and seasonal regimes. The new data also revealed the presence of an unrecognized clade of Alphaproteobacteria, here named SMA-1 (Sargasso Mesopelagic Alphaproteobacteria, group 1), in the upper mesopelagic zone. The high-resolution phylogenetic analyses performed herein highlight significant, previously unknown, patterns of evolutionary diversification, within perhaps the most widely distributed heterotrophic marine bacterial clade, and strongly links to ecosystem regimes. PMID:23466704

High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences.

PubMed

Vergin, Kevin L; Beszteri, Bánk; Monier, Adam; Thrash, J Cameron; Temperton, Ben; Treusch, Alexander H; Kilpert, Fabian; Worden, Alexandra Z; Giovannoni, Stephen J

2013-07-01

Advances in next-generation sequencing technologies are providing longer nucleotide sequence reads that contain more information about phylogenetic relationships. We sought to use this information to understand the evolution and ecology of bacterioplankton at our long-term study site in the Western Sargasso Sea. A bioinformatics pipeline called PhyloAssigner was developed to align pyrosequencing reads to a reference multiple sequence alignment of 16S ribosomal RNA (rRNA) genes and assign them phylogenetic positions in a reference tree using a maximum likelihood algorithm. Here, we used this pipeline to investigate the ecologically important SAR11 clade of Alphaproteobacteria. A combined set of 2.7 million pyrosequencing reads from the 16S rRNA V1-V2 regions, representing 9 years at the Bermuda Atlantic Time-series Study (BATS) site, was quality checked and parsed into a comprehensive bacterial tree, yielding 929 036 Alphaproteobacteria reads. Phylogenetic structure within the SAR11 clade was linked to seasonally recurring spatiotemporal patterns. This analysis resolved four new SAR11 ecotypes in addition to five others that had been described previously at BATS. The data support a conclusion reached previously that the SAR11 clade diversified by subdivision of niche space in the ocean water column, but the new data reveal a more complex pattern in which deep branches of the clade diversified repeatedly across depth strata and seasonal regimes. The new data also revealed the presence of an unrecognized clade of Alphaproteobacteria, here named SMA-1 (Sargasso Mesopelagic Alphaproteobacteria, group 1), in the upper mesopelagic zone. The high-resolution phylogenetic analyses performed herein highlight significant, previously unknown, patterns of evolutionary diversification, within perhaps the most widely distributed heterotrophic marine bacterial clade, and strongly links to ecosystem regimes.

Detection of virulent Escherichia coli O157 strains using multiplex PCR and single base sequencing for SNP characterization.

PubMed

Haugum, K; Brandal, L T; Løbersli, I; Kapperud, G; Lindstedt, B-A

2011-06-01

To compare 167 Norwegian human and nonhuman Escherichia coli O157:H7/NM (nonmotile) isolates with respect to an A/T single nucleotide polymorphism (SNP) in the tir gene and to detect specific SNPs that differentiate STEC O157 into distinct virulence clades (1-3 and 8). We developed a multiplex PCR followed by single base sequencing for detection of the SNPs, and examined the association among SNP genotype, virulence profile (stx and eae status), multilocus variable number of tandem repeats analysis (MLVA) profile and clinical outcome. We found an over-representation of the T allele among human strains compared to nonhuman strains, including 5/6 haemolytic-uraemic syndrome cases. Fourteen strains belonged to clade 8, followed by two clade 2 strains. No clade 1 nor 3 isolates were observed. stx1 in combination with either stx2(EDL933) or stx2c were frequently observed among human strains, whereas stx2c was dominating in nonhuman strains. MLVA indicated that only single cases or small outbreaks with E. coli O157 have been observed in Norway through the years 1993-2008. We observed that the tir-255 A/T SNP and the stx status were different between human and nonhuman O157 strains. No major outbreaks were observed, and only a few strains were differentiated into the virulence clades 2 and 8. The detection of virulence clade-specific SNPs enables the rapid designation of virulent E. coli O157 strains, especially in outbreak situations. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

Effects of spatial disturbance on common loon nest site selection and territory success

USGS Publications Warehouse

McCarthy, Kyle P.; DeStefano, Stephen

2011-01-01

The common loon (Gavia immer) breeds during the summer on northern lakes and water bodies that are also often desirable areas for aquatic recreation and human habitation. In northern New England, we assessed how the spatial nature of disturbance affects common loon nest site selection and territory success. We found through classification and regression analysis that distance to and density of disturbance factors can be used to classify observed nest site locations versus random points, suggesting that these factors affect loon nest site selection (model 1: Correct classification = 75%, null = 50%, K = 0.507, P < 0.001; model 2: Correct classification = 78%, null = 50%, K = 0.551, P < 0.001). However, in an exploratory analysis, we were unable to show a relation between spatial disturbance variables and breeding success (P = 0.595, R2 = 0.436), possibly because breeding success was so low during the breeding seasons of 2007–2008. We suggest that by selecting nest site locations that avoid disturbance factors, loons thereby limit the effect that disturbance will have on their breeding success. Still, disturbance may force loons to use sub-optimal nesting habitat, limiting the available number of territories, and overall productivity. We advise that management efforts focus on limiting disturbance factors to allow breeding pairs access to the best nesting territories, relieving disturbance pressures that may force sub-optimal nest placement.

Three cDNAs encoding vitellogenin homologs from Antarctic copepod, Tigriopus kingsejongensis: Cloning and transcriptional analysis in different maturation stages, temperatures, and putative reproductive hormones.

PubMed

Lee, Soo Rin; Lee, Ji-Hyun; Kim, Ah Ran; Kim, Sanghee; Park, Hyun; Baek, Hea Ja; Kim, Hyun-Woo

2016-02-01

Three full-length cDNAs encoding lipoprotein homologs were identified in Tigriopus kingsejongensis, a newly identified copepod from Antarctica. Structural and transcriptional analyses revealed homology with two vitellogenin-like proteins, Tik-Vg1 and Tik-Vg2, which were 1855 and 1795 amino acids in length, respectively, along with a third protein, Tik-MEP, which produced a 1517-residue protein with similarity to a melanin engaging protein (MEP) in insects Phylogenetic analysis showed that Vgs in Maxillopods including two Tik-Vgs belong to the arthropod vitellogenin-like clade, which includes clottable proteins (CPs) in decapod crustaceans and vitellogenins in insects. Tik-MEP clustered together with insect MEPs, which appear to have evolved before the apoB-like and arthropod Vg-like clades. Interestingly, no genes orthologous to those found in the apoB clade were identified in Maxillopoda, suggesting that functions of large lipid transfer proteins (LLTPs) in reproduction and lipid metabolism may be different from those in insect and decapod crustaceans. As suggested by phylogenetic analyses, the two Tik-Vgs belonging to the arthropod Vg-like clade appear to play major roles in oocyte maturation, while Vgs belonging to the apoB clade function primarily in the reproduction of decapod crustaceans. Transcriptional analysis of Tik-Vg expression revealed a 24-fold increase in mature and ovigerous females compared with immature female, whereas expression of Tik-MEP remained low through all reproductive stages. Acute temperature changes did not affect the transcription of Tik-Vg genes, whereas Tik-MEP appeared to be affected by temperature change. Among the three hormones thought to be involved in molting and reproduction in arthropods, only farnesoic acid (FA) induced transcription of the two Tik-Vg genes. Regardless of developmental stage and hormone treatment, Tik-Vg1 and Tik-Vg2 exhibited a strong positive correlation in expression, suggesting that expression of these genes may be regulated by the same transcriptional machinery. Copyright © 2015 Elsevier Inc. All rights reserved.

Comparative genomic analysis of two isolates of Vibrio cholerae O1 Ogawa El Tor isolated during outbreak in Mariupol in 2011.

PubMed

Kuleshov, Konstantin V; Kostikova, Anna; Pisarenko, Sergey V; Kovalev, Dmitry A; Tikhonov, Sergey N; Savelievа, Irina V; Saveliev, Vilory N; Vasilieva, Oksana V; Zinich, Liliia S; Pidchenko, Nadiia N; Kulichenko, Alexander N; Shipulin, German A

2016-10-01

Cholera is a water-borne, severe enteric infection essentially caused by toxigenic strains of Vibrio cholera O1 and O139 serogroups. An outbreak of cholera was registered during May-July 2011 in Mariupol, Ukraine, with 33 cholera cases and 25 carriers of cholera. Following this outbreak, the toxigenic strain of V. cholerae 2011EL-301 was isolated from seawater in the recreation area of Taganrog city on the territory of Russia. The aim of our study was to understand genomic features of Mariupol isolates as well as to evaluate hypothesis about possible interconnection between the outbreak of cholera in Mariupol and the single case of isolation of V. cholerae from the Sea of Azov in Russia. Mariupol isolates were phenotypically characterized and subsequently subjected to whole genome sequencing procedure. Phylogenetic analysis based on high-quality SNPs of V. cholera O1 El Tor isolates of the 7th pandemic clade from different regions showed that clinical and environmental isolates from Mariupol outbreak were attributable to a unique phylogenetic clade within wave 3 of V. cholera O1 El Tor isolates and characterized by six clade-specific SNPs. Whereas Taganrog isolate belonged to distantly related clade which allows us to reject the hypothesis of transmission the outbreak strain of V. cholerae O1 from Ukraine to Russia in 2011. Mariupol isolates shared a common ancestor with Haiti\\Nepal-4\\India clade indicating that outbreak progenitor strain most likely originated in the South Asia region and later was introduced to Ukraine. Moreover, genomic data both based on hqSNPs and similarity of virulence-associated mobile genomic elements of Mariupol isolates suggests that environmental and clinical isolates are a part of joint outbreak which confirms the role of contaminated domestic sewage, as an element of the complex chain of infection spread during cholera outbreak. In general, the genome-wide comparative analysis of both genes and genomic regions of epidemiological importance indicates accessory of this isolates to 'new' clone of toxigenic multiple drug resistance atypical variant of V. cholerae O1 El Tor. Copyright © 2016 Elsevier B.V. All rights reserved.

Comprehensive Phylogenetic Analysis of Bovine Non-aureus Staphylococci Species Based on Whole-Genome Sequencing

PubMed Central

Naushad, Sohail; Barkema, Herman W.; Luby, Christopher; Condas, Larissa A. Z.; Nobrega, Diego B.; Carson, Domonique A.; De Buck, Jeroen

2016-01-01

Non-aureus staphylococci (NAS), a heterogeneous group of a large number of species and subspecies, are the most frequently isolated pathogens from intramammary infections in dairy cattle. Phylogenetic relationships among bovine NAS species are controversial and have mostly been determined based on single-gene trees. Herein, we analyzed phylogeny of bovine NAS species using whole-genome sequencing (WGS) of 441 distinct isolates. In addition, evolutionary relationships among bovine NAS were estimated from multilocus data of 16S rRNA, hsp60, rpoB, sodA, and tuf genes and sequences from these and numerous other single genes/proteins. All phylogenies were created with FastTree, Maximum-Likelihood, Maximum-Parsimony, and Neighbor-Joining methods. Regardless of methodology, WGS-trees clearly separated bovine NAS species into five monophyletic coherent clades. Furthermore, there were consistent interspecies relationships within clades in all WGS phylogenetic reconstructions. Except for the Maximum-Parsimony tree, multilocus data analysis similarly produced five clades. There were large variations in determining clades and interspecies relationships in single gene/protein trees, under different methods of tree constructions, highlighting limitations of using single genes for determining bovine NAS phylogeny. However, based on WGS data, we established a robust phylogeny of bovine NAS species, unaffected by method or model of evolutionary reconstructions. Therefore, it is now possible to determine associations between phylogeny and many biological traits, such as virulence, antimicrobial resistance, environmental niche, geographical distribution, and host specificity. PMID:28066335

Host selection in the forest interior: cowbirds target ground-nesting species

USGS Publications Warehouse

Hahn, D.C.; Hatfield, J.S.

2000-01-01

We investigated patterns of cowbird host selection in a large (1300 ha), unfragmented forest in eastern New York in 1992-3 to determine whether cowbird parasitism rates can be attributed to species-specific traits or to other features associated with nest sites. Nest height was significantly associated with parasitism (P = 0.003) in this community of 23 species (n = 430 nests, 23% parasitized). Further analysis revealed that the difference in mean nest heights between parasitized and unparasitized nests was due to species identity, and within each species there was no difference in mean nest heights between parasitized and unparasitized nests. These results imply that during 1992-3 cowbirds in this forest specialized on species that have low nests and did not necessarily select low nests regardless of species. This was further supported by a negative association across all 23 species between mean nest height and parasitism rate (P = 0.03). Thus, although most of the forest-nesting species in this community experienced cowbird parasitism, there was a tendency for higher parasitism rates on low-nesting species such as the Ovenbird, Black-and-white Warbler, Louisiana Waterthrush, Veery, and Hermit Thrush. The Wood Thrush, a mid-range nester which is heavily parasitized in southern Illinois, experienced only 10% parasitism in our site and ranked 9th in parasitism rate, although it was the most abundant species in this forest in terms of the number of nests found. A long-term study is necessary to determine whether this cowbird population consistently parasitizes the ground-nesting species of this forest community more often than those nesting at higher levels or whether they periodically shift among hosts at different heights and in different habitats across the local landscape.

Draft genome and sequence variant data of the oomycete Pythium insidiosum strain Pi45 from the phylogenetically-distinct Clade-III.

PubMed

Kittichotirat, Weerayuth; Patumcharoenpol, Preecha; Rujirawat, Thidarat; Lohnoo, Tassanee; Yingyong, Wanta; Krajaejun, Theerapong

2017-12-01

Pythium insidiosum is a unique oomycete microorganism, capable of infecting humans and animals. The organism can be phylogenetically categorized into three distinct clades: Clade-I (strains from the Americas); Clade-II (strains from Asia and Australia), and Clade-III (strains from Thailand and the United States). Two draft genomes of the P. insidiosum Clade-I strain CDC-B5653 and Clade-II strain Pi-S are available in the public domain. The genome of P. insidiosum from the distinct Clade-III, which is distantly-related to the other two clades, is lacking. Here, we report the draft genome sequence of the P. insidiosum strain Pi45 (also known as MCC13; isolated from a Thai patient with pythiosis; accession numbers BCFM01000001-BCFM01017277) as a representative strain of the phylogenetically-distinct Clade-III. We also report a genome-scale data set of sequence variants (i.e., SNPs and INDELs) found in P. insidiosum (accessible online at the Mendeley database: http://dx.doi.org/10.17632/r75799jy6c.1).

Why Does a Method That Fails Continue To Be Used: The Answer

PubMed Central

Templeton, Alan R.

2009-01-01

It has been claimed that hundreds of researchers use nested clade phylogeographic analysis (NCPA) based on what the method promises rather than requiring objective validation of the method. The supposed failure of NCPA is based upon the argument that validating it by using positive controls ignored type I error, and that computer simulations have shown a high type I error. The first argument is factually incorrect: the previously published validation analysis fully accounted for both type I and type II errors. The simulations that indicate a 75% type I error rate have serious flaws and only evaluate outdated versions of NCPA. These outdated type I error rates fall precipitously when the 2003 version of single locus NCPA is used or when the 2002 multi-locus version of NCPA is used. It is shown that the treewise type I errors in single-locus NCPA can be corrected to the desired nominal level by a simple statistical procedure, and that multilocus NCPA reconstructs a simulated scenario used to discredit NCPA with 100% accuracy. Hence, NCPA is a not a failed method at all, but rather has been validated both by actual data and by simulated data in a manner that satisfies the published criteria given by its critics. The critics have come to different conclusions because they have focused on the pre-2002 versions of NCPA and have failed to take into account the extensive developments in NCPA since 2002. Hence, researchers can choose to use NCPA based upon objective critical validation that shows that NCPA delivers what it promises. PMID:19335340

The jumping plant-lice of the Neotropical genus Tainarys (Hemiptera: Psylloidea) associated with Anacardiaceae.

PubMed

Burckhardt, Daniel; Queiroz, Dalva L

2017-02-20

The Neotropical psyllid genus Tainarys Brèthes, 1920 is revised to include 14 extant and one fossil species from Dominican amber. Eight species are described as new, viz. Tainarys aroeira sp. nov., T. atra sp. nov., T. hapla sp. nov., T. myracrodrui sp. nov., T. nigricornis sp. nov., T. didyma sp. nov. and T. orientalis sp. nov. from Brazil, the last two also from Uruguay, as well as T. lozadai sp. nov. from Peru. The fifth instar immatures are described for nine species. †Vicinilura Klimaszewski, 1996, erected for the fossil †V. reposta Klimaszewski, 1996 and previously synonymised with Leurolophus Tuthill, 1942, is synonymised here (syn. nov.) with Tainarys and †V. reposta is transferred to become †Tainarys reposta (Klimaszewski), comb. nov. The descriptions are supplemented by illustrations and keys for the identification of adults and immatures. Phylogenetic relationships between species are investigated with a cladistic analysis using 22 adult and six immature morphological characters. The analysis resulted in a single most parsimonious, fully resolved tree. The fossil species is nested within the genus rather than being the sister taxon of the remainder of species. The extant species are restricted to the subtropical and temperate parts of South America. Three pairs of sister clades display an east‒west South American and one a midwest‒southern Brazilian geographical vicariance. Host plants are confirmed for nine and likely for another four species. They are Astronium, Haplorhus, Myracrodruon, Schinopsis and Schinus (Anacardiaceae). All Tainarys species appear to be oligophagous inducing irregular leaf curls on their hosts.

Phylogeography of Cephalotaxus oliveri (Cephalotaxaceae) in relation to habitat heterogeneity, physical barriers and the uplift of the Yungui Plateau.

PubMed

Wang, C B; Wang, T; Su, Y J

2014-11-01

Habitat heterogeneity, physical barriers, and the uplift of the Yungui Plateau were found to deeply affect the phylogeographic pattern and evolutionary history of Cephalotaxus oliveri, a perennial conifer endemic to China. In this study, we explored the phylogeography using three chloroplast sequences (trnL-trnF, trnT-trnD and atpB-rbcL) in 22 natural populations of C. oliveri distributed throughout its range. The Yungui Plateau populations of C. oliveri were revealed to origin ca. 9.15Ma by molecular clock estimation, which is consistent with rapid uplift of the Qinghai-Tibetan Plateau (QTP) ca. 8-10Ma. Additionally, geological effects of the Yungui Plateau were suggested to promote the rapid intra-specific differentiation of C. oliveri in the Pliocene and Early Pleistocene. The relatively low level of genetic diversity (h=0.719, θ=1.17×10(-3)) and high population differentiation (NST=0.771 and GST=0.642) implied restricted gene flow among populations, which was confirmed by the Nested Clade Analysis (NCA). Mismatch distribution and haplotypes network provided evidences of recent demographic population expansion. Furthermore, the statistical dispersal-vicariance analysis indicated that the center of origin was in Central China. The comparison of haplotype distribution patterns indicated that the regions of HNHPS and HBLD were the potential refugia during the Pleistocene ice ages. Our results highlighted that habitat heterogeneity and physical barriers presenting in a species range can predict genetic patterns. Copyright © 2014 Elsevier Inc. All rights reserved.

Nest survival of American Coots relative to grazing, burning, and water depths

USGS Publications Warehouse

Austin, Jane E.; Buhl, Deborah A.

2011-01-01

Water and emergent vegetation are key features influencing nest site selection and success for many marsh-nesting waterbirds. Wetland management practices such as grazing, burning, and water-level manipulations directly affect these features and can influence nest survival. We used model selection and before-after-control-impact approaches to evaluate the effects of water depth and four common land-management practices or treatments, i.e., summer grazing, fall grazing, fall burning, and idle (no active treatment) on nest survival of American coots (Fulica americana) nesting at Grays Lake, a large montane wetland in southeast Idaho. The best model included the variables year × treatment, and quadratic functions of date, water depth, and nest age; height of vegetation at the nest did not improve the best model. However, results from the before-after-control-impact analysis indicate that management practices affected nest success via vegetation and involved interactions of hydrology, residual vegetation, and habitat composition. Nest success in idled fields changed little between pre- and post-treatment periods, whereas nest success declined in fields that were grazed or burned, with the most dramatic declines the year following treatments. The importance of water depth may be amplified in this wetland system because of rapid water-level withdrawal during the nesting season. Water and land-use values for area ranchers, management for nesting waterbirds, and long-term wetland function are important considerations in management of water levels and vegetation.

Nesting ecology of Whimbrels in boreal Alaska

USGS Publications Warehouse

Harwood, Christopher M.; Gill, Robert E.; Powell, Abby

2016-01-01

Breeding ecology studies of boreal waders have been relatively scarce in North America. This paucity is due in part to boreal habitats being difficult to access, and boreal waders being widely dispersed and thus difficult to monitor. Between 2008 and 2014 we studied the nesting ecology of Whimbrels Numenius phaeopus hudsonicus in interior Alaska, a region characterized by an active wildfire regime. Our objectives were to (1) describe the nesting ecology of Whimbrels in tundra patches within the boreal forest, (2) assess the influence of habitat features at multiple scales on nest-site selection, and (3) characterize factors affecting nest survival. Whimbrels nested in the largest patches and exhibited a consistently compressed annual breeding schedule. We hypothesized that these Whimbrels would exhibit synchronous and clustered nesting, but observed synchronous nesting in only 2009 and 2011, and evidence of clustered nesting at just one study area in 2009, providing limited support for the hypothesis. Nests tended to be on hummocks and exhibited lateral concealment around the bowl, suggesting a trade-off between a greater view from the nest and concealment. However, our analysis failed to identify other important habitat features at scales from 1–400 m from the nest. Our best-supported nest survival model showed a strong difference between our two main study areas, but this difference remains largely unexplained. Given the increased frequency, severity, and extent of wildfires predicted under climate change scenarios, our study highlights the importance of monitoring the persistence of boreal tundra patches and the Whimbrels breeding therein.

Avian nest success in midwestern forests fragmented by agriculture

USGS Publications Warehouse

Knutson, M.G.; Niemi, G.J.; Newton, W.E.; Friberg, M.A.

2004-01-01

We studied how forest-bird nest success varied by landscape context from 1996 to 1998 in an agricultural region of southeastern Minnesota, southwestern Wisconsin, and northeastern Iowa. Nest success was 48% for all nests, 82% for cavity-nesting species, and 42% for cup-nesting species. Mayfield-adjusted nest success for five common species ranged from 23% for the American Redstart (Setophaga ruticilla) to 43% for the Eastern Wood-Pewee (Contopus virens). Nest success was lowest for open-cup nesters, species that reject Brown-headed Cowbird (Molothrus ater) eggs, species that nest near forest edges, and Neo-tropical migrants. The proportion of forest core area in a 5-km radius around the plot had a weakly negative relationship with daily survival rate of nests for all species pooled and for medium or high canopy nesters, species associated with interior and edge habitats, open-cup nesters, and nests located between 75 and 199 m from an edge. The proportion of forest core area was positively related to daily survival rate only for ground and low nesters. Our findings are in contrast to a number of studies from the eastern United States reporting strong positive associations between forest area and nesting success. Supported models of habitat associations changed with the spatial scale of analysis and included variables not often considered in studies of forest birds, including the proportion of water, shrubs, and grasslands in the landscape. Forest area may not be a strong indicator of nest success in landscapes where all the available forests are fragmented.

A new species of Alopoglossus lizard (Squamata, Gymnophthalmidae) from the tropical Andes, with a molecular phylogeny of the genus

PubMed Central

Torres-Carvajal, Omar; Lobos, Simón E.

2014-01-01

Abstract We describe a new species of Alopoglossus from the Pacific slopes of the Andes in northern Ecuador based on morphological and molecular evidence. The new species differs most significantly from all other congeners in having a double longitudinal row of widened gular scales, lanceolate dorsal scales in transverse rows, 29–32 dorsal scales in a transverse row at midbody, and 4 longitudinal rows of ventrals at midbody. It is most similar in morphology to A. festae, the only species of Alopoglossus currently recognized in western Ecuador. We analyze the phylogenetic relationships among species of Alopoglossus based on the mitochondrial gene ND4. Cis-Andean [east of the Andes] and Trans-Andean [west of the Andes] species are nested in two separate clades, suggesting that the uplift of these mountains had an important effect in the diversification of Alopoglossus. In addition, we present an updated key to the species of Alopoglossus. PMID:24899852

Variable depth distribution of Trichodesmium clades in the North Pacific Ocean.

PubMed

Rouco, Mónica; Haley, Sheean T; Alexander, Harriet; Wilson, Samuel T; Karl, David M; Dyhrman, Sonya T

2016-12-01

Populations of nitrogen-fixing cyanobacteria in the genus Trichodesmium are critical to ocean ecosystems, yet predicting patterns of Trichodesmium distribution and their role in ocean biogeochemistry is an ongoing challenge. This may, in part, be due to differences in the physiological ecology of Trichodesmium species, which are not typically considered independently in field studies. In this study, the abundance of the two dominant Trichodesmium clades (Clade I and Clade III) was investigated during a survey at Station ALOHA in the North Pacific Subtropical Gyre (NPSG) using a clade-specific qPCR approach. While Clade I dominated the Trichodesmium community, Clade III abundance was >50% in some NPSG samples, in contrast to the western North Atlantic where Clade III abundance was always <10%. Clade I populations were distributed down to depths >80 m, while Clade III populations were only observed in the mixed layer and found to be significantly correlated with depth and temperature. These data suggest active niche partitioning of Trichodesmium species from different clades, as has been observed in other cyanobacteria. Tracking the distribution and physiology of Trichodesmium spp. would contribute to better predictions of the physiological ecology of this biogeochemically important genus in the present and future ocean. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum

PubMed Central

Francis, Aleena; Dhaka, Namrata; Bakshi, Mohit; Jung, Ki-Hong; Sharma, Manoj K.; Sharma, Rita

2016-01-01

Sorghum is a highly efficient C4 crop with potential to mitigate challenges associated with food, feed and fuel. TCP proteins are of particular interest for crop improvement programs due to their well-demonstrated roles in crop domestication and shaping plant architecture thereby, affecting agronomic traits. We identified 20 TCP genes from Sorghum. Except SbTCP8, all are either intronless or contain introns in the untranslated regions. Comparative phylogenetic analysis of Arabidopsis, rice, Brachypodium and Sorghum TCP proteins revealed two distinct classes categorized into ten sub-clades. Sub-clade F is dicot-specific, whereas A2, G1 and I1 groups only contained genes from grasses. Sub-clade B was missing in Sorghum, whereas group A1 was missing in rice indicating species-specific divergence of TCP proteins. TCP proteins of Sorghum are enriched in disorder promoting residues with class I containing higher percent disorder than class II proteins. Seven pairs of paralogous TCP genes were identified from Sorghum, five of which seem to predate Rice-Sorghum divergence. All of them have diverged in their expression. Based on the expression and orthology analysis, five Sorghum genes have been shortlisted for further investigation for their roles in regulating plant morphology. Whereas, three genes have been identified as candidates for engineering abiotic stress tolerance. PMID:27917941

Comparative phylogenomic analysis provides insights into TCP gene functions in Sorghum.

PubMed

Francis, Aleena; Dhaka, Namrata; Bakshi, Mohit; Jung, Ki-Hong; Sharma, Manoj K; Sharma, Rita

2016-12-05

Sorghum is a highly efficient C4 crop with potential to mitigate challenges associated with food, feed and fuel. TCP proteins are of particular interest for crop improvement programs due to their well-demonstrated roles in crop domestication and shaping plant architecture thereby, affecting agronomic traits. We identified 20 TCP genes from Sorghum. Except SbTCP8, all are either intronless or contain introns in the untranslated regions. Comparative phylogenetic analysis of Arabidopsis, rice, Brachypodium and Sorghum TCP proteins revealed two distinct classes categorized into ten sub-clades. Sub-clade F is dicot-specific, whereas A2, G1 and I1 groups only contained genes from grasses. Sub-clade B was missing in Sorghum, whereas group A1 was missing in rice indicating species-specific divergence of TCP proteins. TCP proteins of Sorghum are enriched in disorder promoting residues with class I containing higher percent disorder than class II proteins. Seven pairs of paralogous TCP genes were identified from Sorghum, five of which seem to predate Rice-Sorghum divergence. All of them have diverged in their expression. Based on the expression and orthology analysis, five Sorghum genes have been shortlisted for further investigation for their roles in regulating plant morphology. Whereas, three genes have been identified as candidates for engineering abiotic stress tolerance.

Overexpressed Proteins in Hypervirulent Clade 8 and Clade 6 Strains of Escherichia coli O157:H7 Compared to E. coli O157:H7 EDL933 Clade 3 Strain.

PubMed

Amigo, Natalia; Zhang, Qi; Amadio, Ariel; Zhang, Qunjie; Silva, Wanderson M; Cui, Baiyuan; Chen, Zhongjian; Larzabal, Mariano; Bei, Jinlong; Cataldi, Angel

2016-01-01

Escherichia coli O157:H7 is responsible for severe diarrhea and hemolytic uremic syndrome (HUS), and predominantly affects children under 5 years. The major virulence traits are Shiga toxins, necessary to develop HUS and the Type III Secretion System (T3SS) through which bacteria translocate effector proteins directly into the host cell. By SNPs typing, E. coli O157:H7 was separated into nine different clades. Clade 8 and clade 6 strains were more frequently associated with severe disease and HUS. In this study, we aimed to identify differentially expressed proteins in two strains of E. coli O157:H7 (clade 8 and clade 6), obtained from cattle and compared them with the well characterized reference EDL933 strain (clade 3). Clade 8 and clade 6 strains show enhanced pathogenicity in a mouse model and virulence-related properties. Proteins were extracted and analyzed using the TMT-6plex labeling strategy associated with two dimensional liquid chromatography and mass spectrometry in tandem. We detected 2241 proteins in the cell extract and 1787 proteins in the culture supernatants. Attention was focused on the proteins related to virulence, overexpressed in clade 6 and 8 strains compared to EDL933 strain. The proteins relevant overexpressed in clade 8 strain were the curli protein CsgC, a transcriptional activator (PchE), phage proteins, Stx2, FlgM and FlgD, a dienelactone hydrolase, CheW and CheY, and the SPATE protease EspP. For clade 6 strain, a high overexpression of phage proteins was detected, mostly from Stx2 encoding phage, including Stx2, flagellin and the protease TagA, EDL933_p0016, dienelactone hydrolase, and Haemolysin A, amongst others with unknown function. Some of these proteins were analyzed by RT-qPCR to corroborate the proteomic data. Clade 6 and clade 8 strains showed enhanced transcription of 10 out of 12 genes compared to EDL933. These results may provide new insights in E. coli O157:H7 mechanisms of pathogenesis.

Characterization of Glycosylation Profiles of HIV-1 Transmitted/Founder Envelopes by Mass Spectrometry ▿ †

PubMed Central

Go, Eden P.; Hewawasam, Geetha; Liao, Hua-Xin; Chen, Haiyan; Ping, Li-Hua; Anderson, Jeffrey A.; Hua, David C.; Haynes, Barton F.; Desaire, Heather

2011-01-01

The analysis of HIV-1 envelope carbohydrates is critical to understanding their roles in HIV-1 transmission as well as in binding of envelope to HIV-1 antibodies. However, direct analysis of protein glycosylation by glycopeptide-based mass mapping approaches involves structural simplification of proteins with the use of a protease followed by an isolation and/or enrichment step before mass analysis. The successful completion of glycosylation analysis is still a major analytical challenge due to the complexity of samples, wide dynamic range of glycopeptide concentrations, and glycosylation heterogeneity. Here, we use a novel experimental workflow that includes an up-front complete or partial enzymatic deglycosylation step before trypsin digestion to characterize the glycosylation patterns and maximize the glycosylation coverage of two recombinant HIV-1 transmitted/founder envelope oligomers derived from clade B and C viruses isolated from acute infection and expressed in 293T cells. Our results show that both transmitted/founder Envs had similar degrees of glycosylation site occupancy as well as similar glycan profiles. Compared to 293T-derived recombinant Envs from viruses isolated from chronic HIV-1, transmitted/founder Envs displayed marked differences in their glycosylation site occupancies and in their amounts of complex glycans. Our analysis reveals that the glycosylation patterns of transmitted/founder Envs from two different clades (B and C) are more similar to each other than they are to the glycosylation patterns of chronic HIV-1 Envs derived from their own clades. PMID:21653661

Discriminating micropathogen lineages and their reticulate evolution through graph theory-based network analysis: the case of Trypanosoma cruzi, the agent of Chagas disease.

PubMed

Arnaud-Haond, Sophie; Moalic, Yann; Barnabé, Christian; Ayala, Francisco José; Tibayrenc, Michel

2014-01-01

Micropathogens (viruses, bacteria, fungi, parasitic protozoa) share a common trait, which is partial clonality, with wide variance in the respective influence of clonality and sexual recombination on the dynamics and evolution of taxa. The discrimination of distinct lineages and the reconstruction of their phylogenetic history are key information to infer their biomedical properties. However, the phylogenetic picture is often clouded by occasional events of recombination across divergent lineages, limiting the relevance of classical phylogenetic analysis and dichotomic trees. We have applied a network analysis based on graph theory to illustrate the relationships among genotypes of Trypanosoma cruzi, the parasitic protozoan responsible for Chagas disease, to identify major lineages and to unravel their past history of divergence and possible recombination events. At the scale of T. cruzi subspecific diversity, graph theory-based networks applied to 22 isoenzyme loci (262 distinct Multi-Locus-Enzyme-Electrophoresis -MLEE) and 19 microsatellite loci (66 Multi-Locus-Genotypes -MLG) fully confirms the high clustering of genotypes into major lineages or "near-clades". The release of the dichotomic constraint associated with phylogenetic reconstruction usually applied to Multilocus data allows identifying putative hybrids and their parental lineages. Reticulate topology suggests a slightly different history for some of the main "near-clades", and a possibly more complex origin for the putative hybrids than hitherto proposed. Finally the sub-network of the near-clade T. cruzi I (28 MLG) shows a clustering subdivision into three differentiated lesser near-clades ("Russian doll pattern"), which confirms the hypothesis recently proposed by other investigators. The present study broadens and clarifies the hypotheses previously obtained from classical markers on the same sets of data, which demonstrates the added value of this approach. This underlines the potential of graph theory-based network analysis for describing the nature and relationships of major pathogens, thereby opening stimulating prospects to unravel the organization, dynamics and history of major micropathogen lineages.

[Genetic structure of Hemibarbus labeo and Hemibarbus medius in South China based on mtDNA COI and ND5 genes].

PubMed

Lan, Zhao Jun; Lin, Long Feng; Zhao, Jun

2017-04-18

Both Hemibarbus labeo and H. medius (Cypriniformes: Cyprinidae: Gobioninae) are primary freshwater fishes and are widely distributed. As such, they provide an ideal model for phylogeographical studies. However, the similarity in morphological characters between these two species made the description of their distributions and the validation of species quite challenging. Here we employed variations in the DNA sequences of mitochondrial COI and ND5 genes (2151 bp) to solve this challenge and to study the population genetics structure of these two species. Among the 130 specimens belonging to 8 populations of H. labeo and 9 populations of H. medius from 17 drainage systems in southern China,196 variable sites (9.1% in the full sequences) falling into 50 haplotypes were identified. The haplotype diversity (h) and the nucleotide diversity (π) were 0.964 and 0.019, respectively, indicating a high level of genetic diversity and an evolutionary potential in both species. The result of neighbor-joining tree based on composite nucleotide sequences of the mtDNA COI and ND5 genes showed that the H. labeo and H. medius fell into two major clades (clade1and clade2): clade1was composed of some specimens of Oujiang River, all the specimens of Hanjiang River and Jiulongjiang River, whereas all remaining populations fell in clade2. The genetic distance between clade I and clade II was 0.036, while that between H. labeo and H. medius was 0.027. The haplotype network analyses indicated that the populations of Hanjiang River and Jiulongjiang River had relatively high genetic variation with the rest rivers. The po-pulations of Hainan Island migrated northward to Moyangjaing River. Haplotypes of the rivers of Hainan Island and Moyangjang River had relatively higher genetic variation with the Yangtze River than Pearl River. The populations of Xiangjiang River had no genetic variation with the populations of Guijiang River and Liujiang River. Analysis of molecular variance (AMOVA) indicated that the genetic variance mainly presented in individuals between geographical regions. The genetic variation of populations among regions was 71.2%, the genetic variation among populations within regions was 16.6%, and that within populations within the regions was 12.2%, indicating that most of the genetic variations resided in the populations among regions. The results of mismatch distribution and tests of neutrality suggested that in all populations, H. labeo, H. medius, clade1and clade2 were relatively stable.

Habitat segregation and cryptic adaptation of species of Periophthalmus (Gobioidei: Gobiidae).

PubMed

Polgar, G; Zaccara, S; Babbucci, M; Fonzi, F; Antognazza, C M; Ishak, N; Sulaiman, Z; Crosa, G

2017-05-01

A study was conducted on the habitat distribution of four sympatric species of Periophthalmus (the silver-lined mudskipper Periophthalmus argentilineatus, the slender mudskipper Periophthalmus gracilis, the kalolo mudskipper Periophthalmus kalolo and the Malacca mudskipper Periophthalmus malaccensis) from northern Sulawesi. Molecular phylogenetic reconstructions based on one mtDNA marker (16S) were used to validate the morphological taxa, identifying five molecular clades. Periophthalmus argentilineatus includes two molecular species, which are named Periophthalmus argentilineatus clades F and K. Multivariate direct gradient analysis show that these species form three distinct ecological guilds, with the two molecular species occurring in different guilds. Periophthalmus clade F is ecologically eurytypic; Periophthalmus clade K and P. kalolo are prevalent in ecosystems isolated by strong oceanic currents and at shorter distances from the sea; P. gracilis plus P. malaccensis are prevalent in ecosystems connected by shallow coastal waters, in vegetated habitats at larger distances from the sea. This indicates for the first time that mudskipper species exhibit a range of adaptations to semiterrestrialism not only within genera, but even within morphospecies, delineating a much more complex adaptive scenario than previously assumed. © 2017 The Fisheries Society of the British Isles.

Simultaneous analysis and design

NASA Technical Reports Server (NTRS)

Haftka, R. T.

1984-01-01

Optimization techniques are increasingly being used for performing nonlinear structural analysis. The development of element by element (EBE) preconditioned conjugate gradient (CG) techniques is expected to extend this trend to linear analysis. Under these circumstances the structural design problem can be viewed as a nested optimization problem. There are computational benefits to treating this nested problem as a large single optimization problem. The response variables (such as displacements) and the structural parameters are all treated as design variables in a unified formulation which performs simultaneously the design and analysis. Two examples are used for demonstration. A seventy-two bar truss is optimized subject to linear stress constraints and a wing box structure is optimized subject to nonlinear collapse constraints. Both examples show substantial computational savings with the unified approach as compared to the traditional nested approach.

Wide variation in virulence and genetic diversity of binucleate Rhizoctonia isolates associated with root rot of strawberry in Western Australia.

PubMed

Fang, Xiangling; Finnegan, Patrick M; Barbetti, Martin J

2013-01-01

Strawberry (Fragaria×ananassa) is one of the most important berry crops in the world. Root rot of strawberry caused by Rhizoctonia spp. is a serious threat to commercial strawberry production worldwide. However, there is no information on the genetic diversity and phylogenetic status of Rhizoctonia spp. associated with root rot of strawberry in Australia. To address this, a total of 96 Rhizoctonia spp. isolates recovered from diseased strawberry plants in Western Australia were characterized for their nuclear condition, virulence, genetic diversity and phylogenetic status. All the isolates were found to be binucleate Rhizoctonia (BNR). Sixty-five of the 96 BNR isolates were pathogenic on strawberry, but with wide variation in virulence, with 25 isolates having high virulence. Sequence analysis of the internal transcribed spacers of the ribosomal DNA separated the 65 pathogenic BNR isolates into six distinct clades. The sequence analysis also separated reference BNR isolates from strawberry or other crops across the world into clades that correspond to their respective anastomosis group (AG). Some of the pathogenic BNR isolates from this study were embedded in the clades for AG-A, AG-K and AG-I, while other isolates formed clades that were sister to the clades specific for AG-G, AG-B, AG-I and AG-C. There was no significant association between genetic diversity and virulence of these BNR isolates. This study demonstrates that pathogenic BNR isolates associated with root rot of strawberry in Western Australia have wide genetic diversity, and highlights new genetic groups not previously found to be associated with root rot of strawberry in the world (e.g., AG-B) or in Australia (e.g., AG-G). The wide variation in virulence and genetic diversity identified in this study will be of high value for strawberry breeding programs in selecting, developing and deploying new cultivars with resistance to these multi-genetic groups of BNR.

Phylogenetic relationships, diversification and expansion of chili peppers (Capsicum, Solanaceae)

PubMed Central

Carrizo García, Carolina; Barfuss, Michael H. J.; Sehr, Eva M.; Barboza, Gloria E.; Samuel, Rosabelle; Moscone, Eduardo A.; Ehrendorfer, Friedrich

2016-01-01

Background and Aims Capsicum (Solanaceae), native to the tropical and temperate Americas, comprises the well-known sweet and hot chili peppers and several wild species. So far, only partial taxonomic and phylogenetic analyses have been done for the genus. Here, the phylogenetic relationships between nearly all taxa of Capsicum were explored to test the monophyly of the genus and to obtain a better knowledge of species relationships, diversification and expansion. Methods Thirty-four of approximately 35 Capsicum species were sampled. Maximum parsimony and Bayesian inference analyses were performed using two plastid markers (matK and psbA-trnH) and one single-copy nuclear gene (waxy). The evolutionary changes of nine key features were reconstructed following the parsimony ancestral states method. Ancestral areas were reconstructed through a Bayesian Markov chain Monte Carlo analysis. Key Results Capsicum forms a monophyletic clade, with Lycianthes as a sister group, following both phylogenetic approaches. Eleven well-supported clades (four of them monotypic) can be recognized within Capsicum, although some interspecific relationships need further analysis. A few features are useful to characterize different clades (e.g. fruit anatomy, chromosome base number), whereas some others are highly homoplastic (e.g. seed colour). The origin of Capsicum is postulated in an area along the Andes of western to north-western South America. The expansion of the genus has followed a clockwise direction around the Amazon basin, towards central and south-eastern Brazil, then back to western South America, and finally northwards to Central America. Conclusions New insights are provided regarding interspecific relationships, character evolution, and geographical origin and expansion of Capsicum. A clearly distinct early-diverging clade can be distinguished, centred in western–north-western South America. Subsequent rapid speciation has led to the origin of the remaining clades. The diversification of Capsicum has culminated in the origin of the main cultivated species in several regions of South to Central America. PMID:27245634

Vertical structure of the phytoplankton community associated with a coastal plume in the Gulf of Mexico

USGS Publications Warehouse

Wawrik, B.; Paul, J.H.; Campbell, L.; Griffin, D.; Houchin, L.; Fuentes-Ortega, A.; Muller-Karger, F.

2003-01-01

Low salinity plumes of coastal origin are occasionally found far offshore, where they display a distinct color signature detectable by satellites. The impact of such plumes on carbon fixation and phytoplankton community structure in vertical profiles and on basin wide scales is poorly understood. On a research cruise in June 1999, ocean-color satellite-images (Sea-viewing Wide Field-of-view Sensor, SeaWiFS) were used in locating a Mississippi River plume in the eastern Gulf of Mexico. Profiles sampled within and outside of the plume were analyzed using flow cytometry, HPLC pigment analysis and primary production using 14C incorporation. Additionally, RubisCO large subunit (rbcL) gene expression was measured by hybridization of extracted RNA using 3 full-length RNA gene probes specific for individual phytoplankton clades. We also used a combination of RT-PCR/PCR and TA cloning in order to generate cDNA and DNA rbcL clone libraries from samples taken in the plume. Primary productivity was greatest in the low salinity surface layer of the plume. The plume was also associated with high Synechococcus counts and a strong peak in Form IA rbcL expression. Form IB rbcL (green algal) mRNA was abundant at the subsurface chlorophyll maximum (SCM), whereas Form ID rbcL (chromophytic) expression showed little vertical structure. Phylogenetic analysis of cDNA libraries demonstrated the presence of Form IA rbcL Synechococcus phylotypes in the plume. Below the plume, 2 spatially separated and genetically distinct rbcL clades of Prochlorococcus were observed. This indicated the presence of the high- and low-light adapted clades of Prochlorococcus. A large and very diverse clade of Prymnesiophytes was distributed throughout the water column, whereas a clade of closely related prasinophytes may have dominated at the SCM. These data indicate that the Mississippi river plume may dramatically alter the surface picoplankton composition of the Gulf of Mexico, with Synechococcus displacing Prochlorococcus in the surface waters.

Diversity and community composition of methanogenic archaea in the rumen of Scottish upland sheep assessed by different methods.

PubMed

Snelling, Timothy J; Genç, Buğra; McKain, Nest; Watson, Mick; Waters, Sinéad M; Creevey, Christopher J; Wallace, R John

2014-01-01

Ruminal archaeomes of two mature sheep grazing in the Scottish uplands were analysed by different sequencing and analysis methods in order to compare the apparent archaeal communities. All methods revealed that the majority of methanogens belonged to the Methanobacteriales order containing the Methanobrevibacter, Methanosphaera and Methanobacteria genera. Sanger sequenced 1.3 kb 16S rRNA gene amplicons identified the main species of Methanobrevibacter present to be a SGMT Clade member Mbb. millerae (≥ 91% of OTUs); Methanosphaera comprised the remainder of the OTUs. The primers did not amplify ruminal Thermoplasmatales-related 16S rRNA genes. Illumina sequenced V6-V8 16S rRNA gene amplicons identified similar Methanobrevibacter spp. and Methanosphaera clades and also identified the Thermoplasmatales-related order as 13% of total archaea. Unusually, both methods concluded that Mbb. ruminantium and relatives from the same clade (RO) were almost absent. Sequences mapping to rumen 16S rRNA and mcrA gene references were extracted from Illumina metagenome data. Mapping of the metagenome data to 16S rRNA gene references produced taxonomic identification to Order level including 2-3% Thermoplasmatales, but was unable to discriminate to species level. Mapping of the metagenome data to mcrA gene references resolved 69% to unclassified Methanobacteriales. Only 30% of sequences were assigned to species level clades: of the sequences assigned to Methanobrevibacter, most mapped to SGMT (16%) and RO (10%) clades. The Sanger 16S amplicon and Illumina metagenome mcrA analyses showed similar species richness (Chao1 Index 19-35), while Illumina metagenome and amplicon 16S rRNA analysis gave lower richness estimates (10-18). The values of the Shannon Index were low in all methods, indicating low richness and uneven species distribution. Thus, although much information may be extracted from the other methods, Illumina amplicon sequencing of the V6-V8 16S rRNA gene would be the method of choice for studying rumen archaeal communities.

Phylogenetic analysis of canine distemper virus in South America clade 1 reveals unique molecular signatures of the local epidemic.

PubMed

Fischer, Cristine D B; Gräf, Tiago; Ikuta, Nilo; Lehmann, Fernanda K M; Passos, Daniel T; Makiejczuk, Aline; Silveira, Marcos A T; Fonseca, André S K; Canal, Cláudio W; Lunge, Vagner R

2016-07-01

Canine distemper virus (CDV) is a highly contagious pathogen for domestic dogs and several wild carnivore species. In Brazil, natural infection of CDV in dogs is very high due to the large non-vaccinated dog population, a scenario that calls for new studies on the molecular epidemiology. This study investigates the phylodynamics and amino-acid signatures of CDV epidemic in South America by analyzing a large dataset compiled from publicly available sequences and also by collecting new samples from Brazil. A population of 175 dogs with canine distemper (CD) signs was sampled, from which 89 were positive for CDV, generating 42 new CDV sequences. Phylogenetic analysis of the new and publicly available sequences revealed that Brazilian sequences mainly clustered in South America 1 (SA1) clade, which has its origin estimated to the late 1980's. The reconstruction of the demographic history in SA1 clade showed an epidemic expanding until the recent years, doubling in size every nine years. SA1 clade epidemic distinguished from the world CDV epidemic by the emergence of the R580Q strain, a very rare and potentially detrimental substitution in the viral genome. The R580Q substitution was estimated to have happened in one single evolutionary step in the epidemic history in SA1 clade, emerging shortly after introduction to the continent. Moreover, a high prevalence (11.9%) of the Y549H mutation was observed among the domestic dogs sampled here. This finding was associated (p<0.05) with outcome-death and higher frequency in mixed-breed dogs, the later being an indicator of a continuous exchange of CDV strains circulating among wild carnivores and domestic dogs. The results reported here highlight the diversity of the worldwide CDV epidemic and reveal local features that can be valuable for combating the disease. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular phylogeny of the bivalve superfamily Galeommatoidea (Heterodonta, Veneroida) reveals dynamic evolution of symbiotic lifestyle and interphylum host switching

PubMed Central

2012-01-01

Background Galeommatoidea is a superfamily of bivalves that exhibits remarkably diverse lifestyles. Many members of this group live attached to the body surface or inside the burrows of other marine invertebrates, including crustaceans, holothurians, echinoids, cnidarians, sipunculans and echiurans. These symbiotic species exhibit high host specificity, commensal interactions with hosts, and extreme morphological and behavioral adaptations to symbiotic life. Host specialization to various animal groups has likely played an important role in the evolution and diversification of this bivalve group. However, the evolutionary pathway that led to their ecological diversity is not well understood, in part because of their reduced and/or highly modified morphologies that have confounded traditional taxonomy. This study elucidates the taxonomy of the Galeommatoidea and their evolutionary history of symbiotic lifestyle based on a molecular phylogenic analysis of 33 galeommatoidean and five putative galeommatoidean species belonging to 27 genera and three families using two nuclear ribosomal genes (18S and 28S ribosomal DNA) and a nuclear (histone H3) and mitochondrial (cytochrome oxidase subunit I) protein-coding genes. Results Molecular phylogeny recovered six well-supported major clades within Galeommatoidea. Symbiotic species were found in all major clades, whereas free-living species were grouped into two major clades. Species symbiotic with crustaceans, holothurians, sipunculans, and echiurans were each found in multiple major clades, suggesting that host specialization to these animal groups occurred repeatedly in Galeommatoidea. Conclusions Our results suggest that the evolutionary history of host association in Galeommatoidea has been remarkably dynamic, involving frequent host switches between different animal phyla. Such an unusual pattern of dynamic host switching is considered to have resulted from their commensalistic lifestyle, in which they maintain filter-feeding habits even in symbiotic habitats. The results of the molecular phylogenetic analysis did not correspond with the current taxonomic circumscription. Galeommatidae and Lasaeidae were polyphyletic, and Basterotia, which is traditionally assigned to Cyamioidea, formed a monophyletic clade within Galeommatoidea. PMID:22954375

Reconstructing the recent West Nile virus lineage 2 epidemic in Europe and Italy using discrete and continuous phylogeography

PubMed Central

Veo, Carla; Ebranati, Erika; Carta, Valentina; Rovida, Francesca; Percivalle, Elena; Moreno, Ana; Lelli, Davide; Calzolari, Mattia; Lavazza, Antonio; Chiapponi, Chiara; Baioni, Laura; Capelli, Gioia; Ravagnan, Silvia; Da Rold, Graziana; Lavezzo, Enrico; Palù, Giorgio; Baldanti, Fausto; Barzon, Luisa; Galli, Massimo

2017-01-01

West Nile virus lineage 2 (WNV-2) was mainly confined to sub-Saharan Africa until the early 2000s, when it was identified for the first time in Central Europe causing outbreaks of human and animal infection. The aim of this study was to reconstruct the origin and dispersion of WNV-2 in Central Europe and Italy on a phylodynamic and phylogeographical basis. To this aim, discrete and continuous space phylogeographical models were applied to a total of 33 newly characterised full-length viral genomes obtained from mosquitoes, birds and humans in Northern Italy in the years 2013–2015 aligned with 64 complete sequences isolated mainly in Europe. The European isolates segregated into two highly significant clades: a small one including three sequences and a large clade including the majority of isolates obtained in Central Europe since 2004. Discrete phylogeographical analysis showed that the most probable location of the root of the largest European clade was in Hungary a mean 12.78 years ago. The European clade bifurcated into two highly supported subclades: one including most of the Central/East European isolates and the other encompassing all of the isolates obtained in Greece. The continuous space phylogeographical analysis of the Italian clade showed that WNV-2 entered Italy in about 2008, probably by crossing the Adriatic sea and reaching a central area of the Po Valley. The epidemic then spread simultaneously eastward, to reach the region of the Po delta in 2013, and westward to the border area between Lombardy and Piedmont in 2014; later, the western strain changed direction southward, and reached the central area of the Po valley once again in 2015. Over a period of about seven years, the virus spread all over an area of northern Italy by following the Po river and its main tributaries. PMID:28678837

Evolution and Expansion of the Prokaryote-Like Lipoxygenase Family in the Brown Alga Saccharina japonica

PubMed Central

Teng, Linhong; Han, Wentao; Fan, Xiao; Xu, Dong; Zhang, Xiaowen; Dittami, Simon M.; Ye, Naihao

2017-01-01

Lipoxygenase (LOX) plays important roles in fatty acid oxidation and lipid mediator biosynthesis. In this study, we give first insights into brown algal LOX evolution. Whole genome searches revealed four, three, and eleven LOXs in Ectocarpus siliculosus, Cladosiphon okamuranus, and Saccharina japonica, respectively. In phylogenetic analyses, LOXs from brown algae form a robust clade with those from prokaryotes, suggesting an ancestral origin and slow evolution. Brown algal LOXs were divided into two clades, C1 and C2 in a phylogenetic tree. Compared to the two species of Ectocarpales, LOX gene expansion occurred in the kelp S. japonica through tandem duplication and segmental duplication. Selection pressure analysis showed that LOX genes in brown algae have undergone strong purifying selection, while the selective constraint in the C2 clade was more relaxed than that in the C1 clade. Furthermore, within each clade, LOXs of S. japonica evolved under more relaxed selection constraints than E. siliculosus and C. okamuranus. Structural modeling showed that unlike LOXs of plants and animals, which contain a β barrel in the N-terminal part of the protein, LOXs in brown algae fold into a single domain. Analysis of previously published transcriptomic data showed that LOXs in E. siliculosus are responsive to hyposaline, hypersaline, oxidative, and copper stresses. Moreover, clear divergence of expression patterns was observed among different life stages, as well as between duplicate gene pairs. In E. siliculosus, all four LOXs are male-biased in immature gametophytes, and mature gametophytes showed significantly higher LOX mRNA levels than immature gametophytes and sporophytes. In S. japonica, however, our RNA-Seq data showed that most LOXs are highly expressed in sporophytes. Even the most recently duplicated gene pairs showed divergent expression patterns, suggesting that functional divergence has likely occurred since LOX genes duplicated, which potentially contributes to the production of various oxylipins in brown algae. PMID:29234336

Inferring Foraging Areas of Nesting Loggerhead Turtles Using Satellite Telemetry and Stable Isotopes

PubMed Central

Ceriani, Simona A.; Roth, James D.; Evans, Daniel R.; Weishampel, John F.; Ehrhart, Llewellyn M.

2012-01-01

In recent years, the use of intrinsic markers such as stable isotopes to link breeding and foraging grounds of migratory species has increased. Nevertheless, several assumptions still must be tested to interpret isotopic patterns found in the marine realm. We used a combination of satellite telemetry and stable isotope analysis to (i) identify key foraging grounds used by female loggerheads nesting in Florida and (ii) examine the relationship between stable isotope ratios and post-nesting migration destinations. We collected tissue samples for stable isotope analysis from 14 females equipped with satellite tags and an additional 57 untracked nesting females. Telemetry identified three post-nesting migratory pathways and associated non-breeding foraging grounds: (1) a seasonal continental shelf–constrained migratory pattern along the northeast U.S. coastline, (2) a non-breeding residency in southern foraging areas and (3) a residency in the waters adjacent to the breeding area. Isotopic variability in both δ13C and δ15N among individuals allowed identification of three distinct foraging aggregations. We used discriminant function analysis to examine how well δ13C and δ15N predict female post-nesting migration destination. The discriminant analysis classified correctly the foraging ground used for all but one individual and was used to predict putative feeding areas of untracked turtles. We provide the first documentation that the continental shelf of the Mid- and South Atlantic Bights are prime foraging areas for a large number (61%) of adult female loggerheads from the largest loggerhead nesting population in the western hemisphere and the second largest in the world. Our findings offer insights for future management efforts and suggest that this technique can be used to infer foraging strategies and residence areas in lieu of more expensive satellite telemetry, enabling sample sizes that are more representative at the population level. PMID:23028943

Detection and Resolution of Cryptosporidium Species and Species Mixtures by Genus-Specific Nested PCR-Restriction Fragment Length Polymorphism Analysis, Direct Sequencing, and Cloning ▿

PubMed Central

Ruecker, Norma J.; Hoffman, Rebecca M.; Chalmers, Rachel M.; Neumann, Norman F.

2011-01-01

Molecular methods incorporating nested PCR-restriction fragment length polymorphism (RFLP) analysis of the 18S rRNA gene of Cryptosporidium species were validated to assess performance based on limit of detection (LoD) and for detecting and resolving mixtures of species and genotypes within a single sample. The 95% LoD was determined for seven species (Cryptosporidium hominis, C. parvum, C. felis, C. meleagridis, C. ubiquitum, C. muris, and C. andersoni) and ranged from 7 to 11 plasmid template copies with overlapping 95% confidence limits. The LoD values for genomic DNA from oocysts on microscope slides were 7 and 10 template copies for C. andersoni and C. parvum, respectively. The repetitive nested PCR-RFLP slide protocol had an LoD of 4 oocysts per slide. When templates of two species were mixed in equal ratios in the nested PCR-RFLP reaction mixture, there was no amplification bias toward one species over another. At high ratios of template mixtures (>1:10), there was a reduction or loss of detection of the less abundant species by RFLP analysis, most likely due to heteroduplex formation in the later cycles of the PCR. Replicate nested PCR was successful at resolving many mixtures of Cryptosporidium at template concentrations near or below the LoD. The cloning of nested PCR products resulted in 17% of the cloned sequences being recombinants of the two original templates. Limiting-dilution nested PCR followed by the sequencing of PCR products resulted in no sequence anomalies, suggesting that this method is an effective and accurate way to study the species diversity of Cryptosporidium, particularly for environmental water samples, in which mixtures of parasites are common. PMID:21498746

Comparison of nested-multiplex, Taqman & SYBR Green real-time PCR in diagnosis of amoebic liver abscess in a tertiary health care institute in India.

PubMed

Dinoop, K P; Parija, Subhash Chandra; Mandal, Jharna; Swaminathan, R P; Narayanan, P

2016-01-01

Amoebiasis is a common parasitic infection caused by Entamoeba histolytica and amoebic liver abscess (ALA) is the most common extraintestinal manifestation of amoebiasis. The aim of this study was to standardise real-time PCR assays (Taqman and SYBR Green) to detect E. histolytica from liver abscess pus and stool samples and compare its results with nested-multiplex PCR. Liver abscess pus specimens were subjected to DNA extraction. The extracted DNA samples were subjected to amplification by nested-multiplex PCR, Taqman (18S rRNA) and SYBR Green real-time PCR (16S-like rRNA assays to detect E. histolytica/E. dispar/E. moshkovskii). The amplification products were further confirmed by DNA sequence analysis. Receiver operator characteristic (ROC) curve analysis was done for nested-multiplex and SYBR Green real-time PCR and the area under the curve was calculated for evaluating the accuracy of the tests to dignose ALA. In all, 17, 19 and 25 liver abscess samples were positive for E. histolytica by nested-multiplex PCR, SYBR Green and Taqman real-time PCR assays, respectively. Significant differences in detection of E. histolytica were noted in the real-time PCR assays evaluated ( P<0.0001). The nested-multiplex PCR, SYBR Green real-time PCR and Taqman real-time PCR evaluated showed a positivity rate of 34, 38 and 50 per cent, respectively. Based on ROC curve analysis (considering Taqman real-time PCR as the gold standard), it was observed that SYBR Green real-time PCR was better than conventional nested-multiplex PCR for the diagnosis of ALA. Taqman real-time PCR targeting the 18S rRNA had the highest positivity rate evaluated in this study. Both nested multiplex and SYBR Green real-time PCR assays utilized were evaluated to give accurate results. Real-time PCR assays can be used as the gold standard in rapid and reliable diagnosis, and appropriate management of amoebiasis, replacing the conventional molecular methods.

Phylogeography of Schizopygopsis stoliczkai (Cyprinidae) in Northwest Tibetan Plateau area.

PubMed

Wanghe, Kunyuan; Tang, Yongtao; Tian, Fei; Feng, Chenguang; Zhang, Renyi; Li, Guogang; Liu, Sijia; Zhao, Kai

2017-11-01

Schizopygopsis stoliczkai (Cyprinidae, subfamily Schizothoracinae) is one of the major freshwater fishes endemic to the northwestern margin of the Tibetan Plateau. In the current study, we used mitochondrial DNA markers cytochrome b (Cyt b ) and 16S rRNA (16S), as well as the nuclear marker, the second intron of the nuclear beta-actin gene (Act2), to uncover the phylogeography of S. stoliczkai . In total, we obtained 74 haplotypes from 403 mitochondrial concatenated sequences. The mtDNA markers depict the phylogenetic structures of S. stoliczkai , which consist of clade North and clade South. The split time of the two clades is dated back to 4.27 Mya (95% HPD = 1.96-8.20 Mya). The estimated split time is earlier than the beginning of the ice age of Pleistocene (2.60 Mya), suggesting that the northwestern area of the Tibetan Plateau probably contain at least two glacial refugia for S. stoliczkai . SAMOVA supports the formation of four groups: (i) the Karakash River group; (ii) The Lake Pangong group; (iii) the Shiquan River group; (iv) the Southern Basin group. Clade North included Karakash River, Lake Pangong, and Shiquan River groups, while seven populations of clade South share the haplotypes. Genetic diversity, star-like network, BSP analysis, as well as negative neutrality tests indicate recent expansions events of S. stoliczkai . Conclusively, our results illustrate the phylogeography of S. stoliczkai , implying the Shiquan River is presumably the main refuge for S. stoliczkai .

Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach

PubMed Central

Choi, Young-Joon; Klosterman, Steven J.; Kummer, Volker; Voglmayr, Hermann; Shin, Hyeon-Dong; Thines, Marco

2017-01-01

Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The family Peronosporaceae (Straminipila; Oomycota) consists of obligate biotrophic pathogens that cause downy mildew disease on angiosperms, including a large number of cultivated plants. In the largest downy mildew genus Peronospora, a phylogenetically complex clade includes the economically important downy mildew pathogens of spinach and beet, as well as the type species of the genus Peronospora. To resolve this complex clade at the species level and to infer evolutionary relationships among them, we used multi-locus phylogenetic analysis and species tree estimation. Both approaches discriminated all nine currently accepted species and revealed four previously unrecognized lineages, which are specific to a host genus or species. This is in line with a narrow species concept, i.e. that a downy mildew species is associated with only a particular host plant genus or species. Instead of applying the dubious name Peronospora farinosa, which has been proposed for formal rejection, our results provide strong evidence that Peronospora schachtii is an independent species from lineages on Atriplex and apparently occurs exclusively on Beta vulgaris. The members of the clade investigated, the Peronospora rumicis clade, associate with three different host plant families, Amaranthaceae, Caryophyllaceae, and Polygonaceae, suggesting that they may have speciated following at least two recent inter-family host shifts, rather than contemporary cospeciation with the host plants. PMID:25772799