Bioinformatic as a tool to highlight and characterize extragenomic sequences within Fusarium verticillioides strains isolated from Italian Zea mays kernels

USDA-ARS?s Scientific Manuscript database

Fusarium Link is a genus including ubiquitous plant-pathogenic fungi that may cause severe crop losses. The Fusarium genus is divided in species complexes; the species are grouped by physiological, biological, ecological and genetic similarity. The Fusarium fujikuroi species complex (FFSC) is one of...

An evaluation of the species status of Bactrocera invadens and the Systematics of the Bactrocera dorsalis (Diptera: Tephritidae) complex

USDA-ARS?s Scientific Manuscript database

The genus Bactrocera (Tephritidae) contains over 500 species, including many severe pests of fruits and vegetables. While native to tropical and sub-tropical areas of Africa, India, Southeast Asia and Australasia, a number of the pest species, largely members of the Bactrocera dorsalis complex, have...

Self-organized instability in complex ecosystems.

PubMed

Solé, Ricard V; Alonso, David; McKane, Alan

2002-05-29

Why are some ecosystems so rich, yet contain so many rare species? High species diversity, together with rarity, is a general trend in neotropical forests and coral reefs. However, the origin of such diversity and the consequences of food web complexity in both species abundances and temporal fluctuations are not well understood. Several regularities are observed in complex, multispecies ecosystems that suggest that these ecologies might be organized close to points of instability. We explore, in greater depth, a recent stochastic model of population dynamics that is shown to reproduce: (i) the scaling law linking species number and connectivity; (ii) the observed distributions of species abundance reported from field studies (showing long tails and thus a predominance of rare species); (iii) the complex fluctuations displayed by natural communities (including chaotic dynamics); and (iv) the species-area relations displayed by rainforest plots. It is conjectured that the conflict between the natural tendency towards higher diversity due to immigration, and the ecosystem level constraints derived from an increasing number of links, leaves the system poised at a critical boundary separating stable from unstable communities, where large fluctuations are expected to occur. We suggest that the patterns displayed by species-rich communities, including rarity, would result from such a spontaneous tendency towards instability.

Description of evandromyia spelunca, a new phlebotomine species of the cortelezzii complex, from a cave in Minas Gerais State, Brazil (Diptera: Psychodidae: Phlebotominae).

PubMed

Carvalho, Gustavo M L; Brazil, Reginaldo P; Sanguinette, Cristiani C; Filho, José D Andrade

2011-08-09

The cave fauna of the Brazil is poorly documented, and among the insects those live or frequent caves and their adjacent environments phlebotomine sand flies call for special attention because several species are vectors of pathogens among vertebrates hosts. A new species of sand fly from Minas Gerais is described based in females and males collected in a cave of the municipality of Lassance. The morphological characters of the new species permit to include in the Evandromyia genus, cortelezzii complex. This complex consists of three species: Evandromyia corumbaensis (Galati, Nunes, Oshiro & Rego, 1989), Evandromyia cortelezzii (Brethes, 1923) and Evandromyia sallesi (Galvao & Coutinho, 1940). The new species can be separate from the others of the cortelezzii complex through morphological characters of the male terminalia and female spermathecae.

Epiverta Dieke (Coleoptera: Coccinellidae: Epilachnini): A Complex of Species, Not a Monotypic Genus

PubMed Central

Huo, Lizhi; Szawaryn, Karol; Wang, Xingmin

2017-01-01

Rich sampling and modern research techniques, including SEM, revealed that rarely collected epilachnine species Epiverta chelonia is a complex of four closely related species: E. chelonia (Mader, 1933), E. albopilosa, E. angusta, and E. supinata spp. nov. All Epiverta species are described and illustrated, a key to the species and a distribution map are provided. Lectotype of Solanophila cheloniaMader, 1933 is designated and its type locality delimited to Yunnan Province, Deqin County (China). PMID:28931156

North American velvet ants form one of the world's largest known Müllerian mimicry complexes.

PubMed

Wilson, Joseph S; Jahner, Joshua P; Forister, Matthew L; Sheehan, Erica S; Williams, Kevin A; Pitts, James P

2015-08-17

Color mimicry is often celebrated as one of the most straightforward examples of evolution by natural selection, as striking morphological similarity between species evolves in response to a shared predation pressure. Recently, a large North American mimetic complex was described that included 65 species of Dasymutilla velvet ants (Hymenoptera: Mutillidae). Beyond those 65 species, little is known about how many species participate in this unique Müllerian complex, though several other arthropods are thought to be involved as Müllerian mimics (spider wasps) and Batesian mimics (beetles, antlions, and spiders; see references in). Müllerian mimicry is similarity in appearance or phenotype among harmful species, while Batesian mimicry is similarity in which not all species are harmful. Here, we investigate the extent of the velvet ant mimicry complex beyond Dasymutilla by examining distributional and color pattern similarities in all of the 21 North American diurnal velvet ant genera, including 302 of the 361 named species (nearly 84%), as well as 16 polymorphic color forms and an additional 33 undescribed species. Of the 351 species and color forms that were analyzed (including undescribed species), 336 exhibit some morphological similarities and we hypothesize that they form eight distinct mimicry rings (Figure 1A; Supplemental Information). Two of these eight mimicry rings, red-headed Timulla and black-headed Timulla, were not documented in earlier assessments of mimicry in velvet ants, and are newly described here. These findings identify one of the largest known Müllerian mimicry systems worldwide and provide a novel system to test hypotheses about aposematism and mimicry, especially those regarding the evolution of imperfect mimicry. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

Biological inventory of anchialine pools in the Pu'uhonua o Hōnaunau National Historical Park and Pu'ukoholā Heiau National Historical Site, Hawaii Island

USGS Publications Warehouse

Tango, Lori K.; Foote, David; Magnacca, Karl N.; Foltz, Sarah J.; Cutler, Kerry

2012-01-01

Inventories for major groups of invertebrates were completed at anchialine pool complexes in Pu‘uhonua o Hōnaunau National Historical Park (PUHO) and Pu‘ukoholā Heiau National Historic Site (PUHE) on the island of Hawai‘i. Nine pools within two pool complexes were surveyed at PUHO, along with one extensive pool at the terminus of Makeāhua Gulch at PUHE. At both parks, inventories documented previously unreported diversity, with pool complexes at PUHO exhibiting greater species richness for most taxa than the pool at PUHE. Inventories at PUHO recorded five species of molluscs, four species of crustaceans (including the candidate endangered shrimp Metabetaeus lohena), two species of Orthoptera, four species of Odonata (including the candidate endangered damselfly Megalagrion xanthomelas), fourteen species of Diptera, nine taxa of plankton, and thirteen species of ants; inventories at the PUHE pool produced only one species of mollusc, two species of crustacean, at least one species of Orthoptera, four species of Odonata, thirty species of Diptera, five taxa of plankton, and four species of ants. Further survey work may be necessary to document the full diversity of pool fauna, especially in species-rich groups like the Diptera. Inventory data will be used to generate a network wide database of species presence and distribution, and will aid in developing management plans for anchialine pool resources.

[Reticulate evolution of parthenogenetic species of the Lacertidae rock lizards: inheritance of CLsat tandem repeats and anonymous RAPD markers].

PubMed

Chobanu, D; Rudykh, I A; Riabinina, N L; Grechko, V V; Kramerov, D A; Darevskiĭ, I S

2002-01-01

The genetic relatedness of several bisexual and of four unisexual "Lacerta saxicola complex" lizards was studied, using monomer sequences of the complex-specific CLsat tandem repeats and anonymous RAPD markers. Genomes of parthenospecies were shown to include different satellite monomers. The structure of each such monomer is specific for a certain pair of bisexual species. This fact might be interpreted in favor of co-dominant inheritance of these markers in bisexual species hybridogenesis. This idea is supported by the results obtained with RAPD markers; i.e., unisexual species genomes include only the loci characteristic of certain bisexual species. At the same time, in neither case parthenospecies possess specific, autoapomorphic loci that were not present in this or that bisexual species.

Existence of species complex largely reduced barcoding success for invasive species of Tephritidae: a case study in Bactrocera spp.

PubMed

Jiang, F; Jin, Q; Liang, L; Zhang, A B; Li, Z H

2014-11-01

Fruit flies in the family Tephritidae are the economically important pests that have many species complexes. DNA barcoding has gradually been verified as an effective tool for identifying species in a wide range of taxonomic groups, and there are several publications on rapid and accurate identification of fruit flies based on this technique; however, comprehensive analyses of large and new taxa for the effectiveness of DNA barcoding for fruit flies identification have been rare. In this study, we evaluated the COI barcode sequences for the diagnosis of fruit flies using 1426 sequences for 73 species of Bactrocera distributed worldwide. Tree-based [neighbour-joining (NJ)]; distance-based, such as Best Match (BM), Best Close Match (BCM) and Minimum Distance (MD); and character-based methods were used to evaluate the barcoding success rates obtained with maintaining the species complex in the data set, treating a species complex as a single taxon unit, and removing the species complex. Our results indicate that the average divergence between species was 14.04% (0.00-25.16%), whereas within a species this was 0.81% (0.00-9.71%); the existence of species complexes largely reduced the barcoding success for Tephritidae, for example relatively low success rates (74.4% based on BM and BCM and 84.8% based on MD) were obtained when the sequences from species complexes were included in the analysis, whereas significantly higher success rates were achieved if the species complexes were treated as a single taxon or removed from the data set - BM (98.9%), BCM (98.5%) and MD (97.5%), or BM (98.1%), BCM (97.4%) and MD (98.2%). © 2014 John Wiley & Sons Ltd.

Recurrent evolution of host and vector association in bacteria of the Borrelia burgdorferi sensu lato species complex.

PubMed

Becker, Noémie S; Margos, Gabriele; Blum, Helmut; Krebs, Stefan; Graf, Alexander; Lane, Robert S; Castillo-Ramírez, Santiago; Sing, Andreas; Fingerle, Volker

2016-09-15

The Borrelia burgdorferi sensu lato (s.l.) species complex consists of tick-transmitted bacteria and currently comprises approximately 20 named and proposed genospecies some of which are known to cause Lyme Borreliosis. Species have been defined via genetic distances and ecological niches they occupy. Understanding the evolutionary relationship of species of the complex is fundamental to explaining patterns of speciation. This in turn forms a crucial basis to frame testable hypotheses concerning the underlying processes including host and vector adaptations. Illumina Technology was used to obtain genome-wide sequence data for 93 strains of 14 named genospecies of the B. burgdorferi species complex and genomic data already published for 18 additional strain (including one new species) was added. Phylogenetic reconstruction based on 114 orthologous single copy genes shows that the genospecies represent clearly distinguishable taxa with recent and still ongoing speciation events apparent in Europe and Asia. The position of Borrelia species in the phylogeny is consistent with host associations constituting a major driver for speciation. Interestingly, the data also demonstrate that vector associations are an additional driver for diversification in this tick-borne species complex. This is particularly obvious in B. bavariensis, a rodent adapted species that has diverged from the bird-associated B. garinii most likely in Asia. It now consists of two populations one of which most probably invaded Europe following adaptation to a new vector (Ixodes ricinus) and currently expands its distribution range. The results imply that genotypes/species with novel properties regarding host or vector associations have evolved recurrently during the history of the species complex and may emerge at any time. We suggest that the finding of vector associations as a driver for diversification may be a general pattern for tick-borne pathogens. The core genome analysis presented here provides an important source for investigations of the underlying mechanisms of speciation in tick-borne pathogens.

Description of evandromyia spelunca, a new phlebotomine species of the cortelezzii complex, from a cave in Minas Gerais State, Brazil (Diptera: Psychodidae: Phlebotominae)

PubMed Central

2011-01-01

Background The cave fauna of the Brazil is poorly documented, and among the insects those live or frequent caves and their adjacent environments phlebotomine sand flies call for special attention because several species are vectors of pathogens among vertebrates hosts. A new species of sand fly from Minas Gerais is described based in females and males collected in a cave of the municipality of Lassance. Results The morphological characters of the new species permit to include in the Evandromyia genus, cortelezzii complex. This complex consists of three species: Evandromyia corumbaensis (Galati, Nunes, Oshiro & Rego, 1989), Evandromyia cortelezzii (Brethes, 1923) and Evandromyia sallesi (Galvao & Coutinho, 1940). Conclusions The new species can be separate from the others of the cortelezzii complex through morphological characters of the male terminalia and female spermathecae. PMID:21827682

The current status of the Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae) species complex

PubMed Central

Souza, Nataly A; Brazil, Reginaldo P; Araki, Alejandra S

2017-01-01

Lutzomyia longipalpis s.l. is a complex of sibling species and is the principal vector of American visceral leishmaniasis. The present review summarises the diversity of efforts that have been undertaken to elucidate the number of unnamed species in this species complex and the phylogenetic relationships among them. A wide variety of evidence, including chemical, behavioral and molecular traits, suggests very recent speciation events and complex population structure in this group. Although significant advances have been achieved to date, differential vector capacity and the correlation between structure of parasite and vector populations have yet to be elucidated. Furthermore, increased knowledge about recent epidemiological changes, such as urbanisation, is essential for pursuing effective strategies for sandfly control in the New World. PMID:28225906

The current status of the Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae) species complex.

PubMed

Souza, Nataly A; Brazil, Reginaldo P; Araki, Alejandra S

2017-03-01

Lutzomyia longipalpis s.l. is a complex of sibling species and is the principal vector of American visceral leishmaniasis. The present review summarises the diversity of efforts that have been undertaken to elucidate the number of unnamed species in this species complex and the phylogenetic relationships among them. A wide variety of evidence, including chemical, behavioral and molecular traits, suggests very recent speciation events and complex population structure in this group. Although significant advances have been achieved to date, differential vector capacity and the correlation between structure of parasite and vector populations have yet to be elucidated. Furthermore, increased knowledge about recent epidemiological changes, such as urbanisation, is essential for pursuing effective strategies for sandfly control in the New World.

Stress Corrosion Cracking Control Plans. 3. Copper Alloys

DTIC Science & Technology

1975-06-01

convenience intended to include amines and all other species which can react with copper to produce the cupric -ammonium complex ion or perhap...capability of forming complexes even resembling the cupric -ammonium complex should be considered as potentially causative of SCC as ammonia unless...nitrate, acetate, tartrate , or citrate which also contain copper ions. There is some evidence that oxides of nitrogen (generating ammoniacal species

A revision of the Schinia Volupia (Fitch) species complex Lepidoptera: Noctuidae: Heliothinae)

USDA-ARS?s Scientific Manuscript database

DNA barcode analysis of cytochrome oxidase I (COI) could not differentiate between the species of the Schinia volupia (Fitch) complex including, S. volupia, S. masoni Smith, S. fulleri (McElvare), S. sanrafaeli (Opler), S. miniana (Grote), and S. biforma Smith. Genitalic characters could only differ...

76 FR 14884 - Atlantic Highly Migratory Species; Modification of the Retention of Incidentally-Caught Highly...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-18

... smoothhound shark complex (which includes smooth dogfish and Florida smoothhound (genus Mustelus) in all... address regulatory discards of incidentally-caught species in the smoothhound shark complex by establishing a retention limit for smoothhound sharks in all Atlantic trawl fisheries. The proposed actions are...

Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach.

PubMed

Choi, Young-Joon; Klosterman, Steven J; Kummer, Volker; Voglmayr, Hermann; Shin, Hyeon-Dong; Thines, Marco

2015-05-01

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. Copyright © 2015 Elsevier Inc. All rights reserved.

Species delimitation in Trametes: a comparison of ITS, RPB1, RPB2 and TEF1 gene phylogenies.

PubMed

Carlson, Alexis; Justo, Alfredo; Hibbett, David S

2014-01-01

Trametes is a cosmopolitan genus of white rot polypores, including the "turkey tail" fungus, T. versicolor. Although Trametes is one of the most familiar genera of polypores, its species-level taxonomy is unsettled. The ITS region is the most commonly used molecular marker for species delimitation in fungi, but it has been shown to have a low molecular variation in Trametes resulting in poorly resolved phylogenies and unclear species boundaries, especially in the T. versicolor species complex (T. versicolor sensu stricto, T. ochracea, T. pubescens, T. ectypa). Here we evaluate the performance of three protein-coding genes (TEF1, RPB1, RPB2) for species delimitation and phylogenetic reconstruction in Trametes. We obtained 59 TEF1, 34 RPB1 and 55 RPB2 sequences from 69 individuals, focusing on the T. versicolor complex and performed phylogenetic analyses with maximum likelihood and parsimony methods. All three protein-coding genes outperformed ITS for separating species in the T. versicolor complex. The multigene phylogenetic analysis shows the highest amount of resolution and supported nodes separating T. ectypa, T. ochracea, T. pubescens and T. versicolor with strong support. In addition three slineages are resolved in the species complex of T. elegans. The T. elegans complex includes three species: T. elegans (based on material from Puerto Rico, Belize, the Philippines), T. aesculi (from North America) and T. repanda (from Papua New Guinea, the Philippines, Venezuela). The utility of gene markers varies, with TEF1 having the highest PCR and sequencing success rate and RPB1 offering the best backbone resolution for the genus. © 2014 by The Mycological Society of America.

An integrative approach to unravel the Ceratitis FAR (Diptera, Tephritidae) cryptic species complex: a review

PubMed Central

De Meyer, Marc; Delatte, Hélène; Ekesi, Sunday; Jordaens, Kurt; Kalinová, Blanka; Manrakhan, Aruna; Mwatawala, Maulid; Steck, Gary; Van Cann, Joannes; Vaníčková, Lucie; Břízová, Radka; Virgilio, Massimiliano

2015-01-01

Abstract This paper reviews all information gathered from different disciplines and studies to resolve the species status within the Ceratitis FAR (Ceratitis fasciventris, Ceratitis anonae, Ceratitis rosa) complex, a group of polyphagous fruit fly pest species (Diptera, Tephritidae) from Africa. It includes information on larval and adult morphology, wing morphometrics, cuticular hydrocarbons, pheromones, microsatellites, developmental physiology and geographic distribution. The general consensus is that the FAR complex comprises Ceratitis anonae, two species within Ceratitis rosa (so-called R1 and R2) and two putatitve species under Ceratitis fasciventris. The information regarding the latter is, however, too limited to draw final conclusions on specific status. Evidence for this recognition is discussed with reference to publications providing further details. PMID:26798270

Single-Site Zeolite-Anchored Organoiridium Carbonyl Complexes: Characterization of Structure and Reactivity by Spectroscopy and Computational Chemistry

DOE PAGES

Martinez-Macias, Claudia; Chen, Mingyang; Dixon, David A.; ...

2015-07-03

We formed a family of HY zeolite-supported cationic organoiridium carbonyl complexes by reaction of Ir(CO) 2(acac) (acac=acetylacetonate) to form supported Ir(CO) 2 complexes, which were treated at 298K and 1atm with flowing gas-phase reactants, including C 2H 4, H 2, (CO)-C-12, (CO)-C-13, and D 2O. Mass spectrometry was used to identify effluent gases, and infrared and X-ray absorption spectroscopies were used to characterize the supported species, with the results bolstered by DFT calculations. The support is crystalline and presents a nearly uniform array of bonding sites for the iridium species, so these were characterized by a high degree of uniformity,more » which allowed a precise determination of the species involved in the replacement, for example, of one CO ligand of each Ir(CO) 2 complex with ethylene. The supported species include the following: Ir(CO) 2, Ir(CO)(C 2H 4) 2, Ir(CO)(C 2H 4), Ir(CO)(C 2H 5), and (tentatively) Ir(CO)(H). The data determine a reaction network involving all of these species.« less

Characterization of Mediator Complex and its Associated Proteins from Rice.

PubMed

Samanta, Subhasis; Thakur, Jitendra Kumar

2017-01-01

The Mediator complex is a multi-protein complex that acts as a molecular bridge conveying transcriptional messages from the cis element-bound transcription factor to the RNA Polymerase II machinery. It is found in all eukaryotes including members of the plant kingdom. Increasing number of reports from plants regarding different Mediator subunits involved in a multitude of processes spanning from plant development to environmental interactions have firmly established it as a central hub of plant regulatory networks. Routine isolation of Mediator complex in a particular species is a necessity because of many reasons. First, composition of the Mediator complex varies from species to species. Second, the composition of the Mediator complex in a particular species is not static under all developmental and environmental conditions. Besides this, at times, Mediator complex is used in in vitro transcription systems. Rice, a staple food crop of the world, is used as a model monocot crop. Realizing the need of a reliable protocol for the isolation of Mediator complex from plants, we describe here the isolation of Mediator complex from rice.

A revision of Passiflora L. subgenus Decaloba (DC.) Rchb. supersection Cieca (Medik.) J. M. MacDougal & Feuillet (Passifloraceae)

PubMed Central

Porter-Utley, Kristen

2014-01-01

Abstract Passiflora subgenus Decaloba supersection Cieca is a monophyletic group of herbaceous to woody climbers found in subtropical and tropical regions of the world. The 19 species recognized here are primarily distributed in the southern United States, Mexico, Central America, South America, and the Caribbean. Two species, Passiflora suberosa and Passiflora pallida, are also naturalized in various regions of the Old World. The species of the supersection are recognized by their small, apetalous, usually greenish flowers with the filaments of the corona mostly in two series. The plants commonly lack c-glycosylflavones but possess flavonol 3-O-glycosides. The supersection contains two problematic species complexes, Passiflora suberosa and Passiflora coriacea. Phylogenetic relationships within supersection Cieca are investigated by means of phenetic and cladistic analyses of morphological and molecular (ITS 1 & 2) characters. The morphological and molecular data sets were analyzed separately because of incongruity due to taxon sampling and the complicated evolutionary history of entities within the Passiflora suberosa complex. All analyses confirm the monophyly of the supersection. They also show that the Passiflora suberosa complex is a non-monophyletic group of cryptic species, and inter-taxic hybridization and polyploidy have contributed to the confusing and complex pattern of variation evident within the group. Four taxa that were formerly included in this complex are recognized: Passiflora pallida, Passiflora suberosa subsp. suberosa, Passiflora suberosa subsp. litoralis, and Passiflora tridactylites. On the basis of molecular and morphological data, three species from the Passiflora coriacea complex are recognized: Passiflora coriacea, Passiflora sexocellata, and Passiflora megacoriacea. A key, detailed descriptions, distribution maps, and illustrations are included in the revision. Pollination, dispersal, and herbivory of the group are reviewed. The distribution and ecology of the species within the supersection are also discussed. PMID:25408618

Evaluating mating compatibility within fruit fly cryptic species complexes and the potential role of sex pheromones in pre-mating isolation

PubMed Central

Juárez, M. Laura; Devescovi, Francisco; Břízová, Radka; Bachmann, Guillermo; Segura, Diego F.; Kalinová, Blanka; Fernández, Patricia; Ruiz, M. Josefina; Yang, Jianquan; Teal, Peter E.A.; Cáceres, Carlos; Vreysen, Marc J.B.; Hendrichs, Jorge; Vera, M. Teresa

2015-01-01

Abstract The study of sexual behavior and the identification of the signals involved in mate recognition between con-specifics are key components that can shed some light, as part of an integrative taxonomic approach, in delimitating species within species complexes. In the Tephritidae family several species complexes have received particular attention as they include important agricultural pests such as the Ceratitis fasciventris (Bezzi), Ceratitis anonae (Graham) and Ceratitis rosa Karsch (FAR) complex, the Bactrocera dorsalis (Hendel) complex and the Anastrepha fraterculus (Wiedemann) complex. Here the value and usefulness of a methodology that uses walk-in field cages with host trees to assess, under semi-natural conditions, mating compatibility within these complexes is reviewed, and the same methodology to study the role of chemical communication in pre-mating isolation among Anastrepha fraterculus populations is used. Results showed that under the same experimental conditions it was possible to distinguish an entire range of different outcomes: from full mating compatibility among some populations to complete assortative mating among others. The effectiveness of the methodology in contributing to defining species limits was shown in two species complexes: Anastrepha fraterculus and Bactrocera dorsalis, and in the case of the latter the synonymization of several established species was published. We conclude that walk-in field cages constitute a powerful tool to measure mating compatibility, which is also useful to determine the role of chemical signals in species recognition. Overall, this experimental approach provides a good source of information about reproductive boundaries to delimit species. However, it needs to be applied as part of an integrative taxonomic approach that simultaneously assesses cytogenetic, molecular, physiological and morphological traits in order to reach more robust species delimitations. PMID:26798257

Diversity and phylogeography of Northeast Asian brown frogs allied to Rana dybowskii (Anura, Ranidae).

PubMed

Yang, Bao-Tian; Zhou, Yu; Min, Mi-Sook; Matsui, Masafumi; Dong, Bing-Jun; Li, Pi-Peng; Fong, Jonathan J

2017-07-01

We investigated the species diversity and phylogeography of the Northeast Asian brown frogs allied to Rana dybowskii (the R. dybowskii species complex: R. dybowskii, R. pirica, and R. uenoi) using four mitochondrial and three nuclear loci. Phylogenetic analyses confirmed the existence of three distinct species in this complex; using extensive molecular data, we confirm the validity of Rana uenoi recognized as a distinct species, and infer R. dybowskii and R. pirica to be sister species. Also, we included populations from previously unsampled regions in Northeast China, and identified them to be R. dybowskii. While many species in Northeast Asia diverged due to Pleistocene glaciation, divergence-dating analyses inferred older, Miocene speciation in the R. dybowskii species complex. Ancestral area reconstruction identified the orogenic movement of the Changbai Mountain Range and the opening of the Sea of Japan/East Sea being major events influencing allopatric speciation. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Flat and complex temperate reefs provide similar support for fish: Evidence for a unimodal species-habitat relationship.

PubMed

Paxton, Avery B; Pickering, Emily A; Adler, Alyssa M; Taylor, J Christopher; Peterson, Charles H

2017-01-01

Structural complexity, a form of habitat heterogeneity, influences the structure and function of ecological communities, generally supporting increased species density, richness, and diversity. Recent research, however, suggests the most complex habitats may not harbor the highest density of individuals and number of species, especially in areas with elevated human influence. Understanding nuances in relationships between habitat heterogeneity and ecological communities is warranted to guide habitat-focused conservation and management efforts. We conducted fish and structural habitat surveys of thirty warm-temperate reefs on the southeastern US continental shelf to quantify how structural complexity influences fish communities. We found that intermediate complexity maximizes fish abundance on natural and artificial reefs, as well as species richness on natural reefs, challenging the current paradigm that abundance and other fish community metrics increase with increasing complexity. Naturally occurring rocky reefs of flat and complex morphologies supported equivalent abundance, biomass, species richness, and community composition of fishes. For flat and complex morphologies of rocky reefs to receive equal consideration as essential fish habitat (EFH), special attention should be given to detecting pavement type rocky reefs because their ephemeral nature makes them difficult to detect with typical seafloor mapping methods. Artificial reefs of intermediate complexity also maximized fish abundance, but human-made structures composed of low-lying concrete and metal ships differed in community types, with less complex, concrete structures supporting lower numbers of fishes classified largely as demersal species and metal ships protruding into the water column harboring higher numbers of fishes, including more pelagic species. Results of this study are essential to the process of evaluating habitat function provided by different types and shapes of reefs on the seafloor so that all EFH across a wide range of habitat complexity may be accurately identified and properly managed.

The taxonomy of Psilocybe fagicola-complex.

PubMed

Guzmán, Gastón; Jacobs, James Q; Ramírez-Guillén, Florencia; Murrieta, Dulce; Gándara, Etelvina

2005-04-01

Psilocybe fagicola comprises a complex of more than eight species, six of them in Mexico, and all of them possessing a long pseudorhiza, a characteristic not listed by Heim and Cailleux in 1959 in the original description of the type species, but described by Guzmán in 1978 and 1983. The description of Psilocybe fagicola s.s. is here emended to include the length of the cheilocystidia of (6-) 12-20 (-30) microm, as well as the absence or scarcity of pleurocystidia. Psilocybe xalapensis and P. wassoniorum are considered to be synonymous with P. fagicola s.s. However, Psilocybe banderillensis and P. herrerae from Mexico, P. columbiana from Colombia, and P. keralensis from India are considered to be valid species within this complex. Moreover, P. novoxalapensis and P. teofilae, both from Mexico, are described as new species. Length of spores, presence or absence of pleurocystidia and their variations, and type of cheilocystidia constitute the principal defining characteristics of the species. Setaceous hyphae at the base of the stipe, as well as caulocystidia, lack taxonomic value, as do other morphological characteristics, including pileipellis and subpileipellis. A key to the eight considered species is also presented within the paper.

A test of color-based taxonomy in nudibranchs: Molecular phylogeny and species delimitation of the Felimida clenchi (Mollusca: Chromodorididae) species complex.

PubMed

Padula, Vinicius; Bahia, Juliana; Stöger, Isabella; Camacho-García, Yolanda; Malaquias, Manuel António E; Cervera, Juan Lucas; Schrödl, Michael

2016-10-01

Traditionally, species identification in nudibranch gastropods relies heavily on body color pattern. The Felimida clenchi species complex, a group of brightly colored Atlantic and Mediterranean species in the family Chromodorididae, has a history of exceptional controversy and discussion among taxonomists. The most widely accepted hypothesis is that the complex includes four species (Felimida clenchi, F. neona, F. binza and F. britoi), each with a characteristic body color pattern. In this study, we investigated the taxonomic value of coloration in the Felimida clenchi complex, using molecular phylogenetics, species-delimitation analyses (ABGD, GMYC, PTP), haplotype-network methods, and the anatomy of the reproductive system. None of our analyses recovered the traditional separation into four species. Our results indicated the existence of three species, a result inconsistent with previous taxonomic hypotheses. We distinguished an undescribed species of Felimida and redefined the concepts of F. clenchi and F. binza, both highly polychromatic species. For the first time, molecular data support the existence of extreme color polymorphism in chromatic nudibranch species, with direct implications for the taxonomy of the group and its diversity. The polychromatism observed in the F. clenchi complex apparently correlates with the regional occurrence of similar color patterns in congeneric species, suggesting different mimicry circles. This may represent a parallel in the marine environment to the mechanisms that play a major role in the diversification of color in terrestrial and fresh-water chromatic groups, such as heliconian butterflies. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

Adding complexity to the complex: new insights into the phylogeny, diversification and origin of parthenogenesis in the Aporrectodea caliginosa species complex (Oligochaeta, Lumbricidae).

PubMed

Fernández, Rosa; Almodóvar, Ana; Novo, Marta; Simancas, Bárbara; Díaz Cosín, Darío J

2012-08-01

The importance of the Aporrectodea caliginosa species complex lies in the great abundance and wide distribution of the species which exist within it. For more than a century, chaos has surrounded this complex; morphological criteria has failed to solve the taxonomic status of these species. This present body of work aims to study the phylogeny of this complex by increasing the number of samples used in previous molecular works and by including morphologically-similar species that were never studied using molecular tools (A. giardi, Nicodrilus monticola, N. carochensis and N. tetramammalis). Two basal clades were obtained: one formed by A. caliginosa and A. tuberculata and the other by the rest of the species. This second clade was divided into two more: one with Eurosiberian and another with Mediterranean forms. A. caliginosa and A. longa were divided into two paraphyletic groups. Both A. giardi and A. nocturna showed characteristics consistent with monophyletic groups. Each of the two recovered lineages of A. trapezoides were phylogenetically related to different sexual species. While lineage I of A. trapezoides was monophyletic, lineage II resulted to be paraphyletic, as well as the three Nicodrilus 'species'. The diversification of the complex occurred during the Late Miocene-Early Pliocene (6.92-11.09 Mya). The parthenogenetic forms within the Mediterranean clade would have diversified before the ones in the Eurosiberian clade (3.13-4.64 Mya and 1.05-3.48 Mya, respectively), thus implying the existence not only of at least two different moments in which parthenogenesis arose within this complex of species, but also of two different and independent evolutionary lines. Neither the 4× rule nor the GMYC method for species delimitation were successful for distinguishing taxonomically-distinct species. Copyright © 2012 Elsevier Inc. All rights reserved.

Comparison of the Virulence-Associated Phenotypes of Five Species of Acinetobacter baumannii Complex.

PubMed

Na, In Young; Chung, Eun Seon; Jung, Chang-Yun; Kim, Dae Hun; Shin, Juyoun; Kang, KyeongJin; Kim, Seong-Tae; Ko, Kwan Soo

2016-01-01

In this study, we compared the virulence-associated factors of Acinetobacter baumannii complex species. Sixty-three isolates of five A. baumannii complex species, including 19 A. baumannii, 15 A. nosocomialis, 13 A. seifertii, 13 A. pittii, and 3 A. calcoaceticus isolates, were included in this study. For all isolates, biofilm formation, A549 cell adherence, resistance to normal human serum, and motility were evaluated. A. baumannii complex isolates showed diversity in biofilm formation, A549 cell adherence, and serum resistance, and no strong positive relationships among these virulence characteristics. However, A. seifertii showed relatively consistent virulence-associated phenotypes. In addition, A. baumannii clone ST110 exhibited consistently high virulence-associated phenotypes. Motility was observed in seven isolates, and all four A. baumannii ST110 isolates showed twitching motility. Although some inconsistencies in virulence-associated phenotypes were seen, high virulence characteristics were observed in A. seifertii, which has been mainly reported in Korea and shows high rates of colistin resistance.

Phylogeny of triatomine vectors of Trypanosoma cruzi suggested by mitochondrial DNA sequences.

PubMed

Sainz, Andrés C; Mauro, Laura V; Moriyama, Etsuko N; García, Beatriz A

2004-07-01

The subfamily Triatominae (Hemiptera: Reduviidae) comprises hematophagous insects, most of which are actual or potential vectors of Trypanosoma cruzi, the protozoan agent of Chagas' disease (American trypanosomiasis). DNA sequence comparisons of mitochondrial DNA (mtDNA) genes were used to infer phylogenetic relationships among 32 species of the subfamily Triatominae, 26 belonging to the genus Triatoma and six species of different genera. We analyzed mtDNA fragments of the 12S and 16S ribosomal RNA genes (totaling 848-851 bp) from each of the 32 species, as well as of the cytochrome oxidase I (COI, 1447 bp) gene from nine. The phylogenetic analyses unambiguously supported several clusters within the genus Triatoma. In the morphological classification, T. costalimai was placed tentatively within the infestans complex while T. guazu was not included in any Triatoma complex. The placement of these species in the molecular phylogeny indicated that both belong to the infestans complex. We confirmed with a strong support the inclusion of T. circummaculata, a member of a different complex based on morphology, within the infestans complex. On the other hand, the present phylogenetics analysis did not support the monophyly of the infestans complex species as it was suggested in our previous studies. While no strong inference of polyphyly of the genus Triatoma was provided by the bootstrap analyses, the other species belonging to Triatomini analyzed could not be distinguished from the species of Triatoma.

Chloroplast heterogeneity and historical admixture within the genus Malus.

PubMed

Volk, Gayle M; Henk, Adam D; Baldo, Angela; Fazio, Gennaro; Chao, C Thomas; Richards, Christopher M

2015-07-01

• The genus Malus represents a unique and complex evolutionary context in which to study domestication. Several Malus species have provided novel alleles and traits to the cultivars. The extent of admixture among wild Malus species has not been well described, due in part to limited sampling of individuals within a taxon.• Four chloroplast regions (1681 bp total) were sequenced and aligned for 412 Malus individuals from 30 species. Phylogenetic relationships were reconstructed using maximum parsimony. The distribution of chloroplast haplotypes among species was examined using statistical parsimony, phylogenetic trees, and a median-joining network.• Chloroplast haplotypes are shared among species within Malus. Three major haplotype-sharing networks were identified. One includes species native to China, Western North America, as well as Malus domestica Borkh, and its four primary progenitor species: M. sieversii (Ledeb.) M. Roem., M. orientalis Uglitzk., M. sylvestris (L.) Mill., and M. prunifolia (Willd.) Borkh; another includes five Chinese Malus species, and a third includes the three Malus species native to Eastern North America.• Chloroplast haplotypes found in M. domestica belong to a single, highly admixed network. Haplotypes shared between the domesticated apple and its progenitors may reflect historical introgression or the retention of ancestral polymorphisms. Multiple individuals should be sampled within Malus species to reveal haplotype heterogeneity, if complex maternal contributions to named species are to be recognized. © 2015 Botanical Society of America, Inc.

Improved resolution of major clades within Tuber and taxonomy of species within the Tuber gibbosum complex

Treesearch

Gregory M. Bonito; James M. Trappe; Pat Rawlinson; Rytas Vilgalys

2010-01-01

Tuber gibbosum Harkn., described from northern California, originally was thought to be a single, variable species that fruited from autumn through winter to spring. It has become popular as a culinary truffle in northwestern USA, where it is commercially harvested. Morphological studies suggested it might be a complex that includes at least two...

Current knowledge of the species complex Anastrepha fraterculus (Diptera, Tephritidae) in Brazil

PubMed Central

Vaníčková, Lucie; Hernández-Ortiz, Vicente; Bravo, Iara Sordi Joachim; Dias, Vanessa; Roriz, Alzira Kelly Passos; Laumann, Raul Alberto; Mendonça, Adriana de Lima; Paranhos, Beatriz Aguiar Jordão; do Nascimento, Ruth Rufino

2015-01-01

Abstract The study of the species complex Anastrepha fraterculus (Af complex) in Brazil is especially important in a taxonomical, evolutionary and pest management context, because there are evidences that some of them may occur in sympatry. In this review, we analyzed the main results supporting evidences that three cryptic species occur in Brazil. The taxonomical and phylogenetic relationships based on eggshell morphology, adult morphometrics, as well as cytotaxonomy and genetic differentiations are discussed. We also review available information on sexual behavior including acoustic communication of males during courtship and sexual incompatibility; and chemical signals involved in the communication between sexes, with a special focus on sex pheromones. We examined the role of long- and short-range pheromones (male-produced volatiles and cuticular hydrocarbons, respectively), their implications in sexual isolation, and their possible use for chemotaxonomic differentiation of the putative species of the Af complex. PMID:26798261

Assessing the likely effectiveness of multispecies management for imperiled desert fishes with niche overlap analysis

USGS Publications Warehouse

Laub, P; Budy, Phaedra

2015-01-01

A critical decision in species conservation is whether to target individual species or a complex of ecologically similar species. Management of multispecies complexes is likely to be most effective when species share similar distributions, threats, and response to threats. We used niche overlap analysis to assess ecological similarity of 3 sensitive desert fish species currently managed as an ecological complex. We measured the amount of shared distribution of multiple habitat and life history parameters between each pair of species. Habitat use and multiple life history parameters, including maximum body length, spawning temperature, and longevity, differed significantly among the 3 species. The differences in habitat use and life history parameters among the species suggest they are likely to respond differently to similar threats and that most management actions will not benefit all 3 species equally. Habitat restoration, frequency of stream dewatering, non-native species control, and management efforts in tributaries versus main stem rivers are all likely to impact each of the species differently. Our results demonstrate that niche overlap analysis provides a powerful tool for assessing the likely effectiveness of multispecies versus single-species conservation plans.

Taxonomic revision of the Chinese Limnonectes (Anura, Dicroglossidae) with the description of a new species from China and Myanmar.

PubMed

Suwannapoom, Chatmongkon; Yuan, Zhi-Yong; Chen, Jin-Min; Hou, Mian; Zhao, Hai-Peng; Wang, Li-Jun; Nguyen, Truong Son; Nguyen, Truong Q; Murphy, Robert W; Sullivan, Jaqueline; Mcleod, David S; Che, Jing

2016-03-21

Phylogenetic reconstructions derived from DNA sequence data play a central role in documenting the number of species in a complex. Such analyses are pointing to the existence of many cryptic species, especially in poorly understood groups such as the genus Limnonectes, and the L. kuhlii species complex in particular. To understand the Limnonectes frogs of China, we reconstruct the major matrilineal genealogy of Limnonectes from China and Southeast Asia based on 12S rRNA, tRNA^Val and 16S rRNA gene sequences. Based on new data we recognize five species of Limnonectes in China including L. bannaensis, L. fujianensis, L. fragilis, L. taylori (new record), and a new species from southern China and Myanmar. Phylogenetically, the new species is more closely related to the clade comprising L. taylori, L. megastomias, L. isanensis, L. nguyenorum, and L. jarujini from Thailand than to other Chinese species. This study supports previous findings of sympatric members of a species complex that are not each other's closest relatives.

Evolution of Interstellar Ices

NASA Astrophysics Data System (ADS)

Allamandola, Louis J.; Bernstein, Max P.; Sandford, Scott A.; Walker, Robert L.

1999-10-01

Infrared observations, combined with realistic laboratory simulations, have revolutionized our understanding of interstellar ice and dust, the building blocks of comets. Ices in molecular clouds are dominated by the very simple molecules H2O, CH3OH, NH3, CO, CO2, and probably H2CO and H2. More complex species including nitriles, ketones, and esters are also present, but at lower concentrations. The evidence for these, as well as the abundant, carbon-rich, interstellar, polycyclic aromatic hydrocarbons (PAHs) is reviewed. Other possible contributors to the interstellar/pre-cometary ice composition include accretion of gas-phase molecules and in situ photochemical processing. By virtue of their low abundance, accretion of simple gas-phase species is shown to be the least important of the processes considered in determining ice composition. On the other hand, photochemical processing does play an important role in driving dust evolution and the composition of minor species. Ultraviolet photolysis of realistic laboratory analogs readily produces H2, H2CO, CO2, CO, CH4, HCO, and the moderately complex organic molecules: CH3CH2OH (ethanol), HC(=O)NH2 (formamide), CH3C(=O)NH2 (acetamide), R-CN (nitriles), and hexamethylenetetramine (HMT, C6H12N4), as well as more complex species including amides, ketones, and polyoxymethylenes (POMs). Inclusion of PAHs in the ices produces many species similar to those found in meteorites including aromatic alcohols, quinones and ethers. Photon assisted PAH-ice deuterium exchange also occurs. All of these species are readily formed and are therefore likely cometary constituents.

Thermodynamic Studies to Support Actinide/Lanthanide Separations

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

Rao, Linfeng

2016-09-04

Thermodynamic data on the complexation of Np(V) with HEDTA in a wide pH region were re-modeled by including a dimeric complex species, (NpO 2) 2(OH) 2L 2 6- where L 3- stands for the fully deprotonated HEDTA ligand and better fits were achieved for the spectrophotometric data. The presence of the dimeric complex species in high pH region was verified for the first time by the EXAFS experiments at Stanford Synchrotron Radiation Laboratory (SSRL).

Rapid diversification and secondary sympatry in Australo-Pacific kingfishers (Aves: Alcedinidae: Todiramphus)

PubMed Central

Andersen, Michael J.; Shult, Hannah T.; Cibois, Alice; Thibault, Jean-Claude; Filardi, Christopher E.; Moyle, Robert G.

2015-01-01

Todiramphus chloris is the most widely distributed of the Pacific's ‘great speciators’. Its 50 subspecies constitute a species complex that is distributed over 16 000 km from the Red Sea to Polynesia. We present, to our knowledge, the first comprehensive molecular phylogeny of this enigmatic radiation of kingfishers. Ten Pacific Todiramphus species are embedded within the T. chloris complex, rendering it paraphyletic. Among these is a radiation of five species from the remote islands of Eastern Polynesian, as well as the widespread migratory taxon, Todiramphus sanctus. Our results offer strong support that Pacific Todiramphus, including T. chloris, underwent an extensive range expansion and diversification less than 1 Ma. Multiple instances of secondary sympatry have accumulated in this group, despite its recent origin, including on Australia and oceanic islands in Palau, Vanuatu and the Solomon Islands. Significant ecomorphological and behavioural differences exist between secondarily sympatric lineages, which suggest that pre-mating isolating mechanisms were achieved rapidly during diversification. We found evidence for complex biogeographic patterns, including a novel phylogeographic break in the eastern Solomon Islands that separates a Northern Melanesian clade from Polynesian taxa. In light of our results, we discuss systematic relationships of Todiramphus and propose an updated taxonomy. This paper contributes to our understanding of avian diversification and assembly on islands, and to the systematics of a classically polytypic species complex. PMID:26064600

Species diversity in the marine microturbellarian Astrotorhynchus bifidus sensu lato (Platyhelminthes: Rhabdocoela) from the Northeast Pacific Ocean.

PubMed

Van Steenkiste, Niels W L; Herbert, Elizabeth R; Leander, Brian S

2018-03-01

Increasing evidence suggests that many widespread species of meiofauna are in fact regional complexes of (pseudo-)cryptic species. This knowledge has challenged the 'Everything is Everywhere' hypothesis and also partly explains the meiofauna paradox of widespread nominal species with limited dispersal abilities. Here, we investigated species diversity within the marine microturbellarian Astrotorhynchus bifidus sensu lato in the Northeast Pacific Ocean. We used a multiple-evidence approach combining multi-gene (18S, 28S, COI) phylogenetic analyses, several single-gene and multi-gene species delimitation methods, haplotype networks and conventional taxonomy to designate Primary Species Hypotheses (PSHs). This included the development of rhabdocoel-specific COI barcode primers, which also have the potential to aid in species identification and delimitation in other rhabdocoels. Secondary Species Hypotheses (SSHs) corresponding to morphospecies and pseudo-cryptic species were then proposed based on the minimum consensus of different PSHs. Our results showed that (a) there are at least five species in the A. bifidus complex in the Northeast Pacific Ocean, four of which can be diagnosed based on stylet morphology, (b) the A. bifidus complex is a mixture of sympatric and allopatric species with regional and/or subglobal distributions, (c) sympatry occurs on local (sample sites), regional (Northeastern Pacific) and subglobal (Northern Atlantic, Arctic, Northeastern Pacific) scales. Mechanisms for this co-occurrence are still poorly understood, but we hypothesize they could include habitat differentiation (spatial and/or seasonal) and life history characteristics such as sexual selection and dispersal abilities. Our results also suggest the need for improved sampling and exploration of molecular markers to accurately map gene flow and broaden our understanding of species diversity and distribution of microturbellarians in particular and meiofauna in general. Copyright © 2017 Elsevier Inc. All rights reserved.

Lectotype designation for seven species names in the Daucus guttatus complex (Apiaceae) from the central and eastern Mediterranean basin

USDA-ARS?s Scientific Manuscript database

The Daucus guttatus complex includes 2-4 species growing from central and northern Italy to the Middle East. They are characterized by being usually annuals up to 50 cm high; and the primary umbels up to 7 cm in diameter with less than 25(35) rays. Discolored umbels are frequent, bearing one to seve...

Flat and complex temperate reefs provide similar support for fish: Evidence for a unimodal species-habitat relationship

PubMed Central

Pickering, Emily A.; Adler, Alyssa M.; Taylor, J. Christopher; Peterson, Charles H.

2017-01-01

Structural complexity, a form of habitat heterogeneity, influences the structure and function of ecological communities, generally supporting increased species density, richness, and diversity. Recent research, however, suggests the most complex habitats may not harbor the highest density of individuals and number of species, especially in areas with elevated human influence. Understanding nuances in relationships between habitat heterogeneity and ecological communities is warranted to guide habitat-focused conservation and management efforts. We conducted fish and structural habitat surveys of thirty warm-temperate reefs on the southeastern US continental shelf to quantify how structural complexity influences fish communities. We found that intermediate complexity maximizes fish abundance on natural and artificial reefs, as well as species richness on natural reefs, challenging the current paradigm that abundance and other fish community metrics increase with increasing complexity. Naturally occurring rocky reefs of flat and complex morphologies supported equivalent abundance, biomass, species richness, and community composition of fishes. For flat and complex morphologies of rocky reefs to receive equal consideration as essential fish habitat (EFH), special attention should be given to detecting pavement type rocky reefs because their ephemeral nature makes them difficult to detect with typical seafloor mapping methods. Artificial reefs of intermediate complexity also maximized fish abundance, but human-made structures composed of low-lying concrete and metal ships differed in community types, with less complex, concrete structures supporting lower numbers of fishes classified largely as demersal species and metal ships protruding into the water column harboring higher numbers of fishes, including more pelagic species. Results of this study are essential to the process of evaluating habitat function provided by different types and shapes of reefs on the seafloor so that all EFH across a wide range of habitat complexity may be accurately identified and properly managed. PMID:28873447

DNA barcoding and real-time PCR detection of Bactrocera xanthodes (Tephritidae: Diptera) complex.

PubMed

Li, D; Waite, D W; Gunawardana, D N; McCarthy, B; Anderson, D; Flynn, A; George, S

2018-05-06

Immature fruit fly stages of the family Tephritidae are commonly intercepted on breadfruit from Pacific countries at the New Zealand border but are unable to be identified to the species level using morphological characters. Subsequent molecular identification showed that they belong to Bactrocera xanthodes, which is part of a species complex that includes Bactrocera paraxanthodes, Bactrocera neoxanthodes and an undescribed species. To establish a more reliable molecular identification system for B. xanthodes, a reference database of DNA barcode sequences for the 5'-fragment of COI gene region was constructed for B. xanthodes from Fiji, Samoa and Tonga. To better understand the species complex, B. neoxanthodes from Vanuatu and B. paraxanthodes from New Caledonia were also barcoded. Using the results of this analysis, real-time TaqMan polymerase chain reaction (PCR) assays for the detection of B. xanthodes complex and for the three individual species of the complex were developed and validated. The assay showed high specificity for the target species, with no cross-reaction observed for closely related organisms. Each of the real-time PCR assays is sensitive, detecting the target sequences at concentrations as low as ten copies µl-1 and can be used as either singleplex or multiplex formats. This real-time PCR assay for B. xanthodes has been successfully applied at the borders in New Zealand, leading to the rapid identification of intercepted Tephritidae eggs and larvae. The developed assays will be useful biosecurity tools for rapid detection of species in the B. xanthodes complex worldwide.

The role of the Forest Service in aquatic invasive species research

Treesearch

Susan B. Adams; Kelly M. Burnett; Peter Bisson; Bret Harvey; Keith H. Nislow; Bruce E. Rieman; John Rinne

2010-01-01

Aquatic ecosystems include the most imperiled taxa in the United States, and invasive species are the second leading contributor to this imperilment. The U.S. Department of Agriculture (USDA), Forest Service is legally mandated to sustainably manage aquatic habitats and native species on National Forest System (NFS) lands. Invasive species add complexity and...

Towards a Phylogenetic Approach to the Composition of Species Complexes in the North and Central American Triatoma, Vectors of Chagas Disease

PubMed Central

de la Rúa, Nicholas M.; Bustamante, Dulce M.; Menes, Marianela; Stevens, Lori; Monroy, Carlota; Kilpatrick, William; Rizzo, Donna; Klotz, Stephen A.; Schmidt, Justin; Axen, Heather J.; Dorn, Patricia L.

2014-01-01

Phylogenetic relationships of insect vectors of parasitic diseases are important for understanding the evolution of epidemiologically relevant traits, and may be useful in vector control. The subfamily Triatominae (Hemiptera:Reduviidae) includes ~140 extant species arranged in five tribes comprised of 15 genera. The genus Triatoma is the most species-rich and contains important vectors of Trypanosoma cruzi, the causative agent of Chagas disease. Triatoma species were grouped into complexes originally by morphology and more recently with the addition of information from molecular phylogenetics (the four-complex hypothesis); however, without a strict adherence to monophyly. To date, the validity of proposed species complexes has not been tested by statistical tests of topology. The goal of this study was to clarify the systematics of 19 Triatoma species from North and Central America. We inferred their evolutionary relatedness using two independent data sets: the complete nuclear Internal Transcribed Spacer-2 ribosomal DNA (ITS-2 rDNA) and head morphometrics. In addition, we used the Shimodaira-Hasegawa statistical test of topology to assess the fit of the data to a set of competing systematic hypotheses (topologies). An unconstrained topology inferred from the ITS-2 data was compared to topologies constrained based on the four-complex hypothesis or one inferred from our morphometry results. The unconstrained topology represents a statistically significant better fit of the molecular data than either the four-complex or the morphometric topology. We propose an update to the composition of species complexes in the North and Central American Triatoma, based on a phylogeny inferred from ITS-2 as a first step towards updating the phylogeny of the complexes based on monophyly and statistical tests of topologies. PMID:24681261

Assessing Species Boundaries Using Multilocus Species Delimitation in a Morphologically Conserved Group of Neotropical Freshwater Fishes, the Poecilia sphenops Species Complex (Poeciliidae)

PubMed Central

Bagley, Justin C.; Alda, Fernando; Breitman, M. Florencia; Bermingham, Eldredge; van den Berghe, Eric P.; Johnson, Jerald B.

2015-01-01

Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including ‘non-adaptive radiations’ containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci) from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial ‘major-lineages’ diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively) 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the importance of testing for hybridization versus incomplete lineage sorting, which aids inference of not only species limits but also evolutionary processes influencing genetic diversity. PMID:25849959

Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae).

PubMed

Bagley, Justin C; Alda, Fernando; Breitman, M Florencia; Bermingham, Eldredge; van den Berghe, Eric P; Johnson, Jerald B

2015-01-01

Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including 'non-adaptive radiations' containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci) from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial 'major-lineages' diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively) 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the importance of testing for hybridization versus incomplete lineage sorting, which aids inference of not only species limits but also evolutionary processes influencing genetic diversity.

Comparative “Omics” of the Fusarium fujikuroi Species Complex Highlights Differences in Genetic Potential and Metabolite Synthesis

PubMed Central

Niehaus, Eva-Maria; Münsterkötter, Martin; Proctor, Robert H.; Brown, Daren W.; Sharon, Amir; Idan, Yifat; Oren-Young, Liat; Sieber, Christian M.; Novák, Ondřej; Pěnčík, Aleš; Tarkowská, Danuše; Hromadová, Kristýna; Freeman, Stanley; Maymon, Marcel; Elazar, Meirav; Youssef, Sahar A.; El-Shabrawy, El Said M.; Shalaby, Abdel Baset A.; Houterman, Petra; Brock, Nelson L.; Burkhardt, Immo; Tsavkelova, Elena A.; Dickschat, Jeroen S.; Galuszka, Petr; Güldener, Ulrich; Tudzynski, Bettina

2016-01-01

Species of the Fusarium fujikuroi species complex (FFC) cause a wide spectrum of often devastating diseases on diverse agricultural crops, including coffee, fig, mango, maize, rice, and sugarcane. Although species within the FFC are difficult to distinguish by morphology, and their genes often share 90% sequence similarity, they can differ in host plant specificity and life style. FFC species can also produce structurally diverse secondary metabolites (SMs), including the mycotoxins fumonisins, fusarins, fusaric acid, and beauvericin, and the phytohormones gibberellins, auxins, and cytokinins. The spectrum of SMs produced can differ among closely related species, suggesting that SMs might be determinants of host specificity. To date, genomes of only a limited number of FFC species have been sequenced. Here, we provide draft genome sequences of three more members of the FFC: a single isolate of F. mangiferae, the cause of mango malformation, and two isolates of F. proliferatum, one a pathogen of maize and the other an orchid endophyte. We compared these genomes to publicly available genome sequences of three other FFC species. The comparisons revealed species-specific and isolate-specific differences in the composition and expression (in vitro and in planta) of genes involved in SM production including those for phytohormome biosynthesis. Such differences have the potential to impact host specificity and, as in the case of F. proliferatum, the pathogenic versus endophytic life style. PMID:28040774

Energetic Processing of Interstellar Ices: A Route to Complexity

NASA Technical Reports Server (NTRS)

Moore, Marla H.; Hudson, Reggie L.

2009-01-01

More than 140 gas-phase molecules have been detected in the interstellar (IS) medium or in circumstellar environments including inorganics, organics, ions, and radicals. The significant abundance of large, complex organic molecules, and families of isomers in these regions makes the origin and formation history of these species the subject of debate. Observationally determined condensed-phase species are H2O, CO, CO2, NH3 and CH30H, with CH4, HCOOH, OCS, OCN-, H2CO and NH4(+) present at trace levels. These ices can undergo energetic processing with cosmic rays or far-UV photons to form larger complex organics with abundance levels that make them undetectable in icy mantles. Once warmed, however, it is likely that these complex species would enter the gas-phase where they might be detected by Herschel or Alma. Understanding the role of radiation chemistry and thermal processing of ices and identifying new products are the goals of our laboratory research. In the Cosmic lee Laboratory at NASA Goddard Space Plight Center, we can study both the photo-and radiation chemistries of ices from 8 -- 300 K. Using dear- and mid-IR spectroscopy we can follow the destruction of primary molecules and the formation of radicals and secondary products as a function of energetic processing. During warming we can monitor the trapping of species and the results of any thermal chemistry. An overview of recent and past work will focus on complex secondary radiation products from small condensed-phase IS species. Likely reactions include dimerization, isomerization, H-addition and H-elimination. Another focus of our work is the development of reaction schemes for the formation of complex molecules and the use of such schemes to predict new molecules awaiting detection by Herschel and Alma.

The Mugil curema species complex (Pisces, Mugilidae): a new karyotype for the Pacific white mullet mitochondrial lineage

PubMed Central

Nirchio, Mauro; Oliveira, Claudio; Siccha-Ramirez, Zoila R.; de Sene, Viviani F.; Sola, Luciana; Milana, Valentina; Rossi, Anna Rita

2017-01-01

Abstract Recent molecular phylogenetic analyses have shown that the Mugil curema Valenciennes, 1836 species complex includes M. incilis Hancock, 1830, M. thoburni (Jordan & Starks, 1896) and at least four “M. curema” mitochondrial lineages, considered as cryptic species. The cytogenetic data on some representatives of the species complex have shown a high cytogenetic diversity. This research reports the results of cytogenetic and molecular analyses of white mullet collected in Ecuador. The analyzed specimens were molecularly assigned to the Mugil sp. O, the putative cryptic species present in the Pacific Ocean and showed a 2n = 46 karyotype, which is composed of 2 metacentric and 44 subtelocentric/acrocentric chromosomes. This karyotype is different from the one described for M. incilis (2n = 48) and from those of the two western Atlantic lineages Mugil curema (2n = 28), and Mugil margaritae (2n = 24). Data suggest the need for a morphological analysis to assign a species name to this Pacific lineage. PMID:28919961

The Mugil curema species complex (Pisces, Mugilidae): a new karyotype for the Pacific white mullet mitochondrial lineage.

PubMed

Nirchio, Mauro; Oliveira, Claudio; Siccha-Ramirez, Zoila R; de Sene, Viviani F; Sola, Luciana; Milana, Valentina; Rossi, Anna Rita

2017-01-01

Recent molecular phylogenetic analyses have shown that the Mugil curema Valenciennes, 1836 species complex includes M. incilis Hancock, 1830, M. thoburni (Jordan & Starks, 1896) and at least four " M. curema " mitochondrial lineages, considered as cryptic species. The cytogenetic data on some representatives of the species complex have shown a high cytogenetic diversity. This research reports the results of cytogenetic and molecular analyses of white mullet collected in Ecuador. The analyzed specimens were molecularly assigned to the Mugil sp. O, the putative cryptic species present in the Pacific Ocean and showed a 2n = 46 karyotype, which is composed of 2 metacentric and 44 subtelocentric/acrocentric chromosomes. This karyotype is different from the one described for M. incilis (2n = 48) and from those of the two western Atlantic lineages Mugil curema (2n = 28), and Mugil margaritae (2n = 24). Data suggest the need for a morphological analysis to assign a species name to this Pacific lineage.

Leapfrogging into new territory: How Mascarene ridged frogs diversified across Africa and Madagascar to maintain their ecological niche.

PubMed

Zimkus, Breda M; Lawson, Lucinda P; Barej, Michael F; Barratt, Christopher D; Channing, Alan; Dash, Katrina M; Dehling, J Maximilian; Du Preez, Louis; Gehring, Philip-Sebastian; Greenbaum, Eli; Gvoždík, Václav; Harvey, James; Kielgast, Jos; Kusamba, Chifundera; Nagy, Zoltán T; Pabijan, Maciej; Penner, Johannes; Rödel, Mark-Oliver; Vences, Miguel; Lötters, Stefan

2017-01-01

The Mascarene ridged frog, Ptychadena mascareniensis, is a species complex that includes numerous lineages occurring mostly in humid savannas and open forests of mainland Africa, Madagascar, the Seychelles, and the Mascarene Islands. Sampling across this broad distribution presents an opportunity to examine the genetic differentiation within this complex and to investigate how the evolution of bioclimatic niches may have shaped current biogeographic patterns. Using model-based phylogenetic methods and molecular-clock dating, we constructed a time-calibrated molecular phylogenetic hypothesis for the group based on mitochondrial 16S rRNA and cytochrome b (cytb) genes and the nuclear RAG1 gene from 173 individuals. Haplotype networks were reconstructed and species boundaries were investigated using three species-delimitation approaches: Bayesian generalized mixed Yule-coalescent model (bGMYC), the Poisson Tree Process model (PTP) and a cluster algorithm (SpeciesIdentifier). Estimates of similarity in bioclimatic niche were calculated from species-distribution models (maxent) and multivariate statistics (Principal Component Analysis, Discriminant Function Analysis). Ancestral-area reconstructions were performed on the phylogeny using probabilistic approaches implemented in BioGeoBEARS. We detected high levels of genetic differentiation yielding ten distinct lineages or operational taxonomic units, and Central Africa was found to be a diversity hotspot for these frogs. Most speciation events took place throughout the Miocene, including "out-of-Africa" overseas dispersal events to Madagascar in the East and to São Tomé in the West. Bioclimatic niche was remarkably well conserved, with most species tolerating similar temperature and rainfall conditions common to the Central African region. The P. mascareniensis complex provides insights into how bioclimatic niche shaped the current biogeographic patterns with niche conservatism being exhibited by the Central African radiation and niche divergence shaping populations in West Africa and Madagascar. Central Africa, including the Albertine Rift region, has been an important center of diversification for this species complex. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

75 FR 22832 - Lake Wales Ridge National Wildlife Refuge, Highlands and Polk Counties, FL

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-30

... would continue to focus on maintaining existing habitats for rare, threatened, and endangered species... Island NWR Complex provides fire program staff); (2) rare, threatened, and endangered species monitoring... actions that include managing habitats for rare, threatened, and endangered species. Both Federal- and...

Molecular phylogeny of the Anopheles gambiae complex suggests genetic introgression between principal malaria vectors.

PubMed Central

Besansky, N J; Powell, J R; Caccone, A; Hamm, D M; Scott, J A; Collins, F H

1994-01-01

The six Afrotropical species of mosquitoes comprising the Anopheles gambiae complex include the most efficient vectors of malaria in the world as well as a nonvector species. The accepted interpretation of evolutionary relationships among these species is based on chromosomal inversions and suggests that the two principal vectors, A. gambiae and Anopheles arabiensis, are on distant branches of the phylogenetic tree. However, DNA sequence data indicate that these two species are sister taxa and suggest gene flow between them. These results have important implications for malaria control strategies involving the replacement of vector with nonvector populations. Images PMID:8041714

Evaluation of GenoType NTM-DR Assay for Identification of Mycobacterium chimaera.

PubMed

Mok, Simone; Rogers, Thomas R; Fitzgibbon, Margaret

2017-06-01

Identification of species within the Mycobacterium avium complex (MAC) is difficult, and most current diagnostic laboratory tests cannot distinguish between species included in the complex. Differentiation of species within the MAC is important, as Mycobacterium chimaera has recently emerged as a major cause of invasive cardiovascular infections following open heart surgery. A new commercial diagnostic assay, GenoType NTM-DR ver. 1.0, is intended to differentiate between three species within the MAC, namely, Mycobacterium avium , Mycobacterium intracellulare , and Mycobacterium chimaera In this study, we investigated an archival collection of 173 MAC isolates using 16S rRNA and 16S-23S internal transcribed spacer (ITS) gene sequencing, and GenoType NTM-DR was evaluated for identifying M. chimaera and other species belonging to the MAC. Species identification of 157/173 (91%) isolates with the GenoType NTM-DR assay was in agreement with 16S rRNA and 16S-23S ITS gene sequencing results. Misidentification occurred with 16 isolates which belonged to four species included in the MAC that are rarely encountered in clinical specimens. Despite some limitations of this assay, GenoType NTM-DR had 100% specificity for identifying M. chimaera This novel assay will enable diagnostic laboratories to differentiate species belonging to the Mycobacterium avium complex and to accurately identify M. chimaera It can produce rapid results and is also more cost efficient than gene sequencing methods. Copyright © 2017 American Society for Microbiology.

Cryptic Species Identification and Composition of Bemisia tabaci (Hemiptera: Aleyrodidae) Complex in Henan Province, China

PubMed Central

Hu, Jian; Wang, Lun-Ji; Dong, Jun-Feng; Song, Yue-Qin; Sun, Hui-Zhong

2017-01-01

Abstract Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex, causing significant crop losses in China during the last decade. Although knowledge of cryptic species composition and dynamics within B. tabaci complex is critical for developing sustainable pest management strategies, limited information is available on this pest in the Henan province of China. A systematic survey of the cryptic species composition and distribution of B. tabaci complex in different locations of Henan province was conducted in 2012. The results of RAPD-PCR and the gene for the mitochondrial cytochrome oxidase subunit-1 (mtCOI) based phylogenetic relationships established using Bayesian method indicated there were four known cryptic species MEAM1, MED, Asia II 3, Asia II 9 and a new cryptic species named China 6 in Henan province. In the survey, the invasive cryptic species MED and MEAM1 were found to be predominant with wide spread distribution across the surveyed regions. On the contrary, the indigenous B. tabaci cryptic species including Asia II 3, Asia II 9 and China 6 remained with low prevalence in some surveyed regions. Cryptic species MEAM1 and MED have not completely displaced the native B. tabaci in Henan province. This current study for the first time unifies our knowledge of the diversity and distribution of B. tabaci across Henan province of China. PMID:28973577

Squirrels cannot live by truffles alone: a closer look at a northwest keystone complex.

Treesearch

Sally Duncan

2004-01-01

Tree squirrels in the Pacific Northwest are part of a keystone complex that includes ectomycorrhizal fungi, Douglas-fir, and spotted owls. All three squirrel species—the northern flying squirrel, the Douglas' squirrel, and the Townsend’s squirrel—consume truffles produced by fungal partners of important tree species. The squirrels then spread the spores of these...

Unrewarded Object Combinations in Captive Parrots

PubMed Central

Auersperg, Alice Marie Isabel; Oswald, Natalie; Domanegg, Markus; Gajdon, Gyula Koppany; Bugnyar, Thomas

2015-01-01

In primates, complex object combinations during play are often regarded as precursors of functional behavior. Here we investigate combinatory behaviors during unrewarded object manipulation in seven parrot species, including kea, African grey parrots and Goffin cockatoos, three species previously used as model species for technical problem solving. We further examine a habitually tool using species, the black palm cockatoo. Moreover, we incorporate three neotropical species, the yellow- and the black-billed Amazon and the burrowing parakeet. Paralleling previous studies on primates and corvids, free object-object combinations and complex object-substrate combinations such as inserting objects into tubes/holes or stacking rings onto poles prevailed in the species previously linked to advanced physical cognition and tool use. In addition, free object-object combinations were intrinsically structured in Goffin cockatoos and in kea. PMID:25984564

A new species of inseminating seasonal killifish of the Cynopoecilus melanotaenia complex from southern Brazil (Cyprinodontiformes: Rivulidae)

PubMed Central

Amorim, Pedro F

2016-01-01

Abstract Background The Cynopoecilus melanotaenia complex is a morphologically homogeneous killifish group, endemic from an area encompassing southern Brazil and northeastern Uruguay. It presently comprises four valid species: C. melanotaenia, the type species of the genus, and C. fulgens, C. intimus, and C. nigrovittatus. New information Cynopoecilus feltrini, n. sp., from the lower Tubarão river basin, southern Brazil, is distinguished from all congeners of the C. melanotaenia complex by having frontal E-scales medially overlapped, branchiostegal region orangish red in males and dorsum with few dark brown spots above opercular region. A phylogenetic tree derived from the analysis of a fragment of the mitochondrial gene cytochrome c oxidase subunit I (681 bp) indicates that C. feltrini is a member of the clade that includes all species of the C. melanotaenia complex except C. melanotaenia, as well as that C. feltrini is the sister group of a clade comprising C. fulgens and C. nigrovittatus. PMID:27099548

A reinvestigation of phylogeny and divergence times of the Ablepharus kitaibelii species complex (Sauria, Scincidae) based on mtDNA and nuDNA genes.

PubMed

Skourtanioti, Eirini; Kapli, Paschalia; Ilgaz, Çetin; Kumlutaş, Yusuf; Avcı, Aziz; Ahmadzadeh, Faraham; Crnobrnja-Isailović, Jelka; Gherghel, Iulian; Lymberakis, Petros; Poulakakis, Nikos

2016-10-01

Morphological and DNA data support that the East Mediterranean snake-eyed skink Ablepharus kitaibelii represents a species complex that includes four species A. kitaibelii, A. budaki, A. chernovi, and A. rueppellii, highlighting the need of its taxonomic reevaluation. Here, we used Bayesian and Maximum Likelihood methods to estimate the phylogenetic relationships of all members of the complex based on two mitochondrial (cyt b, 16S rRNA) and two nuclear markers (MC1R, and NKTR) and using Chalcides, Eumeces, and Eutropis as outgroups. The biogeographic history of the complex was also investigated through the application of several phylogeographic (BEAST) and biogeographic (BBM) analyses. Paleogeographic and paleoclimatic data were used to support the inferred phylogeographic patterns. The A. kitaibelli species complex exhibits high genetic diversity, revealing cases of hidden diversity and cases of non-monophyletic species such as A. kitaibelii and A. budaki. Our results indicate that A. pannonicus branches off first and a group that comprises specimens of A. kitaibelli and A. budaki from Kastelorizo Island group (southeast Greece) and southwest Turkey, respectively is differentiated from the rest A. kitaibelli and A. budaki populations and may represent a new species. The estimated divergence times place the origin of the complex in the Middle Miocene (∼16Mya) and the divergence of most currently recognized species in the Late Miocene. The inferred ancestral distribution suggests that the complex originated in Anatolia, supposing that several vicariance and dispersal events that are related with the formation of the Mid-Aegean Trench, the Anatolian Diagonal and the orogenesis of the mountain chains in southern and eastern Anatolia have led to current distribution pattern of A. kitaibelii species complex in the Balkans and Middle East. Copyright © 2016 Elsevier Inc. All rights reserved.

Not a simple case - A first comprehensive phylogenetic hypothesis for the Midas cichlid complex in Nicaragua (Teleostei: Cichlidae: Amphilophus).

PubMed

Geiger, Matthias F; McCrary, Jeffrey K; Schliewen, Ulrich K

2010-09-01

Nicaraguan Midas cichlids from crater lakes have recently attracted attention as potential model systems for speciation research, but no attempt has been made to comprehensively reconstruct phylogenetic relationships of this highly diverse and recently evolved species complex. We present a first AFLP (2793 loci) and mtDNA based phylogenetic hypothesis including all described and several undescribed species from six crater lakes (Apoyeque, Apoyo, Asososca Leon, Masaya, Tiscapa and Xiloá), the two great Lakes Managua and Nicaragua and the San Juan River. Our analyses demonstrate that the relationships between the Midas cichlid members are complex, and that phylogenetic information from different markers and methods do not always yield congruent results. Nevertheless, monophyly support for crater lake assemblages from Lakes Apoyeque, Apoyo, A. Leon is high as compared to those from L. Xiloá indicating occurrence of sympatric speciation. Further, we demonstrate that a 'three species' concept for the Midas cichlid complex is inapplicable and consequently that an individualized and voucher based approach in speciation research of the Midas cichlid complex is necessary at least as long as there is no comprehensive revision of the species complex available. Copyright 2010 Elsevier Inc. All rights reserved.

Novel taxa in the Fusarium fujikuroi species complex from Pinus spp.

PubMed Central

Herron, D.A.; Wingfield, M.J.; Wingfield, B.D.; Rodas, C.A.; Marincowitz, S.; Steenkamp, E.T.

2015-01-01

The pitch canker pathogen Fusarium circinatum has caused devastation to Pinus spp. in natural forests and non-natives in commercially managed plantations. This has drawn attention to the potential importance of Fusarium species as pathogens of forest trees. In this study, we explored the diversity of Fusarium species associated with diseased Pinus patula, P. tecunumanii, P. kesiya and P. maximinoi in Colombian plantations and nurseries. Plants displaying symptoms associated with a F. circinatum-like infection (i.e., stem cankers and branch die-back on trees in plantations and root or collar rot of seedlings) were sampled. A total of 57 isolates were collected and characterised based on DNA sequence data for the translation elongation factor 1-α and β-tubulin gene regions. Phylogenetic analyses of these data allowed for the identification of more than 10 Fusarium species. These included F. circinatum, F. oxysporum, species within the Fusarium solani species complex and seven novel species in the Fusarium fujikuroi species complex (formerly the Gibberella fujikuroi species complex), five of which are described here as new. Selected isolates of the new species were tested for their pathogenicity on Pinus patula and compared with that of F. circinatum. Of these, F. marasasianum, F. parvisorum and F. sororula displayed levels of pathogenicity to P. patula that were comparable with that of F. circinatum. These apparently emerging pathogens thus pose a significant risk to forestry in Colombia and other parts of the world. PMID:26955193

Gene flow in Prunus species in the context of novel trait risk assessment.

PubMed

Cici, S Zahra H; Van Acker, Rene C

2010-01-01

Prunus species are important commercial fruit (plums, apricot, peach and cherries), nut (almond) and ornamental trees cultivated broadly worldwide. This review compiles information from available literature on Prunus species in regard to gene flow and hybridization within this complex of species. The review serves as a resource for environmental risk assessment related to pollen mediated gene flow and the release of transgenic Prunus. It reveals that Prunus species, especially plums and cherries show high potential for transgene flow. A range of characteristics including; genetic diversity, genetic bridging capacity, inter- and intra-specific genetic compatibility, self sterility (in most species), high frequency of open pollination, insect assisted pollination, perennial nature, complex phenotypic architecture (canopy height, heterogeneous crown, number of flowers produced in an individual plant), tendency to escape from cultivation, and the existence of ornamental and road side Prunus species suggest that there is a tremendous and complicated ability for pollen mediated gene movement among Prunus species. Ploidy differences among Prunus species do not necessarily provide genetic segregation. The characteristics of Prunu s species highlight the complexity of maintaining coexistence between GM and non-GM Prunus if there were commercial production of GM Prunus species. The results of this review suggest that the commercialization of one GM Prunus species can create coexistence issues for commercial non-GM Prunus production. Despite advances in molecular markers and genetic analysis in agroecology, there remains limited information on the ecological diversity, metapopulation nature, population dynamics, and direct measures of gene flow among different subgenera represented in the Prunus genus. Robust environmental impact, biosafety and coexistence assessments for GM Prunus species will require better understanding of the mechanisms of gene flow and hybridization among species within the Prunus species complex. © ISBR, EDP Sciences, 2011.

Molecular phylogenetics and historical biogeography of the west-palearctic common toads (Bufo bufo species complex).

PubMed

Garcia-Porta, J; Litvinchuk, S N; Crochet, P A; Romano, A; Geniez, P H; Lo-Valvo, M; Lymberakis, P; Carranza, S

2012-04-01

In most pan-Eurasiatic species complexes, two phenomena have been traditionally considered key processes of their cladogenesis and biogeography. First, it is hypothesized that the origin and development of the Central Asian Deserts generated a biogeographic barrier that fragmented past continuous distributions in Eastern and Western domains. Second, Pleistocene glaciations have been proposed as the main process driving the regional diversification within each of these domains. The European common toad and its closest relatives provide an interesting opportunity to examine the relative contributions of these paleogeographic and paleoclimatic events to the phylogeny and biogeography of a widespread Eurasiatic group. We investigate this issue by applying a multiproxy approach combining information from molecular phylogenies, a multiple correspondence analysis of allozyme data and species distribution models. Our study includes 304 specimens from 164 populations, covering most of the distributional range of the Bufo bufo species complex in the Western Palearctic. The phylogenies (ML and Bayesian analyses) were based on a total of 1988 bp of mitochondrial DNA encompassing three genes (tRNAval, 16S and ND1). A dataset with 173 species of the family Bufonidae was assembled to estimate the separation of the two pan-Eurasiatic species complexes of Bufo and to date the main biogeographic events within the Bufo bufo species complex. The allozyme study included sixteen protein systems, corresponding to 21 presumptive loci. Finally, the distribution models were based on maximum entropy. Our distribution models show that Eastern and Western species complexes are greatly isolated by the Central Asian Deserts, and our dating estimates place this divergence during the Middle Miocene, a moment in which different sources of evidence document a major upturn of the aridification rate of Central Asia. This climate-driven process likely separated the Eastern and Western species. At the level of the Western Palearctic, our dating estimates place most of the deepest phylogenetic structure before the Pleistocene, indicating that Pleistocene glaciations did not have a major role in splitting the major lineages. At a shallow level, the glacial dynamics contributed unevenly to the genetic structuring of populations, with a strong influence in the European-Caucasian populations, and a more relaxed effect in the Iberian populations. Copyright © 2011 Elsevier Inc. All rights reserved.

Incomplete Combustion of Hydrogen: Trapping a Reaction Intermediate

ERIC Educational Resources Information Center

Mattson, Bruce; Hoette, Trisha

2007-01-01

The combustion of hydrogen in air is quite complex with at least 28 mechanistic steps and twelve reaction species. Most of the species involved are radicals (having unpaired electrons) in nature. Among the various species generated, a few are stable, including hydrogen peroxide. In a normal hydrogen flame, the hydrogen peroxide goes on to further…

The Colletotrichum destructivum species complex – hemibiotrophic pathogens of forage and field crops

PubMed Central

Damm, U.; O'Connell, R.J.; Groenewald, J.Z.; Crous, P.W.

2014-01-01

Colletotrichum destructivum is an important plant pathogen, mainly of forage and grain legumes including clover, alfalfa, cowpea and lentil, but has also been reported as an anthracnose pathogen of many other plants worldwide. Several Colletotrichum isolates, previously reported as closely related to C. destructivum, are known to establish hemibiotrophic infections in different hosts. The inconsistent application of names to those isolates based on outdated species concepts has caused much taxonomic confusion, particularly in the plant pathology literature. A multilocus DNA sequence analysis (ITS, GAPDH, CHS-1, HIS3, ACT, TUB2) of 83 isolates of C. destructivum and related species revealed 16 clades that are recognised as separate species in the C. destructivum complex, which includes C. destructivum, C. fuscum, C. higginsianum, C. lini and C. tabacum. Each of these species is lecto-, epi- or neotypified in this study. Additionally, eight species, namely C. americae-borealis, C. antirrhinicola, C. bryoniicola, C. lentis, C. ocimi, C. pisicola, C. utrechtense and C. vignae are newly described. PMID:25492986

Fungus-feeding Thysanoptera: Phlaeothripinae of the Idiothrips genus-group in Australia, with nine new species.

PubMed

Mound, Laurence A; Tree, Desley J

2015-10-29

In a group of fungus-feeding Phlaeothripinae characterized by complex body sculpture, identification keys are provided to three genera and 15 species from Australia, including nine new species. In the genus Azaleothrips one new species is described, and one Asian species is newly recorded from Australia. The genus Stictothrips is recorded from Australia for the first time, with two new species. Within the genus Strepterothrips considerable structural diversity is recorded including three new species in which antennal segment III is greatly reduced and bears no sense cones. Some species in this genus exhibit the unusual condition of having several setae on the pelta, the first abdominal tergite. Problems in the production of generic diagnoses within the Phlaeothripinae are discussed.

Enhancement of C-H Oxidizing Ability in Co-O2  Complexes through an Isolated Heterobimetallic Oxo Intermediate.

PubMed

DeRosha, Daniel E; Mercado, Brandon Q; Lukat-Rodgers, Gudrun; Rodgers, Kenton R; Holland, Patrick L

2017-03-13

The characterization of intermediates formed through the reaction of transition-metal complexes with dioxygen (O 2 ) is important for understanding oxidation in biological and synthetic processes. Here, the reaction of the diketiminate-supported cobalt(I) complex L tBu Co with O 2 gives a rare example of a side-on dioxygen complex of cobalt. Structural, spectroscopic, and computational data are most consistent with its assignment as a cobalt(III)-peroxo complex. Treatment of L tBu Co(O 2 ) with low-valent Fe and Co diketiminate complexes affords isolable oxo species with M 2 O 2 "diamond" cores, including the first example of a crystallographically characterized heterobimetallic bis(μ-oxo) complex of two transition metals. The bimetallic species are capable of cleaving C-H bonds in the supporting ligands, and kinetic studies show that the Fe/Co heterobimetallic species activates C-H bonds much more rapidly than the Co/Co homobimetallic analogue. Thus heterobimetallic oxo intermediates provide a promising route for enhancing the rates of oxidation reactions. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular Identification and Susceptibility of Clinically Relevant Scedosporium spp. in China

PubMed Central

Wang, Hong; Wan, Zhe; Li, Ruoyu; Lu, Qiaoyun

2015-01-01

As various new sibling species within the Scedosporium spp. have been described recently, this study was conducted to investigate distribution and antifungal susceptibility profiles of the different species of Scedosporium spp. in China. Twenty-one clinical strains of Scedosporium from China and two strains from Japan were reidentified by MLSA. The analysis included BT2, CAL, RPB, SOD, and ACT and the combination of the five loci. Pseudallescheria boydii complex (17 strains) and S. apiospermum (6 strains) were identified. P. boydii complex included four closely related subgroups: P. boydii (9 strains), P. ellipsoidea (6 strains), P. fusoidea (1 strain), and P. angusta (1 strain). There were no significant differences in MICs for neither VOR, POS, nor AMB over all the five species in study. For itraconazole, intraspecific diversity was evident. PMID:26550562

Molecular identification and susceptibility of clinically relevant Scedosporium spp. in China.

PubMed

Wang, Hong; Wan, Zhe; Li, Ruoyu; Lu, Qiaoyun; Yu, Jin

2015-01-01

As various new sibling species within the Scedosporium spp. have been described recently, this study was conducted to investigate distribution and antifungal susceptibility profiles of the different species of Scedosporium spp. in China. Twenty-one clinical strains of Scedosporium from China and two strains from Japan were reidentified by MLSA. The analysis included BT2, CAL, RPB, SOD, and ACT and the combination of the five loci. Pseudallescheria boydii complex (17 strains) and S. apiospermum (6 strains) were identified. P. boydii complex included four closely related subgroups: P. boydii (9 strains), P. ellipsoidea (6 strains), P. fusoidea (1 strain), and P. angusta (1 strain). There were no significant differences in MICs for neither VOR, POS, nor AMB over all the five species in study. For itraconazole, intraspecific diversity was evident.

Echinococcus ortleppi, the cattle strain in a crested porcupine (Hystrix cristata): A new host record.

PubMed

Hodžić, Adnan; Alić, Amer; Šupić, Jovana; Škapur, Vedad; Duscher, Georg Gerhard

2018-05-30

Echinococcus granulosus sensu lato, a dog tapeworm is a species complex causing cystic echinococcosis or hydatid disease in a great variety of mammalian intermediate hosts, including humans. This complex comprises five species including Echinococcus ortleppi (G5 genotype or cattle strain). In the present paper, we report the first case of infection with the larval stage of latter cestode in a captive crested porcupine (Hystrix cristata), molecularly confirmed by PCR and sequencing of the cox1 and nad1 genes. The food contaminated with the parasite's eggs is the most likely source of the infection. Our data broaden the knowledge on the host range and geographical distribution of this rarely reported species of Echinococcus in Europe. Copyright © 2018 Elsevier B.V. All rights reserved.

Otolith shape analysis and mitochondrial DNA markers distinguish three sand smelt species in the Atherina boyeri species complex in western Mediterranean

NASA Astrophysics Data System (ADS)

Boudinar, A. S.; Chaoui, L.; Quignard, J. P.; Aurelle, D.; Kara, M. H.

2016-12-01

Atherina boyeri is a common euryhaline teleost fish in the Mediterranean and adjacent areas, which inhabits coastal and estuarine waters, including coastal lagoons and more rarely inland waters. Several recent studies have pointed the possible existence of three distinct groups or species, one lagoon/freshwater group and two 'punctuated and unpunctuated on the flanks' marine groups, within an A. boyeri species complex. This study is a combined approach using otolith shape and molecular markers to better define the structure of the species in the western Mediterranean. Genetic differentiation and species delimitation among nine Atherina boyeri populations from several marine and lagoon/brakish habitat sites in Algeria, Tunisia and France were investigated using three mitochondrial (control region, Cyt b and 16S) and one nuclear markers (2nd intron of S7). For further phylogenetic and phylogeographic study, we added sequences from Genbank covering more areas (Ionian Sea, Adriatic Sea, Tyrrhenian Sea, Black Sea, Atlantic). Five groups were found. Two of them perfectly corresponded to two species already recognized Atherina presbyter and Atherina hepsetus, both living in marine waters; and three additional, including Atherina boyeri (brackish and freshwater environments) and two independent groups of marine punctated and unpunctated individuals. Those findings are corroborated by the study of the otolith contour shape of 362 individuals of seven populations from different habitats using Fourier analysis. Individuals could be discriminated into five groups based on the first two functions (Wilk's lambda = 0.07, p < 0.001). Samples from Ziama inlet, marine punctuated individuals and unpunctuated marine specimens from Annaba's Gulf formed three well separated groups. Specimens from Mellah and Mauguio lagoons formed another group. The last one includes individuals from Bizerte and Thau lagoons. The divergences between them strongly support the potential species within the A. boyeri species complex.

Waterflooding injectate design systems and methods

DOEpatents

Brady, Patrick V.; Krumhansl, James L.

2014-08-19

A method of designing an injectate to be used in a waterflooding operation is disclosed. One aspect includes specifying data representative of chemical characteristics of a liquid hydrocarbon, a connate, and a reservoir rock, of a subterranean reservoir. Charged species at an interface of the liquid hydrocarbon are determined based on the specified data by evaluating at least one chemical reaction. Charged species at an interface of the reservoir rock are determined based on the specified data by evaluating at least one chemical reaction. An extent of surface complexation between the charged species at the interfaces of the liquid hydrocarbon and the reservoir rock is determined by evaluating at least one surface complexation reaction. The injectate is designed and is operable to decrease the extent of surface complexation between the charged species at interfaces of the liquid hydrocarbon and the reservoir rock. Other methods, apparatus, and systems are disclosed.

Cryptic Species Identification and Composition of Bemisia tabaci (Hemiptera: Aleyrodidae) Complex in Henan Province, China.

PubMed

Jiu, Min; Hu, Jian; Wang, Lun-Ji; Dong, Jun-Feng; Song, Yue-Qin; Sun, Hui-Zhong

2017-05-01

Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex, causing significant crop losses in China during the last decade. Although knowledge of cryptic species composition and dynamics within B. tabaci complex is critical for developing sustainable pest management strategies, limited information is available on this pest in the Henan province of China. A systematic survey of the cryptic species composition and distribution of B. tabaci complex in different locations of Henan province was conducted in 2012. The results of RAPD-PCR and the gene for the mitochondrial cytochrome oxidase subunit-1 (mtCOI) based phylogenetic relationships established using Bayesian method indicated there were four known cryptic species MEAM1, MED, Asia II 3, Asia II 9 and a new cryptic species named China 6 in Henan province. In the survey, the invasive cryptic species MED and MEAM1 were found to be predominant with wide spread distribution across the surveyed regions. On the contrary, the indigenous B. tabaci cryptic species including Asia II 3, Asia II 9 and China 6 remained with low prevalence in some surveyed regions. Cryptic species MEAM1 and MED have not completely displaced the native B. tabaci in Henan province. This current study for the first time unifies our knowledge of the diversity and distribution of B. tabaci across Henan province of China. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America.

Structure and function of complex I in animals and plants - a comparative view.

PubMed

Senkler, Jennifer; Senkler, Michael; Braun, Hans-Peter

2017-09-01

The mitochondrial NADH dehydrogenase complex (complex I) has a molecular mass of about 1000 kDa and includes 40-50 subunits in animals, fungi and plants. It is composed of a membrane arm and a peripheral arm and has a conserved L-like shape in all species investigated. However, in plants and possibly some protists it has a second peripheral domain which is attached to the membrane arm on its matrix exposed side at a central position. The extra domain includes proteins resembling prokaryotic gamma-type carbonic anhydrases. We here present a detailed comparison of complex I from mammals and flowering plants. Forty homologous subunits are present in complex I of both groups of species. In addition, five subunits are present in mammalian complex I, which are absent in plants, and eight to nine subunits are present in plant complex I which do not occur in mammals. Based on the atomic structure of mammalian complex I and biochemical insights into complex I architecture from plants we mapped the species-specific subunits. Interestingly, four of the five animal-specific and five of the eight to nine plant-specific subunits are localized at the inner surface of the membrane arm of complex I in close proximity. We propose that the inner surface of the membrane arm represents a workbench for attaching proteins to complex I, which are not directly related to respiratory electron transport, like nucleoside kinases, acyl-carrier proteins or carbonic anhydrases. We speculate that further enzyme activities might be bound to this micro-location in other groups of organisms. © 2017 Scandinavian Plant Physiology Society.

Interaction complexity matters: disentangling services and disservices of ant communities driving yield in tropical agroecosystems

PubMed Central

Wielgoss, Arno; Tscharntke, Teja; Rumede, Alfianus; Fiala, Brigitte; Seidel, Hannes; Shahabuddin, Saleh; Clough, Yann

2014-01-01

Owing to complex direct and indirect effects, impacts of higher trophic levels on plants is poorly understood. In tropical agroecosystems, ants interact with crop mutualists and antagonists, but little is known about how this integrates into the final ecosystem service, crop yield. We combined ant exclusion and introduction of invasive and native-dominant species in cacao agroecosystems to test whether (i) ant exclusion reduces yield, (ii) dominant species maximize certain intermediate ecosystem services (e.g. control of specific pests) rather than yield, which depends on several, cascading intermediate services and (iii) even, species-rich ant communities result in highest yields. Ants provided services, including reduced leaf herbivory and fruit pest damage and indirect pollination facilitation, but also disservices, such as increased mealybug density, phytopathogen dissemination and indirect pest damage enhancement. Yields were highest with unmanipulated, species-rich, even communities, whereas ant exclusion decreased yield by 27%. Introduction of an invasive-dominant ant decreased species density and evenness and resulted in 34% lower yields, whereas introduction of a non-invasive-dominant species resulted in similar species density and yields as in the unmanipulated control. Species traits and ant community structure affect services and disservices for agriculture in surprisingly complex ways, with species-rich and even communities promoting highest yield. PMID:24307667

What Explains Patterns of Diversification and Richness among Animal Phyla?

PubMed Central

Jezkova, Tereza; Wiens, John J.

2016-01-01

Animal phyla vary dramatically in species richness (from 1 species to >1.2 million), but the causes of this variation remain largely unknown. Animals have also evolved striking variation in morphology and ecology, including sessile marine taxa lacking heads, eyes, limbs, and complex organs (e.g. sponges), parasitic worms (e.g. nematodes, platyhelminths), and taxa with eyes, skeletons, limbs, and complex organs that dominate terrestrial ecosystems (arthropods, chordates). Relating this remarkable variation in traits to the diversification and richness of animal phyla is a fundamental yet unresolved problem in biology. Here, we test the impacts of 18 traits (including morphology, ecology, reproduction, and development) on diversification and richness of extant animal phyla. Using phylogenetic multiple regression, the best-fitting model includes five traits that explain ~74% of the variation in diversification rates (dioecy, parasitism, eyes/photoreceptors, a skeleton, non-marine habitat). However, a model including just three (skeleton, parasitism, habitat) explains nearly as much variation (~67%). Diversification rates then largely explain richness patterns. Our results also identify many striking traits that have surprisingly little impact on diversification (e.g. head, limbs, and complex circulatory and digestive systems). Overall, our results reveal the key factors that shape large-scale patterns of diversification and richness across >80% of all extant, described species. PMID:28221832

What Explains Patterns of Diversification and Richness among Animal Phyla?

PubMed

Jezkova, Tereza; Wiens, John J

2017-03-01

Animal phyla vary dramatically in species richness (from one species to >1.2 million), but the causes of this variation remain largely unknown. Animals have also evolved striking variation in morphology and ecology, including sessile marine taxa lacking heads, eyes, limbs, and complex organs (e.g., sponges), parasitic worms (e.g., nematodes, platyhelminths), and taxa with eyes, skeletons, limbs, and complex organs that dominate terrestrial ecosystems (arthropods, chordates). Relating this remarkable variation in traits to the diversification and richness of animal phyla is a fundamental yet unresolved problem in biology. Here, we test the impacts of 18 traits (including morphology, ecology, reproduction, and development) on diversification and richness of extant animal phyla. Using phylogenetic multiple regression, the best-fitting model includes five traits that explain ∼74% of the variation in diversification rates (dioecy, parasitism, eyes/photoreceptors, a skeleton, nonmarine habitat). However, a model including just three (skeleton, parasitism, habitat) explains nearly as much variation (∼67%). Diversification rates then largely explain richness patterns. Our results also identify many striking traits that have surprisingly little impact on diversification (e.g., head, limbs, and complex circulatory and digestive systems). Overall, our results reveal the key factors that shape large-scale patterns of diversification and richness across >80% of all extant, described species.

Genetic constraints on wing pattern variation in Lycaeides butterflies: A case study on mapping complex, multifaceted traits in structured populations.

PubMed

Lucas, Lauren K; Nice, Chris C; Gompert, Zachariah

2018-03-13

Patterns of phenotypic variation within and among species can be shaped and constrained by trait genetic architecture. This is particularly true for complex traits, such as butterfly wing patterns, that consist of multiple elements. Understanding the genetics of complex trait variation across species boundaries is difficult, as it necessitates mapping in structured populations and can involve many loci with small or variable phenotypic effects. Here, we investigate the genetic architecture of complex wing pattern variation in Lycaeides butterflies as a case study of mapping multivariate traits in wild populations that include multiple nominal species or groups. We identify conserved modules of integrated wing pattern elements within populations and species. We show that trait covariances within modules have a genetic basis and thus represent genetic constraints that can channel evolution. Consistent with this, we find evidence that evolutionary changes in wing patterns among populations and species occur in the directions of genetic covariances within these groups. Thus, we show that genetic constraints affect patterns of biological diversity (wing pattern) in Lycaeides, and we provide an analytical template for similar work in other systems. © 2018 John Wiley & Sons Ltd.

Phylogenetic and population genetic analyses of Phaeosphaeria nodorum and its close relatives indicate cryptic species and an origin in the Fertile Crescent.

PubMed

McDonald, Megan C; Razavi, Mohammad; Friesen, Timothy L; Brunner, Patrick C; McDonald, Bruce A

2012-11-01

The origin of the fungal wheat pathogen Phaeosphaeria nodorum remains unclear despite earlier intensive global population genetic and phylogeographical studies. We sequenced 1683 bp distributed across three loci in 355 globally distributed Phaeosphaeria isolates, including 74 collected in Iran near the center of origin of wheat. We identified nine phylogenetically distinct clades, including two previously unknown species tentatively named P1 and P2 collected in Iran. Coalescent analysis indicates that P1 and P2 are sister species of P. nodorum and the other Phaeosphaeria species identified in our analysis. Two species, P. nodorum and P. avenaria f. sp. tritici 1 (Pat1), comprised ~85% of the sampled isolates, making them the dominant wheat-infecting pathogens within the species complex. We designed a PCR-RFLP assay to distinguish P. nodorum from Pat1. Approximately 4% of P. nodorum and Pat1 isolates showed evidence of hybridization. Measures of private allelic richness at SSR and sequence loci suggest that the center of origin of P. nodorum coincides with its host in the Fertile Crescent. We hypothesize that the origin of this species complex is also in the Fertile Crescent, with four species out of nine found exclusively in the Iranian collections. Copyright © 2012 Elsevier Inc. All rights reserved.

The Diaporthe sojae species complex: Phylogenetic re-assessment of pathogens associated with soybean, cucurbits and other field crops.

PubMed

Udayanga, Dhanushka; Castlebury, Lisa A; Rossman, Amy Y; Chukeatirote, Ekachai; Hyde, Kevin D

2015-05-01

Phytopathogenic species of Diaporthe are associated with a number of soybean diseases including seed decay, pod and stem blight and stem canker and lead to considerable crop production losses worldwide. Accurate morphological identification of the species that cause these diseases has been difficult. In this study, we determined the phylogenetic relationships and species boundaries of Diaporthe longicolla, Diaporthe phaseolorum, Diaporthe sojae and closely related taxa. Species boundaries for this complex were determined based on combined phylogenetic analysis of five gene regions: partial sequences of calmodulin (CAL), beta-tubulin (TUB), histone-3 (HIS), translation elongation factor 1-α (EF1-α), and the nuclear ribosomal internal transcribed spacers (ITS). Phylogenetic analyses revealed that this large complex of taxa is comprised of soybean pathogens as well as species associated with herbaceous field crops and weeds. Diaporthe arctii, Diaporthe batatas, D. phaseolorum and D. sojae are epitypified. The seed decay pathogen D. longicolla was determined to be distinct from D. sojae. D. phaseolorum, originally associated with stem and leaf blight of Lima bean, was not found to be associated with soybean. A new species, Diaporthe ueckerae on Cucumis melo, is introduced with description and illustrations. Published by Elsevier Ltd.

Molecular Evidences of a Hidden Complex Scenario in Leporinus cf. friderici

PubMed Central

Silva-Santos, Rosane; Ramirez, Jorge L.; Galetti, Pedro M.; Freitas, Patrícia D.

2018-01-01

The megadiversity of the neotropical ichthyofauna has been associated to recent diversification processes, reflecting in subtle or lacking morphological differentiation between species, challenging the classical taxonomic identification. Leporinus friderici occurs in several river basins of South America, and its nominal taxonomic validity has been questioned. Its wide distribution within the Brazilian Shield suggests that this species could be genetically structured among the hydrographic basins, despite a sharp morphological similarity. In this study, we performed phylogenetic analyses, based on three nuclear (recombination activating gene 1, RAG1, recombination activating gene 2, RAG2, and myosin heavy chain 6 cardiac muscle alpha gene, Myh6) and two mitochondrial (COI and Cytochrome b, Cytb) markers, in specimens morphologically similar to L. friderici and related species from different hydrographic basins in South America. Our phylogenetic tree identified four well-supported clades, which point out to the existence of taxonomic inconsistencies within this fish group. A clade named L. cf. friderici sensu stricto included eight Molecular Operational Taxonomic Units recently diversified in the Brazilian Shield basins. These results were also confirmed by a single-gene species delimitation analysis. It is suggested that this clade includes a species complex, characterizing taxonomic uncertainties. Another clade recovered only L. friderici from the Suriname rivers, validating this nominal species in its type locality. A third no-named clade, characterized by deeper species divergence, recovered five different nominal species interleaved with other undescribed forms previously also recognized as L. cf. friderici, indicating taxonomic errors. The fourth clade only included L. taeniatus. Our results showed a complex scenario involving the morphotype L. cf. friderici and allowed us to address aspects related to evolutionary diversification of this fish group and historical processes involved with, highlighting the importance of revealing hidden biodiversity for the taxonomy and conservationist action plans of these fish. PMID:29497440

Relative Importance of Coral Cover, Habitat Complexity and Diversity in Determining the Structure of Reef Fish Communities

PubMed Central

Komyakova, Valeriya; Munday, Philip L.; Jones, Geoffrey P.

2013-01-01

The structure of coral reef habitat has a pronounced influence on the diversity, composition and abundance of reef-associated fishes. However, the particular features of the habitat that are most critical are not always known. Coral habitats can vary in many characteristics, notably live coral cover, topographic complexity and coral diversity, but the relative effects of these habitat characteristics are often not distinguished. Here, we investigate the strength of the relationships between these habitat features and local fish diversity, abundance and community structure in the lagoon of Lizard Island, Great Barrier Reef. In a spatial comparison using sixty-six 2m2 quadrats, fish species richness, total abundance and community structure were examined in relation to a wide range of habitat variables, including topographic complexity, habitat diversity, coral diversity, coral species richness, hard coral cover, branching coral cover and the cover of corymbose corals. Fish species richness and total abundance were strongly associated with coral species richness and cover, but only weakly associated with topographic complexity. Regression tree analysis showed that coral species richness accounted for most of the variation in fish species richness (63.6%), while hard coral cover explained more variation in total fish abundance (17.4%), than any other variable. In contrast, topographic complexity accounted for little spatial variation in reef fish assemblages. In degrading coral reef environments, the potential effects of loss of coral cover and topographic complexity are often emphasized, but these findings suggest that reduced coral biodiversity may ultimately have an equal, or greater, impact on reef-associated fish communities. PMID:24349455

Relative importance of coral cover, habitat complexity and diversity in determining the structure of reef fish communities.

PubMed

Komyakova, Valeriya; Munday, Philip L; Jones, Geoffrey P

2013-01-01

The structure of coral reef habitat has a pronounced influence on the diversity, composition and abundance of reef-associated fishes. However, the particular features of the habitat that are most critical are not always known. Coral habitats can vary in many characteristics, notably live coral cover, topographic complexity and coral diversity, but the relative effects of these habitat characteristics are often not distinguished. Here, we investigate the strength of the relationships between these habitat features and local fish diversity, abundance and community structure in the lagoon of Lizard Island, Great Barrier Reef. In a spatial comparison using sixty-six 2m(2) quadrats, fish species richness, total abundance and community structure were examined in relation to a wide range of habitat variables, including topographic complexity, habitat diversity, coral diversity, coral species richness, hard coral cover, branching coral cover and the cover of corymbose corals. Fish species richness and total abundance were strongly associated with coral species richness and cover, but only weakly associated with topographic complexity. Regression tree analysis showed that coral species richness accounted for most of the variation in fish species richness (63.6%), while hard coral cover explained more variation in total fish abundance (17.4%), than any other variable. In contrast, topographic complexity accounted for little spatial variation in reef fish assemblages. In degrading coral reef environments, the potential effects of loss of coral cover and topographic complexity are often emphasized, but these findings suggest that reduced coral biodiversity may ultimately have an equal, or greater, impact on reef-associated fish communities.

Molecular and Phenotypic Data Supporting Distinct Species Statuses for Scedosporium apiospermum and Pseudallescheria boydii and the Proposed New Species Scedosporium dehoogii▿ † ‡

PubMed Central

Gilgado, Fèlix; Cano, Josep; Gené, Josepa; Sutton, Deanna A.; Guarro, Josep

2008-01-01

Based on the morphological, physiologic, and molecular (β-tubulin gene) study of 141 isolates of the Pseudallescheria boydii species complex (including several synonyms) and relatives, the new species Scedosporium dehoogii is proposed. Scedosporium apiospermum and P. boydii are considered two different species and the new name Scedosporium boydii is proposed for the anamorph of the latter species. A summary of the key morphological and physiological features for distinguishing the species of Pseudallescheria/Scedosporium is provided. PMID:18077629

Molecular and phenotypic data supporting distinct species statuses for Scedosporium apiospermum and Pseudallescheria boydii and the proposed new species Scedosporium dehoogii.

PubMed

Gilgado, Fèlix; Cano, Josep; Gené, Josepa; Sutton, Deanna A; Guarro, Josep

2008-02-01

Based on the morphological, physiologic, and molecular (beta-tubulin gene) study of 141 isolates of the Pseudallescheria boydii species complex (including several synonyms) and relatives, the new species Scedosporium dehoogii is proposed. Scedosporium apiospermum and P. boydii are considered two different species and the new name Scedosporium boydii is proposed for the anamorph of the latter species. A summary of the key morphological and physiological features for distinguishing the species of Pseudallescheria/Scedosporium is provided.

Revision of the African pollen beetle genera Tarchonanthogethes and Xenostrongylogethes, with insect-host plant relationships, identification key, and cladistic analysis of the Anthystrix genus-complex (Coleoptera: Nitidulidae: Meligethinae).

PubMed

Audisio, Paolo; Cline, Andrew R; Trizzino, Marco; Mancini, Emiliano; Antonini, Gloria; Sabatelli, Simone; Cerretti, Pierfilippo

2015-02-19

The Afrotropical endemic pollen beetle genera Tarchonanthogethes Audisio & Cline and Xenostrongylogethes Audisio & Cline, of the Anthystrix genus-complex, are revised. Eleven new species of Tarchonanthogethes (T. autumnalis, sp. nov., T. bisignatus, sp. nov., T. fasciatus, sp. nov., T. gratiellae, sp. nov., T. hermani, sp. nov., T. hystrix, sp. nov., T. lilliputianus, sp. nov., T. maasai, sp. nov., T. manconiae, sp. nov., T. pectinipes, sp. nov., T. thalycriformis, sp. nov.) and one new Xenostrongylogethes (X. cychramoides, sp. nov.) are described, illustrated and compared with related taxa. Tarchonanthogethes hirtus Kirejtshuk & Easton, 1988 is synonymized with T. martini (syn. nov.). Meligethes assutus Easton, 1960 from Kenya is transferred from Afrogethes Audisio & Cline to Tarchonanthogethes (comb. nov.). Meligethes singularis Grouvelle, 1919 from southern Africa is transferred from Tarchonanthogethes to Meligethinus Grouvelle, 1906 (comb. nov.). Larval host-plants for Tarchonanthogethes and Xenostrongylogethes include dioecious bushes and trees of Tarchonantheae Asteraceae (genera Brachylaena R.Br. and Tarchonanthus L.). All species currently attributed to the genera Anthystrix Kirejtshuk, Sebastiangethes Audisio, Kirk-Spriggs & Cline, Tarchonanthogethes and Xenostrongylogethes (Anthystrix genus-complex) are included in a morphology-based cladistic analysis to provide a rigorous hypothesis of phylogenetic relationships. An identification key to all 25 known species in the Anthystrix genus-complex, including all available data on insect host plant relationships, is presented.

Tapping the promise of genomics in species with complex, nonmodel genomes.

PubMed

Hirsch, Candice N; Buell, C Robin

2013-01-01

Genomics is enabling a renaissance in all disciplines of plant biology. However, many plant genomes are complex and remain recalcitrant to current genomic technologies. The complexities of these nonmodel plant genomes are attributable to gene and genome duplication, heterozygosity, ploidy, and/or repetitive sequences. Methods are available to simplify the genome and reduce these barriers, including inbreeding and genome reduction, making these species amenable to current sequencing and assembly methods. Some, but not all, of the complexities in nonmodel genomes can be bypassed by sequencing the transcriptome rather than the genome. Additionally, comparative genomics approaches, which leverage phylogenetic relatedness, can aid in the interpretation of complex genomes. Although there are limitations in accessing complex nonmodel plant genomes using current sequencing technologies, genome manipulation and resourceful analyses can allow access to even the most recalcitrant plant genomes.

The importance of motivation, weapons, and foul odors in driving encounter competition in carnivores.

PubMed

Allen, Maximilian L; Wilmers, Christopher C; Elbroch, L Mark; Golla, Julie M; Wittmer, Heiko U

2016-08-01

Encounter competition is interference competition in which animals directly contend for resources. Ecological theory predicts the trait that determines the resource holding potential (RHP), and hence the winner of encounter competition, is most often body size or mass. The difficulties of observing encounter competition in complex organisms in natural environments, however, has limited opportunities to test this theory across diverse species. We studied the outcome of encounter competition contests among mesocarnivores at deer carcasses in California to determine the most important variables for winning these contests. We found some support for current theory in that body mass is important in determining the winner of encounter competition, but we found that other factors including hunger and species-specific traits were also important. In particular, our top models were "strength and hunger" and "size and hunger," with models emphasizing the complexity of variables influencing outcomes of encounter competition. In addition, our wins above predicted (WAP) statistic suggests that an important aspect that determines the winner of encounter competition is species-specific advantages that increase their RHP, as bobcats (Lynx rufus) and spotted skunks (Spilogale gracilis) won more often than predicted based on mass. In complex organisms, such as mesocarnivores, species-specific adaptations, including strategic behaviors, aggressiveness, and weapons, contribute to competitive advantages and may allow certain species to take control or defend resources better than others. Our results help explain how interspecific competition shapes the occurrence patterns of species in ecological communities. © 2016 by the Ecological Society of America.

Species and ecological diversity within the Cladosporium cladosporioides complex (Davidiellaceae, Capnodiales)

PubMed Central

Bensch, K.; Groenewald, J.Z.; Dijksterhuis, J.; Starink-Willemse, M.; Andersen, B.; Summerell, B.A.; Shin, H.-D.; Dugan, F.M.; Schroers, H.-J.; Braun, U.; Crous, P.W.

2010-01-01

The genus Cladosporium is one of the largest genera of dematiaceous hyphomycetes, and is characterised by a coronate scar structure, conidia in acropetal chains and Davidiella teleomorphs. Based on morphology and DNA phylogeny, the species complexes of C. herbarum and C. sphaerospermum have been resolved, resulting in the elucidation of numerous new taxa. In the present study, more than 200 isolates belonging to the C. cladosporioides complex were examined and phylogenetically analysed on the basis of DNA sequences of the nuclear ribosomal RNA gene operon, including the internal transcribed spacer regions ITS1 and ITS2, the 5.8S nrDNA, as well as partial actin and translation elongation factor 1-α gene sequences. For the saprobic, widely distributed species Cladosporium cladosporioides, both a neotype and epitype are designated in order to specify a well established circumscription and concept of this species. Cladosporium tenuissimum and C. oxysporum, two saprobes abundant in the tropics, are epitypified and shown to be allied to, but distinct from C. cladosporioides. Twenty-two species are newly described on the basis of phylogenetic characters and cryptic morphological differences. The most important phenotypic characters for distinguishing species within the C. cladosporioides complex, which represents a monophyletic subclade within the genus, are shape, width, length, septation and surface ornamentation of conidia and conidiophores; length and branching patterns of conidial chains and hyphal shape, width and arrangement. Many of the treated species, e.g., C. acalyphae, C. angustisporum, C. australiense, C. basiinflatum, C. chalastosporoides, C. colocasiae, C. cucumerinum, C. exasperatum, C. exile, C. flabelliforme, C. gamsianum, and C. globisporum are currently known only from specific hosts, or have a restricted geographical distribution. A key to all species recognised within the C. cladosporioides complex is provided. PMID:20877444

Whole-tree silvic identifications and the microsatellite genetic structure of a red oak species complex in an Indiana old-growth forest

Treesearch

Preston R. Aldrich; George R. Parker; Charles H. Michler; Jeanne Romero-Severson

2003-01-01

The red oaks (Quercus section Lobatae) include important timber species, but we know little about their gene pools. Red oak species can be difficult to identify, possibly because of extensive interspecific hybridization, although most evidence of this is morphological. We used 15 microsatellite loci to examine the genetic...

Phylogenomics and species delimitation of a complex radiation of Neotropical suboscine birds (Pachyramphus).

PubMed

Musher, Lukas J; Cracraft, Joel

2018-01-01

Phylogeographic studies within the Neotropics continue to uncover hidden diversity, the extent of which remains poorly known. In birds, molecular studies are producing evidence that species-level diversity is substantially underestimated. Many avian taxa comprise large complexes of subspecies that often represent species-level taxa by various criteria. One such group of Neotropical suboscine birds, the becards (Pachyramphus), ranges from Argentina through northern Mexico. Their taxonomic limits have been complex and controversial as the genus has bounced around a number of suboscine families. Additionally, the phylogenetic relationships within Pachyramphus are unresolved due to insufficient sampling of taxa and populations across species' ranges. We used target capture of ultraconserved elements for 62 individuals representing 42 taxa, and sequenced two mitochondrial genes and two nuclear introns covering 265 individuals of 51 taxa, including all recognized species, resulting in the most densely and completely sampled phylogenetic hypothesis for Pachyramphus to date. We delimited species using a traditional taxonomic approach and then tested them under a Bayesian multi-species coalescent framework. In doing so, we provide evidence for multiple young, previously undetected evolutionary lineages within Pachyramphus. Deep, well-supported branches and a high number of intraspecific lineages across the tree suggest that at least 50% of species diversity may be unrecognized. Copyright © 2017 Elsevier Inc. All rights reserved.

Polymorphism at the defensin gene in the Anopheles gambiae complex: testing different selection hypotheses

PubMed Central

Simard, Frédéric; Licht, Monica; Besansky, Nora J.; Lehmann, Tovi

2007-01-01

Genetic variation in defensin, a gene encoding a major effector molecule of insects immune response was analyzed within and between populations of three members of the Anopheles gambiae complex. The species selected included the two anthropophilic species, An. gambiae and An. arabiensis and the most zoophilic species of the complex, An. quadriannulatus. The first species was represented by four populations spanning its extreme genetic and geographical ranges, whereas each of the other two species was represented by a single population. We found (i) reduced overall polymorphism in the mature peptide region and in the total coding region, together with specific reductions in rare and moderately frequent mutations (sites) in the coding region compared with non coding regions, (ii) markedly reduced rate of nonsynonymous diversity compared with synonymous variation in the mature peptide and virtually identical mature peptide across the three species, and (iii) increased divergence between species in the mature peptide together with reduced differentiation between populations of An. gambiae in the same DNA region. These patterns suggest a strong purifying selection on the mature peptide and probably the whole coding region. Because An. quadriannulatus is not exposed to human pathogens, identical mature peptide and similar pattern of polymorphism across species implies that human pathogens played no role as selective agents on this peptide. PMID:17161659

Disentangling the complexity of tropical small-scale fisheries dynamics using supervised Self-Organizing Maps.

PubMed

Mendoza-Carranza, Manuel; Ejarque, Elisabet; Nagelkerke, Leopold A J

2018-01-01

Tropical small-scale fisheries are typical for providing complex multivariate data, due to their diversity in fishing techniques and highly diverse species composition. In this paper we used for the first time a supervised Self-Organizing Map (xyf-SOM), to recognize and understand the internal heterogeneity of a tropical marine small-scale fishery, using as model the fishery fleet of San Pedro port, Tabasco, Mexico. We used multivariate data from commercial logbooks, including the following four factors: fish species (47), gear types (bottom longline, vertical line+shark longline and vertical line), season (cold, warm), and inter-annual variation (2007-2012). The size of the xyf-SOM, a fundamental characteristic to improve its predictive quality, was optimized for the minimum distance between objects and the maximum prediction rate. The xyf-SOM successfully classified individual fishing trips in relation to the four factors included in the model. Prediction percentages were high (80-100%) for bottom longline and vertical line + shark longline, but lower prediction values were obtained for vertical line (51-74%) fishery. A confusion matrix indicated that classification errors occurred within the same fishing gear. Prediction rates were validated by generating confidence interval using bootstrap. The xyf-SOM showed that not all the fishing trips were targeting the most abundant species and the catch rates were not symmetrically distributed around the mean. Also, the species composition is not homogeneous among fishing trips. Despite the complexity of the data, the xyf-SOM proved to be an excellent tool to identify trends in complex scenarios, emphasizing the diverse and complex patterns that characterize tropical small scale-fishery fleets.

Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum.

PubMed

Walkowiak, Sean; Rowland, Owen; Rodrigue, Nicolas; Subramaniam, Rajagopal

2016-12-09

The Fusarium graminearum species complex is composed of many distinct fungal species that cause several diseases in economically important crops, including Fusarium Head Blight of wheat. Despite being closely related, these species and individuals within species have distinct phenotypic differences in toxin production and pathogenicity, with some isolates reported as non-pathogenic on certain hosts. In this report, we compare genomes and gene content of six new isolates from the species complex, including the first available genomes of F. asiaticum and F. meridionale, with four other genomes reported in previous studies. A comparison of genome structure and gene content revealed a 93-99% overlap across all ten genomes. We identified more than 700 k base pairs (kb) of single nucleotide polymorphisms (SNPs), insertions, and deletions (indels) within common regions of the genome, which validated the species and genetic populations reported within species. We constructed a non-redundant pan gene list containing 15,297 genes from the ten genomes and among them 1827 genes or 12% were absent in at least one genome. These genes were co-localized in telomeric regions and select regions within chromosomes with a corresponding increase in SNPs and indels. Many are also predicted to encode for proteins involved in secondary metabolism and other functions associated with disease. Genes that were common between isolates contained high levels of nucleotide variation and may be pseudogenes, allelic, or under diversifying selection. The genomic resources we have contributed will be useful for the identification of genes that contribute to the phenotypic variation and niche specialization that have been reported among members of the F. graminearum species complex.

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.

Intraspecific Adaptations to Thermal Gradients in a Cosmopolitan Coccolithophore

NASA Astrophysics Data System (ADS)

Matson, P. G.; Ladd, T. M.; Iglesias-Rodriguez, D.

2016-02-01

The species concept in marine phytoplankton has enormous biological complexity. Differences in genomic, morphological, physiological, biogeochemical, and ecological/biogeographic properties between strains of the same species can be comparable or even exceed those between species. This complexity is particularly pronounced in the cosmopolitan coccolithophore species Emiliania huxleyi. This bloom-forming species is found at nearly every latitude in a variety of environments including upwelling regions, and exposed to large temperature gradients. We present results from experiments using two strains of E. huxleyi isolated from different latitudes and environmental conditions. Tests involved semi-continuous culturing in lab manipulation experiments to determine how carbon fixation, growth, and morphology respond to temperature-driven alterations in physico-chemical conditions. This talk will discuss the observed differences in physiology within an ecological context and the implications of these biogeochemical differences in modeling carbon fluxes driven by phytoplankton.

Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma)

USGS Publications Warehouse

Leache, A.D.; Koo, M.S.; Spencer, C.L.; Papenfuss, T.J.; Fisher, R.N.; McGuire, J.A.

2009-01-01

Lineage separation and divergence form a temporally extended process whereby populations may diverge genetically, morphologically, or ecologically, and these contingent properties of species provide the operational criteria necessary for species delimitation.We inferred the historical process of lineage formation in the coast horned lizard (Phrynosoma coronatum) species complex by evaluating a diversity of operational species criteria, including divergence in mtDNA (98 specimens; 2,781 bp) and nuclear loci (RAG-1, 1,054 bp; BDNF 529 bp), ecological niches (11 bioclimatic variables; 285 unique localities), and cranial horn shapes (493 specimens; 16 landmarks). A phylogenetic analysis of mtDNA recovers 5 phylogeographic groups arranged latitudinally along the Baja California Peninsula and in California. The 2 southern phylogeographic groups exhibit concordance between genetic, morphological, and ecological divergence; however, differentiation is weak or absent at more recent levels defined by phylogeographic breaks in California. Interpreting these operational species criteria together suggests that there are 3 ecologically divergent and morphologically diagnosable species within the P. coronatum complex. Our 3-species taxonomic hypothesis invokes a deep coalescence event when fitting the mtDNA genealogy into the species tree, which is not unexpected for populations that have diverged recently. Although the hypothesis that the 3 phylogeographic groups distributed across California each represent distinctive species is not supported by all of the operational species criteria evaluated in this study, the conservation status of the imperiled populations represented by these genealogical units remains critical.

Global diversity of the Ganoderma lucidum complex (Ganodermataceae, Polyporales) inferred from morphology and multilocus phylogeny.

PubMed

Zhou, Li-Wei; Cao, Yun; Wu, Sheng-Hua; Vlasák, Josef; Li, De-Wei; Li, Meng-Jie; Dai, Yu-Cheng

2015-06-01

Species of the Ganoderma lucidum complex are used in many types of health products. However, the taxonomy of this complex has long been chaotic, thus limiting its uses. In the present study, 32 collections of the complex from Asia, Europe and North America were analyzed from both morphological and molecular phylogenetic perspectives. The combined dataset, including an outgroup, comprised 33 ITS, 24 tef1α, 24 rpb1 and 21 rpb2 sequences, of which 19 ITS, 20 tef1α, 20 rpb1 and 17 rpb2 sequences were newly generated. A total of 13 species of the complex were recovered in the multilocus phylogeny. These 13 species were not strongly supported as a single monophyletic lineage, and were further grouped into three lineages that cannot be defined by their geographic distributions. Clade A comprised Ganoderma curtisii, Ganoderma flexipes, Ganoderma lingzhi, Ganoderma multipileum, Ganoderma resinaceum, Ganoderma sessile, Ganoderma sichuanense and Ganoderma tropicum, Clade B comprised G. lucidum, Ganoderma oregonense and Ganoderma tsugae, and Clade C comprised Ganoderma boninense and Ganoderma zonatum. A dichotomous key to the 13 species is provided, and their key morphological characters from context, pores, cuticle cells and basidiospores are presented in a table. The taxonomic positions of these species are briefly discussed. Noteworthy, the epitypification of G. sichuanense is rejected. Copyright © 2014 Elsevier Ltd. All rights reserved.

DNA barcoding of Bemisia tabaci complex (Hemiptera: Aleyrodidae) reveals southerly expansion of the dominant whitefly species on cotton in Pakistan.

PubMed

Ashfaq, Muhammad; Hebert, Paul D N; Mirza, M Sajjad; Khan, Arif M; Mansoor, Shahid; Shah, Ghulam S; Zafar, Yusuf

2014-01-01

Although whiteflies (Bemisia tabaci complex) are an important pest of cotton in Pakistan, its taxonomic diversity is poorly understood. As DNA barcoding is an effective tool for resolving species complexes and analyzing species distributions, we used this approach to analyze genetic diversity in the B. tabaci complex and map the distribution of B. tabaci lineages in cotton growing areas of Pakistan. Sequence diversity in the DNA barcode region (mtCOI-5') was examined in 593 whiteflies from Pakistan to determine the number of whitefly species and their distributions in the cotton-growing areas of Punjab and Sindh provinces. These new records were integrated with another 173 barcode sequences for B. tabaci, most from India, to better understand regional whitefly diversity. The Barcode Index Number (BIN) System assigned the 766 sequences to 15 BINs, including nine from Pakistan. Representative specimens of each Pakistan BIN were analyzed for mtCOI-3' to allow their assignment to one of the putative species in the B. tabaci complex recognized on the basis of sequence variation in this gene region. This analysis revealed the presence of Asia II 1, Middle East-Asia Minor 1, Asia 1, Asia II 5, Asia II 7, and a new lineage "Pakistan". The first two taxa were found in both Punjab and Sindh, but Asia 1 was only detected in Sindh, while Asia II 5, Asia II 7 and "Pakistan" were only present in Punjab. The haplotype networks showed that most haplotypes of Asia II 1, a species implicated in transmission of the cotton leaf curl virus, occurred in both India and Pakistan. DNA barcodes successfully discriminated cryptic species in B. tabaci complex. The dominant haplotypes in the B. tabaci complex were shared by India and Pakistan. Asia II 1 was previously restricted to Punjab, but is now the dominant lineage in southern Sindh; its southward spread may have serious implications for cotton plantations in this region.

In vitro antifungal activity of silver nanoparticles against ocular pathogenic filamentous fungi.

PubMed

Xu, Yan; Gao, Chuanwen; Li, Xiaohua; He, Yi; Zhou, Lutan; Pang, Guangren; Sun, Shengtao

2013-03-01

Fungal keratitis is emerging as a major cause of vision loss in a developing country such as China because of higher incidence and the unavailability of effective antifungals. It is urgent to explore broad-spectrum antifungals to effectively suppress ocular fungal pathogens, and to develop new antifungal eye drops to combat this vision-threatening infection. The aim of this study is to investigate the antifungal activity of silver nanoparticles (nano-Ag) in comparison with that of natamycin against ocular pathogenic filamentous fungi in vitro. Susceptibility tests were performed against 216 strains of fungi isolated from patients with fungal keratitis from the Henan Eye Institute in China by broth dilution antifungal susceptibility test of filamentous fungi approved by the Clinical and Laboratory Standards Institute M38-A document. The isolates included 112 Fusarium isolates (82 Fusarium solani species complex, 20 Fusarium verticillioides species complex, and 10 Fusarium oxysporum species complex), 94 Aspergillus isolates (61 Aspergillus flavus species complex, 11 Aspergillus fumigatus species complex, 12 Aspergillus versicolor species complex, and 10 Aspergillus niger species complex), and 10 Alternaria alternata isolates. The minimum inhibitory concentration (MIC) range and mode, the MIC for 50% of the strains tested (MIC50 value), and the MIC90 value were provided for the isolates with the SPSS statistical package. MIC50 value of nano-Ag were 1, 0.5, and 0.5 μg/mL for Fusarium spp., Aspergillus spp., and Al. alternata, respectively. MIC90 values of nano-Ag were 1, 1, and 1 μg/mL for Fusarium spp., Aspergillus spp., and Al. alternata, respectively. MIC50 values of natamycin were 4, 32, and 4 μg/mL for Fusarium spp., Aspergillus spp., and Al. alternata, respectively. MIC90 values of natamycin were 8, 32, and 4 μg/mL for Fusarium spp., Aspergillus spp., and Al. alternata, respectively. Nano-Ag, relative to natamycin, exhibits potent in vitro activity against ocular pathogenic filamentous fungi.

Toward more diverse forests: helping trees "get along" in a new organization

Treesearch

Noreen Parks; Timothy Harrington; Warren. Devine

2010-01-01

Interactions among plant species and their growth patterns help shape a forest. Various management practices can enhance forest complexity and in return yield benefits that include enhanced growth of desired species, slowing the spread of root disease, and improved wildlife habitat.Based on...

Complex biogeographic scenarios revealed in the diversification of the largest woodpecker radiation in the New World.

PubMed

Navarro-Sigüenza, Adolfo G; Vázquez-Miranda, Hernán; Hernández-Alonso, Germán; García-Trejo, Erick A; Sánchez-González, Luis A

2017-07-01

Phylogenetic relationships and patterns of evolution within Melanerpes, one of the most diverse groups of New World woodpeckers (22-23 lineages), have been complicated due to complex plumages and morphological adaptations. In an attempt to resolve these issues, we obtained sequence data from four nuclear introns and two mitochondrial protein-coding genes for 22 of the 24 currently recognized species in the genus. We performed phylogenetic analyses involving Maximum Likelihood and Bayesian Inference, species-tree divergence dating, and biogeographic reconstructions. Tree topologies from the concatenated and species-tree analyses of the mtDNA and nDNA showed broadly similar patterns, with three relatively well-supported groups apparent: (a) the Sphyrapicus clade (four species); (b) the typical Melanerpes clade, which includes temperate and subtropical dry forest black-backed species; and (c) the mostly barred-backed species, here referred to as the "Centurus" clade. The phylogenetic position of Melanerpes superciliaris regarding the rest of Melanerpes is ambiguous as it is recovered as sister to the rest of Melanerpes or as sister to a group including Sphyrapicus+Melanerpes. Our species tree estimations recovered the same well-delimited highly-supported clades. Geographic range evolution (estimated in BioGeoBEARS) was best explained by a DIVALIKE+j model, which includes vicariance, founder effect speciation, and anagenetic dispersal (range expansion) as important processes involved in the diversification of the largest radiation of woodpeckers in the New World. Copyright © 2017 Elsevier Inc. All rights reserved.

Environmental Conditions and Threatened and Endangered Species Populations near the Titain, Atlas, and Delta Launch Complexes, Cape Canaveral Air Station

NASA Technical Reports Server (NTRS)

Oddy, Donna M.; Stolen, Eric D.; Schmalzer, Paul A.; Hensley, Melissa A.; Hall, Patrice; Larson, Vickie L.; Turek, Shannon R.

1999-01-01

Launches of Delta, Atlas, and Titan rockets from Cape Canaveral Air Station (CCAS) have potential environmental effects. These could occur from direct impacts of launches or indirectly from habitat alterations. This report summarizes a three-year study (1995-1998) characterizing the environment, with particular attention to threatened and endangered species, near Delta, Atlas, and Titan launch facilities. Cape Canaveral has been modified by Air Force development and by 50 years of fire suppression. The dominant vegetation type around the Delta and Atlas launch complexes is coastal oak hammock forest. Oak scrub is the predominant upland vegetation type near the Titan launch complexes. Compositionally, these are coastal scrub communities that has been unburned for greater than 40 years and have developed into closed canopy, low-stature forests. Herbaceous vegetation around active and inactive facilities, coastal strand and dune vegetation near the Atlantic Ocean, and exotic vegetation in disturbed areas are common. Marsh and estuarine vegetation is most common west of the Titan complexes. Launch effects to vegetation include scorch, acid, and particulate deposition. Discernable, cumulative effects are limited to small areas near the launch complexes. Water quality samples were collected at the Titan, Atlas, and Delta launch complexes in September 1995 (wet season) and January 1996 (dry season). Samples were analyzed for heavy metals, chloride, total organic carbon, calcium, iron, magnesium, sodium, total alkalinity, pH, and conductivity. Differences between fresh, brackish, and saline surface waters were evident. The natural buffering capacity of the environment surrounding the CCAS launch complexes is adequate for neutralizing acid deposition in rainfall and launch deposition. Populations of the Florida Scrub-Jay (Aphelocoma coerulescens), a Federally- listed, threatened species, reside near the launch complexes. Thirty-seven to forty-one scrub-jay territories were located at Titan, Atlas, and Delta launch complexes between 1995 and 1997. No direct impacts to scrub-jays were observed as a result of normal launches. The explosion of the Delta rocket in January 1997 caused direct impacts to the habitat of several scrub-jays families, from fire and debris; however, no scrub-jay mortality was observed. Mortality exceeded reproductive output at all areas over the course of the study. Populations of the southeastern beach mouse (Peromyscus polionotus niveiventris) populations, a Federally listed, threatened species, reside near all the launch complexes. Hurricane Erin and several other tropical storms impacted several areas at the inception of the study in 1995 causing coastal habitat alterations as a result of salt-water intrusion. Both the habitat and the beach mice populations recovered during the course of the study. No direct impacts to southeastern beach mice were observed as a result of normal launch operations. Direct impacts were observed to the habitat as a result of the explosion of the Delta rocket in January 1997. This alteration of the habitant resulted in a shift in use with the mice moving on to the newly burned part of the site. Waterbirds use wetlands and aquatic systems near the launch complexes. Species include the Federally-listed, endangered Wood Stork (Mycteria americana) and several state-listed species of special concern including the Snowy Egret (Egretta thula thula), Reddish Egret (Egretta rufescens rufescens), White Ibis (Eudocimus albus), Roseate Spoonbill (Ajaia ajaja), Tricolored Heron (Egretta tricolor ruficolis), and Little Blue Heron (Egretta caerulea). No impacts to these populations resulting from any launch operations were observed. Gopher tortoises (Gopherus polyphemus) also occur around the launch complexes. Most of those observed appeared to be in good condition; however, upper respiratory tract disease is known to occur in the population. Cape Canaveral Air Station, including areas near active launch complexes, remains important habitat for a variety of native plants and animals including threatened and endangered species. Direct negative effects of current launch systems appear limited. Additional monitoring of these populations and habitats is required to determine if subtle, long-term changes are occurring, to determine if new launch systems and facilities cause other effects, and to determine the effects of habitat restoration and management.

Cutaneous Disseminated and Extracutaneous Sporotrichosis: Current Status of a Complex Disease

PubMed Central

Bonifaz, Alexandro; Tirado-Sánchez, Andrés

2017-01-01

Sporotrichosis is an implantation or inoculation mycosis caused by species of Sporothrix schenckii complex; its main manifestations are limited to skin; however, cutaneous-disseminated, disseminated (visceral) and extracutaneous variants of sporotrichosis can be associated with immunosuppression, including HIV-AIDS, chronic alcoholism or more virulent strains. The most common extracutaneous form of sporotrichosis includes pulmonary, osteoarticular and meningeal. The laboratory diagnosis requires observing yeast forms and isolating the fungus; the two main causative agents are Sporothrix schenckii (ss) and Sporothrix brasiliensis. Antibody levels and species recognition by Polimerase Chain Reaction using biological samples or cultures are also useful. The treatment of choice for most cases is amphotericin B and subsequent itraconazole for maintenance therapy. PMID:29371525

Cutaneous Disseminated and Extracutaneous Sporotrichosis: Current Status of a Complex Disease.

PubMed

Bonifaz, Alexandro; Tirado-Sánchez, Andrés

2017-02-10

Sporotrichosis is an implantation or inoculation mycosis caused by species of Sporothrix schenckii complex; its main manifestations are limited to skin; however, cutaneous-disseminated, disseminated (visceral) and extracutaneous variants of sporotrichosis can be associated with immunosuppression, including HIV-AIDS, chronic alcoholism or more virulent strains. The most common extracutaneous form of sporotrichosis includes pulmonary, osteoarticular and meningeal. The laboratory diagnosis requires observing yeast forms and isolating the fungus; the two main causative agents are Sporothrix schenckii ( ss ) and Sporothrix brasiliensis . Antibody levels and species recognition by Polimerase Chain Reaction using biological samples or cultures are also useful. The treatment of choice for most cases is amphotericin B and subsequent itraconazole for maintenance therapy.

Taxonomic review of the Oriental flower beetle Coilodera penicillata species complex (Coleoptera: Scarabaeidae: Cetoniinae).

PubMed

Qiu, Jian-Yue; Xu, Hao; Chen, L I

2017-11-20

The taxonomy of the Coilodera penicillata Hope, 1831 (Coleoptera: Scarabaeidae: Cetoniinae) species complex, which is recognized by the black body and elytra with larger tomentose maculae, is revised. Six Indochinese species assigned to this complex, including C. grandimaculata new species from Tibet, China. Coilodera nigroscutellaris Moser, 1902 revised status and C. formosana Moser, 1910 revised status formerly treated as two subspecies of C. penicillata Hope, 1831 are elevated to species rank. The distribution of C. penicillata in China is confirmed based on examination of specimens from Yunnan and Tibet, and almost all previous Chinese literature records should be referred to C. nigroscutellaris. Coilodera dives (Gory & Percheron, 1833) revised status previously synonymized with C. penicillata is herein considered as a valid species based on the examination of types and additional specimens, and C. miksici Antoine, 1986 new synonymy is regarded as a junior synonym of C. dives. A lectotype is designated for Coilodera dives (Gory & Percheron, 1833). The record of C. mearesii (Westwood, 1842) in southeastern China is attributed to a misidentification of C. nigroscutellaris, and it is here newly recoreded from Tibet near the Nepal-China border. Diagnosis characters and intraspecific variations are illustrated for all six species, new distribution records and a key to species are also presented. Ecological information is provided for all species.

Morphological and genetic evolution in eastern populations of the Macrhybopsis aestivalis complex (Cypriniformes: Cyprinidae), with the descriptions of four new species.

PubMed

Gilbert, Carter R; Mayden, Richard L; Powers, Steven L

2017-03-30

For many years the North American cyprinid fish Macrhybopsis aestivalis (common name: Speckled Chub) was regarded as a single widespread and morphologically variable species, occurring in rivers throughout much of the Mississippi Valley and geographically adjacent eastern Gulf slope drainages, west to the Rio Grande basin in Texas, New Mexico, and Mexico. Eisenhour (1997) completed a morphological study of western populations of the Speckled Chub, the results of which appeared thereafter in published form (Eisenhour 1999, 2004). He demonstrated the existence of five valid species west of the Mississippi River (aestivalis, marconis, australis, tetranema, hyostoma), of which the name aestivalis was shown to be restricted to the population occurring in the Rio Grande and the geographically adjacent Rio San Fernando system, in northeastern Mexico. Eisenhour (2004) considered populations throughout the middle Mississippi Valley and its major tributaries to be a single morphologically variable species (hyostoma), and he also indicated that populations of Macrhybopsis from eastern Gulf slope drainages may represent a complex of species. Genetic confirmation of Eisenhour's conclusions regarding western species appeared in the publication by Underwood et al. (2003), who also showed that western populations of M. hyostoma, as presently recognized, are genetically much more complex than previously considered.     Meanwhile, the present authors were involved in a companion study of eastern populations of Macrhybopsis, for which a genetic summary of the eastern Gulf coast species was published by Mayden & Powers (2004). Based on their findings, four species were recognized from southeastern drainages (identified as species A-D), although no formal taxonomic descriptions were included. Their genetic data, in combination with meristic, morphometric and other morphological data presented herein, form the basis for a revised classification of eastern Macrhybopsis populations, including formal descriptions of the four new species from eastern Gulf coast drainages.

A new species of bark beetle, Dendroctonus mesoamericanus sp nov. (Curculionidae: Scolytinae), in southern Mexico and Central America

Treesearch

Francisco Armendariz-Toledano; Alicia Nino; Brian T. Sullivan; Lawrence R. Kirkendall; Gerado Zunig

2015-01-01

The bark beetle Dendroctonus mesoamericanus sp. nov. is described from a population in Parque Nacional Lagunas de Montebello, La Trinitaria, Chiapas, Mexico. This species belongs to the D. frontalis complex, which includes D. adjunctus Blandford 1897, D. approximatus Dietz 1890, D....

Holodiscus (K. Koch) Maxim.: ocean-spray

Treesearch

Nancy L. Shaw; Emerenciana G. Hurd; Peter F. Stickney

2008-01-01

Holodiscus is a taxonomically complex genus including about 6 species of western North America and northern South America (Hitchcock and others 1961; Ley 1943). The 2 generally recognized North American species (table 1) - creambush ocean-spray and gland ocean-spray - are deciduous, multistemmed shrubs with simple, alternate, deciduous, toothed to shallowly lobed,...

REAL-TIME QUANTITATIVE PCR DETECTION OF MYCOBACTERIUM AVIUM COMPLEX ORGANISMS IN DRINKING WATER

EPA Science Inventory

The Mycobacterium avium Complex (MAC) includes the species M. avium (MA), M. intracellulare (MI), and others. MAC are listed on the U.S. Environmental Protection Agency's Contaminant Candidate List (CCL) due to their association with human disease and occurrence in public drinkin...

Multilocus Phylogeography and Species Delimitation in the Cumberland Plateau Salamander, Plethodon kentucki: Incongruence among Data Sets and Methods

PubMed Central

Kuchta, Shawn R.; Brown, Ashley D.; Converse, Paul E.; Highton, Richard

2016-01-01

Species are a fundamental unit of biodiversity, yet can be challenging to delimit objectively. This is particularly true of species complexes characterized by high levels of population genetic structure, hybridization between genetic groups, isolation by distance, and limited phenotypic variation. Previous work on the Cumberland Plateau Salamander, Plethodon kentucki, suggested that it might constitute a species complex despite occupying a relatively small geographic range. To examine this hypothesis, we sampled 135 individuals from 43 populations, and used four mitochondrial loci and five nuclear loci (5693 base pairs) to quantify phylogeographic structure and probe for cryptic species diversity. Rates of evolution for each locus were inferred using the multidistribute package, and time calibrated gene trees and species trees were inferred using BEAST 2 and *BEAST 2, respectively. Because the parameter space relevant for species delimitation is large and complex, and all methods make simplifying assumptions that may lead them to fail, we conducted an array of analyses. Our assumption was that strongly supported species would be congruent across methods. Putative species were first delimited using a Bayesian implementation of the GMYC model (bGMYC), Geneland, and Brownie. We then validated these species using the genealogical sorting index and BPP. We found substantial phylogeographic diversity using mtDNA, including four divergent clades and an inferred common ancestor at 14.9 myr (95% HPD: 10.8–19.7 myr). By contrast, this diversity was not corroborated by nuclear sequence data, which exhibited low levels of variation and weak phylogeographic structure. Species trees estimated a far younger root than did the mtDNA data, closer to 1.0 myr old. Mutually exclusive putative species were identified by the different approaches. Possible causes of data set discordance, and the problem of species delimitation in complexes with high levels of population structure and introgressive hybridization, are discussed. PMID:26974148

Rapid and accurate identification of Mycobacterium tuberculosis complex and common non-tuberculous mycobacteria by multiplex real-time PCR targeting different housekeeping genes.

PubMed

Nasr Esfahani, Bahram; Rezaei Yazdi, Hadi; Moghim, Sharareh; Ghasemian Safaei, Hajieh; Zarkesh Esfahani, Hamid

2012-11-01

Rapid and accurate identification of mycobacteria isolates from primary culture is important due to timely and appropriate antibiotic therapy. Conventional methods for identification of Mycobacterium species based on biochemical tests needs several weeks and may remain inconclusive. In this study, a novel multiplex real-time PCR was developed for rapid identification of Mycobacterium genus, Mycobacterium tuberculosis complex (MTC) and the most common non-tuberculosis mycobacteria species including M. abscessus, M. fortuitum, M. avium complex, M. kansasii, and the M. gordonae in three reaction tubes but under same PCR condition. Genetic targets for primer designing included the 16S rDNA gene, the dnaJ gene, the gyrB gene and internal transcribed spacer (ITS). Multiplex real-time PCR was setup with reference Mycobacterium strains and was subsequently tested with 66 clinical isolates. Results of multiplex real-time PCR were analyzed with melting curves and melting temperature (T (m)) of Mycobacterium genus, MTC, and each of non-tuberculosis Mycobacterium species were determined. Multiplex real-time PCR results were compared with amplification and sequencing of 16S-23S rDNA ITS for identification of Mycobacterium species. Sensitivity and specificity of designed primers were each 100 % for MTC, M. abscessus, M. fortuitum, M. avium complex, M. kansasii, and M. gordonae. Sensitivity and specificity of designed primer for genus Mycobacterium was 96 and 100 %, respectively. According to the obtained results, we conclude that this multiplex real-time PCR with melting curve analysis and these novel primers can be used for rapid and accurate identification of genus Mycobacterium, MTC, and the most common non-tuberculosis Mycobacterium species.

Mucor nidicola sp. nov., a fungal species isolated from an invasive paper wasp nest.

PubMed

Madden, A A; Stchigel, A M; Guarro, J; Sutton, D; Starks, P T

2012-07-01

A strain of a novel mucoralean fungus was isolated from a nest of the invasive paper wasp, Polistes dominulus. Phylogenetic analysis based on the internal transcribed spacer (ITS) regions and 5.8S rRNA gene sequences, along with physiological tests, revealed that this strain represents a novel species within the genus Mucor. The novel species also includes a representative that had previously been characterized as part of the Mucor hiemalis complex. Unlike the type strain of M. hiemalis, these two strains can grow at 37 °C and sporulate at 35 °C. Here, we present a partial resolution of the M. hiemalis species complex and propose the novel species Mucor nidicola sp. nov. to accommodate the isolate; the type strain of M. nidicola is F53(T) (=NRRL 54520(T)=UAMH 11442(T)=CBS 130359(T)).

High Levels of Diversity Uncovered in a Widespread Nominal Taxon: Continental Phylogeography of the Neotropical Tree Frog Dendropsophus minutus

PubMed Central

Gehara, Marcelo; Crawford, Andrew J.; Orrico, Victor G. D.; Rodríguez, Ariel; Lötters, Stefan; Fouquet, Antoine; Barrientos, Lucas S.; Brusquetti, Francisco; De la Riva, Ignacio; Ernst, Raffael; Urrutia, Giuseppe Gagliardi; Glaw, Frank; Guayasamin, Juan M.; Hölting, Monique; Jansen, Martin; Kok, Philippe J. R.; Kwet, Axel; Lingnau, Rodrigo; Lyra, Mariana; Moravec, Jiří; Pombal, José P.; Rojas-Runjaic, Fernando J. M.; Schulze, Arne; Señaris, J. Celsa; Solé, Mirco; Rodrigues, Miguel Trefaut; Twomey, Evan; Haddad, Celio F. B.; Vences, Miguel; Köhler, Jörn

2014-01-01

Species distributed across vast continental areas and across major biomes provide unique model systems for studies of biotic diversification, yet also constitute daunting financial, logistic and political challenges for data collection across such regions. The tree frog Dendropsophus minutus (Anura: Hylidae) is a nominal species, continentally distributed in South America, that may represent a complex of multiple species, each with a more limited distribution. To understand the spatial pattern of molecular diversity throughout the range of this species complex, we obtained DNA sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and the 16S rhibosomal gene (16S) for 407 samples of D. minutus and closely related species distributed across eleven countries, effectively comprising the entire range of the group. We performed phylogenetic and spatially explicit phylogeographic analyses to assess the genetic structure of lineages and infer ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may represent currently unrecognized distinct species. One major clade, containing 25 divergent lineages, includes samples from the type locality of D. minutus. We defined that clade as the D. minutus complex. The remaining lineages together with the D. minutus complex constitute the D. minutus species group. Historical analyses support an Amazonian origin for the D. minutus species group with a subsequent dispersal to eastern Brazil where the D. minutus complex originated. According to our dataset, a total of eight mtDNA lineages have ranges >100,000 km2. One of them occupies an area of almost one million km2 encompassing multiple biomes. Our results, at a spatial scale and resolution unprecedented for a Neotropical vertebrate, confirm that widespread amphibian species occur in lowland South America, yet at the same time a large proportion of cryptic diversity still remains to be discovered. PMID:25208078

High levels of diversity uncovered in a widespread nominal taxon: continental phylogeography of the neotropical tree frog Dendropsophus minutus.

PubMed

Gehara, Marcelo; Crawford, Andrew J; Orrico, Victor G D; Rodríguez, Ariel; Lötters, Stefan; Fouquet, Antoine; Barrientos, Lucas S; Brusquetti, Francisco; De la Riva, Ignacio; Ernst, Raffael; Urrutia, Giuseppe Gagliardi; Glaw, Frank; Guayasamin, Juan M; Hölting, Monique; Jansen, Martin; Kok, Philippe J R; Kwet, Axel; Lingnau, Rodrigo; Lyra, Mariana; Moravec, Jiří; Pombal, José P; Rojas-Runjaic, Fernando J M; Schulze, Arne; Señaris, J Celsa; Solé, Mirco; Rodrigues, Miguel Trefaut; Twomey, Evan; Haddad, Celio F B; Vences, Miguel; Köhler, Jörn

2014-01-01

Species distributed across vast continental areas and across major biomes provide unique model systems for studies of biotic diversification, yet also constitute daunting financial, logistic and political challenges for data collection across such regions. The tree frog Dendropsophus minutus (Anura: Hylidae) is a nominal species, continentally distributed in South America, that may represent a complex of multiple species, each with a more limited distribution. To understand the spatial pattern of molecular diversity throughout the range of this species complex, we obtained DNA sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and the 16S rhibosomal gene (16S) for 407 samples of D. minutus and closely related species distributed across eleven countries, effectively comprising the entire range of the group. We performed phylogenetic and spatially explicit phylogeographic analyses to assess the genetic structure of lineages and infer ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may represent currently unrecognized distinct species. One major clade, containing 25 divergent lineages, includes samples from the type locality of D. minutus. We defined that clade as the D. minutus complex. The remaining lineages together with the D. minutus complex constitute the D. minutus species group. Historical analyses support an Amazonian origin for the D. minutus species group with a subsequent dispersal to eastern Brazil where the D. minutus complex originated. According to our dataset, a total of eight mtDNA lineages have ranges >100,000 km2. One of them occupies an area of almost one million km2 encompassing multiple biomes. Our results, at a spatial scale and resolution unprecedented for a Neotropical vertebrate, confirm that widespread amphibian species occur in lowland South America, yet at the same time a large proportion of cryptic diversity still remains to be discovered.

Environmental Conditions and Threatened and Endangered Species Populations near the Titan, Atlas, and Delta Launch Complexes, Cape Canaveral Air Station

NASA Technical Reports Server (NTRS)

Oddy, Donna M.; Stolen, Eric D.; Schmalzer, Paul A.; Hensley, Melissa A.; Hall, Patrice; Larson, Vickie L.; Turek, Shannon R.

1999-01-01

Launches of Delta, Atlas, and Titan rockets from Cape Canaveral Air Station (CCAS) have potential environmental effects. These could occur from direct impacts of launches or indirectly from habitat alterations. This report summarizes a three-year study (1 995-1 998) characterizing the environment, with particular attention to threatened and endangered species, near Delta, Atlas, and Titan launch facilities. Cape Canaveral has been modified by Air Force development and by 50 years of fire suppression. The dominant vegetation type around the Delta and Atlas launch complexes is coastal oak hammock forest. Oak scrub is the predominant upland vegetation type near the Titan launch complexes. Compositionally, these are coastal scrub communities that has been unburned for > 40 years and have developed into closed canopy, low-stature forests. Herbaceous vegetation around active and inactive facilities, coastal strand and dune vegetation near the Atlantic Ocean, and exotic vegetation in disturbed areas are common. Marsh and estuarine vegetation is most common west of the Titan complexes. Launch effects to vegetation include scorch, acid, and particulate deposition. Discernable, cumulative effects are limited to small areas near the launch complexes. Water quality samples were collected at the Titan, Atlas, and Delta launch complexes in September 1995 (wet season) and January 1996 (dry season). Samples were analyzed for heavy metals, chloride, total organic carbon, calcium, iron, magnesium, sodium, total alkalinity, pH, and conductivity. Differences between fresh, brackish, and saline surface waters were evident. The natural buffering capacity of the environment surrounding the CCAS launch complexes is adequate for neutralizing acid deposition in rainfall and launch deposition. Populations of the Florida Scrub-Jay (Aphelocoma coerulescens), a Federally-listed, threatened species, reside near the launch complexes. Thirty-seven to forty-one scrub-jay territories were located at Titan, Atlas, and Delta launch complexes between 1995 and 1997. No direct impacts to scrub-jays were observed as a result of normal launches. The explosion of the Delta rocket in January 1997 caused direct impacts to the habitat of several scrub-jays families, from fire and debris; however, no scrub-jay mortality was observed. Mortality exceeded reproductive output at all areas over the course of the study. Populations of the southeastern beach mouse (Peromyscus polionotus niveiventris) populations, a Federally listed, threatened species, reside near all the launch complexes. Hurricane Erin and several other tropical storms impacted several areas at the inception of the study in 1995 causing coastal habitat alterations as a result of salt-water intrusion. Both the habitat and the beach mice populations recovered during the course of the study. No direct impacts to southeastern beach mice were observed as a result of normal launch operations. Direct impacts were observed to the habitat as a result of the explosion of the Delta rocket in January 1997. This alteration of the habitat resulted in a shift in use with the mice moving on to the newly burned part of the site. Waterbirds use wetlands and aquatic systems near the launch complexes. Species include the Federally-listed, endangered Wood Stork (Mycferia americana) and several state-listed species of special concern including the Snowy Egret (Egretfa thula fhula), Reddish Egret (Egreffa rufescens rufescens), White Ibis (Eudocimus albus), Roseate Spoonbill (Ajaia ajaja), Tricolored Heron (Egreffa tricolor ruficolis), and Little Blue Heron (Egreffa caerulea). No impacts to these populations resulting from any launch operations were observed. Gopher tortoises (Gopherus polyphemus) also occur around the launch complexes. Most of those observed appeared to be in good condition; however, upper respiratory tract disease is known to occur in the population. Cape Canaveral Air Station, including areas near active launch colexes, remains important habitat for a variety of native plants and animals including threatened and endangered species. Direct negative effects of current launch systems appear limited. Additional monitoring of these populations and habitats is required to determine if subtle, long-term changes are occurring, to determine if new launch systems and facilities cause other effects, and to determine the effects of habitat restoration and management.

Review of the crevalle jacks, Caranx hippos complex (Teleostei: Carangidae), with a description of a new species from West Africa

USGS Publications Warehouse

Smith-Vaniz, W.F.; Carpenter, K.E.

2007-01-01

The Caranx hippos species complex comprises three extant species: crevalle jack (Caranx hippos) (Linnaeus, 1766) from both the western and eastern Atlantic oceans; Pacific crevalle jack (Caranx caninus) Gu??nther, 1868 from the eastern Pacific Ocean; and longfin crevalle jack (Caranx fischeri) new species, from the eastern Atlantic, including the Mediterranean Sea and Ascension Island. Adults of all three species are superficially similar with a black blotch on the lower half of the pectoral fin, a black spot on the upper margin of opercle, one or two pairs of enlarged symphyseal canines on the lower jaw, and a similar pattern of breast squamation. Each species has a different pattern of hyperostotic bone development and anal-fin color. The two sympatric eastern Atlantic species also differ from each other in number of dorsal- and anal-fin rays, and in large adults of C. fischeri the lobes of these fins are longer and the body is deeper. Caranx hippos from opposite sides of the Atlantic are virtually indistinguishable externally but differ consistently in the expression of hyperostosis of the first dorsal-fin pterygiophore. The fossil species Caranx carangopsis Steindachner 1859 appears to have been based on composite material of Trachurus sp. and a fourth species of the Caranx hippos complex. Patterns of hyperostotic bone development are compared in the nine (of 15 total) species of Caranx sensu stricto that exhibit hyperostosis.

Hybridization could be a common phenomenon within the highly diverse lizard genus Liolaemus.

PubMed

Olave, Melisa; Avila, Luciano J; Sites, Jack W; Morando, Mariana

2018-03-26

Hybridization is likely to occur more often between closely related taxa that have had insufficient time to diverge to the point of reproductive incompatibility; hybridization between deeply divergent lineages is rare. In squamate reptiles, hybridization has been proposed as a possible explanation for the extensive paraphyly observed in mitochondrial gene trees in several species complexes of the South American lizard genus Liolaemus. One of the best-documented cases is within the L. boulengeri and L. rothi complexes, which diverged ~5.5 million years ago. Here, we describe a comprehensive study for approaching the hybridization hypothesis between these lizard species complexes. We explored the level of gene tree discordance using the novel 'extra lineage contribution' statistics (XLC, presented in this study) that quantifies the level of gene tree discordance contribution per individual within a species. We included molecular data (12 nuclear and two mitochondrial genes) from 127 individuals, and results of a coalescent model-based analysis show that the most likely explanation for the gene tree-species tree discordance is interspecific hybridization. Our best-supported hypothesis suggests current and past hybridization between L. rothi (rothi complex) and L. tehuelche (boulengeri complex), and independently between L. rothi and L. boulengeri and L. telsen (boulengeri complex). The hybrid descendants are characterized by intermediate phenotypes between the parental species, but are more similar to L. rothi in body size. We discuss the possible role of hybridization in Liolaemus evolution. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Disentangling the complexity of tropical small-scale fisheries dynamics using supervised Self-Organizing Maps

PubMed Central

Ejarque, Elisabet; Nagelkerke, Leopold A. J.

2018-01-01

Tropical small-scale fisheries are typical for providing complex multivariate data, due to their diversity in fishing techniques and highly diverse species composition. In this paper we used for the first time a supervised Self-Organizing Map (xyf-SOM), to recognize and understand the internal heterogeneity of a tropical marine small-scale fishery, using as model the fishery fleet of San Pedro port, Tabasco, Mexico. We used multivariate data from commercial logbooks, including the following four factors: fish species (47), gear types (bottom longline, vertical line+shark longline and vertical line), season (cold, warm), and inter-annual variation (2007–2012). The size of the xyf-SOM, a fundamental characteristic to improve its predictive quality, was optimized for the minimum distance between objects and the maximum prediction rate. The xyf-SOM successfully classified individual fishing trips in relation to the four factors included in the model. Prediction percentages were high (80–100%) for bottom longline and vertical line + shark longline, but lower prediction values were obtained for vertical line (51–74%) fishery. A confusion matrix indicated that classification errors occurred within the same fishing gear. Prediction rates were validated by generating confidence interval using bootstrap. The xyf-SOM showed that not all the fishing trips were targeting the most abundant species and the catch rates were not symmetrically distributed around the mean. Also, the species composition is not homogeneous among fishing trips. Despite the complexity of the data, the xyf-SOM proved to be an excellent tool to identify trends in complex scenarios, emphasizing the diverse and complex patterns that characterize tropical small scale-fishery fleets. PMID:29782501

Allopatric Speciation within a Cryptic Species Complex of Australasian Octopuses

PubMed Central

Amor, Michael D.; Norman, Mark D.; Cameron, Hayley E.; Strugnell, Jan M.

2014-01-01

Despite extensive revisions over recent decades, the taxonomy of benthic octopuses (Family Octopodidae) remains in a considerable flux. Among groups of unresolved status is a species complex of morphologically similar shallow-water octopods from subtropical Australasia, including: Allopatric populations of Octopus tetricus on the eastern and western coasts of Australia, of which the Western Australian form is speculated to be a distinct or sub-species; and Octopus gibbsi from New Zealand, a proposed synonym of Australian forms. This study employed a combination of molecular and morphological techniques to resolve the taxonomic status of the ‘tetricus complex’. Phylogenetic analyses (based on five mitochondrial genes: 12S rRNA, 16S rRNA, COI, COIII and Cytb) and Generalised Mixed Yule Coalescent (GMYC) analysis (based on COI, COIII and Cytb) distinguished eastern and Western Australian O. tetricus as distinct species, while O. gibbsi was found to be synonymous with the east Australian form (BS = >97, PP = 1; GMYC p = 0.01). Discrete morphological differences in mature male octopuses (based on sixteen morphological traits) provided further evidence of cryptic speciation between east (including New Zealand) and west coast populations; although females proved less useful in morphological distinction among members of the tetricus complex. In addition, phylogenetic analyses suggested populations of octopuses currently treated under the name Octopus vulgaris are paraphyletic; providing evidence of cryptic speciation among global populations of O. vulgaris, the most commercially valuable octopus species worldwide. PMID:24964133

Detection of quantification of Mycobacterium avium complex organisms in drinking water

EPA Science Inventory

The Mycobacterium avium Complex (MAC) includes the species M. avium (MA), M. intracellulare (MI), and others. MAC are listed on the U. S. Environmental Protection Agency’s Contaminant Candidate List 2 (CCL2) due to their association with human disease and occurrence in public dr...

Accurate and Practical Identification of 20 Fusarium Species by Seven-Locus Sequence Analysis and Reverse Line Blot Hybridization, and an In Vitro Antifungal Susceptibility Study▿†

PubMed Central

Wang, He; Xiao, Meng; Kong, Fanrong; Chen, Sharon; Dou, Hong-Tao; Sorrell, Tania; Li, Ruo-Yu; Xu, Ying-Chun

2011-01-01

Eleven reference and 25 clinical isolates of Fusarium were subject to multilocus DNA sequence analysis to determine the species and haplotypes of the fusarial isolates from Beijing and Shandong, China. Seven loci were analyzed: the translation elongation factor 1 alpha gene (EF-1α); the nuclear rRNA internal transcribed spacer (ITS), large subunit (LSU), and intergenic spacer (IGS) regions; the second largest subunit of the RNA polymerase gene (RPB2); the calmodulin gene (CAM); and the mitochondrial small subunit (mtSSU) rRNA gene. We also evaluated an IGS-targeted PCR/reverse line blot (RLB) assay for species/haplotype identification of Fusarium. Twenty Fusarium species and seven species complexes were identified. Of 25 clinical isolates (10 species), the Gibberella (Fusarium) fujikuroi species complex was the commonest (40%) and was followed by the Fusarium solani species complex (FSSC) (36%) and the F. incarnatum-F. equiseti species complex (12%). Six FSSC isolates were identified to the species level as FSSC-3+4, and three as FSSC-5. Twenty-nine IGS, 27 EF-1α, 26 RPB2, 24 CAM, 18 ITS, 19 LSU, and 18 mtSSU haplotypes were identified; 29 were unique, and haplotypes for 24 clinical strains were novel. By parsimony informative character analysis, the IGS locus was the most phylogenetically informative, and the rRNA gene regions were the least. Results by RLB were concordant with multilocus sequence analysis for all isolates. Amphotericin B was the most active drug against all species. Voriconazole MICs were high (>8 μg/ml) for 15 (42%) isolates, including FSSC. Analysis of larger numbers of isolates is required to determine the clinical utility of the seven-locus sequence analysis and RLB assay in species classification of fusaria. PMID:21389150

Diapause in ticks of the medically important Ixodes ricinus species complex

PubMed Central

Gray, Jeremy S.; Kahl, Olaf; Lane, Robert S.; Levin, Michael L.; Tsao, Jean I.

2017-01-01

Four members of the Ixodes ricinus species complex, Ixodes pacificus, Ixodes persulcatus, Ixodes ricinus and Ixodes scapularis, have, between them, a worldwide distribution within the northern hemisphere. They are responsible for the transmission of several animal and human pathogens, including the causal agents of Lyme borreliosis, tick-borne encephalitis, human granulocytic anaplasmosis and human babesiosis. Despite the importance of these ticks as vectors, the knowledge and understanding of the role that diapause plays in their complex life cycles are confused and incomplete. In view of the continuing geographic spread of these tick species, as well as the effects of climate change on vector-borne diseases, it is timely encourage research on diapause phenomena to improve understanding of their biology and of pathogen transmission dynamics. In our review we seek to clarify thinking on the topic and to address gaps in our knowledge that require the attention of researchers. PMID:27263092

On cicadas of Hyalessa maculaticollis complex (Hemiptera, Cicadidae) of China.

PubMed

Wang, Xu; Hayashi, Masami; Wei, Cong

2014-01-01

The genus Hyalessa China is reviewed based on the discovery of male of the type species H. ronshana China as well as the description of one new species (H. batangensis sp. n.). The species formerly included in the genus Sonata Lee are removed to Hyalessa as new combinations. Intraspecific variations of H. maculaticollis are enumerated based on materials collected from various locations from China. The identity of Sonata and the systematic placement of Hyalessa are discussed. A key to all species of Hyalessa is provided.

Serological cross-reactivity among Sporothrix schenckii, Ceratocystis, Europhium, and Graphium species.

PubMed Central

Ishizaki, H; Wheat, R W; Kiel, D P; Conant, N F

1978-01-01

Ethanol-precipitable culture filtrate antigens of 100 strains of 75 species of the Sporothrix-Ceratocystis-Europhium-Graphium complex and 1 species of Botrytis were examined for neutral sugar components and for serological cross-reactivity with S. schenckii rabbit antiserum and human sporotrichosis sera by capillary precipitin and double immunodiffusion assay. Results revealed that cross-reactive species (60 of 77, ca. 80%) produced exoconidial forms and rhamnose- and mannose-containing polysaccharides and included Ceratocystis, the three known Europhium, and several Graphium-form species. Endoconidial-form Ceratocystis species did not cross-react. Images PMID:99369

The hyper-diverse ant genus Tetramorium Mayr (Hymenoptera, Formicidae) in the Malagasy region taxonomic revision of the T. naganum, T. plesiarum, T. schaufussii, and T. severini species groups

PubMed Central

Hita Garcia, Francisco; Fisher, Brian L.

2014-01-01

Abstract The taxonomy of the Tetramorium naganum, T. plesiarum, T. schaufussii, and T. severini species groups are revised for the Malagasy region. A total of 31 species are treated, of which 22 are newly described and nine redescribed. This increases the richness of the hyper-diverse genus Tetramorium in the Malagasy region to 106 species, which makes it the most species-rich genus in the region. Twenty-nine of the treated species are endemic to Madagascar, one is endemic to the Comoros, and one species is found predominantly in Madagascar but also on the island of Reunion. The T. naganum species group contains five species, which are mainly distributed in the rainforests and montane rainforests of eastern and northern Madagascar: T. alperti sp. n., T. dalek sp. n., T. enkidu sp. n., T. gilgamesh sp. n., and T. naganum Bolton, 1979. The T. plesiarum species group holds five species: T. bressleri sp. n., T. hobbit sp. n., T. gollum sp. n., T. mars sp. n., and T. plesiarum Bolton, 1979. All five are arid-adapted species occurring in the southwest and west of Madagascar. The second-most species-rich group in the region is the T. schaufussii species group with 20 species, most of which inhabit rainforests or montane rainforests of eastern and northern Madagascar. This group includes two species complexes each containing ten species: the T. cognatum complex with the species T. aspis sp. n., T. camelliae sp. n., T. cognatum Bolton, 1979, T. freya sp. n., T. gladius sp. n., T. karthala sp. n., T. myrmidon sp. n., T. proximum Bolton, 1979, T. rumo sp. n., and T. tenuinode sp. n.; and the T. schaufussii complex with the species T. merina sp. n., T. monticola sp. n., T. nassonowii Forel, 1892 stat. n., T. obiwan sp. n., T. pseudogladius sp. n., T. rala sp. n., T. schaufussii Forel, 1891, T. sikorae Forel, 1892 (= T. latior (Santschi, 1926)), T. scutum sp. n., T. xanthogaster Santschi, 1911. The last group treated in this study is the T. severini species group, which contains only the species T. severini (Emery, 1895). This very conspicuous species is widely distributed in the rainforests and montane rainforests of eastern and northern Madagascar. All four groups are fully revised with group diagnoses, illustrated species-level identification keys, and detailed descriptions for all species that include multifocused montage images and distribution maps. PMID:25009414

Aspergillus flavus: human pathogen, allergen and mycotoxin producer.

PubMed

Hedayati, M T; Pasqualotto, A C; Warn, P A; Bowyer, P; Denning, D W

2007-06-01

Aspergillus infections have grown in importance in the last years. However, most of the studies have focused on Aspergillus fumigatus, the most prevalent species in the genus. In certain locales and hospitals, Aspergillus flavus is more common in air than A. fumigatus, for unclear reasons. After A. fumigatus, A. flavus is the second leading cause of invasive aspergillosis and it is the most common cause of superficial infection. Experimental invasive infections in mice show A. flavus to be 100-fold more virulent than A. fumigatus in terms of inoculum required. Particularly common clinical syndromes associated with A. flavus include chronic granulomatous sinusitis, keratitis, cutaneous aspergillosis, wound infections and osteomyelitis following trauma and inoculation. Outbreaks associated with A. flavus appear to be associated with single or closely related strains, in contrast to those associated with A. fumigatus. In addition, A. flavus produces aflatoxins, the most toxic and potent hepatocarcinogenic natural compounds ever characterized. Accurate species identification within Aspergillus flavus complex remains difficult due to overlapping morphological and biochemical characteristics, and much taxonomic and population genetics work is necessary to better understand the species and related species. The flavus complex currently includes 23 species or varieties, including two sexual species, Petromyces alliaceus and P. albertensis. The genome of the highly related Aspergillus oryzae is completed and available; that of A. flavus in the final stages of annotation. Our understanding of A. flavus lags far behind that of A. fumigatus. Studies of the genomics, taxonomy, population genetics, pathogenicity, allergenicity and antifungal susceptibility of A. flavus are all required.

Experimental hybridization and reproductive isolation between two sympatric species of tephritid fruit flies in the Anastrepha fraterculus species group.

PubMed

Rull, Juan; Tadeo, Eduardo; Lasa, Rodrigo; Rodríguez, Christian L; Altuzar-Molina, Alma; Aluja, Martín

2017-06-06

Among tephritid fruit flies, hybridization has been found to produce local adaptation and speciation, and in the case of pest species, induce behavioral and ecological alterations that can adversely impact efficient pest management. The fraterculus species group within Anastrepha (Diptera: Tephritidae), is a rapidly radiating aggregate, which includes cryptic species complexes, numerous sister species, and several pest species. Molecular studies have highlighted the possibility of introgression between A. fraterculus and A. obliqua. Reproductive isolation has been studied among morphotypes of the A. fraterculus species complex as a tool for species delimitation. Here we examined the existence and strength of prezygotic and postzygotic isolation between sympatric populations of two closely related species within the highly derived fraterculus group (A. fraterculus and A. obliqua), coexisting in nature. Although adults of both species showed a strong tendency for assortative mating, a small proportion of hybrid pairings in both directions were observed. We also observed asymmetric postzygotic isolation, with one hybrid cross displaying a strong reduction in fecundity and F1 egg fertility. Survival was greater for the progeny of homotypic and hybrid crosses in the maternal host. There was a marked female biased sex ratio distortion for both F1 hybrid adults. Hybridization between A. fraterculus and A. obliqua in nature may be difficult but possible; these two species display stronger reproductive isolation than all pairs of species previously examined in the A. fraterculus species complex. Asymmetric postzygotic isolation is suggestive of Wolbachia mediated cytoplasmic incompatibilities that may be exploited in area-wide pest management. © 2017 Institute of Zoology, Chinese Academy of Sciences.

The oak (Quercus) biodiversity of California and adjacent regions

Treesearch

Kevin C. Nixon

2002-01-01

Twenty species of oak (Quercus) are known from California. The white oak group is the most diverse, and includes a complex of scrub oak species that are often encountered in chaparral, mixed forest and desert margin habitats. The Protobalanus group (e.g., Quercus chrysolepis) is a unique and distinctive clade of western North...

QTL analysis of Fusarium root rot resistance in an Andean x Middle American common bean RIL population

USDA-ARS?s Scientific Manuscript database

Aims Fusarium root rot (FRR) is a soil-borne disease that constrains common bean (Phaseolus vulgaris L.) production. FRR causal pathogens include clade 2 members of the Fusarium solani species complex. Here we characterize common bean reaction to four Fusarium species and identify genomic regions as...

Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach

USDA-ARS?s Scientific Manuscript database

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 angiosperm...

A peroxynitrite complex of copper: formation from a copper-nitrosyl complex, transformation to nitrite and exogenous phenol oxidative coupling or nitration.

PubMed

Park, Ga Young; Deepalatha, Subramanian; Puiu, Simona C; Lee, Dong-Heon; Mondal, Biplab; Narducci Sarjeant, Amy A; del Rio, Diego; Pau, Monita Y M; Solomon, Edward I; Karlin, Kenneth D

2009-11-01

Reaction of nitrogen monoxide with a copper(I) complex possessing a tridentate alkylamine ligand gives a Cu(I)-(*NO) adduct, which when exposed to dioxygen generates a peroxynitrite (O=NOO(-))-Cu(II) species. This undergoes thermal transformation to produce a copper(II) nitrito (NO(2) (-)) complex and 0.5 mol equiv O(2). In the presence of a substituted phenol, the peroxynitrite complex effects oxidative coupling, whereas addition of chloride ion to dissociate the peroxynitrite moiety instead leads to phenol ortho nitration. Discussions include the structures (including electronic description) of the copper-nitrosyl and copper-peroxynitrite complexes and the formation of the latter, based on density functional theory calculations and accompanying spectroscopic data.

Bu-2470, a new peptide antibiotic complex. I. Production, isolation and properties of Bu-2470 A, B1 and B2.

PubMed

Konishi, M; Sugawara, K; Tomita, K; Matsumoto, K; Miyaki, T; Fujisawa, K; Tsukiura, H; Kawaguchi, H

1983-06-01

A strain of Bacillus circulans produced a complex of basic peptide antibiotics designated Bu-2470, which was found to contain four active components, A, B1, B2a and B2b. Bu-2470 A specifically inhibited various Pseudomonas species including P. aeruginosa, P. maltophilia and P. putida, but otherwise its antibacterial spectrum was limited to certain Gram-negative organisms. Bu-2470 B1 and B2 (B2a + B2b) showed broad antibiotic activity against Gram-positive and Gram-negative bacteria including Pseudomonas species. The physicochemical and biological properties of Bu-2470 B1 and B2 are very similar to those of the octapeptin group of antibiotics.

Additions to Philippine Slender Skinks of the Brachymeles bonitae Complex (Reptilia: Squamata: Scincidae) III: a new species from Tablas Island.

PubMed

Davis, Drew R; Geheber, Aaron D; Watters, Jessa L; Penrod, Michelle L; Feller, Kathryn D; Ashford, Alissa; Kouri, Josh; Nguyen, Daniel; Shauberger, Kathryn; Sheatsley, Kyra; Winfrey, Claire; Wong, Rachel; Sanguila, Marites B; Brown, Rafe M; Siler, Cameron D

2016-06-28

Studies of the diversity of Philippine amphibians and reptiles have resulted in the continued description of cryptic species. Species formerly thought to range across multiple recognized faunal regions are now considered to be assemblages of multiple unique species, each restricted to a single faunal region. This pattern continues to hold true when considering Philippine skinks of the genus Brachymeles. Recent studies have resulted in the description of numerous unique species with many exhibiting various degrees of digit loss or limb reduction, as well as suggesting that unique lineages are still present in the B. bonitae Complex. In this paper, we describe a new species of fossorial skink within this species complex from Tablas Island based on collections made nearly 50 years ago. Although no genetic data are available for the new species, examinations of morphological data (qualitative traits, meristic counts, and mensural measurements) support its distinction from all other members of the genus. Brachymeles dalawangdaliri sp. nov. is differentiated from other members of the genus based on a suite of unique phenotypic characteristics, including a small body size (SVL 66.0-80.9 mm), bidactyl fore-limbs, digitless, unidactyl, or bidactyl hind limbs, a high number of presacral vertebrae (49), the absence of auricular openings, and distinct dorsal head scale patterns. The description of the new species increases the diversity of endemic vertebrates recognized to occur in the Romblon Island Group in the central Philippines.

A new genus and two new species of feather lice (Phthiraptera: Ischnocera: Philopteridae) from New Zealand endemic passerines (Aves: Passeriformes).

PubMed

Valim, Michel P; Palma, Ricardo L

2015-03-09

The first descriptions of New Zealand endemic feather lice belonging to the Brueelia-complex (Phthiraptera: Ischnocera: Philopteridae) are given. The new genus Melibrueelia and new species M. novaeseelandiae are described, illustrated and compared with morphologically close taxa within the complex. The type host of M. novaeseelandiae is the tui, Prosthemadera novaeseelandiae (Gmelin, 1788), and an additional host is the bellbird, Anthornis melanura (Sparrman, 1786) (Passeriformes: Meliphagidae), both endemic to New Zealand. Also, the new species Brueelia callaeincola is described and illustrated from four endemic bird species belonging to two endemic genera and an endemic family: Philesturnus carunculatus (Gmelin, 1789) (the type host), Ph. rufusater (Lesson, 1828), Callaeas cinerea (Gmelin, 1788) and C. wilsoni (Bonaparte, 1851) (Passeriformes: Callaeidae). Brief discussions on possible evolutionary histories of the new taxa are included.

Spatial Variation in Host Feeding Patterns of Culex tarsalis and the Culex pipiens complex (Diptera: Culicidae) in California

PubMed Central

THIEMANN, T. C.; LEMENAGER, D. A.; KLUH, S.; CARROLL, B. D.; LOTHROP, H. D.; REISEN, W. K.

2012-01-01

West Nile virus (family Flaviviridae, genus Flavivirus, WNV) is now endemic in California across a variety of ecological regions that support a wide diversity of potential avian and mammalian host species. Because different avian hosts have varying competence for WNV, determining the blood-feeding patterns of Culex (Diptera: Culicidae) vectors is a key component in understanding the maintenance and amplification of the virus as well as tangential transmission to humans and horses. We investigated the blood-feeding patterns of Culex tarsalis Coquillett and members of the Culex pipiens L. complex from southern to northern California. Nearly 100 different host species were identified from 1,487 bloodmeals, by using the mitochondrial gene cytochrome c oxidase I (COI). Cx. tarsalis fed on a higher diversity of hosts and more frequently on nonhuman mammals than did the Cx. pipiens complex. Several WNV-competent host species, including house finch and house sparrow, were common bloodmeal sources for both vector species across several biomes and could account for WNV maintenance and amplification in these areas. Highly competent American crow, western scrub-jay and yellow-billed magpie also were fed upon often when available and are likely important as amplifying hosts for WNV in some areas. Neither species fed frequently on humans (Cx. pipiens complex [0.4%], Cx. tarsalis [0.2%]), but with high abundance, both species could serve as both enzootic and bridge vectors for WNV. PMID:22897051

Cytogenetic Analysis of the South American Fruit Fly Anastrepha fraterculus (Diptera:Tephritidae) Species Complex: Construction of Detailed Photographic Polytene Chromosome Maps of the Argentinian Af. sp.1 Member

PubMed Central

Augustinos, Antonios A.; Drosopoulou, Elena; Lanzavecchia, Silvia B.; Cladera, Jorge L.; Caceres, Carlos; Bourtzis, Kostas; Mavragani-Tsipidou, Penelope; Zacharopoulou, Antigone

2016-01-01

Genetic and cytogenetic studies constitute a significant basis for understanding the biology of insect pests and the design and the construction of genetic tools for biological control strategies. Anastrepha fraterculus is an important pest of the Tephritidae family. It is distributed from southern Texas through eastern Mexico, Central America and South America causing significant crop damage and economic losses. Currently it is considered as a species complex; until now seven members have been described based on multidisciplinary approaches. Here we report the cytogenetic analysis of an Argentinian population characterized as Af. sp.1 member of the Anastrepha fraterculus species complex. The mitotic karyotype and the first detailed photographic maps of the salivary gland polytene chromosomes are presented. The mitotic metaphase complement consists of six (6) pairs of chromosomes, including one pair of heteromorphic sex chromosomes, with the male being the heterogametic sex. The analysis of the salivary gland polytene complement shows a total number of five long chromosomes that correspond to the five autosomes of the mitotic karyotype and a heterochromatic network corresponding to the sex chromosomes. Comparison of the polytene chromosome maps between this species and Anastrepha ludens shows significant similarity. The polytene maps presented here are suitable for cytogenetic studies that could shed light on the species limits within this species complex and support the development of genetic tools for sterile insect technique (SIT) applications. PMID:27362546

Identification of a New Mullet Species Complex Based on an Integrative Molecular and Cytogenetic Investigation of Mugil hospes (Mugilidae: Mugiliformes).

PubMed

Nirchio, Mauro; Paim, Fabilene G; Milana, Valentina; Rossi, Anna R; Oliveira, Claudio

2018-01-01

Mullets are very common fishes included in the family Mugilidae, (Mugiliformes), which are characterized by both a remarkably uniform external morphology and internal anatomy. Recently, within this family, different species complexes were molecularly identified within Mugil , a genus which is characterized by lineages that sometimes show very different karyotypes. Here we report the results of cytogenetic and molecular analyses conducted on Mugil hospes , commonly known as the hospe mullet, from Ecuador. The study aims to verify whether the original described species from the Pacific Ocean corresponds to that identified in the Atlantic Ocean, and to identify species-specific chromosome markers that can add new comparative data about Mugilidae karyotype evolution. The karyotype of M. hospes from Ecuador is composed of 48 acrocentric chromosomes and shows two active nucleolar organizer regions (NORs). In situ hybridization, using different types of repetitive sequences (rDNAs, U1 snDNA, telomeric repeats) as probes, identified species-specific chromosome markers that have been compared with those of other species of the genus Mugil . Cytochrome c oxidase subunit I (COI) sequence analysis shows only 92-93% similarity with sequences previously deposited under this species name in GenBank, all of which were from the Atlantic Ocean. Phylogenetic reconstructions indicate the presence of three well-supported hospe mullet lineages whose molecular divergence is compatible with the presence of distinct species. Indeed, the first lineage includes samples from Ecuador, whereas the other two lineages include the Atlantic samples and correspond to M. brevirostris from Brazil and Mugil sp. R from Belize/Venezuela. Results here provided reiterate the pivotal importance of an integrative molecular and cytogenetic approach in the reconstruction of the relationships within Mugilidae.

Identification of a New Mullet Species Complex Based on an Integrative Molecular and Cytogenetic Investigation of Mugil hospes (Mugilidae: Mugiliformes)

PubMed Central

Nirchio, Mauro; Paim, Fabilene G.; Milana, Valentina; Rossi, Anna R.; Oliveira, Claudio

2018-01-01

Mullets are very common fishes included in the family Mugilidae, (Mugiliformes), which are characterized by both a remarkably uniform external morphology and internal anatomy. Recently, within this family, different species complexes were molecularly identified within Mugil, a genus which is characterized by lineages that sometimes show very different karyotypes. Here we report the results of cytogenetic and molecular analyses conducted on Mugil hospes, commonly known as the hospe mullet, from Ecuador. The study aims to verify whether the original described species from the Pacific Ocean corresponds to that identified in the Atlantic Ocean, and to identify species-specific chromosome markers that can add new comparative data about Mugilidae karyotype evolution. The karyotype of M. hospes from Ecuador is composed of 48 acrocentric chromosomes and shows two active nucleolar organizer regions (NORs). In situ hybridization, using different types of repetitive sequences (rDNAs, U1 snDNA, telomeric repeats) as probes, identified species-specific chromosome markers that have been compared with those of other species of the genus Mugil. Cytochrome c oxidase subunit I (COI) sequence analysis shows only 92–93% similarity with sequences previously deposited under this species name in GenBank, all of which were from the Atlantic Ocean. Phylogenetic reconstructions indicate the presence of three well-supported hospe mullet lineages whose molecular divergence is compatible with the presence of distinct species. Indeed, the first lineage includes samples from Ecuador, whereas the other two lineages include the Atlantic samples and correspond to M. brevirostris from Brazil and Mugil sp. R from Belize/Venezuela. Results here provided reiterate the pivotal importance of an integrative molecular and cytogenetic approach in the reconstruction of the relationships within Mugilidae. PMID:29459882

Taxonomy and species boundaries in the coral genus Favia Milne Edwards and Haime, 1857 (Cnidaria: Scleractinia) from Thailand revealed by morphological and genetic data

NASA Astrophysics Data System (ADS)

Kongjandtre, N.; Ridgway, T.; Cook, L. G.; Huelsken, T.; Budd, A. F.; Hoegh-Guldberg, O.

2012-06-01

While Faviidae is a widely and uniformly distributed coral family throughout the Indo-Pacific, the extensive phenotypic plasticity of colony surface and corallite features often confounds the use of macromorphological characters in species identification, and contributes to conflict between traditional classification and molecular analyses of the group. Recent advances in morphological and molecular techniques now provide a suite of methods to re-address coral taxonomy in complex groups, such as that represented by the Faviidae. This study combines morphologic measurements including "3D coordinates landmarks" data with phylogenetic assessments of nuclear (ITS) and mitochondrial (COI-trnM) DNA to assess species boundaries in nine species of Faviidae with para-septothecal walls from Thailand. Strong concordance was found between morphological features and a priori groupings based on both morphospecies and genetically defined groups (ITS and COI-trnM). Favia truncatus was the most well-defined species based on morphological analyses, and it was also shown to be monophyletic using phylogenetic analyses. Besides F. truncatus, the only other species that was found to be monophyletic in analyses of both genes was F. cf. helianthoides, but its skeletal morphology overlapped with the F. favus species complex (comprised of F. favus, F. speciosa, F. matthaii and F. rotumana). Although not genetically monophyletic, the F. favus species complex and F. pallida were fairly well delineated morphologically. Morphospecies within the F. favus species complex are therefore possibly a result of genetic drift and/or stable polymorphisms driven by divergent selection. These results represent a first step toward a taxonomic revision of the Indo-Pacific Favia, which will integrate morphological methods with the study of type material, genetic information, reproductive data, and tests of phenotypic plasticity—given that multiple lines of evidence are needed to resolve ambiguous species and assign species names.

The effect of size and competition on tree growth rate in old-growth coniferous forests

USGS Publications Warehouse

Das, Adrian

2012-01-01

Tree growth and competition play central roles in forest dynamics. Yet models of competition often neglect important variation in species-specific responses. Furthermore, functions used to model changes in growth rate with size do not always allow for potential complexity. Using a large data set from old-growth forests in California, models were parameterized relating growth rate to tree size and competition for four common species. Several functions relating growth rate to size were tested. Competition models included parameters for tree size, competitor size, and competitor distance. Competitive strength was allowed to vary by species. The best ranked models (using Akaike’s information criterion) explained between 18% and 40% of the variance in growth rate, with each species showing a strong response to competition. Models indicated that relationships between competition and growth varied substantially among species. The results also suggested that the relationship between growth rate and tree size can be complex and that how we model it can affect not only our ability to detect that complexity but also whether we obtain misleading results. In this case, for three of four species, the best model captured an apparent and unexpected decline in potential growth rate for the smallest trees in the data set.

The Hyalella (Crustacea: Amphipoda) species cloud of the ancient Lake Titicaca originated from multiple colonizations.

PubMed

Adamowicz, Sarah J; Marinone, María Cristina; Menu-Marque, Silvina; Martin, Jeffrey W; Allen, Daniel C; Pyle, Michelle N; De Los Ríos, Patricio; Sobel, Crystal N; Ibañez, Carla; Pinto, Julio; Witt, Jonathan D S

2018-08-01

Ancient lakes are renowned for their exceptional diversity of endemic species. As model systems for the study of sympatric speciation, it is necessary to understand whether a given hypothesized species flock is of monophyletic or polyphyletic origin. Here, we present the first molecular characterization of the Hyalella (Crustacea: Amphipoda) species complex of Lake Titicaca, using COI and 28S DNA sequences, including samples from the connected Small and Large Lakes that comprise Lake Titicaca as well as from a broader survey of southern South American sites. At least five evolutionarily distant lineages are present within Lake Titicaca, which were estimated to have diverged from one another 12-20 MYA. These major lineages are dispersed throughout the broader South American Hyalella phylogeny, with each lineage representing at least one independent colonization of the lake. Moreover, complex genetic relationships are revealed between Lake Titicaca individuals and those from surrounding water bodies, which may be explained by repeated dispersal into and out of the lake, combined with parallel intralacustrine diversification within two separate clades. Although further work in deeper waters will be required to determine the number of species present and modes of diversification, our results strongly indicate that this amphipod species cloud is polyphyletic with a complex geographic history. Copyright © 2018 Elsevier Inc. All rights reserved.

Biology, taxonomy, and IPM strategies of Bactrocera tau Walker and complex species (Diptera; Tephritidae) in Asia: a comprehensive review.

PubMed

Jaleel, Waqar; Lu, Lihua; He, Yurong

2018-06-02

Bactrocera flies are the serious pests of fruit, vegetables, and nuts over the world. Bactrocera tau Walker is an economically important pest of agricultural crops. In Asia, approximately 30-40% losses of agricultural products are caused by B. tau infestation every year. In Asia, the B. tau contains a complex of sibling species that called the tau complex. However, the basic studies of B. tau and complex species are very important for integrated management. A comprehensive review of the B. tau and complex species has not been provided elsewhere. So, considering the importance of B. tau and complex species, this study provides the published information on ecology, nomenclature, identification tools, geographical distribution, potential invasion, and IPM tactics of B. tau and complex species, which would be more informative for publication facilitating related to integrated pest management (IPM) strategies of B. tau and complex species. In IPM of B. tau and complex species, the phytochemical and biological controls have not been applied successfully in Asia; there is an urgent need to study and applications of these two mentioned control techniques against the B. tau and complex species in Asia.

DNA Barcoding of Bemisia tabaci Complex (Hemiptera: Aleyrodidae) Reveals Southerly Expansion of the Dominant Whitefly Species on Cotton in Pakistan

PubMed Central

Ashfaq, Muhammad; Hebert, Paul D. N.; Mirza, M. Sajjad; Khan, Arif M.; Mansoor, Shahid; Shah, Ghulam S.; Zafar, Yusuf

2014-01-01

Background Although whiteflies (Bemisia tabaci complex) are an important pest of cotton in Pakistan, its taxonomic diversity is poorly understood. As DNA barcoding is an effective tool for resolving species complexes and analyzing species distributions, we used this approach to analyze genetic diversity in the B. tabaci complex and map the distribution of B. tabaci lineages in cotton growing areas of Pakistan. Methods/Principal Findings Sequence diversity in the DNA barcode region (mtCOI-5′) was examined in 593 whiteflies from Pakistan to determine the number of whitefly species and their distributions in the cotton-growing areas of Punjab and Sindh provinces. These new records were integrated with another 173 barcode sequences for B. tabaci, most from India, to better understand regional whitefly diversity. The Barcode Index Number (BIN) System assigned the 766 sequences to 15 BINs, including nine from Pakistan. Representative specimens of each Pakistan BIN were analyzed for mtCOI-3′ to allow their assignment to one of the putative species in the B. tabaci complex recognized on the basis of sequence variation in this gene region. This analysis revealed the presence of Asia II 1, Middle East-Asia Minor 1, Asia 1, Asia II 5, Asia II 7, and a new lineage “Pakistan”. The first two taxa were found in both Punjab and Sindh, but Asia 1 was only detected in Sindh, while Asia II 5, Asia II 7 and “Pakistan” were only present in Punjab. The haplotype networks showed that most haplotypes of Asia II 1, a species implicated in transmission of the cotton leaf curl virus, occurred in both India and Pakistan. Conclusions DNA barcodes successfully discriminated cryptic species in B. tabaci complex. The dominant haplotypes in the B. tabaci complex were shared by India and Pakistan. Asia II 1 was previously restricted to Punjab, but is now the dominant lineage in southern Sindh; its southward spread may have serious implications for cotton plantations in this region. PMID:25099936

Evolution of Cuticular Hydrocarbons in the Hymenoptera: a Meta-Analysis.

PubMed

Kather, Ricarda; Martin, Stephen J

2015-10-01

Chemical communication is the oldest form of communication, spreading across all forms of life. In insects, cuticular hydrocarbons (CHC) function as chemical cues for the recognition of mates, species, and nest-mates in social insects. Although much is known about the function of individual hydrocarbons and their biosynthesis, a phylogenetic overview is lacking. Here, we review the CHC profiles of 241 species of Hymenoptera, one of the largest and most important insect orders, which includes the Symphyta (sawflies), the polyphyletic Parasitica (parasitoid wasps), and the Aculeata (wasps, bees, and ants). We investigated whether these taxonomic groups differed in the presence and absence of CHC classes and whether the sociality of a species (solitarily vs. social) had an effect on CHC profile complexity. We found that the main CHC classes (i.e., n-alkanes, alkenes, and methylalkanes) were all present early in the evolutionary history of the Hymenoptera, as evidenced by their presence in ancient Symphyta and primitive Parasitica wasps. Throughout all groups within the Hymenoptera, the more complex a CHC the fewer species that produce it, which may reflect the Occam's razor principle that insects' only biosynthesize the most simple compound that fulfil its needs. Surprisingly, there was no difference in the complexity of CHC profiles between social and solitary species, with some of the most complex CHC profiles belonging to the Parasitica. This profile complexity has been maintained in the ants, but some specialization in biosynthetic pathways has led to a simplification of profiles in the aculeate wasps and bees. The absence of CHC classes in some taxa or species may be due to gene silencing or down-regulation rather than gene loss, as demonstrated by sister species having highly divergent CHC profiles, and cannot be predicted by their phylogenetic history. The presence of highly complex CHC profiles prior to the vast radiation of the social Hymenoptera indicates a 'spring-loaded' system where the diversity of CHC needed for the complex communication systems of social insects were already present for natural selection to act upon, rather than having evolved independently. This diversity may have aided the multiple independent evolution of sociality within the Aculeata.

The 'species complex' issue in clinically relevant fungi: A case study in Scedosporium apiospermum.

PubMed

Chen, Min; Zeng, Jingsi; De Hoog, G Sybren; Stielow, Benjamin; Gerrits Van Den Ende, A H G; Liao, Wanqing; Lackner, Michaela

2016-02-01

The genus Scedosporium currently comprises six species, Scedosporium apiospermum, Scedosporium boydii, Pseudallescheria angusta, Scedosporium minutisporum, Scedosporium dehoogii, and Scedosporium aurantiacum, most of which can be distinguished with the primary fungal DNA barcode, the ITS1/2 region of the rDNA gene cluster. In the present study, four additional genetic loci were explored from a phylogenetic point of view enabling a barcoding approach based on K2P pairwise distances to resolve the taxa Scedosporium. We included partial γ-actin (ACT), β-tubulin (BT2), elongation factor 1α (TEF1), and the small ribosomal protein 60S L10 (L1) (RP60S). Phylogenetic inference of each marker individually showed that four out of six species within Scedosporium can be distinguished unambiguously, while strains of S. apiospermum, S. boydii, and P. angusta showed occasional recombination, and accordingly, no genealogical concordance between markers was obtainable. We defined S. apiospermum, S. boydii, and P. angusta as the 'S. apiospermum species complex' since observed differences were not consistent between lineages, and no clinical differences are known between entities within the complex. While BT2 revealed the best performance among the genetic loci tested at the lineage level, barcoding of the ITS region is sufficient for distinction of all entities in Scedosporium at the species or 'complex' level. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

One new species of Amphinemura and description of the female of A. ancistroidea Li & Yang (Plecoptera: Nemouridae) from Guangxi Zhuang Autonomous Region of southern China.

PubMed

Mo, Raorao; Yang, Ding; Wang, Guoquan; Li, Weihai

2017-06-11

A new nemourid species, Amphinemura yao sp. nov. is described from the Daoyao Mountains of Guangxi Zhuang Autonomous Region of southern China. Amphinemura ancistroidea Li & Yang, 2007 is newly recorded from Guangxi and the female is described for the first time including the internal vaginal complex. The new species is compared with related taxa.

Evaluating the SWAT model for a low-gradient forested watershed in coastal South Carolina

Treesearch

D.M. Amatya; M.K. Jha.

2011-01-01

Modeling the hydrology of low�]gradient forested watersheds on shallow, poorly drained soils of the coastal plain is a challenging task due to complexities in watershed delineation, microtopography, evapotranspiration, runoff generation processes and pathways including flooding and submergence caused by tropical storms, and complexity of vegetation species....

Potential for using Fusarium to control Fusarium disease in forest nurseries

Treesearch

Robert L. James; R. Kasten Dumroese

2007-01-01

The taxon Fusarium oxysporum contains a complex of fungi that are very important pathogens of many plant species worldwide, including seedlings grown in forest nurseries. All members of this complex appear very similar morphologically, and can often be differentiated only on the basis of genetic analyses. Strains of F. oxysporum...

The first European stand of Paramecium sonneborni (P. aurelia complex), a species known only from North America (Texas, USA).

PubMed

Przyboś, Ewa; Tarcz, Sebastian; Rautian, Maria; Lebedeva, Natalia

2014-06-01

P. aurelia is currently defined as a complex of 15 sibling species including 14 species designated by Sonneborn (1975) and one, P. sonneborni, by Aufderheide et al. (1983). The latter was known from only one stand (Texas, USA). The main reason for the present study was a new stand of Paramecium in Cyprus, with strains recognized as P. sonneborni based on the results of strain crosses, cytological slides, and molecular analyses of three loci (ITS1-5.8S-ITS2-5'LSU rDNA, COI, CytB). The new stand of P. sonneborni in Europe shows that the species, previously considered endemic, may have a wider range. This demonstrates the impact of under-sampling on the knowledge of the biogeography of microbial eukaryotes. Phylogenetic trees based on all the studied fragments revealed that P. sonneborni forms a separate cluster that is closer to P. jenningsi and P. schewiakoffi than to the other members of the P. aurelia complex. Copyright © 2014 Elsevier GmbH. All rights reserved.

Pyrroloindolone synthesis via a Cp*Co(III)-catalyzed redox-neutral directed C-H alkenylation/annulation sequence.

PubMed

Ikemoto, Hideya; Yoshino, Tatsuhiko; Sakata, Ken; Matsunaga, Shigeki; Kanai, Motomu

2014-04-09

A unique synthetic utility of a Cp*Co(III) catalyst in comparison with related Cp*Rh(III) catalysts is described. A C2-selective indole alkenylation/annulation sequence proceeded smoothly with catalytic amount of a [Cp*Co(III)(C6H6)](PF6)2 complex and KOAc. Intramolecular addition of an alkenyl-Cp*Co species to a carbamoyl moiety gave pyrroloindolones in 58-89% yield in one pot. Clear difference was observed between the catalytic activity of the Cp*Co(III) complex and those of Cp*Rh(III) complexes, highlighting the unique nucleophilic activity of the organocobalt species. The Cp*Co(III) catalysis was also suitable for simple alkenylation process of N-carbamoyl indoles, and broad range of alkynes, including terminal alkynes, were applicable to give C2-alkenylated indoles in 50-99% yield. Mechanistic studies on C-H activation step under Cp*Co(III) catalysis with the aid of an acetate unit as well as evaluation of the difference between organo-Co(III) species and organo-Rh(III) species are also described.

Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples

PubMed Central

Arulandhu, Alfred J.; Staats, Martijn; Hagelaar, Rico; Voorhuijzen, Marleen M.; Prins, Theo W.; Scholtens, Ingrid; Costessi, Adalberto; Duijsings, Danny; Rechenmann, François; Gaspar, Frédéric B.; Barreto Crespo, Maria Teresa; Holst-Jensen, Arne; Birck, Matthew; Burns, Malcolm; Haynes, Edward; Hochegger, Rupert; Klingl, Alexander; Lundberg, Lisa; Natale, Chiara; Niekamp, Hauke; Perri, Elena; Barbante, Alessandra; Rosec, Jean-Philippe; Seyfarth, Ralf; Sovová, Tereza; Van Moorleghem, Christoff; van Ruth, Saskia; Peelen, Tamara

2017-01-01

Abstract DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories. A DNA metabarcoding method was developed that makes use of 12 DNA barcode markers that have demonstrated universal applicability across a wide range of plant and animal taxa and that facilitate the identification of species in samples containing degraded DNA. The DNA metabarcoding method was developed based on Illumina MiSeq amplicon sequencing of well-defined experimental mixtures, for which a bioinformatics pipeline with user-friendly web-interface was developed. The performance of the DNA metabarcoding method was assessed in an international validation trial by 16 laboratories, in which the method was found to be highly reproducible and sensitive enough to identify species present in a mixture at 1% dry weight content. The advanced multi-locus DNA metabarcoding method assessed in this study provides reliable and detailed data on the composition of complex food products, including information on the presence of CITES-listed species. The method can provide improved resolution for species identification, while verifying species with multiple DNA barcodes contributes to an enhanced quality assurance. PMID:29020743

Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples.

PubMed

Arulandhu, Alfred J; Staats, Martijn; Hagelaar, Rico; Voorhuijzen, Marleen M; Prins, Theo W; Scholtens, Ingrid; Costessi, Adalberto; Duijsings, Danny; Rechenmann, François; Gaspar, Frédéric B; Barreto Crespo, Maria Teresa; Holst-Jensen, Arne; Birck, Matthew; Burns, Malcolm; Haynes, Edward; Hochegger, Rupert; Klingl, Alexander; Lundberg, Lisa; Natale, Chiara; Niekamp, Hauke; Perri, Elena; Barbante, Alessandra; Rosec, Jean-Philippe; Seyfarth, Ralf; Sovová, Tereza; Van Moorleghem, Christoff; van Ruth, Saskia; Peelen, Tamara; Kok, Esther

2017-10-01

DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories. A DNA metabarcoding method was developed that makes use of 12 DNA barcode markers that have demonstrated universal applicability across a wide range of plant and animal taxa and that facilitate the identification of species in samples containing degraded DNA. The DNA metabarcoding method was developed based on Illumina MiSeq amplicon sequencing of well-defined experimental mixtures, for which a bioinformatics pipeline with user-friendly web-interface was developed. The performance of the DNA metabarcoding method was assessed in an international validation trial by 16 laboratories, in which the method was found to be highly reproducible and sensitive enough to identify species present in a mixture at 1% dry weight content. The advanced multi-locus DNA metabarcoding method assessed in this study provides reliable and detailed data on the composition of complex food products, including information on the presence of CITES-listed species. The method can provide improved resolution for species identification, while verifying species with multiple DNA barcodes contributes to an enhanced quality assurance. © The Authors 2017. Published by Oxford University Press.

Habitat availability and gene flow influence diverging local population trajectories under scenarios of climate change: a place-based approach.

PubMed

Schwalm, Donelle; Epps, Clinton W; Rodhouse, Thomas J; Monahan, William B; Castillo, Jessica A; Ray, Chris; Jeffress, Mackenzie R

2016-04-01

Ecological niche theory holds that species distributions are shaped by a large and complex suite of interacting factors. Species distribution models (SDMs) are increasingly used to describe species' niches and predict the effects of future environmental change, including climate change. Currently, SDMs often fail to capture the complexity of species' niches, resulting in predictions that are generally limited to climate-occupancy interactions. Here, we explore the potential impact of climate change on the American pika using a replicated place-based approach that incorporates climate, gene flow, habitat configuration, and microhabitat complexity into SDMs. Using contemporary presence-absence data from occupancy surveys, genetic data to infer connectivity between habitat patches, and 21 environmental niche variables, we built separate SDMs for pika populations inhabiting eight US National Park Service units representing the habitat and climatic breadth of the species across the western United States. We then predicted occurrence probability under current (1981-2010) and three future time periods (out to 2100). Occurrence probabilities and the relative importance of predictor variables varied widely among study areas, revealing important local-scale differences in the realized niche of the American pika. This variation resulted in diverse and - in some cases - highly divergent future potential occupancy patterns for pikas, ranging from complete extirpation in some study areas to stable occupancy patterns in others. Habitat composition and connectivity, which are rarely incorporated in SDM projections, were influential in predicting pika occupancy in all study areas and frequently outranked climate variables. Our findings illustrate the importance of a place-based approach to species distribution modeling that includes fine-scale factors when assessing current and future climate impacts on species' distributions, especially when predictions are intended to manage and conserve species of concern within individual protected areas. © 2015 John Wiley & Sons Ltd.

Herschel Observations of Extraordinary Sources: Analysi sof the HIFI 1.2 THz Wide Spectral Survey toward Orion KL II. Chemical Implications

NASA Astrophysics Data System (ADS)

Crockett, N. R.; Bergin, E. A.; Neill, J. L.; Favre, C.; Blake, G. A.; Herbst, E.; Anderson, D. E.; Hassel, G. E.

2015-06-01

We present chemical implications arising from spectral models fit to the Herschel/HIFI spectral survey toward the Orion Kleinmann-Low nebula (Orion KL). We focus our discussion on the eight complex organics detected within the HIFI survey utilizing a novel technique to identify those molecules emitting in the hottest gas. In particular, we find the complex nitrogen bearing species CH3CN, C2H3CN, C2H5CN, and NH2CHO systematically trace hotter gas than the oxygen bearing organics CH3OH, C2H5OH, CH3OCH3, and CH3OCHO, which do not contain nitrogen. If these complex species form predominantly on grain surfaces, this may indicate N-bearing organics are more difficult to remove from grain surfaces than O-bearing species. Another possibility is that hot (Tkin ∼ 300 K) gas phase chemistry naturally produces higher complex cyanide abundances while suppressing the formation of O-bearing complex organics. We compare our derived rotation temperatures and molecular abundances to chemical models, which include gas-phase and grain surface pathways. Abundances for a majority of the detected complex organics can be reproduced over timescales ≳105 years, with several species being underpredicted by less than 3σ. Derived rotation temperatures for most organics, furthermore, agree reasonably well with the predicted temperatures at peak abundance. We also find that sulfur bearing molecules that also contain oxygen (i.e., SO, SO2, and OCS) tend to probe the hottest gas toward Orion KL, indicating the formation pathways for these species are most efficient at high temperatures. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.

Mining sequence variations in representative polyploid sugarcane germplasm accessions

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

Yang, Xiping; Song, Jian; You, Qian

Sugarcane (Saccharum spp.) is one of the most important economic crops because of its high sugar production and biofuel potential. Due to the high polyploid level and complex genome of sugarcane, it has been a huge challenge to investigate genomic sequence variations, which are critical for identifying alleles contributing to important agronomic traits. In order to mine the genetic variations in sugarcane, genotyping by sequencing (GBS), was used to genotype 14 representative Saccharum complex accessions. GBS is a method to generate a large number of markers, enabled by next generation sequencing (NGS) and the genome complexity reduction using restriction enzymes.more » To use GBS for high throughput genotyping highly polyploid sugarcane, the GBS analysis pipelines in 14 Saccharum complex accessions were established by evaluating different alignment methods, sequence variants callers, and sequence depth for single nucleotide polymorphism (SNP) filtering. By using the established pipeline, a total of 76,251 non-redundant SNPs, 5642 InDels, 6380 presence/absence variants (PAVs), and 826 copy number variations (CNVs) were detected among the 14 accessions. In addition, non-reference based universal network enabled analysis kit and Stacks de novo called 34,353 and 109,043 SNPs, respectively. In the 14 accessions, the percentages of single dose SNPs ranged from 38.3% to 62.3% with an average of 49.6%, much more than the portions of multiple dosage SNPs. Concordantly called SNPs were used to evaluate the phylogenetic relationship among the 14 accessions. The results showed that the divergence time between the Erianthus genus and the Saccharum genus was more than 10 million years ago (MYA). The Saccharum species separated from their common ancestors ranging from 0.19 to 1.65 MYA. The GBS pipelines including the reference sequences, alignment methods, sequence variant callers, and sequence depth were recommended and discussed for the Saccharum complex and other related species. A large number of sequence variations were discovered in the Saccharum complex, including SNPs, InDels, PAVs, and CNVs. Genome-wide SNPs were further used to illustrate sequence features of polyploid species and demonstrated the divergence of different species in the Saccharum complex. The results of this study showed that GBS was an effective NGS-based method to discover genomic sequence variations in highly polyploid and heterozygous species.« less

Mining sequence variations in representative polyploid sugarcane germplasm accessions

DOE PAGES

Yang, Xiping; Song, Jian; You, Qian; ...

2017-08-09

Sugarcane (Saccharum spp.) is one of the most important economic crops because of its high sugar production and biofuel potential. Due to the high polyploid level and complex genome of sugarcane, it has been a huge challenge to investigate genomic sequence variations, which are critical for identifying alleles contributing to important agronomic traits. In order to mine the genetic variations in sugarcane, genotyping by sequencing (GBS), was used to genotype 14 representative Saccharum complex accessions. GBS is a method to generate a large number of markers, enabled by next generation sequencing (NGS) and the genome complexity reduction using restriction enzymes.more » To use GBS for high throughput genotyping highly polyploid sugarcane, the GBS analysis pipelines in 14 Saccharum complex accessions were established by evaluating different alignment methods, sequence variants callers, and sequence depth for single nucleotide polymorphism (SNP) filtering. By using the established pipeline, a total of 76,251 non-redundant SNPs, 5642 InDels, 6380 presence/absence variants (PAVs), and 826 copy number variations (CNVs) were detected among the 14 accessions. In addition, non-reference based universal network enabled analysis kit and Stacks de novo called 34,353 and 109,043 SNPs, respectively. In the 14 accessions, the percentages of single dose SNPs ranged from 38.3% to 62.3% with an average of 49.6%, much more than the portions of multiple dosage SNPs. Concordantly called SNPs were used to evaluate the phylogenetic relationship among the 14 accessions. The results showed that the divergence time between the Erianthus genus and the Saccharum genus was more than 10 million years ago (MYA). The Saccharum species separated from their common ancestors ranging from 0.19 to 1.65 MYA. The GBS pipelines including the reference sequences, alignment methods, sequence variant callers, and sequence depth were recommended and discussed for the Saccharum complex and other related species. A large number of sequence variations were discovered in the Saccharum complex, including SNPs, InDels, PAVs, and CNVs. Genome-wide SNPs were further used to illustrate sequence features of polyploid species and demonstrated the divergence of different species in the Saccharum complex. The results of this study showed that GBS was an effective NGS-based method to discover genomic sequence variations in highly polyploid and heterozygous species.« less

Restoring complexity: second-growth forests and habitat diversity.

Treesearch

Valerie Rapp

2002-01-01

Old-growth forests supply many important values, including critical habitat for some wildlife species. These forests are most useful for some wildlife species when they exist in large blocks. But many areas dedicated to old-growth values on federal lands are fragmented by patches of second-growth forests planted after timber harvest. These second-growth forests are...

Population diversity and evidence of introgression among the black oaks of California

Treesearch

Richard S. Dodd; Nasser Kashani; Zara Afzal-Rafii

2002-01-01

The black oaks of California include 4 tree species (California black oak, coast live oak, Shreve oak, interior live oak) that are known to hybridize. Complex patterns of population variation within each species are likely to result from these hybrid combinations and from subsequent introgressions. We have been studying population variation using biochemical and...

Genome sequence of Fusarium isolate MYA-4552 from the midgut of Anoplophora glabripennis, an invasive, wood-boring beetle

USDA-ARS?s Scientific Manuscript database

The Fusarium solani species complex (FSSC) is a clade of environmentally ubiquitous fungi that includes plant, animal and insect associates. Here we report the draft genome sequence of the undescribed species FSSC 6 (isolate MYA-4552), housed in the gut of the wood-boring cerambycid beetle Anoplopho...

Trophic redundancy reduces vulnerability to extinction cascades

PubMed Central

Sanders, Dirk; Thébault, Elisa; Kehoe, Rachel; Frank van Veen, F. J.

2018-01-01

Current species extinction rates are at unprecedentedly high levels. While human activities can be the direct cause of some extinctions, it is becoming increasingly clear that species extinctions themselves can be the cause of further extinctions, since species affect each other through the network of ecological interactions among them. There is concern that the simplification of ecosystems, due to the loss of species and ecological interactions, increases their vulnerability to such secondary extinctions. It is predicted that more complex food webs will be less vulnerable to secondary extinctions due to greater trophic redundancy that can buffer against the effects of species loss. Here, we demonstrate in a field experiment with replicated plant-insect communities, that the probability of secondary extinctions is indeed smaller in food webs that include trophic redundancy. Harvesting one species of parasitoid wasp led to secondary extinctions of other, indirectly linked, species at the same trophic level. This effect was markedly stronger in simple communities than for the same species within a more complex food web. We show that this is due to functional redundancy in the more complex food webs and confirm this mechanism with a food web simulation model by highlighting the importance of the presence and strength of trophic links providing redundancy to those links that were lost. Our results demonstrate that biodiversity loss, leading to a reduction in redundant interactions, can increase the vulnerability of ecosystems to secondary extinctions, which, when they occur, can then lead to further simplification and run-away extinction cascades. PMID:29467292

Preferential uptake of soil nitrogen forms by grassland plant species.

PubMed

Weigelt, Alexandra; Bol, Roland; Bardgett, Richard D

2005-02-01

In this study, we assessed whether a range of temperate grassland species showed preferential uptake for different chemical forms of N, including inorganic N and a range of amino acids that commonly occur in temperate grassland soil. Preferential uptake of dual-labelled (13C and 15N) glycine, serine, arginine and phenylalanine, as compared to inorganic N, was tested using plants growing in pots with natural field soil. We selected five grass species representing a gradient from fertilised, productive pastures to extensive, low productivity pastures (Lolium perenne, Holcus lanatus, Anthoxanthum odoratum, Deschampsia flexuosa, and Nardus stricta). Our data show that all grass species were able to take up directly a diversity of soil amino acids of varying complexity. Moreover, we present evidence of marked inter-species differences in preferential use of chemical forms of N of varying complexity. L. perenne was relatively more effective at using inorganic N and glycine compared to the most complex amino acid phenylalanine, whereas N. stricta showed a significant preference for serine over inorganic N. Total plant N acquisition, measured as root and shoot concentration of labelled compounds, also revealed pronounced inter-species differences which were related to plant growth rate: plants with higher biomass production were found to take up more inorganic N. Our findings indicate that species-specific differences in direct uptake of different N forms combined with total N acquisition could explain changes in competitive dominance of grass species in grasslands of differing fertility.

Gill monogenean communities (Platyhelminthes, Monogenea, Dactylogyridae) of butterflyfishes from tropical Indo-West Pacific Islands.

PubMed

Reverter, Miriam; Cutmore, Scott C; Bray, Rodney; Cribb, Thomas H; Sasal, Pierre

2016-10-01

We studied the monogenean communities of 34 species of butterflyfish from the tropical Indo-West Pacific, identifying 13 dactylogyrid species (including two species that are presently undescribed). Monogenean assemblages differed significantly between host species in terms of taxonomic structure, intensity and prevalence. Parasite richness ranged from 0 (Chaetodon lunulatus) to 11 (C. auriga, C. citrinellus and C. lunula). Host specificity varied between the dactylogyrids species, being found on 2-29 of the 34 chaetodontid species examined. Sympatric butterflyfish species were typically parasitized by different combinations of dactylogyrid species, suggesting the existence of complex host-parasite interactions. We identified six clusters of butterflyfish species based on the similarities of their dactylogyrid communities. Dactylogyrid richness and diversity were not related to host size, diet specialization, depth range or phylogeny of butterflyfish species. However, there was a weak positive correlation between monogenean richness and diversity and host geographical range. Most communities of dactylogyrids were dominated by Haliotrema aurigae and H. angelopterum, indicating the importance of the genus Haliotrema in shaping monogenean communities of butterflyfishes. This study casts light on the structure of the monogenean communities of butterflyfishes, suggesting that the diversity and complexity of community structures arises from a combination of host species-specific parameters.

Review of the Hispaniolan Parachondria (Chondropomorus) complex (Gastropoda: Littorinoidea: Annulariidae).

PubMed

Watters, G Thomas

2016-06-23

The Parachondria (Chondropomorus) complex in Hispaniola is reviewed. Nineteen species are recognized including eight new species: Parachondria anatolensis n. sp., Parachondria arcisensis n. sp., Parachondria daedalus n. sp., Parachondria heatheraikenae n. sp., Parachondria isabellinus n. sp., Parachondria muchai n. sp., Parachondria silvaticus n. sp., and Parachondria stigmosus n. sp. Distributional and habitat notes are given for additional taxa. Chondropoma marinum "Weinland" Reeve, 1863, is regarded as a nomen dubium. Chondropoma (Chondropomorus) moroni Bartsch, 1946, is reidentified as Crossepoma emilianum (Weinland, 1862). Chondropoma simplex Pfeiffer, 1852, regarded by Bartsch (1946) as a Chondropomorus, is considered a Chondropoma.

Retention of Habitat Complexity Minimizes Disassembly of Reef Fish Communities following Disturbance: A Large-Scale Natural Experiment

PubMed Central

Emslie, Michael J.; Cheal, Alistair J.; Johns, Kerryn A.

2014-01-01

High biodiversity ecosystems are commonly associated with complex habitats. Coral reefs are highly diverse ecosystems, but are under increasing pressure from numerous stressors, many of which reduce live coral cover and habitat complexity with concomitant effects on other organisms such as reef fishes. While previous studies have highlighted the importance of habitat complexity in structuring reef fish communities, they employed gradient or meta-analyses which lacked a controlled experimental design over broad spatial scales to explicitly separate the influence of live coral cover from overall habitat complexity. Here a natural experiment using a long term (20 year), spatially extensive (∼115,000 kms2) dataset from the Great Barrier Reef revealed the fundamental importance of overall habitat complexity for reef fishes. Reductions of both live coral cover and habitat complexity had substantial impacts on fish communities compared to relatively minor impacts after major reductions in coral cover but not habitat complexity. Where habitat complexity was substantially reduced, species abundances broadly declined and a far greater number of fish species were locally extirpated, including economically important fishes. This resulted in decreased species richness and a loss of diversity within functional groups. Our results suggest that the retention of habitat complexity following disturbances can ameliorate the impacts of coral declines on reef fishes, so preserving their capacity to perform important functional roles essential to reef resilience. These results add to a growing body of evidence about the importance of habitat complexity for reef fishes, and represent the first large-scale examination of this question on the Great Barrier Reef. PMID:25140801

Retention of habitat complexity minimizes disassembly of reef fish communities following disturbance: a large-scale natural experiment.

PubMed

Emslie, Michael J; Cheal, Alistair J; Johns, Kerryn A

2014-01-01

High biodiversity ecosystems are commonly associated with complex habitats. Coral reefs are highly diverse ecosystems, but are under increasing pressure from numerous stressors, many of which reduce live coral cover and habitat complexity with concomitant effects on other organisms such as reef fishes. While previous studies have highlighted the importance of habitat complexity in structuring reef fish communities, they employed gradient or meta-analyses which lacked a controlled experimental design over broad spatial scales to explicitly separate the influence of live coral cover from overall habitat complexity. Here a natural experiment using a long term (20 year), spatially extensive (∼ 115,000 kms(2)) dataset from the Great Barrier Reef revealed the fundamental importance of overall habitat complexity for reef fishes. Reductions of both live coral cover and habitat complexity had substantial impacts on fish communities compared to relatively minor impacts after major reductions in coral cover but not habitat complexity. Where habitat complexity was substantially reduced, species abundances broadly declined and a far greater number of fish species were locally extirpated, including economically important fishes. This resulted in decreased species richness and a loss of diversity within functional groups. Our results suggest that the retention of habitat complexity following disturbances can ameliorate the impacts of coral declines on reef fishes, so preserving their capacity to perform important functional roles essential to reef resilience. These results add to a growing body of evidence about the importance of habitat complexity for reef fishes, and represent the first large-scale examination of this question on the Great Barrier Reef.

Systematics of the Dendropsophus leucophyllatus species complex (Anura: Hylidae): Cryptic diversity and the description of two new species

PubMed Central

Caminer, Marcel A.; Milá, Borja; Jansen, Martin; Fouquet, Antoine; Venegas, Pablo J.; Chávez, Germán; Lougheed, Stephen C.

2017-01-01

Genetic data in studies of systematics of Amazonian amphibians frequently reveal that purportedly widespread single species in reality comprise species complexes. This means that real species richness may be significantly higher than current estimates. Here we combine genetic, morphological, and bioacoustic data to assess the phylogenetic relationships and species boundaries of two Amazonian species of the Dendropsophus leucophyllatus species group: D. leucophyllatus and D. triangulum. Our results uncovered the existence of five confirmed and four unconfirmed candidate species. Among the confirmed candidate species, three have available names: Dendropsophus leucophyllatus, Dendropsophus triangulum, and Dendropsophus reticulatus, this last being removed from the synonymy of D. triangulum. A neotype of D. leucophyllatus is designated. We describe the remaining two confirmed candidate species, one from Bolivia and another from Peru. All confirmed candidate species are morphologically distinct and have much smaller geographic ranges than those previously reported for D. leucophyllatus and D. triangulum sensu lato. Dendropsophus leucophyllatus sensu stricto occurs in the Guianan region. Dendropsophus reticulatus comb. nov. corresponds to populations in the Amazon basin of Brazil, Ecuador, and Peru previously referred to as D. triangulum. Dendropsophus triangulum sensu stricto is the most widely distributed species; it occurs in Amazonian Ecuador, Peru and Brazil, reaching the state of Pará. We provide accounts for all described species including an assessment of their conservation status. PMID:28248998

On cicadas of Hyalessa maculaticollis complex (Hemiptera, Cicadidae) of China

PubMed Central

Wang, Xu; Hayashi, Masami; Wei, Cong

2014-01-01

Abstract The genus Hyalessa China is reviewed based on the discovery of male of the type species H. ronshana China as well as the description of one new species (H. batangensis sp. n.). The species formerly included in the genus Sonata Lee are removed to Hyalessa as new combinations. Intraspecific variations of H. maculaticollis are enumerated based on materials collected from various locations from China. The identity of Sonata and the systematic placement of Hyalessa are discussed. A key to all species of Hyalessa is provided. PMID:24478586

Next-generation sequencing yields the complete mitochondrial genome of the flathead mullet, Mugil cephalus cryptic species in East Australia (Teleostei: Mugilidae).

PubMed

Shen, Kang-Ning; Chen, Ching-Hung; Hsiao, Chung-Der; Durand, Jean-Dominique

2016-09-01

In this study, the complete mitogenome sequence of a cryptic species from East Australia (Mugil sp. H) belonging to the worldwide Mugil cephalus species complex (Teleostei: Mugilidae) has been sequenced by next-generation sequencing method. The assembled mitogenome, consisting of 16,845 bp, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a non-coding control region of D-loop. D-loop consists of 1067 bp length, and is located between tRNA-Pro and tRNA-Phe. The overall base composition of East Australia M. cephalus is 28.4% for A, 29.3% for C, 15.4% for G and 26.9% for T. The complete mitogenome may provide essential and important DNA molecular data for further phylogenetic and evolutionary analysis for flathead mullet species complex.

A new species of the Cyrtodactylus (Geckoella) collegalensis (Beddome, 1870) complex (Squamata: Gekkonidae) from Western India.

PubMed

Agarwal, Ishan; Mirza, Zeeshan A; Pal, Saunak; Maddock, Simon T; Mishra, Anurag; Bauer, Aaron M

2016-09-23

A new species of Cyrtodactylus (Geckoella) from the C. collegalensis complex is described based on a series of specimens from western and central India. Morphological and molecular data support the distinctiveness of the new form, which can be diagnosed from other Cyrtodactylus (including other Geckoella) species by its small body size (snout to vent length to 56 mm), the absence of precloacal and femoral pores, no enlarged preanal or femoral scales, and a dorsal scalation consisting wholly of small, granular scales. The new species is most closely related to C. collegalensis, C. speciosus and C. yakhuna, from which it differs by the presence of a patch of enlarged roughly hexagonal scales on the canthus rostralis and beneath the angle of jaw, its relatively long limbs and narrow body, and a dorsal colour pattern of 4-6 pairs of dark spots.

Sensitivity of Above-Ground Biomass Estimates to Height-Diameter Modelling in Mixed-Species West African Woodlands

PubMed Central

Aynekulu, Ermias; Pitkänen, Sari; Packalen, Petteri

2016-01-01

It has been suggested that above-ground biomass (AGB) inventories should include tree height (H), in addition to diameter (D). As H is a difficult variable to measure, H-D models are commonly used to predict H. We tested a number of approaches for H-D modelling, including additive terms which increased the complexity of the model, and observed how differences in tree-level predictions of H propagated to plot-level AGB estimations. We were especially interested in detecting whether the choice of method can lead to bias. The compared approaches listed in the order of increasing complexity were: (B0) AGB estimations from D-only; (B1) involving also H obtained from a fixed-effects H-D model; (B2) involving also species; (B3) including also between-plot variability as random effects; and (B4) involving multilevel nested random effects for grouping plots in clusters. In light of the results, the modelling approach affected the AGB estimation significantly in some cases, although differences were negligible for some of the alternatives. The most important differences were found between including H or not in the AGB estimation. We observed that AGB predictions without H information were very sensitive to the environmental stress parameter (E), which can induce a critical bias. Regarding the H-D modelling, the most relevant effect was found when species was included as an additive term. We presented a two-step methodology, which succeeded in identifying the species for which the general H-D relation was relevant to modify. Based on the results, our final choice was the single-level mixed-effects model (B3), which accounts for the species but also for the plot random effects reflecting site-specific factors such as soil properties and degree of disturbance. PMID:27367857

Decrypting the Polyporus dictyopus complex: Recovery of Atroporus Ryvarden and segregation of Neodictyopus gen. nov. (Polyporales, Basidiomyocta).

PubMed

Palacio, Melissa; Robledo, Gerardo Lucio; Reck, Mateus Arduvino; Grassi, Emanuel; Góes-Neto, Aristóteles; Drechsler-Santos, Elisandro Ricardo

2017-01-01

Polyporus dictyopus, with a large number of heterotypic synonyms, has been traditionally considered a species complex, characterized by wide morphological variation and geographic distribution. Thus, neotropical specimens previously identified as P. dictyopus from Amazonia, Cerrado and Atlantic Forest biomes were studied based on detailed macro- and micromorphological examination and phylogenetic analyses, using distinct ribosomal and protein-coding genomic regions: the nuclear ribosomal internal transcribed spacer (nrITS), nuclear ribosomal large subunit (nrLSU), and RNA polymerase II second subunit (RPB2). Two unrelated generic lineages, each one represented by different species, are reported: Atroporus is recovered and re-circumscribed to include A. diabolicus and A. rufoatratus comb. nov.; Neodictyopus gen. nov. is proposed to accommodate N. dictyopus comb. nov. and two new species, N. atlanticae and N. gugliottae. Our study showed that at least five distinct species were hidden under the name P. dictyopus. Detailed descriptions, pictures, illustrations, and a key are provided for Atroporus and Neodictyopus species.

Decrypting the Polyporus dictyopus complex: Recovery of Atroporus Ryvarden and segregation of Neodictyopus gen. nov. (Polyporales, Basidiomyocta)

PubMed Central

Reck, Mateus Arduvino; Grassi, Emanuel; Góes-Neto, Aristóteles; Drechsler-Santos, Elisandro Ricardo

2017-01-01

Polyporus dictyopus, with a large number of heterotypic synonyms, has been traditionally considered a species complex, characterized by wide morphological variation and geographic distribution. Thus, neotropical specimens previously identified as P. dictyopus from Amazonia, Cerrado and Atlantic Forest biomes were studied based on detailed macro- and micromorphological examination and phylogenetic analyses, using distinct ribosomal and protein-coding genomic regions: the nuclear ribosomal internal transcribed spacer (nrITS), nuclear ribosomal large subunit (nrLSU), and RNA polymerase II second subunit (RPB2). Two unrelated generic lineages, each one represented by different species, are reported: Atroporus is recovered and re-circumscribed to include A. diabolicus and A. rufoatratus comb. nov.; Neodictyopus gen. nov. is proposed to accommodate N. dictyopus comb. nov. and two new species, N. atlanticae and N. gugliottae. Our study showed that at least five distinct species were hidden under the name P. dictyopus. Detailed descriptions, pictures, illustrations, and a key are provided for Atroporus and Neodictyopus species. PMID:29049417

Identification of Leishmania by Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) Mass Spectrometry Using a Free Web-Based Application and a Dedicated Mass-Spectral Library.

PubMed

Lachaud, Laurence; Fernández-Arévalo, Anna; Normand, Anne-Cécile; Lami, Patrick; Nabet, Cécile; Donnadieu, Jean Luc; Piarroux, Martine; Djenad, Farid; Cassagne, Carole; Ravel, Christophe; Tebar, Silvia; Llovet, Teresa; Blanchet, Denis; Demar, Magalie; Harrat, Zoubir; Aoun, Karim; Bastien, Patrick; Muñoz, Carmen; Gállego, Montserrat; Piarroux, Renaud

2017-10-01

Human leishmaniases are widespread diseases with different clinical forms caused by about 20 species within the Leishmania genus. Leishmania species identification is relevant for therapeutic management and prognosis, especially for cutaneous and mucocutaneous forms. Several methods are available to identify Leishmania species from culture, but they have not been standardized for the majority of the currently described species, with the exception of multilocus enzyme electrophoresis. Moreover, these techniques are expensive, time-consuming, and not available in all laboratories. Within the last decade, mass spectrometry (MS) has been adapted for the identification of microorganisms, including Leishmania However, no commercial reference mass-spectral database is available. In this study, a reference mass-spectral library (MSL) for Leishmania isolates, accessible through a free Web-based application (mass-spectral identification [MSI]), was constructed and tested. It includes mass-spectral data for 33 different Leishmania species, including species that infect humans, animals, and phlebotomine vectors. Four laboratories on two continents evaluated the performance of MSI using 268 samples, 231 of which were Leishmania strains. All Leishmania strains, but one, were correctly identified at least to the complex level. A risk of species misidentification within the Leishmania donovani , L. guyanensis , and L. braziliensis complexes was observed, as previously reported for other techniques. The tested application was reliable, with identification results being comparable to those obtained with reference methods but with a more favorable cost-efficiency ratio. This free online identification system relies on a scalable database and can be implemented directly in users' computers. Copyright © 2017 American Society for Microbiology.

A new species of Caligus (Copepoda, Siphonostomatoida) from the plankton of the Caribbean coast of Venezuela with a key to species

PubMed Central

Suárez-Morales, Eduardo; Camisotti, Humberto; Martín, Alberto

2012-01-01

Abstract During a survey of the zooplankton community of Bahía Amuay, Venezuelan Caribbean, specimens of an undescribed species of Caligus Müller were collected. It resembles Caligus xystercus Cressey and Caligus ocyurus Cressey, both known only from the Caribbean Sea. The new species can be distinguished from these and other congeners by a combination of characters including the armature of legs 1 and 4, but mainly by its unique female genital complex. This is the first species of Caligus described from Venezuela. The species is described in full and a key to the species of the genus recorded in Venezuela is provided. PMID:22768004

Observations of Carbon Chain Chemistry in the Envelopes of Low-Mass Protostars

NASA Technical Reports Server (NTRS)

Cordiner, M.; Charnley, S.; Buckle, J. V.; Walsh, C.; Millar, T. J.

2012-01-01

Observational results are reported from our surveys in the Northern Hemisphere (using the Onsala 20 m telescope) and the Southern Hemisphere (using the Mopra 22 m telescope) to search for 3 mm emission lines from carbon-chain-bearing species and other complex molecules in the envelopes of low-mass protostars. Based on a sample of approximately 60 sources, we find that carbon-chain-bearing species including HC3N (and C4H) are highly abundant in the vicinity of more than half of the observed protostars. The origin and evolution of these species, including their likely incorporation into ices in protoplanetary disks will be discussed

DNA barcode variability and host plant usage of fruit flies (Diptera: Tephritidae) in Thailand.

PubMed

Kunprom, Chonticha; Pramual, Pairot

2016-10-01

The objectives of this study were to examine the genetic variation in fruit flies (Diptera: Tephritidae) in Thailand and to test the efficiency of the mitochondrial cytochrome c oxidase subunit I (COI) barcoding region for species-level identification. Twelve fruit fly species were collected from 24 host plant species of 13 families. The number of host plant species for each fruit fly species ranged between 1 and 11, with Bactrocera correcta found in the most diverse host plants. A total of 123 COI sequences were obtained from these fruit fly species. Sequences from the NCBI database were also included, for a total of 17 species analyzed. DNA barcoding identification analysis based on the best close match method revealed a good performance, with 94.4% of specimens correctly identified. However, many specimens (3.6%) had ambiguous identification, mostly due to intra- and interspecific overlap between members of the B. dorsalis complex. A phylogenetic tree based on the mitochondrial barcode sequences indicated that all species, except for the members of the B. dorsalis complex, were monophyletic with strong support. Our work supports recent calls for synonymization of these species. Divergent lineages were observed within B. correcta and B. tuberculata, and this suggested that these species need further taxonomic reexamination.

Hybrid sterility in crosses between two Brazilian sibling species of the Anopheles albitarsis complex.

PubMed

Fontoura, Nathalia Giglio; Araki, Alejandra Saori; Van Der Maas Azevedo, Renata; Galardo, Allan Kardec Ribeiro; Peixoto, Alexandre Afranio; Lima, José Bento Pereira

2014-12-04

Complexes of cryptic species are common in several taxa and this is also the case in the Anopheles genus, a group including all known human malaria vectors. The Anopheles albitarsis complex comprises at least nine cryptic species, some of which are implicated as vectors of human malaria. Several different types of data have been generated for this species complex such as cytogenetics, alloenzymes, morphological and feeding behavioral, hybridization experiments, RAPD-PCR and RFLP and mitochondrial and nuclear markers. Studies focused on its postzygotic isolation are still somewhat rare in the literature despite their importance to understand the speciation process and the level of gene flow potentially occurring among the different sibling species. Hybridization experiments between Anopheles albitarsis s.s. and Anopheles marajoara, as well as backcrosses between hybrids and Anopheles albitarsis s.s., were performed using the induced mating technique. Results were compared to intraspecific crosses. Larva-to-adult viability and sex ratio were also assessed. Male hybrids show very low insemination rates and nearly complete sterility, apparently due to abnormalities in their reproductive organs. Evidence of partial sterility among the hybrid females was also observed. Our data indicated that Anopheles albitarsis s.s. and Anopheles marajoara show a high level of postzygotic isolation with a strong hybrid male sterility. This result is consistent with the Haldane's rule which states that in interspecific crosses the heterogametic sex is the first to be affected. However, the fact that the females are not completely sterile raises the possibility of introgression between these two siblings species.

Species diversity and phylogeographical affinities of the Branchiopoda (Crustacea) of Churchill, Manitoba, Canada.

PubMed

Jeffery, Nicholas W; Elías-Gutiérrez, Manuel; Adamowicz, Sarah J

2011-01-01

The region of Churchill, Manitoba, contains a wide variety of habitats representative of both the boreal forest and arctic tundra and has been used as a model site for biodiversity studies for nearly seven decades within Canada. Much previous work has been done in Churchill to study the Daphnia pulex species complex in particular, but no study has completed a wide-scale survey on the crustacean species that inhabit Churchill's aquatic ecosystems using molecular markers. We have employed DNA barcoding to study the diversity of the Branchiopoda (Crustacea) in a wide variety of freshwater habitats and to determine the likely origins of the Churchill fauna following the last glaciation. The standard animal barcode marker (COI) was sequenced for 327 specimens, and a 3% divergence threshold was used to delineate potential species. We found 42 provisional and valid branchiopod species from this survey alone, including several cryptic lineages, in comparison with the 25 previously recorded from previous ecological works. Using published sequence data, we explored the phylogeographic affinities of Churchill's branchiopods, finding that the Churchill fauna apparently originated from all directions from multiple glacial refugia (including southern, Beringian, and high arctic regions). Overall, these microcrustaceans are very diverse in Churchill and contain multiple species complexes. The present study introduces among the first sequences for some understudied genera, for which further work is required to delineate species boundaries and develop a more complete understanding of branchiopod diversity over a larger spatial scale.

Species Diversity and Phylogeographical Affinities of the Branchiopoda (Crustacea) of Churchill, Manitoba, Canada

PubMed Central

Jeffery, Nicholas W.; Elías-Gutiérrez, Manuel; Adamowicz, Sarah J.

2011-01-01

The region of Churchill, Manitoba, contains a wide variety of habitats representative of both the boreal forest and arctic tundra and has been used as a model site for biodiversity studies for nearly seven decades within Canada. Much previous work has been done in Churchill to study the Daphnia pulex species complex in particular, but no study has completed a wide-scale survey on the crustacean species that inhabit Churchill's aquatic ecosystems using molecular markers. We have employed DNA barcoding to study the diversity of the Branchiopoda (Crustacea) in a wide variety of freshwater habitats and to determine the likely origins of the Churchill fauna following the last glaciation. The standard animal barcode marker (COI) was sequenced for 327 specimens, and a 3% divergence threshold was used to delineate potential species. We found 42 provisional and valid branchiopod species from this survey alone, including several cryptic lineages, in comparison with the 25 previously recorded from previous ecological works. Using published sequence data, we explored the phylogeographic affinities of Churchill's branchiopods, finding that the Churchill fauna apparently originated from all directions from multiple glacial refugia (including southern, Beringian, and high arctic regions). Overall, these microcrustaceans are very diverse in Churchill and contain multiple species complexes. The present study introduces among the first sequences for some understudied genera, for which further work is required to delineate species boundaries and develop a more complete understanding of branchiopod diversity over a larger spatial scale. PMID:21610864

The genera Isorineloricaria and Aphanotorulus (Siluriformes: Loricariidae)
with description of a new species.

PubMed

Ray, C Keith; Armbruster, Jonathan W

2016-02-04

We review the complex history of those species included in the Hypostomus emarginatus species complex and recognize them in Isorineloricaria and Aphanotorulus. Isorineloricaria consists of four valid species: I. acuarius n. sp., I. spinosissima, I. tenuicauda, and I. villarsi. Aphanotorulus consists of six valid species: A. ammophilus, A, emarginatus, A. gomesi, A. horridus, A. phrixosoma, and A. unicolor. Plecostomus annae and Hypostoma squalinum are placed in the synonymy of A. emarginatus; Plecostomus biseriatus, P. scopularius, and P. virescens are placed in the synonymy of A. horridus; Plecostomus winzi is placed in the synonymy of I. tenuicauda, and one new species, I. acuarius is described from the Apure River basin of Venezuela. Aphanotoroulus can be distinguished from Isorineloricaria by having caudal peduncles that do not become greatly lengthed with size and that are oval in cross section (vs. caudal peduncle proportions that get proportionately longer with size and that become round in cross-section), and by having small dark spots (less than half plate diameter) on a light tan background (vs. spots almost as large as lateral plates on a nearly white background.

Versatile aggressive mimicry of cicadas by an Australian predatory katydid.

PubMed

Marshall, David C; Hill, Kathy B R

2009-01-01

In aggressive mimicry, a predator or parasite imitates a signal of another species in order to exploit the recipient of the signal. Some of the most remarkable examples of aggressive mimicry involve exploitation of a complex signal-response system by an unrelated predator species. We have found that predatory Chlorobalius leucoviridis katydids (Orthoptera: Tettigoniidae) can attract male cicadas (Hemiptera: Cicadidae) by imitating the species-specific wing-flick replies of sexually receptive female cicadas. This aggressive mimicry is accomplished both acoustically, with tegminal clicks, and visually, with synchronized body jerks. Remarkably, the katydids respond effectively to a variety of complex, species-specific Cicadettini songs, including songs of many cicada species that the predator has never encountered. We propose that the versatility of aggressive mimicry in C. leucoviridis is accomplished by exploiting general design elements common to the songs of many acoustically signaling insects that use duets in pair-formation. Consideration of the mechanism of versatile mimicry in C. leucoviridis may illuminate processes driving the evolution of insect acoustic signals, which play a central role in reproductive isolation of populations and the formation of species.

Extreme gender flexibility: using a phylogenetic framework to infer the evolution of variation in sex allocation, phylogeography, and speciation in a genus of bidirectional sex changing fishes(Lythrypnus, Gobiidae).

PubMed

Maxfield, Jessica M; Van Tassell, James L; St Mary, Colette M; Joyeux, Jean-Christophe; Crow, Karen D

2012-09-01

The genus Lythrypnus is a group of marine gobies that exhibit extreme gender flexibility as bidirectional sex changers. The genus consists of 20 described species and several undescribed species that are distributed in the Americas. Five species have been characterized with respect to sex allocation and gonad morphology. The hormonal, morphological, and behavioral aspects of sex change have been studied extensively for one species, L. dalli. These data, however, have not been interpreted in an evolutionary context because a phylogenetic hypothesis has not previously been proposed for the genus Lythrypnus. We propose the first phylogenetic hypothesis for the genus based on molecular data from three mitochondrial genes (12s, ND2, and Cytb), one nuclear gene (Rag1) and one nuclear intron (S7). We also include three previously undescribed Lythrypnus species. Our results support the monophyly of the genus with L. heterochroma, an Atlantic species, as the basal taxon. After the divergence of L. heterochroma, there are two main clades, one comprised of species distributed in the Atlantic, the other comprised of species distributed in the Pacific. These data indicate an Atlantic origin for the genus, followed by divergence after the closure of the Isthmus of Panama. Our data also support the monophyly of three previously described species complexes, the L. rhizophora complex and L. dalli complex in the Pacific, and the L. mowbrayi complex in the Atlantic. We mapped patterns of sex allocation within this genus onto the fully resolved and supported topology, and found that sexual plasticity and gender flexibility is likely a synapomorphy for the genus. Overall our results create a well-supported framework to understand the phylogeography of the genus, and to interpret the evolution of sex allocation in Lythrypnus gobies. Copyright © 2012 Elsevier Inc. All rights reserved.

Habitat and Host Indicate Lineage Identity in Colletotrichum gloeosporioides s.l. from Wild and Agricultural Landscapes in North America

PubMed Central

Doyle, Vinson P.; Oudemans, Peter V.; Rehner, Stephen A.; Litt, Amy

2013-01-01

Understanding the factors that drive the evolution of pathogenic fungi is central to revealing the mechanisms of virulence and host preference, as well as developing effective disease control measures. Prerequisite to these pursuits is the accurate delimitation of species boundaries. Colletotrichum gloeosporioides s.l. is a species complex of plant pathogens and endophytic fungi for which reliable species recognition has only recently become possible through a multi-locus phylogenetic approach. By adopting an intensive regional sampling strategy encompassing multiple hosts within and beyond agricultural zones associated with cranberry (Vaccinium macrocarpon Aiton), we have integrated North America strains of Colletotrichum gloeosporioides s.l. from these habitats into a broader phylogenetic framework. We delimit species on the basis of genealogical concordance phylogenetic species recognition (GCPSR) and quantitatively assess the monophyly of delimited species at each of four nuclear loci and in the combined data set with the genealogical sorting index (gsi). Our analysis resolved two principal lineages within the species complex. Strains isolated from cranberry and sympatric host plants are distributed across both of these lineages and belong to seven distinct species or terminal clades. Strains isolated from V. macrocarpon in commercial cranberry beds belong to four species, three of which are described here as new. Another species, C. rhexiae Ellis & Everh., is epitypified. Intensive regional sampling has revealed a combination of factors, including the host species from which a strain has been isolated, the host organ of origin, and the habitat of the host species, as useful indicators of species identity in the sampled regions. We have identified three broadly distributed temperate species, C. fructivorum, C. rhexiae, and C. nupharicola, that could be useful for understanding the microevolutionary forces that may lead to species divergence in this important complex of endophytes and plant pathogens. PMID:23671594

Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism.

PubMed

Hoek, Milan J A van; Merks, Roeland M H

2017-05-16

The human gut contains approximately 10 14 bacteria, belonging to hundreds of different species. Together, these microbial species form a complex food web that can break down nutrient sources that our own digestive enzymes cannot handle, including complex polysaccharides, producing short chain fatty acids and additional metabolites, e.g., vitamin K. Microbial diversity is important for colonic health: Changes in the composition of the microbiota have been associated with inflammatory bowel disease, diabetes, obesity and Crohn's disease, and make the microbiota more vulnerable to infestation by harmful species, e.g., Clostridium difficile. To get a grip on the controlling factors of microbial diversity in the gut, we here propose a multi-scale, spatiotemporal dynamic flux-balance analysis model to study the emergence of metabolic diversity in a spatial gut-like, tubular environment. The model features genome-scale metabolic models (GEM) of microbial populations, resource sharing via extracellular metabolites, and spatial population dynamics and evolution. In this model, cross-feeding interactions emerge readily, despite the species' ability to metabolize sugars autonomously. Interestingly, the community requires cross-feeding for producing a realistic set of short-chain fatty acids from an input of glucose, If we let the composition of the microbial subpopulations change during invasion of adjacent space, a complex and stratified microbiota evolves, with subspecies specializing on cross-feeding interactions via a mechanism of compensated trait loss. The microbial diversity and stratification collapse if the flux through the gut is enhanced to mimic diarrhea. In conclusion, this in silico model is a helpful tool in systems biology to predict and explain the controlling factors of microbial diversity in the gut. It can be extended to include, e.g., complex nutrient sources, and host-microbiota interactions via the intestinal wall.

A Quadruplex Real-Time PCR Assay for the Rapid Detection and Differentiation of the Most Relevant Members of the B. pseudomallei Complex: B. mallei, B. pseudomallei, and B. thailandensis

PubMed Central

Lowe, Chinn-Woan; Thiriot, Joseph D.; Heder, Michael J.; March, Jordon K.; Drake, David S.; Lew, Cynthia S.; Bunnell, Annette J.; Moore, Emily S.; O'Neill, Kim L.; Robison, Richard A.

2016-01-01

The Burkholderia pseudomallei complex classically consisted of B. mallei, B. pseudomallei, and B. thailandensis, but has now expanded to include B. oklahomensis, B. humptydooensis, and three unassigned Burkholderia clades. Methods for detecting and differentiating the B. pseudomallei complex has been the topic of recent research due to phenotypic and genotypic similarities of these species. B. mallei and B. pseudomallei are recognized as CDC Tier 1 select agents, and are the causative agents of glanders and melioidosis, respectively. Although B. thailandensis and B. oklahomensis are generally avirulent, both display similar phenotypic characteristics to that of B. pseudomallei. B. humptydooensis and the Burkholderia clades are genetically similar to the B. pseudomallei complex, and are not associated with disease. Optimal identification of these species remains problematic, and PCR-based methods can resolve issues with B. pseudomallei complex detection and differentiation. Currently, no PCR assay is available that detects the major species of the B. pseudomallei complex. A real-time PCR assay in a multiplex single-tube format was developed to simultaneously detect and differentiate B. mallei, B. pseudomallei, and B. thailandensis, and a common sequence found in B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis. A total of 309 Burkholderia isolates and 5 other bacterial species were evaluated. The assay was 100% sensitive and specific, demonstrated sensitivity beyond culture and GC methods for the isolates tested, and is completed in about an hour with a detection limit between 2.6pg and 48.9pg of gDNA. Bioinformatic analyses also showed the assay is likely 100% specific and sensitive for all 84 fully sequenced B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis strains currently available in GenBank. For these reasons, this assay could be a rapid and sensitive tool in the detection and differentiation for those species of the B. pseudomallei complex with recognized clinical and practical significance. PMID:27736903

A Quadruplex Real-Time PCR Assay for the Rapid Detection and Differentiation of the Most Relevant Members of the B. pseudomallei Complex: B. mallei, B. pseudomallei, and B. thailandensis.

PubMed

Lowe, Chinn-Woan; Satterfield, Benjamin A; Nelson, Daniel B; Thiriot, Joseph D; Heder, Michael J; March, Jordon K; Drake, David S; Lew, Cynthia S; Bunnell, Annette J; Moore, Emily S; O'Neill, Kim L; Robison, Richard A

2016-01-01

The Burkholderia pseudomallei complex classically consisted of B. mallei, B. pseudomallei, and B. thailandensis, but has now expanded to include B. oklahomensis, B. humptydooensis, and three unassigned Burkholderia clades. Methods for detecting and differentiating the B. pseudomallei complex has been the topic of recent research due to phenotypic and genotypic similarities of these species. B. mallei and B. pseudomallei are recognized as CDC Tier 1 select agents, and are the causative agents of glanders and melioidosis, respectively. Although B. thailandensis and B. oklahomensis are generally avirulent, both display similar phenotypic characteristics to that of B. pseudomallei. B. humptydooensis and the Burkholderia clades are genetically similar to the B. pseudomallei complex, and are not associated with disease. Optimal identification of these species remains problematic, and PCR-based methods can resolve issues with B. pseudomallei complex detection and differentiation. Currently, no PCR assay is available that detects the major species of the B. pseudomallei complex. A real-time PCR assay in a multiplex single-tube format was developed to simultaneously detect and differentiate B. mallei, B. pseudomallei, and B. thailandensis, and a common sequence found in B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis. A total of 309 Burkholderia isolates and 5 other bacterial species were evaluated. The assay was 100% sensitive and specific, demonstrated sensitivity beyond culture and GC methods for the isolates tested, and is completed in about an hour with a detection limit between 2.6pg and 48.9pg of gDNA. Bioinformatic analyses also showed the assay is likely 100% specific and sensitive for all 84 fully sequenced B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis strains currently available in GenBank. For these reasons, this assay could be a rapid and sensitive tool in the detection and differentiation for those species of the B. pseudomallei complex with recognized clinical and practical significance.

Comparative morphology of the axial complex and interdependence of internal organ systems in sea urchins (Echinodermata: Echinoidea).

PubMed

Ziegler, Alexander; Faber, Cornelius; Bartolomaeus, Thomas

2009-06-09

The axial complex of echinoderms (Echinodermata) is composed of various primary and secondary body cavities that interact with each other. In sea urchins (Echinoidea), structural differences of the axial complex in "regular" and irregular species have been observed, but the reasons underlying these differences are not fully understood. In addition, a better knowledge of axial complex diversity could not only be useful for phylogenetic inferences, but improve also an understanding of the function of this enigmatic structure. We therefore analyzed numerous species of almost all sea urchin orders by magnetic resonance imaging, dissection, histology, and transmission electron microscopy and compared the results with findings from published studies spanning almost two centuries. These combined analyses demonstrate that the axial complex is present in all sea urchin orders and has remained structurally conserved for a long time, at least in the "regular" species. Within the Irregularia, a considerable morphological variation of the axial complex can be observed with gradual changes in topography, size, and internal architecture. These modifications are related to the growing size of the gastric caecum as well as to the rearrangement of the morphology of the digestive tract as a whole. The structurally most divergent axial complex can be observed in the highly derived Atelostomata in which the reorganization of the digestive tract is most pronounced. Our findings demonstrate a structural interdependence of various internal organs, including digestive tract, mesenteries, and the axial complex.

Respiration and substrate transport rates as well as reactive oxygen species production distinguish mitochondria from brain and liver.

PubMed

Gusdon, Aaron M; Fernandez-Bueno, Gabriel A; Wohlgemuth, Stephanie; Fernandez, Jenelle; Chen, Jing; Mathews, Clayton E

2015-09-10

Aberrant mitochondrial function, including excessive reactive oxygen species (ROS) production, has been implicated in the pathogenesis of human diseases. The use of mitochondrial inhibitors to ascertain the sites in the electron transport chain (ETC) resulting in altered ROS production can be an important tool. However, the response of mouse mitochondria to ETC inhibitors has not been thoroughly assessed. Here we set out to characterize the differences in phenotypic response to ETC inhibitors between the more energetically demanding brain mitochondria and less energetically demanding liver mitochondria in commonly utilized C57BL/6J mice. We show that in contrast to brain mitochondria, inhibiting distally within complex I or within complex III does not increase liver mitochondrial ROS production supported by complex I substrates, and liver mitochondrial ROS production supported by complex II substrates occurred primarily independent of membrane potential. Complex I, II, and III enzymatic activities and membrane potential were equivalent between liver and brain and responded to ETC. inhibitors similarly. Brain mitochondria exhibited an approximately two-fold increase in complex I and II supported respiration compared with liver mitochondria while exhibiting similar responses to inhibitors. Elevated NADH transport and heightened complex II-III coupled activity accounted for increased complex I and II supported respiration, respectively in brain mitochondria. We conclude that important mechanistic differences exist between mouse liver and brain mitochondria and that mouse mitochondria exhibit phenotypic differences compared with mitochondria from other species.

[Adaptation of sensory systems of gamasid mites (Parasitiformes, Gamasina) to dwelling in different environment].

PubMed

Leonovich, S A

2008-01-01

The main complication sensory organs (the palpal organ and the tarsal sensory complex) of several species of gamasid mites were studied in scanning electron microscope. The species examined included permanent ectoparasites (Laelaps agilis, Laelaptidae), parasites of the nasal cavity and respiratory tract of birds (Sternostoma tracheocolum and Ptilonyssus reguli, Rhinonyssidae), dwellers of the sea littoral zone (Parasitus kempersi, Parasitus immanis, Parasitidae), and mites found on soil and on plants (Amblyseius barkeri, Parasitidae). Similar sensillar types, including olfactory SW-WP sensilla, contact chemo-mechanosensory (SW-UP and DW-UP) sensilla, termo-chemo-mechanosensitive (DW-WP) sensilla of two types, and tactile (NP) sensilla were found in all these species, excluding endoparasites, where some sensillar types (in particular, DW-WP sensilla with slit-like pores) are absent. It was shown that the topography of olfactory SW-WP sensilla of the tarsal complex reflects taxonomic position and phylogenetic history of mite genera, whereas the number of certain sensillar types and the degree of their development reflect ecological specialization of species. The palpal organ is characterized by rather uniform structure in mites of different families, dwellers of different environments, except for the endoparasites of the family Rhinonyssidae, where this organ is strongly reduced.

Improvement of MALDI-TOF MS profiling for the differentiation of species within the Acinetobacter calcoaceticus-Acinetobacter baumannii complex.

PubMed

Šedo, Ondrej; Nemec, Alexandr; Křížová, Lenka; Kačalová, Magdaléna; Zdráhal, Zbyněk

2013-12-01

MALDI-TOF MS is currently becoming the method of choice for rapid identification of bacterial species in routine diagnostics. Yet, this method suffers from the inability to differentiate reliably between some closely related bacterial species including those of the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex, namely A. baumannii and Acinetobacter nosocomialis. In the present study, we evaluated a protocol which was different from that used in the Bruker Daltonics identification system (MALDI BioTyper) to improve species identification using a taxonomically precisely defined set of 105 strains representing the four validly named species of the ACB complex. The novel protocol is based on the change in matrix composition from alpha-cyano-4-hydroxycinnamic acid (saturated solution in water:acetonitrile:trifluoroacetic acid, 47.5:50:2.5, v/v) to ferulic acid (12.5mgml(-1) solution in water:acetonitrile:formic acid 50:33:17, v/v), while the other steps of sample processing remain unchanged. Compared to the standard protocol, the novel one extended the range of detected compounds towards higher molecular weight, produced signals with better mass resolution, and allowed the detection of species-specific signals. As a result, differentiation of A. nosocomialis and A. baumannii strains by cluster analysis was improved and 13 A. nosocomialis strains, assigned erroneously or ambiguously by using the standard protocol, were correctly identified. Copyright © 2013 Elsevier GmbH. All rights reserved.

Lipidomics of glycosphingolipids.

PubMed

Farwanah, Hany; Kolter, Thomas

2012-02-02

Glycosphingolipids (GSLs) contain one or more sugars that are attached to a sphingolipid moiety, usually to a ceramide, but in rare cases also to a sphingoid base. A large structural heterogeneity results from differences in number, identity, linkage, and anomeric configuration of the carbohydrate residues, and also from structural differences within the hydrophobic part. GSLs form complex cell-type specific patterns, which change with the species, the cellular differentiation state, viral transformation, ontogenesis, and oncogenesis. Although GSL structures can be assigned to only a few series with a common carbohydrate core, their structural variety and the complex pattern are challenges for their elucidation and quantification by mass spectrometric techniques. We present a general overview of the application of lipidomics for GSL determination. This includes analytical procedures and instrumentation together with recent correlations of GSL molecular species with human diseases. Difficulties such as the structural complexity and the lack of standard substances for complex GSLs are discussed.

Lipidomics of Glycosphingolipids

PubMed Central

Farwanah, Hany; Kolter, Thomas

2012-01-01

Glycosphingolipids (GSLs) contain one or more sugars that are attached to a sphingolipid moiety, usually to a ceramide, but in rare cases also to a sphingoid base. A large structural heterogeneity results from differences in number, identity, linkage, and anomeric configuration of the carbohydrate residues, and also from structural differences within the hydrophobic part. GSLs form complex cell-type specific patterns, which change with the species, the cellular differentiation state, viral transformation, ontogenesis, and oncogenesis. Although GSL structures can be assigned to only a few series with a common carbohydrate core, their structural variety and the complex pattern are challenges for their elucidation and quantification by mass spectrometric techniques. We present a general overview of the application of lipidomics for GSL determination. This includes analytical procedures and instrumentation together with recent correlations of GSL molecular species with human diseases. Difficulties such as the structural complexity and the lack of standard substances for complex GSLs are discussed. PMID:24957371

Unilateral incompatibility in Capsicum (Solanaceae): occurrence and taxonomic distribution.

PubMed

Onus, A Naci; Pickersgill, Barbara

2004-08-01

Unilateral incompatibility (UI) occurs when pollinations between species are successful in one direction but not in the other. Self-incompatible (SI) species frequently show UI with genetically related, self-compatible (SC) species, as pollen of SI species is compatible on the SC pistil, but not vice versa. Many examples of unilateral incompatibility, and all those which have been studied most intensively, are found in the Solanaceae, particularly Lycopersicon, Solanum, Nicotiana and Petunia. The genus Capsicum is evolutionarily somewhat distant from Lycopersicon and Solanum and even further removed from Nicotiana and Petunia. Unilateral incompatibility has also been reported in Capsicum; however, this is the first comprehensive study of crosses between all readily available species in the genus. All readily available (wild and domesticated) species in the genus are used as plant material, including the three genera from the Capsicum pubescens complex plus eight other species. Pollinations were made on pot-grown plants in a glasshouse. The number of pistils pollinated per cross varied (from five to 40 pistils per plant), depending on the numbers of flowers available. Pistils were collected 24 h after pollination and fixed for 3-24 h. After staining, pistils were mounted in a drop of stain, squashed gently under a cover slip and examined microscopically under ultra-violet light for pollen tube growth. Unilateral incompatibility is confirmed in the C. pubescens complex. Its direction conforms to that predominant in the Solanaceae and other families, i.e. pistils of self-incompatible species, or self-compatible taxa closely related to self-incompatible species, inhibit pollen tubes of self-compatible species. Unilateral incompatibility in Capsicum does not seem to have arisen to prevent introgression of self-compatibility into self-incompatible taxa, but as a by-product of divergence of the C. pubescens complex from the remainder of the genus.

Orchid conservation: further links.

PubMed

Fay, Michael F

2016-07-01

Due in great part to their often complex interactions with mycorrhizal fungi, pollinators and host trees, Orchidaceae present particular challenges for conservation. Furthermore, orchids, as potentially the largest family of angiosperms with >26000 species, species complexes and frequent hybrid formation, are complex to catalogue. Following a highlight in 2015, a further seven papers focusing on orchids, their interactions with beneficial organisms, pollinators and mycorrhiza, and other factors relating to their conservation, including threats from human utilization and changing land use, are presented here. The production of an online flora of all known plants and an assessment of the conservation status of all known plant species as far as possible, to guide conservation action are the first two targets of the Global Strategy for Plant Conservation Without knowing how many species there are and how they should be circumscribed, neither of these targets is achievable. Orchids are a fascinating subject for fundamental research with rapid species evolution, specific organ structure and development, but they also suffer from high levels of threat. Effective orchid conservation must take account of the beneficial interactions with fungi and pollinators and the potentially detrimental effects of over-collection and changes in land use. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Wild and synanthropic reservoirs of Leishmania species in the Americas

PubMed Central

Roque, André Luiz R.; Jansen, Ana Maria

2014-01-01

The definition of a reservoir has changed significantly in the last century, making it necessary to study zoonosis from a broader perspective. One important example is that of Leishmania, zoonotic multi-host parasites maintained by several mammal species in nature. The magnitude of the health problem represented by leishmaniasis combined with the complexity of its epidemiology make it necessary to clarify all of the links in transmission net, including non-human mammalian hosts, to develop effective control strategies. Although some studies have described dozens of species infected with these parasites, only a minority have related their findings to the ecological scenario to indicate a possible role of that host in parasite maintenance and transmission. Currently, it is accepted that a reservoir may be one or a complex of species responsible for maintaining the parasite in nature. A reservoir system should be considered unique on a given spatiotemporal scale. In fact, the transmission of Leishmania species in the wild still represents an complex enzootic “puzzle”, as several links have not been identified. This review presents the mammalian species known to be infected with Leishmania spp. in the Americas, highlighting those that are able to maintain and act as a source of the parasite in nature (and are thus considered potential reservoirs). These host/reservoirs are presented separately in each of seven mammal orders – Marsupialia, Cingulata, Pilosa, Rodentia, Primata, Carnivora, and Chiroptera – responsible for maintaining Leishmania species in the wild. PMID:25426421

Two new species of the Fusarium solani species complex isolated from compost and hibiscus (Hibiscus sp.).

PubMed

Šišić, Adnan; Al-Hatmi, Abdullah M S; Baćanović-Šišić, Jelena; Ahmed, Sarah A; Dennenmoser, Dominic; de Hoog, G Sybren; Finckh, Maria R

2018-03-22

Two new species in the Fusarium solani species complex (FSSC) are described and introduced. The new taxa are represented by German isolates CBS 142481 and CBS 142480 collected from commercial yard waste compost and vascular tissue of a wilting branch of hibiscus, respectively. The phylogenetic relationships of the collected strains to one another and within the FSSC were evaluated based on DNA sequences of 6 gene loci. Due to the limited sequence data available for reference strains in GenBank, however, a multi-gene phylogenetic analysis included partial sequences for the internal transcribed spacer region and intervening 5.8S nrRNA gene (ITS), translation elongation factor 1-alpha (tef1) and the RNA polymerase II second largest subunit (rpb2). Morphological and molecular phylogenetic data independently showed that these strains are distinct populations of the FSSC, nested within Clade 3. Thus, we introduce Fusarium stercicola and Fusarium witzenhausenense as novel species in the complex. In addition, 19 plant species of 7 legume genera were evaluated for their potential to host the newly described taxa. Eighteen plant species were successfully colonized, with 6 and 9 of these being symptomatic hosts for F. stercicola and F. witzenhausenense, respectively. As plants of the family Fabaceae are very distant to the originally sourced material from which the new taxa were recovered, our results suggest that F. stercicola and F. witzenhausenense are not host-specific and are ecologically fit to sustain stable populations in variety of habitats.

The Trichoderma harzianum demon: complex speciation history resulting in coexistence of hypothetical biological species, recent agamospecies and numerous relict lineages

PubMed Central

2010-01-01

Background The mitosporic fungus Trichoderma harzianum (Hypocrea, Ascomycota, Hypocreales, Hypocreaceae) is an ubiquitous species in the environment with some strains commercially exploited for the biological control of plant pathogenic fungi. Although T. harzianum is asexual (or anamorphic), its sexual stage (or teleomorph) has been described as Hypocrea lixii. Since recombination would be an important issue for the efficacy of an agent of the biological control in the field, we investigated the phylogenetic structure of the species. Results Using DNA sequence data from three unlinked loci for each of 93 strains collected worldwide, we detected a complex speciation process revealing overlapping reproductively isolated biological species, recent agamospecies and numerous relict lineages with unresolved phylogenetic positions. Genealogical concordance and recombination analyses confirm the existence of two genetically isolated agamospecies including T. harzianum sensu stricto and two hypothetical holomorphic species related to but different from H. lixii. The exact phylogenetic position of the majority of strains was not resolved and therefore attributed to a diverse network of recombining strains conventionally called 'pseudoharzianum matrix'. Since H. lixii and T. harzianum are evidently genetically isolated, the anamorph - teleomorph combination comprising H. lixii/T. harzianum in one holomorph must be rejected in favor of two separate species. Conclusions Our data illustrate a complex speciation within H. lixii - T. harzianum species group, which is based on coexistence and interaction of organisms with different evolutionary histories and on the absence of strict genetic borders between them. PMID:20359347

The hydro-chemical and physical conditions of the environment of the immature stages of some species of the simulium (Edwardsellum) damnosum complex (Diptera).

PubMed

Grunewald, J

1976-12-01

Water samples were collected from breeding sites of species of the Simulium (Edwardsellum) damnoslm complex in Upper Volta, Liberia and Cameroon during the dry season; and in Tanzania and Kenya at various seasons during a period of two years. The following 20 factors were analysed at 45 breeding sites: water temperature, current velocity, pH value, conductivity free carbon dioxide, oxygen content, calcium, magnesium, potassium, sodium, alkalinity, chloride, sulphate, nitrite, nitrate, ammonium, phosphate, silicate, total iron and organic substance (consumption of potassium permanganate). A number of notable differences in the chemical composition of the water of the breeding sites of 13 S. damnosum complex species were found, particularly with regard to the pH and conductivity. On the basis of these differences the various species can be divided into three main groups: Group I: 3 species (S. sanctipauli, S. yahense, "Menge"); breeding in sites with pH values always below 7 and conductivity values below 50 mumhos. Group II: 8 species (S. sirbanum, S. sudanense, S. damnosum s.s., S. squamosum, "Sanje", "Nkusi", "Nyamagasani", "Jovi"); breeding in watercourses with neutral, weakly acid or weakly alkaline reactions and conductivity values ranging from 50 to 150 mumhos. Group III: 2 species ("Kibwezi", "Kisiwani"); breeding in watercourses characterized by highly alkaline reactions with pH values between 7.7 and 10 and by conductivity values between 400 and 950 mumhos. The vectors of Onchocerca volvulus are included in group I and II only.

Reproductive cycles of deer.

PubMed

Asher, G W

2011-04-01

The cervids are a complex assemblage of taxa showing extreme diversity in morphology, physiology, ecology and geographical distribution. Reproductive strategies adopted by various species are also diverse, and include a range from highly seasonal to completely aseasonal birth patterns. The recent growth in knowledge on cervid reproduction is strongly biased towards the larger-bodied, gregarious mixed grazer-browser species that have adapted well to human management and commercialisation. These species tend to represent 'K-selected' climax species characterised by very productive annual breeding success, singleton births and long breeding life (10+ years). Conversely, we know relatively little about the reproductive patterns of the 'r-selected' smaller-bodied, solitary (and often highly territorial), forest-dwelling browser species, often characterised by great fecundity (twinning) and shorter breeding life (<10 years). This group includes many of the endangered cervid taxa. This review extends earlier reviews to include more recent work on cervid reproductive cycles, particularly in relation to environmental factors influencing gestation length. Copyright © 2010 Elsevier B.V. All rights reserved.

Highlighting Astyanax Species Diversity through DNA Barcoding

PubMed Central

Oliveira, Carlos Alexandre Miranda; de Melo, Filipe Augusto Gonçalves; Bertaco, Vinicius de Araújo; de Astarloa, Juan M. Díaz; Rosso, Juan J.; Foresti, Fausto; Oliveira, Claudio

2016-01-01

DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions. PMID:27992537

Parasites Affect Food Web Structure Primarily through Increased Diversity and Complexity

PubMed Central

Dunne, Jennifer A.; Lafferty, Kevin D.; Dobson, Andrew P.; Hechinger, Ryan F.; Kuris, Armand M.; Martinez, Neo D.; McLaughlin, John P.; Mouritsen, Kim N.; Poulin, Robert; Reise, Karsten; Stouffer, Daniel B.; Thieltges, David W.; Williams, Richard J.; Zander, Claus Dieter

2013-01-01

Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite data. Our analyses show that adding parasites usually increases link density and connectance (simple measures of complexity), particularly when including concomitant links (links from predators to parasites of their prey). However, we clarify prior claims that parasites “dominate” food web links. Although parasites can be involved in a majority of links, in most cases classic predation links outnumber classic parasitism links. Regarding network structure, observed changes in degree distributions, 14 commonly studied metrics, and link probabilities are consistent with scale-dependent changes in structure associated with changes in diversity and complexity. Parasite and free-living species thus have similar effects on these aspects of structure. However, two changes point to unique roles of parasites. First, adding parasites and concomitant links strongly alters the frequency of most motifs of interactions among three taxa, reflecting parasites' roles as resources for predators of their hosts, driven by trophic intimacy with their hosts. Second, compared to free-living consumers, many parasites' feeding niches appear broader and less contiguous, which may reflect complex life cycles and small body sizes. This study provides new insights about generic versus unique impacts of parasites on food web structure, extends the generality of food web theory, gives a more rigorous framework for assessing the impact of any species on trophic organization, identifies limitations of current food web models, and provides direction for future structural and dynamical models. PMID:23776404

Parasites affect food web structure primarily through increased diversity and complexity

USGS Publications Warehouse

Dunne, Jennifer A.; Lafferty, Kevin D.; Dobson, Andrew P.; Hechinger, Ryan F.; Kuris, Armand M.; Martinez, Neo D.; McLaughlin, John P.; Mouritsen, Kim N.; Poulin, Robert; Reise, Karsten; Stouffer, Daniel B.; Thieltges, David W.; Williams, Richard J.; Zander, Claus Dieter

2013-01-01

Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite data. Our analyses show that adding parasites usually increases link density and connectance (simple measures of complexity), particularly when including concomitant links (links from predators to parasites of their prey). However, we clarify prior claims that parasites ‘‘dominate’’ food web links. Although parasites can be involved in a majority of links, in most cases classic predation links outnumber classic parasitism links. Regarding network structure, observed changes in degree distributions, 14 commonly studied metrics, and link probabilities are consistent with scale-dependent changes in structure associated with changes in diversity and complexity. Parasite and free-living species thus have similar effects on these aspects of structure. However, two changes point to unique roles of parasites. First, adding parasites and concomitant links strongly alters the frequency of most motifs of interactions among three taxa, reflecting parasites’ roles as resources for predators of their hosts, driven by trophic intimacy with their hosts. Second, compared to free-living consumers, many parasites’ feeding niches appear broader and less contiguous, which may reflect complex life cycles and small body sizes. This study provides new insights about generic versus unique impacts of parasites on food web structure, extends the generality of food web theory, gives a more rigorous framework for assessing the impact of any species on trophic organization, identifies limitations of current food web models, and provides direction for future structural and dynamical models.

Parasites affect food web structure primarily through increased diversity and complexity.

PubMed

Dunne, Jennifer A; Lafferty, Kevin D; Dobson, Andrew P; Hechinger, Ryan F; Kuris, Armand M; Martinez, Neo D; McLaughlin, John P; Mouritsen, Kim N; Poulin, Robert; Reise, Karsten; Stouffer, Daniel B; Thieltges, David W; Williams, Richard J; Zander, Claus Dieter

2013-01-01

Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite data. Our analyses show that adding parasites usually increases link density and connectance (simple measures of complexity), particularly when including concomitant links (links from predators to parasites of their prey). However, we clarify prior claims that parasites "dominate" food web links. Although parasites can be involved in a majority of links, in most cases classic predation links outnumber classic parasitism links. Regarding network structure, observed changes in degree distributions, 14 commonly studied metrics, and link probabilities are consistent with scale-dependent changes in structure associated with changes in diversity and complexity. Parasite and free-living species thus have similar effects on these aspects of structure. However, two changes point to unique roles of parasites. First, adding parasites and concomitant links strongly alters the frequency of most motifs of interactions among three taxa, reflecting parasites' roles as resources for predators of their hosts, driven by trophic intimacy with their hosts. Second, compared to free-living consumers, many parasites' feeding niches appear broader and less contiguous, which may reflect complex life cycles and small body sizes. This study provides new insights about generic versus unique impacts of parasites on food web structure, extends the generality of food web theory, gives a more rigorous framework for assessing the impact of any species on trophic organization, identifies limitations of current food web models, and provides direction for future structural and dynamical models.

Soil actinomycetes in the National Forest Park in northeastern China

NASA Astrophysics Data System (ADS)

Shirokikh, I. G.; Shirokikh, A. A.

2017-01-01

The taxonomic and functional structure of actinomycete complexes in the litters and upper horizons of the soils under an artificial coniferous-broad-leaved forest located around the town of Chanchun (Tszilin province, PRC). The complex of actinomycetes included representatives of the Streptomyces, Micromonospora, Streptosporangium, and Streptoverticillium genera and oligosporous forms. In the actinomycete complexes, streptomycetes prevailed in the abundance (61-95%) and frequency of occurrence (100%). In the parcels of Korean pine ( Pinus koraiensis) and Mongolian oak ( Quercus mongolica), streptomycetes of 19 species from 8 series and 4 sections were isolated. The most representative, as in European forest biomes, was the Cinereus Achromogenes series. A distinguishing feature of the streptomycete complex in the biomes studied was the high participation of species from the Imperfectus series. The verification of the functional activity of natural isolates made it possible to reveal strains with high antagonistic and cellulolytic abilities. A high similarity of actinomycete complexes was found in Eurasian forest ecosystems remote from each other, probably due to the similarity of plant polymers decomposable by actinomycetes.

A new Cernosvitoviella species (Clitellata: Enchytraeidae) and its comparison with other Cernosvitoviella species from Sphagnum mires in Hungary.

PubMed

Dózsa-Farkas, Klára; Csitári, Bianka; Felföldi, Tamás

2017-04-18

Results of a comparative investigation on five Cernosvitoviella species from Hungarian Sphagnum mires including their distribution and the description of a new species, Cernosvitoviella farkasi sp. n., are presented in this paper. Cernosvitoviella atrata, C. aggtelekiensis, C. crassoductus and C. farkasi sp. n. could be easily distinguished from each other based on both morphological and molecular taxonomic analyses. However, C. minor seems to be a species complex on the basis of these investigations, so it was referred as C. minor sensu lato. The status of the C. minor variants requires further studies.

Distributional Patterns of Pseudacteon Associated with the Solenopsis saevissima Complex in South America

PubMed Central

Patrock, Richard J. W.; Porter, Sanford D.; Gilbert, Lawrence E.; Folgarait, Patricia J.

2009-01-01

Classical biological control efforts against imported fire ants have largely involved the use of Pseudacteon parasitoids. To facilitate further exploration for species and population biotypes a database of collection records for Pseudacteon species was organized, including those from the literature and other sources. These data were then used to map the geographical ranges of species associated with the imported fire ants in their native range in South America. In addition, we found geographical range metrics for all species in the genus and related these metrics to latitude and host use. Approximately equal numbers of Pseudacteon species were found in temperate and tropical regions, though the majority of taxa found only in temperate areas were found in the Northern Hemisphere. No significant differences in sizes of geographical ranges were found between Pseudacteon associated with the different host complexes of fire ants despite the much larger and systemic collection effort associated with the S. saevissima host group. The geographical range of the flies was loosely associated with both the number of hosts and the geographical range of their hosts. Pseudacteon with the most extensive ranges had either multiple hosts or hosts with broad distributions. Mean species richnesses of Pseudacteon in locality species assemblages associated with S. saevissima complex ants was 2.8 species, but intensively sampled locations were usually much higher. Possible factors are discussed related to variation in the size of geographical range, and areas in southern South America are outlined that are likely to have been under-explored for Pseudacteon associated with imported fire ants. PMID:20050779

Empirical Evidence Supporting Frequent Cryptic Speciation in Epiphyllous Liverworts: A Case Study of the Cololejeunea lanciloba Complex

PubMed Central

Yu, Ying; Heinrichs, Jochen; Zhu, Rui-Liang; Schneider, Harald

2013-01-01

Cryptic species are frequently recovered in plant lineages, and considered an important cause for divergent of morphological disparity and species diversity. The identification of cryptic species has important implications for the assessment of conservation needs of species aggregates. The mechanisms and processes of the origin of cryptic species diversity are still poorly understand based on the lack of studies especially in context of environment factors. Here we explored evidence for cryptic species within the epiphyllous liverworts Cololejeunea lanciloba complex based on two loci, the plastid trnL-F region and the nuclear ribosomal ITS region. Several analytic approaches were employed to delimit species based on DNA sequence variation including phylogenetic reconstruction, statistical parsimony networks analysis and two recently introduced species delimitation criteria: Rosenberg’s reciprocal monophyly and Rodrigo’s randomly distinct. We found evidence for thirteen genetically distinct putative species, each consisting of more than one haplotype, rather than four morphologically-circumscribed species. The results implied that the highly conserved phenotypes are not congruent with the genetic differentiation, contributing to incorrect assessments of the biodiversity of epiphyllous liverworts. We hypothesize that evolution of cryptic species recovered may be caused by selection of traits critical to the survival in epiphyllous habitats combined with limited developmental options designed in the small body. PMID:24367634

DFT Study on the Complexation of Bambus[6]uril with the Perchlorate and Tetrafluoroborate Anions.

PubMed

Toman, Petr; Makrlík, Emanuel; Vaňura, Petr

2011-12-01

By using quantum mechanical DFT calculations, the most probable structures of the bambus[6]uril.ClO4- and bambus[6]uril.BF4- anionic complex species were derived. In these two complexes having C3 symmetry, each of the considered anions, included in the macrocyclic cavity, is bound by 12 weak hydrogen bonds between methine hydrogen atoms on the convex face of glycoluril units and the respective anion.

Comparative embryology of eleven species of stony corals (Scleractinia).

PubMed

Okubo, Nami; Mezaki, Takuma; Nozawa, Yoko; Nakano, Yoshikatsu; Lien, Yi-Ting; Fukami, Hironobu; Hayward, David C; Ball, Eldon E

2013-01-01

A comprehensive understanding of coral reproduction and development is needed because corals are threatened in many ways by human activity. Major threats include the loss of their photosynthetic symbionts (Symbiodinium) caused by rising temperatures (bleaching), reduced ability to calcify caused by ocean acidification, increased storm severity associated with global climate change and an increase in predators caused by runoff from human agricultural activity. In spite of these threats, detailed descriptions of embryonic development are not available for many coral species. The current consensus is that there are two major groups of stony corals, the "complex" and the "robust". In this paper we describe the embryonic development of four "complex" species, Pseudosiderastrea tayamai, Galaxea fascicularis, Montipora hispida, and Pavona Decussata, and seven "robust" species, Oulastrea crispata, Platygyra contorta, Favites abdita, Echinophyllia aspera, Goniastrea favulus, Dipsastraea speciosa (previously Favia speciosa), and Phymastrea valenciennesi (previously Montastrea valenciennesi). Data from both histologically sectioned embryos and whole mounts are presented. One apparent difference between these two major groups is that before gastrulation the cells of the complex corals thus far described (mainly Acropora species) spread and flatten to produce the so-called prawn chip, which lacks a blastocoel. Our present broad survey of robust and complex corals reveals that prawn chip formation is not a synapomorphy of complex corals, as Pavona Decussata does not form a prawn chip and has a well-developed blastocoel. Although prawn chip formation cannot be used to separate the two clades, none of the robust corals which we surveyed has such a stage. Many robust coral embryos pass through two periods of invagination, separated by a return to a spherical shape. However, only the second of these periods is associated with endoderm formation. We have therefore termed the first invagination a pseudo-blastopore.

Comparative Embryology of Eleven Species of Stony Corals (Scleractinia)

PubMed Central

Okubo, Nami; Mezaki, Takuma; Nozawa, Yoko; Nakano, Yoshikatsu; Lien, Yi-Ting; Fukami, Hironobu; Hayward, David C.; Ball, Eldon E.

2013-01-01

A comprehensive understanding of coral reproduction and development is needed because corals are threatened in many ways by human activity. Major threats include the loss of their photosynthetic symbionts (Symbiodinium) caused by rising temperatures (bleaching), reduced ability to calcify caused by ocean acidification, increased storm severity associated with global climate change and an increase in predators caused by runoff from human agricultural activity. In spite of these threats, detailed descriptions of embryonic development are not available for many coral species. The current consensus is that there are two major groups of stony corals, the "complex" and the "robust". In this paper we describe the embryonic development of four "complex" species, Pseudosiderastrea tayamai, Galaxea fascicularis, Montipora hispida, and Pavona Decussata, and seven "robust" species, Oulastrea crispata, Platygyra contorta, Favites abdita, Echinophyllia aspera, Goniastrea favulus, Dipsastraea speciosa (previously Favia speciosa), and Phymastrea valenciennesi (previously Montastrea valenciennesi). Data from both histologically sectioned embryos and whole mounts are presented. One apparent difference between these two major groups is that before gastrulation the cells of the complex corals thus far described (mainly Acropora species) spread and flatten to produce the so-called prawn chip, which lacks a blastocoel. Our present broad survey of robust and complex corals reveals that prawn chip formation is not a synapomorphy of complex corals, as Pavona Decussata does not form a prawn chip and has a well-developed blastocoel. Although prawn chip formation cannot be used to separate the two clades, none of the robust corals which we surveyed has such a stage. Many robust coral embryos pass through two periods of invagination, separated by a return to a spherical shape. However, only the second of these periods is associated with endoderm formation. We have therefore termed the first invagination a pseudo-blastopore. PMID:24367633

Cryptic Speciation Patterns in Iranian Rock Lizards Uncovered by Integrative Taxonomy

PubMed Central

Ahmadzadeh, Faraham; Flecks, Morris; Carretero, Miguel A.; Mozaffari, Omid; Böhme, Wolfgang; Harris, D. James; Freitas, Susana; Rödder, Dennis

2013-01-01

While traditionally species recognition has been based solely on morphological differences either typological or quantitative, several newly developed methods can be used for a more objective and integrative approach on species delimitation. This may be especially relevant when dealing with cryptic species or species complexes, where high overall resemblance between species is coupled with comparatively high morphological variation within populations. Rock lizards, genus Darevskia, are such an example, as many of its members offer few diagnostic morphological features. Herein, we use a combination of genetic, morphological and ecological criteria to delimit cryptic species within two species complexes, D. chlorogaster and D. defilippii, both distributed in northern Iran. Our analyses are based on molecular information from two nuclear and two mitochondrial genes, morphological data (15 morphometric, 16 meristic and four categorical characters) and eleven newly calculated spatial environmental predictors. The phylogeny inferred for Darevskia confirmed monophyly of each species complex, with each of them comprising several highly divergent clades, especially when compared to other congeners. We identified seven candidate species within each complex, of which three and four species were supported by Bayesian species delimitation within D. chlorogaster and D. defilippii, respectively. Trained with genetically determined clades, Ecological Niche Modeling provided additional support for these cryptic species. Especially those within the D. defilippii-complex exhibit well-differentiated niches. Due to overall morphological resemblance, in a first approach PCA with mixed variables only showed the separation between the two complexes. However, MANCOVA and subsequent Discriminant Analysis performed separately for both complexes allowed for distinction of the species when sample size was large enough, namely within the D. chlorogaster-complex. In conclusion, the results support four new species, which are described herein. PMID:24324611

Mammals of the Braulio Carrillo- La Selva Complex, Costa Rica

USGS Publications Warehouse

Timm, Robert M.; Wilson, Don E.; Clauson, Barbara L.; LaVal, Richard K.; Vaughan, Christopher S.

1989-01-01

Costa Rica's La Selva-Braulio Carrillo complex encompasses a 60-km protected corridor of Caribbean rain and cloud forest extending from 30 m at the La Selva Biological Station to 2,906 m at the top of Volcán Barva. The 52,000-ha complex covers four life zones and two transitional zones, including tropical wet forest, tropical wet forest cool-transition, tropical premontane wet-transition rain forest, tropical premontane rain forest, lower montane rain forest, and montane rain forest. Located in the northeastern part of the country, the area is representative of Central American Caribbean slope forests that extend from Mexico to Panama. The extensive elevational gradient of the complex provides protected habitat for a variety of altitudinal migrants. With support from the National Geographic Society and Rice Foundation, the Organization for Tropical Studies organized a biological survey of the complex in early 1986. The mammal team worked at six sites along the elevational transect established by the expedition: 300 m, 700 m, 1,000 m, 1,500 m, 2,050 m, and 2,600 m. We supplemented our collecting records with unpublished records made available by colleagues, records in the published literature, and specimens in museum collections. In addition, observations recorded by a variety of observers at the La Selva Biological Station are summarized. The mammal fauna of the complex comprises 142 species including 79 bats, 23 rodents, 15 carnivores, 7 marsupials, 6 edentates, 4 artiodactyls, 3 primates, 2 rabbits, 2 shrews, and 1 perissodactyl. At least 10 additional species are likely to occur there. The only species of mammal likely to have been extirpated from the area is the giant anteater. Recognizing the importance of the area to wildlife and to mankind in general, the government of Costa Rica added 13,500 ha to the complex on 13 April 1986. This area, previously known as the “Zona Protectora,” provided the mid-elevational link between the lowlands of the La Selva Biological Station and the montane forests of Braulio Carrillo National Park. Unfortunately, destruction of the rain forests surrounding the complex will soon render it an isolated island of protected forest. Thus, the area will become increasingly valuable as a refuge for many species with home ranges that require extensive tracts of undisturbed habitat.

A Multistep Equilibria-Redox-Complexation Demonstration to Illustrate Le Chatelier's Principle.

ERIC Educational Resources Information Center

Berger, Tomas G.; Mellon, Edward K.

1996-01-01

Describes a process that can be used to illustrate a number of chemical principles including Le Chatelier's principle, redox chemistry, equilibria versus steady state situations, and solubility of species. (JRH)

Isomerization of Cyclooctadiene to Cyclooctyne with a Zinc/Zirconium Heterobimetallic Complex.

PubMed

Butler, Michael J; White, Andrew J P; Crimmin, Mark R

2016-06-06

Reaction of a zinc/zirconium heterobimetallic complex with 1,5-cyclooctadiene (1,5-COD) results in slow isomerization to 1,3-cyclooctadiene (1,3-COD), along with the formation of a new complex that includes a cyclooctyne ligand bridging two metal centers. While analogous magnesium/zirconium and aluminum/zirconium heterobimetallic complexes are competent for the catalytic isomerization of 1,5-COD to 1,3-COD, only in the case of the zinc species is the cyclooctyne adduct observed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Isomerization of Cyclooctadiene to Cyclooctyne with a Zinc/Zirconium Heterobimetallic Complex

PubMed Central

Butler, Michael J.; White, Andrew J. P.

2016-01-01

Abstract Reaction of a zinc/zirconium heterobimetallic complex with 1,5‐cyclooctadiene (1,5‐COD) results in slow isomerization to 1,3‐cyclooctadiene (1,3‐COD), along with the formation of a new complex that includes a cyclooctyne ligand bridging two metal centers. While analogous magnesium/zirconium and aluminum/zirconium heterobimetallic complexes are competent for the catalytic isomerization of 1,5‐COD to 1,3‐COD, only in the case of the zinc species is the cyclooctyne adduct observed. PMID:27071992

Benchmarking novel approaches for modelling species range dynamics.

PubMed

Zurell, Damaris; Thuiller, Wilfried; Pagel, Jörn; Cabral, Juliano S; Münkemüller, Tamara; Gravel, Dominique; Dullinger, Stefan; Normand, Signe; Schiffers, Katja H; Moore, Kara A; Zimmermann, Niklaus E

2016-08-01

Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21st century. To anticipate and mitigate biodiversity loss, models are needed that reliably project species' range dynamics and extinction risks. Recently, several new approaches to model range dynamics have been developed to supplement correlative species distribution models (SDMs), but applications clearly lag behind model development. Indeed, no comparative analysis has been performed to evaluate their performance. Here, we build on process-based, simulated data for benchmarking five range (dynamic) models of varying complexity including classical SDMs, SDMs coupled with simple dispersal or more complex population dynamic models (SDM hybrids), and a hierarchical Bayesian process-based dynamic range model (DRM). We specifically test the effects of demographic and community processes on model predictive performance. Under current climate, DRMs performed best, although only marginally. Under climate change, predictive performance varied considerably, with no clear winners. Yet, all range dynamic models improved predictions under climate change substantially compared to purely correlative SDMs, and the population dynamic models also predicted reasonable extinction risks for most scenarios. When benchmarking data were simulated with more complex demographic and community processes, simple SDM hybrids including only dispersal often proved most reliable. Finally, we found that structural decisions during model building can have great impact on model accuracy, but prior system knowledge on important processes can reduce these uncertainties considerably. Our results reassure the clear merit in using dynamic approaches for modelling species' response to climate change but also emphasize several needs for further model and data improvement. We propose and discuss perspectives for improving range projections through combination of multiple models and for making these approaches operational for large numbers of species. © 2016 John Wiley & Sons Ltd.

A sociogram for the cranes of the world.

PubMed

Ellis, D H; Swengel, S R; Archibald, G W; Kepler, C B

1998-05-01

The behavioral repertoire for the world's 15 species of cranes includes over 100 behavioral acts with clear social significance. Each species performs at least 60 discrete social postures, vocalizations, displays, and activities. Because all but a handful of the stereotyped social displays are common to all species, the presence or absence of social displays was useful only to a limited degree in comparing the relatedness of established crane taxonomic groups. However, the breadth of the repertoire for each species and for the family Gruidae tentatively places cranes at the apex of social complexity (at least for stereotyped displays) in the animal world.

A sociogram for the cranes of the world

USGS Publications Warehouse

Ellis, D.H.; Swengel, S.R.; Archibald, George W.; Kepler, C.B.

1998-01-01

The behavioral repertoire for the world's 15 species of cranes includes over 100 behavioral acts with clear social significance. Each species performs at least 60 discrete social postures, vocalizations, displays, and activities. Because all but a handful of the stereotyped social displays are common to all species, the presence or absence of social displays was useful only to a limited degree in comparing the relatedness of established crane taxonomic groups. However, the breadth of the repertoire for each species and for the family Gruidae tentatively places cranes at the apex of social complexity (at least for stereotyped displays) in the animal world.

Early evolution of Tubulogenerina during the Paleogene of Europe

USGS Publications Warehouse

Gibson, T.G.; Barbin, V.; Poignant, A.; Sztrakos, K.

1991-01-01

The early evolution of Tubulogenerina took place in Europe where eight species occur in lower Eocene to uppermost Oligocene or lower Miocene strata. Species diversity within Tubulogenerina dropped significantly in the early Oligocne; only a single species persisted from the late Eocene, and it became extinct before the end of the early Oligocene. Morphologic changes during the European phylogeny of Tubulogenerina include (1) the development of costate and more complex tubulopore ornamentation, and (2) the change from a single elongated apertural slit with a single toothplate to multiple apertures and toothplates. Three new Tubulogenerina species are described. -from Authors

Functionalized active-nucleus complex sensor

DOEpatents

Pines, Alexander; Wemmer, David E.; Spence, Megan; Rubin, Seth

2003-11-25

A functionalized active-nucleus complex sensor that selectively associates with one or more target species, and a method for assaying and screening for one or a plurality of target species utilizing one or a plurality of functionalized active-nucleus complexes with at least two of the functionalized active-nucleus complexes having an attraction affinity to different corresponding target species. The functionalized active-nucleus complex has an active-nucleus and a targeting carrier. The method involves functionalizing an active-nucleus, for each functionalized active-nucleus complex, by incorporating the active-nucleus into a macromolucular or molecular complex that is capable of binding one of the target species and then bringing the macromolecular or molecular complexes into contact with the target species and detecting the occurrence of or change in a nuclear magnetic resonance signal from each of the active-nuclei in each of the functionalized active-nucleus complexes.

Speciation on the Rocks: Integrated Systematics of the Heteronotia spelea Species Complex (Gekkota; Reptilia) from Western and Central Australia

PubMed Central

Pepper, Mitzy; Doughty, Paul; Fujita, Matthew K.; Moritz, Craig; Keogh, J. Scott

2013-01-01

The isolated uplands of the Australian arid zone are known to provide mesic refuges in an otherwise xeric landscape, and divergent lineages of largely arid zone taxa have persisted in these regions following the onset of Miocene aridification. Geckos of the genus Heteronotia are one such group, and have been the subject of many genetic studies, including H. spelea, a strongly banded form that occurs in the uplands of the Pilbara and Central Ranges regions of the Australian arid zone. Here we assess the systematics of these geckos based on detailed examination of morphological and genetic variation. The H. spelea species complex is a monophyletic lineage to the exclusion of the H. binoei and H. planiceps species complexes. Within the H. spelea complex, our previous studies based on mtDNA and nine nDNA loci found populations from the Central Ranges to be genetically divergent from Pilbara populations. Here we supplement our published molecular data with additional data gathered from central Australian samples. In the spirit of integrative species delimitation, we combine multi-locus, coalescent-based lineage delimitation with extensive morphological analyses to test species boundaries, and we describe the central populations as a new species, H. fasciolatus sp. nov. In addition, within the Pilbara there is strong genetic evidence for three lineages corresponding to northeastern (type), southern, and a large-bodied melanic population isolated in the northwest. Due to its genetic distinctiveness and extreme morphological divergence from all other Heteronotia, we describe the melanic form as a new species, H. atra sp. nov. The northeastern and southern Pilbara populations are morphologically indistinguishable with the exception of a morpho-type in the southeast that has a banding pattern resembling H. planiceps from the northern monsoonal tropics. Pending more extensive analyses, we therefore treat Pilbara H. spelea as a single species with phylogenetic structure and morphological heterogeneity. PMID:24244289

DNA Barcoding in a Crop Genebank: Resolving the Capsicum annuum Species Complex.

USDA-ARS?s Scientific Manuscript database

Variability within eight cpDNA introns including trnS-trnfM, trnL-trnT, trnH-psbA, trnF-trnL, trnD-trnT, trnC-rpoB, rps16, and matK, and the nuclear waxy intron was examined in seven species of Capsicum (C. annuum, C. baccatum, C. chinense, C. frutescens, C. pubescens, C. chacoense, and C. rhomboide...

Genetic differentiation of two California red oak species, Quercus parvula var. shreveii and Q. wislizeni, based on AFLP genetic markers

Treesearch

Nasser Kashani; Richard S. Dodd

2002-01-01

Oaks are renowned for posing problems in defining species boundaries. One example is the case of the interior live oak complex that is usually taken to include two varieties of Quercus wislizeni from the Coast Ranges of California and the Sierra Nevada, and Q. parvula var. shreveii from the central coast of...

Genome Sequence of Fusarium Isolate MYA-4552 from the Midgut of Anoplophora glabripennis, an Invasive, Wood-Boring Beetle.

PubMed

Herr, Joshua R; Scully, Erin D; Geib, Scott M; Hoover, Kelli; Carlson, John E; Geiser, David M

2016-07-21

The Fusarium solani species complex (FSSC) is a clade of environmentally ubiquitous fungi that includes plant, animal, and insect associates. Here, we report the draft genome sequence of the undescribed species FSSC 6 (isolate MYA-4552), housed in the gut of the wood-boring cerambycid beetle Anoplophora glabripennis. Copyright © 2016 Herr et al.

Reef flattening effects on total richness and species responses in the Caribbean.

PubMed

Newman, Steven P; Meesters, Erik H; Dryden, Charlie S; Williams, Stacey M; Sanchez, Cristina; Mumby, Peter J; Polunin, Nicholas V C

2015-11-01

There has been ongoing flattening of Caribbean coral reefs with the loss of habitat having severe implications for these systems. Complexity and its structural components are important to fish species richness and community composition, but little is known about its role for other taxa or species-specific responses. This study reveals the importance of reef habitat complexity and structural components to different taxa of macrofauna, total species richness, and individual coral and fish species in the Caribbean. Species presence and richness of different taxa were visually quantified in one hundred 25-m(2) plots in three marine reserves in the Caribbean. Sampling was evenly distributed across five levels of visually estimated reef complexity, with five structural components also recorded: the number of corals, number of large corals, slope angle, maximum sponge and maximum octocoral height. Taking advantage of natural heterogeneity in structural complexity within a particular coral reef habitat (Orbicella reefs) and discrete environmental envelope, thus minimizing other sources of variability, the relative importance of reef complexity and structural components was quantified for different taxa and individual fish and coral species on Caribbean coral reefs using boosted regression trees (BRTs). Boosted regression tree models performed very well when explaining variability in total (82·3%), coral (80·6%) and fish species richness (77·3%), for which the greatest declines in richness occurred below intermediate reef complexity levels. Complexity accounted for very little of the variability in octocorals, sponges, arthropods, annelids or anemones. BRTs revealed species-specific variability and importance for reef complexity and structural components. Coral and fish species occupancy generally declined at low complexity levels, with the exception of two coral species (Pseudodiploria strigosa and Porites divaricata) and four fish species (Halichoeres bivittatus, H. maculipinna, Malacoctenus triangulatus and Stegastes partitus) more common at lower reef complexity levels. A significant interaction between country and reef complexity revealed a non-additive decline in species richness in areas of low complexity and the reserve in Puerto Rico. Flattening of Caribbean coral reefs will result in substantial species losses, with few winners. Individual structural components have considerable value to different species, and their loss may have profound impacts on population responses of coral and fish due to identity effects of key species, which underpin population richness and resilience and may affect essential ecosystem processes and services. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

LC-IMS-MS Feature Finder. Detecting Multidimensional Liquid Chromatography, Ion Mobility, and Mass Spectrometry Features in Complex Datasets

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

Crowell, Kevin L.; Slysz, Gordon W.; Baker, Erin Shammel

2013-09-05

We introduce a command line software application LC-IMS-MS Feature Finder that searches for molecular ion signatures in multidimensional liquid chromatography-ion mobility spectrometry-mass spectrometry (LC-IMS-MS) data by clustering deisotoped peaks with similar monoisotopic mass, charge state, LC elution time, and ion mobility drift time values. The software application includes an algorithm for detecting and quantifying co-eluting chemical species, including species that exist in multiple conformations that may have been separated in the IMS dimension.

Development of a PCR-RFLP method based on the transcription elongation factor 1-α gene to differentiate Fusarium graminearum from other species within the Fusarium graminearum species complex.

PubMed

Garmendia, Gabriela; Umpierrez-Failache, Mariana; Ward, Todd J; Vero, Silvana

2018-04-01

Fusarium head blight (FHB) is a destructive disease of cereals crops worldwide and a major food safety concern due to grain contamination with trichothecenes and other mycotoxins. Fusarium graminearum, a member of the Fusarium graminearum species complex (FGSC) is the dominant FHB pathogen in many parts of the world. However, a number of other Fusarium species, including other members of the FGSC, may also be present for example in Argentina, New Zealand, Ethiopia, Nepal, Unites States in cereals such as wheat and barley. Proper species identification is critical to research aimed at improving disease and mycotoxin control programs. Identification of Fusarium species is are often unreliable by traditional, as many species are morphologically cryptic. DNA sequence-based methods offer a reliable means of species identification, but can be expensive when applied to the analyses of population samples. To facilitate identification of the major causative agent of FHB, this work describes an easy and inexpensive method to differentiate F. graminearum from the remaining species within the FGSC and from the other common Fusarium species causing FHB in cereals. The developed method is based on a PCR-RFLP of the transcription elongation factor (TEF 1-α) gene using the restriction enzyme BsaHI. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular species composition of plant cardiolipin determined by liquid chromatography mass spectrometry

PubMed Central

Zhou, Yonghong; Peisker, Helga

2016-01-01

Cardiolipin (CL), an anionic phospholipid of the inner mitochondrial membrane, provides essential functions for stabilizing respiratory complexes and is involved in mitochondrial morphogenesis and programmed cell death in animals. The role of CL and its metabolism in plants are less well understood. The measurement of CL in plants, including its molecular species composition, is hampered by the fact that CL is of extremely low abundance, and that plants contain large amounts of interfering compounds including galactolipids, neutral lipids, and pigments. We used solid phase extraction by anion exchange chromatography to purify CL from crude plant lipid extracts. LC/MS was used to determine the content and molecular species composition of CL. Thus, up to 23 different molecular species of CL were detected in different plant species, including Arabidopsis, mung bean, spinach, barley, and tobacco. Similar to animals, plant CL is dominated by highly unsaturated species, mostly containing linoleic and linolenic acid. During phosphate deprivation or exposure to an extended dark period, the amount of CL decreased in Arabidopsis, accompanied with an increased degree in unsaturation. The mechanism of CL remodeling during stress, and the function of highly unsaturated CL molecular species, remains to be defined. PMID:27179363

Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota

PubMed Central

Ellegaard, Kirsten M.; Engel, Philipp

2016-01-01

Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities. PMID:27708630

Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota.

PubMed

Ellegaard, Kirsten M; Engel, Philipp

2016-01-01

Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities.

Links between Genetic Groups, Indole Alkaloid Profiles and Ecology within the Grass-Parasitic Claviceps purpurea Species Complex.

PubMed

Negård, Mariell; Uhlig, Silvio; Kauserud, Håvard; Andersen, Tom; Høiland, Klaus; Vrålstad, Trude

2015-04-28

The grass parasitic fungus Claviceps purpurea sensu lato produces sclerotia with toxic indole alkaloids. It constitutes several genetic groups with divergent habitat preferences that recently were delimited into separate proposed species. We aimed to 1) analyze genetic variation of C. purpurea sensu lato in Norway, 2) characterize the associated indole alkaloid profiles, and 3) explore relationships between genetics, alkaloid chemistry and ecology. Approximately 600 sclerotia from 14 different grass species were subjected to various analyses including DNA sequencing and HPLC-MS. Molecular results, supported by chemical and ecological data, revealed one new genetic group (G4) in addition to two of the three known; G1 (C. purpurea sensu stricto) and G2 (C. humidiphila). G3 (C. spartinae) was not found. G4, which was apparently con-specific with the recently described C. arundinis sp. nov, was predominantly found in very wet habitats on Molinia caerulea and infrequently in saline habitats on Leymus arenarius. Its indole-diterpene profile resembled G2, while its ergot alkaloid profile differed from G2 in high amounts of ergosedmam. In contrast to G1, indole-diterpenes were consistently present in G2 and G4. Our study supports and complements the newly proposed species delimitation of the C. purpurea complex, but challenges some species characteristics including host spectrum, habitat preferences and sclerotial floating ability.

Links between Genetic Groups, Indole Alkaloid Profiles and Ecology within the Grass-Parasitic Claviceps purpurea Species Complex

PubMed Central

Negård, Mariell; Uhlig, Silvio; Kauserud, Håvard; Andersen, Tom; Høiland, Klaus; Vrålstad, Trude

2015-01-01

The grass parasitic fungus Claviceps purpurea sensu lato produces sclerotia with toxic indole alkaloids. It constitutes several genetic groups with divergent habitat preferences that recently were delimited into separate proposed species. We aimed to 1) analyze genetic variation of C. purpurea sensu lato in Norway, 2) characterize the associated indole alkaloid profiles, and 3) explore relationships between genetics, alkaloid chemistry and ecology. Approximately 600 sclerotia from 14 different grass species were subjected to various analyses including DNA sequencing and HPLC-MS. Molecular results, supported by chemical and ecological data, revealed one new genetic group (G4) in addition to two of the three known; G1 (C. purpurea sensu stricto) and G2 (C. humidiphila). G3 (C. spartinae) was not found. G4, which was apparently con-specific with the recently described C. arundinis sp. nov, was predominantly found in very wet habitats on Molinia caerulea and infrequently in saline habitats on Leymus arenarius. Its indole-diterpene profile resembled G2, while its ergot alkaloid profile differed from G2 in high amounts of ergosedmam. In contrast to G1, indole-diterpenes were consistently present in G2 and G4. Our study supports and complements the newly proposed species delimitation of the C. purpurea complex, but challenges some species characteristics including host spectrum, habitat preferences and sclerotial floating ability. PMID:25928134

Relating geomorphic change and grazing to avian communities in riparian forests

USGS Publications Warehouse

Scott, M.L.; Skagen, S.K.; Merligliano, M.F.

2003-01-01

Avian conservation in riparian or bottomland forests requires an understanding of the physical and biotic factors that sustain the structural complexity of riparian vegetation. Riparian forests of western North America are dependent upon flow-related geomorphic processes necessary for establishment of new cottonwood and willow patches. In June 1995, we examined how fluvial geomorphic processes and long-term grazing influence the structural complexity of riparian vegetation and the abundance and diversity of breeding birds along the upper Missouri River in central Montana, a large, flow-regulated, and geomorphically constrained reach. Use by breeding birds was linked to fluvial geomorphic processes that influence the structure of these patches. Species richness and bird diversity increased with increasing structural complexity of vegetation (F1,32 = 75.49, p < 0.0001; F1,32 = 79.76, p < 0.0001, respectively). Bird species composition was significantly correlated with vegetation strata diversity (rs,33 = 0.98, p < 0.0001). Bird abundance in canopy and tall-shrub foraging guilds increased significantly with increasing tree cover and tall-shrub cover (F1,22 = 34.68, p < 0.0001; F1,20 = 22.22, p < 0.0001, respectively). Seventeen bird species, including five species of concern (e.g., Red-eyed Vireo [Vireo olivaceus]), were significantly associated (p < 0.10) with structurally complex forest patches, whereas only six bird species were significantly associated with structurally simple forest patches. We related the structural complexity of 34 riparian vegetation patches to geomorphic change, woody vegetation establishment, and grazing history over a 35-year post-dam period (1953–1988). The structural complexity of habitat patches was positively related to recent sediment accretion (t33 = 3.31, p = 0.002) and vegetation establishment (t20.7 = −3.63, p = 0.002) and negatively related to grazing activity (t19.6 = 3.75, p = 0.001). Avian conservation along rivers like the upper Missouri requires maintenance of the geomorphic processes responsible for tree establishment and management of land-use activities in riparian forests.

Fifty years of oxacalix[3]arenes: A review

PubMed Central

Cottet, Kevin; Marcos, Paula M

2012-01-01

Summary Hexahomotrioxacalix[3]arenes, commonly called oxacalix[3]arenes, were first reported in 1962. Since then, their chemistry has been expanded to include numerous derivatives and complexes. This review describes the syntheses of the parent compounds, their derivatives, and their complexation behaviour towards cations. Extraction data are presented, as are crystal structures of the macrocycles and their complexes with guest species. Applications in fields as diverse as ion selective electrode modifiers, fluorescence sensors, fullerene separations and biomimetic chemistry are described. PMID:22423288

The Andean Paepalanthus pilosus complex (Eriocaulaceae): a revision with three new taxa

PubMed Central

Hensold, Nancy

2016-01-01

Abstract A herbarium-based revision is provided for Paepalanthus pilosus and allies, five commonly confused species of cushion plants native to Andean paramo. These are placed in the recircumscribed Paepalanthus subsect. Cryptanthella Suess. The group includes Paepalanthus pilosus, Paepalanthus dendroides, and Paepalanthus lodiculoides. An additional two species and one variety are newly described: Paepalanthus caryonauta, Paepalanthus huancabambensis, and Paepalanthus pilosus var. leoniae. The latter two are Peruvian endemics, while Paepalanthus caryonauta is known from four countries, and has long been confused with other species. An additional, possibly undescribed taxon is noted from the Serrania de Perijá, Colombia. Five new synonyms and three lectotypes are proposed, and the common misapplication of some names is noted. Within the Paepalanthus pilosus complex, species differences were found in timing of peduncle elongation, sex ratio, and leaf, perianth, diaspore and nectary morphology. Ecological differences are suggested by specimen data and a review of ecological literature. Descriptions, photographs and maps are provided for all species, as is a key to the groups of eriocaulaceous cushion plants from Andean South America. PMID:27489483

Reaction landscape of a pentadentate N5-ligated Mn(II) complex with O2˙- and H2O2 includes conversion of a peroxomanganese(III) adduct to a bis(μ-oxo)dimanganese(III,IV) species.

PubMed

Leto, Domenick F; Chattopadhyay, Swarup; Day, Victor W; Jackson, Timothy A

2013-09-28

Herein we describe the chemical reactivity of the mononuclear [Mn(II)(N4py)(OTf)](OTf) (1) complex with hydrogen peroxide and superoxide. Treatment of 1 with one equivalent superoxide at -40 °C in MeCN formed the peroxomanganese(III) adduct, [Mn(III)(O2)(N4py)](+) (2) in ~30% yield. Complex 2 decayed over time and the formation of the bis(μ-oxo)dimanganese(III,IV) complex, [Mn(III)Mn(IV)(μ-O)2(N4py)2](3+) (3) was observed. When 2 was formed in higher yields (~60%) using excess superoxide, the [Mn(III)(O2)(N4py)](+) species thermally decayed to Mn(II) species and 3 was formed in no greater than 10% yield. Treatment of [Mn(III)(O2)(N4py)](+) with 1 resulted in the formation of 3 in ~90% yield, relative to the concentration of [Mn(III)(O2)(N4py)](+). This reaction mimics the observed chemistry of Mn-ribonucleotide reductase, as it features the conversion of two Mn(II) species to an oxo-bridged Mn(III)Mn(IV) compound using O2(-) as oxidant. Complex 3 was independently prepared through treatment of 1 with H2O2 and base at -40 °C. The geometric and electronic structures of 3 were probed using electronic absorption, electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD), variable-temperature, variable-field MCD (VTVH-MCD), and X-ray absorption (XAS) spectroscopies. Complex 3 was structurally characterized by X-ray diffraction (XRD), which revealed the N4py ligand bound in an unusual tetradentate fashion.

Herpetofauna of the cedar glades and associated habitats of the Inner Central Basin of middle Tennessee

USGS Publications Warehouse

Niemiller, M.L.; Graham, Reynolds R.; Glorioso, B.M.; Spiess, J.; Miller, B.T.

2011-01-01

The cedar glades and barrens of the Inner Central Basin (ICB) of middle Tennessee support a unique and diverse flora and fauna and represent some of the state's most valued natural areas. We conducted herpetofaunal inventories of the cedar glades, associated barrens, cedar-hardwood forest, and adjacent aquatic habitats of the Stones River drainage of Middle Tennessee, focusing our sampling effort primarily at seven state- or federally owned properties in Rutherford and Wilson counties. These properties included Stones River National Battlefield (SRNB), Flat Rock State Natural Area (FRSNA), Vesta Cedar Glade State Natural Area (VSNA), Fall Creek Recreation Area (FCRA) on J. Percy Priest Wildlife Management Area, Cedars of Lebanon State Forest (CLSF), Cedars of Lebanon State Forest Natural Area (CLSNA), and Cedars of Lebanon State Park (CLSP). We used a variety of inventory techniques in terrestrial, aquatic, and subterranean habitats to survey these properties periodically from 1989 to 2010. We documented 49 species (22 amphibian and 27 reptile) accounting for 75.4% of the 65 herpetofaunal species thought to occur in the ICB, including records for Cemophora coccinea, Aneides aeneus, Gyrinophilus palleucus, Ambystoma barbouri, and Pseudotriton montanus. We found differences in alpha and beta diversity between sites, with the CLSF complex containing a high of 41 herpetofaunal species and FRSNA containing a low of 23 species. Beta diversity comparisons indicated similarity in amphibian species composition between FRSNA and CLSF and between SRNB and CLSF (9 shared species), and in reptile species composition between VSNA and the CLSF complex (16 shared species). We compare the results of our inventory with two previous studies conducted in the area and discuss the relative abundance, conservation, and threats to the herpetofaunal community of these habitats.

Molecular systematics and undescribed diversity of Madagascan scolecophidian snakes (Squamata: Serpentes).

PubMed

Nagy, Zoltán T; Marion, Angela B; Glaw, Frank; Miralles, Aurélien; Nopper, Joachim; Vences, Miguel; Hedges, S Blair

2015-11-10

We provide an updated molecular phylogenetic analysis of global diversity of typhlopid and xenotyphlopid blindsnakes, adding a set of Madagascan samples and sequences of an additional mitochondrial gene to an existing supermatrix of nuclear and mitochondrial gene segments. Our data suggest monophyly of Madagascan typhlopids, exclusive of introduced Indotyphlops braminus. The Madagascar-endemic typhlopid clade includes two species previously assigned to the genus Lemuriatyphlops (in the subfamily Asiatyphlopinae), which were not each others closest relatives. This contradicts a previous study that described Lemuriatyphlops based on a sequence of the cytochrome oxidase subunit 1 gene from a single species and found this species not forming a clade with the other Malagasy species included. Based on our novel phylogenetic assessment we include all species in this endemic typhlopid clade in the genus Madatyphlops and in the subfamily Madatyphlopinae and consider Lemuriatyphlops as junior synonym. Within Madatyphlops, we identify several candidate species. For some of these (those in the M. arenarius complex), our preliminary data suggest sympatric occurrence and morphological differentiation, thus the existence of undescribed species. We also comment on the genus-level classification of several non-Madagascan typhlopids. We suggest that African species included in Madatyphlops (Afrotyphlops calabresii, A. cuneirostris, A. platyrhynchus, and Rhinotyphlops leucocephalus) should not be included in this genus. We furthermore argue that recent claims of Sundatyphlops, Antillotyphlops, and Cubatyphlops being "undiagnosable" or "not monophyletic" were based on errors in tree reconstruction and failure to notice diagnostic characters, and thus regard these three genera as valid.

Reaction factoring and bipartite update graphs accelerate the Gillespie Algorithm for large-scale biochemical systems.

PubMed

Indurkhya, Sagar; Beal, Jacob

2010-01-06

ODE simulations of chemical systems perform poorly when some of the species have extremely low concentrations. Stochastic simulation methods, which can handle this case, have been impractical for large systems due to computational complexity. We observe, however, that when modeling complex biological systems: (1) a small number of reactions tend to occur a disproportionately large percentage of the time, and (2) a small number of species tend to participate in a disproportionately large percentage of reactions. We exploit these properties in LOLCAT Method, a new implementation of the Gillespie Algorithm. First, factoring reaction propensities allows many propensities dependent on a single species to be updated in a single operation. Second, representing dependencies between reactions with a bipartite graph of reactions and species requires only storage for reactions, rather than the required for a graph that includes only reactions. Together, these improvements allow our implementation of LOLCAT Method to execute orders of magnitude faster than currently existing Gillespie Algorithm variants when simulating several yeast MAPK cascade models.

Reaction Factoring and Bipartite Update Graphs Accelerate the Gillespie Algorithm for Large-Scale Biochemical Systems

PubMed Central

Indurkhya, Sagar; Beal, Jacob

2010-01-01

ODE simulations of chemical systems perform poorly when some of the species have extremely low concentrations. Stochastic simulation methods, which can handle this case, have been impractical for large systems due to computational complexity. We observe, however, that when modeling complex biological systems: (1) a small number of reactions tend to occur a disproportionately large percentage of the time, and (2) a small number of species tend to participate in a disproportionately large percentage of reactions. We exploit these properties in LOLCAT Method, a new implementation of the Gillespie Algorithm. First, factoring reaction propensities allows many propensities dependent on a single species to be updated in a single operation. Second, representing dependencies between reactions with a bipartite graph of reactions and species requires only storage for reactions, rather than the required for a graph that includes only reactions. Together, these improvements allow our implementation of LOLCAT Method to execute orders of magnitude faster than currently existing Gillespie Algorithm variants when simulating several yeast MAPK cascade models. PMID:20066048

Trophic signatures of seabirds suggest shifts in oceanic ecosystems

PubMed Central

Gagne, Tyler O.; Hyrenbach, K. David; Hagemann, Molly E.; Van Houtan, Kyle S.

2018-01-01

Pelagic ecosystems are dynamic ocean regions whose immense natural capital is affected by climate change, pollution, and commercial fisheries. Trophic level–based indicators derived from fishery catch data may reveal the food web status of these systems, but the utility of these metrics has been debated because of targeting bias in fisheries catch. We analyze a unique, fishery-independent data set of North Pacific seabird tissues to inform ecosystem trends over 13 decades (1890s to 2010s). Trophic position declined broadly in five of eight species sampled, indicating a long-term shift from higher–trophic level to lower–trophic level prey. No species increased their trophic position. Given species prey preferences, Bayesian diet reconstructions suggest a shift from fishes to squids, a result consistent with both catch reports and ecosystem models. Machine learning models further reveal that trophic position trends have a complex set of drivers including climate, commercial fisheries, and ecomorphology. Our results show that multiple species of fish-consuming seabirds may track the complex changes occurring in marine ecosystems. PMID:29457134

Trophic signatures of seabirds suggest shifts in oceanic ecosystems.

PubMed

Gagne, Tyler O; Hyrenbach, K David; Hagemann, Molly E; Van Houtan, Kyle S

2018-02-01

Pelagic ecosystems are dynamic ocean regions whose immense natural capital is affected by climate change, pollution, and commercial fisheries. Trophic level-based indicators derived from fishery catch data may reveal the food web status of these systems, but the utility of these metrics has been debated because of targeting bias in fisheries catch. We analyze a unique, fishery-independent data set of North Pacific seabird tissues to inform ecosystem trends over 13 decades (1890s to 2010s). Trophic position declined broadly in five of eight species sampled, indicating a long-term shift from higher-trophic level to lower-trophic level prey. No species increased their trophic position. Given species prey preferences, Bayesian diet reconstructions suggest a shift from fishes to squids, a result consistent with both catch reports and ecosystem models. Machine learning models further reveal that trophic position trends have a complex set of drivers including climate, commercial fisheries, and ecomorphology. Our results show that multiple species of fish-consuming seabirds may track the complex changes occurring in marine ecosystems.

Ceratocystis larium sp. nov., a new species from Styrax benzoin wounds associated with incense harvesting in Indonesia.

PubMed

van Wyk, M; Wingfield, B D; Clegg, P A; Wingfield, M J

2009-06-01

Styrax benzoin trees, native to the island Sumatra, Indonesia are wounded to produce resin that is collected and burned as incense. These wounds on trees commonly develop into expanding cankers that lead to tree death. The aim of this study was to consider whether Ophiostomatoid fungi, typically associated with wounds on trees might be associated with resin harvesting on S. benzoin. Samples were collected from the edges of artificially induced wounds, and particularly where cankers and staining of the vascular tissue was evident. Tissue samples were incubated in moist chambers and carrot baiting was also used to detect the presence of Ceratocystis spp. Fruiting structures with morphology typical of species in the C. fimbriata s.l. species complex and species in the anamorph genus Thielaviopsis were found, on both the incubated wood and the carrot baits. DNA sequences were generated for the Internal Transcribed Spacer regions 1 and 2 including the 5.8S rRNA gene, part of the beta-tubulin and the Transcription Elongation Factor 1-alpha gene regions. These data were compared with those of other species in the C. fimbriata s.l. species complex and Thielaviopsis using phylogenetic analysis. Morphology of the isolates in culture as well as phylogenetic inference showed that the Thielaviopsis sp. present on the wounds was T. basicola. The Ceratocystis sp. from S. benzoin represents a new taxon in the C. fimbriata s.l. complex described here as C. larium sp. nov.

Comparison of transmission of Papaya leaf curl China virus among four cryptic species of the whitefly Bemisia tabaci complex

PubMed Central

Guo, Tao; Guo, Qi; Cui, Xi-Yun; Liu, Yin-Quan; Hu, Jian; Liu, Shu-Sheng

2015-01-01

Begomoviruses are transmitted by cryptic species of the whitefly Bemisia tabaci complex, often in a species-specific manner. Papaya leaf curl China virus (PaLCuCNV) has been recorded to infect several crops including papaya, tomato and tobacco in China. To help assess the risks of spread of this virus, we compared the acquisition, retention and transmission of PaLCuCNV among four species of whiteflies, Middle East-Asia Minor 1 (MEAM1), Mediterranean (MED), Asia 1 and Asia II 7. All four species of whiteflies are able to acquire, retain and transmit the virus, but with different levels of efficiency. Transmission tests using tomato as the host plant showed that MEAM1 transmitted PaLCuCNV with substantially higher efficiency than did MED, Asia 1 and Asia II 7. Furthermore, accumulation of PaLCuCNV in the whiteflies was positively associated with its efficiency of transmitting the virus. Altogether, these findings indicate that MEAM1 is the most efficient vector for PaLCuCNV in the four species of whiteflies, and suggest that risks of PaLCuCNV pandemics are high in regions where MEAM1 occurs. PMID:26486606

Versatile Aggressive Mimicry of Cicadas by an Australian Predatory Katydid

PubMed Central

Marshall, David C.; Hill, Kathy B. R.

2009-01-01

Background In aggressive mimicry, a predator or parasite imitates a signal of another species in order to exploit the recipient of the signal. Some of the most remarkable examples of aggressive mimicry involve exploitation of a complex signal-response system by an unrelated predator species. Methodology/Principal Findings We have found that predatory Chlorobalius leucoviridis katydids (Orthoptera: Tettigoniidae) can attract male cicadas (Hemiptera: Cicadidae) by imitating the species-specific wing-flick replies of sexually receptive female cicadas. This aggressive mimicry is accomplished both acoustically, with tegminal clicks, and visually, with synchronized body jerks. Remarkably, the katydids respond effectively to a variety of complex, species-specific Cicadettini songs, including songs of many cicada species that the predator has never encountered. Conclusions/Significance We propose that the versatility of aggressive mimicry in C. leucoviridis is accomplished by exploiting general design elements common to the songs of many acoustically signaling insects that use duets in pair-formation. Consideration of the mechanism of versatile mimicry in C. leucoviridis may illuminate processes driving the evolution of insect acoustic signals, which play a central role in reproductive isolation of populations and the formation of species. PMID:19142230

Comparison of transmission of Papaya leaf curl China virus among four cryptic species of the whitefly Bemisia tabaci complex.

PubMed

Guo, Tao; Guo, Qi; Cui, Xi-Yun; Liu, Yin-Quan; Hu, Jian; Liu, Shu-Sheng

2015-10-21

Begomoviruses are transmitted by cryptic species of the whitefly Bemisia tabaci complex, often in a species-specific manner. Papaya leaf curl China virus (PaLCuCNV) has been recorded to infect several crops including papaya, tomato and tobacco in China. To help assess the risks of spread of this virus, we compared the acquisition, retention and transmission of PaLCuCNV among four species of whiteflies, Middle East-Asia Minor 1 (MEAM1), Mediterranean (MED), Asia 1 and Asia II 7. All four species of whiteflies are able to acquire, retain and transmit the virus, but with different levels of efficiency. Transmission tests using tomato as the host plant showed that MEAM1 transmitted PaLCuCNV with substantially higher efficiency than did MED, Asia 1 and Asia II 7. Furthermore, accumulation of PaLCuCNV in the whiteflies was positively associated with its efficiency of transmitting the virus. Altogether, these findings indicate that MEAM1 is the most efficient vector for PaLCuCNV in the four species of whiteflies, and suggest that risks of PaLCuCNV pandemics are high in regions where MEAM1 occurs.

Continental Drift and Speciation of the Cryptococcus neoformans and Cryptococcus gattii Species Complexes

PubMed Central

Freij, Joudeh B.; Hann-Soden, Christopher; Taylor, John

2017-01-01

ABSTRACT Genomic analysis has placed the origins of two human-pathogenic fungi, the Cryptococcus gattii species complex and the Cryptococcus neoformans species complex, in South America and Africa, respectively. Molecular clock calculations suggest that the two species separated ~80 to 100 million years ago. This time closely approximates the breakup of the supercontinent Pangea, which gave rise to South America and Africa. On the basis of the geographic distribution of these two species complexes and the coincidence of the evolutionary divergence and Pangea breakup times, we propose that a spatial separation caused by continental drift resulted in the emergence of the C. gattii and C. neoformans species complexes from a Pangean ancestor. We note that, despite the spatial and temporal separation that occurred approximately 100 million years ago, these two species complexes are morphologically similar, share virulence factors, and cause very similar diseases. Continuation of these phenotypic characteristics despite ancient separation suggests the maintenance of similar selection pressures throughout geologic ages. PMID:28435888

Continental Drift and Speciation of the Cryptococcus neoformans and Cryptococcus gattii Species Complexes.

PubMed

Casadevall, Arturo; Freij, Joudeh B; Hann-Soden, Christopher; Taylor, John

2017-01-01

Genomic analysis has placed the origins of two human-pathogenic fungi, the Cryptococcus gattii species complex and the Cryptococcus neoformans species complex, in South America and Africa, respectively. Molecular clock calculations suggest that the two species separated ~80 to 100 million years ago. This time closely approximates the breakup of the supercontinent Pangea, which gave rise to South America and Africa. On the basis of the geographic distribution of these two species complexes and the coincidence of the evolutionary divergence and Pangea breakup times, we propose that a spatial separation caused by continental drift resulted in the emergence of the C. gattii and C. neoformans species complexes from a Pangean ancestor. We note that, despite the spatial and temporal separation that occurred approximately 100 million years ago, these two species complexes are morphologically similar, share virulence factors, and cause very similar diseases. Continuation of these phenotypic characteristics despite ancient separation suggests the maintenance of similar selection pressures throughout geologic ages.

A re-assessment of species diversity within the 'revolutum' group of Echinostoma Rudolphi, 1809 (Digenea: Echinostomatidae) in Europe.

PubMed

Faltýnková, Anna; Georgieva, Simona; Soldánová, Miroslava; Kostadinova, Aneta

2015-01-01

Species of Echinostoma Rudolphi, 1809 (Digenea: Echinostomatidae) belonging to the 'revolutum' species complex were re-examined based on material gathered in an extensive sampling programme in eight countries in Europe. The morphology of the life-cycle stages was studied in naturally and experimentally infected snail and bird hosts. A review, with an updated synonymy, is presented for six European species, including one new to science, i.e. Echinostoma revolutum (Frölich, 1802) (sensu stricto) (type-species), E. bolschewense (Kotova, 1939), E. miyagawai Ishii, 1932, E. nasincovae n. sp., E. paraulum Dietz, 1909 and Echinostoma sp. IG), and keys to the identification of their cercariae and adults are provided.

The Scirtothrips dorsalis Species Complex: Endemism and Invasion in a Global Pest

PubMed Central

Dickey, Aaron M.; Kumar, Vivek; Hoddle, Mark S.; Funderburk, Joe E.; Morgan, J. Kent; Jara-Cavieres, Antonella; Shatters, Robert G. Jr.; Osborne, Lance S.; McKenzie, Cindy L.

2015-01-01

Invasive arthropods pose unique management challenges in various environments, the first of which is correct identification. This apparently mundane task is particularly difficult if multiple species are morphologically indistinguishable but accurate identification can be determined with DNA barcoding provided an adequate reference set is available. Scirtothrips dorsalis is a highly polyphagous plant pest with a rapidly expanding global distribution and this species, as currently recognized, may be comprised of cryptic species. Here we report the development of a comprehensive DNA barcode library for S. dorsalis and seven nuclear markers via next-generation sequencing for identification use within the complex. We also report the delimitation of nine cryptic species and two morphologically distinguishable species comprising the S. dorsalis species complex using histogram analysis of DNA barcodes, Bayesian phylogenetics, and the multi-species coalescent. One member of the complex, here designated the South Asia 1 cryptic species, is highly invasive, polyphagous, and likely the species implicated in tospovirus transmission. Two other species, South Asia 2, and East Asia 1 are also highly polyphagous and appear to be at an earlier stage of global invasion. The remaining members of the complex are regionally endemic, varying in their pest status and degree of polyphagy. In addition to patterns of invasion and endemism, our results provide a framework both for identifying members of the complex based on their DNA barcode, and for future species delimiting efforts. PMID:25893251

Urban habitat complexity affects species richness but not environmental filtering of morphologically-diverse ants

PubMed Central

Nash, Michael A.; Christie, Fiona J.; Hahs, Amy K.; Livesley, Stephen J.

2015-01-01

Habitat complexity is a major determinant of structure and diversity of ant assemblages. Following the size-grain hypothesis, smaller ant species are likely to be advantaged in more complex habitats compared to larger species. Habitat complexity can act as an environmental filter based on species size and morphological traits, therefore affecting the overall structure and diversity of ant assemblages. In natural and semi-natural ecosystems, habitat complexity is principally regulated by ecological successions or disturbance such as fire and grazing. Urban ecosystems provide an opportunity to test relationships between habitat, ant assemblage structure and ant traits using novel combinations of habitat complexity generated and sustained by human management. We sampled ant assemblages in low-complexity and high-complexity parks, and high-complexity woodland remnants, hypothesizing that (i) ant abundance and species richness would be higher in high-complexity urban habitats, (ii) ant assemblages would differ between low- and high-complexity habitats and (iii) ants living in high-complexity habitats would be smaller than those living in low-complexity habitats. Contrary to our hypothesis, ant species richness was higher in low-complexity habitats compared to high-complexity habitats. Overall, ant assemblages were significantly different among the habitat complexity types investigated, although ant size and morphology remained the same. Habitat complexity appears to affect the structure of ant assemblages in urban ecosystems as previously observed in natural and semi-natural ecosystems. However, the habitat complexity filter does not seem to be linked to ant morphological traits related to body size. PMID:26528416

Complex life cycles in a pond food web: effects of life stage structure and parasites on network properties, trophic positions and the fit of a probabilistic niche model.

PubMed

Preston, Daniel L; Jacobs, Abigail Z; Orlofske, Sarah A; Johnson, Pieter T J

2014-03-01

Most food webs use taxonomic or trophic species as building blocks, thereby collapsing variability in feeding linkages that occurs during the growth and development of individuals. This issue is particularly relevant to integrating parasites into food webs because parasites often undergo extreme ontogenetic niche shifts. Here, we used three versions of a freshwater pond food web with varying levels of node resolution (from taxonomic species to life stages) to examine how complex life cycles and parasites alter web properties, the perceived trophic position of organisms, and the fit of a probabilistic niche model. Consistent with prior studies, parasites increased most measures of web complexity in the taxonomic species web; however, when nodes were disaggregated into life stages, the effects of parasites on several network properties (e.g., connectance and nestedness) were reversed, due in part to the lower trophic generality of parasite life stages relative to free-living life stages. Disaggregation also reduced the trophic level of organisms with either complex or direct life cycles and was particularly useful when including predation on parasites, which can inflate trophic positions when life stages are collapsed. Contrary to predictions, disaggregation decreased network intervality and did not enhance the fit of a probabilistic niche model to the food webs with parasites. Although the most useful level of biological organization in food webs will vary with the questions of interest, our results suggest that disaggregating species-level nodes may refine our perception of how parasites and other complex life cycle organisms influence ecological networks.

Multidrug-resistant Fusarium in keratitis: a clinico-mycological study of keratitis infections in Chennai, India.

PubMed

Tupaki-Sreepurna, Ananya; Al-Hatmi, Abdullah M S; Kindo, Anupma J; Sundaram, Murugan; de Hoog, G Sybren

2017-04-01

In this study, we aimed to present the first molecular epidemiological data from Chennai, India, analyse keratitis cases that have been monitored in a university hospital during 2 years, identify the responsible Fusarium species and determine antifungal susceptibilities. A total of 10 cases of keratitis were included in the study. Fusarium isolates were identified using the second largest subunit of the RNA polymerase gene (RPB2) and the translation elongation factor 1 alpha (TEF1). Antifungal susceptibility was tested by the broth microdilution method according to the Clinical and Laboratory Standards Institute (CLSI) methodology. The aetiological agents belonged to Fusarium solani species complex (FSSC) (n = 9) and Fusarium sambucinum species complex (FSAMSC) (n = 1), and the identified species were Fusarium keratoplasticum (n = 7), Fusarium falciforme (n = 2) and Fusarium sporotrichioides (n = 1). All strains showed multidrug resistance to azoles and caspofungin but exhibited lower minimum inhibitory concentration (MIC) to natamycin and amphotericin B. Fusarium keratoplasticum and Fusarium falciforme belonging to the Fusarium solani species complex were the major aetiological agents of Fusarium keratitis in this study. Early presentation and 5% topical natamycin was associated with better patient outcome. Preventative measures and monitoring of local epidemiological data play an important role in clinical practice. © 2016 Blackwell Verlag GmbH.

The economic origins of ultrasociality.

PubMed

Gowdy, John; Krall, Lisi

2016-01-01

Ultrasociality refers to the social organization of a few species, including humans and some social insects, having a complex division of labor, city-states, and an almost exclusive dependence on agriculture for subsistence. We argue that the driving forces in the evolution of these ultrasocial societies were economic. With the agricultural transition, species could directly produce their own food and this was such a competitive advantage that those species now dominate the planet. Once underway, this transition was propelled by the selection of within-species groups that could best capture the advantages of (1) actively managing the inputs to food production, (2) a more complex division of labor, and (3) increasing returns to larger scale and larger group size. Together these factors reoriented productive life and radically altered the structure of these societies. Once agriculture began, populations expanded as these economic drivers opened up new opportunities for the exploitation of resources and the active management of inputs to food production. With intensified group-level competition, larger populations and intensive resource exploitation became competitive advantages, and the "social conquest of Earth" was underway. Ultrasocial species came to dominate the earth's ecosystems. Ultrasociality also brought a loss of autonomy for individuals within the group. We argue that exploring the common causes and consequences of ultrasociality in humans and the social insects that adopted agriculture can provide fruitful insights into the evolution of complex human society.

Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae).

PubMed

Garrigos, Yareli Esquer; Hugueny, Bernard; Koerner, Kellie; Ibañez, Carla; Bonillo, Celine; Pruvost, Patrice; Causse, Romain; Cruaud, Corinne; Gaubert, Philippe

2013-01-01

Specimens stored in museum collections represent a crucial source of morphological and genetic information, notably for taxonomically problematic groups and extinct taxa. Although fluid-preserved specimens of groups such as teleosts may constitute an almost infinite source of DNA, few ancient DNA protocols have been applied to such material. In this study, we describe a non-invasive Guanidine-based (GuSCN) ancient DNA extraction protocol adapted to fluid-preserved specimens that we use to re-assess the systematics of the genus Orestias (Cyprinodontidae: Teleostei). The latter regroups pupfishes endemic to the inter-Andean basin that have been considered as a 'species flock', and for which the morphology-based taxonomic delimitations have been hotly debated. We extracted DNA from the type specimens of Orestias kept at the Muséum National d'Histoire Naturelle of Paris, France, including the extinct species O. cuvieri. We then built the first molecular (control region [CR] and rhodopsin [RH]) phylogeny including historical and recently collected representatives of all the Orestias complexes as recognized by Parenti (1984a): agassizii, cuvieri, gilsoni and mulleri. Our ancient DNA extraction protocol was validated after PCR amplification through an approach based on fragment-by-fragment chimera detection. After optimization, we were able to amplify < 200 bp fragments from both mitochondrial and nuclear DNA (CR and RH, respectively) from probably formalin-fixed type specimens bathed entirely in the extraction fluid. Most of the individuals exhibited few modifications of their external structures after GuSCN bath. Our approach combining type material and 'fresh' specimens allowed us to taxonomically delineate four clades recovered from the well-resolved CR tree into four redefined complexes: agassizii (sensu stricto, i.e. excluding luteus-like species), luteus, cuvieri and gilsoni. The mulleri complex is polyphyletic. Our phylogenetic analyses based on both mitochondrial and nuclear DNA revealed a main, deep dichotomy within the genus Orestias, separating the agassizii complex from a clade grouped under shallow dichotomies as (luteus, (cuvieri, gilsoni)). This 'deep and shallow' diversification pattern could fit within a scenario of ancient divergence between the agassizii complex and the rest of Orestias, followed by a recent diversification or adaptive radiation within each complex during the Pleistocene, in- and outside the Lake Titicaca. We could not recover the reciprocal monophyly of any of the 15 species or morphotypes that were considered in our analyses, possibly due to incomplete lineage sorting and/or hybridization events. As a consequence, our results starkly question the delineation of a series of diagnostic characters listed in the literature for Orestias. Although not included in our phylogenetic analysis, the syntype of O. jussiei could not be assigned to the agassizii complex as newly defined. The CR sequence of the extinct O. cuvieri was recovered within the cuvieri clade (same haplotype as one representative of O. pentlandii), so the mtDNA of the former species might still be represented in the wild.

Changing Names with Changed Address: Integrated Taxonomy and Species Delimitation in the Holarctic Colymbetes paykulli Group (Coleoptera: Dytiscidae)

PubMed Central

Drotz, Marcus K.; Brodin, Tomas; Nilsson, Anders N.

2015-01-01

Species delimitation of geographically isolated forms is a long-standing problem in less studied insect groups. Often taxonomic decisions are based directly on morphologic variation, and lack a discussion regarding sample size and the efficiency of migration barriers or dispersal/migration capacity of the studied species. These problems are here exemplified in a water beetle complex from the Bering Sea region that separates North America from Eurasia. Only a few sampled specimens occur from this particular area and they are mostly found in museum and private collections. Here we utilize the theory of integrated taxonomy to discuss the speciation of the Holarctic Colymbetes paykulli water beetle complex, which historically has included up to five species of which today only two are recognized. Three delimitation methods are used; landmark based morphometry of body shape, variation in reticulation patterns of the pronotum exo-skeleton and sequence variation of the partial mitochondrial gene Cyt b. Our conclusion is that the Palearctic and Nearctic populations of C. paykulli are given the status of separate species, based on the fact that all methods showed significant separation between populations. As a consequence the name of the Palearctic species is C. paykulli Erichson and the Nearctic species should be known as C. longulus LeConte. There is no clear support for delineation between Palearctic and Nearctic populations of C. dahuricus based on mtDNA. However, significant difference in size and reticulation patterns from the two regions is shown. The combined conclusion is that the C. dahuricus complex needs a more thorough investigation to fully disentangle its taxonomic status. Therefore it is here still regarded as a Holarctic species. This study highlights the importance to study several diagnosable characters that has the potential to discriminate evolutionary lineage during speciation. PMID:26619278

Species richness and variety of life in Arizona’s ponderosa pine forest type

Treesearch

David R. Patton; Richard W. Hofstetter; John D. Bailey; Mary Ann Benoit

2014-01-01

Species richness (SR) is a tool that managers can use to include diversity in planning and decision-making and is a convenient and useful way to characterize the first level of biological diversity. A richness list derived from existing inventories enhances a manager’s understanding of the complexity of the plant and animal communities they manage. Without a list of...

Fungal pathogen (mis-) identifications: a case study with DNA barcodes on Melampsora rusts of aspen and white poplar.

PubMed

Feau, Nicolas; Vialle, Agathe; Allaire, Mathieu; Tanguay, Philippe; Joly, David L; Frey, Pascal; Callan, Brenda E; Hamelin, Richard C

2009-01-01

Wide variation and overlap in morphological characters have led to confusion in species identification within the fungal rust genus Melampsora. The Melampsora species with uredinial-telial stages on white poplar and aspens are especially prone to misidentification. This group includes the Melampsora populnea species complex and the highly destructive pine twisting rust, Melampsora pinitorqua, which alternates between hosts in Populus section Populus and Pinus. Our objective was to compare morphologically based identification to genetic material extracted from Melampsora species pathogenic to aspen and white poplar. We compared morphometric traits and DNA barcodes obtained from internal transcribed spacer (ITS), large ribosomal RNA subunit (28S), and mitochondrial cytochrome oxidase 1 (CO1) sequences to delimit within this taxonomically difficult group. Eight different Melampsora species were initially defined based on host specificity and morphometric data. DNA barcodes were then overlaid on these initial species definitions. The DNA barcodes, specifically those defined on ITS and 28S sequences, provided a highly accurate means of identifying and resolving Melampsora taxa. We highlighted species misidentification in specimens from Canadian herbaria related to either Melampsora medusae f. sp. tremuloidae or Melampsora aecidioides. Finally, we evidenced that the north-American species found on Populus alba, M. aecidioides is closely related but distinct from the four species of the M. populnea complex (Melampsora larici-tremulae, Melampsora magnusiana, Melampsora pinitorqua, and Melampsora rostrupii) found in Eurasia.

Molecular screening of 246 Portuguese Aspergillus isolates among different clinical and environmental sources.

PubMed

Sabino, Raquel; Veríssimo, Cristina; Parada, Helena; Brandão, João; Viegas, Carla; Carolino, Elisabete; Clemons, Karl V; Stevens, David A

2014-07-01

Clinical and environmental samples from Portugal were screened for the presence of Aspergillus and the distributions of the species complexes were determined in order to understand how their distributions differ based on their source. Fifty-seven Aspergillus isolates from clinical samples were collected from 10 health institutions. Six species complexes were detected by internal transcribed spacer sequencing; Fumigati, Flavi, and Nigri were found most frequently (50.9%, 21.0%, and 15.8%, respectively). β-tubulin and calmodulin sequencing resulted in seven cryptic species (A. awamorii, A. brasiliensis, A. fructus, A. lentulus, A. sydowii, A. tubingensis, Emericella echinulata) being identified among the 57 isolates. Thirty-nine isolates of Aspergillus were recovered from beach sand and poultry farms, 31 from swine farms, and 80 from hospital environments, for a total 189 isolates. Eleven species complexes were found in these 189 isolates, and those belonging to the Versicolores species complex were found most frequently (23.8%). There was a significant association between the different environmental sources and distribution of the species complexes; the hospital environment had greater variability of species complexes than other environmental locations. A high prevalence of cryptic species within the Circumdati complex was detected in several environments; from the isolates analyzed, at least four cryptic species were identified, most of them growing at 37ºC. Because Aspergillus species complexes have different susceptibilities to antifungals, knowing the species-complex epidemiology for each setting, as well as the identification of cryptic species among the collected clinical isolates, is important. This may allow preventive and corrective measures to be taken, which may result in decreased exposure to those organisms and a better prognosis. © The Author 2014. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

MICOBACTERIUM PARATUBERCULOSIS AND NONTUBERCULOUS MYCOBACTERIAL IN POTABLE WATER

EPA Science Inventory

Nontuberculous mycobacteria (NTM) include Mycobacterium species that are not members of the Mycobacterium tuberculosis Complex. Members of the NTM group are important causes of disease in birds and mammals. Mycobacterium avium, Mycobacterium intracellulare and Mycobacterium parat...

Lactobacillus species: taxonomic complexity and controversial susceptibilities.

PubMed

Goldstein, Ellie J C; Tyrrell, Kerin L; Citron, Diane M

2015-05-15

The genus Lactobacillus is a taxonomically complex and is composed of over 170 species that cannot be easily differentiated phenotypically and often require molecular identification. Although they are part of the normal human gastrointestinal and vaginal flora, they can also be occasional human pathogens. They are extensively used in a variety of commercial products including probiotics. Their antimicrobial susceptibilities are poorly defined in part because of their taxonomic complexity and are compounded by the different methods recommended by Clinical Laboratory Standards Institute and International Dairy Foundation. Their use as probiotics for prevention of Clostridium difficile infection is prevalent among consumers worldwide but raises the question of will the use of any concurrent antibiotic effect their ability to survive. Lactobacillus species are generally acid resistant and are able to survive ingestion. They are generally resistant to metronidazole, aminoglycosides and ciprofloxacin with L. acidophilus being susceptible to penicillin and vancomycin, whereas L. rhamnosus and L. casei are resistant to metronidazole and vancomycin. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Time-resolved EPR study on the photoexcited triplet state of the electron-donor-acceptor complex formed in the system of fac-tris[2-(4-octyl-phenyl) pyridine] iridium(III) and tetracene.

PubMed

Zhebin, Fu; Shuhei, Yoshioka; Hisao, Murai

2014-01-09

The physical properties of the phosphorescent organic light-emitting diode material fac-tris(phenylpyridine) iridium(III), Ir(ppy)3, have been reported with experimental and theoretical studies. Here, the photochemical properties of the excited triplet state of partially modified fac-tris[2-(4-octyl-phenyl) pyridine] iridium(III), Ir(C8ppy)3, were investigated using time-resolved electron paramagnetic resonance (tr-EPR) and optical methods by adding tetracene in the toluene solution. The tr-EPR observation at 77 K revealed the following two species: the excited triplet state of tetracene and another triplet species with zero field splitting parameters of |D| = 0.088 cm(-1) and |E| = 0.018 cm(-1) with characteristic spin polarization. The latter species was assigned to the electron-donor-acceptor (EDA) complex formed between Ir(C8ppy)3 and tetracene. The mechanism of formation and the properties of this EDA complex, including the information on the principal axes of (3)Ir(C8ppy)3*, are discussed.

The interplay of cognition and cooperation

PubMed Central

Brosnan, Sarah F.; Salwiczek, Lucie; Bshary, Redouan

2010-01-01

Cooperation often involves behaviours that reduce immediate payoffs for actors. Delayed benefits have often been argued to pose problems for the evolution of cooperation because learning such contingencies may be difficult as partners may cheat in return. Therefore, the ability to achieve stable cooperation has often been linked to a species' cognitive abilities, which is in turn linked to the evolution of increasingly complex central nervous systems. However, in their famous 1981 paper, Axelrod and Hamilton stated that in principle even bacteria could play a tit-for-tat strategy in an iterated Prisoner's Dilemma. While to our knowledge this has not been documented, interspecific mutualisms are present in bacteria, plants and fungi. Moreover, many species which have evolved large brains in complex social environments lack convincing evidence in favour of reciprocity. What conditions must be fulfilled so that organisms with little to no brainpower, including plants and single-celled organisms, can, on average, gain benefits from interactions with partner species? On the other hand, what conditions favour the evolution of large brains and flexible behaviour, which includes the use of misinformation and so on? These questions are critical, as they begin to address why cognitive complexity would emerge when ‘simple’ cooperation is clearly sufficient in some cases. This paper spans the literature from bacteria to humans in our search for the key variables that link cooperation and deception to cognition. PMID:20679113

Cryptic lineage diversity, body size divergence, and sympatry in a species complex of Australian lizards (Gehyra).

PubMed

Moritz, Craig C; Pratt, Renae C; Bank, Sarah; Bourke, Gayleen; Bragg, Jason G; Doughty, Paul; Keogh, J Scott; Laver, Rebecca J; Potter, Sally; Teasdale, Luisa C; Tedeschi, Leonardo G; Oliver, Paul M

2018-01-01

Understanding the joint evolutionary and ecological underpinnings of sympatry among close relatives remains a key challenge in biology. This problem can be addressed through joint phylogenomic and phenotypic analysis of complexes of closely related lineages within, and across, species and hence representing the speciation continuum. For a complex of tropical geckos from northern Australia-Gehyra nana and close relatives-we combine mtDNA phylogeography, exon-capture sequencing, and morphological data to resolve independently evolving lineages and infer their divergence history and patterns of morphological evolution. Gehyra nana is found to include nine divergent lineages and is paraphyletic with four other species from the Kimberley region of north-west Australia. Across these 13 taxa, 12 of which are restricted to rocky habitats, several lineages overlap geographically, including on the diverse Kimberley islands. Morphological evolution is dominated by body size shifts, and both body size and shape have evolved gradually across the group. However, larger body size shifts are observed among overlapping taxa than among closely related parapatric lineages of G. nana, and sympatric lineages are more divergent than expected at random. Whether elevated body size differences among sympatric lineages are due to ecological sorting or character displacement remains to be determined. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Bacterial biodiversity-ecosystem functioning relations are modified by environmental complexity.

PubMed

Langenheder, Silke; Bulling, Mark T; Solan, Martin; Prosser, James I

2010-05-26

With the recognition that environmental change resulting from anthropogenic activities is causing a global decline in biodiversity, much attention has been devoted to understanding how changes in biodiversity may alter levels of ecosystem functioning. Although environmental complexity has long been recognised as a major driving force in evolutionary processes, it has only recently been incorporated into biodiversity-ecosystem functioning investigations. Environmental complexity is expected to strengthen the positive effect of species richness on ecosystem functioning, mainly because it leads to stronger complementarity effects, such as resource partitioning and facilitative interactions among species when the number of available resource increases. Here we implemented an experiment to test the combined effect of species richness and environmental complexity, more specifically, resource richness on ecosystem functioning over time. We show, using all possible combinations of species within a bacterial community consisting of six species, and all possible combinations of three substrates, that diversity-functioning (metabolic activity) relationships change over time from linear to saturated. This was probably caused by a combination of limited complementarity effects and negative interactions among competing species as the experiment progressed. Even though species richness and resource richness both enhanced ecosystem functioning, they did so independently from each other. Instead there were complex interactions between particular species and substrate combinations. Our study shows clearly that both species richness and environmental complexity increase ecosystem functioning. The finding that there was no direct interaction between these two factors, but that instead rather complex interactions between combinations of certain species and resources underlie positive biodiversity ecosystem functioning relationships, suggests that detailed knowledge of how individual species interact with complex natural environments will be required in order to make reliable predictions about how altered levels of biodiversity will most likely affect ecosystem functioning.

Bacterial Biodiversity-Ecosystem Functioning Relations Are Modified by Environmental Complexity

PubMed Central

Langenheder, Silke; Bulling, Mark T.; Solan, Martin; Prosser, James I.

2010-01-01

Background With the recognition that environmental change resulting from anthropogenic activities is causing a global decline in biodiversity, much attention has been devoted to understanding how changes in biodiversity may alter levels of ecosystem functioning. Although environmental complexity has long been recognised as a major driving force in evolutionary processes, it has only recently been incorporated into biodiversity-ecosystem functioning investigations. Environmental complexity is expected to strengthen the positive effect of species richness on ecosystem functioning, mainly because it leads to stronger complementarity effects, such as resource partitioning and facilitative interactions among species when the number of available resource increases. Methodology/Principal Findings Here we implemented an experiment to test the combined effect of species richness and environmental complexity, more specifically, resource richness on ecosystem functioning over time. We show, using all possible combinations of species within a bacterial community consisting of six species, and all possible combinations of three substrates, that diversity-functioning (metabolic activity) relationships change over time from linear to saturated. This was probably caused by a combination of limited complementarity effects and negative interactions among competing species as the experiment progressed. Even though species richness and resource richness both enhanced ecosystem functioning, they did so independently from each other. Instead there were complex interactions between particular species and substrate combinations. Conclusions/Significance Our study shows clearly that both species richness and environmental complexity increase ecosystem functioning. The finding that there was no direct interaction between these two factors, but that instead rather complex interactions between combinations of certain species and resources underlie positive biodiversity ecosystem functioning relationships, suggests that detailed knowledge of how individual species interact with complex natural environments will be required in order to make reliable predictions about how altered levels of biodiversity will most likely affect ecosystem functioning. PMID:20520808

Food-web complexity across hydrothermal vents on the Azores triple junction

NASA Astrophysics Data System (ADS)

Portail, Marie; Brandily, Christophe; Cathalot, Cécile; Colaço, Ana; Gélinas, Yves; Husson, Bérengère; Sarradin, Pierre-Marie; Sarrazin, Jozée

2018-01-01

The assessment and comparison of food webs across various hydrothermal vent sites can enhance our understanding of ecological processes involved in the structure and function of biodiversity. The Menez Gwen, Lucky Strike and Rainbow vent fields are located on the Azores triple junction of the Mid-Atlantic Ridge. These fields have distinct depths (from 850 to 2320 m) and geological contexts (basaltic and ultramafic), but share similar faunal assemblages defined by the presence of foundation species that include Bathymodiolus azoricus, alvinocarid shrimp and gastropods. We compared the food webs of 13 faunal assemblages at these three sites using carbon and nitrogen stable isotope analyses (SIA). Results showed that photosynthesis-derived organic matter is a negligible basal source for vent food webs, at all depths. The contribution of methanotrophy versus autotrophy based on Calvin-Benson-Bassham (CBB) or reductive tricarboxylic acid (rTCA) cycles varied between and within vent fields according to the concentrations of reduced compounds (e.g. CH4, H2S). Species that were common to vent fields showed high trophic flexibility, suggesting weak trophic links to the metabolism of chemosynthetic primary producers. At the community level, a comparison of SIA-derived metrics between mussel assemblages from two vent fields (Menez Gwen & Lucky Strike) showed that the functional structure of food webs was highly similar in terms of basal niche diversification, functional specialization and redundancy. Coupling SIA to functional trait approaches included more variability within the analyses, but the functional structures were still highly comparable. These results suggest that despite variable environmental conditions (physico-chemical factors and basal sources) and faunal community structure, functional complexity remained relatively constant among mussel assemblages. This functional similarity may be favoured by the propensity of species to adapt to fluid variations and practise trophic flexibility. Furthermore, the different pools of species at vent fields may play similar functions in the community such as the change in composition does not affect the overall functional structure. Finally, the absence of a relationship between the functional structure and taxonomic diversity as well as the high overlap between species' isotopic niches within communities indicates that co-occuring species may have redundant functions. Therefore, the addition of species within in a functional group does not necessarily lead to more complexity. Overall, this study highlights the complexity of food webs within chemosynthetic communities and emphasizes the need to better characterize species' ecological niches and biotic interactions.

Review of the Trifolium amabile Complex in Peru, with the Description of a New Species

PubMed Central

2016-01-01

Here, we describe Trifolium absconditum sp. nov., a new species of the T. amabile complex from South America. It differs from other Peruvian Trifolia of the complex by having smaller stipules, leaves, inflorescences, and floral pieces. A key for Peruvian species of the complex is presented, and typifications for them are made when necessary and material is available in Peruvian herbaria. Thus, the number of Peruvian species in the complex is elevated to three: T. amabile, T. absconditum, and a resurrected T. peruvianum. Finally, it is suggested that Chile must be excluded from the distribution of this complex. PMID:27127681

The Enhancer of split complex arose prior to the diversification of schizophoran flies and is strongly conserved between Drosophila and stalk-eyed flies (Diopsidae)

PubMed Central

2011-01-01

Background In Drosophila, the Enhancer of split complex (E(spl)-C) comprises 11 bHLH and Bearded genes that function during Notch signaling to repress proneural identity in the developing peripheral nervous system. Comparison with other insects indicates that the basal state for Diptera is a single bHLH and Bearded homolog and that the expansion of the gene complex occurred in the lineage leading to Drosophila. However, comparative genomic data from other fly species that would elucidate the origin and sequence of gene duplication for the complex is lacking. Therefore, in order to examine the evolutionary history of the complex within Diptera, we reconstructed, using several fosmid clones, the entire E(spl)-complex in the stalk-eyed fly, Teleopsis dalmanni and collected additional homologs of E(spl)-C genes from searches of dipteran EST databases and the Glossina morsitans genome assembly. Results Comparison of the Teleopsis E(spl)-C gene organization with Drosophila indicates complete conservation in gene number and orientation between the species except that T. dalmanni contains a duplicated copy of E(spl)m5 that is not present in Drosophila. Phylogenetic analysis of E(spl)-complex bHLH and Bearded genes for several dipteran species clearly demonstrates that all members of the complex were present prior to the diversification of schizophoran flies. Comparison of upstream regulatory elements and 3' UTR domains between the species also reveals strong conservation for many of the genes and identifies several novel characteristics of E(spl)-C regulatory evolution including the discovery of a previously unidentified, highly conserved SPS+A domain between E(spl)mγ and E(spl)mβ. Conclusion Identifying the phylogenetic origin of E(spl)-C genes and their associated regulatory DNA is essential to understanding the functional significance of this well-studied gene complex. Results from this study provide numerous insights into the evolutionary history of the complex and will help refine the focus of studies examining the adaptive consequences of this gene expansion. PMID:22151427

Landscape moderation of biodiversity patterns and processes - eight hypotheses.

PubMed

Tscharntke, Teja; Tylianakis, Jason M; Rand, Tatyana A; Didham, Raphael K; Fahrig, Lenore; Batáry, Péter; Bengtsson, Janne; Clough, Yann; Crist, Thomas O; Dormann, Carsten F; Ewers, Robert M; Fründ, Jochen; Holt, Robert D; Holzschuh, Andrea; Klein, Alexandra M; Kleijn, David; Kremen, Claire; Landis, Doug A; Laurance, William; Lindenmayer, David; Scherber, Christoph; Sodhi, Navjot; Steffan-Dewenter, Ingolf; Thies, Carsten; van der Putten, Wim H; Westphal, Catrin

2012-08-01

Understanding how landscape characteristics affect biodiversity patterns and ecological processes at local and landscape scales is critical for mitigating effects of global environmental change. In this review, we use knowledge gained from human-modified landscapes to suggest eight hypotheses, which we hope will encourage more systematic research on the role of landscape composition and configuration in determining the structure of ecological communities, ecosystem functioning and services. We organize the eight hypotheses under four overarching themes. Section A: 'landscape moderation of biodiversity patterns' includes (1) the landscape species pool hypothesis-the size of the landscape-wide species pool moderates local (alpha) biodiversity, and (2) the dominance of beta diversity hypothesis-landscape-moderated dissimilarity of local communities determines landscape-wide biodiversity and overrides negative local effects of habitat fragmentation on biodiversity. Section B: 'landscape moderation of population dynamics' includes (3) the cross-habitat spillover hypothesis-landscape-moderated spillover of energy, resources and organisms across habitats, including between managed and natural ecosystems, influences landscape-wide community structure and associated processes and (4) the landscape-moderated concentration and dilution hypothesis-spatial and temporal changes in landscape composition can cause transient concentration or dilution of populations with functional consequences. Section C: 'landscape moderation of functional trait selection' includes (5) the landscape-moderated functional trait selection hypothesis-landscape moderation of species trait selection shapes the functional role and trajectory of community assembly, and (6) the landscape-moderated insurance hypothesis-landscape complexity provides spatial and temporal insurance, i.e. high resilience and stability of ecological processes in changing environments. Section D: 'landscape constraints on conservation management' includes (7) the intermediate landscape-complexity hypothesis-landscape-moderated effectiveness of local conservation management is highest in structurally simple, rather than in cleared (i.e. extremely simplified) or in complex landscapes, and (8) the landscape-moderated biodiversity versus ecosystem service management hypothesis-landscape-moderated biodiversity conservation to optimize functional diversity and related ecosystem services will not protect endangered species. Shifting our research focus from local to landscape-moderated effects on biodiversity will be critical to developing solutions for future biodiversity and ecosystem service management. © 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society.

The CO-H2 van der Waals complex and complex organic molecules in cold molecular clouds: A TMC-1C survey

NASA Astrophysics Data System (ADS)

Potapov, A.; Sánchez-Monge, Á.; Schilke, P.; Graf, U. U.; Möller, Th.; Schlemmer, S.

2016-10-01

Context. Almost 200 different species have been detected in the interstellar medium (ISM) during the last decades, revealing not only simple species but complex molecules with more than six atoms. Other exotic compounds, like the weakly-bound dimer (H2)2, have also been detected in astronomical sources like Jupiter. Aims: We aim to detect, for the first time, the CO-H2 van der Waals complex in the ISM, which could be a sensitive indicator for low temperatures if detected. Methods: We used the IRAM 30 m telescope, located in Pico Veleta (Spain), to search for the CO-H2 complex in a cold, dense core in TMC-1C (with a temperature of ~10 K). All the brightest CO-H2 transitions in the 3 mm (80-110 GHz) band were observed with a spectral resolution of 0.5-0.7 km s-1, reaching a rms noise level of ~2 mK. The simultaneous observation of a broad frequency band, 16 GHz, allowed us to conduct a serendipitous spectral line survey. Results: We did not detected any lines belonging to the CO-H2 complex. We set up a new, more stringent upper limit for its abundance to be [CO-H2]/[CO] ~ 5 × 10-6, while we expect the abundance of the complex to be in the range ~10-8-10-3. The spectral line survey has allowed us to detect 75 lines associated with 41 different species (including isotopologues). We detect a number of complex organic species, for example methyl cyanide (CH3CN), methanol (CH3OH), propyne (CH3CCH), and ketene (CH2CO), associated with cold gas (excitation temperatures ~7 K), confirming the presence of these complex species not only in warm objects but also in cold regimes. Based on observations carried out with the IRAM 30 m Telescope. IRAM is supported by INSU/CNRS (France), MPG (Germany) and IGN (Spain).Reduced spectra (FITS files) are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/594/A117

A new species of Labidocera (Copepoda, Calanoida, Pontellidae) collected from Okinawa, southwestern Japan, with establishment of five Indo-West Pacific species groups in the L.detruncata species complex.

PubMed

Hirabayashi, Takeshi; Ohtsuka, Susumu

2014-01-01

Labidocerachuraumi sp. n. is described from Okinawa, southwestern Japan. The female of the new species differs from other congeners in genital compound somite with right postero-lateral and left antero-lateral processes. The male is distinguished from other congeners by the structure of the fifth leg. This new species is assigned to a newly proposed species group, the Labidoceramadurae species group, within the Labidoceradetruncata species complex. In this species complex five Indo-West Pacific species groups are recognized (cervi, detruncata, gangetica, madurae, and pavo) and defined on the basis of difference in sexual dimorphism.

Bimetallic d10 -Metal Complexes of a Bipyridine Substituted N-Heterocyclic Carbene.

PubMed

Kaub, Christoph; Lebedkin, Sergei; Li, Alina; Kruppa, Sebastian V; Strebert, Patrick H; Kappes, Manfred M; Riehn, Christoph; Roesky, Peter W

2018-04-20

The hybrid ligand 3-(2,2'-bipyridine-6-ylmethyl)-1-mesityl-1H-imidazolylidene (NHC Bipy ) featuring both carbene and N-donor sites, was selectively complexed with various d 10 metal cations in order to examine its coordination behavior with regard to homo and heterometallic structures. Respective silver complexes can be obtained by the silver oxide route and are suitable transmetallation reagents for the synthesis of gold(I) compounds. Starting from the mononuclear complexes [(NHC Bipy )AuCl], [(NHC Bipy )Au(C 6 F 5 )] and [(NHC Bipy ) 2 Au][ClO 4 ], open-chain as well as cyclic heterobimetallic complexes containing Cu + , Ag + , Zn 2+ , Cd 2+ , and Hg 2+ were synthesized. Furthermore, the homobimetallic species [(NHC Bipy ) 2 M 2 ][ClO 4 ] 2 (M=Cu, Ag) were obtained. All bimetallic compounds were fully characterized including single-crystal X-ray analysis. Their photoluminescence (PL) properties were investigated in the solid state at temperatures between 15 and 295 K and compared with those of the mononuclear species. There is a clear difference in PL properties between the open chain and the cyclic heterobimetallic complexes. The latter species show different PL properties, depending on the metals involved. In addition, collision-induced dissociation (CID) experiments were performed on electrosprayed cations of the cyclic heterobimetallic compounds, to compare the metal binding at the carbene and N-donor sites. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pseudotetrahedral manganese complexes supported by the anionic tris(phosphino)borate ligand [PhBPiPr3

PubMed Central

Lu, Connie C.; Peters, Jonas C.

2008-01-01

This paper presents aspects of the coordination chemistry of mono- and divalent manganese complexes supported by the anionic tris(phosphino)borate ligand, [PhBPiPr3] (where [PhBPiPr3] = [PhB(CH2PiPr2)3]−). The Mn(II) halide complexes, [PhBPiPr3]MnCl (1 and [PhBPiPr3]MnI (2), have been characterized by X-ray diffraction, SQUID magnetometry, and EPR spectroscopy. Compound 2 serves as a precursor to a series of Mn azide, alkyl, and amide species: [PhBPiPr3]Mn(N3) (3), [PhBPiPr3]Mn(CH2Ph) (4), [PhBPiPr3]Mn(Me) (5), [PhBPiPr3]Mn(NH(2,6-iPr2-C6H3)) (6), [PhBPiPr3]Mn(dbabh) (7), and [PhBPiPr3]Mn(1-Ph(isoindolate)) (8). The complexes 2 – 8 feature a divalent-metal center and are pseudotetrahedral. They collectively represent an uncommon structural motif for low-coordinate, polyphosphine-supported Mn complexes. Two Mn(I) species have also been prepared. These include the Tl-Mn adduct, [PhBPiPr3]Tl-MnBr(CO)4 (9), and the octahedral complex [PhBPiPr3]Mn(CNtBu)3 (10). Some of our initial synthetic efforts to generate [PhBPiPr3]Mn≡Nx species are briefly described, as are DFT studies that probe the electronic viability of these types of multiply bonded target structures. PMID:17029370

[Evaluation of ten fish species to be included as part of renal diet, due to their protein, phosphorus and fatty acids content].

PubMed

Castro-González, Maria Isabel; Maafs-Rodríguez, Ana Gabriela; Pérez-Gil Romo, Fernando

2012-06-01

Because renal disease is highly complex, its nutritional treatment is complicated and many foods are restricted, including fish because its phosphorus content. The aim of the present study was to analyze ten fillet fish species, commonly consumed in Mexico (Cyprinus carpio carpio, Ophichthus rex, Symphurus elongatus, Eucinostomus entomelas, Chirostoma patzcuaro, Bairdiella chrysoura, Salmo salar Oreochromis urolepis hornorum, Sphyraena guachancho, Istiophorus albicans), to determine their phosphorus (P), protein (Pr), cholesterol, sodium, potassium, vitamins D3 and E, and n-3 PUFA (EPA+DHA) according to the AOAC techniques, in order to identify which species could be included in renal diet; particularly because of their risk:benefit relations (calculated with those results). Protein values ranged from 16.5 to 33.5g/100 g of fillet; the specie with the highest phosphorus contest was Salmo salar, and with the lowest, Symphurus elongatus. EPA+DHA quantity ranged from 79.64 mg/100 g to 1,381.53 mg/100 g. Considering de P/Pr relation recommended to renal patients, all analyzed species (except Salmo salar, Ophichthus rex and Istiophorus albicans) could be included in their diet. As for the P/EPA+DHA relation, the species most recommended to renal patients are Symphurus elongatus, Bairdiella chrysoura and Sphyraena guachancho.

Co-Option and De Novo Gene Evolution Underlie Molluscan Shell Diversity

PubMed Central

Aguilera, Felipe; McDougall, Carmel

2017-01-01

Abstract Molluscs fabricate shells of incredible diversity and complexity by localized secretions from the dorsal epithelium of the mantle. Although distantly related molluscs express remarkably different secreted gene products, it remains unclear if the evolution of shell structure and pattern is underpinned by the differential co-option of conserved genes or the integration of lineage-specific genes into the mantle regulatory program. To address this, we compare the mantle transcriptomes of 11 bivalves and gastropods of varying relatedness. We find that each species, including four Pinctada (pearl oyster) species that diverged within the last 20 Ma, expresses a unique mantle secretome. Lineage- or species-specific genes comprise a large proportion of each species’ mantle secretome. A majority of these secreted proteins have unique domain architectures that include repetitive, low complexity domains (RLCDs), which evolve rapidly, and have a proclivity to expand, contract and rearrange in the genome. There are also a large number of secretome genes expressed in the mantle that arose before the origin of gastropods and bivalves. Each species expresses a unique set of these more ancient genes consistent with their independent co-option into these mantle gene regulatory networks. From this analysis, we infer lineage-specific secretomes underlie shell diversity, and include both rapidly evolving RLCD-containing proteins, and the continual recruitment and loss of both ancient and recently evolved genes into the periphery of the regulatory network controlling gene expression in the mantle epithelium. PMID:28053006

Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks.

PubMed

Kim, Inhae; Lee, Heetak; Han, Seong Kyu; Kim, Sanguk

2014-10-01

The modular architecture of protein-protein interaction (PPI) networks is evident in diverse species with a wide range of complexity. However, the molecular components that lead to the evolution of modularity in PPI networks have not been clearly identified. Here, we show that weak domain-linear motif interactions (DLIs) are more likely to connect different biological modules than strong domain-domain interactions (DDIs). This molecular division of labor is essential for the evolution of modularity in the complex PPI networks of diverse eukaryotic species. In particular, DLIs may compensate for the reduction in module boundaries that originate from increased connections between different modules in complex PPI networks. In addition, we show that the identification of biological modules can be greatly improved by including molecular characteristics of protein interactions. Our findings suggest that transient interactions have played a unique role in shaping the architecture and modularity of biological networks over the course of evolution.

Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri

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

Prochnik, Simon E.; Umen, James; Nedelcu, Aurora

2010-07-01

Analysis of the Volvox carteri genome reveals that this green alga's increased organismal complexity and multicellularity are associated with modifications in protein families shared with its unicellular ancestor, and not with large-scale innovations in protein coding capacity. The multicellular green alga Volvox carteri and its morphologically diverse close relatives (the volvocine algae) are uniquely suited for investigating the evolution of multicellularity and development. We sequenced the 138 Mb genome of V. carteri and compared its {approx}14,500 predicted proteins to those of its unicellular relative, Chlamydomonas reinhardtii. Despite fundamental differences in organismal complexity and life history, the two species have similarmore » protein-coding potentials, and few species-specific protein-coding gene predictions. Interestingly, volvocine algal-specific proteins are enriched in Volvox, including those associated with an expanded and highly compartmentalized extracellular matrix. Our analysis shows that increases in organismal complexity can be associated with modifications of lineage-specific proteins rather than large-scale invention of protein-coding capacity.« less

Activation of Dioxygen by Iron and Manganese Complexes: A Heme and Nonheme Perspective

PubMed Central

Sahu, Sumit; Goldberg, David P.

2016-01-01

The rational design of well-defined, first-row transition metal complexes that can activate dioxygen has been a challenging goal for the synthetic inorganic chemist. The activation of O2 is important in part because of its central role in the functioning of metalloenzymes, which utilize O2 to perform a number of challenging reactions including the highly selective oxidation of various substrates. There is also great interest in utilizing O2, an abundant and environmentally benign oxidant, in synthetic catalytic oxidation systems. This Perspective brings together recent examples of biomimetic Fe and Mn complexes that can activate O2 in heme or nonheme-type ligand environments. The use of oxidants such as hypervalent iodine (e.g., ArIO), peracids (e.g., m-CPBA), peroxides (e.g., H2O2) or even superoxide is a popular choice for accessing well-characterized metal–superoxo, metal–peroxo, or metal–oxo species, but the instances of biomimetic Fe/Mn complexes that react with dioxygen to yield such observable metal–oxygen species are surprisingly few. This Perspective focuses on mononuclear Fe and Mn complexes that exhibit reactivity with O2 and lead to spectroscopically observable metal–oxygen species, and/or oxidize biologically relevant substrates. Analysis of these examples reveals that solvent, spin state, redox potential, external co-reductants, and ligand architecture can all play important roles in the O2 activation process. PMID:27576170

Global minimum profile error (GMPE) - a least-squares-based approach for extracting macroscopic rate coefficients for complex gas-phase chemical reactions.

PubMed

Duong, Minh V; Nguyen, Hieu T; Mai, Tam V-T; Huynh, Lam K

2018-01-03

Master equation/Rice-Ramsperger-Kassel-Marcus (ME/RRKM) has shown to be a powerful framework for modeling kinetic and dynamic behaviors of a complex gas-phase chemical system on a complicated multiple-species and multiple-channel potential energy surface (PES) for a wide range of temperatures and pressures. Derived from the ME time-resolved species profiles, the macroscopic or phenomenological rate coefficients are essential for many reaction engineering applications including those in combustion and atmospheric chemistry. Therefore, in this study, a least-squares-based approach named Global Minimum Profile Error (GMPE) was proposed and implemented in the MultiSpecies-MultiChannel (MSMC) code (Int. J. Chem. Kinet., 2015, 47, 564) to extract macroscopic rate coefficients for such a complicated system. The capability and limitations of the new approach were discussed in several well-defined test cases.

Identification and Spectroscopic Characterization of Nonheme Iron(III) Hypochlorite Intermediates.

PubMed

Draksharapu, Apparao; Angelone, Davide; Quesne, Matthew G; Padamati, Sandeep K; Gómez, Laura; Hage, Ronald; Costas, Miquel; Browne, Wesley R; de Visser, Sam P

2015-03-27

Fe III -hypohalite complexes have been implicated in a wide range of important enzyme-catalyzed halogenation reactions including the biosynthesis of natural products and antibiotics and post-translational modification of proteins. The absence of spectroscopic data on such species precludes their identification. Herein, we report the generation and spectroscopic characterization of nonheme Fe III -hypohalite intermediates of possible relevance to iron halogenases. We show that Fe III -OCl polypyridylamine complexes can be sufficiently stable at room temperature to be characterized by UV/Vis absorption, resonance Raman and EPR spectroscopies, and cryo-ESIMS. DFT methods rationalize the pathways to the formation of the Fe III -OCl, and ultimately Fe IV =O, species and provide indirect evidence for a short-lived Fe II -OCl intermediate. The species observed and the pathways involved offer insight into and, importantly, a spectroscopic database for the investigation of iron halogenases.

Identification and Spectroscopic Characterization of Nonheme Iron(III) Hypochlorite Intermediates**

PubMed Central

Draksharapu, Apparao; Angelone, Davide; Quesne, Matthew G; Padamati, Sandeep K; Gómez, Laura; Hage, Ronald; Costas, Miquel; Browne, Wesley R; de Visser, Sam P

2015-01-01

FeIII–hypohalite complexes have been implicated in a wide range of important enzyme-catalyzed halogenation reactions including the biosynthesis of natural products and antibiotics and post-translational modification of proteins. The absence of spectroscopic data on such species precludes their identification. Herein, we report the generation and spectroscopic characterization of nonheme FeIII–hypohalite intermediates of possible relevance to iron halogenases. We show that FeIII-OCl polypyridylamine complexes can be sufficiently stable at room temperature to be characterized by UV/Vis absorption, resonance Raman and EPR spectroscopies, and cryo-ESIMS. DFT methods rationalize the pathways to the formation of the FeIII-OCl, and ultimately FeIV=O, species and provide indirect evidence for a short-lived FeII-OCl intermediate. The species observed and the pathways involved offer insight into and, importantly, a spectroscopic database for the investigation of iron halogenases. PMID:25663379

Complex Dynamics of an Impulsive Control System in which Predator Species Share a Common Prey

NASA Astrophysics Data System (ADS)

Pei, Yongzhen; Liu, Shaoying; Li, Changguo

2009-06-01

In an ecosystem, multiple predator species often share a common prey and the interactions between the predators are neutral. In view of this fact, we propose a three-species prey-predator system with the functional responses and impulsive controls to model the process of pest management. It is proved that the system has a locally stable pest-eradication periodic solution under the assumption that the impulsive period is less than some critical value. In particular, two single control strategies (biological control alone or chemical control alone) are proposed. Finally, we compare three pest control strategies and find that if we choose narrow-spectrum pesticides that are targeted to a specific pest’s life cycle to kill the pest, then the combined strategy is preferable. Numerical results show that our system has complex dynamics including period-doubling bifurcation, quasi-periodic oscillation, chaos, intermittency and crises.

Catalogue of distribution of lizards (Reptilia: Squamata) from the Brazilian Amazonia. IV. Alopoglossidae, Gymnophthalmidae.

PubMed

Ribeiro-Júnior, Marco A; Amaral, Silvana

2017-05-22

We present distribution data of all Alopoglossidae and Gymnophthalmidae lizards known from the Brazilian Amazonia, totaling 54 species-level taxa, belonging to 17 genera and two families. This represents 22 more species-level taxa than previously reported. Data were based on 17,431 specimens deposited in three North American and eight Brazilian museums, including the main collections harboring Amazonian material. Most species (~80%) are endemic to Amazonia; non-endemic species are mainly associated with open vegetation (savanna) enclaves or open dry (semideciduous) forest in Amazonia, with a few exceptions. As a whole, seven taxa (including one species complex) are widespread in Amazonia, six are restricted to eastern Amazonia, seven to western Amazonia, two to southwestern Amazonia, 11 to southern Amazonia, 11 to northern Amazonia (either in part of it or widespread in the Guiana region), and six to the southern peripheral portion of Amazonia. Besides, four species present unique distributions. Considering this study and the other three catalogues of distribution of lizards already published, the total number of lizard species from Brazilian Amazonia increased from 97 to 142 species-level tava. It represents an increase of 45 species from the region since the last revision.

Effects of Methyl Eugenol Feeding on Mating Compatibility of Asian Population of Bactrocera dorsalis (Diptera: Tephritidae) with African Population and with B. carambolae

PubMed Central

Haq, Ihsan ul; Vreysen, Marc J. B.; Schutze, Mark; Hendrichs, Jorge; Shelly, Todd

2016-01-01

Males of some species included in the Bactrocera dorsalis complex are strongly attracted to methyl eugenol (ME) (1,2-dimethoxy-4-(2-propenyl) benzene), a natural compound occurring in a variety of plant species. ME feeding of males of the B. dorsalis complex is known to enhance their mating competitiveness. Within B. dorsalis, recent studies show that Asian and African populations of B. dorsalis are sexually compatible, while populations of B. dorsalis and Bactrocera carambolae are relatively incompatible. The objectives of this study were to examine whether ME feeding by males affects mating compatibility between Asian and African populations of B. dorsalis and ME feeding reduces male mating incompatibility between B. dorsalis (Asian population) and B. carambolae. The data confirmed that Asian and African populations of B. dorsalis are sexually compatible for mating and showed that ME feeding only increased the number of matings. Though ME feeding also increased the number of matings of B. dorsalis (Asian population) and B. carambolae males but the sexual incompatibility between both species was not reduced by treatment with ME. These results conform to the efforts resolving the biological species limits among B. dorsalis complex and have implications for fruit fly control programs in fields and horticultural trade. PMID:26362991

Larval Habitats Characterization and Species Composition of Anopheles Mosquitoes in Tunisia, with Particular Attention to Anopheles maculipennis Complex

PubMed Central

Tabbabi, Ahmed; Boussès, Philippe; Rhim, Adel; Brengues, Cécile; Daaboub, Jabeur; Ben-Alaya-Bouafif, Nissaf; Fontenille, Didier; Bouratbine, Aïda; Simard, Frédéric; Aoun, Karim

2015-01-01

In Tunisia, malaria transmission has been interrupted since 1980. However, the growing number of imported cases and the persistence of putative vectors stress the need for additional studies to assess the risk of malaria resurgence in the country. In this context, our aim was to update entomological data concerning Anopheles mosquitoes in Tunisia. From May to October of 2012, mosquito larval specimens were captured in 60 breeding sites throughout the country and identified at the species level using morphological keys. Environmental parameters of the larval habitats were recorded. Specimens belonging to the An. maculipennis complex were further identified to sibling species by the ribosomal deoxyribonucleic acid (rDNA)–internal transcribed spacer 2 (ITS2) polymerase chain reaction (PCR) technique. In total, 647 Anopheles larvae were collected from 25 habitats. Four species, including An. labranchiae, An. multicolor, An. sergentii, and An. algeriensis, were morphologically identified. rDNA-ITS2 PCR confirmed that An. labranchiae is the sole member of the An. maculipennis complex in Tunisia. An. labranchiae was collected throughout northern and central Tunisia, and it was highly associated with rural habitat, clear water, and sunlight areas. Larvae of An. multicolor and An. sergentii existed separately or together and were collected in southern Tunisia in similar types of breeding places. PMID:25561567

Global revision of the dulotic ant genus Polyergus (Hymenoptera: Formicidae, Formicinae, Formicini).

PubMed

Trager, James C

2013-01-01

The genus Polyergus is characterized, and all valid species reinstated and re-described, and five new species described, based on morphometric, ecological, host-association, and biogeographic characteristics. Polyergus contains 14 species: 3 Palaearctic, 11 Nearctic. The rufescens group comprises western Eurasian rufescens Latreille 1804 including its former eastern subspecies tianschanicus Kuznetsov-Ugamsky 1927 new synonymy, and the following American species, informally called the breviceps complex: breviceps Emery 1893 sensu stricto, revised status, bicolor Wasmann 1901 new status, mexicanus Forel 1899 new status, topoffi new species, and vinosus new species. The lucidus group comprises longicornis M. R. Smith 1947 new status, lucidus Mayr 1870 sensu stricto, revised status, montivagus Wheeler 1915 new status, oligergus new species, ruber new species, and sanwaldi new species. The samurai group comprises two blackish forms: the western Asian P. nigerrimus Marikovsky 1963 and eastern Asian P. samurai Yano 1911. Polyergus texana Buckley 1866 is excluded from Polyergus.

First discovery of Quercus-feeding Nepticulidae (Lepidoptera) in South America, with description of new species and designation of the S. nigriverticella complex in the S. saginella group.

PubMed

Remeikis, Andrius; Stonis, Jonas R

2015-12-11

We describe three new species: Stigmella crassifoliae Remeikis & Stonis, sp. nov. (a leaf-miner on Quercus crassifolia and Q. crispipilis from the highlands of Guatemala), S. robleae Remeikis & Stonis, sp. nov., and S. humboldti Remeikis & Stonis, sp. nov. (leaf-miners on Quercus humboldtii from the Colombian Andes). No Quercus-feeding Nepticulidae species were previously known from South America. All new species are illustrated with photographs of the leaf-mines, cocoons, adults, and genitalia. In the S. saginella species group, for the species possessing in male genitalia M-shaped gnathos with caudal processes closely juxtaposed and phallus without cornuti, a new species complex (the S. nigriverticella complex) is defined. We also provide a pictorial key to the species of the new complex.

Biotechnology of Aureobasidium pullulans: A phylogenetic perspective

USDA-ARS?s Scientific Manuscript database

Aureobasidium pullulans is a fungus historically included among the "black yeasts." Although many strains are predominantly yeast-like, the species is actually polymorphic, exhibiting complex forms ranging from blastic conidia and swollen cells to pseudophyphae, hyphae, and chlamydospores. A. pull...

Clinical and Taxonomic Status of Pathogenic Nonpigmented or Late-Pigmenting Rapidly Growing Mycobacteria

PubMed Central

Brown-Elliott, Barbara A.; Wallace, Richard J.

2002-01-01

The history, taxonomy, geographic distribution, clinical disease, and therapy of the pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria (RGM) are reviewed. Community-acquired disease and health care-associated disease are highlighted for each species. The latter grouping includes health care-associated outbreaks and pseudo-outbreaks as well as sporadic disease cases. Treatment recommendations for each species and type of disease are also described. Special emphasis is on the Mycobacterium fortuitum group, including M. fortuitum, M. peregrinum, and the unnamed third biovariant complex with its recent taxonomic changes and newly recognized species (including M. septicum, M. mageritense, and proposed species M. houstonense and M. bonickei). The clinical and taxonomic status of M. chelonae, M. abscessus, and M. mucogenicum is also detailed, along with that of the closely related new species, M. immunogenum. Additionally, newly recognized species, M. wolinskyi and M. goodii, as well as M. smegmatis sensu stricto, are included in a discussion of the M. smegmatis group. Laboratory diagnosis of RGM using phenotypic methods such as biochemical testing and high-performance liquid chromatography and molecular methods of diagnosis are also discussed. The latter includes PCR-restriction fragment length polymorphism analysis, hybridization, ribotyping, and sequence analysis. Susceptibility testing and antibiotic susceptibility patterns of the RGM are also annotated, along with the current recommendations from the National Committee for Clinical Laboratory Standards (NCCLS) for mycobacterial susceptibility testing. PMID:12364376

Clinical and taxonomic status of pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria.

PubMed

Brown-Elliott, Barbara A; Wallace, Richard J

2002-10-01

The history, taxonomy, geographic distribution, clinical disease, and therapy of the pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria (RGM) are reviewed. Community-acquired disease and health care-associated disease are highlighted for each species. The latter grouping includes health care-associated outbreaks and pseudo-outbreaks as well as sporadic disease cases. Treatment recommendations for each species and type of disease are also described. Special emphasis is on the Mycobacterium fortuitum group, including M. fortuitum, M. peregrinum, and the unnamed third biovariant complex with its recent taxonomic changes and newly recognized species (including M. septicum, M. mageritense, and proposed species M. houstonense and M. bonickei). The clinical and taxonomic status of M. chelonae, M. abscessus, and M. mucogenicum is also detailed, along with that of the closely related new species, M. immunogenum. Additionally, newly recognized species, M. wolinskyi and M. goodii, as well as M. smegmatis sensu stricto, are included in a discussion of the M. smegmatis group. Laboratory diagnosis of RGM using phenotypic methods such as biochemical testing and high-performance liquid chromatography and molecular methods of diagnosis are also discussed. The latter includes PCR-restriction fragment length polymorphism analysis, hybridization, ribotyping, and sequence analysis. Susceptibility testing and antibiotic susceptibility patterns of the RGM are also annotated, along with the current recommendations from the National Committee for Clinical Laboratory Standards (NCCLS) for mycobacterial susceptibility testing.

Ecological and epidemiological status of species of the Phlebotomus perniciosus complex (Diptera: Psychodidae, Phlebotominae) in Morocco.

PubMed

Zarrouk, Asmae; Kahime, Kholoud; Boussaa, Samia; Belqat, Boutaïna

2016-03-01

Leishmania infantum (Kinetoplastida: Trypanosomatidae) infection is transmitted by an infected female sand fly (Diptera: Psychodidae, Phlebotominae) of the subgenus Larroussius: Phlebotomus ariasi, Phlebotomus perniciosus, and Phlebotomus longicuspis in the Mediterranean basin. In Morocco, the vectorial role of P. ariasi was demonstrated, while that of P. longicuspis and P. perniciosus is not elucidated. In addition, Moroccan P. longicuspis and P. perniciosus populations present a higher morphologic and genetic variability. It was classified as P. perniciosus complex, including typical (PN) and atypical (PNA) morphs of P. perniciosus, P. longicuspis sensu stricto (LCss), and a sibling species of P. longicuspis (LCx). With the aim to study the ecological and epidemiological status of P. perniciosus complex species in Morocco, entomological surveys were carried out during three entomological seasons (2012, 2013, and 2014). We collected a total of 6298 specimens from 81 localities of northern, central, and southern Morocco. After describing the geographical distribution of P. perniciosus complex trough Morocco according to many variables (altitude, latitude, and longitude), we discuss the resulting epidemiological implications of its species. Our results highlight the geographical distribution of the two morphs of P. perniciosus through Morocco: PN is limited to the north, while PNA is widespread in northern, central, and southern Morocco. In terms of vectorial role, we hypothesize the potential involvement of PN, LCss, and LCx, at least, with P. ariasi, in the epidemiological cycle of L. infantum in Morocco.

Up and down the blind alley: population divergence with scant gene flow in an endangered tropical lineage of Andean palms (Ceroxylon quindiuense clade: Ceroxyloideae).

PubMed

Sanín, María José; Zapata, Patricia; Pintaud, Jean-Christophe; Galeano, Gloria; Bohórquez, Adriana; Tohme, Joseph; Hansen, Michael Møller

2017-02-10

Given the geographical complexity of the Andes, species distributions hold interesting information regarding the history of isolation and gene flow across geographic barriers and ecological gradients. Moreover, current threats to the region’s enormous plant diversity pose an additional challenge to the understanding of these patterns. We explored the geographic structure of genetic diversity within the Ceroxylon quindiuense species complex (wax palms) at a regional scale, using a model-based approach to disentangle the historical mechanisms by which these species have dispersed over a range encompassing 17° of latitude in the tropical Andes. A total of 10 microsatellite loci were cross-amplified in 8 populations of the 3 species comprising the C. quindiuense complex. Analyses performed include estimates of molecular diversity and genetic structure, testing for genetic bottlenecks and an evaluation of the colonization scenario under approximate Bayesian computation. We showed that there was a geographical diversity gradient reflecting the orogenetic pattern of the northern Andes and its end at the cordilleras facing the Caribbean Sea. A general pattern of diversity suggests that the cordilleras of Colombia have served as historical recipients of gene flow occurring only scantly along the northern Andes. We provided evidence of important isolation between the largest populations of this complex, suggesting that both historical constraints to dispersal but also current anthropogenic effects might explain the high levels of population structuring. We provide a list of advisable measures for conservation stakeholders.

Evolutionary history of tall fescue morphotypes inferred from molecular phylogenetics of the Lolium-Festuca species complex

PubMed Central

2010-01-01

Background The agriculturally important pasture grass tall fescue (Festuca arundinacea Schreb. syn. Lolium arundinaceum (Schreb.) Darbysh.) is an outbreeding allohexaploid, that may be more accurately described as a species complex consisting of three major (Continental, Mediterranean and rhizomatous) morphotypes. Observation of hybrid infertility in some crossing combinations between morphotypes suggests the possibility of independent origins from different diploid progenitors. This study aims to clarify the evolutionary relationships between each tall fescue morphotype through phylogenetic analysis using two low-copy nuclear genes (encoding plastid acetyl-CoA carboxylase [Acc1] and centroradialis [CEN]), the nuclear ribosomal DNA internal transcribed spacer (rDNA ITS) and the chloroplast DNA (cpDNA) genome-located matK gene. Other taxa within the closely related Lolium-Festuca species complex were also included in the study, to increase understanding of evolutionary processes in a taxonomic group characterised by multiple inter-specific hybridisation events. Results Putative homoeologous sequences from both nuclear genes were obtained from each polyploid species and compared to counterparts from 15 diploid taxa. Phylogenetic reconstruction confirmed F. pratensis and F. arundinacea var. glaucescens as probable progenitors to Continental tall fescue, and these species are also likely to be ancestral to the rhizomatous morphotype. However, these two morphotypes are sufficiently distinct to be located in separate clades based on the ITS-derived data set. All four of the generated data sets suggest independent evolution of the Mediterranean and Continental morphotypes, with minimal affinity between cognate sequence haplotypes. No obvious candidate progenitor species for Mediterranean tall fescues were identified, and only two putative sub-genome-specific haplotypes were identified for this morphotype. Conclusions This study describes the first phylogenetic analysis of the Festuca genus to include representatives of each tall fescue morphotype, and to use low copy nuclear gene-derived sequences to identify putative progenitors of the polyploid species. The demonstration of distinct tall fescue lineages has implications for both taxonomy and molecular breeding strategies, and may facilitate the generation of morphotype and/or sub-genome-specific molecular markers. PMID:20937141

Bambus[6]uril as a novel macrocyclic receptor for the nitrate anion.

PubMed

Toman, Petr; Makrlík, Emanuel; Vanura, Petr

2013-01-01

By using quantum mechanical DFT calculations, the most probable structure of the bambus[6]uril x NO3(-) anionic complex species was derived. In this complex having C3 symmetry, the nitrate anion NO3(-), included in the macrocyclic cavity, is bound by twelve weak hydrogen bonds between methine hydrogen atoms on the convex face of glycoluril units and the considered NO3(-) ion.

Modeling uranium(VI) adsorption onto montmorillonite under varying carbonate concentrations: A surface complexation model accounting for the spillover effect on surface potential

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

Tournassat, C.; Tinnacher, R. M.; Grangeon, S.

The prediction of U(VI) adsorption onto montmorillonite clay is confounded by the complexities of: (1) the montmorillonite structure in terms of adsorption sites on basal and edge surfaces, and the complex interactions between the electrical double layers at these surfaces, and (2) U(VI) solution speciation, which can include cationic, anionic and neutral species. Previous U(VI)-montmorillonite adsorption and modeling studies have typically expanded classical surface complexation modeling approaches, initially developed for simple oxides, to include both cation exchange and surface complexation reactions. However, previous models have not taken into account the unique characteristics of electrostatic surface potentials that occur at montmorillonitemore » edge sites, where the electrostatic surface potential of basal plane cation exchange sites influences the surface potential of neighboring edge sites (‘spillover’ effect).« less

Modeling uranium(VI) adsorption onto montmorillonite under varying carbonate concentrations: A surface complexation model accounting for the spillover effect on surface potential

DOE PAGES

Tournassat, C.; Tinnacher, R. M.; Grangeon, S.; ...

2017-10-06

The prediction of U(VI) adsorption onto montmorillonite clay is confounded by the complexities of: (1) the montmorillonite structure in terms of adsorption sites on basal and edge surfaces, and the complex interactions between the electrical double layers at these surfaces, and (2) U(VI) solution speciation, which can include cationic, anionic and neutral species. Previous U(VI)-montmorillonite adsorption and modeling studies have typically expanded classical surface complexation modeling approaches, initially developed for simple oxides, to include both cation exchange and surface complexation reactions. However, previous models have not taken into account the unique characteristics of electrostatic surface potentials that occur at montmorillonitemore » edge sites, where the electrostatic surface potential of basal plane cation exchange sites influences the surface potential of neighboring edge sites (‘spillover’ effect).« less

Angiosperm flora on the páramos of northwestern Colombia: diversity and affinities

PubMed Central

Alzate-Guarín, Fernando; Murillo-Serna, Jhon Steven

2016-01-01

Abstract Páramos are high-elevation isolated ecosystems in the Andes characterized by specific flora. This flora includes a number of endemic species and some taxa phylogenetically related to temperate lineages (van der Hammen and Cleef 1986). There are six páramo units or complexes in the Department of Antioquia, located in northwestern Colombia. For five years, we conducted botanic explorations in order to quantify the richness of angiosperm flora in these units. We estimate the richness of angiosperms in these páramos at 693 species, 277 genera, and 86 families, which represent almost 10% of the floral diversity in Antioquia, but contained in only 0.7% of its area. We found that Frontino-Urrao is the most species-rich páramo with 465 species from 225 genera. Our results show that the most diverse angiosperm families of the páramos of Antioquia are Asteraceae, Orchidaceae, Melastomataceae, and Poaceae, which together represent 245 species. Groupings between páramos by Sørensen’s similarity index show that the complexes of the Central Andes Cordillera form a cluster of greater affinity than Páramos from other regions. Of the species found, 80 have a CITES or IUCN diagnosis. The expeditions allowed the identification of 21 species not previously registered in Antioquia and a considerable number of endemisms (35 species), further proof of the high plant diversity in these ecosystems. PMID:27829798

Characterization of divalent and trivalent species generated in the chemical and electrochemical oxidation of a dimeric pincer complex of nickel.

PubMed

Spasyuk, Denis M; Gorelsky, Serge I; van der Est, Art; Zargarian, Davit

2011-03-21

The electrolytic and chemical oxidation of the dimeric pincer complex [κ(P),κ(C),κ(N),μ(N)-(2,6-(i-Pr(2)POC(6)H(3)CH(2)NBn)Ni](2) (1; Bn = CH(2)Ph) has been investigated by various analytic techniques. Cyclic voltammetry measurements have shown that 1 undergoes a quasi-reversible, one electron, Ni-based redox process (ΔE(0)(1/2) = -0.07 V vs Cp(2)Fe/[Cp(2)Fe](+)), and spectroelectrochemical measurements conducted on the product of the electrolytic oxidation, [1](+•), have shown multiple low-energy electronic transitions in the range of 10,000-15,000 cm(-1). Computational studies using Density Functional Theory (B3LYP) have corroborated the experimentally obtained structure of 1, provided the electronic structure description, and helped interpret the experimentally obtained absorption spectra for 1 and [1](+·). These calculations indicate that the radical cation [1](+·) is a dimeric, mixed-valent species (class III) wherein most of the spin density is delocalized over the two nickel centers (Ni(+2.5)(2)N(2)), but some spin density is also present over the two nitrogen atoms (Ni(2+)(2)N(2)·). Examination of alternative structures for open shell species generated from 1 has shown that the spin density distribution is highly sensitive toward changes in the ligand environment of the Ni ions. NMR, UV-vis, electron paramagnetic resonance (EPR), and single crystal X-ray diffraction analyses have shown that chemical oxidation of 1 with N-Bromosuccinimide (NBS) follows a complex process that gives multiple products, including the monomeric trivalent species κ(P),κ(C),κ(N)-{2,6-(i-Pr(2)PO)(C(6)H(3))(CH═NBn)}NiBr(2) (2). These studies also indicate that oxidation of 1 with 1 equiv of NBS gives an unstable, paramagnetic intermediate that decomposes to a number of divalent species, including succinimide and the monomeric divalent complexes κ(P),κ(C),κ(N)-{2,6-(i-Pr(2)PO)(C(6)H(3))(CH═NBn)}NiBr (3) and κ(P),κ(C),κ(N)-{2,6-(i-Pr(2)PO)(C(6)H(3))(CH(2)N(H)Bn)}NiBr(2) (4); a second equivalent of NBS then oxidizes 3 and 4 to 2 and other unidentified products. The divalent complex 3 was synthesized independently and shown to react with NBS or bromine to form its trivalent homologue 2. The new complexes 2 and 3 have been characterized fully.

Biomass and fire dynamics in a temperate forest-grassland mosaic: Integrating multi-species herbivory, climate, and fire with the FireBGCv2/GrazeBGC system

Treesearch

Robert A. Riggs; Robert E. Keane; Norm Cimon; Rachel Cook; Lisa Holsinger; John Cook; Timothy DelCurto; L.Scott Baggett; Donald Justice; David Powell; Martin Vavra; Bridgett Naylor

2015-01-01

Landscape fire succession models (LFSMs) predict spatially-explicit interactions between vegetation succession and disturbance, but these models have yet to fully integrate ungulate herbivory as a driver of their processes. We modified a complex LFSM, FireBGCv2, to include a multi-species herbivory module, GrazeBGC. The system is novel in that it explicitly...

Using Field and Satellite Measurements to Improve Snow and Riming Processes in Cloud Resolving Models

NASA Technical Reports Server (NTRS)

Colle, Brian A.; Molthan, Andrew L.

2013-01-01

The representation of clouds in climate and weather models is a driver in forecast uncertainty. Cloud microphysics parameterizations are challenged by having to represent a diverse range of ice species. Key characteristics of predicted ice species include habit and fall speed, and complex interactions that result from mixed-phased processes like riming. Our proposed activity leverages Global Precipitation Measurement (GPM) Mission ground validation studies to improve parameterizations

Macrobenthos of Yenisei Bay and the adjacent Kara Sea shelf

NASA Astrophysics Data System (ADS)

Galkin, S. V.; Vedenin, A. A.

2015-07-01

Trawl samples were collected in the northern region of Yenisei Bay and adjacent parts of the Kara Sea shelf. A total of eight stations were taken. We found more than 200 species of benthic organisms. A consecutive replacement of benthic communities is observed when going to the north from the Ob and Yenisei estuaries to the open parts of the sea. We could distinguish four different species complexes in the investigated area: a brackish-water complex where Saduria entomon is dominant; an intermediate complex where S. sibirica, S. sabini and Portlandia aestuariorum are dominant; a transitional complex with P. arctica as a dominant species and with a small amount of Ophiocten sericeum; a marine complex where O. sericeum is dominant. When salinity increased, some brackish-water species were replaced by related euryhaline species. One such example was the replacement of brackish-water Saduria entomon isopods by two euryhaline species: S. sibirica and S. sabini. The consecutive replacement of benthic communities showed a break near Sverdrup Island. In this area the marine complex was replaced by a transitional complex with P. arctica.

Preparation and properties of a monomeric high-spin Mn(V)-oxo complex.

PubMed

Taguchi, Taketo; Gupta, Rupal; Lassalle-Kaiser, Benedikt; Boyce, David W; Yachandra, Vittal K; Tolman, William B; Yano, Junko; Hendrich, Michael P; Borovik, A S

2012-02-01

Oxomanganese(V) species have been implicated in a variety of biological and synthetic processes, including their role as a key reactive center within the oxygen-evolving complex in photosynthesis. Nearly all mononuclear Mn(V)-oxo complexes have tetragonal symmetry, producing low-spin species. A new high-spin Mn(V)-oxo complex that was prepared from a well-characterized oxomanganese(III) complex having trigonal symmetry is now reported. Oxidation experiments with [FeCp(2)](+) were monitored with optical and electron paramagnetic resonance (EPR) spectroscopies and support a high-spin oxomanganese(V) complex formulation. The parallel-mode EPR spectrum has a distinctive S = 1 signal at g = 4.01 with a six-line hyperfine pattern having A(z) = 113 MHz. The presence of an oxo ligand was supported by resonance Raman spectroscopy, which revealed O-isotope-sensitive peaks at 737 and 754 cm(-1) assigned as a Fermi doublet centered at 746 cm(-1)(Δ(18)O = 31 cm(-1)). Mn Kβ X-ray emission spectra showed Kβ' and Kβ(1,3) bands at 6475.92 and 6490.50 eV, respectively, which are characteristic of a high-spin Mn(V) center. © 2012 American Chemical Society

Investigation of the host-guest complexation between 4-sulfocalix[4]arene and nedaplatin for potential use in drug delivery

NASA Astrophysics Data System (ADS)

Fahmy, Sherif Ashraf; Ponte, Fortuna; Abd El-Rahman, Mohamed K.; Russo, Nino; Sicilia, Emilia; Shoeib, Tamer

2018-03-01

Macromolecules including macrocyclic species have been reported to have the potential to encapsulate biologically active compounds such as drugs through host-guest complexation to increase their solubility, stability and bioavailability. In this paper the first experimental and theoretical investigation of the complexation between nedaplatin, a second generation antineoplastic drug, and p-4-sulfocalix[4]arene, a macromolecule possessing a bipolar amphiphilic structure with good biocompatibility and relatively low haemolytic toxicity for potential use as a drug delivery system is presented. Data from 1H NMR, UV, Job's plot analysis, HPLC and DFT calculations are detailed and suggest the formation of a 1:1 complex. The stability constant of the complex was experimentally estimated to be 3.6 × 104 M- 1 and 2.1 × 104 M- 1 which correspond to values of - 6.2 and - 5.9 kcal mol- 1, respectively for the free energy of complexation while the interaction free energy is calculated to be - 4.9 kcal mol- 1. The formed species is shown to be stabilised in solution through hydrogen bonding between the host and the guest which may allow for this strategy to be effective for potential use in drug delivery.

A new species of Labidocera (Copepoda, Calanoida, Pontellidae) collected from Okinawa, southwestern Japan, with establishment of five Indo-West Pacific species groups in the L. detruncata species complex

PubMed Central

Hirabayashi, Takeshi; Ohtsuka, Susumu

2014-01-01

Abstract Labidocera churaumi sp. n. is described from Okinawa, southwestern Japan. The female of the new species differs from other congeners in genital compound somite with right postero-lateral and left antero-lateral processes. The male is distinguished from other congeners by the structure of the fifth leg. This new species is assigned to a newly proposed species group, the Labidocera madurae species group, within the Labidocera detruncata species complex. In this species complex five Indo-West Pacific species groups are recognized (cervi, detruncata, gangetica, madurae, and pavo) and defined on the basis of difference in sexual dimorphism. PMID:25349514

Molecular identification of Aspergillus species collected for the Transplant-Associated Infection Surveillance Network.

PubMed

Balajee, S Arunmozhi; Kano, Rui; Baddley, John W; Moser, Stephen A; Marr, Kieren A; Alexander, Barbara D; Andes, David; Kontoyiannis, Dimitrios P; Perrone, Giancarlo; Peterson, Stephen; Brandt, Mary E; Pappas, Peter G; Chiller, Tom

2009-10-01

A large aggregate collection of clinical isolates of aspergilli (n = 218) from transplant patients with proven or probable invasive aspergillosis was available from the Transplant-Associated Infection Surveillance Network, a 6-year prospective surveillance study. To determine the Aspergillus species distribution in this collection, isolates were subjected to comparative sequence analyses by use of the internal transcribed spacer and beta-tubulin regions. Aspergillus fumigatus was the predominant species recovered, followed by A. flavus and A. niger. Several newly described species were identified, including A. lentulus and A. calidoustus; both species had high in vitro MICs to multiple antifungal drugs. Aspergillus tubingensis, a member of the A. niger species complex, is described from clinical specimens; all A. tubingensis isolates had low in vitro MICs to antifungal drugs.

Taxonomic Synopsis of the Ponto-Mediterranean Ants of Temnothorax nylanderi Species-Group

PubMed Central

Csősz, Sándor; Heinze, Jürgen; Mikó, István

2015-01-01

In the current revisionary work, the Temnothorax nylanderi species-group of myrmicine ants is characterized. Eighteen species belonging to this group in the Ponto-Mediterranean region are described or redefined based on an integrative approach that combines exploratory analyses of morphometric data and of a 658bp fragment of the mitochondrial gene for the cytochrome c oxidase subunit I (CO I). The species group is subdivided into five species complexes: T. angustifrons complex, T. lichtensteini complex, T. nylanderi complex, T. parvulus complex, T. sordidulus complex, and two species, T. angulinodis sp. n. and T. flavicornis (Emery, 1870) form their own lineages. We describe seven new species (T. angulinodis sp. n., T. angustifrons sp. n., T. ariadnae sp. n., T. helenae sp. n., T. lucidus sp. n., T. similis sp. n., T. subtilis sp. n.), raise T. tergestinus (FINZI, 1928) stat.n. to species level, and propose a new junior synonymy for T. saxonicus (SEIFERT, 1995) syn.n. (junior synonym of T. tergestinus). We describe the worker caste and provide high quality images and distributional maps for all eighteen species. Furthermore, we provide a decision tree as an alternative identification key that visually gives an overview of this species-group. We make the first application to Formicidae of the Semantic Phenotype approach that has been used in previous taxonomic revisions. PMID:26536033

[Identification of potentially invasive species of black flies [Diptera: Simuliidae] from Armenia based on an analysis of variability in the mtDNA barcode of the cox1 gene and chromosomal polymorphism].

PubMed

Andrianov, B V; Goryacheva, I I; Vlasov, S V; Gorelova, T V; Harutyunova, M V; Harutyunova, K V; Mayilyan, K R; Zakharov, I A

2015-03-01

Black flies (Diptera, Simuliidae) are well known for their medical, environmental, and veterinary importance. The simuliid fauna of Armenia includes 53 species. A number of dominant species are of ecological importance. Complex analysis, which involved morphometric, cytogenetic, and molecular genetic approaches, was conducted to characterize the species status of black flies inhabiting the territory of Armenia. It was shown that the predominant simuliid species, Simulium paraequinum and Simulium kiritshenkoi, belong to a group of species with minimal variability of the cox1 gene. The recently discovered species, Simulium noellery and Simulium [B.] erythrocephalum, which are new to Armenia, can be considered as potentially invasive, which is supported by the low level of variability of the cox1 gene.

Species delimitation of the Hyphydrus ovatus complex in western Palaearctic with an update of species distributions (Coleoptera, Dytiscidae)

PubMed Central

Bergsten, Johannes; Weingartner, Elisabeth; Hájek, Jiří

2017-01-01

Abstract The species status of Hyphydrus anatolicus Guignot, 1957 and H. sanctus Sharp, 1882, previously often confused with the widespread H. ovatus (Linnaeus, 1760), are tested with molecular and morphological characters. Cytochrome c oxidase subunit 1 (CO1) was sequenced for 32 specimens of all three species. Gene-trees were inferred with parsimony, time-free bayesian and strict clock bayesian analyses. The GMYC model was used to estimate species limits. All three species were reciprocally monophyletic with CO1 and highly supported. The GMYC species delimitation analysis unequivocally delimited the three species with no other than the three species solution included in the confidence interval. A likelihood ratio test rejected the one-species null model. Important morphological characters distinguishing the species are provided and illustrated. New distributional data are given for the following species: Hyphydrus anatolicus from Slovakia and Ukraine, and H. aubei Ganglbauer, 1891, and H. sanctus from Turkey. PMID:28769697

Genetic Diversity and Phylogenetic Analysis of the Iranian Leishmania Parasites Based on HSP70 Gene PCR-RFLP and Sequence Analysis.

PubMed

Nemati, Sara; Fazaeli, Asghar; Hajjaran, Homa; Khamesipour, Ali; Anbaran, Mohsen Falahati; Bozorgomid, Arezoo; Zarei, Fatah

2017-08-01

Despite the broad distribution of leishmaniasis among Iranians and animals across the country, little is known about the genetic characteristics of the causative agents. Applying both HSP70 PCR-RFLP and sequence analyses, this study aimed to evaluate the genetic diversity and phylogenetic relationships among Leishmania spp. isolated from Iranian endemic foci and available reference strains. A total of 36 Leishmania isolates from almost all districts across the country were genetically analyzed for the HSP70 gene using both PCR-RFLP and sequence analysis. The original HSP70 gene sequences were aligned along with homologous Leishmania sequences retrieved from NCBI, and subjected to the phylogenetic analysis. Basic parameters of genetic diversity were also estimated. The HSP70 PCR-RFLP presented 3 different electrophoretic patterns, with no further intraspecific variation, corresponding to 3 Leishmania species available in the country, L. tropica, L. major, and L. infantum. Phylogenetic analyses presented 5 major clades, corresponding to 5 species complexes. Iranian lineages, including L. major, L. tropica, and L. infantum, were distributed among 3 complexes L. major, L. tropica, and L. donovani. However, within the L. major and L. donovani species complexes, the HSP70 phylogeny was not able to distinguish clearly between the L. major and L. turanica isolates, and between the L. infantum, L. donovani, and L. chagasi isolates, respectively. Our results indicated that both HSP70 PCR-RFLP and sequence analyses are medically applicable tools for identification of Leishmania species in Iranian patients. However, the reduced genetic diversity of the target gene makes it inevitable that its phylogeny only resolves the major groups, namely, the species complexes.

Phylogeography of the sergeants Abudefduf sexfasciatus and A. vaigiensis reveals complex introgression patterns between two widespread and sympatric Indo-West Pacific reef fishes.

PubMed

Bertrand, Joris A M; Borsa, Philippe; Chen, Wei-Jen

2017-05-01

On evolutionary timescales, sea level oscillations lead to recurrent spatio-temporal variation in species distribution and population connectivity. In this situation, applying classical concepts of biogeography is challenging yet necessary to understand the mechanisms underlying biodiversity in highly diverse marine ecosystems such as coral reefs. We aimed at studying the outcomes of such complex biogeographic dynamics on reproductive isolation by sampling populations across a wide spatial range of a species-rich fish genus: the sergeants (Pomacentridae: Abudefduf). We generated a mutlilocus data set that included ten morpho-species from 32 Indo-West Pacific localities. We observed a pattern of mito-nuclear discordance in two common and widely distributed species: Abudefduf sexfasciatus and Abudefduf vaigiensis. The results showed three regional sublineages (Indian Ocean, Coral Triangle region, western Pacific) in A. sexfasciatus (0.6-1.5% divergence at cytb). The other species, A. vaigiensis, is polyphyletic and consists of three distinct genetic lineages (A, B and C) (9% divergence at cytb) whose geographic ranges overlap. Although A. vaigiensis A and A. sexfasciatus were found to be distinct based on nuclear information, A. vaigiensis A was found to be nested within A. sexfasciatus in the mitochondrial gene tree. A. sexfasciatus from the Coral Triangle region and A. vaigiensis A were not differentiated from each other at the mitochondrial locus. We then used coalescent-based simulation to characterize a spatially widespread but weak gene flow between the two species. We showed that these fishes are good candidates to investigate the evolutionary complexity of the discrepancies between phenotypic and genetic similarity in closely related species. © 2017 John Wiley & Sons Ltd.

A new Eastern Central Atlantic skate Raja parva sp. nov. (Rajoidei: Rajidae) belonging to the Raja miraletus species complex.

PubMed

Last, Peter R; Séret, Bernard

2016-08-05

An investigation of combined CO1 and NADH2 data for rajid skates referable to Raja miraletus provided evidence that populations ranging from southern Africa to the North-East Atlantic and Mediterranean Sea, once considered to represent a cline, belong to a species complex consisting of at least four valid species. Raja miraletus appears to be confined to the Mediterranean Sea, and the North-East Atlantic from the Bay of Biscay south to Morocco and Madeira. The southernmost species, referable to the resurrected Raja ocellifera, occurs off southern Africa, off Namibia and from False Bay to Durban (South Africa). Two species occur off tropical West Africa, including Raja parva sp. nov. (Senegal, Liberia and Angola but is probably more widespread within the region), and another unidentified species needing further investigation. Raja cf. miraletus, confirmed from Mauritania and Senegal, appears to be a larger skate with a broader disc, more broadly pointed snout, larger spiracles, and a slightly longer and broader tail. Raja parva sp. nov. differs from nominal members of the complex in having an unusually long procaudal tail (exceeding 22% TL), as well as a combination of other external characters. Past investigators observed morphological and anatomical differences between these forms but these were thought to be due to intraspecific variability. They postulated that an upwelling at Cape Blanco (21°N) may have isolated the Mediterranean form (R. miraletus) from Mauritania-Senegal form (now known to be two species). Similarly, the Benguela Current and upwelling off Cape Frio (18°S) were thought to be responsible for separating the Angolan form (R. parva) and South African form (R. ocellifera).

Four new species of Pyropia (Bangiales, Rhodophyta) from the west coast of North America: the Pyropia lanceolata species complex updated

PubMed Central

Lindstrom, Sandra C.; Hughey, Jeffery R.; Rosas, Luis E. Aguilar

2015-01-01

Abstract Recent molecular studies indicate that the Pyropia lanceolata species complex on the west coast of North America is more speciose than previously thought. Based on extensive rbcL gene sequencing of representative specimens we recognize seven species in the complex, three of which are newly described: Pyropia montereyensis sp. nov., Pyropia columbiensis sp. nov., and Pyropia protolanceolata sp. nov. The new species are all lanceolate, at least when young, and occur in the upper mid to high intertidal zone primarily in winter and early spring. Pyropia montereyensis and Pyropia columbiensis are sister taxa that are distributed south and north of Cape Mendocino, respectively, and both occur slightly lower on the shore than Pyropia lanceolata or Pyropia pseudolanceolata. Pyropia protolanceolata is known thus far only from Morro Rock and the Monterey Peninsula, California; it occurs basally to the other species in the complex in the molecular phylogeny. A fourth newly described species, Pyropia bajacaliforniensis sp. nov., is more closely related to Pyropia nereocystis than to species in this complex proper. It is a thin species with undulate margins known only from Moss Landing, Monterey Bay, California, and northern Baja California; it also occurs in the high intertidal in spring. Porphyra mumfordii, a high intertidal winter species that has frequently been confused with species in the Pyropia lanceolata complex, has now been confirmed to occur from Calvert Island, British Columbia, to Pescadero State Park, California. PMID:26312033

Climate and the complexity of migratory phenology: sexes, migratory distance, and arrival distributions

NASA Astrophysics Data System (ADS)

Macmynowski, Dena P.; Root, Terry L.

2007-05-01

The intra- and inter-season complexity of bird migration has received limited attention in climatic change research. Our phenological analysis of 22 species collected in Chicago, USA, (1979 2002) evaluates the relationship between multi-scalar climate variables and differences (1) in arrival timing between sexes, (2) in arrival distributions among species, and (3) between spring and fall migration. The early migratory period for earliest arriving species (i.e., short-distance migrants) and earliest arriving individuals of a species (i.e., males) most frequently correlate with climate variables. Compared to long-distance migrant species, four times as many short-distance migrants correlate with spring temperature, while 8 of 11 (73%) of long-distance migrant species’ arrival is correlated with the North Atlantic Oscillation (NAO). While migratory phenology has been correlated with NAO in Europe, we believe that this is the first documentation of a significant association in North America. Geographically proximate conditions apparently influence migratory timing for short-distance migrants while continental-scale climate (e.g., NAO) seemingly influences the phenology of Neotropical migrants. The preponderance of climate correlations is with the early migratory period, not the median of arrival, suggesting that early spring conditions constrain the onset or rate of migration for some species. The seasonal arrival distribution provides considerable information about migratory passage beyond what is apparent from statistical analyses of phenology. A relationship between climate and fall phenology is not detected at this location. Analysis of the within-season complexity of migration, including multiple metrics of arrival, is essential to detect species’ responses to changing climate as well as evaluate the underlying biological mechanisms.

The complex evolutionary dynamics of ancient and recent polyploidy in Leucaena (Leguminosae; Mimosoideae).

PubMed

Govindarajulu, Rajanikanth; Hughes, Colin E; Alexander, Patrick J; Bailey, C Donovan

2011-12-01

The evolutionary history of Leucaena has been impacted by polyploidy, hybridization, and divergent allopatric species diversification, suggesting that this is an ideal group to investigate the evolutionary tempo of polyploidy and the complexities of reticulation and divergence in plant diversification. Parsimony- and ML-based phylogenetic approaches were applied to 105 accessions sequenced for six sequence characterized amplified region-based nuclear encoded loci, nrDNA ITS, and four cpDNA regions. Hypotheses for the origin of tetraploid species were inferred using results derived from a novel species tree and established gene tree methods and from data on genome sizes and geographic distributions. The combination of comprehensively sampled multilocus DNA sequence data sets and a novel methodology provide strong resolution and support for the origins of all five tetraploid species. A minimum of four allopolyploidization events are required to explain the origins of these species. The origin(s) of one tetraploid pair (L. involucrata/L. pallida) can be equally explained by two unique allopolyploidizations or a single event followed by divergent speciation. Alongside other recent findings, a comprehensive picture of the complex evolutionary dynamics of polyploidy in Leucaena is emerging that includes paleotetraploidization, diploidization of the last common ancestor to Leucaena, allopatric divergence among diploids, and recent allopolyploid origins for tetraploid species likely associated with human translocation of seed. These results provide insights into the role of divergence and reticulation in a well-characterized angiosperm lineage and into traits of diploid parents and derived tetraploids (particularly self-compatibility and year-round flowering) favoring the formation and establishment of novel tetraploids combinations.

EVIDENCE FOR THE MACROPHAGE INDUCING GENE IN MYCOBACTERIUM INTRACELLULARE

EPA Science Inventory

Background: The Mycobacterium avium Complex (MAC) includes the species M. avium (MA), M. intracellulare (MI), and possibly others. Organisms belonging to the MAC are phylogenetically closely related, opportunistic pathogens. The macrophage inducing gene (mig) is the only well-des...

ASSAYING PARTICLE-BOUND POLYCYCLIC AROMATIC HYDROCARBONS (PAH) FROM ARCHIVED PM2.5 FILTERS

EPA Science Inventory

Airborne particulate matter contains numerous organic species, including several polycyclic aromatic hydrocarbons (PAHs) that are known or suspected carcinogens. Existing methods for measuring airborne PAHs are complex and costly, primarily because they are designed to collect...

Not "Alona" monacantha Sars, 1901, but Coronatella hardingi (Brehm, 1957) Crustacea: Branchiopoda: Cladocera) in the Afrotropics.

PubMed

Damme, Kay Van

2016-07-20

Many taxa formerly housed in the lump genus Alona Baird, 1843 remain data-deficient. These species are often overlooked or wrongly identified during faunistic and ecological studies. "Alona" hardingi (Brehm, 1957) is a lesser known taxon, hidden for decades under records of "Alona" monacantha Sars, 1901. Both taxa have recently been allocated to the genus Coronatella Dybowski & Grochowski, 1894, yet without revision of the former. The morphology of Coronatella hardingi (Brehm, 1957), a widespread and abundant species in Afrotropical freshwater habitats, is examined here for the first time, including the first description of the male. The species is redescribed, based on populations from Southern Africa and confirmed as a good species and a valid sibling of the Neotropical C. monacantha (Sars, 1901) and the SE Asian C. acuticostata (Sars, 1903). The study of the Afrotropical C. hardingi allows a better understanding of this small tropical species complex, for which a diagnosis is included.

Cycadophila, a new genus (Coleoptera: Erotylidae: Pharaxonothinae) inhabiting Cycas debaoensis (Cycadaceae) in Asia.

PubMed

Xu, Guang; Tang, William; Skelley, Paul; Liu, Nian; Rich, Stephen

2015-07-17

Asian species assigned to Pharaxonotha Reitter formed a separate clade from New World species of the genus and are distinguished on the basis of morphology and analysis of 16S rRNA gene sequences. Cycadophila, new genus, is described based on a consideration of four Asian species in comparison with New World Pharaxonotha. This new genus includes two new species (Cycadophila debaonica new species and Cycadophila fupingensis new species) and two previously described species (Cycadophila nigra (Gorham) new combination and Cycadophila yunnanensis (Grouvelle) new combination). These latter two may represent species complexes. Lectotypes are designated for Thallis nigra Gorham and Pharaxonotha yunnanensis Grouvelle. Larvae of C. debaonica and C. fupingensis are described based on individuals collected on the cones of Cycas debaoensis Y. C. Zhong & C. J. Chen (Cycadaceae), a cycad native to Guangxi and Yunnan provinces, China.

Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Identification of Molds of the Fusarium Genus

PubMed Central

Stubbe, Dirk; De Cremer, Koen; Piérard, Denis; Normand, Anne-Cécile; Piarroux, Renaud; Detandt, Monique; Hendrickx, Marijke

2014-01-01

The rates of infection with Fusarium molds are increasing, and a diverse number of Fusarium spp. belonging to different species complexes can cause infection. Conventional species identification in the clinical laboratory is time-consuming and prone to errors. We therefore evaluated whether matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a useful alternative. The 289 Fusarium strains from the Belgian Coordinated Collections of Microorganisms (BCCM)/Institute of Hygiene and Epidemiology Mycology (IHEM) culture collection with validated sequence-based identities and comprising 40 species were used in this study. An identification strategy was developed, applying a standardized MALDI-TOF MS assay and an in-house reference spectrum database. In vitro antifungal testing was performed to assess important differences in susceptibility between clinically relevant species/species complexes. We observed that no incorrect species complex identifications were made by MALDI-TOF MS, and 82.8% of the identifications were correct to the species level. This success rate was increased to 91% by lowering the cutoff for identification. Although the identification of the correct species complex member was not always guaranteed, antifungal susceptibility testing showed that discriminating between Fusarium species complexes can be important for treatment but is not necessarily required between members of a species complex. With this perspective, some Fusarium species complexes with closely related members can be considered as a whole, increasing the success rate of correct identifications to 97%. The application of our user-friendly MALDI-TOF MS identification approach resulted in a dramatic improvement in both time and accuracy compared to identification with the conventional method. A proof of principle of our MALDI-TOF MS approach in the clinical setting using recently isolated Fusarium strains demonstrated its validity. PMID:25411180

Interleukin-8 responses of multi-layer gingival epithelia to subgingival biofilms: role of the "red complex" species.

PubMed

Belibasakis, Georgios N; Thurnheer, Thomas; Bostanci, Nagihan

2013-01-01

Periodontitis is an infectious inflammatory disease that results in the destruction of the tooth-supporting (periodontal) tissues. The Gram-negative anaerobic species Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola, (also known as the "red complex" species) are highly associated with subgingival biofilms at periodontitis-affected sites. A major chemokine produced by the gingival epithelium in response to biofilm challenge, is interleukin (IL)-8. The aim of this in vitro study was to investigate the relative effect of the "red complex" species as constituents of subgingival biofilms, on the regulation of IL-8 by gingival epithelia. Multi-layered organotypic human gingival epithelial cultures were challenged with a 10-species in vitro subgingival biofilm model, or its 7-species variant, excluding the "red complex". IL-8 gene expression and secretion analyses were performed by qPCR and ELISA, respectively. After 3 h, both biofilms up-regulated IL-8 gene expression, but the presence of the "red complex" resulted in 3-fold greater response. IL-8 secretion was also up-regulated by both biofilms, with no differences between them. After 24 h, the 10-species biofilm reduced IL-8 secretion to 50% of the control, but this was not affected when the "red complex" was absent. In conclusion, as part of biofilms, "red complex" species differentially regulate IL-8 in gingival epithelia, potentially affecting the chemotactic responses of the tissue.

Independent evolution of complex life history adaptations in two families of fishes, live-bearing halfbeaks (zenarchopteridae, beloniformes) and poeciliidae (cyprinodontiformes).

PubMed

Reznick, David; Meredith, Robert; Collette, Bruce B

2007-11-01

We have previously documented multiple, independent origins of placentas in the fish family Poeciliidae. Here we summarize similar analyses of fishes in the family Zenarchopteridae. This family includes three live-bearing genera. Earlier studies documented the presence of superfetation, or the ability to carry multiple litters of young in different stages of development in the same ovary, in some species in all three genera. There is also one earlier report of matrotrophy, or extensive postfertilization maternal provisioning, in two of these genera. We present detailed life-history data for approximately half of the species in all three genera and combine them with the best available phylogeny to make inferences about the pattern of life-history evolution within this family. Three species of Hemirhamphodon have superfetation but lack matrotrophy. Most species in Nomorhamphus and Dermogenys either lack superfetation and matrotrophy or have both superfetation and matrotrophy. Our phylogenetic analysis shows that matrotrophy may have evolved independently in each genus. In Dermogenys, matrotrophic species produce fewer, larger offspring than nonmatrotrophic species. In Nomorhamphus; matrotrophic species instead produce more and smaller offspring than lecithotrophic species. However, the matrotrophic species in both genera have significantly smaller masses of reproductive tissue relative to their body sizes. All aspects of these results are duplicated in the fish family Poeciliidae. We discuss the possible adaptive significance of matrotrophy in the light of these new results. The two families together present a remarkable opportunity to study the evolution of a complex trait because they contain multiple, independent origins of the trait that often include close relatives that vary in either the presence or absence of the matrotrophy or in the degree to which matrotrophy is developed. These are the raw materials that are required for either an analysis of the adaptive significance of the trait or for studies of the genetic mechanisms that underlie the evolution of the trait.

The Seasonality and Ecology of the Anopheles gambiae complex (Dipetra: Culicidae) in Liberia Using Molecular Identification.

PubMed

Fahmy, N T; Villinski, J T; Bolay, F; Stoops, C A; Tageldin, R A; Fakoli, L; Okasha, O; Obenauer, P J; Diclaro, J W

2015-05-01

Members of the Anopheles gambiae sensu lato (Giles) complex define a group of seven morphologically indistinguishable species, including the principal malaria vectors in Sub-Saharan Africa. Members of this complex differ in behavior and ability to transmit malaria; hence, precise identification of member species is critical to monitoring and evaluating malaria threat levels. We collected mosquitoes from five counties in Liberia every other month from May 2011 until May 2012, using various trapping techniques. A. gambiae complex members were identified using molecular techniques based on differences in the ribosomal DNA (rDNA) region between species and the molecular forms (S and M) of A. gambiae sensu stricto (s.s) specimens. In total, 1,696 A. gambiae mosquitoes were collected and identified. DNA was extracted from legs of each specimen with species identification determined by multiplex polymerase chain reaction using specific primers. The molecular forms (M or S) of A. gambiae s.s were determined by restriction fragment length polymorphism. Bivariate and multivariate logistic regression models identified environmental variables associated with genomic differentiation. Our results indicate widespread occurrence of A. gambiae s.s., the principal malaria vector in the complex, although two Anopheles melas Theobald/A. merus Donitz mosquitoes were detected. We found 72.6, 25.5, and 1.9% of A. gambiae s.s specimens were S, M, and hybrid forms, respectively. Statistical analysis indicates that the S form was more likely to be found in rural areas during rainy seasons and indoor catchments. This information will enhance vector control efforts in Liberia. Published by Oxford University Press on behalf of Entomological Society of America 2015. This work is written by US Government employees and is in the public domain in the US.

Using hand proportions to test taxonomic boundaries within the Tupaia glis species complex (Scandentia, Tupaiidae)

USGS Publications Warehouse

Sargos, Eric J.; Woodman, Neal; Reese, Aspen T.; Olson, Link E.

2013-01-01

Treeshrews (order Scandentia) comprise 2 families of squirrel-sized terrestrial, arboreal, and scansorial mammals distributed throughout much of tropical South and Southeast Asia. The last comprehensive taxonomic revision of treeshrews was published in 1913, and a well-supported phylogeny clarifying relationships among all currently recognized extant species within the order has only recently been published. Within the family Tupaiidae, 2 widely distributed species, the northern treeshrew, Tupaia belangeri (Wagner, 1841), and the common treeshrew, T. glis (Diard, 1820), represent a particularly vexing taxonomic complex. These 2 species are currently distinguished primarily based on their respective distributions north and south of the Isthmus of Kra on the Malay Peninsula and on their different mammae counts. This problematic species complex includes 54 published synonyms, many of which represent putative island endemics. The widespread T. glis and T. belangeri collectively comprise a monophyletic assemblage representing the sister lineage to a clade composed of the golden-bellied treeshrew, T. chrysogaster Miller, 1903 (Mentawai Islands), and the long-footed treeshrew, T. longipes (Thomas, 1893) (Borneo). As part of a morphological investigation of the T. glis–T. belangeri complex, we studied the proportions of hand bones, which have previously been shown to be useful in discriminating species of soricids (true shrews). We measured 38 variables from digital X-ray images of 148 museum study skins representing several subspecies of T. glis, T. belangeri, T. chrysogaster, and T. longipes and analyzed these data using principal components and cluster analyses. Manus proportions among these 4 species readily distinguish them, particularly in the cases of T. chrysogaster and T. longipes. We then tested the distinctiveness of several of the populations comprising T. glis and T. longipes. T. longipes longipes and T. l. salatana Lyon, 1913, are distinguishable from each other, and populations of T. "glis" from Bangka Island and Sumatra are distinct from those on the Malay Peninsula, supporting the recognition of T. salatana, T. discolor Lyon, 1906, and T. ferruginea Raffles, 1821 as distinct species in Indonesia. These relatively small, potentially vulnerable treeshrew populations occur in the Sundaland biodiversity hotspot and will require additional study to determine their appropriate conservation status.

Biodiversity of complexes of mycotoxigenic fungal species associated with Fusarium ear rot of maize and Aspergillus rot of grape.

PubMed

Logrieco, A; Moretti, A; Perrone, G; Mulè, G

2007-10-20

Fusarium ear rot of maize and Aspergillus rot of grape are two examples of important plant diseases caused by complexes of species of mycotoxigenic fungi. These complexes of species tend to be closely related, produce different classes of mycotoxins, and can induce disease under different environmental conditions. The infection of maize and grape with multiple fungal species and the resulting production of large classes of mycotoxins is an example of mutual aggressiveness of microorganisms toward host species as well as to humans and animals that eat feed or food derived from the infected and contaminated plants. Infection of crop plant with a complex of microbial species certainly represents a greater threat to a crop plant and to human and animal health than infection of the plant with a single fungal species.

Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae).

PubMed

Šašić, Ljiljana; Ačanski, Jelena; Vujić, Ante; Ståhls, Gunilla; Radenković, Snežana; Milić, Dubravka; Obreht Vidaković, Dragana; Đan, Mihajla

2016-01-01

The Merodon aureus species group (Diptera: Syrphidae: Eristalinae) comprises a number of different sub-groups and species complexes. In this study we focus on resolving the taxonomic status of the entity previously identified as M. cinereus B, here identified as M. atratus species complex. We used an integrative approach based on morphological descriptions, combined with supporting characters that were obtained from molecular analyses of the mitochondrial cytochrome c oxidase I gene as well as from geometric morphometry of wing and surstylus shapes and environmental niche comparisons. All applied data and methods distinguished and supported three morphologically cryptic species: M. atratus stat. nov., M. virgatus sp. nov. and M. balkanicus sp. nov., which constitute the M. atratus species complex. We present an identification key for the sub-groups and species complexes of the M. aureus species group occurring in Europe, describe the taxa and discuss the utility of the applied methods for species delimitation. The estimated divergence times for the species splits of these taxa coincide with the Pleistocene Günz-Mindel interglaciation and the Great interglaciation (between the Ris and Mindel glacial periods).

Complex dynamics in the Leslie-Gower type of the food chain system with multiple delays

NASA Astrophysics Data System (ADS)

Guo, Lei; Song, Zi-Gen; Xu, Jian

2014-08-01

In this paper, we present a Leslie-Gower type of food chain system composed of three species, which are resource, consumer, and predator, respectively. The digestion time delays corresponding to consumer-eat-resource and predator-eat-consumer are introduced for more realistic consideration. It is called the resource digestion delay (RDD) and consumer digestion delay (CDD) for simplicity. Analyzing the corresponding characteristic equation, the stabilities of the boundary and interior equilibrium points are studied. The food chain system exhibits the species coexistence for the small values of digestion delays. Large RDD/CDD may destabilize the species coexistence and induce the system dynamic into recurrent bloom or system collapse. Further, the present of multiple delays can control species population into the stable coexistence. To investigate the effect of time delays on the recurrent bloom of species population, the Hopf bifurcation and periodic solution are investigated in detail in terms of the central manifold reduction and normal form method. Finally, numerical simulations are performed to display some complex dynamics, which include multiple periodic solution and chaos motion for the different values of system parameters. The system dynamic behavior evolves into the chaos motion by employing the period-doubling bifurcation.

Genetic effects on mating success and partner choice in a social mammal

PubMed Central

Tung, Jenny; Charpentier, Marie JE; Mukherjee, Sayan; Altmann, Jeanne; Alberts, Susan C

2012-01-01

Mating behavior has profound consequences for two phenomena – individual reproductive success and the maintenance of species boundaries – that contribute to evolutionary processes. Studies of mating behavior in relation to individual reproductive success are common in many species, but studies of mating behavior in relation to genetic variation and species boundaries are less commonly conducted in socially complex species. Here, we leveraged extensive observations of a wild yellow baboon (Papio cynocephalus) population that has experienced recent gene flow from a close sister taxon, the anubis baboon (Papio anubis), to examine how admixture-related genetic background affects mating behavior. We identified novel effects of genetic background on mating patterns, including an advantage accruing to anubis-like males and assortative mating among both yellow-like and anubis-like pairs. These genetic effects acted alongside social dominance rank, inbreeding avoidance, and age to produce highly nonrandom mating patterns. Our results suggest that this population may be undergoing admixture-related evolutionary change, driven in part by nonrandom mating. However, the strength of the genetic effects is mediated by behavioral plasticity and social interactions, emphasizing the strong influence of social context on mating behavior in socially complex species. PMID:22673655

Environmental Screening for the Scedosporium apiospermum Species Complex in Public Parks in Bangkok, Thailand.

PubMed

Luplertlop, Natthanej; Pumeesat, Potjaman; Muangkaew, Watcharamat; Wongsuk, Thanwa; Alastruey-Izquierdo, Ana

2016-01-01

The Scedosporium apiospermum species complex, comprising filamentous fungal species S. apiospermum sensu stricto, S. boydii, S. aurantiacum, S. dehoogii and S. minutispora, are important pathogens that cause a wide variety of infections. Although some species (S. boydii and S. apiospermum) have been isolated from patients in Thailand, no environmental surveys of these fungi have been performed in Thailand or surrounding countries. In this study, we isolated and identified species of these fungi from 68 soil and 16 water samples randomly collected from 10 parks in Bangkok. After filtration and subsequent inoculation of samples on Scedo-Select III medium, colony morphological examinations and microscopic observations were performed. Scedosporium species were isolated from soil in 8 of the 10 parks, but were only detected in one water sample. Colony morphologies of isolates from 41 of 68 soil samples (60.29%) and 1 of 15 water samples (6.67%) were consistent with that of the S. apiospermum species complex. Each morphological type was selected for species identification based on DNA sequencing and phylogenetic analysis of the β-tubulin gene. Three species of the S. apiospermum species complex were identified: S. apiospermum (71 isolates), S. aurantiacum (6 isolates) and S. dehoogii (5 isolates). In addition, 16 sequences could not be assigned to an exact Scedosporium species. According to our environmental survey, the S. apiospermum species complex is widespread in soil in Bangkok, Thailand.

Environmental Screening for the Scedosporium apiospermum Species Complex in Public Parks in Bangkok, Thailand

PubMed Central

Pumeesat, Potjaman; Muangkaew, Watcharamat; Wongsuk, Thanwa; Alastruey-Izquierdo, Ana

2016-01-01

The Scedosporium apiospermum species complex, comprising filamentous fungal species S. apiospermum sensu stricto, S. boydii, S. aurantiacum, S. dehoogii and S. minutispora, are important pathogens that cause a wide variety of infections. Although some species (S. boydii and S. apiospermum) have been isolated from patients in Thailand, no environmental surveys of these fungi have been performed in Thailand or surrounding countries. In this study, we isolated and identified species of these fungi from 68 soil and 16 water samples randomly collected from 10 parks in Bangkok. After filtration and subsequent inoculation of samples on Scedo-Select III medium, colony morphological examinations and microscopic observations were performed. Scedosporium species were isolated from soil in 8 of the 10 parks, but were only detected in one water sample. Colony morphologies of isolates from 41 of 68 soil samples (60.29%) and 1 of 15 water samples (6.67%) were consistent with that of the S. apiospermum species complex. Each morphological type was selected for species identification based on DNA sequencing and phylogenetic analysis of the β-tubulin gene. Three species of the S. apiospermum species complex were identified: S. apiospermum (71 isolates), S. aurantiacum (6 isolates) and S. dehoogii (5 isolates). In addition, 16 sequences could not be assigned to an exact Scedosporium species. According to our environmental survey, the S. apiospermum species complex is widespread in soil in Bangkok, Thailand. PMID:27467209

Taxonomic revision of Israeli snakes belonging to the Platyceps rhodorachis species complex (Reptilia: Squamata: Colubridae).

PubMed

Sinaiko, Guy; Magory-Cohen, Tali; Meiri, Shai; Dor, Roi

2018-02-15

The Platyceps rhodorachis species complex encompasses a widespread group of morphologically similar colubrid snakes. The number and identities of species from this complex in Israel have recently been debated. Studies from the previous decade concluded that there are two species in Israel and its vicinity (compared with one previously recognized), but their identity remained contested. We estimated the number of species and their taxonomic identity using morphological and molecular data. We found some evidence for clinal variation in many of the characters used to differentiate the species, and a great overlap in traits of putative species. Genetic data revealed very low sequence divergence, with all putative species being paraphyletic. Platyceps rogersi emerged as genetically closer to Platyceps saharicus rather than to its putative conspecific, P. karelini. The phylogenetic and taxonomic results thus indicate that the Israeli populations of the P. rhodorachis complex all belong to a single species, Platyceps saharicus (Schätti McCarthy 2004).

Radiation and diversification within the Ligularia-Cremanthodium-Parasenecio complex (Asteraceae) triggered by uplift of the Qinghai-Tibetan Plateau.

PubMed

Liu, Jian-Quan; Wang, Yu-Jing; Wang, Ai-Lan; Hideaki, Ohba; Abbott, Richard J

2006-01-01

The Ligularia-Cremanthodium-Parasenecio (L-C-P) complex of the Tussilagininae (Asteraceae: Senecioneae) contains more than 200 species that are endemic to the Qinghai-Tibetan Plateau in eastern Asia. These species are morphologically distinct; however, their relationships appear complex. A phylogenetic analysis of members of the complex and selected taxa of the tribe Senecioneae was conducted using chloroplast (ndhF and trnL-F) and nuclear (ITS) sequences. Phylogenetic trees were constructed from individual and combined datasets of the three different sequences. All analyses suggested that Doronicum, a genus that has been included in the Tussilagininae, should be excluded from this subtribe and placed at the base of the tribe Senecioneae. In addition, the Tussilagininae should be broadly circumscribed to include the Tephroseridinae. Within the expanded Tussilagininae containing all 13 genera occurring in eastern Asia, Tussilago and Petasites diverged early as a separate lineage, while the remaining 11 genera comprise an expanded L-C-P complex clade. We suggest that the L-C-P clade, which is largely unresolved, most likely originated as a consequence of an explosive radiation. The few monophyletic subclades identified in the L-C-P clade with robust support further suggest that some genera of Tussilagininae from eastern Asia require generic re-circumscriptions given the occurrence of subclades containing species of the same genus in different parts of the phylogentic tree due to homoplasy of important morphological characters used to delimit them. Molecular-clock analyses suggest that the explosive radiation of the L-C-P complex occurred mostly within the last 20 million years, which falls well within the period of recent major uplifts of the Qinghai-Tibetan Plateau between the early Miocene to the Pleistocene. It is proposed that significant increases in geological and ecological diversity that accompanied such uplifting, most likely promoted rapid and continuous allopatric speciation in small and isolated populations, and allowed fixation or acquisition of similar morphological characters within unrelated lineages. This phenomenon, possibly combined with interspecific diploid hybridization because of secondary sympatry during relatively stable stages between different uplifts, could be a major cause of high species diversity in the Qinghai-Tibetan Plateau and adjacent areas of eastern Asia.

Genetic variation and origin of parthenogenesis in the Aspidoscelis cozumela complex: evidence from mitochondrial genes.

PubMed

Manríquez-Morán, Norma L; Cruz, Fausto R Méndez-de la; Murphy, Robert W

2014-01-01

Parthenogenesis is a form of clonal reproduction. Eggs develop in the absence of sperm and offspring are genetically identical to their mother. Although common in invertebrates, it occurs in only a few species of squamate reptiles. Parthenogenetic reptiles have their origin in interspecific hybridization, and their populations are exclusively female. Because of its high mutation rate and maternal inheritance, mitochondrial DNA sequence data can evaluate the origin and evolution of all-female vertebrates. Partial sequences from two mitochondrial genes, Cytb and ND4, were analyzed to investigate questions about the origin of parthenogenesis in the Aspidoscelis cozumela complex, which includes A. cozumela, A. maslini and A. rodecki. Low levels of divergence were detected among parthenogenetic species, and between them and A. angusticeps, confirming it as the maternal species of the parthenoforms. A gene tree was constructed using sequences from three populations of A. angusticeps and nine of its unisexual daughter species. The phylogeny suggests that two independent hybridization events between A. angusticeps and A. deppii formed three unisexual species. One hybridization resulted in A. rodecki and the other formed A. maslini and A. cozumela. Although A. cozumela has the haplotype characteristic of A. maslini from Puerto Morelos, it is considered to be a different species based on karyological and morphological characteristics and its geographical isolation.

Hybridization and population structure of the Culex pipiens complex in the islands of Macaronesia

PubMed Central

Gomes, Bruno; Alves, Joana; Sousa, Carla A; Santa-Ana, Marta; Vieira, Inês; Silva, Teresa L; Almeida, António PG; Donnelly, Martin J; Pinto, João

2012-01-01

The Culex pipiens complex includes two widespread mosquito vector species, Cx. pipiens and Cx. quinquefasciatus. The distribution of these species varies in latitude, with the former being present in temperate regions and the latter in tropical and subtropical regions. However, their distribution range overlaps in certain areas and interspecific hybridization has been documented. Genetic introgression between these species may have epidemiological repercussions for West Nile virus (WNV) transmission. Bayesian clustering analysis based on multilocus genotypes of 12 microsatellites was used to determine levels of hybridization between these two species in Macaronesian islands, the only contact zone described in West Africa. The distribution of the two species reflects both the islands' biogeography and historical aspects of human colonization. Madeira Island displayed a homogenous population of Cx. pipiens, whereas Cape Verde showed a more intriguing scenario with extensive hybridization. In the islands of Brava and Santiago, only Cx. quinquefasciatus was found, while in Fogo and Maio high hybrid rates (∼40%) between the two species were detected. Within the admixed populations, second-generation hybrids (∼50%) were identified suggesting a lack of isolation mechanisms. The observed levels of hybridization may locally potentiate the transmission to humans of zoonotic arboviruses such as WNV. PMID:22957190

Design and control strategies for CELSS - Integrating mechanistic paradigms and biological complexities

NASA Technical Reports Server (NTRS)

Moore, B., III; Kaufmann, R.; Reinhold, C.

1981-01-01

Systems analysis and control theory consideration are given to simulations of both individual components and total systems, in order to develop a reliable control strategy for a Controlled Ecological Life Support System (CELSS) which includes complex biological components. Because of the numerous nonlinearities and tight coupling within the biological component, classical control theory may be inadequate and the statistical analysis of factorial experiments more useful. The range in control characteristics of particular species may simplify the overall task by providing an appropriate balance of stability and controllability to match species function in the overall design. The ultimate goal of this research is the coordination of biological and mechanical subsystems in order to achieve a self-supporting environment.

The capuchin monkey as a flight candidate

NASA Technical Reports Server (NTRS)

Winget, C. M.

1977-01-01

The highly evolved nervous system and associated complex behavioral capabilities of the nonhuman primates make them good candidates for certain studies in the space environment since deleterious changes in these more complex aspects of a biological status can only be demonstrated by species which share such highly evolved features with man. Important assets which urge the selection of the capuchin monkey for space experiments include his small size, high intelligence, relative disease resistance, nutritional requirements, and lower volume life support systems. The species is particularly suited for experiments on the nervous system or on process under neural control because of the similarity of capuchin and human blood chemistry profiles and endocrine systems involved in the maintenance of homeostasis and vasomotor tone.

Catalytic hydroboration by an imido-hydrido complex of Mo(IV).

PubMed

Khalimon, Andrey Y; Farha, Philip; Kuzmina, Lyudmila G; Nikonov, Georgii I

2012-01-11

The imido-hydrido complex (ArN)Mo(H)(Cl)(PMe(3))(3) catalyses a variety of hydroboration reactions, including the first example of catalytic addition of HBCat to nitriles to form the bis(borylated) amines RCH(2)N(BCat)(2). The latter species easily undergoes chemoselective coupling with aldehydes R'C(O)H to yield imines RCH(2)N=C(H)R'. This journal is © The Royal Society of Chemistry 2012

Assessing Species Diversity Using Metavirome Data: Methods and Challenges.

PubMed

Herath, Damayanthi; Jayasundara, Duleepa; Ackland, David; Saeed, Isaam; Tang, Sen-Lin; Halgamuge, Saman

2017-01-01

Assessing biodiversity is an important step in the study of microbial ecology associated with a given environment. Multiple indices have been used to quantify species diversity, which is a key biodiversity measure. Measuring species diversity of viruses in different environments remains a challenge relative to measuring the diversity of other microbial communities. Metagenomics has played an important role in elucidating viral diversity by conducting metavirome studies; however, metavirome data are of high complexity requiring robust data preprocessing and analysis methods. In this review, existing bioinformatics methods for measuring species diversity using metavirome data are categorised broadly as either sequence similarity-dependent methods or sequence similarity-independent methods. The former includes a comparison of DNA fragments or assemblies generated in the experiment against reference databases for quantifying species diversity, whereas estimates from the latter are independent of the knowledge of existing sequence data. Current methods and tools are discussed in detail, including their applications and limitations. Drawbacks of the state-of-the-art method are demonstrated through results from a simulation. In addition, alternative approaches are proposed to overcome the challenges in estimating species diversity measures using metavirome data.

A phylogeny of Astyanax (Characiformes: Characidae) in Central and North America.

PubMed

Schmitter-Soto, Juan J

2016-05-06

A phylogeny is presented for 34 species of Astyanax, 27 of them once included within A. aeneus or A. fasciatus in Central America and Mexico, based on 52 morphological characters (mostly osteological, but also pigmentation and meristics), with three outgroups. Monophyly is not supported for A. aeneus s. lat., as Brazilian species such as A. fasciatus s. str. and others occur also within that clade. There were only five resolved clades, three of them including both Brazilian and Central American species, one purely Nicaraguan, and one for central-northern Mexico and Texas. Coincidence with previous cladistic hypotheses is only partial. The genus Bramocharax Gill is not recovered, and thus confirmed as a synonym of Astyanax Baird & Girard. The findings point at a more complex biogeographic history of the region than usually recognized.

Ecological Distribution and CQ11 Genetic Structure of Culex pipiens Complex (Diptera: Culicidae) in Italy.

PubMed

Di Luca, Marco; Toma, Luciano; Boccolini, Daniela; Severini, Francesco; La Rosa, Giuseppe; Minelli, Giada; Bongiorno, Gioia; Montarsi, Fabrizio; Arnoldi, Daniele; Capelli, Gioia; Rizzoli, Annapaola; Romi, Roberto

2016-01-01

Mosquitoes in the Culex pipiens complex are considered to be involved in the transmission of a range of pathogens, including West Nile virus (WNV). Although its taxonomic status is still debated, the complex includes species, both globally distributed or with a more limited distribution, morphologically similar and characterised by different physiological and behavioural traits, which affect their ability as vectors. In many European countries, Cx. pipiens and its sibling species Culex torrentium occur in sympatry, exhibiting similar bionomic and morphological characters, but only Cx. pipiens appears to play a vector role in WNV transmission. This species consists of two biotypes, pipiens and molestus, which can interbreed when in sympatry, and their hybrids can act as WNV-bridge vectors, due to intermediate ecological features. Considering the yearly WNV outbreaks since 2008 and given the morphological difficulties in recognising species and biotypes, our aim was to molecularly identify and characterised Cx. pipiens and Cx. torrentium in Italy, using recently developed molecular assays. Culex torrentium was not detected; as in other European countries, the pipiens and molestus biotypes were widely found in sympatry with hybrids in most environments. The UPGMA cluster analysis applied to CQ11 genotypic frequencies mainly revealed two groups of Cx. pipiens populations that differed in ecological features. The high propensity of the molestus biotype to exist in hypogean environments, where the habitat's physical characteristics hinder and preclude the gene flow, was shown. These results confirmed the CQ11 assay as a reliable diagnostic method, consistent with the ecological and physiological aspects of the populations analysed. Since the assessment of the actual role of three biotypes in the WNV circulation remains a crucial point to be elucidated, this extensive molecular screening of Cx. pipiens populations can provide new insights into the ecology of the species and may give useful indications to plan and implement WNV surveillance activities in Italy.

Ecological Distribution and CQ11 Genetic Structure of Culex pipiens Complex (Diptera: Culicidae) in Italy

PubMed Central

Di Luca, Marco; Toma, Luciano; Boccolini, Daniela; Severini, Francesco; La Rosa, Giuseppe; Minelli, Giada; Bongiorno, Gioia; Montarsi, Fabrizio; Arnoldi, Daniele; Capelli, Gioia; Rizzoli, Annapaola; Romi, Roberto

2016-01-01

Mosquitoes in the Culex pipiens complex are considered to be involved in the transmission of a range of pathogens, including West Nile virus (WNV). Although its taxonomic status is still debated, the complex includes species, both globally distributed or with a more limited distribution, morphologically similar and characterised by different physiological and behavioural traits, which affect their ability as vectors. In many European countries, Cx. pipiens and its sibling species Culex torrentium occur in sympatry, exhibiting similar bionomic and morphological characters, but only Cx. pipiens appears to play a vector role in WNV transmission. This species consists of two biotypes, pipiens and molestus, which can interbreed when in sympatry, and their hybrids can act as WNV-bridge vectors, due to intermediate ecological features. Considering the yearly WNV outbreaks since 2008 and given the morphological difficulties in recognising species and biotypes, our aim was to molecularly identify and characterised Cx. pipiens and Cx. torrentium in Italy, using recently developed molecular assays. Culex torrentium was not detected; as in other European countries, the pipiens and molestus biotypes were widely found in sympatry with hybrids in most environments. The UPGMA cluster analysis applied to CQ11 genotypic frequencies mainly revealed two groups of Cx. pipiens populations that differed in ecological features. The high propensity of the molestus biotype to exist in hypogean environments, where the habitat’s physical characteristics hinder and preclude the gene flow, was shown. These results confirmed the CQ11 assay as a reliable diagnostic method, consistent with the ecological and physiological aspects of the populations analysed. Since the assessment of the actual role of three biotypes in the WNV circulation remains a crucial point to be elucidated, this extensive molecular screening of Cx. pipiens populations can provide new insights into the ecology of the species and may give useful indications to plan and implement WNV surveillance activities in Italy. PMID:26741494

The Colletotrichum acutatum species complex

PubMed Central

Damm, U.; Cannon, P.F.; Woudenberg, J.H.C.; Crous, P.W.

2012-01-01

Colletotrichum acutatum is known as an important anthracnose pathogen of a wide range of host plants worldwide. Numerous studies have reported subgroups within the C. acutatum species complex. Multilocus molecular phylogenetic analysis (ITS, ACT, TUB2, CHS-1, GAPDH, HIS3) of 331 strains previously identified as C. acutatum and other related taxa, including strains from numerous hosts with wide geographic distributions, confirmed the molecular groups previously recognised and identified a series of novel taxa. Thirty-one species are accepted, of which 21 have not previously been recognised. Colletotrichum orchidophilum clusters basal to the C. acutatum species complex. There is a high phenotypic diversity within this complex, and some of the species appear to have preferences to specific hosts or geographical regions. Others appear to be plurivorous and are present in multiple regions. In this study, only C. salicis and C. rhombiforme formed sexual morphs in culture, although sexual morphs have been described from other taxa (especially as laboratory crosses), and there is evidence of hybridisation between different species. One species with similar morphology to C. acutatum but not belonging to this species complex was also described here as new, namely C. pseudoacutatum. Taxonomic novelties: New combinations - Colletotrichum limetticola (R.E. Clausen) Damm, P.F. Cannon & Crous, C. lupini (Bondar) Damm, P.F. Cannon & Crous, C. salicis (Fuckel) Damm, P.F. Cannon & Crous. New species - C. acerbum Damm, P.F. Cannon & Crous, C. australe Damm, P.F. Cannon & Crous, C. brisbanense Damm, P.F. Cannon & Crous, C. cosmi Damm, P.F. Cannon & Crous, C. costaricense Damm, P.F. Cannon & Crous, C. cuscutae Damm, P.F. Cannon & Crous, C. guajavae Damm, P.F. Cannon & Crous, C. indonesiense Damm, P.F. Cannon & Crous, C. johnstonii Damm, P.F. Cannon & Crous, C. kinghornii Damm, P.F. Cannon & Crous, C. laticiphilum Damm, P.F. Cannon & Crous, C. melonis Damm, P.F. Cannon & Crous, C. orchidophilum Damm, P.F. Cannon & Crous, C. paxtonii Damm, P.F. Cannon & Crous, C. pseudoacutatum Damm, P.F. Cannon & Crous C. pyricola Damm, P.F. Cannon & Crous, C. rhombiforme Damm, P.F. Cannon & Crous, C. scovillei Damm, P.F. Cannon & Crous, C. sloanei Damm, P.F. Cannon & Crous, C. tamarilloi Damm, P.F. Cannon & Crous, C. walleri Damm, P.F. Cannon & Crous. Typifications: Epitypifications - C. acutatum J.H. Simmonds, C. limetticola (R.E. Clausen) Damm, P.F. Cannon & Crous, C. nymphaeae (Pass.) Aa, C. phormii (Henn.) D.F. Farr & Rossman, C. salicis (Fuckel) Damm, P.F. Cannon & Crous. Lectotypifications - C. nymphaeae (Pass.) Aa, C. orchidearum Allesch. PMID:23136458

Pyramidal Cells in Prefrontal Cortex of Primates: Marked Differences in Neuronal Structure Among Species

PubMed Central

Elston, Guy N.; Benavides-Piccione, Ruth; Elston, Alejandra; Manger, Paul R.; DeFelipe, Javier

2010-01-01

The most ubiquitous neuron in the cerebral cortex, the pyramidal cell, is characterized by markedly different dendritic structure among different cortical areas. The complex pyramidal cell phenotype in granular prefrontal cortex (gPFC) of higher primates endows specific biophysical properties and patterns of connectivity, which differ from those in other cortical regions. However, within the gPFC, data have been sampled from only a select few cortical areas. The gPFC of species such as human and macaque monkey includes more than 10 cortical areas. It remains unknown as to what degree pyramidal cell structure may vary among these cortical areas. Here we undertook a survey of pyramidal cells in the dorsolateral, medial, and orbital gPFC of cercopithecid primates. We found marked heterogeneity in pyramidal cell structure within and between these regions. Moreover, trends for gradients in neuronal complexity varied among species. As the structure of neurons determines their computational abilities, memory storage capacity and connectivity, we propose that these specializations in the pyramidal cell phenotype are an important determinant of species-specific executive cortical functions in primates. PMID:21347276

The Cladophora complex (Chlorophyta): new views based on 18S rRNA gene sequences.

PubMed

Bakker, F T; Olsen, J L; Stam, W T; van den Hoek, C

1994-12-01

Evolutionary relationships among species traditionally ascribed to the Siphonocladales/Cladophorales have remained unclear due to a lack of phylogenetically informative characters and extensive morphological plasticity resulting in morphological convergence. This study explores some of the diversity within the generic complex Cladophora and its siphonocladalaen allies. Twelve species of Cladophora representing 6 of the 11 morphological sections recognized by van den Hoek were analyzed along with 8 siphonocladalaen species using 18S rRNA gene sequences. The final alignment consisted of 1460 positions containing 92 phylogenetically informative substitutions. Weighting schemes (EOR weighting, combinatorial weighting) were applied in maximum parsimony analysis to correct for substitution bias. Stem characters were weighted 0.66 relative to single-stranded characters to correct for secondary structural constraints. Both weighting approaches resulted in greater phylogenetic resolution. Results confirm that there is no basis for the independent recognition of the Cladophorales and Siphonocladales. The Siphonocladales is polyphyletic, and Cladophora is paraphyletic. All analyses support two principal lineages, of which one contains predominantly tropical members including almost all siphonocladalean taxa, while the other lineage consists of mostly warm- to cold-temperate species of Cladophora.

First report of Neoechinorhynchus (Acanthocephala: Neoechinorhynchidae) from marine fish of the eastern seaboard of Vietnam, with the description of six new species

PubMed Central

Amin, O.M.; Ha, N.V.; Ha, D.N.

2011-01-01

The occurrence of acanthocephalans of the genus Neoechinorhynchus Stiles and Hassall, 1905 in Vietnamese waters is reported for the first time. Six new species are described from seven species of marine fish of the families Belonidae, Clupeidae, Megalopidae, Mugilidae, and Sciaenidae, collected in Halong Bay of the eastern seaboard of Vietnam in 2008 and 2009. These are Neoechinorhynchus (Neoechinorhynchus) plaquensis n. sp. characterized by dermal plaques covering the entire trunk; Neoechinorhynchus manubriensis n. sp. with very long anterior proboscis hooks having roots with prominent anterior manubria and very small and equal middle and posterior hooks, two pseudoretractors in the receptacle, simple vagina, and terminal gonopore; Neoechinorhynchus pennahia n. sp. with equal anterior and middle proboscis and somewhat smaller posterior hooks, and terminal female gonopore; Neoechinorhynchus ampullata with many giant nuclei in the body wall and lemnisci and a parareceptacle structure complex which includes pumping ampullas reported for the first time; Neoechinorhynchus (Neoechinorhynchus) longinucleatus n. sp. with very long giant nuclei in the Lemnisci, anteriorly twisted vagina, and subterminal female gonopore. Neoechinorhynchus (Neoechinorhynchus) ascus n. sp. is the second species of Neoechinorhynchus found with the parareceptacle structure/ampulla complex. Neoechinorhynchus (Neoechinorhynchus) johnii Yamaguti, 1929 of Bilqees, 1972 is not N. johnii because of proboscis armature and other discrepancies with the Yamaguti material. Notes on host distribution and feeding habits are also included. PMID:21395202

Novel molecular approach to define pest species status and tritrophic interactions from historical Bemisia specimens.

PubMed

Tay, W T; Elfekih, S; Polaszek, A; Court, L N; Evans, G A; Gordon, K H J; De Barro, P J

2017-03-27

Museum specimens represent valuable genomic resources for understanding host-endosymbiont/parasitoid evolutionary relationships, resolving species complexes and nomenclatural problems. However, museum collections suffer DNA degradation, making them challenging for molecular-based studies. Here, the mitogenomes of a single 1912 Sri Lankan Bemisia emiliae cotype puparium, and of a 1942 Japanese Bemisia puparium are characterised using a Next-Generation Sequencing approach. Whiteflies are small sap-sucking insects including B. tabaci pest species complex. Bemisia emiliae's draft mitogenome showed a high degree of homology with published B. tabaci mitogenomes, and exhibited 98-100% partial mitochondrial DNA Cytochrome Oxidase I (mtCOI) gene identity with the B. tabaci species known as Asia II-7. The partial mtCOI gene of the Japanese specimen shared 99% sequence identity with the Bemisia 'JpL' genetic group. Metagenomic analysis identified bacterial sequences in both Bemisia specimens, while hymenopteran sequences were also identified in the Japanese Bemisia puparium, including complete mtCOI and rRNA genes, and various partial mtDNA genes. At 88-90% mtCOI sequence identity to Aphelinidae wasps, we concluded that the 1942 Bemisia nymph was parasitized by an Eretmocerus parasitoid wasp. Our approach enables the characterisation of genomes and associated metagenomic communities of museum specimens using 1.5 ng gDNA, and to infer historical tritrophic relationships in Bemisia whiteflies.

Quantum chemical study of the structure and properties of citrinin

USDA-ARS?s Scientific Manuscript database

Citrinin is a well known polyketide mycotoxin produced by fungal species that naturally occur in certain agricultural commodities, including red yeast rice. This toxin possesses complex intramolecular hydrogen bonding interactions which influence its mode of action and selective detection. Detailed ...

Comparative typing analyses of clinical and environmental strains of the Cryptococcus neoformans/Cryptococcus gattii species complex from Ivory Coast.

PubMed

Kassi, Fulgence K; Bellet, Virginie; Drakulovski, Pascal; Krasteva, Donika; Roger, Frédéric; Valérie, Bedia-Tanoh A; Aboubakar, Touré; Doumbia, Adama; Kouakou, Gisèle A; Delaporte, Eric; Reynes, Jacques; Yavo, William; Menan, Hervé I E; Bertout, Sebastien

2018-01-01

The aim of this study was to assess the biotope of the Cryptococcus neoformans/Cryptococcus gattii species complex from Ivory Coast, and clarify the possible epidemiological relationship between environmental and clinical strains. Samples from Eucalyptus camaldulensis (n=136), Mangifera indica (n=13) and pigeon droppings (n=518) were collected from different sites close to the living environment of Ivorian HIV patients with cryptococcosis (n=10, 50 clinical strains). Clinical and environmental strains were characterized by molecular serotyping and genotyping [RFLP analysis of the URA5 gene, (GACA)4, (GTG)5 and M13 PCR fingerprinting] and compared.Results/Key findings. Environmental strains were recovered only from the pigeon droppings. In vitro susceptibility profiles showed that all strains were susceptible to fluconazole, flucytosine and amphotericin B. All environmental strains consisted of C. neoformans (A, AFLP1/VNI), whereas clinical strains included C. neoformans (A, AFLP1/VNI), C. neoformans x Cryptococcus deneoformans hybrids (AD, AFLP3/VNIII) and Cryptococcus deuterogattii (B, AFLP6/VGII). Two patients were co-infected with both C. neoformans and C. neoformans x C. deneoformans hybrids. We noticed a low genetic diversity among the environmental samples compared to the high diversity of the clinical samples. Some clinical strains were genetically more similar to environmental strains than to other clinical strains, including those from the same patient. These results provide new information on the ecology and epidemiology of the C. neoformans/C. gattii species complex in Ivory Coast.

Species delimitation in the Stenocereus griseus (Cactaceae) species complex reveals a new species, S. huastecorum

PubMed Central

Alvarado-Sizzo, Hernán; Parra, Fabiola; Arreola-Nava, Hilda Julieta; Terrazas, Teresa; Sánchez, Cristian

2018-01-01

The Stenocereus griseus species complex (SGSC) has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC. PMID:29342184

Species delimitation in the Stenocereus griseus (Cactaceae) species complex reveals a new species, S. huastecorum.

PubMed

Alvarado-Sizzo, Hernán; Casas, Alejandro; Parra, Fabiola; Arreola-Nava, Hilda Julieta; Terrazas, Teresa; Sánchez, Cristian

2018-01-01

The Stenocereus griseus species complex (SGSC) has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC.

Evolution of complex fruiting-body morphologies in homobasidiomycetes.

PubMed Central

Hibbett, David S; Binder, Manfred

2002-01-01

The fruiting bodies of homobasidiomycetes include some of the most complex forms that have evolved in the fungi, such as gilled mushrooms, bracket fungi and puffballs ('pileate-erect') forms. Homobasidiomycetes also include relatively simple crust-like 'resupinate' forms, however, which account for ca. 13-15% of the described species in the group. Resupinate homobasidiomycetes have been interpreted either as a paraphyletic grade of plesiomorphic forms or a polyphyletic assemblage of reduced forms. The former view suggests that morphological evolution in homobasidiomycetes has been marked by independent elaboration in many clades, whereas the latter view suggests that parallel simplification has been a common mode of evolution. To infer patterns of morphological evolution in homobasidiomycetes, we constructed phylogenetic trees from a dataset of 481 species and performed ancestral state reconstruction (ASR) using parsimony and maximum likelihood (ML) methods. ASR with both parsimony and ML implies that the ancestor of the homobasidiomycetes was resupinate, and that there have been multiple gains and losses of complex forms in the homobasidiomycetes. We also used ML to address whether there is an asymmetry in the rate of transformations between simple and complex forms. Models of morphological evolution inferred with ML indicate that the rate of transformations from simple to complex forms is about three to six times greater than the rate of transformations in the reverse direction. A null model of morphological evolution, in which there is no asymmetry in transformation rates, was rejected. These results suggest that there is a 'driven' trend towards the evolution of complex forms in homobasidiomycetes. PMID:12396494

Idiosyncratic species effects confound size-based predictions of responses to climate change.

PubMed

Twomey, Marion; Brodte, Eva; Jacob, Ute; Brose, Ulrich; Crowe, Tasman P; Emmerson, Mark C

2012-11-05

Understanding and predicting the consequences of warming for complex ecosystems and indeed individual species remains a major ecological challenge. Here, we investigated the effect of increased seawater temperatures on the metabolic and consumption rates of five distinct marine species. The experimental species reflected different trophic positions within a typical benthic East Atlantic food web, and included a herbivorous gastropod, a scavenging decapod, a predatory echinoderm, a decapod and a benthic-feeding fish. We examined the metabolism-body mass and consumption-body mass scaling for each species, and assessed changes in their consumption efficiencies. Our results indicate that body mass and temperature effects on metabolism were inconsistent across species and that some species were unable to meet metabolic demand at higher temperatures, thus highlighting the vulnerability of individual species to warming. While body size explains a large proportion of the variation in species' physiological responses to warming, it is clear that idiosyncratic species responses, irrespective of body size, complicate predictions of population and ecosystem level response to future scenarios of climate change.

Neural Regulation Of Chromatophore Function In Cephalopods

DTIC Science & Technology

2015-05-19

which include octopus , squid and cuttlefish, are the only animals able to generate active body patterns directly controlled by the nervous system...Pattering Behavior, the ability of cephalopod mollusks to generate numerous and highly complex body patterns. Cephalopods, which include octopus , squid...cephalopod species, Octopus vulgaris with the Fiorito lab at the Stazione Zoologica in Napoli, Italy and showed that regeneration follows a

Fluorescence and NMR spectroscopy together with molecular simulations reveal amphiphilic characteristics of a Burkholderia biofilm exopolysaccharide.

PubMed

Kuttel, Michelle M; Cescutti, Paola; Distefano, Marco; Rizzo, Roberto

2017-06-30

Biofilms are a collective mode of bacterial life in which a self-produced matrix confines cells in close proximity to each other. Biofilms confer many advantages, including protection from chemicals (including antibiotics), entrapment of useful extracellular enzymes and nutrients, as well as opportunities for efficient recycling of molecules from dead cells. Biofilm matrices are aqueous gel-like structures composed of polysaccharides, proteins, and DNA stabilized by intermolecular interactions that may include non-polar connections. Recently, polysaccharides extracted from biofilms produced by species of the Burkholderia cepacia complex were shown to possess clusters of rhamnose, a 6-deoxy sugar with non-polar characteristics. Molecular dynamics simulations are well suited to characterizing the structure and dynamics of polysaccharides, but only relatively few such studies exist of their interaction with non-polar molecules. Here we report an investigation into the hydrophobic properties of the exopolysaccharide produced by Burkholderia multivorans strain C1576. Fluorescence experiments with two hydrophobic fluorescent probes established that this polysaccharide complexes hydrophobic species, and NMR experiments confirmed these interactions. Molecular simulations to model the hydrodynamics of the polysaccharide and the interaction with guest species revealed a very flexible, amphiphilic carbohydrate chain that has frequent dynamic interactions with apolar molecules; both hexane and a long-chain fatty acid belonging to the quorum-sensing system of B. multivorans were tested. A possible role of the non-polar domains of the exopolysaccharide in facilitating the diffusion of aliphatic species toward specific targets within the biofilm aqueous matrix is proposed. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Redox Species of Redox Flow Batteries: A Review.

PubMed

Pan, Feng; Wang, Qing

2015-11-18

Due to the capricious nature of renewable energy resources, such as wind and solar, large-scale energy storage devices are increasingly required to make the best use of the renewable power. The redox flow battery is considered suitable for large-scale applications due to its modular design, good scalability and flexible operation. The biggest challenge of the redox flow battery is the low energy density. The redox active species is the most important component in redox flow batteries, and the redox potential and solubility of redox species dictate the system energy density. This review is focused on the recent development of redox species. Different categories of redox species, including simple inorganic ions, metal complexes, metal-free organic compounds, polysulfide/sulfur and lithium storage active materials, are reviewed. The future development of redox species towards higher energy density is also suggested.

Discovery of Aspergillus frankstonensis sp. nov. during environmental sampling for animal and human fungal pathogens.

PubMed

Talbot, Jessica J; Houbraken, Jos; Frisvad, Jens C; Samson, Robert A; Kidd, Sarah E; Pitt, John; Lindsay, Sue; Beatty, Julia A; Barrs, Vanessa R

2017-01-01

Invasive fungal infections (IFI) due to species in Aspergillus section Fumigati (ASF), including the Aspergillus viridinutans species complex (AVSC), are increasingly reported in humans and cats. The risk of exposure to these medically important fungi in Australia is unknown. Air and soil was sampled from the domiciles of pet cats diagnosed with these IFI and from a nature reserve in Frankston, Victoria, where Aspergillus viridinutans sensu stricto was discovered in 1954. Of 104 ASF species isolated, 61% were A. fumigatus sensu stricto, 9% were AVSC (A. felis-clade and A. frankstonensis sp. nov.) and 30% were other species (30%). Seven pathogenic ASF species known to cause disease in humans and animals (A. felis-clade, A. fischeri, A. thermomutatus, A. lentulus, A. laciniosus A. fumisynnematus, A. hiratsukae) comprised 25% of isolates overall. AVSC species were only isolated from Frankston soil where they were abundant, suggesting a particular ecological niche. Phylogenetic, morphological and metabolomic analyses of these isolates identified a new species, A. frankstonensis that is phylogenetically distinct from other AVSC species, heterothallic and produces a unique array of extrolites, including the UV spectrum characterized compounds DOLD, RAIMO and CALBO. Shared morphological and physiological characteristics with other AVSC species include slow sporulation, optimal growth at 37°C, no growth at 50°C, and viriditoxin production. Overall, the risk of environmental exposure to pathogenic species in ASF in Australia appears to be high, but there was no evidence of direct environmental exposure to AVSC species in areas where humans and cats cohabitate.

Stability and Unimolecular Reactivity of Palladate(II) Complexes [Ln PdR3 ]- (L=Phosphine, R=Organyl, n=0 and 1).

PubMed

Kolter, Marlene; Koszinowski, Konrad

2016-10-24

The reduction of Pd II precatalysts to catalytically active Pd 0 species is a key step in many palladium-mediated cross-coupling reactions. Besides phosphines, the stoichiometrically used organometallic reagents can afford this reduction, but do so in a poorly understood way. To elucidate the mechanism of this reaction, we have treated solutions of Pd(OAc) 2 and a phosphine ligand L in tetrahydrofuran with RMgCl (R=Ph, Bn, Bu) as well as other organometallic reagents. Analysis of these model systems by electrospray- ionization mass spectrometry found palladate(II) complexes [L n PdR 3 ] - (n=0 and 1), thus pointing to the occurrence of transmetallation reactions. Upon gas-phase fragmentation, the [L n PdR 3 ] - anions preferentially underwent a reductive elimination to yield Pd 0 species. The sequence of the transmetallation and reductive elimination, thus, constitutes a feasible mechanism for the reduction of the Pd(OAc) 2 precatalyst. Other species of interest observed include the Pd IV complex [PdBn 5 ] - , which did not fragment via a reductive elimination but lost BnH instead. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Unmasking the complexity of species identification in Australasian flying-foxes

PubMed Central

Danks, Melissa; Lott, Matthew J.; Dennison, Siobhan; Frankham, Greta J.; King, Andrew; Eldridge, Mark D. B.; Johnson, Rebecca N.; Divljan, Anja

2018-01-01

Pteropus (flying-foxes) are a speciose group of non-echolocating large bats, with five extant Australian species and 24 additional species distributed amongst the Pacific Islands. In 2015, an injured flying-fox with unusual facial markings was found in Sydney, Australia, following severe and widespread storms. Based on an initial assessment, the individual belonged to Pteropus but could not be readily identified to species. As a consequence, four hypotheses for its identification/origin were posited: the specimen represented (1) an undescribed Australian species; or (2) a morphological variant of a recognised Australian species; or (3) a hybrid individual; or (4) a vagrant from the nearby Southwest Pacific Islands. We used a combination of morphological and both mitochondrial- and nuclear DNA-based identification methods to assess these hypotheses. Based on the results, we propose that this morphologically unique Pteropus most likely represents an unusual P. alecto (black flying-fox) potentially resulting from introgression from another Pteropus species. Unexpectedly, this individual, and the addition of reference sequence data from newly vouchered specimens, revealed a previously unreported P. alecto mitochondrial DNA lineage. This lineage was distinct from currently available haplotypes. It also suggests long-term hybridisation commonly occurs between P. alecto and P. conspicillatus (spectacled flying-fox). This highlights the importance of extensive reference data, and the inclusion of multiple vouchered specimens for each species to encompass both intraspecific and interspecific variation to provide accurate and robust species identification. Moreover, our additional reference data further demonstrates the complexity of Pteropus species relationships, including hybridisation, and potential intraspecific biogeographical structure that may impact on their management and conservation. PMID:29634748

Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation.

PubMed

Govindarajulu, Rajanikanth; Hughes, Colin E; Bailey, C Donovan

2011-12-01

Leucaena comprises 17 diploid species, five tetraploid species, and a complex series of hybrids whose evolutionary histories have been influenced by human seed translocation, cultivation, and subsequent spontaneous hybridization. Here we investigated patterns of evolutionary divergence among diploid Leucaena through comprehensively sampled multilocus phylogenetic and population genetic approaches to address species delimitation, interspecific relationships, hybridization, and the predominant mode of speciation among diploids. Parsimony- and maximum-likelihood-based phylogenetic approaches were applied to 59 accessions sequenced for six SCAR-based nuclear loci, nrDNA ITS, and four cpDNA regions. Population genetic comparisons included 1215 AFLP loci representing 42 populations and 424 individuals. Phylogenetic results provided a well-resolved hypothesis of divergent species relationships, recovering previously recognized clades of diploids as well as newly resolved relationships. Phylogenetic and population genetic assessments identified two cryptic species that are consistent with geography and morphology. Findings from this study highlight the importance and utility of multilocus data in the recovery of complex evolutionary histories. The results are consistent with allopatric divergence representing the predominant mode of speciation among diploid Leucaena. These findings contrast with the potential hybrid origin of several tetraploid species and highlight the importance of human translocation of seed to the origin of these tetraploids. The recognition of one previously unrecognized species (L. cruziana) and the elevation of another taxon (L. collinsii subsp. zacapana) to specific status (L. zacapana) is consistent with a growing number of newly diagnosed species from neotropical seasonally dry forests, suggesting these communities harbor greater species diversity than previously recognized.

Review of fish diversity in the Lake Huron basin

USGS Publications Warehouse

Roseman, E.F.; Schaeffer, J.S.; Steen, P.J.

2009-01-01

Lake Huron has a rich aquatic habitat diversity that includes shallow embayments, numerous tributaries, shallow mid-lake reef complexes, archipelagos, and profundal regions. These habitats provide support for warm, cool, and cold water fish communities. Diversity of fishes in Lake Huron reflects post-glaciation colonization events, current climate conditions, accidental and intentional introductions of non-indigenous species, and extinctions. Most extinction events have been largely associated with habitat alterations, exploitation of fisheries, and interactions with non-indigenous species. The most recent historical survey of extirpated and imperiled species conducted in the late 1970s identified 79 fish species in Lake Huron proper and about 50 additional species in tributaries. Of those 129 species, 20 are now considered extirpated or imperiled. Extirpated species include Arctic grayling, paddlefish, weed shiner, deepwater cisco, blackfin cisco, shortnose cisco, and kiyi. Six species have declined appreciably due to loss of clear-water stream habitat: the river redhorse, river darter, black redhorse, pugnose shiner, lake chubsucker, redside dace, eastern sand darter, and channel darter. While numerous agencies, universities, and other organizations routinely monitor nearshore and offshore fish distribution and abundance, there is a need for more rigorous examination of the distribution and abundance of less-common species to better understand their ecology. This information is critical to the development of management plans aimed at ecosystem remediation and restoration.

Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex

PubMed Central

Garrido-Sanz, Daniel; Meier-Kolthoff, Jan P.; Göker, Markus; Martín, Marta; Rivilla, Rafael; Redondo-Nieto, Miguel

2016-01-01

The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR) with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH) identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI) approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as PGPR. PMID:26915094

Modeling of Wildlife-Associated Zoonoses: Applications and Caveats

PubMed Central

Lewis, Bryan L.; Marathe, Madhav; Eubank, Stephen; Blackburn, Jason K.

2012-01-01

Abstract Wildlife species are identified as an important source of emerging zoonotic disease. Accordingly, public health programs have attempted to expand in scope to include a greater focus on wildlife and its role in zoonotic disease outbreaks. Zoonotic disease transmission dynamics involving wildlife are complex and nonlinear, presenting a number of challenges. First, empirical characterization of wildlife host species and pathogen systems are often lacking, and insight into one system may have little application to another involving the same host species and pathogen. Pathogen transmission characterization is difficult due to the changing nature of population size and density associated with wildlife hosts. Infectious disease itself may influence wildlife population demographics through compensatory responses that may evolve, such as decreased age to reproduction. Furthermore, wildlife reservoir dynamics can be complex, involving various host species and populations that may vary in their contribution to pathogen transmission and persistence over space and time. Mathematical models can provide an important tool to engage these complex systems, and there is an urgent need for increased computational focus on the coupled dynamics that underlie pathogen spillover at the human–wildlife interface. Often, however, scientists conducting empirical studies on emerging zoonotic disease do not have the necessary skill base to choose, develop, and apply models to evaluate these complex systems. How do modeling frameworks differ and what considerations are important when applying modeling tools to the study of zoonotic disease? Using zoonotic disease examples, we provide an overview of several common approaches and general considerations important in the modeling of wildlife-associated zoonoses. PMID:23199265

Wolbachia infection complexity among insects in the tropical rice-field community.

PubMed

Kittayapong, P; Jamnongluk, W; Thipaksorn, A; Milne, J R; Sindhusake, C

2003-04-01

Wolbachia are a group of intracellular bacteria that cause reproductive alterations in their arthropod hosts. Widely discordant host and Wolbachia phylogenies indicate that horizontal transmission of these bacteria among species sometimes occurs. A likely means of horizontal transfer is through the feeding relations of organisms within communities. Feeding interactions among insects within the rice-field insect community have been well documented in the past. Here, we present the results of a polymerase chain reaction-based survey and phylogenetic analysis of Wolbachia strains in the rice-field insect community of Thailand. Our field survey indicated that 49 of 209 (23.4%) rice-field insect species were infected with Wolbachia. Of the 49 infected species, 27 were members of two feeding complexes: (i) a group of 13 hoppers preyed on by 2 mirid species and parasitized by a fly species, and (ii) 2 lepidopteran pests parasitized by 9 wasp species. Wolbachia strains found in three hoppers, Recilia dorsalis, Nephotettix malayanus and Nisia nervosa, the two mirid predators, Cyrtorhinus lividipennis and Tytthus chinensis, and the fly parasitoid, Tomosvaryella subvirescens, were all in the same Wolbachia clade. In the second complex, the two lepidopteran pests, Cnaphalocrocis medinalis and Scirpophaga incertulas, were both infected with Wolbachia from the same clade, as was the parasitoid Tropobracon schoenobii. However, none of the other infected parasitoid species in this feeding complex was infected by Wolbachia from this clade. Mean (+/- SD) genetic distance of Wolbachia wsp sequences among interacting species pairs of the hopper feeding complex (0.118 +/- 0.091 nucleotide sequence differences), but not for the other two complexes, was significantly smaller than that between noninteracting species pairs (0.162 +/- 0.079 nucleotide sequence differences). Our results suggest that some feeding complexes, such as the hopper complex described here, could be an important means by which Wolbachia spreads among species within arthropod communities.

A Statistical Model for Estimation of Fish Density Including Correlation in Size, Space, Time and between Species from Research Survey Data

PubMed Central

Bastardie, Francois

2014-01-01

Trawl survey data with high spatial and seasonal coverage were analysed using a variant of the Log Gaussian Cox Process (LGCP) statistical model to estimate unbiased relative fish densities. The model estimates correlations between observations according to time, space, and fish size and includes zero observations and over-dispersion. The model utilises the fact the correlation between numbers of fish caught increases when the distance in space and time between the fish decreases, and the correlation between size groups in a haul increases when the difference in size decreases. Here the model is extended in two ways. Instead of assuming a natural scale size correlation, the model is further developed to allow for a transformed length scale. Furthermore, in the present application, the spatial- and size-dependent correlation between species was included. For cod (Gadus morhua) and whiting (Merlangius merlangus), a common structured size correlation was fitted, and a separable structure between the time and space-size correlation was found for each species, whereas more complex structures were required to describe the correlation between species (and space-size). The within-species time correlation is strong, whereas the correlations between the species are weaker over time but strong within the year. PMID:24911631

Ecology and Life Cycle Patterns of Echinococcus Species.

PubMed

Romig, T; Deplazes, P; Jenkins, D; Giraudoux, P; Massolo, A; Craig, P S; Wassermann, M; Takahashi, K; de la Rue, M

2017-01-01

The genus Echinococcus is composed of eight generally recognized species and one genotypic cluster (Echinococcus canadensis cluster) that may in future be resolved into one to three species. For each species, we review existing information on transmission routes and life cycles in different geographical contexts and - where available - include basic biological information of parasites and hosts (e.g., susceptibility of host species). While some Echinococcus spp. are transmitted in life cycles that involve predominantly domestic animals (e.g., dog - livestock cycles), others are wildlife parasites that do or do not interact with domestic transmission. In many cases, life cycle patterns of the same parasite species differ according to geography. Simple life cycles contrast with transmission patterns that are highly complex, involving multihost systems that may include both domestic and wild mammals. Wildlife transmission may be primary or secondary, i.e., resulting from spillovers from domestic animals. For most of the species and regions, existing information does not yet permit a conclusive description of transmission systems. Such data, however, would be highly relevant, e.g., for anticipation of geographical changes of the presence and frequency of these parasites in a warming world, or for initiating evidence-based control strategies. Copyright © 2017 Elsevier Ltd. All rights reserved.

Predicting the consequences of species loss using size-structured biodiversity approaches.

PubMed

Brose, Ulrich; Blanchard, Julia L; Eklöf, Anna; Galiana, Nuria; Hartvig, Martin; R Hirt, Myriam; Kalinkat, Gregor; Nordström, Marie C; O'Gorman, Eoin J; Rall, Björn C; Schneider, Florian D; Thébault, Elisa; Jacob, Ute

2017-05-01

Understanding the consequences of species loss in complex ecological communities is one of the great challenges in current biodiversity research. For a long time, this topic has been addressed by traditional biodiversity experiments. Most of these approaches treat species as trait-free, taxonomic units characterizing communities only by species number without accounting for species traits. However, extinctions do not occur at random as there is a clear correlation between extinction risk and species traits. In this review, we assume that large species will be most threatened by extinction and use novel allometric and size-spectrum concepts that include body mass as a primary species trait at the levels of populations and individuals, respectively, to re-assess three classic debates on the relationships between biodiversity and (i) food-web structural complexity, (ii) community dynamic stability, and (iii) ecosystem functioning. Contrasting current expectations, size-structured approaches suggest that the loss of large species, that typically exploit most resource species, may lead to future food webs that are less interwoven and more structured by chains of interactions and compartments. The disruption of natural body-mass distributions maintaining food-web stability may trigger avalanches of secondary extinctions and strong trophic cascades with expected knock-on effects on the functionality of the ecosystems. Therefore, we argue that it is crucial to take into account body size as a species trait when analysing the consequences of biodiversity loss for natural ecosystems. Applying size-structured approaches provides an integrative ecological concept that enables a better understanding of each species' unique role across communities and the causes and consequences of biodiversity loss. © 2016 Cambridge Philosophical Society.

Inter-species variation in the oligomeric states of the higher plant Calvin cycle enzymes glyceraldehyde-3-phosphate dehydrogenase and phosphoribulokinase

PubMed Central

Lloyd, Julie C.; Raines, Christine A.

2011-01-01

In darkened leaves the Calvin cycle enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) form a regulatory multi-enzyme complex with the small chloroplast protein CP12. GAPDH also forms a high molecular weight regulatory mono-enzyme complex. Given that there are different reports as to the number and subunit composition of these complexes and that enzyme regulatory mechanisms are known to vary between species, it was reasoned that protein–protein interactions may also vary between species. Here, this variation is investigated. This study shows that two different tetramers of GAPDH (an A2B2 heterotetramer and an A4 homotetramer) have the capacity to form part of the PRK/GAPDH/CP12 complex. The role of the PRK/GAPDH/CP12 complex is not simply to regulate the ‘non-regulatory’ A4 GAPDH tetramer. This study also demonstrates that the abundance and nature of PRK/GAPDH/CP12 interactions are not equal in all species and that whilst NAD enhances complex formation in some species, this is not sufficient for complex formation in others. Furthermore, it is shown that the GAPDH mono-enzyme complex is more abundant as a 2(A2B2) complex, rather than the larger 4(A2B2) complex. This smaller complex is sensitive to cellular metabolites indicating that it is an important regulatory isoform of GAPDH. This comparative study has highlighted considerable heterogeneity in PRK and GAPDH protein interactions between closely related species and the possible underlying physiological basis for this is discussed. PMID:21498632

Inter-species variation in the oligomeric states of the higher plant Calvin cycle enzymes glyceraldehyde-3-phosphate dehydrogenase and phosphoribulokinase.

PubMed

Howard, Thomas P; Lloyd, Julie C; Raines, Christine A

2011-07-01

In darkened leaves the Calvin cycle enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) form a regulatory multi-enzyme complex with the small chloroplast protein CP12. GAPDH also forms a high molecular weight regulatory mono-enzyme complex. Given that there are different reports as to the number and subunit composition of these complexes and that enzyme regulatory mechanisms are known to vary between species, it was reasoned that protein-protein interactions may also vary between species. Here, this variation is investigated. This study shows that two different tetramers of GAPDH (an A2B2 heterotetramer and an A4 homotetramer) have the capacity to form part of the PRK/GAPDH/CP12 complex. The role of the PRK/GAPDH/CP12 complex is not simply to regulate the 'non-regulatory' A4 GAPDH tetramer. This study also demonstrates that the abundance and nature of PRK/GAPDH/CP12 interactions are not equal in all species and that whilst NAD enhances complex formation in some species, this is not sufficient for complex formation in others. Furthermore, it is shown that the GAPDH mono-enzyme complex is more abundant as a 2(A2B2) complex, rather than the larger 4(A2B2) complex. This smaller complex is sensitive to cellular metabolites indicating that it is an important regulatory isoform of GAPDH. This comparative study has highlighted considerable heterogeneity in PRK and GAPDH protein interactions between closely related species and the possible underlying physiological basis for this is discussed.

Wide recognition of Culex pipiens and lack of detection of Culex torrentium through biomolecular differentiation of mosquitoes in the Emilia-Romagna region, Northern Italy.

PubMed

Calzolari, M; Bonilauri, P; Bellini, R; Becker, S; Dottori, M

2016-12-01

The Culex pipiens complex includes species with reported differences in vector competence for arthropod-borne viruses, many of which are of significant importance to human health such as the West Nile virus and the Sindbis virus. This group of mosquitoes is difficult to distinguish morphologically; particularly as adult females. In Europe, the two species of the complex, Culex pipiens Linnaeus 1758 and Culex torrentium Martini 1925, are often found sympatrically. With the aim to characterize the presence and spread of both species in the Emilia-Romagna region, Northern Italy, mosquitoes of the complex - collected during the West Nile virus surveillance plans - were tested by multiplex real-time PCR for the detection of the two species Cx. pipiens and Cx. torrentium. A total of 24 165 mosquitoes, collected between 2012 and 2014 from 105 sites, and sorted in 204 pools, were tested. All tested pools were found to be composed of Cx. pipiens, whereas Cx. torrentium was not detected. These results indicate a likely absence of Cx. torrentium mosquitoes within the surveyed territory, whereas Cx. pipiens is widely distributed in the area mentioned. This is in line with previous reports, which describe a pre-alpine distribution of Cx. torrentium in Italy. © 2016 The Royal Entomological Society.

Identification of Pathogenic Fusarium spp. Causing Maize Ear Rot and Potential Mycotoxin Production in China

PubMed Central

Duan, Canxing; Qin, Zihui; Yang, Zhihuan; Li, Weixi; Sun, Suli; Zhu, Zhendong; Wang, Xiaoming

2016-01-01

Ear rot is a serious disease that affects maize yield and grain quality worldwide. The mycotoxins are often hazardous to humans and livestock. In samples collected in China between 2009 and 2014, Fusarium verticillioides and F. graminearum species complex were the dominant fungi causing ear rot. According to the TEF-1α gene sequence, F. graminearum species complex in China included three independent species: F. graminearum, F. meridionale, and F. boothii. The key gene FUM1 responsible for the biosynthesis of fumonisin was detected in all 82 F. verticillioides isolates. Among these, 57 isolates mainly produced fumonisin B1, ranging from 2.52 to 18,416.44 µg/g for each gram of dry hyphal weight, in vitro. Three different toxigenic chemotypes were detected among 78 F. graminearum species complex: 15-ADON, NIV and 15-ADON+NIV. Sixty and 16 isolates represented the 15-ADON and NIV chemotypes, respectively; two isolates carried both 15-ADON and NIV-producing segments. All the isolates carrying NIV-specific segment were F. meridionale. The in vitro production of 15-ADON, 3-ADON, DON, and ZEN varied from 5.43 to 81,539.49; 6.04 to 19,590.61; 13.35 to 19,795.33; and 1.77 to 430.24 µg/g of dry hyphal weight, respectively. Altogether, our present data demonstrate potential main mycotoxin production of dominant pathogenic Fusarium in China. PMID:27338476

Larval habitats characterization and species composition of Anopheles mosquitoes in Tunisia, with particular attention to Anopheles maculipennis complex.

PubMed

Tabbabi, Ahmed; Boussès, Philippe; Rhim, Adel; Brengues, Cécile; Daaboub, Jabeur; Ben-Alaya-Bouafif, Nissaf; Fontenille, Didier; Bouratbine, Aïda; Simard, Frédéric; Aoun, Karim

2015-03-01

In Tunisia, malaria transmission has been interrupted since 1980. However, the growing number of imported cases and the persistence of putative vectors stress the need for additional studies to assess the risk of malaria resurgence in the country. In this context, our aim was to update entomological data concerning Anopheles mosquitoes in Tunisia. From May to October of 2012, mosquito larval specimens were captured in 60 breeding sites throughout the country and identified at the species level using morphological keys. Environmental parameters of the larval habitats were recorded. Specimens belonging to the An. maculipennis complex were further identified to sibling species by the ribosomal deoxyribonucleic acid (rDNA)-internal transcribed spacer 2 (ITS2) polymerase chain reaction (PCR) technique. In total, 647 Anopheles larvae were collected from 25 habitats. Four species, including An. labranchiae, An. multicolor, An. sergentii, and An. algeriensis, were morphologically identified. rDNA-ITS2 PCR confirmed that An. labranchiae is the sole member of the An. maculipennis complex in Tunisia. An. labranchiae was collected throughout northern and central Tunisia, and it was highly associated with rural habitat, clear water, and sunlight areas. Larvae of An. multicolor and An. sergentii existed separately or together and were collected in southern Tunisia in similar types of breeding places. © The American Society of Tropical Medicine and Hygiene.

Sustaining salmonid populations: A caring understanding of naturalness of taxa

USGS Publications Warehouse

Nielsen, Jennifer L.; Regier, Henry A.; Knudsen, E. Eric

2004-01-01

Species of the family of Salmonidae occur naturally in Northern Hemisphere waters that remain clear and cool to cold in summer. For purposes of reproduction, salmonids generally behaviorally respond to the currents of streams and lakes in recently glaciated areas. For feeding and maturation, many larger species migrate into existing systems of large lakes, seas, and oceans. The subfamilies include Salmoninae, Coregoninae, and Thymallinae. In many locales and regions of the hemisphere, numerous species of these subfamilies evolved and self-organized into species flocks or taxocenes of bewildering complexity. For example, any individual species may play different or unique ecological roles in different taxocenes. The northern Pacific and Atlantic Ocean ecosystems, with their seas and tributaries, each contained a metacomplex of such taxocenes that, in their natural state some centuries ago, resembled each other but differed in many ways. Humans have valued all species of this family for subsistence, ceremonial, naturalist, gustatory, angling, and commercial reasons for centuries. Modern progressive humans (MPHs), whose industrial and commercial enterprises have gradually spread over this hemisphere in recent time, now affect aquatic ecosystems at all scales from local to global. These human effects mingle in complex ways that together induce uniquely natural salmonid taxocenes to disintegrate with the loss of species, including those groups least tolerant to human manipulations, but extending more recently to those taxa more adapted to anthropogenic change. As we leave the modern era, dominated by MPHs, will we find ways to live sustainably with salmonid taxocenes that still exhibit self-organizational integrity, or will only individual, isolated populations of salmonid species, derived from those most tolerant of MPHs, survive? To achieve future sustainability of salmonids, we suggest implementation of a search for intuitive knowledge based on faith in the wisdom of nature and a caring-sharing, behavioral structure based on "survival of the wisest" for both humans and salmonids.

Embryonic and larval development in the Midas cichlid fish species flock (Amphilophus spp.): a new evo-devo model for the investigation of adaptive novelties and species differences.

PubMed

Kratochwil, Claudius F; Sefton, Maggie M; Meyer, Axel

2015-02-26

Central American crater lake cichlid fish of the Midas species complex (Amphilophus spp.) are a model system for sympatric speciation and fast ecological diversification and specialization. Midas cichlids have been intensively analyzed from an ecological and morphological perspective. Genomic resources such as transcriptomic and genomic data sets, and a high-quality draft genome are available now. Many ecologically relevant species-specific traits and differences such as pigmentation and cranial morphology arise during development. Detailed descriptions of the early development of the Midas cichlid in particular, will help to investigate the ontogeny of species differences and adaptations. We describe the embryonic and larval development of the crater lake cichlid, Amphilophus xiloaensis, until seven days after fertilization. Similar to previous studies on teleost development, we describe six periods of embryogenesis - the zygote, cleavage, blastula, gastrula, segmentation, and post-hatching period. Furthermore, we define homologous stages to well-described teleost models such as medaka and zebrafish, as well as other cichlid species such as the Nile tilapia and the South American cichlid Cichlasoma dimerus. Key morphological differences between the embryos of Midas cichlids and other teleosts are highlighted and discussed, including the presence of adhesive glands and different early chromatophore patterns, as well as variation in developmental timing. The developmental staging of the Midas cichlid will aid researchers in the comparative investigation of teleost ontogenies. It will facilitate comparative developmental biological studies of Neotropical and African cichlid fish in particular. In the past, the species flocks of the African Great Lakes have received the most attention from researchers, but some lineages of the 300-400 species of Central American lakes are fascinating model systems for adaptive radiation and rapid phenotypic evolution. The availability of genetic resources, their status as a model system for evolutionary research, and the possibility to perform functional experiments including transgenesis makes the Midas cichlid complex a very attractive model for evolutionary-developmental research.

Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae)

PubMed Central

Ačanski, Jelena; Vujić, Ante; Ståhls, Gunilla; Radenković, Snežana; Milić, Dubravka; Obreht Vidaković, Dragana; Đan, Mihajla

2016-01-01

The Merodon aureus species group (Diptera: Syrphidae: Eristalinae) comprises a number of different sub-groups and species complexes. In this study we focus on resolving the taxonomic status of the entity previously identified as M. cinereus B, here identified as M. atratus species complex. We used an integrative approach based on morphological descriptions, combined with supporting characters that were obtained from molecular analyses of the mitochondrial cytochrome c oxidase I gene as well as from geometric morphometry of wing and surstylus shapes and environmental niche comparisons. All applied data and methods distinguished and supported three morphologically cryptic species: M. atratus stat. nov., M. virgatus sp. nov. and M. balkanicus sp. nov., which constitute the M. atratus species complex. We present an identification key for the sub-groups and species complexes of the M. aureus species group occurring in Europe, describe the taxa and discuss the utility of the applied methods for species delimitation. The estimated divergence times for the species splits of these taxa coincide with the Pleistocene Günz-Mindel interglaciation and the Great interglaciation (between the Ris and Mindel glacial periods). PMID:27532618

A description of the nearshore fish communities in the Huron-Erie Corridor using multiple gear types

USGS Publications Warehouse

Francis, James T.; Chiotti, Justin A.; Boase, James C.; Thomas, Mike V.; Manny, Bruce A.; Roseman, Edward F.

2013-01-01

Great Lakes coastal wetlands provide a critical habitat for many fish species throughout their life cycles. Once home to one of the largest wetland complexes in the Great Lakes, coastal wetlands in the Huron–Erie Corridor (HEC) have decreased dramatically since the early 1900s. We characterized the nearshore fish communities at three different wetland complexes in the HEC using electrofishing, seines, and fyke nets. Species richness was highest in the Detroit River (63), followed by the St. Clair Delta (56), and Western Lake Erie (47). The nearshore fish communities in the Detroit River and St. Clair Delta consisted primarily of shiners, bluntnose minnow, centrarchids, and brook silverside, while the Western Lake Erie sites consisted of high proportions of non-native taxa including common carp, gizzard shad, goldfish, and white perch. Species richness estimates using individual-based rarefaction curves were higher when using electrofishing data compared to fyke nets or seine hauls at each wetland. Twelve fish species were captured exclusively during electrofishing assessments, while one species was captured exclusively in fyke nets, and none exclusively during seine hauls. Western Lake Erie wetlands were more indicative of degraded systems with lower species richness, lower proportion of turbidity intolerant species, and increased abundance of non-native taxa. This work highlights the importance of coastal wetlands in the HEC by capturing 69 different fish species utilizing these wetlands to fulfill life history requirements and provides insight when selecting gears to sample nearshore littoral areas.

The Colletotrichum boninense species complex

PubMed Central

Damm, U.; Cannon, P.F.; Woudenberg, J.H.C.; Johnston, P.R.; Weir, B.S.; Tan, Y.P.; Shivas, R.G.; Crous, P.W.

2012-01-01

Although only recently described, Colletotrichum boninense is well established in literature as an anthracnose pathogen or endophyte of a diverse range of host plants worldwide. It is especially prominent on members of Amaryllidaceae, Orchidaceae, Proteaceae and Solanaceae. Reports from literature and preliminary studies using ITS sequence data indicated that C. boninense represents a species complex. A multilocus molecular phylogenetic analysis (ITS, ACT, TUB2, CHS-1, GAPDH, HIS3, CAL) of 86 strains previously identified as C. boninense and other related strains revealed 18 clades. These clades are recognised here as separate species, including C. boninense s. str., C. hippeastri, C. karstii and 12 previously undescribed species, C. annellatum, C. beeveri, C. brassicicola, C. brasiliense, C. colombiense, C. constrictum, C. cymbidiicola, C. dacrycarpi, C. novae-zelandiae, C. oncidii, C. parsonsiae and C. torulosum. Seven of the new species are only known from New Zealand, perhaps reflecting a sampling bias. The new combination C. phyllanthi was made, and C. dracaenae Petch was epitypified and the name replaced with C. petchii. Typical for species of the C. boninense species complex are the conidiogenous cells with rather prominent periclinal thickening that also sometimes extend to form a new conidiogenous locus or annellations as well as conidia that have a prominent basal scar. Many species in the C. boninense complex form teleomorphs in culture. Taxonomic novelties: New combination - Colletotrichum phyllanthi (H. Surendranath Pai) Damm, P.F. Cannon & Crous. Name replacement - C. petchii Damm, P.F. Cannon & Crous. New species - C. annellatum Damm, P.F. Cannon & Crous, C. beeveri Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. brassicicola Damm, P.F. Cannon & Crous, C. brasiliense Damm, P.F. Cannon, Crous & Massola, C. colombiense Damm, P.F. Cannon, Crous, C. constrictum Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. cymbidiicola Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. dacrycarpi Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. novae-zelandiae Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. oncidii Damm, P.F. Cannon & Crous, C. parsonsiae Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. torulosum Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir. Typifications: Epitypifications - C. dracaenae Petch. PMID:23136457

The dominant Anopheles vectors of human malaria in the Asia-Pacific region: occurrence data, distribution maps and bionomic précis

PubMed Central

2011-01-01

Background The final article in a series of three publications examining the global distribution of 41 dominant vector species (DVS) of malaria is presented here. The first publication examined the DVS from the Americas, with the second covering those species present in Africa, Europe and the Middle East. Here we discuss the 19 DVS of the Asian-Pacific region. This region experiences a high diversity of vector species, many occurring sympatrically, which, combined with the occurrence of a high number of species complexes and suspected species complexes, and behavioural plasticity of many of these major vectors, adds a level of entomological complexity not comparable elsewhere globally. To try and untangle the intricacy of the vectors of this region and to increase the effectiveness of vector control interventions, an understanding of the contemporary distribution of each species, combined with a synthesis of the current knowledge of their behaviour and ecology is needed. Results Expert opinion (EO) range maps, created with the most up-to-date expert knowledge of each DVS distribution, were combined with a contemporary database of occurrence data and a suite of open access, environmental and climatic variables. Using the Boosted Regression Tree (BRT) modelling method, distribution maps of each DVS were produced. The occurrence data were abstracted from the formal, published literature, plus other relevant sources, resulting in the collation of DVS occurrence at 10116 locations across 31 countries, of which 8853 were successfully geo-referenced and 7430 were resolved to spatial areas that could be included in the BRT model. A detailed summary of the information on the bionomics of each species and species complex is also presented. Conclusions This article concludes a project aimed to establish the contemporary global distribution of the DVS of malaria. The three articles produced are intended as a detailed reference for scientists continuing research into the aspects of taxonomy, biology and ecology relevant to species-specific vector control. This research is particularly relevant to help unravel the complicated taxonomic status, ecology and epidemiology of the vectors of the Asia-Pacific region. All the occurrence data, predictive maps and EO-shape files generated during the production of these publications will be made available in the public domain. We hope that this will encourage data sharing to improve future iterations of the distribution maps. PMID:21612587

The dominant Anopheles vectors of human malaria in the Asia-Pacific region: occurrence data, distribution maps and bionomic précis.

PubMed

Sinka, Marianne E; Bangs, Michael J; Manguin, Sylvie; Chareonviriyaphap, Theeraphap; Patil, Anand P; Temperley, William H; Gething, Peter W; Elyazar, Iqbal R F; Kabaria, Caroline W; Harbach, Ralph E; Hay, Simon I

2011-05-25

The final article in a series of three publications examining the global distribution of 41 dominant vector species (DVS) of malaria is presented here. The first publication examined the DVS from the Americas, with the second covering those species present in Africa, Europe and the Middle East. Here we discuss the 19 DVS of the Asian-Pacific region. This region experiences a high diversity of vector species, many occurring sympatrically, which, combined with the occurrence of a high number of species complexes and suspected species complexes, and behavioural plasticity of many of these major vectors, adds a level of entomological complexity not comparable elsewhere globally. To try and untangle the intricacy of the vectors of this region and to increase the effectiveness of vector control interventions, an understanding of the contemporary distribution of each species, combined with a synthesis of the current knowledge of their behaviour and ecology is needed. Expert opinion (EO) range maps, created with the most up-to-date expert knowledge of each DVS distribution, were combined with a contemporary database of occurrence data and a suite of open access, environmental and climatic variables. Using the Boosted Regression Tree (BRT) modelling method, distribution maps of each DVS were produced. The occurrence data were abstracted from the formal, published literature, plus other relevant sources, resulting in the collation of DVS occurrence at 10116 locations across 31 countries, of which 8853 were successfully geo-referenced and 7430 were resolved to spatial areas that could be included in the BRT model. A detailed summary of the information on the bionomics of each species and species complex is also presented. This article concludes a project aimed to establish the contemporary global distribution of the DVS of malaria. The three articles produced are intended as a detailed reference for scientists continuing research into the aspects of taxonomy, biology and ecology relevant to species-specific vector control. This research is particularly relevant to help unravel the complicated taxonomic status, ecology and epidemiology of the vectors of the Asia-Pacific region. All the occurrence data, predictive maps and EO-shape files generated during the production of these publications will be made available in the public domain. We hope that this will encourage data sharing to improve future iterations of the distribution maps.

Life-history habitat matching in invading non-native plant species

USGS Publications Warehouse

Stohlgren, T.J.; Crosier, C.; Chong, G.W.; Guenther, D.; Evangelista, P.

2005-01-01

We briefly reviewed the literature on habitat matching in invading non-native plant species. Then we hypothesized that the richness and cover of native annual and perennial plant species integrate complex local information of vegetation and soils that would help to predict invasion success by similarly adapted non-native plant species. We tested these ‘life-history habitat matching’ relationships in 603 0.1-ha plots, including 294 plots in Colorado, which were relatively high for the cover of native perennial plant species, and for 309 0.1-ha plots in southern Utah, which were relatively high in the cover of native annual plant species. We found strong positive relationships between the richness and foliar cover for both native and non-native species, whether they were annual or perennial species (0.34 > r2 < 0.53; P < 0.0001). We also found significant positive relationships between the cover of native annual species at a site and the richness (r2 = 0.13; P < 0.0001) and the foliar cover (r2 = 0.06; P < 0.0001) of non-native annual species. The proportion of non-native annual species in the flora of a plot also increased significantly with the foliar cover of native annual species. Conversely, the richness and cover of non-native annual species were significantly negatively associated with the foliar cover of native perennial species (r2 = 0.05 and 0.06, respectively; P < 0.0001). The cover of non-native annual or perennial species was not significantly correlated with soil texture variables, %N, or %C. We conclude that there may be a high degree of life-history habitat matching by non-native annual species in these study sites. Information on native annual and perennial species richness and cover may help characterize the complex soils, climate, and disturbance environment in which similarly adapted non-native plant species establish and gain foliar cover.

Tephritid Integrative Taxonomy: Where We Are Now, with a Focus on the Resolution of Three Tropical Fruit Fly Species Complexes.

PubMed

Schutze, Mark K; Virgilio, Massimiliano; Norrbom, Allen; Clarke, Anthony R

2017-01-31

Accurate species delimitation underpins good taxonomy. Formalization of integrative taxonomy in the past decade has provided a framework for using multidisciplinary data to make species delimitation hypotheses more rigorous. We address the current state of integrative taxonomy by using as a case study an international project targeted at resolving three important tephritid species complexes: Bactrocera dorsalis complex, Anastrepha fraterculus complex, and Ceratitis FAR (C. fasciventris, C. anonae, C. rosa) complex. The integrative taxonomic approach has helped deliver significant advances in resolving these complexes: It has been used to identify some taxa as belonging to the same biological species as well as to confirm hidden cryptic diversity under a single taxonomic name. Nevertheless, the general application of integrative taxonomy has not been without issue, revealing challenges that must be considered when undertaking an integrative taxonomy project. Scrutiny of this international case study provides a unique opportunity to document lessons learned for the benefit of not only tephritid taxonomists, but also the wider taxonomic community.

Pinpointing the level of isolation between two cryptic species sharing the same microhabitat: a case study with a scarabaeid species complex

USDA-ARS?s Scientific Manuscript database

We explored biological processes underlying speciation within dung beetles belonging to the vacca species complex (Scarabaeidae: Onthophagus). The two taxa of this complex, O. vacca and O. medius, not only are known to have a large overlapping Palearctic distribution range but also share the same co...

On the dangers of model complexity without ecological justification in species distribution modeling

Treesearch

David M. Bell; Daniel R. Schlaepfer

2016-01-01

Although biogeographic patterns are the product of complex ecological processes, the increasing com-plexity of correlative species distribution models (SDMs) is not always motivated by ecological theory,but by model fit. The validity of model projections, such as shifts in a species’ climatic niche, becomesquestionable particularly during extrapolations, such as for...

Positive selection drives the evolution of a major histocompatibility complex gene in an endangered Mexican salamander species complex.

PubMed

Tracy, Karen E; Kiemnec-Tyburczy, Karen M; DeWoody, J Andrew; Parra-Olea, Gabriela; Zamudio, Kelly R

2015-06-01

Immune gene evolution can be critical to species survival in the face of infectious disease. In particular, polymorphism in the genes of the major histocompatibility complex (MHC) helps vertebrates combat novel and diverse pathogens by increasing the number of pathogen-derived proteins that can initiate the host's acquired immune response. In this study, we used a combination of presumably adaptive and neutral markers to investigate MHC evolution in populations of five salamander species within the Ambystoma velasci complex, a group consisting of 15 recently diverged species, several of which are endangered. We isolated 31 unique MHC class II β alleles from 75 total individuals from five species in this complex. MHC heterozygosity was significantly lower than expected for all five species, and we found no clear relationship between number of MHC alleles and species range, life history, or level of heterozygosity. We inferred a phylogeny representing the evolutionary history of Ambystoma MHC, with which we found signatures of positive selection on the overall gene, putative peptide-binding residues, and allelic lineages. We identified several instances of trans-species polymorphism, a hallmark of balancing selection observed in other groups of closely related species. In contrast, we did not detect comparable allelic diversity or signatures of selection on neutral loci. Additionally, we identified 17 supertypes among the 44 unique Ambystoma alleles, indicating that these sequences may encode functionally distinct MHC variants. We therefore have strong evidence that positive selection is a major evolutionary force driving patterns of MHC polymorphism in this recently radiated species complex.

Insectivorous bats respond to vegetation complexity in urban green spaces.

PubMed

Suarez-Rubio, Marcela; Ille, Christina; Bruckner, Alexander

2018-03-01

Structural complexity is known to determine habitat quality for insectivorous bats, but how bats respond to habitat complexity in highly modified areas such as urban green spaces has been little explored. Furthermore, it is uncertain whether a recently developed measure of structural complexity is as effective as field-based surveys when applied to urban environments. We assessed whether image-derived structural complexity (MIG) was as/more effective than field-based descriptors in this environment and evaluated the response of insectivorous bats to structural complexity in urban green spaces. Bat activity and species richness were assessed with ultrasonic devices at 180 locations within green spaces in Vienna, Austria. Vegetation complexity was assessed using 17 field-based descriptors and by calculating the mean information gain (MIG) using digital images. Total bat activity and species richness decreased with increasing structural complexity of canopy cover, suggesting maneuverability and echolocation (sensorial) challenges for bat species using the canopy for flight and foraging. The negative response of functional groups to increased complexity was stronger for open-space foragers than for edge-space foragers. Nyctalus noctula , a species foraging in open space, showed a negative response to structural complexity, whereas Pipistrellus pygmaeus , an edge-space forager, was positively influenced by the number of trees. Our results show that MIG is a useful, time- and cost-effective tool to measure habitat complexity that complemented field-based descriptors. Response of insectivorous bats to structural complexity was group- and species-specific, which highlights the need for manifold management strategies (e.g., increasing or reinstating the extent of ground vegetation cover) to fulfill different species' requirements and to conserve insectivorous bats in urban green spaces.

Lipoic acid metabolism and mitochondrial redox regulation.

PubMed

Solmonson, Ashley D; DeBerardinis, Ralph J

2017-11-30

Lipoic acid is an essential cofactor for mitochondrial metabolism and is synthesized de novo using intermediates from mitochondrial fatty acid synthesis type II, S-adenosylmethionine and iron-sulfur clusters. This cofactor is required for catalysis by multiple mitochondrial 2-ketoacid dehydrogenase complexes, including pyruvate dehydrogenase, alpha-ketoglutarate dehydrogenase, and branched-chain ketoacid dehydrogenase. Lipoic acid also plays a critical role in stabilizing and regulating these multi-enzyme complexes.  Many of these dehydrogenases are regulated by reactive oxygen species, mediated through the disulfide bond of the prosthetic lipoyl moiety.  Collectively, its functions explain why lipoic acid is required for cell growth, mitochondrial activity and coordination of fuel metabolism. Lipoic acid is an essential cofactor for mitochondrial metabolism and is synthesized de novo using intermediates from mitochondrial fatty acid synthesis type II, S-adenosylmethionine and iron-sulfur clusters. This cofactor is required for catalysis by multiple mitochondrial 2-ketoacid dehydrogenase complexes, including pyruvate dehydrogenase, alpha-ketoglutarate dehydrogenase, and branched-chain ketoacid dehydrogenase. Lipoic acid also plays a critical role in stabilizing and regulating these multi-enzyme complexes.  Many of these dehydrogenases are regulated by reactive oxygen species, mediated through the disulfide bond of the prosthetic lipoyl moiety.  Collectively, its functions explain why lipoic acid is required for cell growth, mitochondrial activity and coordination of fuel metabolism. Copyright © 2017, The American Society for Biochemistry and Molecular Biology.

Local variation and parallel evolution: morphological and genetic diversity across a species complex of neotropical crater lake cichlid fishes

PubMed Central

Elmer, Kathryn R.; Kusche, Henrik; Lehtonen, Topi K.; Meyer, Axel

2010-01-01

The polychromatic and trophically polymorphic Midas cichlid fish species complex (Amphilophus cf. citrinellus) is an excellent model system for studying the mechanisms of speciation and patterns of phenotypic diversification in allopatry and in sympatry. Here, we first review research to date on the species complex and the geological history of its habitat. We analyse body shape variation from all currently described species in the complex, sampled from six crater lakes (maximally 1.2–23.9 kyr old) and both great lakes in Nicaragua. We find that Midas cichlid populations in each lake have their own characteristic body shape. In lakes with multiple sympatric species of Midas cichlid, each species has a distinct body shape. Across the species complex, most body shape change relates to body depth, head, snout and mouth shape and caudal peduncle length. There is independent parallel evolution of an elongate limnetic species in at least two crater lakes. Mitochondrial genetic diversity is higher in crater lakes with multiple species. Midas cichlid species richness increases with the size and age of the crater lakes, though no such relationship exists for the other syntopic fishes. We suggest that crater lake Midas cichlids follow the predicted pattern of an adaptive radiation, with early divergence of each crater lake colonization, followed by intralacustrine diversification and speciation by ecological adaptation and sexual selection. PMID:20439280

Genetic and Morphological Analyses Demonstrate That Schizolecis guntheri (Siluriformes: Loricariidae) Is Likely to Be a Species Complex

PubMed Central

Souza, Camila S.; Costa-Silva, Guilherme J.; Roxo, Fábio F.; Foresti, Fausto; Oliveira, Claudio

2018-01-01

Schizolecis is a monotypic genus of Siluriformes widely distributed throughout isolated coastal drainages of southeastern Brazil. Previous studies have shown that fish groups found in isolated river basins tend to differentiate over time in the absence of gene flow, resulting in allopatric speciation. In this study, we used partial sequences of the mitochondrial gene COI with the analysis of the General Mixed Yule Coalescent model (GMYC) and the Automatic Barcode Gap Discovery (ABGD) for single locus species delimitation, and a Principal Component Analysis (PCA) of external morphology to test the hypothesis that Schizolecis guntheri is a complex of species. We analyzed 94 samples of S. guntheri for GMYC and ABGD, and 82 samples for PCA from 22 coastal rivers draining to the Atlantic in southeastern Brazil from the Paraná State to the north of the Rio de Janeiro State. As a result, the GMYC model and the ABGD delimited five operational taxonomy units (OTUs – a nomenclature referred to in the present study of the possible new species delimited for the genetic analysis), a much higher number compared to the traditional alfa taxonomy that only recognizes S. guntheri across the isolated coastal rivers of Brazil. Furthermore, the PCA analysis suggests that S. guntheri is highly variable in aspects of external body proportions, including dorsal-fin spine length, pectoral-fin spine length, pelvic-fin spine length, lower caudal-fin spine length, caudal peduncle depth, anal width and mandibular ramus length. However, no exclusive character was found among the isolated populations that could be used to describe a new species of Schizolecis. Therefore, we can conclude, based on our results of PCA contrasting with the results of GMYC and ABGD, that S. guntheri represents a complex of species. PMID:29552028

Seagrass Radiation after Messinian Salinity Crisis Reflected by Strong Genetic Structuring and Out-of-Africa Scenario (Ruppiaceae)

PubMed Central

Triest, Ludwig; Sierens, Tim

2014-01-01

Many aquatic plant and seagrass species are widespread and the origin of their continent-wide ranges might result from high gene flow levels. The response of species when extending northwards since the Last Glacial Maximum can be opposed to the structuring of their populations that survived glaciation cycles in southern regions. The peri-Mediterranean is a complex series of sea basins, coastlines, islands and river deltas with a unique history since the Messinian Crisis that potentially influenced allopatric processes of aquatic life. We tested whether vast ranges across Europe and the peri-Mediterranean of a global seagrass group (Ruppia species complexes) can be explained by either overall high levels of gene flow or vicariance through linking population genetics, phylogeography and shallow phylogenetics. A multigene approach identified haplogroup lineages of two species complexes, of ancient and recent hybrids with most of the diversity residing in the South. High levels of connectivity over long distances were only observed at recently colonized northern ranges and in recently-filled seas following the last glaciation. A strong substructure in the southern Mediterranean explained an isolation-by-distance model across Europe. The oldest lineages of the southern Mediterranean Ruppia dated back to the period between the end of the Messinian and Late Pliocene. An imprint of ancient allopatric origin was left at basin level, including basal African lineages. Thus both vicariance in the South and high levels of connectivity in the North explained vast species ranges. Our findings highlight the need for interpreting global distributions of these seagrass and euryhaline species in the context of their origin and evolutionary significant units for setting up appropriate conservation strategies. PMID:25100173

Genetic and Morphological Analyses Demonstrate That Schizolecis guntheri (Siluriformes: Loricariidae) Is Likely to Be a Species Complex.

PubMed

Souza, Camila S; Costa-Silva, Guilherme J; Roxo, Fábio F; Foresti, Fausto; Oliveira, Claudio

2018-01-01

Schizolecis is a monotypic genus of Siluriformes widely distributed throughout isolated coastal drainages of southeastern Brazil. Previous studies have shown that fish groups found in isolated river basins tend to differentiate over time in the absence of gene flow, resulting in allopatric speciation. In this study, we used partial sequences of the mitochondrial gene COI with the analysis of the General Mixed Yule Coalescent model (GMYC) and the Automatic Barcode Gap Discovery (ABGD) for single locus species delimitation, and a Principal Component Analysis (PCA) of external morphology to test the hypothesis that Schizolecis guntheri is a complex of species. We analyzed 94 samples of S. guntheri for GMYC and ABGD, and 82 samples for PCA from 22 coastal rivers draining to the Atlantic in southeastern Brazil from the Paraná State to the north of the Rio de Janeiro State. As a result, the GMYC model and the ABGD delimited five operational taxonomy units (OTUs - a nomenclature referred to in the present study of the possible new species delimited for the genetic analysis), a much higher number compared to the traditional alfa taxonomy that only recognizes S. guntheri across the isolated coastal rivers of Brazil. Furthermore, the PCA analysis suggests that S. guntheri is highly variable in aspects of external body proportions, including dorsal-fin spine length, pectoral-fin spine length, pelvic-fin spine length, lower caudal-fin spine length, caudal peduncle depth, anal width and mandibular ramus length. However, no exclusive character was found among the isolated populations that could be used to describe a new species of Schizolecis . Therefore, we can conclude, based on our results of PCA contrasting with the results of GMYC and ABGD, that S. guntheri represents a complex of species.

Mapping Arid Vegetation Species Distributions in the White Mountains, Eastern California, Using AVIRIS, Topography, and Geology

NASA Technical Reports Server (NTRS)

VandeVen, C.; Weiss, S. B.

2001-01-01

Our challenge is to model plant species distributions in complex montane environments using disparate sources of data, including topography, geology, and hyperspectral data. From an ecologist's point of view, species distributions are determined by local environment and disturbance history, while spectral data are 'ancillary.' However, a remote sensor's perspective says that spectral data provide picture of what vegetation is there, topographic and geologic data are ancillary. In order to bridge the gap, all available data should be used to get the best possible prediction of species distributions using complex multivariate techniques implemented on a GIS. Vegetation reflects local climatic and nutrient conditions, both of which can be modeled, allowing predictive mapping of vegetation distributions. Geologic substrate strongly affects chemical, thermal, and physical properties of soils, while climatic conditions are determined by local topography. As elevation increases, precipitation increases and temperature decreases. Aspect, slope, and surrounding topography determine potential insolation, so that south-facing slopes are warmer and north-facing slopes cooler at a given elevation. Topographic position (ridge, slope, canyon, or meadow) and slope angle affect sediment accumulation and soil depth. These factors combine as complex environmental gradients, and underlie many features of plant distributions. Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data, digital elevation models, digitized geologic maps, and 378 ground control points were used to predictively map species distributions in the central and southern White Mountains, along the western boundary of the Basin and Range province. Minimum Noise Fraction (MNF) bands were calculated from the visible and near-infrared AVIRIS bands, and combined with digitized geologic maps and topographic variables using Canonical Correspondence Analysis (CCA). CCA allows for modeling species 'envelopes' in multidimensional environmental space, which can then be projected across entire landscapes.

Molecular systematics of the parasitic protozoan Giardia intestinalis.

PubMed

Monis, P T; Andrews, R H; Mayrhofer, G; Ey, P L

1999-09-01

The long-standing controversy regarding whether Giardia intestinalis is a single species prevalent in both human and animal hosts or a species complex consisting of morphologically similar organisms that differ in host range and other biotypic characteristics is an issue with important medical, veterinary, and environmental management implications. In the past decade, highly distinct genotypes (some apparently confined to particular host groups) have been identified by genetic analysis of samples isolated from different host species. The aim of this study was to undertake a phylogenetic analysis of G. intestinalis that were representative of all known major genetic groups and compare them with other Giardia species, viz. G. ardeae, G. muris, and G. microti. Segments from four "housekeeping" genes (specifying glutamate dehydrogenase, triose phosphate isomerase, elongation factor 1 alpha, and 18S ribosomal RNA) were examined by analysis of 0.48-0.69-kb nucleotide sequences determined from DNA amplified in polymerase chain reactions from each locus. In addition, isolates were compared by allozymic analysis of electrophoretic data obtained for 21 enzymes representing 23 gene loci. The results obtained from these independent techniques and different loci were essentially congruous. Analyses using G. ardeae and/or G. muris as outgroups supported the monophyly of G. intestinalis and also showed that this species includes genotypes that represent at least seven deeply rooted lineages, herein designated assemblages A-G. Inclusion of G. microti in the analysis of 18S rRNA sequence data demonstrated the monophyly of Giardia with the same median body morphology but did not support the monophyly of G. intestinalis, instead placing G. microti within G. intestinalis. The findings support the hypothesis that G. intestinalis is a species complex and suggest that G. microti is a member of this complex.

Contrasting Evolutionary Paths Among Indo-Pacific Pomacentrus Species Promoted by Extensive Pericentric Inversions and Genome Organization of Repetitive Sequences.

PubMed

Getlekha, Nuntaporn; Cioffi, Marcelo de Bello; Maneechot, Nuntiya; Bertollo, Luiz Antônio Carlos; Supiwong, Weerayuth; Tanomtong, Alongklod; Molina, Wagner Franco

2018-02-01

Pomacentrus (damselfishes) is one of the most characteristic groups of fishes in the Indo-Pacific coral reef. Its 77 described species exhibit a complex taxonomy with cryptic lineages across their extensive distribution. Periods of evolutionary divergences between them are very variable, and the cytogenetic events that followed their evolutionary diversification are largely unknown. In this respect, analyses of chromosomal divergence, within a phylogenetic perspective, are particularly informative regarding karyoevolutionary trends. As such, we conducted conventional cytogenetic and cytogenomic analyses in four Pomacentrus species (Pomacentrus similis, Pomacentrus auriventris, Pomacentrus moluccensis, and Pomacentrus cuneatus), through the mapping of repetitive DNA classes and transposable elements, including 18S rDNA, 5S rDNA, (CA) 15 , (GA) 15 , (CAA) 10 , Rex6, and U2 snDNA as markers. P. auriventris and P. similis, belonging to the Pomacentrus coelestis complex, have indistinguishable karyotypes (2n = 48; NF = 48), with a peculiar syntenic organization of ribosomal genes. On the other hand, P. moluccensis and P. cuneatus, belonging to another clade, exhibit very different karyotypes (2n = 48, NF = 86 and 92, respectively), with a large number of bi-armed chromosomes, where multiple pericentric inversions played a significant role in their karyotype organization. In this sense, different chromosomal pathways followed the phyletic diversification in the Pomacentrus genus, making possible the characterization of two well-contrasting species groups regarding their karyotype features. Despite this, pericentric inversions act as an effective postzygotic barrier in many organisms, which appear to be also the case for P. moluccensis and P. cuneatus; the extensive chromosomal similarities in the two species of P. coelestis complex suggest minor participation of chromosomal postzygotic barriers in the phyletic diversification of these species.

Vibrio Iron Transport: Evolutionary Adaptation to Life in Multiple Environments

PubMed Central

Mey, Alexandra R.; Wyckoff, Elizabeth E.

2015-01-01

SUMMARY Iron is an essential element for Vibrio spp., but the acquisition of iron is complicated by its tendency to form insoluble ferric complexes in nature and its association with high-affinity iron-binding proteins in the host. Vibrios occupy a variety of different niches, and each of these niches presents particular challenges for acquiring sufficient iron. Vibrio species have evolved a wide array of iron transport systems that allow the bacteria to compete for this essential element in each of its habitats. These systems include the secretion and uptake of high-affinity iron-binding compounds (siderophores) as well as transport systems for iron bound to host complexes. Transporters for ferric and ferrous iron not complexed to siderophores are also common to Vibrio species. Some of the genes encoding these systems show evidence of horizontal transmission, and the ability to acquire and incorporate additional iron transport systems may have allowed Vibrio species to more rapidly adapt to new environmental niches. While too little iron prevents growth of the bacteria, too much can be lethal. The appropriate balance is maintained in vibrios through complex regulatory networks involving transcriptional repressors and activators and small RNAs (sRNAs) that act posttranscriptionally. Examination of the number and variety of iron transport systems found in Vibrio spp. offers insights into how this group of bacteria has adapted to such a wide range of habitats. PMID:26658001

Novel species including Mycobacterium fukienense sp. is found from tuberculosis patients in Fujian Province, China, using phylogenetic analysis of Mycobacterium chelonae/abscessus complex.

PubMed

Zhang, Yuan Yuan; Li, Yan Bing; Huang, Ming Xiang; Zhao, Xiu Qin; Zhang, Li Shui; Liu, Wen En; Wan, Kang Lin

2013-11-01

To identify the novel species 'Mycobacterium fukienense' sp. nov of Mycobacterium chelonae/abscessus complex from tuberculosis patients in Fujian Province, China. Five of 27 clinical Mycobacterium isolates (Cls) were previously identified as M. chelonae/abscessus complex by sequencing the hsp65, rpoB, 16S-23S rRNA internal transcribed spacer region (its), recA and sodA house-keeping genes commonly used to describe the molecular characteristics of Mycobacterium. Clinical Mycobacterium isolates were classified according to the gene sequence using a clustering analysis program. Sequence similarity within clusters and diversity between clusters were analyzed. The 5 isolates were identified with distinct sequences exhibiting 99.8% homology in the hsp65 gene. However, a complete lack of homology was observed among the sequences of the rpoB, 16S-23S rRNA internal transcribed spacer region (its), sodA, and recA genes as compared with the M. abscessus. Furthermore, no match for rpoB, sodA, and recA genes was identified among the published sequences. The novel species, Mycobacterium fukienense, is identified from tuberculosis patients in Fujian Province, China, which does not belong to any existing subspecies of M. chelonea/abscessus complex. Copyright © 2013 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Environmental studies conducted at the Fenton Hill Hot Dry Rock geothermal development site

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

Miera, F.R. Jr.; Langhorst, G.; McEllin, S.

1984-05-01

An environmental investigation of Hot Dry Rock (HDR) geothermal development was conducted at Fenton Hill, New Mexico, during 1976-1979. Activities at the Fenton Hill Site included an evaluation of baseline data for biotic and abiotic ecosystem components. Identification of contaminants produced by HDR processes that had the potential for reaching the surrounding environment is also discussed. Three dominant vegetative communities were identified in the vicinity of the site. These included grass-forb, aspen, and mixed conifer communities. The grass-forb area was identified as having the highest number of species encountered, with Phleum pratense and Dactylis glomerata being the dominant grass species.more » Frequency of occurrence and mean coverage values are also given for other species in the three main vegetative complexes. Live trapping of small mammals was conducted to determine species composition, densities, population, and diversity estimates for this component of the ecosystem. The data indicate that Peromyscus maniculatus was the dominant species across all trapping sites during the study. Comparisons of relative density of small mammals among the various trapping sites show the grass-forb vegetative community to have had the highest overall density. Comparisons of small mammal diversity for the three main vegetative complexes indicate that the aspen habitat had the highest diversity and the grass-forb habitat had the lowest. Analyses of waste waters from the closed circulation loop indicate that several trace contaminants (e.g., arsenic, cadmium, fluoride, boron, and lithium) were present at concentrations greater than those reported for surface waters of the region.« less

Burkholderia puraquae sp. nov., a novel species of the Burkholderia cepacia complex isolated from hospital settings and agricultural soils.

PubMed

Martina, Pablo; Leguizamon, Mariana; Prieto, Claudia I; Sousa, Silvia A; Montanaro, Patricia; Draghi, Walter O; Stämmler, Maren; Bettiol, Marisa; de Carvalho, Carla C C R; Palau, Juliana; Figoli, Cecilia; Alvarez, Florencia; Benetti, Silvina; Lejona, Sergio; Vescina, Cecilia; Ferreras, Julián; Lasch, Peter; Lagares, Antonio; Zorreguieta, Angeles; Leitão, Jorge H; Yantorno, Osvaldo M; Bosch, Alejandra

2018-01-01

Bacteria from the Burkholderia cepacia complex (Bcc) are capable of causing severe infections in patients with cystic fibrosis (CF). These opportunistic pathogens are also widely distributed in natural and man-made environments. After a 12-year epidemiological surveillance involving Bcc bacteria from respiratory secretions of Argentinean patients with CF and from hospital settings, we found six isolates of the Bcc with a concatenated species-specific allele sequence that differed by more than 3 % from those of the Bcc with validly published names. According to the multilocus sequence analysis (MLSA), these isolates clustered with the agricultural soil strain, Burkholderia sp. PBP 78, which was already deposited in the PubMLST database. The isolates were examined using a polyphasic approach, which included 16S rRNA, recA, Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), DNA base composition, average nucleotide identities (ANIs), fatty acid profiles, and biochemical characterizations. The results of the present study demonstrate that the seven isolates represent a single novel species within the Bcc, for which the name Burkholderia puraquae sp. nov. is proposed. Burkholderia puraquae sp. nov. CAMPA 1040 T (=LMG 29660 T =DSM 103137 T ) was designated the type strain of the novel species, which can be differentiated from other species of the Bcc mainly from recA gene sequence analysis, MLSA, ANIb, MALDI-TOF MS analysis, and some biochemical tests, including the ability to grow at 42 °C, aesculin hydrolysis, and lysine decarboxylase and β-galactosidase activities.

Species-richness of the Anopheles annulipes Complex (Diptera: Culicidae) Revealed by Tree and Model-Based Allozyme Clustering Analyses

DTIC Science & Technology

2007-01-01

including tree- based methods such as the unweighted pair group method of analysis ( UPGMA ) and Neighbour-joining (NJ) (Saitou & Nei, 1987). By...based Bayesian approach and the tree-based UPGMA and NJ cluster- ing methods. The results obtained suggest that far more species occur in the An...unlikely that groups that differ by more than these levels are conspecific. Genetic distances were clustered using the UPGMA and NJ algorithms in MEGA

Whole-Genome Sequences of 94 Environmental Isolates of Bacillus cereus Sensu Lato

PubMed Central

Feldgarden, Michael; Kolter, Roberto; Mahillon, Jacques

2013-01-01

Bacillus cereus sensu lato is a species complex that includes the anthrax pathogen Bacillus anthracis and other bacterial species of medical, industrial, and ecological importance. Their phenotypes of interest are typically linked to large plasmids that are closely related to the anthrax plasmids pXO1 and pXO2. Here, we present the draft genome sequences of 94 isolates of B. cereus sensu lato, which were chosen for their plasmid content and environmental origins. PMID:24092776

Use of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of molds of the Fusarium genus.

PubMed

Triest, David; Stubbe, Dirk; De Cremer, Koen; Piérard, Denis; Normand, Anne-Cécile; Piarroux, Renaud; Detandt, Monique; Hendrickx, Marijke

2015-02-01

The rates of infection with Fusarium molds are increasing, and a diverse number of Fusarium spp. belonging to different species complexes can cause infection. Conventional species identification in the clinical laboratory is time-consuming and prone to errors. We therefore evaluated whether matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a useful alternative. The 289 Fusarium strains from the Belgian Coordinated Collections of Microorganisms (BCCM)/Institute of Hygiene and Epidemiology Mycology (IHEM) culture collection with validated sequence-based identities and comprising 40 species were used in this study. An identification strategy was developed, applying a standardized MALDI-TOF MS assay and an in-house reference spectrum database. In vitro antifungal testing was performed to assess important differences in susceptibility between clinically relevant species/species complexes. We observed that no incorrect species complex identifications were made by MALDI-TOF MS, and 82.8% of the identifications were correct to the species level. This success rate was increased to 91% by lowering the cutoff for identification. Although the identification of the correct species complex member was not always guaranteed, antifungal susceptibility testing showed that discriminating between Fusarium species complexes can be important for treatment but is not necessarily required between members of a species complex. With this perspective, some Fusarium species complexes with closely related members can be considered as a whole, increasing the success rate of correct identifications to 97%. The application of our user-friendly MALDI-TOF MS identification approach resulted in a dramatic improvement in both time and accuracy compared to identification with the conventional method. A proof of principle of our MALDI-TOF MS approach in the clinical setting using recently isolated Fusarium strains demonstrated its validity. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Structural basis for the Nanos-mediated recruitment of the CCR4-NOT complex and translational repression.

PubMed

Bhandari, Dipankar; Raisch, Tobias; Weichenrieder, Oliver; Jonas, Stefanie; Izaurralde, Elisa

2014-04-15

The RNA-binding proteins of the Nanos family play an essential role in germ cell development and survival in a wide range of metazoan species. They function by suppressing the expression of target mRNAs through the recruitment of effector complexes, which include the CCR4-NOT deadenylase complex. Here, we show that the three human Nanos paralogs (Nanos1-3) interact with the CNOT1 C-terminal domain and determine the structural basis for the specific molecular recognition. Nanos1-3 bind CNOT1 through a short CNOT1-interacting motif (NIM) that is conserved in all vertebrates and some invertebrate species. The crystal structure of the human Nanos1 NIM peptide bound to CNOT1 reveals that the peptide opens a conserved hydrophobic pocket on the CNOT1 surface by inserting conserved aromatic residues. The substitutions of these aromatic residues in the Nanos1-3 NIMs abolish binding to CNOT1 and abrogate the ability of the proteins to repress translation. Our findings provide the structural basis for the recruitment of the CCR4-NOT complex by vertebrate Nanos, indicate that the NIMs are the major determinants of the translational repression mediated by Nanos, and identify the CCR4-NOT complex as the main effector complex for Nanos function.

Mitochondrial dysfunction in myocardium obtained from clinically normal dogs, clinically normal anesthetized dogs, and dogs with dilated cardiomyopathy.

PubMed

Sleeper, Meg M; Rosato, Bradley P; Bansal, Seema; Avadhani, Narayan G

2012-11-01

To compare mitochondrial complex I and complex IV activity in myocardial mitochondria of clinically normal dogs, clinically normal dogs exposed to inhalation anesthesia, and dogs affected with dilated cardiomyopathy. Myocardial samples obtained from 21 euthanized dogs (6 clinically normal [control] dogs, 5 clinically normal dogs subjected to inhalation anesthesia with isoflurane prior to euthanasia, 5 dogs with juvenile-onset dilated cardiomyopathy, and 5 dogs with adult-onset dilated cardiomyopathy). Activity of mitochondrial complex I and complex IV was assayed spectrophotometrically in isolated mitochondria from left ventricular tissue obtained from the 4 groups of dogs. Activity of complex I and complex IV was significantly decreased in anesthetized dogs, compared with activities in the control dogs and dogs with juvenile-onset or adult-onset dilated cardiomyopathy. Inhalation anesthesia disrupted the electron transport chain in the dogs, which potentially led to an outburst of reactive oxygen species that caused mitochondrial dysfunction. Inhalation anesthesia depressed mitochondrial function in dogs, similar to results reported in other species. This effect is important to consider when anesthetizing animals with myocardial disease and suggested that antioxidant treatments may be beneficial in some animals. Additionally, this effect should be considered when designing studies in which mitochondrial enzyme activity will be measured. Additional studies that include a larger number of animals are warranted.

Reticulate evolution in stick insects: the case of Clonopsis (Insecta Phasmida).

PubMed

Milani, Liliana; Ghiselli, Fabrizio; Pellecchia, Marco; Scali, Valerio; Passamonti, Marco

2010-08-25

Phasmids show noteworthy abilities to overcome species-specific reproductive isolation mechanisms, including hybridization, polyploidy, parthenogenesis, hybridogenesis and androgenesis. From an evolutionary standpoint, such tangled reproductive interactions lead to the complex phyletic relationships known as "reticulate evolution". Moroccan stick insects of the genus Clonopsis include one bisexual (C. felicitatis) and two closely related parthenogenetic forms (C. gallica, C. soumiae), which represent a polyploid series in chromosome number, but with apparent diploid karyotypes. Moreover, two Clonopsis strains of ameiotic males have been described, C. androgenes-35 and C. androgenes-53. As a consequence, Clonopsis stick insects may have experienced complex micro-evolutionary events, which we try to disentangle in this study. Mitochondrial cox2 analysis supports a recent divergence of Clonopsis, while AFLPs evidence genetic differentiation not linked to karyotypes, so that parthenogenetic C. gallica and C. soumiae appear to be a mix of strains of polyphyletic origin rather than single parthenogenetic species. Moreover, an admixed hybrid origin seems to be confirmed for C. androgenes. On the whole, Clonopsis is an intriguing case of reticulate evolution. Actually, complex cladogenetic events should be taken into account to explain the observed genetic structure, including diploidization of polyploid karyotypes, possibly coupled with hybridization and androgenesis. We also proposed a "working hypothesis" to account for the observed data, which deserves further studies, but fits the observed data very well.

Reticulate evolution in stick insects: the case of Clonopsis (Insecta Phasmida)

PubMed Central

2010-01-01

Background Phasmids show noteworthy abilities to overcome species-specific reproductive isolation mechanisms, including hybridization, polyploidy, parthenogenesis, hybridogenesis and androgenesis. From an evolutionary standpoint, such tangled reproductive interactions lead to the complex phyletic relationships known as "reticulate evolution". Moroccan stick insects of the genus Clonopsis include one bisexual (C. felicitatis) and two closely related parthenogenetic forms (C. gallica, C. soumiae), which represent a polyploid series in chromosome number, but with apparent diploid karyotypes. Moreover, two Clonopsis strains of ameiotic males have been described, C. androgenes-35 and C. androgenes-53. As a consequence, Clonopsis stick insects may have experienced complex micro-evolutionary events, which we try to disentangle in this study. Results Mitochondrial cox2 analysis supports a recent divergence of Clonopsis, while AFLPs evidence genetic differentiation not linked to karyotypes, so that parthenogenetic C. gallica and C. soumiae appear to be a mix of strains of polyphyletic origin rather than single parthenogenetic species. Moreover, an admixed hybrid origin seems to be confirmed for C. androgenes. Conclusion On the whole, Clonopsis is an intriguing case of reticulate evolution. Actually, complex cladogenetic events should be taken into account to explain the observed genetic structure, including diploidization of polyploid karyotypes, possibly coupled with hybridization and androgenesis. We also proposed a "working hypothesis" to account for the observed data, which deserves further studies, but fits the observed data very well. PMID:20738851

Tutorial on Protein Ontology Resources

PubMed Central

Arighi, Cecilia; Drabkin, Harold; Christie, Karen R.; Ross, Karen; Natale, Darren

2017-01-01

The Protein Ontology (PRO) is the reference ontology for proteins in the Open Biomedical Ontologies (OBO) foundry and consists of three sub-ontologies representing protein classes of homologous genes, proteoforms (e.g., splice isoforms, sequence variants, and post-translationally modified forms), and protein complexes. PRO defines classes of proteins and protein complexes, both species-specific and species non-specific, and indicates their relationships in a hierarchical framework, supporting accurate protein annotation at the appropriate level of granularity, analyses of protein conservation across species, and semantic reasoning. In this first section of this chapter, we describe the PRO framework including categories of PRO terms and the relationship of PRO to other ontologies and protein resources. Next, we provide a tutorial about the PRO website (proconsortium.org) where users can browse and search the PRO hierarchy, view reports on individual PRO terms, and visualize relationships among PRO terms in a hierarchical table view, a multiple sequence alignment view, and a Cytoscape network view. Finally, we describe several examples illustrating the unique and rich information available in PRO. PMID:28150233

Distribution of 10 periodontal bacterial species in children and adolescents over a 7-year period.

PubMed

Nakano, K; Miyamoto, E; Tamura, K; Nemoto, H; Fujita, K; Nomura, R; Ooshima, T

2008-10-01

There is scant information available regarding the distribution of periodontal bacterial species in children and adolescents over an extended period. The purpose of this study was to compare bacterial profiles in the same individuals over a period of 7 years. Twenty-six children and adolescents from whom dental plaque and saliva specimens were obtained during both the first (1999-2000) and second (2006-2007) periods, were analyzed. Bacterial DNA was extracted from each specimen and the presence of 10 periodontal bacterial species was determined using a PCR method, with a focus on the red complex species of Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia. Subjects with red complex species in saliva specimens obtained during the second collection possessed a significantly higher number of total bacterial species than those without. The detection rate of the red complex species in the second collection period samples was significantly greater in subjects who had two or more species detected in samples taken during the first collection compared with the other subjects. Subjects possessing red complex species may be at possible risk for infection with a high number of periodontal bacterial species during adolescent and younger adult years.

Cryptic or pseudocryptic: can morphological methods inform copepod taxonomy? An analysis of publications and a case study of the Eurytemora affinis species complex

PubMed Central

Lajus, Dmitry; Sukhikh, Natalia; Alekseev, Victor

2015-01-01

Interest in cryptic species has increased significantly with current progress in genetic methods. The large number of cryptic species suggests that the resolution of traditional morphological techniques may be insufficient for taxonomical research. However, some species now considered to be cryptic may, in fact, be designated pseudocryptic after close morphological examination. Thus the “cryptic or pseudocryptic” dilemma speaks to the resolution of morphological analysis and its utility for identifying species. We address this dilemma first by systematically reviewing data published from 1980 to 2013 on cryptic species of Copepoda and then by performing an in-depth morphological study of the former Eurytemora affinis complex of cryptic species. Analyzing the published data showed that, in 5 of 24 revisions eligible for systematic review, cryptic species assignment was based solely on the genetic variation of forms without detailed morphological analysis to confirm the assignment. Therefore, some newly described cryptic species might be designated pseudocryptic under more detailed morphological analysis as happened with Eurytemora affinis complex. Recent genetic analyses of the complex found high levels of heterogeneity without morphological differences; it is argued to be cryptic. However, next detailed morphological analyses allowed to describe a number of valid species. Our study, using deep statistical analyses usually not applied for new species describing, of this species complex confirmed considerable differences between former cryptic species. In particular, fluctuating asymmetry (FA), the random variation of left and right structures, was significantly different between forms and provided independent information about their status. Our work showed that multivariate statistical approaches, such as principal component analysis, can be powerful techniques for the morphological discrimination of cryptic taxons. Despite increasing cryptic species designations, morphological techniques have great potential in determining copepod taxonomy. PMID:26120427

Colobopsis explodens sp. n., model species for studies on “exploding ants” (Hymenoptera, Formicidae), with biological notes and first illustrations of males of the Colobopsis cylindrica group

PubMed Central

Laciny, Alice; Zettel, Herbert; Kopchinskiy, Alexey; Pretzer, Carina; Pal, Anna; Salim, Kamariah Abu; Rahimi, Mohammad Javad; Hoenigsberger, Michaela; Lim, Linda; Jaitrong, Weeyawat; Druzhinina, Irina S.

2018-01-01

Abstract A taxonomic description of all castes of Colobopsis explodens Laciny & Zettel, sp. n. from Borneo, Thailand, and Malaysia is provided, which serves as a model species for biological studies on “exploding ants” in Southeast Asia. The new species is a member of the Colobopsis cylindrica (COCY) group and falls into a species complex that has been repeatedly summarized under the name Colobopsis saundersi (Emery, 1889) (formerly Camponotus saundersi). The COCY species group is known under its vernacular name “exploding ants” for a unique behaviour: during territorial combat, workers of some species sacrifice themselves by rupturing their gaster and releasing sticky and irritant contents of their hypertrophied mandibular gland reservoirs to kill or repel rivals. This study includes first illustrations and morphometric characterizations of males of the COCY group: Colobopsis explodens Laciny & Zettel, sp. n. and Colobopsis badia (Smith, 1857). Characters of male genitalia and external morphology are compared with other selected taxa of Camponotini. Preliminary notes on the biology of C. explodens Laciny & Zettel, sp. n. are provided. To fix the species identity of the closely related C. badia, a lectotype from Singapore is designated. The following taxonomic changes within the C. saundersi complex are proposed: Colobopsis solenobia (Menozzi, 1926), syn. n. and Colobopsis trieterica (Menozzi, 1926), syn. n. are synonymized with Colobopsis corallina Roger, 1863, a common endemic species of the Philippines. Colobopsis saginata Stitz, 1925, stat. n., hitherto a subspecies of C. badia, is raised to species level. PMID:29706783

Colobopsis explodens sp. n., model species for studies on "exploding ants" (Hymenoptera, Formicidae), with biological notes and first illustrations of males of the Colobopsis cylindrica group.

PubMed

Laciny, Alice; Zettel, Herbert; Kopchinskiy, Alexey; Pretzer, Carina; Pal, Anna; Salim, Kamariah Abu; Rahimi, Mohammad Javad; Hoenigsberger, Michaela; Lim, Linda; Jaitrong, Weeyawat; Druzhinina, Irina S

2018-01-01

A taxonomic description of all castes of Colobopsis explodens Laciny & Zettel, sp. n. from Borneo, Thailand, and Malaysia is provided, which serves as a model species for biological studies on "exploding ants" in Southeast Asia. The new species is a member of the Colobopsis cylindrica (COCY) group and falls into a species complex that has been repeatedly summarized under the name Colobopsis saundersi (Emery, 1889) (formerly Camponotus saundersi ). The COCY species group is known under its vernacular name "exploding ants" for a unique behaviour: during territorial combat, workers of some species sacrifice themselves by rupturing their gaster and releasing sticky and irritant contents of their hypertrophied mandibular gland reservoirs to kill or repel rivals. This study includes first illustrations and morphometric characterizations of males of the COCY group: Colobopsis explodens Laciny & Zettel, sp. n. and Colobopsis badia (Smith, 1857). Characters of male genitalia and external morphology are compared with other selected taxa of Camponotini. Preliminary notes on the biology of C. explodens Laciny & Zettel, sp. n. are provided. To fix the species identity of the closely related C. badia , a lectotype from Singapore is designated. The following taxonomic changes within the C. saundersi complex are proposed: Colobopsis solenobia (Menozzi, 1926), syn. n. and Colobopsis trieterica (Menozzi, 1926), syn. n. are synonymized with Colobopsis corallina Roger, 1863, a common endemic species of the Philippines. Colobopsis saginata Stitz, 1925, stat. n ., hitherto a subspecies of C. badia , is raised to species level.

Themes and Variations: Regulation of RpoN-Dependent Flagellar Genes across Diverse Bacterial Species

PubMed Central

Tsang, Jennifer; Hoover, Timothy R.

2014-01-01

Flagellar biogenesis in bacteria is a complex process in which the transcription of dozens of structural and regulatory genes is coordinated with the assembly of the flagellum. Although the overall process of flagellar biogenesis is conserved among bacteria, the mechanisms used to regulate flagellar gene expression vary greatly among different bacterial species. Many bacteria use the alternative sigma factor σ 54 (also known as RpoN) to transcribe specific sets of flagellar genes. These bacteria include members of the Epsilonproteobacteria (e.g., Helicobacter pylori and Campylobacter jejuni), Gammaproteobacteria (e.g., Vibrio and Pseudomonas species), and Alphaproteobacteria (e.g., Caulobacter crescentus). This review characterizes the flagellar transcriptional hierarchies in these bacteria and examines what is known about how flagellar gene regulation is linked with other processes including growth phase, quorum sensing, and host colonization. PMID:24672734

The Laboratory Production of Complex Organic Molecules in Simulated Interstellar Ices

NASA Technical Reports Server (NTRS)

Dworkin, J. P.; Sandford, S. A.; Bernstein, M. P.; Allamandola, L. J.

2002-01-01

Much of the volatiles in interstellar dense clouds exist in ices surrounding dust grains. Their low temperatures preclude most chemical reactions, but ionizing radiation can drive reactions that produce a suite of new species, many of which are complex organics. The Astrochemistry Lab at NASA Ames studies the UV radiation processing of interstellar ice analogs to better identify the resulting products and establish links between interstellar chemistry, the organics in meteorites, and the origin of life on Earth. Once identified, the spectral properties of the products can be quantified to assist with the search for these species in space. Of particular interest are findings that UV irradiation of interstellar ice analogs produces molecules of importance in current living organisms, including quinones, amphiphiles, and amino acids.

Nocardia transvalensis Disseminated Infection in an Immunocompromised Patient with Idiopathic Thrombocytopenic Purpura

PubMed Central

García-Méndez, Jorge; Carrillo-Casas, Erika M.; Rangel-Cordero, Andrea; Leyva-Leyva, Margarita; Xicohtencatl-Cortes, Juan; Arenas, Roberto; Hernández-Castro, Rigoberto

2016-01-01

Nocardia transvalensis complex includes a wide range of microorganisms with specific antimicrobial resistance patterns. N. transvalensis is an unusual Nocardia species. However, it must be differentiated due to its natural resistance to aminoglycosides while other Nocardia species are susceptible. The present report describes a Nocardia species involved in an uncommon clinical case of a patient with idiopathic thrombocytopenic purpura and pulmonary nocardiosis. Microbiological and molecular techniques based on the sequencing of the 16S rRNA gene allowed diagnosis of Nocardia transvalensis sensu stricto. The successful treatment was based on trimethoprim-sulfamethoxazole and other drugs. We conclude that molecular identification of Nocardia species is a valuable technique to guide good treatment and prognosis and recommend its use for daily bases diagnosis. PMID:27313917

Nocardia transvalensis Disseminated Infection in an Immunocompromised Patient with Idiopathic Thrombocytopenic Purpura.

PubMed

García-Méndez, Jorge; Carrillo-Casas, Erika M; Rangel-Cordero, Andrea; Leyva-Leyva, Margarita; Xicohtencatl-Cortes, Juan; Arenas, Roberto; Hernández-Castro, Rigoberto

2016-01-01

Nocardia transvalensis complex includes a wide range of microorganisms with specific antimicrobial resistance patterns. N. transvalensis is an unusual Nocardia species. However, it must be differentiated due to its natural resistance to aminoglycosides while other Nocardia species are susceptible. The present report describes a Nocardia species involved in an uncommon clinical case of a patient with idiopathic thrombocytopenic purpura and pulmonary nocardiosis. Microbiological and molecular techniques based on the sequencing of the 16S rRNA gene allowed diagnosis of Nocardia transvalensis sensu stricto. The successful treatment was based on trimethoprim-sulfamethoxazole and other drugs. We conclude that molecular identification of Nocardia species is a valuable technique to guide good treatment and prognosis and recommend its use for daily bases diagnosis.

Range-wide threats to a foundation tree species from disturbance interactions

Treesearch

Whalen W. Dillon; Ross K. Meentemeyer; John B. Vogler; Richard C. Cobb; Margaret R. Metz; David M. Rizzo

2013-01-01

The geographic range of tanoak, Notholithocarpus densiflorus (Hook. & Arn.) Manos, Cannon & S. H. Oh (Fagaceae), encompasses tremendous physiographic variability, diverse plant communities, and complex disturbance regimes (e.g., development, timber harvest, and wildfire) that now also include serious threats posed by the invasive forest...

Dietary breadth is positively correlated with venom complexity in cone snails.

PubMed

Phuong, Mark A; Mahardika, Gusti N; Alfaro, Michael E

2016-05-26

Although diet is believed to be a major factor underlying the evolution of venom, few comparative studies examine both venom composition and diet across a radiation of venomous species. Cone snails within the family, Conidae, comprise more than 700 species of carnivorous marine snails that capture their prey by using a cocktail of venomous neurotoxins (conotoxins or conopeptides). Venom composition across species has been previously hypothesized to be shaped by (a) prey taxonomic class (i.e., worms, molluscs, or fish) and (b) dietary breadth. We tested these hypotheses under a comparative phylogenetic framework using ecological data from past studies in conjunction with venom duct transcriptomes sequenced from 12 phylogenetically disparate cone snail species, including 10 vermivores (worm-eating), one molluscivore, and one generalist. We discovered 2223 unique conotoxin precursor peptides that encoded 1864 unique mature toxins across all species, >90 % of which are new to this study. In addition, we identified two novel gene superfamilies and 16 novel cysteine frameworks. Each species exhibited unique venom profiles, with venom composition and expression patterns among species dominated by a restricted set of gene superfamilies and mature toxins. In contrast with the dominant paradigm for interpreting Conidae venom evolution, prey taxonomic class did not predict venom composition patterns among species. We also found a significant positive relationship between dietary breadth and measures of conotoxin complexity. The poor performance of prey taxonomic class in predicting venom components suggests that cone snails have either evolved species-specific expression patterns likely as a consequence of the rapid evolution of conotoxin genes, or that traditional means of categorizing prey type (i.e., worms, mollusc, or fish) and conotoxins (i.e., by gene superfamily) do not accurately encapsulate evolutionary dynamics between diet and venom composition. We also show that species with more generalized diets tend to have more complex venoms and utilize a greater number of venom genes for prey capture. Whether this increased gene diversity confers an increased capacity for evolutionary change remains to be tested. Overall, our results corroborate the key role of diet in influencing patterns of venom evolution in cone snails and other venomous radiations.

The golden mimicry complex uses a wide spectrum of defence to deter a community of predators

PubMed Central

Pekár, Stano; Petráková, Lenka; Bulbert, Matthew W; Whiting, Martin J; Herberstein, Marie E

2017-01-01

Mimicry complexes typically consist of multiple species that deter predators using similar anti-predatory signals. Mimics in these complexes are assumed to vary in their level of defence from highly defended through to moderately defended, or not defended at all. Here, we report a new multi-order mimicry complex that includes at least 140 different putative mimics from four arthropod orders including ants, wasps, bugs, tree hoppers and spiders. All members of this mimicry complex are characterised by a conspicuous golden body and an ant Gestalt, but vary substantially in their defensive traits. However, they were similarly effective at deterring predators - even mildly defended mimics were rarely eaten by a community of invertebrate and vertebrate predators both in the wild and during staged trials. We propose that despite the predominance of less defended mimics the three predatory guilds avoid the mimics because of the additive influence of the various defensive traits. DOI: http://dx.doi.org/10.7554/eLife.22089.001 PMID:28170317

Peptaibol, secondary-metabolite, and hydrophobin pattern of commercial biocontrol agents formulated with species of the Trichoderma harzianum complex.

PubMed

Degenkolb, Thomas; Fog Nielsen, Kristian; Dieckmann, Ralf; Branco-Rocha, Fabiano; Chaverri, Priscila; Samuels, Gary J; Thrane, Ulf; von Döhren, Hans; Vilcinskas, Andreas; Brückner, Hans

2015-04-01

The production of bioactive polypeptides (peptaibiotics) in vivo is a sophisticated adaptation strategy of both mycoparasitic and saprotrophic Trichoderma species for colonizing and defending their natural habitats. This feature is of major practical importance, as the detection of peptaibiotics in plant-protective Trichoderma species, which are successfully used against economically relevant bacterial and fungal plant pathogens, certainly contributes to a better understanding of these complex antagonistic interactions. We analyzed five commercial biocontrol agents (BCAs), namely Canna(®) , Trichosan(®) , Vitalin(®) , Promot(®) WP, and TrichoMax(®) , formulated with recently described species of the Trichoderma harzianum complex, viz. T. afroharzianum, T. simmonsii, and T. guizhouense. By using the well-established, HPLC/MS-based peptaibiomics approach, it could unequivocally be demonstrated that all of these formulations contained new and recurrent peptaibols, i.e., peptaibiotics carrying an acetylated N-terminus, the C-terminus of which is reduced to a 1,2-amino alcohol. Their chain lengths, including the amino alcohol, were 11, 14, and 18 residues, respectively. Peptaibols were also to be the dominating secondary metabolites in plate cultures of the four strains obtained from four of the Trichoderma- based BCAs, contributing 95% of the UHPLC-UV/VIS peak areas and 99% of the total ion count MS peak area from solid media. Furthermore, species-specific hydrophobins, as well as non-peptaibiotic secondary metabolites, were detected, the latter being known for their antifungal, siderophore, or plant-growth-promoting activities. Notably, none of the isolates produced low-molecular weight mycotoxins. Copyright © 2015 Verlag Helvetica Chimica Acta AG, Zürich.

More of the same: a diminutive new species of the Limnonectes kuhlii complex from northern Vietnam (Anura: Dicroglossidae).

PubMed

Mcleod, David S; Kurlbaum, Scuyler; Hoang, Ngoc Van

2015-04-15

A new species in the dicroglossid genus Limnonectes known only from Ha Giang province, Vietnam is described. Analysis of DNA sequence data from the mitochondrial 12S and 16S gene regions places the species within the Limnonectes kuhlii Complex and demonstrates it to be the sister taxon to an Indochinese clade containing L. isanensis, L. jarujini, L. megastomias, and L. taylori. The new species occurs in syntopy with L. bannaensis. Both molecular and morphological data support the recognition of this lineage as a new species. Notably, the relatively diminutive size of this species distinguishes Limnonectes nguyenorum sp. nov. from all other members of the L. kuhlii Complex.

Two New Species of Liuixalus (Rhacophoridae, Anura): Evidence from Morphological and Molecular Analyses.

PubMed

Qin, Shaobo; Mo, Yunming; Jiang, Ke; Cai, Bo; Xie, Feng; Jiang, Jianping; Murphy, Robert W; Li, Jia-Tang; Wang, Yuezhao

2015-01-01

Due to small body sizes, superficial similarities in morphologies, and obscure activity behaviors, the phylogeny and taxonomy of species in the genus Liuixalus were very troublesome. Some species might comprise a complex of cryptic species. To investigate the species of group, we constructed the matrilineal genealogy of the genus using 16s rRNA mitochondrial DNA sequences. Analyses recovered six well supported matrilines that involved L. romeri, L. ocellatus, L. hainanus, L. calcarius, Liuixalus shiwandashan sp. nov. and Liuixalus jinxiuensis sp. nov., though the historical relationships among them remained unresolved. Currently, Liuixalus included 4 species, distributed eastwards from northern Vietnam to Hong Kong, China. Based on genealogical and morphological distinctiveness, we described Liuixalus jinxiuensis sp. nov. from the type locality Mt. Dayao, Jinxiu, China and Liuixalus shiwandashan sp. nov. from the type locality Mt. Shiwanda, China. A combination of morphological measurements, genetic, bioacoustic and osteological analysis was served to diagnose the new taxa.

The Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species

PubMed Central

Tollis, Marc; DeNardo, Dale F.; Cornelius, John A.; Dolby, Greer A.; Edwards, Taylor; Henen, Brian T.; Karl, Alice E.; Murphy, Robert W.

2017-01-01

Agassiz’s desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex. PMID:28562605

The Agassiz's desert tortoise genome provides a resource for the conservation of a threatened species.

PubMed

Tollis, Marc; DeNardo, Dale F; Cornelius, John A; Dolby, Greer A; Edwards, Taylor; Henen, Brian T; Karl, Alice E; Murphy, Robert W; Kusumi, Kenro

2017-01-01

Agassiz's desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.

Complexation of amyloid fibrils with charged conjugated polymers.

PubMed

Ghosh, Dhiman; Dutta, Paulami; Chakraborty, Chanchal; Singh, Pradeep K; Anoop, A; Jha, Narendra Nath; Jacob, Reeba S; Mondal, Mrityunjoy; Mankar, Shruti; Das, Subhadeep; Malik, Sudip; Maji, Samir K

2014-04-08

It has been suggested that conjugated charged polymers are amyloid imaging agents and promising therapeutic candidates for neurological disorders. However, very less is known about their efficacy in modulating the amyloid aggregation pathway. Here, we studied the modulation of Parkinson's disease associated α-synuclein (AS) amyloid assembly kinetics using conjugated polyfluorene polymers (PF, cationic; PFS, anionic). We also explored the complexation of these charged polymers with the various AS aggregated species including amyloid fibrils and oligomers using multidisciplinary biophysical techniques. Our data suggests that both polymers irrespective of their different charges in the side chains increase the fibrilization kinetics of AS and also remarkably change the morphology of the resultant amyloid fibrils. Both polymers were incorporated/aligned onto the AS amyloid fibrils as evident from electron microscopy (EM) and atomic force microscopy (AFM), and the resultant complexes were structurally distinct from their pristine form of both polymers and AS supported by FTIR study. Additionally, we observed that the mechanism of interactions between the polymers with different species of AS aggregates were markedly different.

Phylogeny of the Celastraceae inferred from 26S nuclear ribosomal DNA, phytochrome B, rbcL, atpB, and morphology.

PubMed

Simmons, M P; Savolainen, V; Clevinger, C C; Archer, R H; Davis, J I

2001-06-01

Phylogenetic relationships within Celastraceae (spindle-tree family) were inferred from nucleotide sequence characters from the 5' end of 26S nuclear ribosomal DNA (including expansion segments D1-D3; 84 species sampled), phytochrome B (58 species), rbcL (31 species), atpB (23 species), and morphology (94 species). Among taxa of questionable affinity, Forsellesia is a member of Crossosomataceae, and Goupia is excluded from Celastraceae. However, Brexia, Canotia, Lepuropetalon, Parnassia, Siphonodon, and Stackhousiaceae are supported as members of Celastraceae. Gymnosporia and Tricerma are distinct from Maytenus, Cassine is supported as distinct from Elaeodendron, and Dicarpellum is distinct from Salacia. Catha, Maytenus, and Pristimera are not resolved as natural genera. Hippocrateaceae (including Plagiopteron and Lophopetalum) are a clade nested within a paraphyletic Celastraceae. These data also suggest that the Loesener's classification of Celastraceae sensu stricto and Hallé's classification of Hippocrateaceae are artificial. The diversification of the fruit and aril within Celastraceae appears to be complex, with multiple origins of most fruit and aril forms. Copyright 2001 Academic Press.

Evaluation of a Simple in-House Test to Presumptively Differentiate Mycobacterium tuberculosis Complex from Nontuberculous Mycobacteria by Detection of p-Nitrobenzoic Acid Metabolites

PubMed Central

Wang, Guirong; Yu, Xia; Liang, Qian; Chen, Suting; Wilson, Stuart; Huang, Hairong

2013-01-01

The timely differentiation of Mycobacterium tuberculosis complex (MTC) and non-tubercular mycobacterium (NTM) species is urgently needed in patient care since the routine laboratory method is time consuming and cumbersome. An easy and cheap method which can successfully distinguish MTC from NTM was established and evaluated. 38 mycobacterial type and reference strains and 65 clinical isolates representing 10 species of mycobacterium were included in this study. Metabolites of p-nitrobenzoic acid (PNB) reduction were identified using liquid chromatography and tandem mass spectrometry (LC/MS/MS). A spectrophotometric method was developed to detect these metabolites, which was evaluated on a number of MTC and NTM species. All of the tested NTM species and strains reduced PNB to p-aminobenzoic acid (PABA), while none of the MTC strains showed a similar activity. Spectrophotometric detection of PABA had 100% sensitivity and specificity for MTC and NTM differentiation among the type strains and the clinical isolates tested. PABA was identified as one of the metabolites of PNB reduction. All the tested NTM species metabolized PNB to PABA whereas the MTC members lacked this activity. A simple, specific and cost-effective method based on PABA production was established in order to discriminate MTC from NTM from cultured organisms. PMID:24260497

Polymorphism of Paramecium pentaurelia (Ciliophora, Oligohymenophorea) strains revealed by rDNA and mtDNA sequences.

PubMed

Przyboś, Ewa; Tarcz, Sebastian; Greczek-Stachura, Magdalena; Surmacz, Marta

2011-05-01

Paramecium pentaurelia is one of 15 known sibling species of the Paramecium aurelia complex. It is recognized as a species showing no intra-specific differentiation on the basis of molecular fingerprint analyses, whereas the majority of other species are polymorphic. This study aimed at assessing genetic polymorphism within P. pentaurelia including new strains recently found in Poland (originating from two water bodies, different years, seasons, and clones of one strain) as well as strains collected from distant habitats (USA, Europe, Asia), and strains representing other species of the complex. We compared two DNA fragments: partial sequences (349 bp) of the LSU rDNA and partial sequences (618 bp) of cytochrome B gene. A correlation between the geographical origin of the strains and the genetic characteristics of their genotypes was not observed. Different genotypes were found in Kraków in two types of water bodies (Opatkowice-natural pond; Jordan's Park-artificial pond). Haplotype diversity within a single water body was not recorded. Likewise, seasonal haplotype differences between the strains within the artificial water body, as well as differences between clones originating from one strain, were not detected. The clustering of some strains belonging to different species was observed in the phylogenies. Copyright © 2010 Elsevier GmbH. All rights reserved.

Comparing two remote video survey methods for spatial predictions of the distribution and environmental niche suitability of demersal fishes.

PubMed

Galaiduk, Ronen; Radford, Ben T; Wilson, Shaun K; Harvey, Euan S

2017-12-15

Information on habitat associations from survey data, combined with spatial modelling, allow the development of more refined species distribution modelling which may identify areas of high conservation/fisheries value and consequentially improve conservation efforts. Generalised additive models were used to model the probability of occurrence of six focal species after surveys that utilised two remote underwater video sampling methods (i.e. baited and towed video). Models developed for the towed video method had consistently better predictive performance for all but one study species although only three models had a good to fair fit, and the rest were poor fits, highlighting the challenges associated with modelling habitat associations of marine species in highly homogenous, low relief environments. Models based on baited video dataset regularly included large-scale measures of structural complexity, suggesting fish attraction to a single focus point by bait. Conversely, models based on the towed video data often incorporated small-scale measures of habitat complexity and were more likely to reflect true species-habitat relationships. The cost associated with use of the towed video systems for surveying low-relief seascapes was also relatively low providing additional support for considering this method for marine spatial ecological modelling.

Volatile compounds in cryptic species of the Aneura pinguis complex and Aneura maxima (Marchantiophyta, Metzgeriidae).

PubMed

Wawrzyniak, Rafał; Wasiak, Wiesław; Bączkiewicz, Alina; Buczkowska, Katarzyna

2014-09-01

Aneura pinguis is one of the liverwort species complexes that consist of several cryptic species. Ten samples collected from different regions in Poland are in the focus of our research. Eight of the A. pinguis complex belonging to four cryptic species (A, B, C, E) and two samples of closely related species Aneura maxima were tested for the composition of volatile compounds. The HS-SPME technique coupled to GC/FID and GC/MS analysis has been applied. The fiber coated with DVB/CAR/PDMS has been used. The results of the present study, revealed the qualitative and quantitative differences in the composition of the volatile compounds between the studied species. Mainly they are from the group of sesquiterpenoids, oxygenated sesquiterpenoids and aliphatic hydrocarbons. The statistical methods (CA and PCA) showed that detected volatile compounds allow to distinguish cryptic species of A. pinguis. All examined cryptic species of the A. pinguis complex differ from A. maxima. Species A and E of A. pinguis, in CA and PCA, form separate clusters remote from two remaining cryptic species of A. pinguis (B and C) and A. maxima. Relationship between the cryptic species appeared from the chemical studies are in accordance with that revealed on the basis of DNA sequences. Copyright © 2014 Elsevier Ltd. All rights reserved.

Further insight into reproductive incompatibility between putative cryptic species of the Bemisia tabaci whitefly complex.

PubMed

Qin, Li; Pan, Li-Long; Liu, Shu-Sheng

2016-04-01

The whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), with its global distribution and extensive genetic diversity, is now known to be a complex of over 35 cryptic species. However, a satisfactory resolution of the systematics of this species complex is yet to be achieved. Here, we designed experiments to examine reproductive compatibility among species with different levels of mitochondrial cytochrome oxidase I (mtCOI) divergence. The data show that putative species with mtCOI divergence of >8% between them consistently exhibited complete reproductive isolation. However, two of the putative species, Asia II 9 and Asia II 3, with mtCOI divergence of 4.47% between them, exhibited near complete reproductive compatibility in one direction of their cross, and partial reproductive compatibility in the other direction. Together with some recent reports on this topic from the literature, our data indicates that, while divergence in the mtCOI sequences provides a valid molecular marker for species delimitation in most clades, more genetic markers and more sophisticated molecular phylogeny will be required to achieve adequate delimitation of all species in this whitefly complex. While many attempts have been made to examine the reproductive compatibility among genetic groups of the B. tabaci complex, our study represents the first effort to conduct crossing experiments with putative species that were chosen with considerations of their genetic divergence. In light of the new data, we discuss the best strategy and protocols to conduct further molecular phylogenetic analysis and crossing trials, in order to reveal the overall pattern of reproductive incompatibility among species of this whitefly complex. © 2015 Institute of Zoology, Chinese Academy of Sciences.

An updated checklist of mosquito species (Diptera: Culicidae) from Madagascar.

PubMed

Tantely, Michaël Luciano; Le Goff, Gilbert; Boyer, Sébastien; Fontenille, Didier

2016-01-01

An updated checklist of 235 mosquito species from Madagascar is presented. The number of species has increased considerably compared to previous checklists, particularly the last published in 2003 (178 species). This annotated checklist provides concise information on endemism, taxonomic position, developmental stages, larval habitats, distribution, behavior, and vector-borne diseases potentially transmitted. The 235 species belong to 14 genera: Aedeomyia (3 species), Aedes (35 species), Anopheles (26 species), Coquillettidia (3 species), Culex (at least 50 species), Eretmapodites (4 species), Ficalbia (2 species), Hodgesia (at least one species), Lutzia (one species), Mansonia (2 species), Mimomyia (22 species), Orthopodomyia (8 species), Toxorhynchites (6 species), and Uranotaenia (73 species). Due to non-deciphered species complexes, several species remain undescribed. The main remarkable characteristic of Malagasy mosquito fauna is the high biodiversity with 138 endemic species (59%). Presence and abundance of species, and their association, in a given location could be a bio-indicator of environmental particularities such as urban, rural, forested, deforested, and mountainous habitats. Finally, taking into account that Malagasy culicidian fauna includes 64 species (27%) with a known medical or veterinary interest in the world, knowledge of their biology and host preference summarized in this paper improves understanding of their involvement in pathogen transmission in Madagascar. © M.L. Tantely et al., published by EDP Sciences, 2016.

An updated checklist of mosquito species (Diptera: Culicidae) from Madagascar

PubMed Central

Tantely, Michaël Luciano; Le Goff, Gilbert; Boyer, Sébastien; Fontenille, Didier

2016-01-01

An updated checklist of 235 mosquito species from Madagascar is presented. The number of species has increased considerably compared to previous checklists, particularly the last published in 2003 (178 species). This annotated checklist provides concise information on endemism, taxonomic position, developmental stages, larval habitats, distribution, behavior, and vector-borne diseases potentially transmitted. The 235 species belong to 14 genera: Aedeomyia (3 species), Aedes (35 species), Anopheles (26 species), Coquillettidia (3 species), Culex (at least 50 species), Eretmapodites (4 species), Ficalbia (2 species), Hodgesia (at least one species), Lutzia (one species), Mansonia (2 species), Mimomyia (22 species), Orthopodomyia (8 species), Toxorhynchites (6 species), and Uranotaenia (73 species). Due to non-deciphered species complexes, several species remain undescribed. The main remarkable characteristic of Malagasy mosquito fauna is the high biodiversity with 138 endemic species (59%). Presence and abundance of species, and their association, in a given location could be a bio-indicator of environmental particularities such as urban, rural, forested, deforested, and mountainous habitats. Finally, taking into account that Malagasy culicidian fauna includes 64 species (27%) with a known medical or veterinary interest in the world, knowledge of their biology and host preference summarized in this paper improves understanding of their involvement in pathogen transmission in Madagascar. PMID:27101839

Cyanide and antimony thermodynamic database for the aqueous species and solids for the EPA-MINTEQ geochemical code

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

Sehmel, G.A.

1989-05-01

Thermodynamic data for aqueous species and solids that contain cyanide and antimony were tabulated from several commonly accepted, published sources of thermodynamic data and recent journal article. The review does not include gases or organic complexes of either antimony or cyanide, nor does the review include the sulfur compounds of cyanide. The basic thermodynamic data, ..delta..G/sub f,298//sup o/, ..delta..H/sub f,298//sup o/, and S/sub f//sup o/ values, were chosen to represent each solid phase and aqueous species for which data were available in the appropriate standard state. From these data the equilibrium constants (log K/sub r,298//sup o/) and enthalpies of reactionmore » (..delta..H/sub r,298//sup o/) at 298 K (25/degree/C) were calculated for reactions involving the formation of these aqueous species and solids from the basic components. 34 refs., 14 tabs.« less

The Species Problem and the Value of Teaching and the Complexities of Species

ERIC Educational Resources Information Center

Chung, Carl

2004-01-01

Discussions on species taxa directly refer to a range of complex biological phenomena. Given these phenomena, biologists have developed and continue to appeal to a series of species concepts and do not have a clear definition for it as each species concept tells us part of the story or helps the biologists to explain and understand a subset of…

Genomic Analysis of Phylotype I Strain EP1 Reveals Substantial Divergence from Other Strains in the Ralstonia solanacearum Species Complex

PubMed Central

Li, Peng; Wang, Dechen; Yan, Jinli; Zhou, Jianuan; Deng, Yinyue; Jiang, Zide; Cao, Bihao; He, Zifu; Zhang, Lianhui

2016-01-01

Ralstonia solanacearum species complex is a devastating group of phytopathogens with an unusually wide host range and broad geographical distribution. R. solanacearum isolates may differ considerably in various properties including host range and pathogenicity, but the underlying genetic bases remain vague. Here, we conducted the genome sequencing of strain EP1 isolated from Guangdong Province of China, which belongs to phylotype I and is highly virulent to a range of solanaceous crops. Its complete genome contains a 3.95-Mb chromosome and a 2.05-Mb mega-plasmid, which is considerably bigger than reported genomes of other R. solanacearum strains. Both the chromosome and the mega-plasmid have essential house-keeping genes and many virulence genes. Comparative analysis of strain EP1 with other 3 phylotype I and 3 phylotype II, III, IV strains unveiled substantial genome rearrangements, insertions and deletions. Genome sequences are relatively conserved among the 4 phylotype I strains, but more divergent among strains of different phylotypes. Moreover, the strains exhibited considerable variations in their key virulence genes, including those encoding secretion systems and type III effectors. Our results provide valuable information for further elucidation of the genetic basis of diversified virulences and host range of R. solanacearum species. PMID:27833603

The comparative osteology of the petrotympanic complex (ear region) of extant baleen whales (Cetacea: Mysticeti).

PubMed

Ekdale, Eric G; Berta, Annalisa; Deméré, Thomas A

2011-01-01

Anatomical comparisons of the ear region of baleen whales (Mysticeti) are provided through detailed osteological descriptions and high-resolution photographs of the petrotympanic complex (tympanic bulla and petrosal bone) of all extant species of mysticete cetaceans. Salient morphological features are illustrated and identified, including overall shape of the bulla, size of the conical process of the bulla, morphology of the promontorium, and the size and shape of the anterior process of the petrosal. We place our comparative osteological observations into a phylogenetic context in order to initiate an exploration into petrotympanic evolution within Mysticeti. The morphology of the petrotympanic complex is diagnostic for individual species of baleen whale (e.g., sigmoid and conical processes positioned at midline of bulla in Balaenoptera musculus; confluence of fenestra cochleae and perilymphatic foramen in Eschrichtius robustus), and several mysticete clades are united by derived characteristics. Balaenids and neobalaenids share derived features of the bulla, such as a rhomboid shape and a reduced anterior lobe (swelling) in ventral aspect, and eschrichtiids share derived morphologies of the petrosal with balaenopterids, including loss of a medial promontory groove and dorsomedial elongation of the promontorium. Monophyly of Balaenoidea (Balaenidae and Neobalaenidae) and Balaenopteroidea (Balaenopteridae and Eschrichtiidae) was recovered in phylogenetic analyses utilizing data exclusively from the petrotympanic complex. This study fills a major gap in our knowledge of the complex structures of the mysticete petrotympanic complex, which is an important anatomical region for the interpretation of the evolutionary history of mammals. In addition, we introduce a novel body of phylogenetically informative characters from the ear region of mysticetes. Our detailed anatomical descriptions, illustrations, and comparisons provide valuable data for current and future studies on the phylogenetic relationships, evolution, and auditory physiology of mysticetes and other cetaceans throughout Earth's history.

Fusarium Species from Nepalese Rice and Production of Mycotoxins and Gibberellic Acid by Selected Species

PubMed Central

Desjardins, A. E.; Manandhar, H. K.; Plattner, R. D.; Manandhar, G. G.; Poling, S. M.; Maragos, C. M.

2000-01-01

Infection of cereal grains with Fusarium species can cause contamination with mycotoxins that affect human and animal health. To determine the potential for mycotoxin contamination, we isolated Fusarium species from samples of rice seeds that were collected in 1997 on farms in the foothills of the Nepal Himalaya. The predominant Fusarium species in surface-disinfested seeds with husks were species of the Gibberella fujikuroi complex, including G. fujikuroi mating population A (anamorph, Fusarium verticillioides), G. fujikuroi mating population C (anamorph, Fusarium fujikuroi), and G. fujikuroi mating population D (anamorph, Fusarium proliferatum). The widespread occurrence of mating population D suggests that its role in the complex symptoms of bakanae disease of rice may be significant. Other common species were Gibberella zeae (anamorph, Fusarium graminearum) and Fusarium semitectum, with Fusarium acuminatum, Fusarium anguioides, Fusarium avenaceum, Fusarium chlamydosporum, Fusarium equiseti, and Fusarium oxysporum occasionally present. Strains of mating population C produced beauvericin, moniliformin, and gibberellic acid, but little or no fumonisin, whereas strains of mating population D produced beauvericin, fumonisin, and, usually, moniliformin, but no gibberellic acid. Some strains of G. zeae produced the 8-ketotrichothecene nivalenol, whereas others produced deoxynivalenol. Despite the occurrence of fumonisin-producing strains of mating population D, and of 8-ketotrichothecene-producing strains of G. zeae, Nepalese rice showed no detectable contamination with these mycotoxins. Effective traditional practices for grain drying and storage may prevent contamination of Nepalese rice with Fusarium mycotoxins. PMID:10698766

Barcoding Neotropical birds: assessing the impact of nonmonophyly in a highly diverse group.

PubMed

Chaves, Bárbara R N; Chaves, Anderson V; Nascimento, Augusto C A; Chevitarese, Juliana; Vasconcelos, Marcelo F; Santos, Fabrício R

2015-07-01

In this study, we verified the power of DNA barcodes to discriminate Neotropical birds using Bayesian tree reconstructions of a total of 7404 COI sequences from 1521 species, including 55 Brazilian species with no previous barcode data. We found that 10.4% of species were nonmonophyletic, most likely due to inaccurate taxonomy, incomplete lineage sorting or hybridization. At least 0.5% of the sequences (2.5% of the sampled species) retrieved from GenBank were associated with database errors (poor-quality sequences, NuMTs, misidentification or unnoticed hybridization). Paraphyletic species (5.8% of the total) can be related to rapid speciation events leading to nonreciprocal monophyly between recently diverged sister species, or to absence of synapomorphies in the small COI region analysed. We also performed two series of genetic distance calculations under the K2P model for intraspecific and interspecific comparisons: the first included all COI sequences, and the second included only monophyletic taxa observed in the Bayesian trees. As expected, the mean and median pairwise distances were smaller for intraspecific than for interspecific comparisons. However, there was no precise 'barcode gap', which was shown to be larger in the monophyletic taxon data set than for the data from all species, as expected. Our results indicated that although database errors may explain some of the difficulties in the species discrimination of Neotropical birds, distance-based barcode assignment may also be compromised because of the high diversity of bird species and more complex speciation events in the Neotropics. © 2014 John Wiley & Sons Ltd.

Quantifying Florida Bay habitat suitability for fishes and invertebrates under climate change scenarios.

PubMed

Kearney, Kelly A; Butler, Mark; Glazer, Robert; Kelble, Christopher R; Serafy, Joseph E; Stabenau, Erik

2015-04-01

The Florida Bay ecosystem supports a number of economically important ecosystem services, including several recreational fisheries, which may be affected by changing salinity and temperature due to climate change. In this paper, we use a combination of physical models and habitat suitability index models to quantify the effects of potential climate change scenarios on a variety of juvenile fish and lobster species in Florida Bay. The climate scenarios include alterations in sea level, evaporation and precipitation rates, coastal runoff, and water temperature. We find that the changes in habitat suitability vary in both magnitude and direction across the scenarios and species, but are on average small. Only one of the seven species we investigate (Lagodon rhomboides, i.e., pinfish) sees a sizable decrease in optimal habitat under any of the scenarios. This suggests that the estuarine fauna of Florida Bay may not be as vulnerable to climate change as other components of the ecosystem, such as those in the marine/terrestrial ecotone. However, these models are relatively simplistic, looking only at single species effects of physical drivers without considering the many interspecific interactions that may play a key role in the adjustment of the ecosystem as a whole. More complex models that capture the mechanistic links between physics and biology, as well as the complex dynamics of the estuarine food web, may be necessary to further understand the potential effects of climate change on the Florida Bay ecosystem.

Why is metal bioaccumulation so variable? Biodynamics as a unifying concept

USGS Publications Warehouse

Luoma, Samuel N.; Rainbow, Philip S.

2005-01-01

Ecological risks from metal contaminants are difficult to document because responses differ among species, threats differ among metals, and environmental influences are complex. Unifying concepts are needed to better tie together such complexities. Here we suggest that a biologically based conceptualization, the biodynamic model, provides the necessary unification for a key aspect in risk:  metal bioaccumulation (internal exposure). The model is mechanistically based, but empirically considers geochemical influences, biological differences, and differences among metals. Forecasts from the model agree closely with observations from nature, validating its basic assumptions. The biodynamic metal bioaccumulation model combines targeted, high-quality geochemical analyses from a site of interest with parametrization of key physiological constants for a species from that site. The physiological parameters include metal influx rates from water, influx rates from food, rate constants of loss, and growth rates (when high). We compiled results from 15 publications that forecast species-specific bioaccumulation, and compare the forecasts to bioaccumulation data from the field. These data consider concentrations that cover 7 orders of magnitude. They include 7 metals and 14 species of animals from 3 phyla and 11 marine, estuarine, and freshwater environments. The coefficient of determination (R2) between forecasts and independently observed bioaccumulation from the field was 0.98. Most forecasts agreed with observations within 2-fold. The agreement suggests that the basic assumptions of the biodynamic model are tenable. A unified explanation of metal bioaccumulation sets the stage for a realistic understanding of toxicity and ecological effects of metals in nature.

Quantifying Florida Bay Habitat Suitability for Fishes and Invertebrates Under Climate Change Scenarios

NASA Astrophysics Data System (ADS)

Kearney, Kelly A.; Butler, Mark; Glazer, Robert; Kelble, Christopher R.; Serafy, Joseph E.; Stabenau, Erik

2015-04-01

The Florida Bay ecosystem supports a number of economically important ecosystem services, including several recreational fisheries, which may be affected by changing salinity and temperature due to climate change. In this paper, we use a combination of physical models and habitat suitability index models to quantify the effects of potential climate change scenarios on a variety of juvenile fish and lobster species in Florida Bay. The climate scenarios include alterations in sea level, evaporation and precipitation rates, coastal runoff, and water temperature. We find that the changes in habitat suitability vary in both magnitude and direction across the scenarios and species, but are on average small. Only one of the seven species we investigate ( Lagodon rhomboides, i.e., pinfish) sees a sizable decrease in optimal habitat under any of the scenarios. This suggests that the estuarine fauna of Florida Bay may not be as vulnerable to climate change as other components of the ecosystem, such as those in the marine/terrestrial ecotone. However, these models are relatively simplistic, looking only at single species effects of physical drivers without considering the many interspecific interactions that may play a key role in the adjustment of the ecosystem as a whole. More complex models that capture the mechanistic links between physics and biology, as well as the complex dynamics of the estuarine food web, may be necessary to further understand the potential effects of climate change on the Florida Bay ecosystem.

Armored scale insect endosymbiont diversity at the species level: genealogical patterns of Uzinura diasipipdicola in the Chionaspis pinifoliae-Chionaspis heterophyllae species complex (Hemiptera: Coccoidea: Diaspididae).

PubMed

Andersen, J C; Gwiazdowski, R A; Gdanetz, K; Gruwell, M E

2015-02-01

Armored scale insects and their primary bacterial endosymbionts show nearly identical patterns of co-diversification when viewed at the family level, though the persistence of these patterns at the species level has not been explored in this group. Therefore we investigated genealogical patterns of co-diversification near the species level between the primary endosymbiont Uzinura diaspidicola and its hosts in the Chionaspis pinifoliae-Chionaspis heterophyllae species complex. To do this we generated DNA sequence data from three endosymbiont loci (rspB, GroEL, and 16S) and analyzed each locus independently using statistical parsimony network analyses and as a concatenated dataset using Bayesian phylogenetic reconstructions. We found that for two endosymbiont loci, 16S and GroEL, sequences from U. diaspidicola were broadly associated with host species designations, while for rspB this pattern was less clear as C. heterophyllae (species S1) shared haplotypes with several other Chionaspis species. We then compared the topological congruence of the phylogenetic reconstructions generated from a concatenated dataset of endosymbiont loci (including all three loci, above) to that from a concatenated dataset of armored scale hosts, using published data from two nuclear loci (28S and EF1α) and one mitochondrial locus (COI-COII) from the armored scale hosts. We calculated whether the two topologies were congruent using the Shimodaira-Hasegawa test. We found no significant differences (P = 0.4892) between the topologies suggesting that, at least at this level of resolution, co-diversification of U. diaspidicola with its armored scale hosts also occurs near the species level. This is the first such study of co-speciation at the species level between U. diaspidicola and a group of armored scale insects.

Seven new species of Paleanotus (Annelida: Chrysopetalidae) described from Lizard Island, Great Barrier Reef, and coral reefs of northern Australia and the Indo-Pacific: two cryptic species pairs revealed between western Pacific Ocean and the eastern Indian Ocean.

PubMed

Watson, Charlotte

2015-09-18

Morphological investigation into the paleate genus Paleanotus Schmarda 1861 of the family Chrysopetalidae from northern Australian coral reefs, primarily Lizard Island and outlying reefs, included a complex of very small, slender individuals (length < 5 mm). This complex resolved into 7 new species, described herein: Paleanotus inornatus n. sp., P. adornatus n. sp., P. chrysos n. sp., P. aquifolia n. sp., P. latifolia n. sp., P. silus n. sp., and P. silopsis n. sp. A key is provided to the new species and Paleanotus distinguished from Treptopale and Hyalopale, two closely related genera. Diagnostic features of the apical structure and shape of the notochaetal main paleae plus median paleae shape and raised rib pattern, differentiates each species from the other. Gametous states are described. Two cryptic species pairs (Paleanotus silopsis n. sp. and P. silus n. sp.; Paleanotus aquifolia n. sp. and P. latifolia n. sp.) were identified. In each case one species is restricted to either the NE or NW Australian coast. In each pair the most eastern point for the NW Australian species range occurs at Darwin, western Arnhemland, Northern Territory. Additional material for each species pair extends their respective ranges northwards: NW Australia to Thailand, Andaman Sea, eastern Indian Ocean or NE Australia, Great Barrier Reef to the Philippines, western Pacific Ocean. Cryptic morphology and potential genetic diversity is discussed in Paleanotus inornatus n. sp. and P. adornatus n. sp. that possess overlapping widespread distribution patterns across northern Australia and Indo-Pacific reefs. The smallest bodied taxon, Paleanotus chrysos n. sp. is the only species with a Coral Sea range encompassing Lizard Island, Heron Island and New Caledonia.

Scorpions from Mexico: From Species Diversity to Venom Complexity.

PubMed

Santibáñez-López, Carlos E; Francke, Oscar F; Ureta, Carolina; Possani, Lourival D

2015-12-24

Scorpions are among the oldest terrestrial arthropods, which are distributed worldwide, except for Antarctica and some Pacific islands. Scorpion envenomation represents a public health problem in several parts of the world. Mexico harbors the highest diversity of scorpions in the world, including some of the world's medically important scorpion species. The systematics and diversity of Mexican scorpion fauna has not been revised in the past decade; and due to recent and exhaustive collection efforts as part of different ongoing major revisionary systematic projects, our understanding of this diversity has changed compared with previous assessments. Given the presence of several medically important scorpion species, the study of their venom in the country is also important. In the present contribution, the diversity of scorpion species in Mexico is revised and updated based on several new systematic contributions; 281 different species are recorded. Commentaries on recent venomic, ecological and behavioral studies of Mexican scorpions are also provided. A list containing the most important peptides identified from 16 different species is included. A graphical representation of the different types of components found in these venoms is also revised. A map with hotspots showing the current knowledge on scorpion distribution and areas explored in Mexico is also provided.

Scorpions from Mexico: From Species Diversity to Venom Complexity

PubMed Central

Santibáñez-López, Carlos E.; Francke, Oscar F.; Ureta, Carolina; Possani, Lourival D.

2015-01-01

Scorpions are among the oldest terrestrial arthropods, which are distributed worldwide, except for Antarctica and some Pacific islands. Scorpion envenomation represents a public health problem in several parts of the world. Mexico harbors the highest diversity of scorpions in the world, including some of the world’s medically important scorpion species. The systematics and diversity of Mexican scorpion fauna has not been revised in the past decade; and due to recent and exhaustive collection efforts as part of different ongoing major revisionary systematic projects, our understanding of this diversity has changed compared with previous assessments. Given the presence of several medically important scorpion species, the study of their venom in the country is also important. In the present contribution, the diversity of scorpion species in Mexico is revised and updated based on several new systematic contributions; 281 different species are recorded. Commentaries on recent venomic, ecological and behavioral studies of Mexican scorpions are also provided. A list containing the most important peptides identified from 16 different species is included. A graphical representation of the different types of components found in these venoms is also revised. A map with hotspots showing the current knowledge on scorpion distribution and areas explored in Mexico is also provided. PMID:26712787

The Campanian-Maastrichtian foraminiferal biostratigraphy of the basement sediments from the southern Pannonian Basin (Vojvodina, northern Serbia): implications for the continuation of the Eastern Vardar and Sava zones

NASA Astrophysics Data System (ADS)

Dunčić, Milena; Dulić, Ivan; Popov, Olivera; Bogićević, Goran; Vranjković, Alan

2017-04-01

Micropalaeontological and biostratigraphical studies included Campanian-Maastrichtian complexes from five oil exploration wells drilled in northern Serbia (Vojvodina): the first is a carbonate-clastic complex and second is a complex containing ophiolites intercalated with hemipelagic and pelagic sediments. Within the studied complexes, rich associations of planktonic and benthic foraminifera, calcareous nannoplankton, palynomorphs, as well as shallow and deep-water fossil detritus were determined. The presence of relatively rich associations of planktonic foraminifera allowed recognition of two biozones: the Globotruncana ventricosa Zone, observed in the sediments of the carbonate-clastic complex and the Gansserina gansseri Zone, observed in both complexes. Except biozones, based on documented index species, for some units in both complexes, larger benthic foraminifera species had special biostratigraphical value, and in some of them, the calcareous nannoplankton zones were recognized. The studied complexes represent deep-water formations, generated in oceanic island arc and trough zones. The presence of limestones, which originate from destroyed rudist reefs, is explained by transfer by means of gravitational transport mechanisms of shallow-water sediments to deep-water depositional environments. In this paper, the results of more detailed biostratigraphical and palaeo-ecological studies of foraminifera associations in Campanian-Maastrichtian complexes in Vojvodina are presented. Combined with lithological studies, seven units were determined within the complexes. The obtained results are important as a part of multidisciplinary, regional exploration of both complexes, generated in specific geological conditions, that today constitute a part of the pre-Neogene basement complex in the southeastern part of the Pannonian Basin. The Campanian- Maastrichtian carbonate-clastic complex represents sedimentary cover of the Eastern Vardar Ophiolitic Unit, while the ophiolites intercalated with hemipelagic and pelagic limestones belongs to the Sava Zone.

Absence of Complex I Implicates Rearrangement of the Respiratory Chain in European Mistletoe.

PubMed

Senkler, Jennifer; Rugen, Nils; Eubel, Holger; Hegermann, Jan; Braun, Hans-Peter

2018-05-21

The mitochondrial oxidative phosphorylation (OXPHOS) system, which is based on the presence of five protein complexes, is in the very center of cellular ATP production. Complexes I to IV are components of the respiratory electron transport chain that drives proton translocation across the inner mitochondrial membrane. The resulting proton gradient is used by complex V (the ATP synthase complex) for the phosphorylation of ADP. Occurrence of complexes I to V is highly conserved in eukaryotes, with exceptions being restricted to unicellular parasites that take up energy-rich compounds from their hosts. Here we present biochemical evidence that the European mistletoe (Viscum album), an obligate semi-parasite living on branches of trees, has a highly unusual OXPHOS system. V. album mitochondria completely lack complex I and have greatly reduced amounts of complexes II and V. At the same time, the complexes III and IV form remarkably stable respiratory supercomplexes. Furthermore, complexome profiling revealed the presence of 150 kDa complexes that include type II NAD(P)H dehydrogenases and an alternative oxidase. Although the absence of complex I genes in mitochondrial genomes of mistletoe species has recently been reported, this is the first biochemical proof that these genes have not been transferred to the nuclear genome and that this respiratory complex indeed is not assembled. As a consequence, the whole respiratory chain is remodeled. Our results demonstrate that, in the context of parasitism, multicellular life can cope with lack of one of the OXPHOS complexes and give new insights into the life strategy of mistletoe species. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Complex of Scolytinae Inhabiting Persea borbonia and Persea americana in Florida: Possible Interactions with Other Species

USDA-ARS?s Scientific Manuscript database

A diverse number of Scolytinae (Coleoptera: Curculionidae) have been found inhabiting Persea borbonia and P. americana in Florida during 2009 and 2010. They include the exotic redbay ambrosia beetle, Xyleborus glabratus, vector of Raffaelea lauricola, X. volvulus, X. ferrugineus, Xylosandrus crassiu...

Fumonisins, Tortillas and Neural Tube Defects: Untangling a Complex Issue

USDA-ARS?s Scientific Manuscript database

Fumonisin mycotoxins are found in corn and corn-based foods. Fumonisin B1 (FB1), the most common, disrupts sphingolipid metabolism thereby causing species-specific diseases in animals that include cancer in rodents and (birth) neural tube defects (NTD) in LM/Bc mice. Fumonisins’ affect on human heal...

Characterization of Fusarium strains recovered from wheat with symptoms of head blight in Kentucky

USDA-ARS?s Scientific Manuscript database

Fusarium graminearum species complex (FGSC) members cause Fusarium head blight (FHB) of wheat (Triticum aestivum L.) and small grains in the United States. The U.S. population is diverse, and includes several genetically distinct local emergent subpopulations, some more aggressive and toxigenic than...

Chapter 5 - Development of biophysical gradient layers for the LANDFIRE Prototype Project

Treesearch

Lisa Holsinger; Robert E. Keane; Russell Parsons; Eva Karau

2006-01-01

Distributions of plant species are generally continuous, gradually changing across landscapes and blending into each other due to the influence of, and interactions between, a complex array of biophysical gradients (Whittaker 1967; 1975). Key biophysical gradients for understanding vegetation distributions include moisture, temperature, evaporative demand, nutrient...

Nigeria Anopheles Vector Database: An Overview of 100 Years' Research

PubMed Central

Okorie, Patricia Nkem; McKenzie, F. Ellis; Ademowo, Olusegun George; Bockarie, Moses; Kelly-Hope, Louise

2011-01-01

Anopheles mosquitoes are important vectors of malaria and lymphatic filariasis (LF), which are major public health diseases in Nigeria. Malaria is caused by infection with a protozoan parasite of the genus Plasmodium and LF by the parasitic worm Wuchereria bancrofti. Updating our knowledge of the Anopheles species is vital in planning and implementing evidence based vector control programs. To present a comprehensive report on the spatial distribution and composition of these vectors, all published data available were collated into a database. Details recorded for each source were the locality, latitude/longitude, time/period of study, species, abundance, sampling/collection methods, morphological and molecular species identification methods, insecticide resistance status, including evidence of the kdr allele, and P. falciparum sporozoite rate and W. bancrofti microfilaria prevalence. This collation resulted in a total of 110 publications, encompassing 484,747 Anopheles mosquitoes in 632 spatially unique descriptions at 142 georeferenced locations being identified across Nigeria from 1900 to 2010. Overall, the highest number of vector species reported included An. gambiae complex (65.2%), An. funestus complex (17.3%), An. gambiae s.s. (6.5%). An. arabiensis (5.0%) and An. funestus s.s. (2.5%), with the molecular forms An. gambiae M and S identified at 120 locations. A variety of sampling/collection and species identification methods were used with an increase in molecular techniques in recent decades. Insecticide resistance to pyrethroids and organochlorines was found in the main Anopheles species across 45 locations. Presence of P. falciparum and W. bancrofti varied between species with the highest sporozoite rates found in An. gambiae s.s, An. funestus s.s. and An. moucheti, and the highest microfilaria prevalence in An. gambiae s.l., An. arabiensis, and An. gambiae s.s. This comprehensive geo-referenced database provides an essential baseline on Anopheles vectors and will be an important resource for malaria and LF vector control programmes in Nigeria. PMID:22162764

An Asiatic Chironomid in Brazil: morphology, DNA barcode and bionomics

PubMed Central

Amora, Gizelle; Hamada, Neusa; Fusari, Lívia Maria; Andrade-Souza, Vanderly

2015-01-01

Abstract In most freshwater ecosystems, aquatic insects are dominant in terms of diversity; however, there is a disproportionately low number of records of alien species when compared to other freshwater organisms. The Chironomidae is one aquatic insect family that includes some examples of alien species around the world. During a study on aquatic insects in Amazonas state (Brazil), we collected specimens of Chironomidae that are similar, at the morphological level, to Chironomus kiiensis Tokunaga and Chironomus striatipennis Kieffer, both with distributions restricted to Asia. The objectives of this study were to provide morphological information on this Chironomus population, to investigate its identity using DNA barcoding and, to provide bionomic information about this species. Chironomus DNA barcode data were obtained from GenBank and Barcode of Life Data Systems (BOLD) and, together with our data, were analyzed using the neighbor-joining method with 1000 bootstrap replicates and the genetic distances were estimated using the Kimura-2-parameter. At the morphological level, the Brazilian population cannot be distinguished either from Chironomus striatipennis or Chironomus kiiensis, configuring a species complex but, at the molecular level our studied population is placed in a clade together with Chironomus striatipennis, from South Korea. Bionomic characteristics of the Brazilian Chironomus population differ from the ones of Chironomus kiiensis from Japan, the only species in this species complex with bionomic information available. The Brazilian Chironomus population has a smaller size, the double of the number of eggs and inhabits oligotrophic water, in artificial container. In the molecular analysis, populations of Chironomus striatipennis and Chironomus kiiensis are placed in a clade, formed by two groups: Group A (which includes populations from both named species, from different Asiatic regions and our Brazilian population) and Group B (with populations of Chironomus kiiensis from Japan and South Korea). Genetic distance between the Brazilian population and specimens in Group A suggests that it was recently introduced in Brazil, and that its country of origin is probably South Korea. PMID:26261436

Delimiting Species Boundaries within a Paraphyletic Species Complex: Insights from Morphological, Genetic, and Molecular Data on Paramecium sonneborni (Paramecium aurelia species complex, Ciliophora, Protozoa).

PubMed

Przyboś, Ewa; Tarcz, Sebastian; Rautian, Maria; Sawka, Natalia

2015-09-01

The demarcation of boundaries between protist species is often problematic because of the absence of a uniform species definition, the abundance of cryptic diversity, and the occurrence of convergent morphology. The ciliates belonging to the Paramecium aurelia complex, consisting of 15 species, are a good model for such systematic and evolutionary studies. One member of the complex is P. sonneborni, previously known only from one stand in Texas (USA), but recently found in two new sampling sites in Cyprus (creeks running to Salt Lake and Oroklini Lake near Larnaca). The studied Paramecium sonneborni strains (from the USA and Cyprus) reveal low viability in the F1 and F2 generations of interstrain hybrids and may be an example of ongoing allopatric speciation. Despite its molecular distinctiveness, we postulate that P. sonneborni should remain in the P. aurelia complex, making it a paraphyletic taxon. Morphological studies have revealed that some features of the nuclear apparatus of P. sonneborni correspond to the P. aurelia spp. complex, while others are similar to P. jenningsi and P. schewiakoffi. The observed discordance indicates rapid splitting of the P. aurelia-P. jenningsi-P. schewiakoffi group, in which genetic, morphological, and molecular boundaries between species are not congruent. Copyright © 2015 Elsevier GmbH. All rights reserved.

Positive Selection in Rapidly Evolving Plastid–Nuclear Enzyme Complexes

PubMed Central

Rockenbach, Kate; Havird, Justin C.; Monroe, J. Grey; Triant, Deborah A.; Taylor, Douglas R.; Sloan, Daniel B.

2016-01-01

Rates of sequence evolution in plastid genomes are generally low, but numerous angiosperm lineages exhibit accelerated evolutionary rates in similar subsets of plastid genes. These genes include clpP1 and accD, which encode components of the caseinolytic protease (CLP) and acetyl-coA carboxylase (ACCase) complexes, respectively. Whether these extreme and repeated accelerations in rates of plastid genome evolution result from adaptive change in proteins (i.e., positive selection) or simply a loss of functional constraint (i.e., relaxed purifying selection) is a source of ongoing controversy. To address this, we have taken advantage of the multiple independent accelerations that have occurred within the genus Silene (Caryophyllaceae) by examining phylogenetic and population genetic variation in the nuclear genes that encode subunits of the CLP and ACCase complexes. We found that, in species with accelerated plastid genome evolution, the nuclear-encoded subunits in the CLP and ACCase complexes are also evolving rapidly, especially those involved in direct physical interactions with plastid-encoded proteins. A massive excess of nonsynonymous substitutions between species relative to levels of intraspecific polymorphism indicated a history of strong positive selection (particularly in CLP genes). Interestingly, however, some species are likely undergoing loss of the native (heteromeric) plastid ACCase and putative functional replacement by a duplicated cytosolic (homomeric) ACCase. Overall, the patterns of molecular evolution in these plastid–nuclear complexes are unusual for anciently conserved enzymes. They instead resemble cases of antagonistic coevolution between pathogens and host immune genes. We discuss a possible role of plastid–nuclear conflict as a novel cause of accelerated evolution. PMID:27707788

Genome size evolution at the speciation level: the cryptic species complex Brachionus plicatilis (Rotifera).

PubMed

Stelzer, Claus-Peter; Riss, Simone; Stadler, Peter

2011-04-07

Studies on genome size variation in animals are rarely done at lower taxonomic levels, e.g., slightly above/below the species level. Yet, such variation might provide important clues on the tempo and mode of genome size evolution. In this study we used the flow-cytometry method to study the evolution of genome size in the rotifer Brachionus plicatilis, a cryptic species complex consisting of at least 14 closely related species. We found an unexpectedly high variation in this species complex, with genome sizes ranging approximately seven-fold (haploid '1C' genome sizes: 0.056-0.416 pg). Most of this variation (67%) could be ascribed to the major clades of the species complex, i.e. clades that are well separated according to most species definitions. However, we also found substantial variation (32%) at lower taxonomic levels--within and among genealogical species--and, interestingly, among species pairs that are not completely reproductively isolated. In one genealogical species, called B. 'Austria', we found greatly enlarged genome sizes that could roughly be approximated as multiples of the genomes of its closest relatives, which suggests that whole-genome duplications have occurred early during separation of this lineage. Overall, genome size was significantly correlated to egg size and body size, even though the latter became non-significant after controlling for phylogenetic non-independence. Our study suggests that substantial genome size variation can build up early during speciation, potentially even among isolated populations. An alternative, but not mutually exclusive interpretation might be that reproductive isolation tends to build up unusually slow in this species complex.

Genome size evolution at the speciation level: The cryptic species complex Brachionus plicatilis (Rotifera)

PubMed Central

2011-01-01

Background Studies on genome size variation in animals are rarely done at lower taxonomic levels, e.g., slightly above/below the species level. Yet, such variation might provide important clues on the tempo and mode of genome size evolution. In this study we used the flow-cytometry method to study the evolution of genome size in the rotifer Brachionus plicatilis, a cryptic species complex consisting of at least 14 closely related species. Results We found an unexpectedly high variation in this species complex, with genome sizes ranging approximately seven-fold (haploid '1C' genome sizes: 0.056-0.416 pg). Most of this variation (67%) could be ascribed to the major clades of the species complex, i.e. clades that are well separated according to most species definitions. However, we also found substantial variation (32%) at lower taxonomic levels - within and among genealogical species - and, interestingly, among species pairs that are not completely reproductively isolated. In one genealogical species, called B. 'Austria', we found greatly enlarged genome sizes that could roughly be approximated as multiples of the genomes of its closest relatives, which suggests that whole-genome duplications have occurred early during separation of this lineage. Overall, genome size was significantly correlated to egg size and body size, even though the latter became non-significant after controlling for phylogenetic non-independence. Conclusions Our study suggests that substantial genome size variation can build up early during speciation, potentially even among isolated populations. An alternative, but not mutually exclusive interpretation might be that reproductive isolation tends to build up unusually slow in this species complex. PMID:21473744

Introduction to the symposium Global Perspective on the Culex pipiens Complex in the 21st century: The Interrelationship of Culex pipiens, quinquefasciatus, molestus and others.

PubMed

Linthicum, Kenneth J

2012-12-01

Mosquitoes in the Culex pipiens Complex, including Culex pipiens, Cx. quinquefasciatus, and Cx. molestus, are important pest species and vectors of human and animal diseases throughout the world's tropical, temperate, and Holarctic regions. Diseases transmitted by member of the Pipiens Complex include: St. Louis encephalitis and West Nile virus in North America, West Nile virus on several other continents, Rift Valley fever in Africa, lymphatic filariasis caused by Wuchereria bancrofti in the tropics, and Dirofilaria immitis globally. Here and in the following 14 papers, 3 abstracts and a summary paper are the proceedings of a symposium that gathered many of the world's experts on the Pipiens Complex to explore the current state of knowledge of the taxa. Information presented at the symposium will improve our knowledge of important members of the complex and enhance our ability to conduct efficient surveillance and efficacious control strategies. A background on previous discussions on the Pipiens Complex, and a brief description of current symposium contributors and their topics are discussed.

Reclassification of the Candida haemulonii complex as Candida haemulonii (C. haemulonii group I), C. duobushaemulonii sp. nov. (C. haemulonii group II), and C. haemulonii var. vulnera var. nov.: three multiresistant human pathogenic yeasts.

PubMed

Cendejas-Bueno, E; Kolecka, A; Alastruey-Izquierdo, A; Theelen, B; Groenewald, M; Kostrzewa, M; Cuenca-Estrella, M; Gómez-López, A; Boekhout, T

2012-11-01

The Candida haemulonii species complex is currently known as C. haemulonii groups I and II. Here we describe C. haemulonii group II as a new species, Candida duobushaemulonii sp. nov., and C. haemulonii var. vulnera as new a variety of C. haemulonii group I using phenotypic and molecular methods. These taxa and other relatives of C. haemulonii (i.e., Candida auris and Candida pseudohaemulonii) cannot be differentiated by the commercial methods now used for yeast identification. Four isolates (C. haemulonii var. vulnera) differed from the other isolates of C. haemulonii in the sequence of the internal transcribed spacer (ITS) regions of the nuclear rRNA gene operon. The new species and the new variety have a multiresistant antifungal profile, which includes high MICs of amphotericin B (geometric mean MIC, 1.18 mg/liter for C. haemulonii var. vulnera and 2 mg/liter for C. duobushaemulonii sp. nov) and cross-resistance to azole compounds. Identification of these species should be based on molecular methods, such as sequence analysis of ITS regions and matrix-assisted laser desorption ionization-time of flight mass spectrometry.

Structure and biodiversity of coralligenous assemblages dominated by the precious red coral Corallium rubrum over broad spatial scales

PubMed Central

Casas-Güell, Edgar; Cebrian, Emma; Garrabou, Joaquim; Ledoux, Jean-Baptiste; Linares, Cristina; Teixidó, Núria

2016-01-01

Data on species diversity and structure in coralligenous outcrops dominated by Corallium rubrum are lacking. A hierarchical sampling including 3 localities and 9 sites covering more than 400 km of rocky coasts in NW Mediterranean, was designed to characterize the spatial variability of structure, composition and diversity of perennial species inhabiting coralligenous outcrops. We estimated species/taxa composition and abundance. Eight morpho-functional groups were defined according to their life span and growth to characterize the structural complexity of the outcrops. The species composition and structural complexity differed consistently across all spatial scales considered. The lowest and the highest variability were found among localities (separated by >200 km) and within sites (separated by 1–5 km), respectively supporting differences in diversity indices. The morpho-functional groups displayed a consistent spatial arrangement in terms of the number, size and shape of patches across study sites. These results contribute to filling the gap on the understanding of assemblage composition and structure and to build baselines to assess the response of this of this highly threatened habitat to anthropogenic disturbances. PMID:27857209

The Biofilm Community-Rebels with a Cause.

PubMed

Aruni, A Wilson; Dou, Yuetan; Mishra, Arunima; Fletcher, Hansel M

2015-03-01

Oral Biofilms are one of the most complex and diverse ecosystem developed by successive colonization of more than 600 bacterial taxa. Development starts with the attachment of early colonizers such as Actinomyces species and oral streptococci on the acquired pellicle and tooth enamel. These bacteria not only adhere to tooth surface but also interact with each other and lay foundation for attachment of bridging colonizer such as Fusobacterium nucleatum followed by late colonizers including the red complex species: Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola -the founders of periodontal disease. As the biofilm progresses from supragingival sites to subgingival sites, the environment changes from aerobic to anaerobic thus favoring the growth of mainly Gram-negative obligate anaerobes while restricting the growth of the early Gram-positive facultative aerobes. Microbes present at supragingival level are mainly related to gingivitis and root-caries whereas subgingival species advance the destruction of teeth supporting tissues and thus causing periodontitis. This review summarizes our present understanding and recent developments on the characteristic features of supra- and subgingival biofilms, interaction between different genera and species of bacteria constituting these biofilms and draws our attention to the role of some of the recently discovered members of the oral community.

The Biofilm Community-Rebels with a Cause

PubMed Central

Aruni, A. Wilson; Dou, Yuetan; Mishra, Arunima; Fletcher, Hansel M.

2015-01-01

Oral Biofilms are one of the most complex and diverse ecosystem developed by successive colonization of more than 600 bacterial taxa. Development starts with the attachment of early colonizers such as Actinomyces species and oral streptococci on the acquired pellicle and tooth enamel. These bacteria not only adhere to tooth surface but also interact with each other and lay foundation for attachment of bridging colonizer such as Fusobacterium nucleatum followed by late colonizers including the red complex species: Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola-the founders of periodontal disease. As the biofilm progresses from supragingival sites to subgingival sites, the environment changes from aerobic to anaerobic thus favoring the growth of mainly Gram-negative obligate anaerobes while restricting the growth of the early Gram-positive facultative aerobes. Microbes present at supragingival level are mainly related to gingivitis and root-caries whereas subgingival species advance the destruction of teeth supporting tissues and thus causing periodontitis. This review summarizes our present understanding and recent developments on the characteristic features of supra- and subgingival biofilms, interaction between different genera and species of bacteria constituting these biofilms and draws our attention to the role of some of the recently discovered members of the oral community. PMID:26120510

Infections Caused by Fusarium Species in Pediatric Cancer Patients and Review of Published Literature.

PubMed

Arnoni, Mariana Volpe; Paula, Claudete Rodrigues; Auler, Marcos Ereno; Simões, Cirilo Cesar Naozuka; Nakano, Shirley; Szeszs, Maria Walderez; Melhem, Márcia de Souza Carvalho; Pereira, Virgínia Bodelão Richini; Garces, Hans Garcia; Bagagli, Eduardo; Silva, Eriques Gonçalves; de Macêdo, Melissa Ferreira; Ruiz, Luciana da Silva

2018-03-21

Fusarium species have emerged as responsible for a broad spectrum of infections, including superficial, locally invasive and disseminated ones, especially in the hospital environment. Since there are few reports of invasive and disseminated fusariosis in children, the aim of this study was to report four cases of nosocomial infection caused by this microorganism in children with cancer hospitalized in a public children's hospital located in Brazil. Two of these patients were female and two were male. All patients presented febrile neutropenia, while three patients had acute lymphocytic leukemia and one patient had Wilms' tumor as underlying disease. In two cases, fungi were isolated from blood and identified as Fusarium oxysporum species complex after phenotypic and genotypic studies, while in two other cases fungi were isolated from skin biopsies and identified as Fusarium solani species complex. One patient died 12 days after the onset of cutaneous lesions. All isolates, after susceptibility testing, presented high levels of minimum inhibitory concentration for itraconazole, voriconazole and amphotericin B. Considering the emergence of filamentous fungi as etiologic agents of nosocomial infections, health professionals should be aware of the problems these infections, especially fungal ones, may cause to debilitated patients.

How to be an ant on figs

NASA Astrophysics Data System (ADS)

Bain, Anthony; Harrison, Rhett D.; Schatz, Bertrand

2014-05-01

Mutualistic interactions are open to exploitation by one or other of the partners and a diversity of other organisms, and hence are best understood as being embedded in a complex network of biotic interactions. Figs participate in an obligate mutualism in that figs are dependent on agaonid fig wasps for pollination and the wasps are dependent on fig ovules for brood sites. Ants are common insect predators and abundant in tropical forests. Ants have been recorded on approximately 11% of fig species, including all six subgenera, and often affect the fig-fig pollinator interaction through their predation of either pollinating and parasitic wasps. On monoecious figs, ants are often associated with hemipterans, whereas in dioecious figs ants predominantly prey on fig wasps. A few fig species are true myrmecophytes, with domatia or food rewards for ants, and in at least one species this is linked to predation of parasitic fig wasps. Ants also play a role in dispersal of fig seeds and may be particularly important for hemi-epiphytic species, which require high quality establishment microsites in the canopy. The intersection between the fig-fig pollinator and ant-plant systems promises to provide fertile ground for understanding mutualistic interactions within the context of complex interaction networks.

Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

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

Ovacik, Meric A.; Androulakis, Ioannis P., E-mail: yannis@rci.rutgers.edu; Biomedical Engineering Department, Rutgers University, Piscataway, NJ 08854

2013-09-15

Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogeneticmore » relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.« less

Molecular phylogeny and diversification of a widespread Neotropical rainforest bird group: The Buff-throated Woodcreeper complex, Xiphorhynchus guttatus/susurrans (Aves: Dendrocolaptidae).

PubMed

Rocha, Tainá C; Sequeira, Fernando; Aleixo, Alexandre; Rêgo, Péricles S; Sampaio, Iracilda; Schneider, Horacio; Vallinoto, Marcelo

2015-04-01

The genus Xiphorhynchus is a species rich avian group widely distributed in Neotropical forests of Central and South America. Although recent molecular studies have improved our understanding of the spatial patterns of genetic diversity in some species of this genus, most are still poorly known, including their taxonomy. Here, we address the historical diversification and phylogenetic relationships of the X. guttatus/susurrans complex, using data from two mitochondrial (cyt b and ND2) and one nuclear (β-fibint7) genes. Phylogenetic relationships were inferred with both gene trees and a Bayesian-based species tree under a coalescent framework (∗BEAST). With exception of the nuclear β-fibint7 gene that produced an unresolved tree, both mtDNA and the species tree showed a similar topology and were congruent in recovering five main clades with high statistical support. These clades, however, are not fully concordant with traditional delimitation of some X. guttatus subspecies, since X. g. polystictus, X. g. guttatus, and X. g. connectens are not supported as distinct clades. Interestingly, these three taxa are more closely related to the mostly trans-Andean X. susurrans than the other southern and western Amazonian subspecies of X. guttatus, which constitutes a paraphyletic species. Timing estimates based on the species tree indicated that diversification in X. guttatus occurred between the end of the Pliocene and early Pleistocene, likely associated with the formation of the modern Amazon River and its main southern tributaries (Xingu, Tocantins, and Madeira), in addition to climate-induced changes in the distribution of rainforest biomes. Our study supports with an enlarged dataset a previous proposal for recognizing at least three species level taxa in the X. guttatus/susurrans complex: X. susurrans, X. guttatus, and X. guttatoides. Copyright © 2015 Elsevier Inc. All rights reserved.

Malaria vectors in South America: current and future scenarios.

PubMed

Laporta, Gabriel Zorello; Linton, Yvonne-Marie; Wilkerson, Richard C; Bergo, Eduardo Sterlino; Nagaki, Sandra Sayuri; Sant'Ana, Denise Cristina; Sallum, Maria Anice Mureb

2015-08-19

Malaria remains a significant public health issue in South America. Future climate change may influence the distribution of the disease, which is dependent on the distribution of those Anopheles mosquitoes competent to transmit Plasmodium falciparum. Herein, predictive niche models of the habitat suitability for P. falciparum, the current primary vector Anopheles darlingi and nine other known and/or potential vector species of the Neotropical Albitarsis Complex, were used to document the current situation and project future scenarios under climate changes in South America in 2070. To build each ecological niche model, we employed topography, climate and biome, and the currently defined distribution of P. falciparum, An. darlingi and nine species comprising the Albitarsis Complex in South America. Current and future (i.e., 2070) distributions were forecast by projecting the fitted ecological niche model onto the current environmental situation and two scenarios of simulated climate change. Statistical analyses were performed between the parasite and each vector in both the present and future scenarios to address potential vector roles in the dynamics of malaria transmission. Current distributions of malaria vector species were associated with that of P. falciparum, confirming their role in transmission, especially An. darlingi, An. marajoara and An. deaneorum. Projected climate changes included higher temperatures, lower water availability and biome modifications. Regardless of future scenarios considered, the geographic distribution of P. falciparum was exacerbated in 2070 South America, with the distribution of the pathogen covering 35-46% of the continent. As the current primary vector An. darlingi showed low tolerance for drier environments, the projected climate change would significantly reduce suitable habitat, impacting both its distribution and abundance. Conversely, climate generalist members of the Albitarsis Complex showed significant spatial and temporal expansion potential in 2070, and we conclude these species will become more important in the dynamics of malaria transmission in South America. Our data suggest that climate and landscape effects will elevate the importance of members of the Albitarsis Complex in malaria transmission in South America in 2070, highlighting the need for further studies addressing the bionomics, ecology and behaviours of the species comprising the Albitarsis Complex.

The Case for Adopting the "Species Complex" Nomenclature for the Etiologic Agents of Cryptococcosis.

PubMed

Kwon-Chung, Kyung J; Bennett, John E; Wickes, Brian L; Meyer, Wieland; Cuomo, Christina A; Wollenburg, Kurt R; Bicanic, Tihana A; Castañeda, Elizabeth; Chang, Yun C; Chen, Jianghan; Cogliati, Massimo; Dromer, Françoise; Ellis, David; Filler, Scott G; Fisher, Matthew C; Harrison, Thomas S; Holland, Steven M; Kohno, Shigeru; Kronstad, James W; Lazera, Marcia; Levitz, Stuart M; Lionakis, Michail S; May, Robin C; Ngamskulrongroj, Popchai; Pappas, Peter G; Perfect, John R; Rickerts, Volker; Sorrell, Tania C; Walsh, Thomas J; Williamson, Peter R; Xu, Jianping; Zelazny, Adrian M; Casadevall, Arturo

2017-01-01

Cryptococcosis is a potentially lethal disease of humans/animals caused by Cryptococcus neoformans and Cryptococcus gattii . Distinction between the two species is based on phenotypic and genotypic characteristics. Recently, it was proposed that C. neoformans be divided into two species and C. gattii into five species based on a phylogenetic analysis of 115 isolates. While this proposal adds to the knowledge about the genetic diversity and population structure of cryptococcosis agents, the published genotypes of 2,606 strains have already revealed more genetic diversity than is encompassed by seven species. Naming every clade as a separate species at this juncture will lead to continuing nomenclatural instability. In the absence of biological differences between clades and no consensus about how DNA sequence alone can delineate a species, we recommend using " Cryptococcus neoformans species complex" and " C. gattii species complex" as a practical intermediate step, rather than creating more species. This strategy recognizes genetic diversity without creating confusion.

An overview of the taxonomy, phylogeny, and typification of nectriaceous fungi in Cosmospora, Acremonium, Fusarium, Stilbella, and Volutella

PubMed Central

Gräfenhan, T.; Schroers, H.-J.; Nirenberg, H.I.; Seifert, K.A.

2011-01-01

A comprehensive phylogenetic reassessment of the ascomycete genus Cosmospora (Hypocreales, Nectriaceae) is undertaken using fresh isolates and historical strains, sequences of two protein encoding genes, the second largest subunit of RNA polymerase II (rpb2), and a new phylogenetic marker, the larger subunit of ATP citrate lyase (acl1). The result is an extensive revision of taxonomic concepts, typification, and nomenclatural details of many anamorph- and teleomorph-typified genera of the Nectriaceae, most notably Cosmospora and Fusarium. The combined phylogenetic analysis shows that the present concept of Fusarium is not monophyletic and that the genus divides into two large groups, one basal in the family, the other terminal, separated by a large group of species classified in genera such as Calonectria, Neonectria, and Volutella. All accepted genera received high statistical support in the phylogenetic analyses. Preliminary polythetic morphological descriptions are presented for each genus, providing details of perithecia, micro- and/or macro-conidial synanamorphs, cultural characters, and ecological traits. Eight species are included in our restricted concept of Cosmospora, two of which have previously documented teleomorphs and all of which have Acremonium-like microconidial anamorphs. A key is provided to the three anamorphic species recognised in Atractium, which is removed from synonymy with Fusarium and epitypified for two macroconidial synnematous species and one sporodochial species associated with waterlogged wood. Dialonectria is recognised as distinct from Cosmospora and two species with teleomorph, macroconidia and microconidia are accepted, including the new species D. ullevolea. Seven species, one with a known teleomorph, are classified in Fusicolla, formerly considered a synonym of Fusarium including members of the F. aquaeductuum and F. merismoides species complex, with several former varieties raised to species rank. Originally a section of Nectria, Macroconia is raised to generic rank for five species, all producing a teleomorph and macroconidial anamorph. A new species of the Verticillium-like anamorphic genus Mariannaea is described as M. samuelsii. Microcera is recognised as distinct from Fusarium and a key is included for four macroconidial species, that are usually parasites of scale insects, two of them with teleomorphs. The four accepted species of Stylonectria each produce a teleomorph and micro- and macroconidial synanamorphs. The Volutella species sampled fall into three clades. Pseudonectria is accepted for a perithecial and sporodochial species that occurs on Buxus. Volutella s. str. also includes perithecial and/or sporodochial species and is revised to include a synnematous species formerly included in Stilbella. The third Volutella-like clade remains unnamed. All fungi in this paper are named using a single name system that gives priority to the oldest generic names and species epithets, irrespective of whether they are originally based on anamorph or teleomorph structures. The rationale behind this is discussed. PMID:21523190

Species diversity of Fergusonina Malloch gall flies (Diptera: Fergusoninidae) forming leaf bud galls on snow gum (Eucalyptus pauciflora Sieb. ex Spreng. complex), with a description of a new species from Tasmania

USDA-ARS?s Scientific Manuscript database

A new species of Fergusonina (Diptera: Fergusoninidae) fly is described from terminal leaf bud galls (TLBGs) from the Eucalyptus pauciflora Sieb. ex Spreng. (snow gum) species complex. Fergusonina tasmaniensis Nelson sp.n. is the first species from the genus Fergusonina to be described from Tasmania...

Morphological and molecular characterization of Cladosporium cladosporioides species complex causing pecan tree leaf spot.

PubMed

Walker, C; Muniz, M F B; Rolim, J M; Martins, R R O; Rosenthal, V C; Maciel, C G; Mezzomo, R; Reiniger, L R S

2016-09-16

The objective of this study was to characterize species of the Cladosporium cladosporioides complex isolated from pecan trees (Carya illinoinensis) with symptoms of leaf spot, based on morphological and molecular approaches. Morphological attributes were assessed using monosporic cultures on potato dextrose agar medium, which were examined for mycelial growth, sporulation, color, and conidia and ramoconidia size. Molecular characterization comprised isolation of DNA and subsequent amplification of the translation elongation factor 1α (TEF-1α) region. Three species of the C. cladosporioides complex were identified: C. cladosporioides, Cladosporium pseudocladosporioides, and Cladosporium subuliforme. Sporulation was the most important characteristic differentiating species of this genus. However, morphological features must be considered together with molecular analysis, as certain characters are indistinguishable between species. TEF-1αcan be effectively used to identify and group isolates belonging to the C. cladosporioides complex. The present study provides an important example of a methodology to ascertain similarity between isolates of this complex causing leaf spot in pecan trees, which should facilitate future pathogenicity studies.

Climate warming promotes species diversity, but with greater taxonomic redundancy, in complex environments

PubMed Central

Thakur, Madhav P.; Tilman, David; Purschke, Oliver; Ciobanu, Marcel; Cowles, Jane; Isbell, Forest; Wragg, Peter D.; Eisenhauer, Nico

2017-01-01

Climate warming is predicted to alter species interactions, which could potentially lead to extinction events. However, there is an ongoing debate whether the effects of warming on biodiversity may be moderated by biodiversity itself. We tested warming effects on soil nematodes, one of the most diverse and abundant metazoans in terrestrial ecosystems, along a gradient of environmental complexity created by a gradient of plant species richness. Warming increased nematode species diversity in complex (16-species mixtures) plant communities (by ~36%) but decreased it in simple (monocultures) plant communities (by ~39%) compared to ambient temperature. Further, warming led to higher levels of taxonomic relatedness in nematode communities across all levels of plant species richness. Our results highlight both the need for maintaining species-rich plant communities to help offset detrimental warming effects and the inability of species-rich plant communities to maintain nematode taxonomic distinctness when warming occur. PMID:28740868

Molecular species delimitation methods recover most song-delimited cicada species in the European Cicadetta montana complex.

PubMed

Wade, E J; Hertach, T; Gogala, M; Trilar, T; Simon, C

2015-12-01

Molecular species delimitation is increasingly being used to discover and illuminate species level diversity, and a number of methods have been developed. Here, we compare the ability of two molecular species delimitation methods to recover song-delimited species in the Cicadetta montana cryptic species complex throughout Europe. Recent bioacoustics studies of male calling songs (premating reproductive barriers) have revealed cryptic species diversity in this complex. Maximum likelihood and Bayesian phylogenetic analyses were used to analyse the mitochondrial genes COI and COII and the nuclear genes EF1α and period for thirteen European Cicadetta species as well as the closely related monotypic genus Euboeana. Two molecular species delimitation methods, general mixed Yule-coalescent (GMYC) and Bayesian phylogenetics and phylogeography, identified the majority of song-delimited species and were largely congruent with each other. None of the molecular delimitation methods were able to fully recover a recent radiation of four Greek species. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Detection of human pathogenic Fusarium species in hospital and communal sink biofilms by using a highly specific monoclonal antibody.

PubMed

Al-Maqtoofi, Marwan; Thornton, Christopher R

2016-11-01

The fungus Fusarium is well known as a plant pathogen, but has recently emerged as an opportunistic pathogen of humans. Habitats providing direct human exposure to infectious propagules are largely unknown, but there is growing evidence that plumbing systems are sources of human pathogenic strains in the Fusarium solani species complex (FSSC) and Fusarium oxysporum species complex (FOSC), the most common groups infecting humans. Here, a newly developed Fusarium-specific monoclonal antibody (mAb ED7) was used to track FSSC and FOSC strains in sink drain biofilms by detecting its target antigen, an extracellular 200 kDa carbohydrate, in saline swabs. The antigen was detectable in 52% of swab samples collected from sinks across a University campus and a tertiary care hospital. The mAb was 100% accurate in detecting FSSC, FOSC, and F. dimerum species complex (FDSC) strains that were present, as mixed fungal communities, in 83% of sink drain biofilms. Specificity of the ELISA was confirmed by sequencing of the internally transcribed spacer 1 (ITS1)-5.8S-ITS2 rRNA-encoding regions of culturable yeasts and molds that were recovered using mycological culture, while translation elongation factor (TEF)-1α analysis of Fusarium isolates included FSSC 1-a, FOSC 33, and FDSC ET-gr, the most common clinical pathotypes in each group. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Stress Genes and Proteins in the Archaea

PubMed Central

Macario, Alberto J. L.; Lange, Marianne; Ahring, Birgitte K.; De Macario, Everly Conway

1999-01-01

The field covered in this review is new; the first sequence of a gene encoding the molecular chaperone Hsp70 and the first description of a chaperonin in the archaea were reported in 1991. These findings boosted research in other areas beyond the archaea that were directly relevant to bacteria and eukaryotes, for example, stress gene regulation, the structure-function relationship of the chaperonin complex, protein-based molecular phylogeny of organisms and eukaryotic-cell organelles, molecular biology and biochemistry of life in extreme environments, and stress tolerance at the cellular and molecular levels. In the last 8 years, archaeal stress genes and proteins belonging to the families Hsp70, Hsp60 (chaperonins), Hsp40(DnaJ), and small heat-shock proteins (sHsp) have been studied. The hsp70(dnaK), hsp40(dnaJ), and grpE genes (the chaperone machine) have been sequenced in seven, four, and two species, respectively, but their expression has been examined in detail only in the mesophilic methanogen Methanosarcina mazei S-6. The proteins possess markers typical of bacterial homologs but none of the signatures distinctive of eukaryotes. In contrast, gene expression and transcription initiation signals and factors are of the eucaryal type, which suggests a hybrid archaeal-bacterial complexion for the Hsp70 system. Another remarkable feature is that several archaeal species in different phylogenetic branches do not have the gene hsp70(dnaK), an evolutionary puzzle that raises the important question of what replaces the product of this gene, Hsp70(DnaK), in protein biogenesis and refolding and for stress resistance. Although archaea are prokaryotes like bacteria, their Hsp60 (chaperonin) family is of type (group) II, similar to that of the eukaryotic cytosol; however, unlike the latter, which has several different members, the archaeal chaperonin system usually includes only two (in some species one and in others possibly three) related subunits of ∼60 kDa. These form, in various combinations depending on the species, a large structure or chaperonin complex sometimes called the thermosome. This multimolecular assembly is similar to the bacterial chaperonin complex GroEL/S, but it is made of only the large, double-ring oligomers each with eight (or nine) subunits instead of seven as in the bacterial complex. Like Hsp70(DnaK), the archaeal chaperonin subunits are remarkable for their evolution, but for a different reason. Ubiquitous among archaea, the chaperonins show a pattern of recurrent gene duplication—hetero-oligomeric chaperonin complexes appear to have evolved several times independently. The stress response and stress tolerance in the archaea involve chaperones, chaperonins, other heat shock (stress) proteins including sHsp, thermoprotectants, the proteasome, as yet incompletely understood thermoresistant features of many molecules, and formation of multicellular structures. The latter structures include single- and mixed-species (bacterial-archaeal) types. Many questions remain unanswered, and the field offers extraordinary opportunities owing to the diversity, genetic makeup, and phylogenetic position of archaea and the variety of ecosystems they inhabit. Specific aspects that deserve investigation are elucidation of the mechanism of action of the chaperonin complex at different temperatures, identification of the partners and substitutes for the Hsp70 chaperone machine, analysis of protein folding and refolding in hyperthermophiles, and determination of the molecular mechanisms involved in stress gene regulation in archaeal species that thrive under widely different conditions (temperature, pH, osmolarity, and barometric pressure). These studies are now possible with uni- and multicellular archaeal models and are relevant to various areas of basic and applied research, including exploration and conquest of ecosystems inhospitable to humans and many mammals and plants. PMID:10585970

Evolution of trophic transmission in parasites: Why add intermediate hosts?

USGS Publications Warehouse

Choisy, Marc; Brown, Sam P.; Lafferty, Kevin D.; Thomas, Frédéric

2003-01-01

Although multihost complex life cycles (CLCs) are common in several distantly related groups of parasites, their evolution remains poorly understood. In this article, we argue that under particular circumstances, adding a second host to a single-host life cycle is likely to enhance transmission (i.e., reaching the target host). For instance, in several situations, the propagules of a parasite exploiting a predator species will achieve a higher host-finding success by encysting in a prey of the target predator than by other dispersal modes. In such a case, selection should favor the transition from a singleto a two-host life cycle that includes the prey species as an intermediate host. We use an optimality model to explore this idea, and we discuss it in relation to dispersal strategies known among free-living species, especially animal dispersal. The model found that selection favored a complex life cycle only if intermediate hosts were more abundant than definitive hosts. The selective value of a complex life cycle increased with predation rates by definitive hosts on intermediate hosts. In exploring trade-offs between transmission strategies, we found that more costly trade-offs made it more difficult to evolve a CLC while less costly trade-offs between traits could favor a mixed strategy.

Generation of novel covalent RNA-protein complexes in cells by ultraviolet B irradiation: implications for autoimmunity.

PubMed

Andrade, Felipe; Casciola-Rosen, Livia A; Rosen, Antony

2005-04-01

To determine whether ultraviolet B (UVB) irradiation induces novel modifications in autoantigens targeted during experimental photoinduced epidermal damage. To search for novel UVB-induced autoantigen modifications, lysates made from UVB-irradiated human keratinocytes or HeLa cells were immunoblotted using human autoantibodies that recognize ribonucleoprotein autoantigens. Novel autoantigen structures identified were further characterized using nucleases and RNA hybridization. Human sera that recognize U1-70 kd (U1-70K) and La by immunoblotting also recognized multiple novel species when they were used to immunoblot lysates of UVB-irradiated keratinocytes or HeLa cells. These species were not present in control cells and were not observed when apoptosis was induced by Fas ligation or cytotoxic lymphocyte granule contents. Biochemical analysis using multiple assays revealed that these novel UVB-induced molecular species result from the covalent crosslinking between the U1 RNA and the hYRNA molecules with their associated proteins, including U1-70K, La, and likely components of the Sm particle. These data demonstrate that UVB irradiation of live cells can directly induce covalent RNA-protein complexes, which are recognized by human autoantibodies. As previously described for other autoantigens, these covalent complexes of RNA and proteins may have important consequences in terms of antigen capture and processing.

Evaluation of highly conserved hsp65-specific nested PCR primers for diagnosing Mycobacterium tuberculosis.

PubMed

Priyadarshini, P; Tiwari, K; Das, A; Kumar, D; Mishra, M N; Desikan, P; Nath, G

2017-02-01

To evaluate the sensitivity and specificity of a new nested set of primers designed for the detection of Mycobacterium tuberculosis complex targeting a highly conserved heat shock protein gene (hsp65). The nested primers were designed using multiple sequence alignment assuming the nucleotide sequence of the M. tuberculosis H37Rv hsp65 genome as base. Multidrug-resistant Mycobacterium species along with other non-mycobacterial and fungal species were included to evaluate the specificity of M. tuberculosis hsp65 gene-specific primers. The sensitivity of the primers was determined using serial 10-fold dilutions, and was 100% as shown by the bands in the case of M. tuberculosis complex. None of the other non M. tuberculosis complex bacterial and fungal species yielded any band on nested polymerase chain reaction (PCR). The first round of amplification could amplify 0.3 ng of the template DNA, while nested PCR could detect 0.3 pg. The present hsp65-specific primers have been observed to be sensitive, specific and cost-effective, without requiring interpretation of biochemical tests, real-time PCR, sequencing or high-performance liquid chromatography. These primer sets do not have the drawbacks associated with those protocols that target insertion sequence 6110, 16S rDNA, rpoB, recA and MPT 64.