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Sample records for phylogenetic analyses suggest

  1. Phylogenetic analyses of endoparasitic Acanthocephala based on mitochondrial genomes suggest secondary loss of sensory organs.

    PubMed

    Weber, Mathias; Wey-Fabrizius, Alexandra R; Podsiadlowski, Lars; Witek, Alexander; Schill, Ralph O; Sugár, László; Herlyn, Holger; Hankeln, Thomas

    2013-01-01

    The metazoan taxon Syndermata (Monogononta, Bdelloidea, Seisonidea, Acanthocephala) comprises species with vastly different lifestyles. The focus of this study is on the phylogeny within the syndermatan subtaxon Acanthocephala (thorny-headed worms, obligate endoparasites). In order to investigate the controversially discussed phylogenetic relationships of acanthocephalan subtaxa we have sequenced the mitochondrial (mt) genomes of Echinorhynchus truttae (Palaeacanthocephala), Paratenuisentis ambiguus (Eoacanthocephala), Macracanthorhynchus hirudinaceus (Archiacanthocephala), and Philodina citrina (Bdelloidea). In doing so, we present the largest molecular phylogenetic dataset so far for this question comprising all major subgroups of Acanthocephala. Alongside with publicly available mt genome data of four additional syndermatans as well as 18 other lophotrochozoan (spiralian) taxa and one outgroup representative, the derived protein-coding sequences were used for Maximum Likelihood as well as Bayesian phylogenetic analyses. We achieved entirely congruent results, whereupon monophyletic Archiacanthocephala represent the sister taxon of a clade comprising Eoacanthocephala and monophyletic Palaeacanthocephala (Echinorhynchida). This topology suggests the secondary loss of lateral sensory organs (sensory pores) within Palaeacanthocephala and is further in line with the emergence of apical sensory organs in the stem lineage of Archiacanthocephala.

  2. Moelcular Phylogenetic Analyses of G1P Dehydrogenase and G3P Dehydrogenase Suggest the Late Origin of Archaea-Type Membrane

    NASA Astrophysics Data System (ADS)

    Yokobori, S.; Nakajima, Y.; Akanuma, S.; Yamagishi, A.

    2013-11-01

    Phylogenetic analyses of G1PDH and G3PDH suggested that the common ancestor of Bacteria/Archaea had cellular membrane with G3P formed by G3PDH. The archaeal ancestry acquired G1PDH, and then the membrane with G3P was replaced with that with G1P.

  3. Phylogenetic analyses of a combined data set suggest that the Attheya lineage is the closest living relative of the pennate diatoms (Bacillariophyceae).

    PubMed

    Sorhannus, Ulf; Fox, Martin G

    2012-03-01

    A Bayesian analysis of a seven gene data set was conducted to reconstruct phylogenetic relationships among a sample of centric and pennate diatoms and to test alternative hypotheses about the closest living relative of Bacillariophyceae. A lineage, composed of two Attheya species, was inferred to share the most recent common ancestor with Bacillariophyceae--a relationship that was also corroborated by the combined parsimony analysis. All competing hypotheses about the closest living relative of Bacillariophyceae were rejected because 100% of the trees in the post-burn-in sample in the Bayesian analysis supported the Attheya-Bacillariophyceae clade. According to a partitioned Bremer support analysis, the majority of the genes in the combined data matrix supported the Attheya--Bacillariophyceae relationship. The global topology of the phylogenetic tree indicated that a monophyletic group consisting of Thalassiosirales and Toxarium undulatum formed the deepest branch followed by a node uniting a clade composed of Bacillariophyceae/Attheya species and a lineage made up of Eucampia zoodiacus, Chaetocerotales, Lithodesmiales, Triceratiales, Biddulphiales and Cymatosirales. Except for the phylogenetic positions of Lithodesmiales, Thalassiosira sp and Skeletonema costatum, the optimal tree obtained from the combined parsimony analysis showed the same branching order of taxa as those seen in the consensus tree inferred from three independent Markov chain Monte Carlo analyses. Noteworthy findings are that Toxarium undulatum shares a strongly supported node with Thalassiosirales and that the genus Attheya is not a member of the Chaetocerotales lineage. PMID:21723193

  4. Structural, Biochemical, and Phylogenetic Analyses Suggest That Indole-3-Acetic Acid Methyltransferase Is an Evolutionarily Ancient Member of the SABATH Family1[W][OA

    PubMed Central

    Zhao, Nan; Ferrer, Jean-Luc; Ross, Jeannine; Guan, Ju; Yang, Yue; Pichersky, Eran; Noel, Joseph P.; Chen, Feng

    2008-01-01

    The plant SABATH protein family encompasses a group of related small-molecule methyltransferases (MTs) that catalyze the S-adenosyl-l-methionine-dependent methylation of natural chemicals encompassing widely divergent structures. Indole-3-acetic acid (IAA) methyltransferase (IAMT) is a member of the SABATH family that modulates IAA homeostasis in plant tissues through methylation of IAA's free carboxyl group. The crystal structure of Arabidopsis (Arabidopsis thaliana) IAMT (AtIAMT1) was determined and refined to 2.75 Å resolution. The overall tertiary and quaternary structures closely resemble the two-domain bilobed monomer and the dimeric arrangement, respectively, previously observed for the related salicylic acid carboxyl methyltransferase from Clarkia breweri (CbSAMT). To further our understanding of the biological function and evolution of SABATHs, especially of IAMT, we analyzed the SABATH gene family in the rice (Oryza sativa) genome. Forty-one OsSABATH genes were identified. Expression analysis showed that more than one-half of the OsSABATH genes were transcribed in one or multiple organs. The OsSABATH gene most similar to AtIAMT1 is OsSABATH4. Escherichia coli-expressed OsSABATH4 protein displayed the highest level of catalytic activity toward IAA and was therefore named OsIAMT1. OsIAMT1 exhibited kinetic properties similar to AtIAMT1 and poplar IAMT (PtIAMT1). Structural modeling of OsIAMT1 and PtIAMT1 using the experimentally determined structure of AtIAMT1 reported here as a template revealed conserved structural features of IAMTs within the active-site cavity that are divergent from functionally distinct members of the SABATH family, such as CbSAMT. Phylogenetic analysis revealed that IAMTs from Arabidopsis, rice, and poplar (Populus spp.) form a monophyletic group. Thus, structural, biochemical, and phylogenetic evidence supports the hypothesis that IAMT is an evolutionarily ancient member of the SABATH family likely to play a critical role in IAA

  5. Structural, Biochemical, and Phylogenetic Analyses Suggest That Indole-3-Acetic Acid Methyltransferase Is an Evolutionarily Ancient Member of the SABATH Family

    SciTech Connect

    Zhao,N.; Ferrer, J.; Ross, J.; Guan, J.; Yang, Y.; Pichersky, E.; Noel, J.; Chen, F.

    2008-01-01

    The plant SABATH protein family encompasses a group of related small-molecule methyltransferases (MTs) that catalyze the S-adenosyl-L-methionine-dependent methylation of natural chemicals encompassing widely divergent structures. Indole-3-acetic acid (IAA) methyltransferase (IAMT) is a member of the SABATH family that modulates IAA homeostasis in plant tissues through methylation of IAA's free carboxyl group. The crystal structure of Arabidopsis (Arabidopsis thaliana) IAMT (AtIAMT1) was determined and refined to 2.75 Angstroms resolution. The overall tertiary and quaternary structures closely resemble the two-domain bilobed monomer and the dimeric arrangement, respectively, previously observed for the related salicylic acid carboxyl methyltransferase from Clarkia breweri (CbSAMT). To further our understanding of the biological function and evolution of SABATHs, especially of IAMT, we analyzed the SABATH gene family in the rice (Oryza sativa) genome. Forty-one OsSABATH genes were identified. Expression analysis showed that more than one-half of the OsSABATH genes were transcribed in one or multiple organs. The OsSABATH gene most similar to AtIAMT1 is OsSABATH4. Escherichia coli-expressed OsSABATH4 protein displayed the highest level of catalytic activity toward IAA and was therefore named OsIAMT1. OsIAMT1 exhibited kinetic properties similar to AtIAMT1 and poplar IAMT (PtIAMT1). Structural modeling of OsIAMT1 and PtIAMT1 using the experimentally determined structure of AtIAMT1 reported here as a template revealed conserved structural features of IAMTs within the active-site cavity that are divergent from functionally distinct members of the SABATH family, such as CbSAMT. Phylogenetic analysis revealed that IAMTs from Arabidopsis, rice, and poplar (Populus spp.) form a monophyletic group. Thus, structural, biochemical, and phylogenetic evidence supports the hypothesis that IAMT is an evolutionarily ancient member of the SABATH family likely to play a critical role in

  6. Birth of Archaeal Cells: Molecular Phylogenetic Analyses of G1P Dehydrogenase, G3P Dehydrogenases, and Glycerol Kinase Suggest Derived Features of Archaeal Membranes Having G1P Polar Lipids

    PubMed Central

    2016-01-01

    Bacteria and Eukarya have cell membranes with sn-glycerol-3-phosphate (G3P), whereas archaeal membranes contain sn-glycerol-1-phosphate (G1P). Determining the time at which cells with either G3P-lipid membranes or G1P-lipid membranes appeared is important for understanding the early evolution of terrestrial life. To clarify this issue, we reconstructed molecular phylogenetic trees of G1PDH (G1P dehydrogenase; EgsA/AraM) which is responsible for G1P synthesis and G3PDHs (G3P dehydrogenase; GpsA and GlpA/GlpD) and glycerol kinase (GlpK) which is responsible for G3P synthesis. Together with the distribution of these protein-encoding genes among archaeal and bacterial groups, our phylogenetic analyses suggested that GlpA/GlpD in the Commonote (the last universal common ancestor of all extant life with a cellular form, Commonote commonote) acquired EgsA (G1PDH) from the archaeal common ancestor (Commonote archaea) and acquired GpsA and GlpK from a bacterial common ancestor (Commonote bacteria). In our scenario based on this study, the Commonote probably possessed a G3P-lipid membrane synthesized enzymatically, after which the archaeal lineage acquired G1PDH followed by the replacement of a G3P-lipid membrane with a G1P-lipid membrane. PMID:27774041

  7. Phylogenetic relationship among horseshoe crab species: effect of substitution models on phylogenetic analyses.

    PubMed

    Xia, X

    2000-03-01

    The horseshoe crabs, known as living fossils, have maintained their morphology almost unchanged for the past 150 million years. The little morphological differentiation among horseshoe crab lineages has resulted in substantial controversy concerning the phylogenetic relationship among the extant species of horseshoe crabs, especially among the three species in the Indo-Pacific region. Previous studies suggest that the three species constitute a phylogenetically unresolvable trichotomy, the result of a cladogenetic process leading to the formation of all three Indo-Pacific species in a short geological time. Data from two mitochondrial genes (for 16S ribosomal rRNA and cytochrome oxidase subunit I) and one nuclear gene (for coagulogen) in the four species of horseshoe crabs and outgroup species were used in a phylogenetic analysis with various substitution models. All three genes yield the same tree topology, with Tachypleus-gigas and Carcinoscorpius-rotundicauda grouped together as a monophyletic taxon. This topology is significantly better than all the alternatives when evaluated with the RELL (resampling estimated log-likelihood) method.

  8. Phylogenetic analysis suggests that sociality is associated with reduced effectiveness of selection.

    PubMed

    Settepani, Virginia; Bechsgaard, Jesper; Bilde, Trine

    2016-01-01

    The evolution of sociality in spiders is associated with female bias, reproductive skew and an inbreeding mating system, factors that cause a reduction in effective population size and increase effects of genetic drift. These factors act to decrease the effectiveness of selection, thereby increasing the fixation probability of deleterious mutations. Comparative studies of closely related species with contrasting social traits and mating systems provide the opportunity to test consequences of low effective population size on the effectiveness of selection empirically. We used phylogenetic analyses of three inbred social spider species and seven outcrossing subsocial species of the genus Stegodyphus, and compared dN/dS ratios and codon usage bias between social Inbreeding and subsocial outcrossing mating systems to assess the effectiveness of selection. The overall results do not differ significantly between the social inbreeding and outcrossing species, but suggest a tendency for lower codon usage bias and higher dN/dS ratios in the social inbreeding species compared with their outcrossing congeners. The differences in dN/dS ratio and codon usage bias between social and subsocial species are modest but consistent with theoretical expectations of reduced effectiveness of selection in species with relatively low effective population size. The modest differences are consistent with relatively recent evolution of social mating systems. Additionally, the short terminal branches and lack of speciation of the social lineages, together with low genetic diversity lend support for the transient state of permanent sociality in spiders. PMID:26843931

  9. Phylogenetic analyses of melanoma reveal complex patterns of metastatic dissemination

    PubMed Central

    Sanborn, J. Zachary; Chung, Jongsuk; Purdom, Elizabeth; Wang, Nicholas J.; Kakavand, Hojabr; Wilmott, James S.; Butler, Timothy; Thompson, John F.; Mann, Graham J.; Haydu, Lauren E.; Saw, Robyn P. M.; Busam, Klaus J.; Lo, Roger S.; Collisson, Eric A.; Hur, Joe S.; Spellman, Paul T.; Cleaver, James E.; Gray, Joe W.; Huh, Nam; Murali, Rajmohan; Scolyer, Richard A.; Bastian, Boris C.; Cho, Raymond J.

    2015-01-01

    Melanoma is difficult to treat once it becomes metastatic. However, the precise ancestral relationship between primary tumors and their metastases is not well understood. We performed whole-exome sequencing of primary melanomas and multiple matched metastases from eight patients to elucidate their phylogenetic relationships. In six of eight patients, we found that genetically distinct cell populations in the primary tumor metastasized in parallel to different anatomic sites, rather than sequentially from one site to the next. In five of these six patients, the metastasizing cells had themselves arisen from a common parental subpopulation in the primary, indicating that the ability to establish metastases is a late-evolving trait. Interestingly, we discovered that individual metastases were sometimes founded by multiple cell populations of the primary that were genetically distinct. Such establishment of metastases by multiple tumor subpopulations could help explain why identical resistance variants are identified in different sites after initial response to systemic therapy. One primary tumor harbored two subclones with different oncogenic mutations in CTNNB1, which were both propagated to the same metastasis, raising the possibility that activation of wingless-type mouse mammary tumor virus integration site (WNT) signaling may be involved, as has been suggested by experimental models. PMID:26286987

  10. [Phylogenetic analyses of the family Tetraonchidae (Platyhelminthes: Monogenea)].

    PubMed

    Gerasev, P I

    2004-01-01

    A phylogenetic reconstruction of the monogenean family Tetraonchidae was carried out by methods of parsimony-based cladistics. The analysis included 20 species of tetraonchids and two out-groups (Sundanonchus tomanorum and Dactylogyrus amphibothrium) and was based on 34 morphofunctional characters. Software PAUP 4.0 and Winclada were used for the phylogenetic reconstructions. Obtained results allow proposing a preliminary phylogenetic hypothesis of the family Tetraonchidae along with the discussion of host-parasite association. According to the current taxonomic view, the family Tetraonchidae included two genera. Cladistic analysis showed a monophyly of the family and the genus Tetraonchus Diesing, 1858. Two representative of the former genus, Tetraoncus monenteron and T. borealis, parasitize the pikes (Esocoformes: Esocidae) and the grayling (Salmonidae: Thymallinae) respectively. The genus Salmonchus Spassky et Roytman, 1958 has a complicated structure and its intrageneric relationships were not completely resolved; in general, the analysis allows to recognise several species groups: Salmonchus oncorhynchi--the parasite of the Oncorhynchus masou smolt living during the first year of life in fresh water; four species (S. variabilis, S. gussevi, S. grumosus, S. alaskensis) inhabiting specifically the whitefishes (Salmonidae: Coregoninae); all reminder of Salmonchus species occurring on the salmons (Salmonidae: Salmoninae). The bootstrap test gives a support only for the following clades: family Tetraonchidae (75%), genus Tetraonchus (88%); a group of Salmonchus species associated with the whitefishes (93%) and grouping of four species (S. huhonis, S. pseudolenoki, S. skrjabini and S. lenoki) from the lenoks (Brachymystax) and taimens (Hucho) (61%). PMID:15553772

  11. Empirical evaluation of partitioning schemes for phylogenetic analyses of mitogenomic data: an avian case study.

    PubMed

    Powell, Alexis F L A; Barker, F Keith; Lanyon, Scott M

    2013-01-01

    Whole mitochondrial genome sequences have been used in studies of animal phylogeny for two decades, and current technologies make them ever more available, but methods for their analysis are lagging and best practices have not been established. Most studies ignore variation in base composition and evolutionary rate within the mitogenome that can bias phylogenetic inference, or attempt to avoid it by excluding parts of the mitogenome from analysis. In contrast, partitioned analyses accommodate heterogeneity, without discarding data, by applying separate evolutionary models to differing portions of the mitogenome. To facilitate use of complete mitogenomic sequences in phylogenetics, we (1) suggest a set of categories for dividing mitogenomic datasets into subsets, (2) explore differences in evolutionary dynamics among those subsets, and (3) apply a method for combining data subsets with similar properties to produce effective and efficient partitioning schemes. We demonstrate these procedures with a case study, using the mitogenomes of species in the grackles and allies clade of New World blackbirds (Icteridae). We found that the most useful categories for partitioning were codon position, RNA secondary structure pairing, and the coding/noncoding distinction, and that a scheme with nine data groups outperformed all of the more complex alternatives (up to 44 data groups) that we tested. As hoped, we found that analyses using whole mitogenomic sequences yielded much better-resolved and more strongly-supported hypotheses of the phylogenetic history of that locus than did a conventional 2-kilobase sample (i.e. sequences of the cytochrome b and ND2 genes). Mitogenomes have much untapped potential for phylogenetics, especially of birds, a taxon for which they have been little exploited except in investigations of ordinal-level relationships. PMID:23000817

  12. Improved Phylogenetic Analyses Corroborate a Plausible Position of Martialis heureka in the Ant Tree of Life

    PubMed Central

    Kück, Patrick; Hita Garcia, Francisco; Misof, Bernhard; Meusemann, Karen

    2011-01-01

    Martialinae are pale, eyeless and probably hypogaeic predatory ants. Morphological character sets suggest a close relationship to the ant subfamily Leptanillinae. Recent analyses based on molecular sequence data suggest that Martialinae are the sister group to all extant ants. However, by comparing molecular studies and different reconstruction methods, the position of Martialinae remains ambiguous. While this sister group relationship was well supported by Bayesian partitioned analyses, Maximum Likelihood approaches could not unequivocally resolve the position of Martialinae. By re-analysing a previous published molecular data set, we show that the Maximum Likelihood approach is highly appropriate to resolve deep ant relationships, especially between Leptanillinae, Martialinae and the remaining ant subfamilies. Based on improved alignments, alignment masking, and tree reconstructions with a sufficient number of bootstrap replicates, our results strongly reject a placement of Martialinae at the first split within the ant tree of life. Instead, we suggest that Leptanillinae are a sister group to all other extant ant subfamilies, whereas Martialinae branch off as a second lineage. This assumption is backed by approximately unbiased (AU) tests, additional Bayesian analyses and split networks. Our results demonstrate clear effects of improved alignment approaches, alignment masking and data partitioning. We hope that our study illustrates the importance of thorough, comprehensible phylogenetic analyses using the example of ant relationships. PMID:21731644

  13. Improved phylogenetic analyses corroborate a plausible position of Martialis heureka in the ant tree of life.

    PubMed

    Kück, Patrick; Hita Garcia, Francisco; Misof, Bernhard; Meusemann, Karen

    2011-01-01

    Martialinae are pale, eyeless and probably hypogaeic predatory ants. Morphological character sets suggest a close relationship to the ant subfamily Leptanillinae. Recent analyses based on molecular sequence data suggest that Martialinae are the sister group to all extant ants. However, by comparing molecular studies and different reconstruction methods, the position of Martialinae remains ambiguous. While this sister group relationship was well supported by Bayesian partitioned analyses, Maximum Likelihood approaches could not unequivocally resolve the position of Martialinae. By re-analysing a previous published molecular data set, we show that the Maximum Likelihood approach is highly appropriate to resolve deep ant relationships, especially between Leptanillinae, Martialinae and the remaining ant subfamilies. Based on improved alignments, alignment masking, and tree reconstructions with a sufficient number of bootstrap replicates, our results strongly reject a placement of Martialinae at the first split within the ant tree of life. Instead, we suggest that Leptanillinae are a sister group to all other extant ant subfamilies, whereas Martialinae branch off as a second lineage. This assumption is backed by approximately unbiased (AU) tests, additional Bayesian analyses and split networks. Our results demonstrate clear effects of improved alignment approaches, alignment masking and data partitioning. We hope that our study illustrates the importance of thorough, comprehensible phylogenetic analyses using the example of ant relationships.

  14. Phylogenetic study on Shiraia bambusicola by rDNA sequence analyses.

    PubMed

    Cheng, Tian-Fan; Jia, Xiao-Ming; Ma, Xiao-Hang; Lin, Hai-Ping; Zhao, Yu-Hua

    2004-01-01

    In this study, 18S rDNA and ITS-5.8S rDNA regions of four Shiraia bambusicola isolates collected from different species of bamboos were amplified by PCR with universal primer pairs NS1/NS8 and ITS5/ITS4, respectively, and sequenced. Phylogenetic analyses were conducted on three selected datasets of rDNA sequences. Maximum parsimony, distance and maximum likelihood criteria were used to infer trees. Morphological characteristics were also observed. The positioning of Shiraia in the order Pleosporales was well supported by bootstrap, which agreed with the placement by Amano (1980) according to their morphology. We did not find significant inter-hostal differences among these four isolates from different species of bamboos. From the results of analyses and comparison of their rDNA sequences, we conclude that Shiraia should be classified into Pleosporales as Amano (1980) proposed and suggest that it might be positioned in the family Phaeosphaeriaceae.

  15. Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids

    PubMed Central

    Jansen, Robert K; Kaittanis, Charalambos; Saski, Christopher; Lee, Seung-Bum; Tomkins, Jeffrey; Alverson, Andrew J; Daniell, Henry

    2006-01-01

    Background The Vitaceae (grape) is an economically important family of angiosperms whose phylogenetic placement is currently unresolved. Recent phylogenetic analyses based on one to several genes have suggested several alternative placements of this family, including sister to Caryophyllales, asterids, Saxifragales, Dilleniaceae or to rest of rosids, though support for these different results has been weak. There has been a recent interest in using complete chloroplast genome sequences for resolving phylogenetic relationships among angiosperms. These studies have clarified relationships among several major lineages but they have also emphasized the importance of taxon sampling and the effects of different phylogenetic methods for obtaining accurate phylogenies. We sequenced the complete chloroplast genome of Vitis vinifera and used these data to assess relationships among 27 angiosperms, including nine taxa of rosids. Results The Vitis vinifera chloroplast genome is 160,928 bp in length, including a pair of inverted repeats of 26,358 bp that are separated by small and large single copy regions of 19,065 bp and 89,147 bp, respectively. The gene content and order of Vitis is identical to many other unrearranged angiosperm chloroplast genomes, including tobacco. Phylogenetic analyses using maximum parsimony and maximum likelihood were performed on DNA sequences of 61 protein-coding genes for two datasets with 28 or 29 taxa, including eight or nine taxa from four of the seven currently recognized major clades of rosids. Parsimony and likelihood phylogenies of both data sets provide strong support for the placement of Vitaceae as sister to the remaining rosids. However, the position of the Myrtales and support for the monophyly of the eurosid I clade differs between the two data sets and the two methods of analysis. In parsimony analyses, the inclusion of Gossypium is necessary to obtain trees that support the monophyly of the eurosid I clade. However, maximum

  16. Phylogenetic trait-based analyses of ecological networks

    PubMed Central

    Rafferty, Nicole E.; Ives, Anthony R.

    2013-01-01

    Ecological networks of two interacting guilds of species, such as flowering plants and pollinators, are common in nature, and studying their structure can yield insights into their resilience to environmental disturbances. Here we develop analytical methods for exploring the strengths of interactions within bipartite networks consisting of two guilds of phylogenetically related species. We then apply these methods to investigate the resilience of a plant–pollinator community to anticipated climate change. The methods allow the statistical assessment of, for example, whether closely related pollinators are more likely to visit plants with similar relative frequencies, and whether closely related pollinators tend to visit closely related plants. The methods can also incorporate trait information, allowing us to identify which plant traits are likely responsible for attracting different pollinators. These questions are important for our study of 14 prairie plants and their 22 insect pollinators. Over the last 70 years, six of the plants have advanced their flowering, while eight have not. When we experimentally forced earlier flowering times, five of the six advanced-flowering species experienced higher pollinator visitation rates, whereas only one of the eight other species had more visits; this network thus appears resilient to climate change, because those species with advanced flowering have ample pollinators earlier in the season. Using the methods developed here, we show that advanced-flowering plants did not have a distinct pollinator community from the other eight species. Furthermore, pollinator phylogeny did not explain pollinator community composition; closely related pollinators were not more likely to visit the same plant species. However, differences among pollinator communities visiting different plants were explained by plant height, floral color, and symmetry. As a result, closely related plants attracted similar numbers of pollinators. By parsing

  17. Phylogenetic Analyses of Novel Squamate Adenovirus Sequences in Wild-Caught Anolis Lizards

    PubMed Central

    Ascher, Jill M.; Geneva, Anthony J.; Ng, Julienne; Wyatt, Jeffrey D.; Glor, Richard E.

    2013-01-01

    Adenovirus infection has emerged as a serious threat to the health of captive snakes and lizards (i.e., squamates), but we know relatively little about this virus' range of possible hosts, pathogenicity, modes of transmission, and sources from nature. We report the first case of adenovirus infection in the Iguanidae, a diverse family of lizards that is widely-studied and popular in captivity. We report adenovirus infections from two closely-related species of Anolis lizards (anoles) that were recently imported from wild populations in the Dominican Republic to a laboratory colony in the United States. We investigate the evolution of adenoviruses in anoles and other squamates using phylogenetic analyses of adenovirus polymerase gene sequences sampled from Anolis and a range of other vertebrate taxa. These phylogenetic analyses reveal that (1) the sequences detected from each species of Anolis are novel, and (2) adenoviruses are not necessarily host-specific and do not always follow a co-speciation model under which host and virus phylogenies are perfectly concordant. Together with the fact that the Anolis adenovirus sequences reported in our study were detected in animals that became ill and subsequently died shortly after importation while exhibiting clinical signs consistent with acute adenovirus infection, our discoveries suggest the need for renewed attention to biosecurity measures intended to prevent the spread of adenovirus both within and among species of snakes and lizards housed in captivity. PMID:23593364

  18. Molecular phylogenetic and dating analyses using mitochondrial DNA sequences of eyelid geckos (Squamata: Eublepharidae).

    PubMed

    Jonniaux, Pierre; Kumazawa, Yoshinori

    2008-01-15

    Mitochondrial DNA sequences of approximately 2.3 kbp including the complete NADH dehydrogenase subunit 2 gene and its flanking genes, as well as parts of 12S and 16S rRNA genes were determined from major species of the eyelid gecko family Eublepharidae sensu [Kluge, A.G. 1987. Cladistic relationships in the Gekkonoidea (Squamata, Sauria). Misc. Publ. Mus. Zool. Univ. Michigan 173, 1-54.]. In contrast to previous morphological studies, phylogenetic analyses based on these sequences supported that Eublepharidae and Gekkonidae form a sister group with Pygopodidae, raising the possibility of homoplasious character change in some key features of geckos, such as reduction of movable eyelids and innovation of climbing toe pads. The phylogenetic analyses also provided a well-resolved tree for relationships between the eublepharid species. The Bayesian estimation of divergence times without assuming the molecular clock suggested the Jurassic divergence of Eublepharidae from Gekkonidae and radiations of most eublepharid genera around the Cretaceous. These dating results appeared to be robust against some conditional changes for time estimation, such as gene regions used, taxon representation, and data partitioning. Taken together with geological evidence, these results support the vicariant divergence of Eublepharidae and Gekkonidae by the breakup of Pangea into Laurasia and Gondwanaland, and recent dispersal of two African eublepharid genera from Eurasia to Africa after these landmasses were connected in the Early Miocene.

  19. Molecular phylogenetic and dating analyses using mitochondrial DNA sequences of eyelid geckos (Squamata: Eublepharidae).

    PubMed

    Jonniaux, Pierre; Kumazawa, Yoshinori

    2008-01-15

    Mitochondrial DNA sequences of approximately 2.3 kbp including the complete NADH dehydrogenase subunit 2 gene and its flanking genes, as well as parts of 12S and 16S rRNA genes were determined from major species of the eyelid gecko family Eublepharidae sensu [Kluge, A.G. 1987. Cladistic relationships in the Gekkonoidea (Squamata, Sauria). Misc. Publ. Mus. Zool. Univ. Michigan 173, 1-54.]. In contrast to previous morphological studies, phylogenetic analyses based on these sequences supported that Eublepharidae and Gekkonidae form a sister group with Pygopodidae, raising the possibility of homoplasious character change in some key features of geckos, such as reduction of movable eyelids and innovation of climbing toe pads. The phylogenetic analyses also provided a well-resolved tree for relationships between the eublepharid species. The Bayesian estimation of divergence times without assuming the molecular clock suggested the Jurassic divergence of Eublepharidae from Gekkonidae and radiations of most eublepharid genera around the Cretaceous. These dating results appeared to be robust against some conditional changes for time estimation, such as gene regions used, taxon representation, and data partitioning. Taken together with geological evidence, these results support the vicariant divergence of Eublepharidae and Gekkonidae by the breakup of Pangea into Laurasia and Gondwanaland, and recent dispersal of two African eublepharid genera from Eurasia to Africa after these landmasses were connected in the Early Miocene. PMID:18029117

  20. Suggestions for presenting the results of data analyses

    USGS Publications Warehouse

    Anderson, D.R.; Link, W.A.; Johnson, D.H.; Burnham, K.P.

    2001-01-01

    We give suggestions for the presentation of research results from frequentist, information-theoretic, and Bayesian analysis paradigms, followed by several general suggestions. The information-theoretic and Bayesian methods offer alternative approaches to data analysis and inference compared to traditionally used methods. Guidance is lacking on the presentation of results under these alternative procedures and on nontesting aspects of classical frequentist methods of statistical analysis. Null hypothesis testing has come under intense criticism. We recommend less reporting of the results of statistical tests of null hypotheses in cases where the null is surely false anyway, or where the null hypothesis is of little interest to science or management.

  1. Suggestions for presenting the results of data analyses

    USGS Publications Warehouse

    Anderson, D.R.; Link, W.A.; Johnson, D.H.; Burnham, K.P.

    2001-01-01

    We give suggestions for the presentation of research results from frequentist, information-theoretic, and Bayesian analysis paradigms, followed by several general suggestions. The information-theoretic and Bayesian methods offer alternative approaches to data analysis and inference compared to traditionally used methods. Guidance is lacking on the presentation of results under these alternative procedures and on nontesting aspects of classical frequentists methods of statistical analysis. Null hypothesis testing has come under intense criticism. We recommend less reporting of the results of statistical tests of null hypotheses in cases where the null is surely false anyway, or where the null hypothesis is of little interest to science or management.

  2. Mitochondrial Genome Analyses Suggest Multiple Trichuris Species in Humans, Baboons, and Pigs from Different Geographical Regions

    PubMed Central

    Hawash, Mohamed B. F.; Andersen, Lee O.; Gasser, Robin B.; Stensvold, Christen Rune; Nejsum, Peter

    2015-01-01

    Background The whipworms Trichuris trichiura and Trichuris suis are two parasitic nematodes of humans and pigs, respectively. Although whipworms in human and non-human primates historically have been referred to as T. trichiura, recent reports suggest that several Trichuris spp. are found in primates. Methods and Findings We sequenced and annotated complete mitochondrial genomes of Trichuris recovered from a human in Uganda, an olive baboon in the US, a hamadryas baboon in Denmark, and two pigs from Denmark and Uganda. Comparative analyses using other published mitochondrial genomes of Trichuris recovered from a human and a porcine host in China and from a françois’ leaf-monkey (China) were performed, including phylogenetic analyses and pairwise genetic and amino acid distances. Genetic and protein distances between human Trichuris in Uganda and China were high (~19% and 15%, respectively) suggesting that they represented different species. Trichuris from the olive baboon in US was genetically related to human Trichuris in China, while the other from the hamadryas baboon in Denmark was nearly identical to human Trichuris from Uganda. Baboon-derived Trichuris was genetically distinct from Trichuris from françois’ leaf monkey, suggesting multiple whipworm species circulating among non-human primates. The genetic and protein distances between pig Trichuris from Denmark and other regions were roughly 9% and 6%, respectively, while Chinese and Ugandan whipworms were more closely related. Conclusion and Significance Our results indicate that Trichuris species infecting humans and pigs are phylogenetically distinct across geographical regions, which might have important implications for the implementation of suitable and effective control strategies in different regions. Moreover, we provide support for the hypothesis that Trichuris infecting primates represents a complex of cryptic species with some species being able to infect both humans and non-human primates

  3. Expanded phylogenetic analyses of the class Heterotrichea (Ciliophora, Postciliodesmatophora) using five molecular markers and morphological data.

    PubMed

    Fernandes, Noemi M; Paiva, Thiago da Silva; da Silva-Neto, Inácio D; Schlegel, Martin; Schrago, Carlos G

    2016-02-01

    Most studies of the molecular evolution of Heterotrichea have been based solely on the 18S-rDNA gene, which were inconsistent with morphological classification. Because of the limitations of single locus phylogenies and the recurring problem of lack of resolution of deeper nodes found in previous studies, we present hypotheses of the evolution of internal groups of the class Heterotrichea based on multi-loci analyses (18S-rDNA, 28S-rDNA, ITS1-5.8S-ITS2 region, COI and alpha-tubulin) and morphological data. Phylogenetic trees from protein coding gene data are presented for Heterotrichea for the first time. Phylogenetic analyses included Bayesian inference, maximum likelihood, maximum parsimony methods, and optimal trees were statistically compared to alternative topologies from the literature. Additionally, the Bayesian concordance approach (BCA algorithm) was used to assess the concordance factor between topologies obtained from isolated analyses. Because different loci may evolve at different rates, resulting in different gene topologies, we also estimated a species tree for Heterotrichea using the STAR coalescence-based method. The results show that: (1) single gene trees are inconsistent regarding the position of some heterotrichean families; (2) the concatenation of all data in a total-evidence tree improved the resolution of deep nodes among the heterotrichean families and genera; (3) the coalescent-based species tree is consistent with phylogenies based on the 18S-rDNA gene and shows Spirostomidae as the stem group of Heterotrichea; (4) however, the total-evidence tree suggests that the large Heterotrichea cluster is divided into nine lineages in which Peritromidae diverges at the base of the Heterotrichea tree.

  4. Expanded phylogenetic analyses of the class Heterotrichea (Ciliophora, Postciliodesmatophora) using five molecular markers and morphological data.

    PubMed

    Fernandes, Noemi M; Paiva, Thiago da Silva; da Silva-Neto, Inácio D; Schlegel, Martin; Schrago, Carlos G

    2016-02-01

    Most studies of the molecular evolution of Heterotrichea have been based solely on the 18S-rDNA gene, which were inconsistent with morphological classification. Because of the limitations of single locus phylogenies and the recurring problem of lack of resolution of deeper nodes found in previous studies, we present hypotheses of the evolution of internal groups of the class Heterotrichea based on multi-loci analyses (18S-rDNA, 28S-rDNA, ITS1-5.8S-ITS2 region, COI and alpha-tubulin) and morphological data. Phylogenetic trees from protein coding gene data are presented for Heterotrichea for the first time. Phylogenetic analyses included Bayesian inference, maximum likelihood, maximum parsimony methods, and optimal trees were statistically compared to alternative topologies from the literature. Additionally, the Bayesian concordance approach (BCA algorithm) was used to assess the concordance factor between topologies obtained from isolated analyses. Because different loci may evolve at different rates, resulting in different gene topologies, we also estimated a species tree for Heterotrichea using the STAR coalescence-based method. The results show that: (1) single gene trees are inconsistent regarding the position of some heterotrichean families; (2) the concatenation of all data in a total-evidence tree improved the resolution of deep nodes among the heterotrichean families and genera; (3) the coalescent-based species tree is consistent with phylogenies based on the 18S-rDNA gene and shows Spirostomidae as the stem group of Heterotrichea; (4) however, the total-evidence tree suggests that the large Heterotrichea cluster is divided into nine lineages in which Peritromidae diverges at the base of the Heterotrichea tree. PMID:26549427

  5. Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased.

    PubMed

    Xi, Zhenxiang; Liu, Liang; Davis, Charles C

    2015-11-01

    The development and application of coalescent methods are undergoing rapid changes. One little explored area that bears on the application of gene-tree-based coalescent methods to species tree estimation is gene informativeness. Here, we investigate the accuracy of these coalescent methods when genes have minimal phylogenetic information, including the implementation of the multilocus bootstrap approach. Using simulated DNA sequences, we demonstrate that genes with minimal phylogenetic information can produce unreliable gene trees (i.e., high error in gene tree estimation), which may in turn reduce the accuracy of species tree estimation using gene-tree-based coalescent methods. We demonstrate that this problem can be alleviated by sampling more genes, as is commonly done in large-scale phylogenomic analyses. This applies even when these genes are minimally informative. If gene tree estimation is biased, however, gene-tree-based coalescent analyses will produce inconsistent results, which cannot be remedied by increasing the number of genes. In this case, it is not the gene-tree-based coalescent methods that are flawed, but rather the input data (i.e., estimated gene trees). Along these lines, the commonly used program PhyML has a tendency to infer one particular bifurcating topology even though it is best represented as a polytomy. We additionally corroborate these findings by analyzing the 183-locus mammal data set assembled by McCormack et al. (2012) using ultra-conserved elements (UCEs) and flanking DNA. Lastly, we demonstrate that when employing the multilocus bootstrap approach on this 183-locus data set, there is no strong conflict between species trees estimated from concatenation and gene-tree-based coalescent analyses, as has been previously suggested by Gatesy and Springer (2014).

  6. Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses

    PubMed Central

    2016-01-01

    Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies. PMID:27146442

  7. Chromosomal evolution and phylogenetic analyses in Tayassu pecari and Pecari tajacu (Tayassuidae): tales from constitutive heterochromatin.

    PubMed

    Adega, F; Chaves, R; Guedes-Pinto, H

    2007-04-01

    The mammalian family Tayassuidae (peccaries) is confined to the New World and comprises three recognized extant species, white-lipped (Tayassu pecari), collared (Pecari tajacu) and chacoan (Catagonus wagneri) peccaries, which exhibit distinct morphological and chromosomal features. The phylogenetic relationships among the tayassuids are unclear and have instigated debate over the palaeontological, cytogenetic and molecular aspects. Constitutive heterochromatin analysis can be used in understanding the phylogenetic relationships between related species. Here we describe, for the first time, the constitutive heterochromatin (C-positive heterochromatin) of two tayassuid species, Tayassu pecari and Pecari tajacu. We demonstrate that in situ restriction endonuclease digestion with sequential C-banding could be a complementary tool in the study of constitutive heterochromatin heterogeneity in chromosomes of the Tayassuidae. Our characterization of peccary chromosomes suggests that the Pecari tajacu autosomal karyotype is more primitive and has accumulated great diversity in its constitutive heterochromatin. This idea is supported by several other studies that analysed nuclear and mitochondrial sequences of the living peccary species. Finally, the tayassuid X chromosome primitive form seems to be the one of Tayassu pecari.

  8. Phylogenetic analysis of kindlins suggests subfunctionalization of an ancestral unduplicated kindlin into three paralogs in vertebrates.

    PubMed

    Khan, Ammad Aslam; Janke, Axel; Shimokawa, Takashi; Zhang, Hongquan

    2011-01-01

    Kindlin proteins represent a newly discovered family of evolutionarily conserved FERM domain-containing proteins. This family includes three highly conserved proteins: Kindlin-1, Kindlin-2 and Kindlin-3. All three Kindlin proteins are associated with focal adhesions and are involved in integrin activation. The FERM domain of each Kindlin is bipartite and plays a key role in integrin activation. We herein explore for the first time the evolutionary history of these proteins. The phylogeny of the Kindlins suggests a single ancestral Kindlin protein present in even the earliest metazoan ie, hydra. This protein then underwent duplication events in insects and also experienced genome duplication in vertebrates, leading to the Kindlin family. A comparative study of the Kindlin paralogs showed that Kindlin-2 is the slowest evolving protein among the three family members. The analysis of synonymous and non-synonymous substitutions in orthologous Kindlin sequences in different species showed that all three Kindlins have been evolving under the influence of purifying selection. The expression pattern of Kindlins along with phylogenetic studies supports the subfunctionalization model of gene duplication.

  9. Do homoiologies impede phylogenetic analyses of the fossil hominids? An assessment based on extant papionin craniodental morphology.

    PubMed

    Lycett, Stephen J; Collard, Mark

    2005-11-01

    Homoiologies are phylogenetically misleading resemblances among taxa that can be attributed to phenotypic plasticity. Recently, it has been claimed that homoiologies are widespread in the hominid skull, especially in those regions affected by mastication-related strain, and that their prevalence is a major reason why researchers have so far been unable to obtain a reliable estimate of hominid phylogeny. To evaluate this "homoiology hypothesis", we carried out analyses of a group of extant primates for which a robust molecular phylogeny is available-the papionins. We compiled a craniometric dataset from measurements that differ in their susceptibility to mastication-related strain according to developmental considerations and experimental evidence. We used the coefficient of variation and analysis of variance with post hoc least significant difference comparisons in order to evaluate the variability of the measurements. The prediction from the homoiology hypothesis was that dental measurements, which do not remodel in response to strain, should be less variable than low-to-moderate-strain measurements, and that the latter should be less variable than high-strain measurements. We then performed phylogenetic analyses using characters derived from the measurements and compared the resulting phylogenetic hypotheses to the group's consensus molecular phylogeny. The prediction was that, if the homoiology hypothesis is correct, the agreement between the craniometric and molecular phylogenies would be best in the analyses of dental characters, intermediate in the analyses of low-to-moderate-strain characters, and least in the analyses of high-strain characters. The results of this study support the suggestion that mastication-related mechanical loading can result in variation in hominid cranial characters. However, they do not support the hypothesis that homoiology is a major reason why phylogenetic analyses of hominid crania have so far yielded conflicting and weakly

  10. Phylogenetics.

    PubMed

    Sleator, Roy D

    2011-04-01

    The recent rapid expansion in the DNA and protein databases, arising from large-scale genomic and metagenomic sequence projects, has forced significant development in the field of phylogenetics: the study of the evolutionary relatedness of the planet's inhabitants. Advances in phylogenetic analysis have greatly transformed our view of the landscape of evolutionary biology, transcending the view of the tree of life that has shaped evolutionary theory since Darwinian times. Indeed, modern phylogenetic analysis no longer focuses on the restricted Darwinian-Mendelian model of vertical gene transfer, but must also consider the significant degree of lateral gene transfer, which connects and shapes almost all living things. Herein, I review the major tree-building methods, their strengths, weaknesses and future prospects. PMID:21249334

  11. Molecular phylogenetic analysis of nuclear genes suggests a Cenozoic over-water dispersal origin for the Cuban solenodon.

    PubMed

    Sato, Jun J; Ohdachi, Satoshi D; Echenique-Diaz, Lazaro M; Borroto-Páez, Rafael; Begué-Quiala, Gerardo; Delgado-Labañino, Jorge L; Gámez-Díez, Jorgelino; Alvarez-Lemus, José; Nguyen, Son Truong; Yamaguchi, Nobuyuki; Kita, Masaki

    2016-01-01

    The Cuban solenodon (Solenodon cubanus) is one of the most enigmatic mammals and is an extremely rare species with a distribution limited to a small part of the island of Cuba. Despite its rarity, in 2012 seven individuals of S. cubanus were captured and sampled successfully for DNA analysis, providing new insights into the evolutionary origin of this species and into the origins of the Caribbean fauna, which remain controversial. We conducted molecular phylogenetic analyses of five nuclear genes (Apob, Atp7a, Bdnf, Brca1 and Rag1; total, 4,602 bp) from 35 species of the mammalian order Eulipotyphla. Based on Bayesian relaxed molecular clock analyses, the family Solenodontidae diverged from other eulipotyphlan in the Paleocene, after the bolide impact on the Yucatan Peninsula, and S. cubanus diverged from the Hispaniolan solenodon (S. paradoxus) in the Early Pliocene. The strikingly recent divergence time estimates suggest that S. cubanus and its ancestral lineage originated via over-water dispersal rather than vicariance events, as had previously been hypothesised. PMID:27498968

  12. Molecular phylogenetic analysis of nuclear genes suggests a Cenozoic over-water dispersal origin for the Cuban solenodon.

    PubMed

    Sato, Jun J; Ohdachi, Satoshi D; Echenique-Diaz, Lazaro M; Borroto-Páez, Rafael; Begué-Quiala, Gerardo; Delgado-Labañino, Jorge L; Gámez-Díez, Jorgelino; Alvarez-Lemus, José; Nguyen, Son Truong; Yamaguchi, Nobuyuki; Kita, Masaki

    2016-08-08

    The Cuban solenodon (Solenodon cubanus) is one of the most enigmatic mammals and is an extremely rare species with a distribution limited to a small part of the island of Cuba. Despite its rarity, in 2012 seven individuals of S. cubanus were captured and sampled successfully for DNA analysis, providing new insights into the evolutionary origin of this species and into the origins of the Caribbean fauna, which remain controversial. We conducted molecular phylogenetic analyses of five nuclear genes (Apob, Atp7a, Bdnf, Brca1 and Rag1; total, 4,602 bp) from 35 species of the mammalian order Eulipotyphla. Based on Bayesian relaxed molecular clock analyses, the family Solenodontidae diverged from other eulipotyphlan in the Paleocene, after the bolide impact on the Yucatan Peninsula, and S. cubanus diverged from the Hispaniolan solenodon (S. paradoxus) in the Early Pliocene. The strikingly recent divergence time estimates suggest that S. cubanus and its ancestral lineage originated via over-water dispersal rather than vicariance events, as had previously been hypothesised.

  13. Molecular phylogenetic analysis of nuclear genes suggests a Cenozoic over-water dispersal origin for the Cuban solenodon

    PubMed Central

    Sato, Jun J.; Ohdachi, Satoshi D.; Echenique-Diaz, Lazaro M.; Borroto-Páez, Rafael; Begué-Quiala, Gerardo; Delgado-Labañino, Jorge L.; Gámez-Díez, Jorgelino; Alvarez-Lemus, José; Nguyen, Son Truong; Yamaguchi, Nobuyuki; Kita, Masaki

    2016-01-01

    The Cuban solenodon (Solenodon cubanus) is one of the most enigmatic mammals and is an extremely rare species with a distribution limited to a small part of the island of Cuba. Despite its rarity, in 2012 seven individuals of S. cubanus were captured and sampled successfully for DNA analysis, providing new insights into the evolutionary origin of this species and into the origins of the Caribbean fauna, which remain controversial. We conducted molecular phylogenetic analyses of five nuclear genes (Apob, Atp7a, Bdnf, Brca1 and Rag1; total, 4,602 bp) from 35 species of the mammalian order Eulipotyphla. Based on Bayesian relaxed molecular clock analyses, the family Solenodontidae diverged from other eulipotyphlan in the Paleocene, after the bolide impact on the Yucatan Peninsula, and S. cubanus diverged from the Hispaniolan solenodon (S. paradoxus) in the Early Pliocene. The strikingly recent divergence time estimates suggest that S. cubanus and its ancestral lineage originated via over-water dispersal rather than vicariance events, as had previously been hypothesised. PMID:27498968

  14. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients.

    PubMed

    Fierer, Noah; Lauber, Christian L; Ramirez, Kelly S; Zaneveld, Jesse; Bradford, Mark A; Knight, Rob

    2012-05-01

    Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.

  15. In silico identification of Bell pepper endornavirus from pepper transcriptomes and their phylogenetic and recombination analyses.

    PubMed

    Jo, Yeonhwa; Choi, Hoseong; Yoon, Ju-Yeon; Choi, Seung-Kook; Cho, Won Kyong

    2016-01-10

    Here, we identified eight Bell pepper endornavirus (BPEV) isolates from nine different pepper transcriptomes. BPEV was present with low copy numbers ranging from 0.01% to 0.18% in the host transcriptome. Phylogenetic identified two different groups of BPEV isolates. Sequence alignment of the five BPEV genomes revealed conservation of the 5' and 3' untranslated regions. Recombination analysis identified two possible recombinant events in the isolate Yolo Wonder. Single nucleotide variation profiles revealed the presence of BPEV variants within a single pepper cultivar. Taken together, this study provides phylogenetic and recombination analyses of the genus Endornavirus using pepper transcriptome data.

  16. In silico identification of Bell pepper endornavirus from pepper transcriptomes and their phylogenetic and recombination analyses.

    PubMed

    Jo, Yeonhwa; Choi, Hoseong; Yoon, Ju-Yeon; Choi, Seung-Kook; Cho, Won Kyong

    2016-01-10

    Here, we identified eight Bell pepper endornavirus (BPEV) isolates from nine different pepper transcriptomes. BPEV was present with low copy numbers ranging from 0.01% to 0.18% in the host transcriptome. Phylogenetic identified two different groups of BPEV isolates. Sequence alignment of the five BPEV genomes revealed conservation of the 5' and 3' untranslated regions. Recombination analysis identified two possible recombinant events in the isolate Yolo Wonder. Single nucleotide variation profiles revealed the presence of BPEV variants within a single pepper cultivar. Taken together, this study provides phylogenetic and recombination analyses of the genus Endornavirus using pepper transcriptome data. PMID:26410036

  17. Phylogenetic analysis of of Sarcocystis nesbitti (Coccidia: Sarcocystidae) suggests a snake as its probable definitive host

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sarcocystis nesbitti was first described by Mandour in 1969 from rhesus monkey muscle. Its definitive host remains unknown. 18SrRNA gene of Sarcocystis nesbitti was amplified, sequenced, and subjected to phylogenetic analysis. Among those congeners available for comparison, it shares closest affinit...

  18. Complete genome of a European hepatitis C virus subtype 1g isolate: phylogenetic and genetic analyses

    PubMed Central

    Bracho, Maria A; Saludes, Verónica; Martró, Elisa; Bargalló, Ana; González-Candelas, Fernando; Ausina, Vicent

    2008-01-01

    Background Hepatitis C virus isolates have been classified into six main genotypes and a variable number of subtypes within each genotype, mainly based on phylogenetic analysis. Analyses of the genetic relationship among genotypes and subtypes are more reliable when complete genome sequences (or at least the full coding region) are used; however, so far 31 of 80 confirmed or proposed subtypes have at least one complete genome available. Of these, 20 correspond to confirmed subtypes of epidemic interest. Results We present and analyse the first complete genome sequence of a HCV subtype 1g isolate. Phylogenetic and genetic distance analyses reveal that HCV-1g is the most divergent subtype among the HCV-1 confirmed subtypes. Potential genomic recombination events between genotypes or subtype 1 genomes were ruled out. We demonstrate phylogenetic congruence of previously deposited partial sequences of HCV-1g with respect to our sequence. Conclusion In light of this, we propose changing the current status of its subtype-specific designation from provisional to confirmed. PMID:18533988

  19. Estimating the Effective Sample Size of Tree Topologies from Bayesian Phylogenetic Analyses

    PubMed Central

    Lanfear, Robert; Hua, Xia; Warren, Dan L.

    2016-01-01

    Bayesian phylogenetic analyses estimate posterior distributions of phylogenetic tree topologies and other parameters using Markov chain Monte Carlo (MCMC) methods. Before making inferences from these distributions, it is important to assess their adequacy. To this end, the effective sample size (ESS) estimates how many truly independent samples of a given parameter the output of the MCMC represents. The ESS of a parameter is frequently much lower than the number of samples taken from the MCMC because sequential samples from the chain can be non-independent due to autocorrelation. Typically, phylogeneticists use a rule of thumb that the ESS of all parameters should be greater than 200. However, we have no method to calculate an ESS of tree topology samples, despite the fact that the tree topology is often the parameter of primary interest and is almost always central to the estimation of other parameters. That is, we lack a method to determine whether we have adequately sampled one of the most important parameters in our analyses. In this study, we address this problem by developing methods to estimate the ESS for tree topologies. We combine these methods with two new diagnostic plots for assessing posterior samples of tree topologies, and compare their performance on simulated and empirical data sets. Combined, the methods we present provide new ways to assess the mixing and convergence of phylogenetic tree topologies in Bayesian MCMC analyses. PMID:27435794

  20. Data on phylogenetic analyses of gazelles (genus Gazella) based on mitochondrial and nuclear intron markers

    PubMed Central

    Lerp, Hannes; Klaus, Sebastian; Allgöwer, Stefanie; Wronski, Torsten; Pfenninger, Markus; Plath, Martin

    2016-01-01

    The data provided is related to the article “Phylogenetic analyses of gazelles reveal repeated transitions of key ecological traits and provide novel insights into the origin of the genus Gazella” [1]. The data is based on 48 tissue samples of all nine extant species of the genus Gazella, namely Gazella gazella, Gazella arabica, Gazella bennettii, Gazella cuvieri, Gazella dorcas, Gazella leptoceros, Gazella marica, Gazella spekei, and Gazella subgutturosa and four related taxa (Saiga tatarica, Antidorcas marsupialis, Antilope cervicapra and Eudorcas rufifrons). It comprises alignments of sequences of a cytochrome b data set and of six nuclear intron markers. For the latter new primers were designed based on cattle and sheep genomes. Based on these alignments phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood methods. Furthermore, ancestral character states (inferred with BayesTraits 1.0) and ancestral ranges based on a Dispersal-Extinction-Cladogenesis model were estimated and results׳ files were stored within this article. PMID:27054158

  1. Data on phylogenetic analyses of gazelles (genus Gazella) based on mitochondrial and nuclear intron markers.

    PubMed

    Lerp, Hannes; Klaus, Sebastian; Allgöwer, Stefanie; Wronski, Torsten; Pfenninger, Markus; Plath, Martin

    2016-06-01

    The data provided is related to the article "Phylogenetic analyses of gazelles reveal repeated transitions of key ecological traits and provide novel insights into the origin of the genus Gazella" [1]. The data is based on 48 tissue samples of all nine extant species of the genus Gazella, namely Gazella gazella, Gazella arabica, Gazella bennettii, Gazella cuvieri, Gazella dorcas, Gazella leptoceros, Gazella marica, Gazella spekei, and Gazella subgutturosa and four related taxa (Saiga tatarica, Antidorcas marsupialis, Antilope cervicapra and Eudorcas rufifrons). It comprises alignments of sequences of a cytochrome b data set and of six nuclear intron markers. For the latter new primers were designed based on cattle and sheep genomes. Based on these alignments phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood methods. Furthermore, ancestral character states (inferred with BayesTraits 1.0) and ancestral ranges based on a Dispersal-Extinction-Cladogenesis model were estimated and results׳ files were stored within this article. PMID:27054158

  2. Morphological, molecular and phylogenetic analyses of the spirurid nematode Stegophorus macronectes (Johnston & Mawson, 1942).

    PubMed

    Vidal, V; Ortiz, J; Diaz, J I; Zafrilla, B; Bonete, M J; Ruiz De Ybañez, M R; Palacios, M J; Benzal, J; Valera, F; De La Cruz, C; Motas, M; Bautista, V; Machordom, A; Barbosa, A

    2016-03-01

    Stegophorus macronectes (Johnston & Mawson, 1942) is a gastrointestinal parasite found in Antarctic seabirds. The original description of the species, which was based only on females, is poor and fragmented with some unclear diagnostic characters. This study provides new morphometric and molecular data on this previously poorly described parasite. Nuclear rDNA sequences (18S, 5.8S, 28S and internal transcribed spacer (ITS) regions) were isolated from S. macronectes specimens collected from the chinstrap penguin Pygoscelis antarctica Forster on Deception Island, Antarctica. Using 18S rDNA sequences, phylogenetic analyses (maximum likelihood, maximum parsimony and Bayesian inference) of the order Spirurida were performed to determine the phylogenetic location of this species. Primer pairs of the ITS regions were designed for genus-level identification of specimens, regardless of their cycle, as an alternative to coprological methods. The utility of this molecular method for identification of morphologically altered specimens is also discussed. PMID:25871788

  3. Combined molecular and morphological phylogenetic analyses of the New Zealand wolf spider genus Anoteropsis (Araneae: Lycosidae).

    PubMed

    Vink, Cor J; Paterson, Adrian M

    2003-09-01

    Datasets from the mitochondrial gene regions NADH dehydrogenase subunit I (ND1) and cytochrome c oxidase subunit I (COI) of the 20 species in the New Zealand wolf spider (Lycosidae) genus Anoteropsis were generated. Sequence data were phylogenetically analysed using parsimony and maximum likelihood analyses. The phylogenies generated from the ND1 and COI sequence data and a previously generated morphological dataset were significantly congruent (p<0.001). Sequence data were combined with morphological data and phylogenetically analysed using parsimony. The ND1 region sequenced included part of tRNA(Leu(CUN)), which appears to have an unstable amino-acyl arm and no TpsiC arm in lycosids. Analyses supported the existence of five species groups within Anoteropsis and the monophyly of species represented by multiple samples. A radiation of Anoteropsis species within the last five million years is inferred from the ND1 and COI likelihood phylograms, habitat and geological data, which also indicates that Anoteropsis arrived in New Zealand some time after it separated from Gondwana.

  4. The complete mitochondrial genomes of four cockroaches (Insecta: Blattodea) and phylogenetic analyses within cockroaches.

    PubMed

    Cheng, Xue-Fang; Zhang, Le-Ping; Yu, Dan-Na; Storey, Kenneth B; Zhang, Jia-Yong

    2016-07-15

    Three complete mitochondrial genomes of Blaberidae (Insecta: Blattodea) (Gromphadorhina portentosa, Panchlora nivea, Blaptica dubia) and one complete mt genome of Blattidae (Insecta: Blattodea) (Shelfordella lateralis) were sequenced to further understand the characteristics of cockroach mitogenomes and reconstruct the phylogenetic relationship of Blattodea. The gene order and orientation of these four cockroach genomes were similar to known cockroach mt genomes, and contained 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. The mt genomes of Blattodea exhibited a characteristics of a high A+T composition (70.7%-74.3%) and dominant usage of the TAA stop codon. The AT content of the whole mt genome, PCGs and total tRNAs in G. portentosa was the lowest in known cockroaches. The presence of a 71-bp intergenic spacer region between trnQ and trnM was a unique feature in B. dubia, but absent in other cockroaches, which can be explained by the duplication/random loss model. Based on the nucleotide and amino acid datasets of the 13 PCGs genes, neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and bayesian inference (BI) analyses were used to rebuild the phylogenetic relationship of cockroaches. All phylogenetic analyses consistently placed Isoptera as the sister cluster to Cryptocercidae of Blattodea. Ectobiidae and Blaberidae (Blaberoidea) formed a sister clade to Blattidae. Corydiidae is a sister clade of all the remaining cockroach species with a high value in NJ and MP analyses of nucleotide and amino acid datasets, and ML and BI analyses of the amino acid dataset.

  5. The complete mitochondrial genomes of four cockroaches (Insecta: Blattodea) and phylogenetic analyses within cockroaches.

    PubMed

    Cheng, Xue-Fang; Zhang, Le-Ping; Yu, Dan-Na; Storey, Kenneth B; Zhang, Jia-Yong

    2016-07-15

    Three complete mitochondrial genomes of Blaberidae (Insecta: Blattodea) (Gromphadorhina portentosa, Panchlora nivea, Blaptica dubia) and one complete mt genome of Blattidae (Insecta: Blattodea) (Shelfordella lateralis) were sequenced to further understand the characteristics of cockroach mitogenomes and reconstruct the phylogenetic relationship of Blattodea. The gene order and orientation of these four cockroach genomes were similar to known cockroach mt genomes, and contained 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. The mt genomes of Blattodea exhibited a characteristics of a high A+T composition (70.7%-74.3%) and dominant usage of the TAA stop codon. The AT content of the whole mt genome, PCGs and total tRNAs in G. portentosa was the lowest in known cockroaches. The presence of a 71-bp intergenic spacer region between trnQ and trnM was a unique feature in B. dubia, but absent in other cockroaches, which can be explained by the duplication/random loss model. Based on the nucleotide and amino acid datasets of the 13 PCGs genes, neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and bayesian inference (BI) analyses were used to rebuild the phylogenetic relationship of cockroaches. All phylogenetic analyses consistently placed Isoptera as the sister cluster to Cryptocercidae of Blattodea. Ectobiidae and Blaberidae (Blaberoidea) formed a sister clade to Blattidae. Corydiidae is a sister clade of all the remaining cockroach species with a high value in NJ and MP analyses of nucleotide and amino acid datasets, and ML and BI analyses of the amino acid dataset. PMID:27045773

  6. Phylogenetic Findings Suggest Possible New Habitat and Routes of Infection of Human Eumyctoma

    PubMed Central

    de Hoog, G. Sybren; Ahmed, Sarah A.; Najafzadeh, Mohammad J.; Sutton, Deanna A.; Keisari, Maryam Saradeghi; Fahal, Ahmed H.; Eberhardt, Ursala; Verkleij, Gerard J.; Xin, Lian; Stielow, Benjamin; van de Sande, Wendy W. J.

    2013-01-01

    Eumycetoma is a traumatic fungal infection in tropical and subtropical areas that may lead to severe disability. Madurella mycetomatis is one of the prevalent etiologic agents in arid Northeastern Africa. The source of infection has not been clarified. Subcutaneous inoculation from plant thorns has been hypothesized, but attempts to detect the fungus in relevant material have remained unsuccessful. The present study aims to find clues to reveal the natural habitat of Madurella species using a phylogenetic approach, i.e. by comparison of neighboring taxa with known ecology. Four species of Madurella were included in a large data set of species of Chaetomium, Chaetomidium, Thielavia, and Papulaspora (n = 128) using sequences of the universal fungal barcode gene rDNA ITS and the partial LSU gene sequence. Our study demonstrates that Madurella species are nested within the Chaetomiaceae, a family of fungi that mainly inhabit animal dung, enriched soil, and indoor environments. We hypothesize that cattle dung, ubiquitously present in rural East Africa, plays a significant role in the ecology of Madurella. If cow dung is an essential factor in inoculation by Madurella, preventative measures may involve the use of appropriate footwear in addition to restructuring of villages to reduce the frequency of contact with etiologic agents of mycetoma. On the other hand, the Chaetomiaceae possess a hidden clinical potential which needs to be explored. PMID:23696914

  7. Deceptive desmas: molecular phylogenetics suggests a new classification and uncovers convergent evolution of lithistid demosponges.

    PubMed

    Schuster, Astrid; Erpenbeck, Dirk; Pisera, Andrzej; Hooper, John; Bryce, Monika; Fromont, Jane; Wörheide, Gert

    2015-01-01

    Reconciling the fossil record with molecular phylogenies to enhance the understanding of animal evolution is a challenging task, especially for taxa with a mostly poor fossil record, such as sponges (Porifera). 'Lithistida', a polyphyletic group of recent and fossil sponges, are an exception as they provide the richest fossil record among demosponges. Lithistids, currently encompassing 13 families, 41 genera and >300 recent species, are defined by the common possession of peculiar siliceous spicules (desmas) that characteristically form rigid articulated skeletons. Their phylogenetic relationships are to a large extent unresolved and there has been no (taxonomically) comprehensive analysis to formally reallocate lithistid taxa to their closest relatives. This study, based on the most comprehensive molecular and morphological investigation of 'lithistid' demosponges to date, corroborates some previous weakly-supported hypotheses, and provides novel insights into the evolutionary relationships of the previous 'order Lithistida'. Based on molecular data (partial mtDNA CO1 and 28S rDNA sequences), we show that 8 out of 13 'Lithistida' families belong to the order Astrophorida, whereas Scleritodermidae and Siphonidiidae form a separate monophyletic clade within Tetractinellida. Most lithistid astrophorids are dispersed between different clades of the Astrophorida and we propose to formally reallocate them, respectively. Corallistidae, Theonellidae and Phymatellidae are monophyletic, whereas the families Pleromidae and Scleritodermidae are polyphyletic. Family Desmanthidae is polyphyletic and groups within Halichondriidae--we formally propose a reallocation. The sister group relationship of the family Vetulinidae to Spongillida is confirmed and we propose here for the first time to include Vetulina into a new Order Sphaerocladina. Megascleres and microscleres possibly evolved and/or were lost several times independently in different 'lithistid' taxa, and microscleres

  8. Deceptive Desmas: Molecular Phylogenetics Suggests a New Classification and Uncovers Convergent Evolution of Lithistid Demosponges

    PubMed Central

    Schuster, Astrid; Erpenbeck, Dirk; Pisera, Andrzej; Hooper, John; Bryce, Monika; Fromont, Jane; Wörheide, Gert

    2015-01-01

    Reconciling the fossil record with molecular phylogenies to enhance the understanding of animal evolution is a challenging task, especially for taxa with a mostly poor fossil record, such as sponges (Porifera). ‘Lithistida’, a polyphyletic group of recent and fossil sponges, are an exception as they provide the richest fossil record among demosponges. Lithistids, currently encompassing 13 families, 41 genera and >300 recent species, are defined by the common possession of peculiar siliceous spicules (desmas) that characteristically form rigid articulated skeletons. Their phylogenetic relationships are to a large extent unresolved and there has been no (taxonomically) comprehensive analysis to formally reallocate lithistid taxa to their closest relatives. This study, based on the most comprehensive molecular and morphological investigation of ‘lithistid’ demosponges to date, corroborates some previous weakly-supported hypotheses, and provides novel insights into the evolutionary relationships of the previous ‘order Lithistida’. Based on molecular data (partial mtDNA CO1 and 28S rDNA sequences), we show that 8 out of 13 ‘Lithistida’ families belong to the order Astrophorida, whereas Scleritodermidae and Siphonidiidae form a separate monophyletic clade within Tetractinellida. Most lithistid astrophorids are dispersed between different clades of the Astrophorida and we propose to formally reallocate them, respectively. Corallistidae, Theonellidae and Phymatellidae are monophyletic, whereas the families Pleromidae and Scleritodermidae are polyphyletic. Family Desmanthidae is polyphyletic and groups within Halichondriidae – we formally propose a reallocation. The sister group relationship of the family Vetulinidae to Spongillida is confirmed and we propose here for the first time to include Vetulina into a new Order Sphaerocladina. Megascleres and microscleres possibly evolved and/or were lost several times independently in different

  9. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

    PubMed Central

    Capella-Gutiérrez, Salvador; Silla-Martínez, José M.; Gabaldón, Toni

    2009-01-01

    Summary: Multiple sequence alignments are central to many areas of bioinformatics. It has been shown that the removal of poorly aligned regions from an alignment increases the quality of subsequent analyses. Such an alignment trimming phase is complicated in large-scale phylogenetic analyses that deal with thousands of alignments. Here, we present trimAl, a tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses. trimAl can consider several parameters, alone or in multiple combinations, for selecting the most reliable positions in the alignment. These include the proportion of sequences with a gap, the level of amino acid similarity and, if several alignments for the same set of sequences are provided, the level of consistency across different alignments. Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized. Availability: trimAl has been written in C++, it is portable to all platforms. trimAl is freely available for download (http://trimal.cgenomics.org) and can be used online through the Phylemon web server (http://phylemon2.bioinfo.cipf.es/). Supplementary Material is available at http://trimal.cgenomics.org/publications. Contact: tgabaldon@crg.es PMID:19505945

  10. Variability of sexual organ possession rates and phylogenetic analyses of a parthenogenetic Japanese earthworm, Amynthas vittatus (Oligochaeta: Megascolecidae).

    PubMed

    Minamiya, Yukio; Hayakawa, Hiroshi; Ohga, Kyohei; Shimano, Satoshi; Ito, Masamichi T; Fukuda, Tatsuya

    2011-01-01

    Although earthworms are hermaphroditic animals with biparental sexual reproduction, some parthenogenetic species have been found. Evolutionary trends in parthenogenetic earthworms revealed a reduction in the reproductive organs. To clarify the phylogenetic relationships of parthenogenetic earthworms with different degree of degraded reproductive organs, we conducted a morphological analysis of the reproductive organs and molecular phylogenetic analyses of Amynthas vittatus which usually degraded a part of reproductive organs. Morphological analysis revealed that almost all individuals collected around Mt. Aobayama, Sendai city of northeastern Japan, possessed male pores, while individuals collected from areas located across Hirose River did not. Phylogenetic analysis using mitochondrial DNA sequences of 48 individuals representing 20 populations indicated that almost all individuals collected around Mt. Aobayama belonged to a different lineage from the other populations collected around Sendai, and that almost all individuals collected from across Japan belonged to the latter lineage. We suggest that the difference in the male pore possession rate was caused by histories of each population, but the A. vittatus population found on Mt. Aobayama belongs to a different lineage as compared to the other Japanese populations and not the primitive population. Thus, the parthenogenetic earthworm A. vittatus has undergone at least two morphological evolutionary processes.

  11. Systematic and phylogeographical assessment of the Acanthodactylus erythrurus group (Reptilia: Lacertidae) based on phylogenetic analyses of mitochondrial and nuclear DNA.

    PubMed

    Fonseca, Miguel M; Brito, José C; Paulo, Octávio S; Carretero, Miguel A; Harris, D James

    2009-05-01

    We have used mitochondrial 12S rRNA, 16S rRNA and nuclear beta-fibrinogen (intron 7) sequences to investigate the phylogenetic and phylogeographic relationships between Acanthodactylus erythrurus group species (except for A. boueti). The phylogenetic analyses of the Acanthodactylus genus did not cluster A. guineensis and A. savignyi with the remaining species of the group (A. blanci, A. lineomaculatus and A. erythrurus). Within the A. erythrurus group, the results of the mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) showed a complex phylogeny with geographic structure, but it was not congruent with the present taxonomy. Some taxonomic units, such as A. blanci, A. lineomaculatus, A. e. atlanticus and A. e. belli did not form monophyletic genetic units. The application of a molecular clock suggested that the uplift of the Atlas Mountains in the mid-late Miocene and the reopening of the Strait of Gibraltar could be major biogeographic events responsible for the genetic differentiation in the group. Additionally, diverse micro-evolutionary patterns due to the recent contraction/expansion phases of the habitats in North Africa associated with the high dispersal capabilities of these lizards could be related to the complex phylogenetic patterns observed.

  12. Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations

    PubMed Central

    Ram Mohan, Nikhil; Fullmer, Matthew S.; Makkay, Andrea M.; Wheeler, Ryan; Ventosa, Antonio; Naor, Adit; Gogarten, J. Peter; Papke, R. Thane

    2014-01-01

    Halobacteria require high NaCl concentrations for growth and are the dominant inhabitants of hypersaline environments above 15% NaCl. They are well-documented to be highly recombinogenic, both in frequency and in the range of exchange partners. In this study, we examine the genetic and genomic variation of cultured, naturally co-occurring environmental populations of Halobacteria. Sequence data from multiple loci (~2500 bp) identified many closely and more distantly related strains belonging to the genera Halorubrum and Haloarcula. Genome fingerprinting using a random priming PCR amplification method to analyze these isolates revealed diverse banding patterns across each of the genera and surprisingly even for isolates that are identical at the nucleotide level for five protein coding sequenced loci. This variance in genome structure even between identical multilocus sequence analysis (MLSA) haplotypes indicates that accumulation of genomic variation is rapid: faster than the rate of third codon substitutions. PMID:24782838

  13. Characterization of bud emergence 46 (BEM46) protein: Sequence, structural, phylogenetic and subcellular localization analyses

    SciTech Connect

    Kumar, Abhishek; Kollath-Leiß, Krisztina; Kempken, Frank

    2013-08-30

    Highlights: •All eukaryotes have at least a single copy of a bem46 ortholog. •The catalytic triad of BEM46 is illustrated using sequence and structural analysis. •We identified indels in the conserved domain of BEM46 protein. •Localization studies of BEM46 protein were carried out using GFP-fusion tagging. -- Abstract: The bud emergence 46 (BEM46) protein from Neurospora crassa belongs to the α/β-hydrolase superfamily. Recently, we have reported that the BEM46 protein is localized in the perinuclear ER and also forms spots close by the plasma membrane. The protein appears to be required for cell type-specific polarity formation in N. crassa. Furthermore, initial studies suggested that the BEM46 amino acid sequence is conserved in eukaryotes and is considered to be one of the widespread conserved “known unknown” eukaryotic genes. This warrants for a comprehensive phylogenetic analysis of this superfamily to unravel origin and molecular evolution of these genes in different eukaryotes. Herein, we observe that all eukaryotes have at least a single copy of a bem46 ortholog. Upon scanning of these proteins in various genomes, we find that there are expansions leading into several paralogs in vertebrates. Usingcomparative genomic analyses, we identified insertion/deletions (indels) in the conserved domain of BEM46 protein, which allow to differentiate fungal classes such as ascomycetes from basidiomycetes. We also find that exonic indels are able to differentiate BEM46 homologs of different eukaryotic lineage. Furthermore, we unravel that BEM46 protein from N. crassa possess a novel endoplasmic-retention signal (PEKK) using GFP-fusion tagging experiments. We propose that three residues namely a serine 188S, a histidine 292H and an aspartic acid 262D are most critical residues, forming a catalytic triad in BEM46 protein from N. crassa. We carried out a comprehensive study on bem46 genes from a molecular evolution perspective with combination of functional

  14. Novel evolutionary lineages in Labeobarbus (Cypriniformes; Cyprinidae) based on phylogenetic analyses of mtDNA sequences.

    PubMed

    Beshera, Kebede A; Harris, Phillip M; Mayden, Richard L

    2016-01-01

    Phylogenetic relationships within Labeobarbus, the large-sized hexaploid cyprinids, were examined using cytochrome b gene sequences from a broad range of geographic localities and multiple taxa. Maximum likelihood and Bayesian methods revealed novel lineages from previously unsampled drainages in central (Congo River), eastern (Genale River) and southeastern (Revue and Mussapa Grande rivers) Africa. Relationships of some species of Varicorhinus in Africa (excluding 'V.' maroccanus) render Labeobarbus as paraphyletic. 'Varicorhinus' beso, 'V.' jubae, 'V.' mariae, 'V.' nelspruitensis, and 'V.' steindachneri are transferred to Labeobarbus. Bayesian estimation of time to most recent common ancestor suggested that Labeobarbus originated in the Late Miocene while lineage diversification began during the Late Miocene-Early Pliocene and continued to the late Pleistocene. The relationships presented herein provide phylogenetic resolution within Labeobarbus and advances our knowledge of genetic diversity within the lineage as well as provides some interesting insight into the hydrographic and geologic history of Africa. PMID:27394501

  15. Molecular and Morphological Analyses Reveal Phylogenetic Relationships of Stingrays Focusing on the Family Dasyatidae (Myliobatiformes)

    PubMed Central

    Lim, Kean Chong; Lim, Phaik-Eem; Chong, Ving Ching; Loh, Kar-Hoe

    2015-01-01

    Elucidating the phylogenetic relationships of the current but problematic Dasyatidae (Order Myliobatiformes) was the first priority of the current study. Here, we studied three molecular gene markers of 43 species (COI gene), 33 species (ND2 gene) and 34 species (RAG1 gene) of stingrays to draft out the phylogenetic tree of the order. Nine character states were identified and used to confirm the molecularly constructed phylogenetic trees. Eight or more clades (at different hierarchical level) were identified for COI, ND2 and RAG1 genes in the Myliobatiformes including four clades containing members of the present Dasyatidae, thus rendering the latter non-monophyletic. The uncorrected p-distance between these four ‘Dasytidae’ clades when compared to the distance between formally known families confirmed that these four clades should be elevated to four separate families. We suggest a revision of the present classification, retaining the Dasyatidae (Dasyatis and Taeniurops species) but adding three new families namely, Neotrygonidae (Neotrygon and Taeniura species), Himanturidae (Himantura species) and Pastinachidae (Pastinachus species). Our result indicated the need to further review the classification of Dasyatis microps. By resolving the non-monophyletic problem, the suite of nine character states enables the natural classification of the Myliobatiformes into at least thirteen families based on morphology. PMID:25867639

  16. The mitochondrial genome of Atrijuglans hetaohei Yang (Lepidoptera: Gelechioidea) and related phylogenetic analyses.

    PubMed

    Wang, Qiqi; Zhang, Zhengqing; Tang, Guanghui

    2016-04-25

    Complete mitochondrial genome sequences are of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In this study, the complete mitochondrial genome of Atrijuglans hetaohei Yang is sequenced and analyzed, which is 15,379bp in length (GenBank: KT581634) and contains a typical set of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a non-coding region (control region). Except for cox1 gene that is initiated by CGA codon, all protein-coding genes start with ATN codons and end with the stop codon T, TA or TAA. All tRNAs have a typical clover-leaf secondary structure, except for trnS1, of which the DHU arm could not form a stable stem-loop structure. The secondary structure of rrnL and rrnS consists of 49 helices and 33 helices, respectively. Phylogenetic analyses of the complete mitochondrial genome sequences and of the amino acid sequences for 13 mitochondrial protein-coding genes among related species support the view that A. hetaohei is more closely related to the Gelechioidea than Yponomeutoidea. This result is consistent with a previous classification based on morphology. PMID:26800782

  17. The mitochondrial genome of Atrijuglans hetaohei Yang (Lepidoptera: Gelechioidea) and related phylogenetic analyses.

    PubMed

    Wang, Qiqi; Zhang, Zhengqing; Tang, Guanghui

    2016-04-25

    Complete mitochondrial genome sequences are of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In this study, the complete mitochondrial genome of Atrijuglans hetaohei Yang is sequenced and analyzed, which is 15,379bp in length (GenBank: KT581634) and contains a typical set of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a non-coding region (control region). Except for cox1 gene that is initiated by CGA codon, all protein-coding genes start with ATN codons and end with the stop codon T, TA or TAA. All tRNAs have a typical clover-leaf secondary structure, except for trnS1, of which the DHU arm could not form a stable stem-loop structure. The secondary structure of rrnL and rrnS consists of 49 helices and 33 helices, respectively. Phylogenetic analyses of the complete mitochondrial genome sequences and of the amino acid sequences for 13 mitochondrial protein-coding genes among related species support the view that A. hetaohei is more closely related to the Gelechioidea than Yponomeutoidea. This result is consistent with a previous classification based on morphology.

  18. Comparative phylogenetic analyses uncover the ancient roots of Indo-European folktales

    PubMed Central

    da Silva, Sara Graça; Tehrani, Jamshid J.

    2016-01-01

    Ancient population expansions and dispersals often leave enduring signatures in the cultural traditions of their descendants, as well as in their genes and languages. The international folktale record has long been regarded as a rich context in which to explore these legacies. To date, investigations in this area have been complicated by a lack of historical data and the impact of more recent waves of diffusion. In this study, we introduce new methods for tackling these problems by applying comparative phylogenetic methods and autologistic modelling to analyse the relationships between folktales, population histories and geographical distances in Indo-European-speaking societies. We find strong correlations between the distributions of a number of folktales and phylogenetic, but not spatial, associations among populations that are consistent with vertical processes of cultural inheritance. Moreover, we show that these oral traditions probably originated long before the emergence of the literary record, and find evidence that one tale (‘The Smith and the Devil’) can be traced back to the Bronze Age. On a broader level, the kinds of stories told in ancestral societies can provide important insights into their culture, furnishing new perspectives on linguistic, genetic and archaeological reconstructions of human prehistory. PMID:26909191

  19. Comparative phylogenetic analyses uncover the ancient roots of Indo-European folktales.

    PubMed

    da Silva, Sara Graça; Tehrani, Jamshid J

    2016-01-01

    Ancient population expansions and dispersals often leave enduring signatures in the cultural traditions of their descendants, as well as in their genes and languages. The international folktale record has long been regarded as a rich context in which to explore these legacies. To date, investigations in this area have been complicated by a lack of historical data and the impact of more recent waves of diffusion. In this study, we introduce new methods for tackling these problems by applying comparative phylogenetic methods and autologistic modelling to analyse the relationships between folktales, population histories and geographical distances in Indo-European-speaking societies. We find strong correlations between the distributions of a number of folktales and phylogenetic, but not spatial, associations among populations that are consistent with vertical processes of cultural inheritance. Moreover, we show that these oral traditions probably originated long before the emergence of the literary record, and find evidence that one tale ('The Smith and the Devil') can be traced back to the Bronze Age. On a broader level, the kinds of stories told in ancestral societies can provide important insights into their culture, furnishing new perspectives on linguistic, genetic and archaeological reconstructions of human prehistory. PMID:26909191

  20. Characterization of the mitochondrial genome of the Malabar trevally Carangoides malabaricus and related phylogenetic analyses.

    PubMed

    Li, Min; Huang, Zirong; Chen, Zuozhi

    2016-01-01

    The Malabar trevally Carangoides malabaricus is a widely distributed inshore fish species and commercially important in some tropical regions. This study presented the complete mitochondrial genome of C. malabaricus as well as its phylogenetic position in Carangidae. The entire sequence was 16,561 bp in length, including the typical structure of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, 1 control regions and 1 L-strand replication origin. The arrangement of the genes was in line with other teleosts. The genome was composed of 29.6% C, 27.8% A, 26.2% T and 16.4% G, showing an obvious anti G bias. Phylogenetic analyses using the concatenated sequence of the protein-coding genes showed similar results in the Neighbour-Joining and Bayesian inference trees. Three clades were formed as Subfamilies Caranginae, Seriolinae and Trachinotinae in Carangidae based on the current dataset. C. malabaricus was most closely related to the species in the same genus.

  1. Geomicrobiology of Hydrothermal Vents in Yellowstone Lake: Phylogenetic and Functional Analysis suggest Importance of Geochemistry (Invited)

    NASA Astrophysics Data System (ADS)

    Inskeep, W. P.; Macur, R.; Jay, Z.; Clingenpeel, S.; Tenney, A.; Lavalvo, D.; Shanks, W. C.; McDermott, T.; Kan, J.; Gorby, Y.; Morgan, L. A.; Yooseph, S.; Varley, J.; Nealson, K.

    2010-12-01

    outflow channels of YNP. Analysis of functional genes present in the consensus metagenome sequence representing these populations indicate metabolic potential for oxidation of reduced sulfur and hydrogen, both of which are present at high concentrations in these vent ecosystems. Metagenome sequence of biomass associated with sediments from hydrothermal vents at Mary Bay (50 m depth) suggest greater archaeal and bacterial diversity in this environment, which may be due to higher concentrations of hydrogen, iron, and manganese measured in these environments. Results from metagenome sequence and modest 16S rRNA gene surveys from hydrothermal vent biomass indicate that several groups of novel thermophilic archaea inhabit these sites, and in many cases, are represented by organisms not found in YNP terrestrial geothermal environments that have been characterized to date. The hydrothermal vents from Inflated Plain and West Thumb indicate a linkage between various geochemical attributes (sulfide, hydrogen) and the metabolic potential associated with dominant Aquificales populations present in these communities.

  2. Phylogenetic analyses of chikungunya virus among travelers in Rio de Janeiro, Brazil, 2014-2015

    PubMed Central

    Conteville, Liliane Costa; Zanella, Louise; Marín, Michel Abanto; de Filippis, Ana Maria Bispo; Nogueira, Rita Maria Ribeiro; Vicente, Ana Carolina Paulo; de Mendonça, Marcos César Lima

    2016-01-01

    Chikungunya virus (CHIKV) is a mosquito-borne pathogen that emerged in Brazil by late 2014. In the country, two CHIKV foci characterized by the East/Central/South Africa and Asian genotypes, were established in North and Northeast regions. We characterized, by phylogenetic analyses of full and partial genomes, CHIKV from Rio de Janeiro state (2014-2015). These CHIKV strains belong to the Asian genotype, which is the determinant of the current Northern Brazilian focus, even though the genome sequence presents particular single nucleotide variations. This study provides the first genetic characterisation of CHIKV in Rio de Janeiro and highlights the potential impact of human mobility in the spread of an arthropod-borne virus. PMID:27120007

  3. Phylogenetic analyses of chikungunya virus among travelers in Rio de Janeiro, Brazil, 2014-2015.

    PubMed

    Conteville, Liliane Costa; Zanella, Louise; Marín, Michel Abanto; Filippis, Ana Maria Bispo de; Nogueira, Rita Maria Ribeiro; Vicente, Ana Carolina Paulo; Mendonça, Marcos César Lima de

    2016-05-01

    Chikungunya virus (CHIKV) is a mosquito-borne pathogen that emerged in Brazil by late 2014. In the country, two CHIKV foci characterized by the East/Central/South Africa and Asian genotypes, were established in North and Northeast regions. We characterized, by phylogenetic analyses of full and partial genomes, CHIKV from Rio de Janeiro state (2014-2015). These CHIKV strains belong to the Asian genotype, which is the determinant of the current Northern Brazilian focus, even though the genome sequence presents particular single nucleotide variations. This study provides the first genetic characterisation of CHIKV in Rio de Janeiro and highlights the potential impact of human mobility in the spread of an arthropod-borne virus.

  4. Multilocus phylogenetic analyses, pullulan production and xylanase activity of tropical isolates of Aureobasidium pullulans.

    PubMed

    Manitchotpisit, Pennapa; Leathers, Timothy D; Peterson, Stephen W; Kurtzman, Cletus P; Li, Xin-Liang; Eveleigh, Douglas E; Lotrakul, Pongtharin; Prasongsuk, Sehanat; Dunlap, Christopher A; Vermillion, Karl E; Punnapayak, Hunsa

    2009-10-01

    Aureobasidium pullulans is the source of the commercially valuable polysaccharide pullulan and the enzyme xylanase. Isolates are typically off-white to pale pink or black on solid media, while some tropical isolates have been described as 'color variants' with bright pigments of red, yellow or purple. We sequenced 5 loci (internal transcribed spacer, intergenic spacer 1, translation elongation factor-1 alpha, beta tubulin, and RNA polymerase II) from 45 new isolates from Thailand. Based on the phylogenetic analyses, isolates were classified into 12 clades. Each clade showed different colors on different culture media including two clades with 'color variants' and some clades exhibited high levels of pullulan production or xylanase activity. Colony characteristics do not correlate perfectly with DNA sequence phylogeny or the physiological characters, but DNA sequence differences rapidly identify isolates with genetic novelty. PMID:19619651

  5. Usefulness of cpDNA markers for phylogenetic and phylogeographic analyses of closely related cactus species.

    PubMed

    Bonatelli, I A S; Zappi, D C; Taylor, N P; Moraes, E M

    2013-02-28

    Although plastid DNA has been widely explored as a marker of choice for phylogeny and phylogeography studies, little is known about its utility for examining relationships between closely related species. The slow evolutionary rates inherent to chloroplast (cp) DNA make it difficult to perform lower level taxonomic analyses, particularly at the population level. We characterized the nucleotide variation and investigated the utility of eight noncoding cpDNA regions in four closely related species of the Pilosocereus aurisetus group (Cactaceae), an endemic taxon of eastern South America. The plastid intergenic spacers 5'-trnS-trnG, 3'-trnS-trnG and trnT-trnL were the most variable regions and were the most useful for lower level taxonomic comparisons, especially when used together. We conclude that an adequate combination of regions alongside indels as an additional character improves the usefulness of cpDNA for phylogenetic studies.

  6. Mitochondrial genome of the Chinese gizzard shad Clupanodon thrissa (Clupeiformes: Clupeidae) and related phylogenetic analyses.

    PubMed

    Li, Min; Zou, Keshu; Chen, Zuozhi; Chen, Tao

    2012-12-01

    The complete mitochondrial genome sequence of the single species from the Genus Clupanodon, the Chinese gizzard shad, Clupanodon thrissa, was determined. The entire sequence is 16,692 bp in length, including the typical structure of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 rRNA genes, and 2 noncoding regions (control region and L-strand replication origin). With the exception of ND6 and eight tRNA genes, all other genes are encoded on the heavy strand and the organization of genes is similar to that observed in most other vertebrates. Phylogenetic analyses using the protein coding gene sequences reveal that C. thrissa is most closely related to Konosirus punctatus within the family Clupeidae and subfamily Dorosomatinae is not a monophyletic group.

  7. Cephalothrix gen. nov. (Cyanobacteria): towards an intraspecific phylogenetic evaluation by multilocus analyses.

    PubMed

    da Silva Malone, Camila Francieli; Rigonato, Janaína; Laughinghouse, Haywood Dail; Schmidt, Éder Carlos; Bouzon, Zenilda Laurita; Wilmotte, Annick; Fiore, Marli Fátima; Sant'Anna, Célia Leite

    2015-09-01

    For more than a decade, the taxonomy of the Phormidiaceae has been problematic, since morphologically similar organisms represent phylogenetically distinct entities. Based on 16S rRNA gene sequence analyses, the polyphyletic genus Phormidium and other gas-vacuolated oscillatorioids appear scattered throughout the cyanobacterial tree of life. Recently, several studies have focused on understanding the oscillatorioid taxa at the generic level. At the specific level, few studies have characterized cyanobacterial strains using combined datasets (morphology, ultrastructure and molecular multilocus analyses). Using a multifaceted approach, we propose a new, well-defined genus, Cephalothrix gen. nov., by analysing seven filamentous strains that are morphologically 'intermediate' between gas-vacuolated taxa and Phormidium. Furthermore, we characterize two novel species: Cephalothrix komarekiana sp. nov. (strains CCIBt 3277, CCIBt 3279, CCIBt 3523, CCALA 155, SAG 75.79 and UTEX 1580) and Cephalothrix lacustris sp. nov. (strain CCIBt 3261). The generic name and specific epithets are proposed under the provisions of the International Code of Nomenclature for Algae, Fungi, and Plants.

  8. Phylogenetic relationships within caniform carnivores based on analyses of the mitochondrial 12S rRNA gene.

    PubMed

    Ledje, C; Arnason, U

    1996-12-01

    The complete 12S rRNA gene of 32 carnivore species, including four feliforms and 28 caniforms, was sequenced. The sequences were aligned on the basis of their secondary structures and used in phylogenetic analyses that addressed several evolutionary relationships within the Caniformia. The analyses showed an unresolved polytomy of the basic caniform clades; pinnipeds, mustelids, procyonids, skunks, Ailurus (lesser panda), ursids, and canids. The polytomy indicates a major diversification of caniforms during a relatively short period of time. The lesser panda was distinct from other caniforms, suggesting its inclusion in a monotypic family, Ailuridae. The giant panda and the bears were joined on the same branch. The skunks are traditionally included in the family Mustelidae. The present analysis, however, showed a less close molecular relationship between the skunks and the remaining Mustelidae (sensu stricto) than between Mustelidae (sensu stricto) and Procyonidae, making Mustelidae (sensu lato) paraphyletic. The results suggest that the skunks should be included in a separate family, Mephitidae. Within the Pinnipedia, the grouping of walrus, sea lions, and fur seals was strongly supported. Analyses of a combined set of 12S rRNA and cytochrome b data were generally consistent with the findings based on each gene. PMID:8995061

  9. Large-scale phylogenetic analyses reveal the causes of high tropical amphibian diversity.

    PubMed

    Pyron, R Alexander; Wiens, John J

    2013-11-01

    Many groups show higher species richness in tropical regions but the underlying causes remain unclear. Despite many competing hypotheses to explain latitudinal diversity gradients, only three processes can directly change species richness across regions: speciation, extinction and dispersal. These processes can be addressed most powerfully using large-scale phylogenetic approaches, but most previous studies have focused on small groups and recent time scales, or did not separate speciation and extinction rates. We investigate the origins of high tropical diversity in amphibians, applying new phylogenetic comparative methods to a tree of 2871 species. Our results show that high tropical diversity is explained by higher speciation in the tropics, higher extinction in temperate regions and limited dispersal out of the tropics compared with colonization of the tropics from temperate regions. These patterns are strongly associated with climate-related variables such as temperature, precipitation and ecosystem energy. Results from models of diversity dependence in speciation rate suggest that temperate clades may have lower carrying capacities and may be more saturated (closer to carrying capacity) than tropical clades. Furthermore, we estimate strikingly low tropical extinction rates over geological time scales, in stark contrast to the dramatic losses of diversity occurring in tropical regions presently. PMID:24026818

  10. Phylogenetic Analyses Reveal Monophyletic Origin of the Ergot Alkaloid Gene dmaW in Fungi

    PubMed Central

    Liu, Miao; Panaccione, Daniel G.; Schardl, Christopher L.

    2009-01-01

    Ergot alkaloids are indole-derived mycotoxins that are important in agriculture and medicine. Ergot alkaloids are produced by a few representatives of two distantly related fungal lineages, the Clavicipitaceae and the Trichocomaceae. Comparison of the ergot alkaloid gene clusters from these two lineages revealed differences in the relative positions and orientations of several genes. The question arose: is ergot alkaloid biosynthetic capability from a common origin? We used a molecular phylogenetic approach to gain insights into the evolution of ergot alkaloid biosynthesis. The 4-γ,γ-dimethylallyltryptophan synthase gene, dmaW, encodes the first step in the pathway. Amino acid sequences deduced from dmaW and homologs were submitted to phylogenetic analysis, and the results indicated that dmaW of Aspergillus fumigatus (mitosporic Trichocomaceae) has the same origin as corresponding genes from clavicipitaceous fungi. Relationships of authentic dmaW genes suggest that they originated from multiple gene duplications with subsequent losses of original or duplicate versions in some lineages. PMID:19812724

  11. Phylogenetic analyses in cornus substantiate ancestry of xylem supercooling freezing behavior and reveal lineage of desiccation related proteins.

    PubMed

    Karlson, Dale T; Xiang, Qiu-Yun; Stirm, Vicki E; Shirazi, A M; Ashworth, Edward N

    2004-07-01

    The response of woody plant tissues to freezing temperature has evolved into two distinct behaviors: an avoidance strategy, in which intracellular water supercools, and a freeze-tolerance strategy, where cells tolerate the loss of water to extracellular ice. Although both strategies involve extracellular ice formation, supercooling cells are thought to resist freeze-induced dehydration. Dehydrin proteins, which accumulate during cold acclimation in numerous herbaceous and woody plants, have been speculated to provide, among other things, protection from desiccative extracellular ice formation. Here we use Cornus as a model system to provide the first phylogenetic characterization of xylem freezing behavior and dehydrin-like proteins. Our data suggest that both freezing behavior and the accumulation of dehydrin-like proteins in Cornus are lineage related; supercooling and nonaccumulation of dehydrin-like proteins are ancestral within the genus. The nonsupercooling strategy evolved within the blue- or white-fruited subgroup where representative species exhibit high levels of freeze tolerance. Within the blue- or white-fruited lineage, a single origin of dehydrin-like proteins was documented and displayed a trend for size increase in molecular mass. Phylogenetic analyses revealed that an early divergent group of red-fruited supercooling dogwoods lack a similar protein. Dehydrin-like proteins were limited to neither nonsupercooling species nor to those that possess extreme freeze tolerance.

  12. The Mitochondrial Genomes of Aquila fasciata and Buteo lagopus (Aves, Accipitriformes): Sequence, Structure and Phylogenetic Analyses

    PubMed Central

    Jiang, Lan; Chen, Juan; Wang, Ping; Ren, Qiongqiong; Yuan, Jian; Qian, Chaoju; Hua, Xinghong; Guo, Zhichun; Zhang, Lei; Yang, Jianke; Wang, Ying; Zhang, Qin; Ding, Hengwu; Bi, De; Zhang, Zongmeng; Wang, Qingqing; Chen, Dongsheng; Kan, Xianzhao

    2015-01-01

    The family Accipitridae is one of the largest groups of non-passerine birds, including 68 genera and 243 species globally distributed. In the present study, we determined the complete mitochondrial sequences of two species of accipitrid, namely Aquila fasciata and Buteo lagopus, and conducted a comparative mitogenome analysis across the family. The mitogenome length of A. fasciata and B. lagopus are 18,513 and 18,559 bp with an A + T content of 54.2% and 55.0%, respectively. For both the two accipitrid birds mtDNAs, obvious positive AT-skew and negative GC-skew biases were detected for all 12 PCGs encoded by the H strand, whereas the reverse was found in MT-ND6 encoded by the L strand. One extra nucleotide‘C’is present at the position 174 of MT-ND3 gene of A. fasciata, which is not observed at that of B. lagopus. Six conserved sequence boxes in the Domain II, named boxes F, E, D, C, CSBa, and CSBb, respectively, were recognized in the CRs of A. fasciata and B. lagopus. Rates and patterns of mitochondrial gene evolution within Accipitridae were also estimated. The highest dN/dS was detected for the MT-ATP8 gene (0.32493) among Accipitridae, while the lowest for the MT-CO1 gene (0.01415). Mitophylogenetic analysis supported the robust monophyly of Accipitriformes, and Cathartidae was basal to the balance of the order. Moreover, we performed phylogenetic analyses using two other data sets (two mitochondrial loci, and combined nuclear and mitochondrial loci). Our results indicate that the subfamily Aquilinae and all currently polytypic genera of this subfamily are monophyletic. These two novel mtDNA data will be useful in refining the phylogenetic relationships and evolutionary processes of Accipitriformes. PMID:26295156

  13. Evolutionary relationships of the Critically Endangered frog Ericabatrachus baleensis Largen, 1991 with notes on incorporating previously unsampled taxa into large-scale phylogenetic analyses

    PubMed Central

    2014-01-01

    Background The phylogenetic relationships of many taxa remain poorly known because of a lack of appropriate data and/or analyses. Despite substantial recent advances, amphibian phylogeny remains poorly resolved in many instances. The phylogenetic relationships of the Ethiopian endemic monotypic genus Ericabatrachus has been addressed thus far only with phenotypic data and remains contentious. Results We obtained fresh samples of the now rare and Critically Endangered Ericabatrachus baleensis and generated DNA sequences for two mitochondrial and four nuclear genes. Analyses of these new data using de novo and constrained-tree phylogenetic reconstructions strongly support a close relationship between Ericabatrachus and Petropedetes, and allow us to reject previously proposed alternative hypotheses of a close relationship with cacosternines or Phrynobatrachus. Conclusions We discuss the implications of our results for the taxonomy, biogeography and conservation of E. baleensis, and suggest a two-tiered approach to the inclusion and analyses of new data in order to assess the phylogenetic relationships of previously unsampled taxa. Such approaches will be important in the future given the increasing availability of relevant mega-alignments and potential framework phylogenies. PMID:24612655

  14. Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae

    PubMed Central

    2011-01-01

    Background Previous DNA-based phylogenetic studies of the Delphinidae family suggest it has undergone rapid diversification, as characterised by unresolved and poorly supported taxonomic relationships (polytomies) for some of the species within this group. Using an increased amount of sequence data we test between alternative hypotheses of soft polytomies caused by rapid speciation, slow evolutionary rate and/or insufficient sequence data, and hard polytomies caused by simultaneous speciation within this family. Combining the mitogenome sequences of five new and 12 previously published species within the Delphinidae, we used Bayesian and maximum-likelihood methods to estimate the phylogeny from partitioned and unpartitioned mitogenome sequences. Further ad hoc tests were then conducted to estimate the support for alternative topologies. Results We found high support for all the relationships within our reconstructed phylogenies, and topologies were consistent between the Bayesian and maximum-likelihood trees inferred from partitioned and unpartitioned data. Resolved relationships included the placement of the killer whale (Orcinus orca) as sister taxon to the rest of the Globicephalinae subfamily, placement of the Risso's dolphin (Grampus griseus) within the Globicephalinae subfamily, removal of the white-beaked dolphin (Lagenorhynchus albirostris) from the Delphininae subfamily and the placement of the rough-toothed dolphin (Steno bredanensis) as sister taxon to the rest of the Delphininae subfamily rather than within the Globicephalinae subfamily. The additional testing of alternative topologies allowed us to reject all other putative relationships, with the exception that we were unable to reject the hypothesis that the relationship between L. albirostris and the Globicephalinae and Delphininae subfamilies was polytomic. Conclusion Despite their rapid diversification, the increased sequence data yielded by mitogenomes enables the resolution of a strongly

  15. Morphological Examination and Phylogenetic Analyses of Phycopeltis spp. (Trentepohliales, Ulvophyceae) from Tropical China

    PubMed Central

    Zhu, Huan; Zhao, Zhijuan; Xia, Shuang; Hu, Zhengyu; Liu, Guoxiang

    2015-01-01

    During an investigation of Trentepohliales (Ulvophyceae) from tropical areas in China, four species of the genus Phycopeltis were identified: Phycopeltis aurea, P. epiphyton, P. flabellata and P. prostrata. The morphological characteristics of both young and adult thalli were observed and compared. Three species (P. flabellata, P. aurea and P. epiphyton) shared a symmetrical development with dichotomously branching vegetative cells during early stages; conversely, P. prostrata had dishevelled filaments with no dichotomously branching filaments and no symmetrical development. The adult thalli of the former three species shared common morphological characteristics, such as equally dichotomous filaments, absence of erect hair and gametangia formed in prostate vegetative filaments. Phylogenetic analyses based on SSU and ITS rDNA sequences showed that the three morphologically similar species were in a clade that was sister to a clade containing T. umbrina and T. abietina, thus confirming morphological monophyly. Conversely, Phycopeltis prostrata, a species with erect filaments, sessile gametangia on the basal erect hair, larger length/width ratio of vegetative cells and very loosely coalescent prostrate filaments, branched separately from the core Phycopeltis group and the T. umbrina and T. abietina clade. Based on morphological and molecular evidence, the genus Phycopeltis was paraphyletic. Furthermore, the traditional taxonomic criteria for Phycopeltis must be reassessed based on phylogeny using more species. A new circumscription of the Phycopeltis and the erection of new genera are recommended. PMID:25643363

  16. SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates.

    PubMed Central

    Schmitz, J; Ohme, M; Zischler, H

    2001-01-01

    Transpositions of Alu sequences, representing the most abundant primate short interspersed elements (SINE), were evaluated as molecular cladistic markers to analyze the phylogenetic affiliations among the primate infraorders. Altogether 118 human loci, containing intronic Alu elements, were PCR analyzed for the presence of Alu sequences at orthologous sites in each of two strepsirhine, New World and Old World monkey species, Tarsius bancanus, and a nonprimate outgroup. Fourteen size-polymorphic amplification patterns exhibited longer fragments for the anthropoids (New World and Old World monkeys) and T. bancanus whereas shorter fragments were detected for the strepsirhines and the outgroup. From these, subsequent sequence analyses revealed three Alu transpositions, which can be regarded as shared derived molecular characters linking tarsiers and anthropoid primates. Concerning the other loci, scenarios are represented in which different SINE transpositions occurred independently in the same intron on the lineages leading both to the common ancestor of anthropoids and to T. bancanus, albeit at different nucleotide positions. Our results demonstrate the efficiency and possible pitfalls of SINE transpositions used as molecular cladistic markers in tracing back a divergence point in primate evolution over 40 million years old. The three Alu insertions characterized underpin the monophyly of haplorhine primates (Anthropoidea and Tarsioidea) from a novel perspective. PMID:11156996

  17. Mutational and Phylogenetic Analyses of the Mycobacterial mbt Gene Cluster ▿§

    PubMed Central

    Chavadi, Sivagami Sundaram; Stirrett, Karen L.; Edupuganti, Uthamaphani R.; Vergnolle, Olivia; Sadhanandan, Gigani; Marchiano, Emily; Martin, Che; Qiu, Wei-Gang; Soll, Clifford E.; Quadri, Luis E. N.

    2011-01-01

    The mycobactin siderophore system is present in many Mycobacterium species, including M. tuberculosis and other clinically relevant mycobacteria. This siderophore system is believed to be utilized by both pathogenic and nonpathogenic mycobacteria for iron acquisition in both in vivo and ex vivo iron-limiting environments, respectively. Several M. tuberculosis genes located in a so-called mbt gene cluster have been predicted to be required for the biosynthesis of the core scaffold of mycobactin based on sequence analysis. A systematic and controlled mutational analysis probing the hypothesized essential nature of each of these genes for mycobactin production has been lacking. The degree of conservation of mbt gene cluster orthologs remains to be investigated as well. In this study, we sought to conclusively establish whether each of nine mbt genes was required for mycobactin production and to examine the conservation of gene clusters orthologous to the M. tuberculosis mbt gene cluster in other bacteria. We report a systematic mutational analysis of the mbt gene cluster ortholog found in Mycobacterium smegmatis. This mutational analysis demonstrates that eight of the nine mbt genes investigated are essential for mycobactin production. Our genome mining and phylogenetic analyses reveal the presence of orthologous mbt gene clusters in several bacterial species. These gene clusters display significant organizational differences originating from an intricate evolutionary path that might have included horizontal gene transfers. Altogether, the findings reported herein advance our understanding of the genetic requirements for the biosynthesis of an important mycobacterial secondary metabolite with relevance to virulence. PMID:21873494

  18. The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses.

    PubMed

    Schultz, Jörg; Müller, Tobias; Achtziger, Marco; Seibel, Philipp N; Dandekar, Thomas; Wolf, Matthias

    2006-07-01

    The internal transcribed spacer 2 (ITS2) is a phylogenetic marker which has been of broad use in generic and infrageneric level classifications, as its sequence evolves comparably fast. Only recently, it became clear, that the ITS2 might be useful even for higher level systematic analyses. As the secondary structure is highly conserved within all eukaryotes it serves as a valuable template for the construction of highly reliable sequence-structure alignments, which build a fundament for subsequent analyses. Thus, any phylogenetic study using ITS2 has to consider both sequence and structure. We have integrated a homology based RNA structure prediction algorithm into a web server, which allows the detection and secondary structure prediction for ITS2 in any given sequence. Furthermore, the resource contains more than 25,000 pre-calculated secondary structures for the currently known ITS2 sequences. These can be taxonomically searched and browsed. Thus, our resource could become a starting point for ITS2-based phylogenetic analyses and is therefore complementary to databases of other phylogenetic markers, which focus on higher level analyses. The current version of the ITS2 database can be accessed via http://its2.bioapps.biozentrum.uni-wuerzburg.de.

  19. Comprehensive Phylogenetic Reconstruction of Amoebozoa Based on Concatenated Analyses of SSU-rDNA and Actin Genes

    PubMed Central

    Lahr, Daniel J. G.; Grant, Jessica; Nguyen, Truc; Lin, Jian Hua; Katz, Laura A.

    2011-01-01

    Evolutionary relationships within Amoebozoa have been the subject of controversy for two reasons: 1) paucity of morphological characters in traditional surveys and 2) haphazard taxonomic sampling in modern molecular reconstructions. These along with other factors have prevented the erection of a definitive system that resolves confidently both higher and lower-level relationships. Additionally, the recent recognition that many protosteloid amoebae are in fact scattered throughout the Amoebozoa suggests that phylogenetic reconstructions have been excluding an extensive and integral group of organisms. Here we provide a comprehensive phylogenetic reconstruction based on 139 taxa using molecular information from both SSU-rDNA and actin genes. We provide molecular data for 13 of those taxa, 12 of which had not been previously characterized. We explored the dataset extensively by generating 18 alternative reconstructions that assess the effect of missing data, long-branched taxa, unstable taxa, fast evolving sites and inclusion of environmental sequences. We compared reconstructions with each other as well as against previously published phylogenies. Our analyses show that many of the morphologically established lower-level relationships (defined here as relationships roughly equivalent to Order level or below) are congruent with molecular data. However, the data are insufficient to corroborate or reject the large majority of proposed higher-level relationships (above the Order-level), with the exception of Tubulinea, Archamoebae and Myxogastrea, which are consistently recovered. Moreover, contrary to previous expectations, the inclusion of available environmental sequences does not significantly improve the Amoebozoa reconstruction. This is probably because key amoebozoan taxa are not easily amplified by environmental sequencing methodology due to high rates of molecular evolution and regular occurrence of large indels and introns. Finally, in an effort to facilitate

  20. Evolution of the chordate body plan: new insights from phylogenetic analyses of deuterostome phyla.

    PubMed

    Cameron, C B; Garey, J R; Swalla, B J

    2000-04-25

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

  1. Phylogenetic analyses and expression studies reveal two distinct groups of calreticulin isoforms in higher plants.

    PubMed

    Persson, Staffan; Rosenquist, Magnus; Svensson, Karin; Galvão, Rafaelo; Boss, Wendy F; Sommarin, Marianne

    2003-11-01

    Calreticulin (CRT) is a multifunctional protein mainly localized to the endoplasmic reticulum in eukaryotic cells. Here, we present the first analysis, to our knowledge, of evolutionary diversity and expression profiling among different plant CRT isoforms. Phylogenetic studies and expression analysis show that higher plants contain two distinct groups of CRTs: a CRT1/CRT2 group and a CRT3 group. To corroborate the existence of these isoform groups, we cloned a putative CRT3 ortholog from Brassica rapa. The CRT3 gene appears to be most closely related to the ancestral CRT gene in higher plants. Distinct tissue-dependent expression patterns and stress-related regulation were observed for the isoform groups. Furthermore, analysis of posttranslational modifications revealed differences in the glycosylation status among members within the CRT1/CRT2 isoform group. Based on evolutionary relationship, a new nomenclature for plant CRTs is suggested. The presence of two distinct CRT isoform groups, with distinct expression patterns and posttranslational modifications, supports functional specificity among plant CRTs and could account for the multiple functional roles assigned to CRTs.

  2. Evolution of the chordate body plan: new insights from phylogenetic analyses of deuterostome phyla.

    PubMed

    Cameron, C B; Garey, J R; Swalla, B J

    2000-04-25

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

  3. Multilocus phylogenetic analyses and phenotypic characterization of tropical isolates of Aureobasidium pullulans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aureobasidium pullulans is the source of the commercial polysaccharide, pullulan, and the enzyme, xylanase. The purpose of this study was to classify Aureobasidium isolates using multilocus phylogenetic analysis and determine specific characteristics of each clade....

  4. Fine-scale genetic structure analyses suggest further male than female dispersal in mountain gorillas

    PubMed Central

    2014-01-01

    Background Molecular studies in social mammals rarely compare the inferences gained from genetic analyses with field information, especially in the context of dispersal. In this study, we used genetic data to elucidate sex-specific dispersal dynamics in the Virunga Massif mountain gorilla population (Gorilla beringei beringei), a primate species characterized by routine male and female dispersal from stable mixed-sex social groups. Specifically, we conducted spatial genetic structure analyses for each sex and linked our genetically-based observations with some key demographic and behavioural data from this population. Results To investigate the spatial genetic structure of mountain gorillas, we analysed the genotypes of 193 mature individuals at 11 microsatellite loci by means of isolation-by-distance and spatial autocorrelation analyses. Although not all males and females disperse, female gorillas displayed an isolation-by-distance pattern among groups and a signal of dispersal at short distances from their natal group based on spatial autocorrelation analyses. In contrast, male genotypes were not correlated with spatial distance, thus suggesting a larger mean dispersal distance for males as compared to females. Both within sex and mixed-sex pairs were on average genetically more related within groups than among groups. Conclusions Our study provides evidence for an intersexual difference in dispersal distance in the mountain gorilla. Overall, it stresses the importance of investigating spatial genetic structure patterns on a sex-specific basis to better understand the dispersal dynamics of the species under investigation. It is currently poorly understood why some male and female gorillas disperse while others remain in the natal group. Our results on average relatedness within and across groups confirm that groups often contain close relatives. While inbreeding avoidance may play a role in driving female dispersal, we note that more detailed dyadic genetic

  5. Incorporating clade identity in analyses of phylogenetic community structure: an example with hummingbirds.

    PubMed

    Parra, Juan L; McGuire, Jimmy A; Graham, Catherine H

    2010-11-01

    An important challenge in community ecology is to determine how processes occurring at multiple spatial, temporal, and phylogenetic scales influence the structure of local communities. While indexes of phylogenetic structure, which measure how related species are in a community, provide insight into the processes that shape species coexistence, they fail to pinpoint the phylogenetic scales at which those processes occur. Here, we explore a framework to identify the species and clades responsible for the inferred patterns of phylogenetic structure within a given community. Further, we evaluate how communities that share the nonrandom representation of species from a given clade in the phylogeny are distributed across geography and environmental gradients. Using Ecuadorian hummingbird communities, we found that multiple patterns of phylogenetic structure often occur within a local assemblage. We also identified four geographic regions where species from certain clades exhibit nonrandom representation: the eastern Amazonian lowlands, the western dry lowlands, the Andes at middle elevations, and the Andes at high elevations. The environmental gradients along which changes in the local coexistence of species occurred were mainly elevation, annual precipitation, and seasonality in both temperature and precipitation. Finally, we show how these patterns can be used to generate hypotheses about the processes that allow species coexistence.

  6. Molecular cloning, expression and phylogenetic analyses of parvalbumin in tilapia, Oreochromis mossambicus.

    PubMed

    Lee, Shyh-Jye; Ju, Chi-Ching; Chu, Shian-Ling; Chien, Ming-Shan; Chan, Tun-Hao; Liao, Wen-Liang

    2007-01-01

    The gene expression of parvalbumin (Pvalb), a high-affinity calcium-binding protein and the major fish allergen, was significantly increased in the tilapia fry treated with methyltestosterone (MT) as examined using a subtractive hybridization assay. Using the real-time quantitative PCR, we further confirmed the increased Pvalb expression in the MT-treated tilapia fry. The 568 base pairs (bp) tilapia Pvalb (tPvalb) cDNA clone was fully sequenced and found to contain a coding region of 330 bp, which encodes a 108 amino acids protein with a molecular weight of 11,370.5 and an calculated isoelectric point of 4.56. The predicted secondary structure of tPvalb is comprised of seven alpha helices. It contains two characteristic EF-hand calcium-binding motifs, one PKC and five casein kinase II consensus phosphorylation sites. The tPvalb is highly homologous to the selected fish Pvalbs at a similarity ranging from 53% to 80%. The phylogenetic tree analysis showed that the tPvalb is closest to the Scomber japonicus Pvalb. The tPvalb was found to express in the heart, muscle, gill, kidney, brain and ovary of adult fish by RT-PCR analysis. In situ hybridization also revealed that the tPvalb was highly expressed in the hypothalamus and sarcoplasmic reticulum. A tPvalb glutathione S-transferase (GST) fusion protein was generated and digested by thrombin to remove the GST moiety. Further Western analysis showed that the tPvalb protein was cross-reacted to an anti-rat Pvalb antibody. Those results suggest that Pvalb is evolutionally conserved in tilapia. PMID:17094115

  7. Genetic analyses of Xanthomonas axonopodis pv. dieffenbachiae strains reveal distinct phylogenetic groups.

    PubMed

    Donahoo, R S; Jones, J B; Lacy, G H; Stromberg, V K; Norman, D J

    2013-03-01

    A comprehensive analysis of 175 Xanthomonas axonopodis pv. dieffenbachiae strains isolated from 10 Araceae hosts was done to identify pathogen variation. The strains were subjected to repetitive extragenic palindromic sequence polymerase chain reaction and four major phylogenetic clusters were generated. A subset of 40 strains isolated from Anthurium, Dieffenbachia, and Syngonium was further defined by amplified fragment length polymorphism and fatty acid methyl ester analysis and the same four phylogenetic clusters were observed. Comparison of representative strains in the first three clusters using DNA-DNA hybridization and multilocus sequence analysis supports the previous reclassification of strains in cluster I, including the X. axonopodis pv. dieffenbachiae pathovar reference strain (LMG695), to X. citri. Our research findings indicate that strains in cluster I, isolated primarily from anthurium, probably represent an undescribed pathovar. Other phylogenetic subclusters consisting primarily of strains isolated from xanthosoma and philodendron in clusters III and IV, respectively, may yet represent other undescribed species or pathovars of Xanthomonas. PMID:23134337

  8. Specific chicken repeat 1 (CR1) retrotransposon insertion suggests phylogenetic affinity of rockfowls (genus Picathartes) to crows and ravens (Corvidae).

    PubMed

    Treplin, Simone; Tiedemann, Ralph

    2007-04-01

    While the monophyly of the order Passeriformes as well as its suborders suboscines (Tyranni) and oscines (Passeri) is well established, both on morphological and molecular grounds, lower phylogenetic relationships have been a continuous matter of debate, especially within oscines. This is particularly true for the rockfowls (genus Picathartes), which phylogenetic classification has been an ongoing puzzle. Sequence-based molecular studies failed in deriving unambiguously resolved and supported hypotheses. We present here a novel approach: use of retrotransposon insertions as phylogenetic markers in passerine birds. Chicken repeat 1 (CR1) is the most important non-LTR retrotransposon in birds. We present two truncated CR1 loci in passerine birds, not only found in representatives of Corvinae (jays, crows and allies), but also in the West-African Picathartes species which provide new evidence for a closer relationship of these species to Corvidae than has previously been thought. Additionally, we show that not only the absence/presence pattern of a CR1 insertion, but also the CR1 sequences themselves contain phylogenetic information.

  9. Gene expression and molecular phylogenetic analyses of beta-glucosidase in the termite Reticulitermes speratus (Isoptera: Rhinotermitidae).

    PubMed

    Shimada, Keisuke; Maekawa, Kiyoto

    2014-06-01

    Beta-glucosidase (BG) is known as a multifunctional enzyme for social maintenance in terms of both cellulose digestion and social communication in termites. However, the expression profiles of each BG gene and their evolutionary history are not well understood. First, we cloned two types of BG homologs (RsBGI and RsBGII) from the termite Reticulitermes speratus (Kolbe). Gene expression analyses showed that RsBGI expression levels of primary queens and kings from 30 to 100 days after colony foundation were high, but those of reproductives dropped after day 400. Extremely low gene expression levels of RsBGI were observed in eggs, whereas workers had significantly higher expression levels than those of soldiers and other colony members. Consequently, RsBGI gene expression levels changed among each developmental stage, and RsBGI was shown to be involved in cellulose digestion. On the other hand, the RsBGII gene was consistently expressed in all castes and developmental stages examined, and notable expression changes were not observed among them, including in eggs. It was indicated that RsBGII is a main component involved in social communication, for example, the egg-recognition pheromone shown in this species previously. Finally, we obtained partial gene homologs from other termite and cockroach species, including the woodroach (genus Cryptocercus), which is the sister group to termites, and performed molecular phylogenetic analyses. The results showed that the origin of the BG gene homologs preceded the divergence of termites and cockroaches, suggesting that the acquisition of multifunctionality of the BG gene also occurred in cockroach lineages.

  10. The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships

    PubMed Central

    2011-01-01

    Background The phylogenetic relationships of the lophophorate lineages, ectoprocts, brachiopods and phoronids, within Lophotrochozoa are still controversial. We sequenced an additional mitochondrial genome of the most species-rich lophophorate lineage, the ectoprocts. Although it is known that there are large differences in the nucleotide composition of mitochondrial sequences of different lineages as well as in the amino acid composition of the encoded proteins, this bias is often not considered in phylogenetic analyses. We applied several approaches for reducing compositional bias and saturation in the phylogenetic analyses of the mitochondrial sequences. Results The complete mitochondrial genome (16,089 bp) of Flustra foliacea (Ectoprocta, Gymnolaemata, Cheilostomata) was sequenced. All protein-encoding, rRNA and tRNA genes are transcribed from the same strand. Flustra shares long intergenic sequences with the cheilostomate ectoproct Bugula, which might be a synapomorphy of these taxa. Further synapomorphies might be the loss of the DHU arm of the tRNA L(UUR), the loss of the DHU arm of the tRNA S(UCN) and the unique anticodon sequence GAG of the tRNA L(CUN). The gene order of the mitochondrial genome of Flustra differs strongly from that of the other known ectoprocts. Phylogenetic analyses of mitochondrial nucleotide and amino acid data sets show that the lophophorate lineages are more closely related to trochozoan phyla than to deuterostomes or ecdysozoans confirming the Lophotrochozoa hypothesis. Furthermore, they support the monophyly of Cheilostomata and Ectoprocta. However, the relationships of the lophophorate lineages within Lophotrochozoa differ strongly depending on the data set and the used method. Different approaches for reducing heterogeneity in nucleotide and amino acid data sets and saturation did not result in a more robust resolution of lophotrochozoan relationships. Conclusion The contradictory and usually weakly supported phylogenetic

  11. Molecular and Phylogenetic Analyses of the Complete MADS-Box Transcription Factor Family in Arabidopsis

    PubMed Central

    Par̆enicová, Lucie; de Folter, Stefan; Kieffer, Martin; Horner, David S.; Favalli, Cristina; Busscher, Jacqueline; Cook, Holly E.; Ingram, Richard M.; Kater, Martin M.; Davies, Brendan; Angenent, Gerco C.; Colombo, Lucia

    2003-01-01

    MADS-box transcription factors are key regulators of several plant development processes. Analysis of the complete Arabidopsis genome sequence revealed 107 genes encoding MADS-box proteins, of which 84% are of unknown function. Here, we provide a complete overview of this family, describing the gene structure, gene expression, genome localization, protein motif organization, and phylogenetic relationship of each member. We have divided this transcription factor family into five groups (named MIKC, Mα, Mβ, Mγ, and Mδ) based on the phylogenetic relationships of the conserved MADS-box domain. This study provides a solid base for functional genomics studies into this important family of plant regulatory genes, including the poorly characterized group of M-type MADS-box proteins. MADS-box genes also constitute an excellent system with which to study the evolution of complex gene families in higher plants. PMID:12837945

  12. The Complete Chloroplast Genome Sequences of Five Epimedium Species: Lights into Phylogenetic and Taxonomic Analyses

    PubMed Central

    Zhang, Yanjun; Du, Liuwen; Liu, Ao; Chen, Jianjun; Wu, Li; Hu, Weiming; Zhang, Wei; Kim, Kyunghee; Lee, Sang-Choon; Yang, Tae-Jin; Wang, Ying

    2016-01-01

    Epimedium L. is a phylogenetically and economically important genus in the family Berberidaceae. We here sequenced the complete chloroplast (cp) genomes of four Epimedium species using Illumina sequencing technology via a combination of de novo and reference-guided assembly, which was also the first comprehensive cp genome analysis on Epimedium combining the cp genome sequence of E. koreanum previously reported. The five Epimedium cp genomes exhibited typical quadripartite and circular structure that was rather conserved in genomic structure and the synteny of gene order. However, these cp genomes presented obvious variations at the boundaries of the four regions because of the expansion and contraction of the inverted repeat (IR) region and the single-copy (SC) boundary regions. The trnQ-UUG duplication occurred in the five Epimedium cp genomes, which was not found in the other basal eudicotyledons. The rapidly evolving cp genome regions were detected among the five cp genomes, as well as the difference of simple sequence repeats (SSR) and repeat sequence were identified. Phylogenetic relationships among the five Epimedium species based on their cp genomes showed accordance with the updated system of the genus on the whole, but reminded that the evolutionary relationships and the divisions of the genus need further investigation applying more evidences. The availability of these cp genomes provided valuable genetic information for accurately identifying species, taxonomy and phylogenetic resolution and evolution of Epimedium, and assist in exploration and utilization of Epimedium plants. PMID:27014326

  13. Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens.

    PubMed

    Chen, Jie; Moinard, Magalie; Xu, Jianping; Wang, Shouxian; Foulongne-Oriol, Marie; Zhao, Ruilin; Hyde, Kevin D; Callac, Philippe

    2016-01-01

    The internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene cluster is widely used in fungal taxonomy and phylogeographic studies. The medicinal and edible mushroom Agaricus subrufescens has a worldwide distribution with a high level of polymorphism in the ITS region. A previous analysis suggested notable ITS sequence heterogeneity within the wild French isolate CA487. The objective of this study was to investigate the pattern and potential mechanism of ITS sequence heterogeneity within this strain. Using PCR, cloning, and sequencing, we identified three types of ITS sequences, A, B, and C with a balanced distribution, which differed from each other at 13 polymorphic positions. The phylogenetic comparisons with samples from different continents revealed that the type C sequence was similar to those found in Oceanian and Asian specimens of A. subrufescens while types A and B sequences were close to those found in the Americas or in Europe. We further investigated the inheritance of these three ITS sequence types by analyzing their distribution among single-spore isolates from CA487. In this analysis, three co-dominant markers were used firstly to distinguish the homokaryotic offspring from the heterokaryotic offspring. The homokaryotic offspring were then analyzed for their ITS types. Our genetic analyses revealed that types A and B were two alleles segregating at one locus ITSI, while type C was not allelic with types A and B but was located at another unlinked locus ITSII. Furthermore, type C was present in only one of the two constitutive haploid nuclei (n) of the heterokaryotic (n+n) parent CA487. These data suggest that there was a relatively recent introduction of the type C sequence and a duplication of the ITS locus in this strain. Whether other genes were also transferred and duplicated and their impacts on genome structure and stability remain to be investigated. PMID:27228131

  14. Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens

    PubMed Central

    Chen, Jie; Moinard, Magalie; Xu, Jianping; Wang, Shouxian; Foulongne-Oriol, Marie; Zhao, Ruilin; Hyde, Kevin D.; Callac, Philippe

    2016-01-01

    The internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene cluster is widely used in fungal taxonomy and phylogeographic studies. The medicinal and edible mushroom Agaricus subrufescens has a worldwide distribution with a high level of polymorphism in the ITS region. A previous analysis suggested notable ITS sequence heterogeneity within the wild French isolate CA487. The objective of this study was to investigate the pattern and potential mechanism of ITS sequence heterogeneity within this strain. Using PCR, cloning, and sequencing, we identified three types of ITS sequences, A, B, and C with a balanced distribution, which differed from each other at 13 polymorphic positions. The phylogenetic comparisons with samples from different continents revealed that the type C sequence was similar to those found in Oceanian and Asian specimens of A. subrufescens while types A and B sequences were close to those found in the Americas or in Europe. We further investigated the inheritance of these three ITS sequence types by analyzing their distribution among single-spore isolates from CA487. In this analysis, three co-dominant markers were used firstly to distinguish the homokaryotic offspring from the heterokaryotic offspring. The homokaryotic offspring were then analyzed for their ITS types. Our genetic analyses revealed that types A and B were two alleles segregating at one locus ITSI, while type C was not allelic with types A and B but was located at another unlinked locus ITSII. Furthermore, type C was present in only one of the two constitutive haploid nuclei (n) of the heterokaryotic (n+n) parent CA487. These data suggest that there was a relatively recent introduction of the type C sequence and a duplication of the ITS locus in this strain. Whether other genes were also transferred and duplicated and their impacts on genome structure and stability remain to be investigated. PMID:27228131

  15. [Molecular Identification and Phylogenetic Analyses of Coxsackievirus A24v Causing an Outbreak of Acute Hemorrhagic Conjunctivitis in Jiangxi, China, in 2010].

    PubMed

    Yan, Dongmei; Xiong, Ying; Zhang, Yang; Yang, Qiai; Zhang, Shuxia; Gong, Tian; Zhu, Tian; Wang, Donavan; Zhu, Hui; Xu, Wenbo

    2015-05-01

    To identify the cause of an outbreak of acute hemorrhagic conjunctivitis (AHC) in Jiangxi (China) in 2010, 20 eye conjunctival swabs were first collected from AHC patients. Then, viruses were isola- ted and tested for human enterovirus 70, coxsackievirus A24 variant (CV-A24v) and adenovirus using the polymerase chain reaction. All CV-A24v isolates underwent sequencing of 3C and VP1 coding regions. Then, a phylogenetic tree was constructed for Jiangxi CV-A24v and worldwide CV-A24v based on,3C and VP1 regions, respectively. Ten out of 20 specimens were positive for CV-A24v, implying that the outbreak was caused by CV-A24v. The phylogenetic tree based on the 3C region showed that Jiangxi CV- A24v belonged to cluster 5 in genotype IV (GIV-C5) with strains isolated throughout the world after 2010, and were divided further into A and B lineages. Phylogenetic analyses of the VP1 region showed that all of the worldwide CV-A24v strains isolated after 2000 could be divided into five groups (1-5). Jiangxi CV-A24v was classified into group 5 and also divided further into A and B lineages upon analyses of the 3C region. These data suggested that CV-A24v causing AHC outbreaks in China in 2010 belonged to GIV-C3 and GIV-C5. At least two transmission lineages were circulated in Jiangxi in 2010. The classification of CV-A24v isolated after 2010 worldwide using the phylogenetic tree based on the VP1 region was almost consistent with that based on the 3C region and also had significant chronological clustering.

  16. Centrohelida is still searching for a phylogenetic home: analyses of seven Raphidiophrys contractilis genes.

    PubMed

    Sakaguchi, Miako; Inagaki, Yuji; Hashimoto, Tetsuo

    2007-12-15

    By recent advance in evolutionary biology, the majority of eukaryotes are classified into six eukaryotic assemblages called as "supergroups". However, several eukaryotic groups show no clear evolutionary affinity to any of the six supergroups. Centrohelida, one of major heliozoan groups, are such an unresolved lineage. In this study, we newly determined the genes encoding translation elongation factor 2 (EF2), cytosolic heat shock protein 70 (HSP70), and cytosolic heat shock protein 90 (HSP90) from the centroheliozoan Raphidiophrys contractilis. The three Raphidiophrys genes were then combined with previously determined actin, alpha-tubulin, beta-tubulin, and SSU rRNA sequences to phylogenetically analyze the position of Centrohelida in global eukaryotic phylogeny. Although the multi-gene data sets examined in this study are the largest ones including the centroheliozoan sequences, the relationships between Centrohelida and the eukaryotic groups considered were unresolved. Our careful investigation revealed that the phylogenetic estimates were highly sensitive to genes included in the multi-gene alignment. The signal of SSU rRNA and that of alpha-tubulin appeared to conflict with one another: the former strongly prefers a monophyly of Diplomonadida (e.g., Giardia), Parabasalia (e.g., Trichomonas), Heterolobosea (e.g., Naegleria), and Euglenozoa (e.g., Trypanosoma), while the latter unites Diplomonadida, Parabasalia, Metazoa, and Fungi. In addition, EF2 robustly unites Rhodophyta and Viridiplantae, while the remaining genes considered in this study do not positively support the particular relationship. Thus, it is difficult to identify the phylogenetic relatives of Centrohelida in the present study, since strong (and some are conflicting) gene-specific "signals" are predominant in the current multi-gene data. We concluded that larger scale multi-gene phylogenies are necessary to elucidate the origin and evolution of Centrohelida. PMID:17931802

  17. Genome and Phylogenetic Analyses of Trypanosoma evansi Reveal Extensive Similarity to T. brucei and Multiple Independent Origins for Dyskinetoplasty

    PubMed Central

    Carnes, Jason; Anupama, Atashi; Balmer, Oliver; Jackson, Andrew; Lewis, Michael; Brown, Rob; Cestari, Igor; Desquesnes, Marc; Gendrin, Claire; Hertz-Fowler, Christiane; Imamura, Hideo; Ivens, Alasdair; Kořený, Luděk; Lai, De-Hua; MacLeod, Annette; McDermott, Suzanne M.; Merritt, Chris; Monnerat, Severine; Moon, Wonjong; Myler, Peter; Phan, Isabelle; Ramasamy, Gowthaman; Sivam, Dhileep; Lun, Zhao-Rong; Lukeš, Julius; Stuart, Ken; Schnaufer, Achim

    2015-01-01

    Two key biological features distinguish Trypanosoma evansi from the T. brucei group: independence from the tsetse fly as obligatory vector, and independence from the need for functional mitochondrial DNA (kinetoplast or kDNA). In an effort to better understand the molecular causes and consequences of these differences, we sequenced the genome of an akinetoplastic T. evansi strain from China and compared it to the T. b. brucei reference strain. The annotated T. evansi genome shows extensive similarity to the reference, with 94.9% of the predicted T. b. brucei coding sequences (CDS) having an ortholog in T. evansi, and 94.6% of the non-repetitive orthologs having a nucleotide identity of 95% or greater. Interestingly, several procyclin-associated genes (PAGs) were disrupted or not found in this T. evansi strain, suggesting a selective loss of function in the absence of the insect life-cycle stage. Surprisingly, orthologous sequences were found in T. evansi for all 978 nuclear CDS predicted to represent the mitochondrial proteome in T. brucei, although a small number of these may have lost functionality. Consistent with previous results, the F1FO-ATP synthase γ subunit was found to have an A281 deletion, which is involved in generation of a mitochondrial membrane potential in the absence of kDNA. Candidates for CDS that are absent from the reference genome were identified in supplementary de novo assemblies of T. evansi reads. Phylogenetic analyses show that the sequenced strain belongs to a dominant group of clonal T. evansi strains with worldwide distribution that also includes isolates classified as T. equiperdum. At least three other types of T. evansi or T. equiperdum have emerged independently. Overall, the elucidation of the T. evansi genome sequence reveals extensive similarity of T. brucei and supports the contention that T. evansi should be classified as a subspecies of T. brucei. PMID:25568942

  18. Stable isotope and signature fatty acid analyses suggest reef manta rays feed on demersal zooplankton.

    PubMed

    Couturier, Lydie I E; Rohner, Christoph A; Richardson, Anthony J; Marshall, Andrea D; Jaine, Fabrice R A; Bennett, Michael B; Townsend, Kathy A; Weeks, Scarla J; Nichols, Peter D

    2013-01-01

    Assessing the trophic role and interaction of an animal is key to understanding its general ecology and dynamics. Conventional techniques used to elucidate diet, such as stomach content analysis, are not suitable for large threatened marine species. Non-lethal sampling combined with biochemical methods provides a practical alternative for investigating the feeding ecology of these species. Stable isotope and signature fatty acid analyses of muscle tissue were used for the first time to examine assimilated diet of the reef manta ray Manta alfredi, and were compared with different zooplankton functional groups (i.e. near-surface zooplankton collected during manta ray feeding events and non-feeding periods, epipelagic zooplankton, demersal zooplankton and several different zooplankton taxa). Stable isotope δ(15)N values confirmed that the reef manta ray is a secondary consumer. This species had relatively high levels of docosahexaenoic acid (DHA) indicating a flagellate-based food source in the diet, which likely reflects feeding on DHA-rich near-surface and epipelagic zooplankton. However, high levels of ω6 polyunsaturated fatty acids and slightly enriched δ(13)C values in reef manta ray tissue suggest that they do not feed solely on pelagic zooplankton, but rather obtain part of their diet from another origin. The closest match was with demersal zooplankton, suggesting it is an important component of the reef manta ray diet. The ability to feed on demersal zooplankton is likely linked to the horizontal and vertical movement patterns of this giant planktivore. These new insights into the habitat use and feeding ecology of the reef manta ray will assist in the effective evaluation of its conservation needs.

  19. Stable Isotope and Signature Fatty Acid Analyses Suggest Reef Manta Rays Feed on Demersal Zooplankton

    PubMed Central

    Couturier, Lydie I. E.; Rohner, Christoph A.; Richardson, Anthony J.; Marshall, Andrea D.; Jaine, Fabrice R. A.; Bennett, Michael B.; Townsend, Kathy A.; Weeks, Scarla J.; Nichols, Peter D.

    2013-01-01

    Assessing the trophic role and interaction of an animal is key to understanding its general ecology and dynamics. Conventional techniques used to elucidate diet, such as stomach content analysis, are not suitable for large threatened marine species. Non-lethal sampling combined with biochemical methods provides a practical alternative for investigating the feeding ecology of these species. Stable isotope and signature fatty acid analyses of muscle tissue were used for the first time to examine assimilated diet of the reef manta ray Manta alfredi, and were compared with different zooplankton functional groups (i.e. near-surface zooplankton collected during manta ray feeding events and non-feeding periods, epipelagic zooplankton, demersal zooplankton and several different zooplankton taxa). Stable isotope δ15N values confirmed that the reef manta ray is a secondary consumer. This species had relatively high levels of docosahexaenoic acid (DHA) indicating a flagellate-based food source in the diet, which likely reflects feeding on DHA-rich near-surface and epipelagic zooplankton. However, high levels of ω6 polyunsaturated fatty acids and slightly enriched δ13C values in reef manta ray tissue suggest that they do not feed solely on pelagic zooplankton, but rather obtain part of their diet from another origin. The closest match was with demersal zooplankton, suggesting it is an important component of the reef manta ray diet. The ability to feed on demersal zooplankton is likely linked to the horizontal and vertical movement patterns of this giant planktivore. These new insights into the habitat use and feeding ecology of the reef manta ray will assist in the effective evaluation of its conservation needs. PMID:24167562

  20. Multilocus phylogenetic analyses reveal unexpected abundant diversity and significant disjunct distribution pattern of the Hedgehog Mushrooms (Hydnum L.).

    PubMed

    Feng, Bang; Wang, Xiang-Hua; Ratkowsky, David; Gates, Genevieve; Lee, Su See; Grebenc, Tine; Yang, Zhu L

    2016-01-01

    Hydnum is a fungal genus proposed by Linnaeus in the early time of modern taxonomy. It contains several ectomycorrhizal species which are commonly consumed worldwide. However, Hydnum is one of the most understudied fungal genera, especially from a molecular phylogenetic view. In this study, we extensively gathered specimens of Hydnum from Asia, Europe, America and Australasia, and analyzed them by using sequences of four gene fragments (ITS, nrLSU, tef1α and rpb1). Our phylogenetic analyses recognized at least 31 phylogenetic species within Hydnum, 15 of which were reported for the first time. Most Australasian species were recognized as strongly divergent old relics, but recent migration between Australasia and the Northern Hemisphere was also detected. Within the Northern Hemisphere, frequent historical biota exchanges between the Old World and the New World via both the North Atlantic Land Bridge and the Bering Land Bridge could be elucidated. Our study also revealed that most Hydnum species found in subalpine areas of the Hengduan Mountains in southwestern China occur in northeastern/northern China and Europe, indicating that the composition of the mycobiota in the Hengduan Mountains reigion is more complicated than what we have known before. PMID:27151256

  1. Multilocus phylogenetic analyses reveal unexpected abundant diversity and significant disjunct distribution pattern of the Hedgehog Mushrooms (Hydnum L.)

    PubMed Central

    Feng, Bang; Wang, Xiang-Hua; Ratkowsky, David; Gates, Genevieve; Lee, Su See; Grebenc, Tine; Yang, Zhu L.

    2016-01-01

    Hydnum is a fungal genus proposed by Linnaeus in the early time of modern taxonomy. It contains several ectomycorrhizal species which are commonly consumed worldwide. However, Hydnum is one of the most understudied fungal genera, especially from a molecular phylogenetic view. In this study, we extensively gathered specimens of Hydnum from Asia, Europe, America and Australasia, and analyzed them by using sequences of four gene fragments (ITS, nrLSU, tef1α and rpb1). Our phylogenetic analyses recognized at least 31 phylogenetic species within Hydnum, 15 of which were reported for the first time. Most Australasian species were recognized as strongly divergent old relics, but recent migration between Australasia and the Northern Hemisphere was also detected. Within the Northern Hemisphere, frequent historical biota exchanges between the Old World and the New World via both the North Atlantic Land Bridge and the Bering Land Bridge could be elucidated. Our study also revealed that most Hydnum species found in subalpine areas of the Hengduan Mountains in southwestern China occur in northeastern/northern China and Europe, indicating that the composition of the mycobiota in the Hengduan Mountains reigion is more complicated than what we have known before. PMID:27151256

  2. Phylogenetic relationships of the Cobitoidea (Teleostei: Cypriniformes) inferred from mitochondrial and nuclear genes with analyses of gene evolution.

    PubMed

    Liu, Si-Qing; Mayden, Richard L; Zhang, Jia-Bo; Yu, Dan; Tang, Qiong-Ying; Deng, Xin; Liu, Huan-Zhang

    2012-10-15

    The superfamily Cobitoidea of the order Cypriniformes is a diverse group of fishes, inhabiting freshwater ecosystems across Eurasia and North Africa. The phylogenetic relationships of this well-corroborated natural group and diverse clade are critical to not only informing scientific communities of the phylogeny of the order Cypriniformes, the world's largest freshwater fish order, but are key to every area of comparative biology examining the evolution of traits, functional structures, and breeding behaviors to their biogeographic histories, speciation, anagenetic divergence, and divergence time estimates. In the present study, two mitochondrial gene sequences (COI, ND4+5) and four single-copy nuclear gene segments (RH1, RAG1, EGR2B, IRBP) were used to infer the phylogenetic relationships of the Cobitoidea as reconstructed from maximum likelihood (ML) and partitioned Bayesian Analysis (BA). Analyses of the combined mitochondrial/nuclear gene datasets revealed five strongly supported monophyletic Cobitoidea families and their sister-group relationships: Botiidae+(Vaillantellidae+(Cobitidae+(Nemacheilidae+Balitoridae))). These recovered relationships are in agreement with previous systematic studies on the order Cypriniformes and/or those focusing on the superfamily Cobitoidea. Using these relationships, our analyses revealed pattern lineage- or ecological-group-specific evolution of these genes for the Cobitoidea. These observations and results corroborate the hypothesis that these group-specific-ancestral ecological characters have contributed in the diversification and/or adaptations within these groups. Positive selections were detected in RH1 of nemacheilids and in RAG1 of nemacheilids and genus Vaillantella, which indicated that evolution of RH1 (related to eye's optic sense) and RAG1 (related to immunity) genes appeared to be important for the diversification of these groups. The balitorid lineage (those species inhabiting fast-flowing riverine habitats) had

  3. Mitochondrial cytochrome b of the Lyakhov mammoth (Proboscidea, Mammalia): new data and phylogenetic analyses of Elephantidae.

    PubMed

    Debruyne, Régis; Barriel, Véronique; Tassy, Pascal

    2003-03-01

    The phylogenetic relationships between recent Elephantidae (Proboscidea, Mammalia), that is to say extant elephants (Asian and African) and extinct woolly mammoth, have remained unclear to date. The prevailing morphological scheme (mammoth grouped with Asian elephant) is either supported or questioned by the molecular results. Recently, the monophyly of woolly mammoths on mitochondrial grounds has been demonstrated (Thomas, et al., 2000), but it conflicts with previous studies (Barriel et al., 1999; Derenko et al., 1997). Here, we report the partial sequencing of two mitochondrial genes: 128 bp of 12S rDNA and 561 bp of cytochrome b for the Lyakhov mammoth, a 49,000-year-old Siberian individual. We use the most comprehensive sample of mammoth (11 sequences) to determine whether the sequences achieved by former studies were congruent or not. The monophyly of a major subset of mammoths sequences (including ours) is recovered. Such a result is assumed to be a good criterion for ascertaining the origin of ancient DNA. Our sequence is incongruent with that of Yang et al. (1996), though obtained for the same individual. As far as the latter sequence is concerned, a contamination by non-identified exogenous DNA is suspected. The robustness and reliability of the sister group relation between Mammuthus primigenius and Loxodonta africana are examined: down-weighting saturated substitutions has no impact on the topology; analyzing data partitions proves that the support of this clade can be assigned to the most conservative phylogenetic signal; insufficient taxonomic and/or characters sampling contributed to former discordant conclusions. We therefore assume the monophyly of "real mammoth sequences" and the (Mammuthus, Loxodonta) clade.

  4. Molecular Epidemiology and Phylogenetic Analyses of Influenza B Virus in Thailand during 2010 to 2014

    PubMed Central

    Tewawong, Nipaporn; Suwannakarn, Kamol; Prachayangprecha, Slinporn; Korkong, Sumeth; Vichiwattana, Preeyaporn; Vongpunsawad, Sompong; Poovorawan, Yong

    2015-01-01

    Influenza B virus remains a major contributor to the seasonal influenza outbreak and its prevalence has increased worldwide. We investigated the epidemiology and analyzed the full genome sequences of influenza B virus strains in Thailand between 2010 and 2014. Samples from the upper respiratory tract were collected from patients diagnosed with influenza like-illness. All samples were screened for influenza A/B viruses by one-step multiplex real-time RT-PCR. The whole genome of 53 influenza B isolates were amplified, sequenced, and analyzed. From 14,418 respiratory samples collected during 2010 to 2014, a total of 3,050 tested positive for influenza virus. Approximately 3.27% (471/14,418) were influenza B virus samples. Fifty three isolates of influenza B virus were randomly chosen for detailed whole genome analysis. Phylogenetic analysis of the HA gene showed clusters in Victoria clades 1A, 1B, 3, 5 and Yamagata clades 2 and 3. Both B/Victoria and B/Yamagata lineages were found to co-circulate during this time. The NA sequences of all isolates belonged to lineage II and consisted of viruses from both HA Victoria and Yamagata lineages, reflecting possible reassortment of the HA and NA genes. No significant changes were seen in the NA protein. The phylogenetic trees generated through the analysis of the PB1 and PB2 genes closely resembled that of the HA gene, while trees generated from the analysis of the PA, NP, and M genes showed similar topology. The NS gene exhibited the pattern of genetic reassortment distinct from those of the PA, NP or M genes. Thus, antigenic drift and genetic reassortment among the influenza B virus strains were observed in the isolates examined. Our findings indicate that the co-circulation of two distinct lineages of influenza B viruses and the limitation of cross-protection of the current vaccine formulation provide support for quadrivalent influenza vaccine in this region. PMID:25602617

  5. Molecular phylogenetics of cixiid planthoppers (Hemiptera: Fulgoromorpha): new insights from combined analyses of mitochondrial and nuclear genes.

    PubMed

    Ceotto, Paula; Kergoat, Gaël J; Rasplus, Jean-Yves; Bourgoin, Thierry

    2008-08-01

    The planthopper family Cixiidae (Hemiptera: Fulgoromorpha) comprises approximately 160 genera and 2000 species divided in three subfamilies: Borystheninae, Bothriocerinae and Cixiinae, the later with 16 tribes. The current paper represents the first attempt to estimate phylogenetic relationships within Cixiidae based on molecular data. We use a total of 3652bp sequence alignment of four genes: the mitochondrial coding genes Cytochrome c Oxidase subunit 1 (Cox1) and Cytochrome b (Cytb), a portion of the nuclear 18S rDNA and two non-contiguous portions of the nuclear 28S rDNA. The phylogenetic relationships of 72 terminal specimens were reconstructed using both maximum parsimony and Bayesian inference methods. Through the analysis of this empirical dataset, we also provide comparisons among different a priori partitioning strategies and the use of mixture models in a Bayesian framework. Our comparisons suggest that mixture models overcome the benefits obtained by partitioning the data according to codon position and gene identity, as they provide better accuracy in phylogenetic reconstructions. The recovered maximum parsimony and Bayesian inference phylogenies suggest that the family Cixiidae is paraphyletic in respect with Delphacidae. The paraphyly of the subfamily Cixiinae is also recovered by both approaches. In contrast to a morphological phylogeny recently proposed for cixiids, subfamilies Borystheninae and Bothriocerinae form a monophyletic group. PMID:18539050

  6. Novel Evolutionary Lineages Revealed in the Chaetothyriales (Fungi) Based on Multigene Phylogenetic Analyses and Comparison of ITS Secondary Structure

    PubMed Central

    Réblová, Martina; Untereiner, Wendy A.; Réblová, Kamila

    2013-01-01

    Cyphellophora and Phialophora (Chaetothyriales, Pezizomycota) comprise species known from skin infections of humans and animals and from a variety of environmental sources. These fungi were studied based on the comparison of cultural and morphological features and phylogenetic analyses of five nuclear loci, i.e., internal transcribed spacer rDNA operon (ITS), large and small subunit nuclear ribosomal DNA (nuc28S rDNA, nuc18S rDNA), β-tubulin, DNA replication licensing factor (mcm7) and second largest subunit of RNA polymerase II (rpb2). Phylogenetic results were supported by comparative analysis of ITS1 and ITS2 secondary structure of representatives of the Chaetothyriales and the identification of substitutions among the taxa analyzed. Base pairs with non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript and unique evolutionary motifs in the ITS2 that characterize whole clades or individual taxa were mapped on predicted secondary structure models. Morphological characteristics, structural data and phylogenetic analyses of three datasets, i.e., ITS, ITS-β-tubulin and 28S-18S-rpb2-mcm7, define a robust clade containing eight species of Cyphellophora (including the type) and six species of Phialophora. These taxa are now accommodated in the Cyphellophoraceae, a novel evolutionary lineage within the Chaetothyriales. Cyphellophora is emended and expanded to encompass species with both septate and nonseptate conidia formed on discrete, intercalary, terminal or lateral phialides. Six new combinations in Cyphellophora are proposed and a dichotomous key to species accepted in the genus is provided. Cyphellophora eugeniae and C. hylomeconis, which grouped in the Chaetothyriaceae, represent another novel lineage and are introduced as the type species of separate genera. PMID:23723988

  7. Towards a phylogenetic generic classification of Thelypteridaceae: Additional sampling suggests alterations of neotropical taxa and further study of paleotropical genera.

    PubMed

    Almeida, Thaís Elias; Hennequin, Sabine; Schneider, Harald; Smith, Alan R; Batista, João Aguiar Nogueira; Ramalho, Aline Joseph; Proite, Karina; Salino, Alexandre

    2016-01-01

    Thelypteridaceae is one of the largest fern families, having about 950 species and a cosmopolitan distribution but with most species occurring in tropical and subtropical regions. Its generic classification remains controversial, with different authors recognizing from one up to 32 genera. Phylogenetic relationships within the family have not been exhaustively studied, but previous studies have confirmed the monophyly of the lineage. Thus far, sampling has been inadequate for establishing a robust hypothesis of infrafamilial relationships within the family. In order to understand phylogenetic relationships within Thelypteridaceae and thus to improve generic reclassification, we expand the molecular sampling, including new samples of Old World taxa and, especially, many additional neotropical representatives. We also explore the monophyly of exclusively or mostly neotropical genera Amauropelta, Goniopteris, Meniscium, and Steiropteris. Our sampling includes 68 taxa and 134 newly generated sequences from two plastid genomic regions (rps4-trnS and trnL-trnF), plus 73 rps4 and 72 trnL-trnF sequences from GenBank. These data resulted in a concatenated matrix of 1980 molecular characters for 149 taxa. The combined data set was analyzed using maximum parsimony and bayesian inference of phylogeny. Our results are consistent with the general topological structure found in previous studies, including two main lineages within the family: phegopteroid and thelypteroid. The thelypteroid lineage comprises two clades; one of these included the segregates Metathelypteris, Coryphopteris, and Amauropelta (including part of Parathelypteris), whereas the other comprises all segregates of Cyclosorus s.l., such as Goniopteris, Meniscium, and Steiropteris (including Thelypteris polypodioides, previously incertae sedis). The three mainly neotropical segregates were found to be monophyletic but nested in a broadly defined Cyclosorus. The fourth mainly neotropical segregate, Amauropelta

  8. Towards a phylogenetic generic classification of Thelypteridaceae: Additional sampling suggests alterations of neotropical taxa and further study of paleotropical genera.

    PubMed

    Almeida, Thaís Elias; Hennequin, Sabine; Schneider, Harald; Smith, Alan R; Batista, João Aguiar Nogueira; Ramalho, Aline Joseph; Proite, Karina; Salino, Alexandre

    2016-01-01

    Thelypteridaceae is one of the largest fern families, having about 950 species and a cosmopolitan distribution but with most species occurring in tropical and subtropical regions. Its generic classification remains controversial, with different authors recognizing from one up to 32 genera. Phylogenetic relationships within the family have not been exhaustively studied, but previous studies have confirmed the monophyly of the lineage. Thus far, sampling has been inadequate for establishing a robust hypothesis of infrafamilial relationships within the family. In order to understand phylogenetic relationships within Thelypteridaceae and thus to improve generic reclassification, we expand the molecular sampling, including new samples of Old World taxa and, especially, many additional neotropical representatives. We also explore the monophyly of exclusively or mostly neotropical genera Amauropelta, Goniopteris, Meniscium, and Steiropteris. Our sampling includes 68 taxa and 134 newly generated sequences from two plastid genomic regions (rps4-trnS and trnL-trnF), plus 73 rps4 and 72 trnL-trnF sequences from GenBank. These data resulted in a concatenated matrix of 1980 molecular characters for 149 taxa. The combined data set was analyzed using maximum parsimony and bayesian inference of phylogeny. Our results are consistent with the general topological structure found in previous studies, including two main lineages within the family: phegopteroid and thelypteroid. The thelypteroid lineage comprises two clades; one of these included the segregates Metathelypteris, Coryphopteris, and Amauropelta (including part of Parathelypteris), whereas the other comprises all segregates of Cyclosorus s.l., such as Goniopteris, Meniscium, and Steiropteris (including Thelypteris polypodioides, previously incertae sedis). The three mainly neotropical segregates were found to be monophyletic but nested in a broadly defined Cyclosorus. The fourth mainly neotropical segregate, Amauropelta

  9. The different potential of sponge bacterial symbionts in N₂ release indicated by the phylogenetic diversity and abundance analyses of denitrification genes, nirK and nosZ.

    PubMed

    Zhang, Xia; He, Liming; Zhang, Fengli; Sun, Wei; Li, Zhiyong

    2013-01-01

    Nitrogen cycle is a critical biogeochemical process of the oceans. The nitrogen fixation by sponge cyanobacteria was early observed. Until recently, sponges were found to be able to release nitrogen gas. However the gene-level evidence for the role of bacterial symbionts from different species sponges in nitrogen gas release is limited. And meanwhile, the quanitative analysis of nitrogen cycle-related genes of sponge microbial symbionts is relatively lacking. The nirK gene encoding nitrite reductase which catalyzes soluble nitrite into gas NO and nosZ gene encoding nitrous oxide reductase which catalyzes N₂O into N₂ are two key functional genes in the complete denitrification pathway. In this study, using nirK and nosZ genes as markers, the potential of bacterial symbionts in six species of sponges in the release of N2 was investigated by phylogenetic analysis and real-time qPCR. As a result, totally, 2 OTUs of nirK and 5 OTUs of nosZ genes were detected by gene library-based saturated sequencing. Difference phylogenetic diversity of nirK and nosZ genes were observed at OTU level in sponges. Meanwhile, real-time qPCR analysis showed that Xestospongia testudinaria had the highest abundance of nosZ gene, while Cinachyrella sp. had the greatest abundance of nirK gene. Phylogenetic analysis showed that the nirK and nosZ genes were probably of Alpha-, Beta-, and Gammaproteobacteria origin. The results from this study suggest that the denitrification potential of bacteria varies among sponges because of the different phylogenetic diversity and relative abundance of nosZ and nirK genes in sponges. Totally, both the qualitative and quantitative analyses of nirK and nosZ genes indicated the different potential of sponge bacterial symbionts in the release of nitrogen gas. PMID:23762300

  10. Reproductive mode evolution in lizards revisited: updated analyses examining geographic, climatic and phylogenetic effects support the cold-climate hypothesis.

    PubMed

    Watson, C M; Makowsky, R; Bagley, J C

    2014-12-01

    Viviparity, the bearing of live young, has evolved well over 100 times among squamate reptiles. This reproductive strategy is hypothesized to allow maternal control of the foetus' thermal environment and thereby to increase the fitness of the parents and offspring. Two hypotheses have been posited to explain this phenomenon: (i) the cold-climate hypothesis (CCH), which advocates low temperatures as the primary selective force; and (ii) the maternal manipulation hypothesis (MMH), which advocates temperature variability as the primary selective force. Here, we investigate whether climatic and geographic variables associated with the CCH vs. the MMH best explain the current geographical distributions of viviparity in lizards while incorporating recent advances in comparative methods, squamate phylogenetics and geospatial analysis. To do this, we compared nonphylogenetic and phylogenetic models predicting viviparity based on point-of-capture data from 20,994 museum specimens representing 215 lizard species in conjunction with spatially explicit bioclimatic and geographic (elevation and latitude) data layers. The database we analysed emphasized Nearctic lizards from three species-rich genera (Phrynosoma, Plestiodon and Sceloporus); however, we additionally analysed a less substantial, but worldwide sample of species to verify the universality of our Nearctic results. We found that maximum temperature of the warmest month (and, less commonly, elevation and maximum temperature of the driest quarter) was frequently the best predictor of viviparity and showed an association consistent with the CCH. Our results strongly favour the CCH over the MMH in explaining lizard reproductive mode evolution. PMID:25365910

  11. Reproductive mode evolution in lizards revisited: updated analyses examining geographic, climatic and phylogenetic effects support the cold-climate hypothesis.

    PubMed

    Watson, C M; Makowsky, R; Bagley, J C

    2014-12-01

    Viviparity, the bearing of live young, has evolved well over 100 times among squamate reptiles. This reproductive strategy is hypothesized to allow maternal control of the foetus' thermal environment and thereby to increase the fitness of the parents and offspring. Two hypotheses have been posited to explain this phenomenon: (i) the cold-climate hypothesis (CCH), which advocates low temperatures as the primary selective force; and (ii) the maternal manipulation hypothesis (MMH), which advocates temperature variability as the primary selective force. Here, we investigate whether climatic and geographic variables associated with the CCH vs. the MMH best explain the current geographical distributions of viviparity in lizards while incorporating recent advances in comparative methods, squamate phylogenetics and geospatial analysis. To do this, we compared nonphylogenetic and phylogenetic models predicting viviparity based on point-of-capture data from 20,994 museum specimens representing 215 lizard species in conjunction with spatially explicit bioclimatic and geographic (elevation and latitude) data layers. The database we analysed emphasized Nearctic lizards from three species-rich genera (Phrynosoma, Plestiodon and Sceloporus); however, we additionally analysed a less substantial, but worldwide sample of species to verify the universality of our Nearctic results. We found that maximum temperature of the warmest month (and, less commonly, elevation and maximum temperature of the driest quarter) was frequently the best predictor of viviparity and showed an association consistent with the CCH. Our results strongly favour the CCH over the MMH in explaining lizard reproductive mode evolution.

  12. Examining Relationships Among Several Oyster Pathogens in the Genus Bonamia Using Molecular Data, in Phylogenetic Analyses

    NASA Astrophysics Data System (ADS)

    White, D.; Burreson, E.

    2006-12-01

    Bonamiasis is a disease that affects oyster stocks around the world and is caused by intracellular protozoan parasites. Bonamia species can rapidly spread through oyster stocks and cause clinical disease in the host. The type species in the genus, Bonamia ostreae, was described from the European flat oyster Ostrea edulis. Since that time, several bonamia-like species have been observed in the following oyster hosts: Crassostrea ariakensis deployed in North Carolina, USA, Ostrea pulchana from Argentina, Ostrea chilensis from Chile, and in Ostrea angasi from Australia. There is, however, much debate over the species identity of these undescribed Bonamia parasites. An hypothesis that I will test is whether the species of Bonamia that occurs in the aforementioned oysters are representative of one species of Bonamia, Bonamia exitiosa, or are representative of different, currently undescribed, species of Bonamia. To test this hypothesis, molecular techniques to include the polymerase chain reaction (PCR) and simultaneous bi-directional sequencing (SBS) reactions were utilized to target the internal transcribed spacer (ITS) region of the ribosomal RNA gene complex for each of the undescribed Bonamia species and for Bonamia exitiosa. Phylogenetic analysis of the sequenced data in addition to pertinent morphological data, geographic distribution information, and possible host dispersals are included in this study to provide additional information for testing hypotheses developed based on molecular data.

  13. Invalidation of Diphyllobothrium hottai (Cestoda: Diphyllobothriidae) based on morphological and molecular phylogenetic analyses.

    PubMed

    Banzai-Umehara, Azusa; Suzuki, Mika; Akiyama, Takahiro; Ooi, Hong-Kean; Kawakami, Yasushi

    2016-10-01

    Diphyllobothrium hottai Yazaki, Fukumoto & Abe, 1988 was described based on the morphology of adult worms recovered from golden hamsters that had been experimentally infected with plerocercoids obtained from Japanese surf smelts (Hypomesus pretiosus japonicus) and olive rainbow smelts (Osmerus eperlanus mordax). Although D. hottai was considered to be distinct from Diphyllobothrium ditremum (Creplin, 1825), their taxonomic relationship requires further clarification. In our study, D. hottai and D. ditremum obtained from hamsters experimentally infected with plerocercoids isolated from Japanese surf smelts were compared using morphological and molecular methods. The criterion usually used to differentiate between D. hottai and D. ditremum is the difference in the angle between the long axis of the cirrus sac and that of the seminal vesicle. However, we found variation of the angle within the same individual and, one specimen showed both of the different angles that were supposedly unique to each of the species. Furthermore, phylogenetic analysis of the complete sequences of the mitochondrial cytochrome c oxidase subunit 1 and cytochrome b genes revealed that both species were genetically indistinguishable. Therefore, D. hottai is considered to be a junior synonym of D. ditremum. PMID:27353020

  14. Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements

    PubMed Central

    Joly-Lopez, Zoé; Hoen, Douglas R.; Blanchette, Mathieu; Bureau, Thomas E.

    2016-01-01

    Once perceived as merely selfish, transposable elements (TEs) are now recognized as potent agents of adaptation. One way TEs contribute to evolution is through TE exaptation, a process whereby TEs, which persist by replicating in the genome, transform into novel host genes, which persist by conferring phenotypic benefits. Known exapted TEs (ETEs) contribute diverse and vital functions, and may facilitate punctuated equilibrium, yet little is known about this process. To better understand TE exaptation, we designed an approach to resolve the phylogenetic context and timing of exaptation events and subsequent patterns of ETE diversification. Starting with known ETEs, we search in diverse genomes for basal ETEs and closely related TEs, carefully curate the numerous candidate sequences, and infer detailed phylogenies. To distinguish TEs from ETEs, we also weigh several key genomic characteristics including repetitiveness, terminal repeats, pseudogenic features, and conserved domains. Applying this approach to the well-characterized plant ETEs MUG and FHY3, we show that each group is paraphyletic and we argue that this pattern demonstrates that each originated in not one but multiple exaptation events. These exaptations and subsequent ETE diversification occurred throughout angiosperm evolution including the crown group expansion, the angiosperm radiation, and the primitive evolution of angiosperms. In addition, we detect evidence of several putative novel ETE families. Our findings support the hypothesis that TE exaptation generates novel genes more frequently than is currently thought, often coinciding with key periods of evolution. PMID:27189548

  15. Morphological and Phylogenetic Characterization of New Gephyrocapsa Isolates Suggests Introgressive Hybridization in the Emiliania/Gephyrocapsa Complex (Haptophyta).

    PubMed

    Bendif, El Mahdi; Probert, Ian; Young, Jeremy R; von Dassow, Peter

    2015-07-01

    The coccolithophore genus Gephyrocapsa contains a cosmopolitan assemblage of pelagic species, including the bloom-forming Gephyrocapsa oceanica, and is closely related to the emblematic coccolithophore Emiliania huxleyi within the Noëlaerhabdaceae. These two species have been extensively studied and are well represented in culture collections, whereas cultures of other species of this family are lacking. We report on three new strains of Gephyrocapsa isolated into culture from samples from the Chilean coastal upwelling zone using a novel flow cytometric single-cell sorting technique. The strains were characterized by morphological analysis using scanning electron microscopy and phylogenetic analysis of 6 genes (nuclear 18S and 28S rDNA, plastidial 16S and tufA, and mitochondrial cox1 and cox3 genes). Morphometric features of the coccoliths indicate that these isolates are distinct from G. oceanica and best correspond to G. muellerae. Surprisingly, both plastidial and mitochondrial gene phylogenies placed these strains within the E. huxleyi clade and well separated from G. oceanica isolates, making Emiliania appear polyphyletic. The only nuclear sequence difference, 1bp in the 28S rDNA region, also grouped E. huxleyi with the new Gephyrocapsa isolates and apart from G. oceanica. Specifically, the G. muellerae morphotype strains clustered with the mitochondrial β clade of E. huxleyi, which, like G. muellerae, has been associated with cold (temperate and sub-polar) waters. Among putative evolutionary scenarios that could explain these results we discuss the possibility that E. huxleyi is not a valid taxonomic unit, or, alternatively the possibility of past hybridization and introgression between each E. huxleyi clade and older Gephyrocapsa clades. In either case, the results support the transfer of Emiliania to Gephyrocapsa. These results have important implications for relating morphological species concepts to ecological and evolutionary units of diversity.

  16. Coalescent species delimitation in milksnakes (genus Lampropeltis) and impacts on phylogenetic comparative analyses.

    PubMed

    Ruane, Sara; Bryson, Robert W; Pyron, R Alexander; Burbrink, Frank T

    2014-03-01

    Both gene-tree discordance and unrecognized diversity are sources of error for accurate estimation of species trees, and can affect downstream diversification analyses by obscuring the correct number of nodes, their density, and the lengths of the branches subtending them. Although the theoretical impact of gene-tree discordance on evolutionary analyses has been examined previously, the effect of unsampled and cryptic diversity has not. Here, we examine how delimitation of previously unrecognized diversity in the milksnake (Lampropeltis triangulum) and use of a species-tree approach affects both estimation of the Lampropeltis phylogeny and comparative analyses with respect to the timing of diversification. Coalescent species delimitation indicates that L. triangulum is not monophyletic and that there are multiple species of milksnake, which increases the known species diversity in the genus Lampropeltis by 40%. Both genealogical and temporal discordance occurs between gene trees and the species tree, with evidence that mitochondrial DNA (mtDNA) introgression is a main factor. This discordance is further manifested in the preferred models of diversification, where the concatenated gene tree strongly supports an early burst of speciation during the Miocene, in contrast to species-tree estimates where diversification follows a birth-death model and speciation occurs mostly in the Pliocene and Pleistocene. This study highlights the crucial interaction among coalescent-based phylogeography and species delimitation, systematics, and species diversification analyses.

  17. Phylogenetics: bats united, microbats divided.

    PubMed

    Springer, Mark S

    2013-11-18

    Phylogenetic analyses on four new bat genomes provide convincing support for the placement of bats relative to other placental mammals, suggest that microbats are an unnatural group, and have important implications for understanding the evolution of echolocation.

  18. Morphological analyses suggest a new taxonomic circumscription for Hymenaea courbaril L. (Leguminosae, Caesalpinioideae).

    PubMed

    Souza, Isys Mascarenhas; Funch, Ligia Silveira; de Queiroz, Luciano Paganucci

    2014-01-01

    Hymenaea is a genus of the Resin-producing Clade of the tribe Detarieae (Leguminosae: Caesalpinioideae) with 14 species. Hymenaea courbaril is the most widespread species of the genus, ranging from southern Mexico to southeastern Brazil. As currently circumscribed, Hymenaea courbaril is a polytypic species with six varieties: var. altissima, var. courbaril, var. longifolia, var. stilbocarpa, var. subsessilis, and var. villosa. These varieties are distinguishable mostly by traits related to leaflet shape and indumentation, and calyx indumentation. We carried out morphometric analyses of 14 quantitative (continuous) leaf characters in order to assess the taxonomy of Hymenaea courbaril under the Unified Species Concept framework. Cluster analysis used the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) based on Bray-Curtis dissimilarity matrices. Principal Component Analyses (PCA) were carried out based on the same morphometric matrix. Two sets of Analyses of Similarity and Non Parametric Multivariate Analysis of Variance were carried out to evaluate statistical support (1) for the major groups recovered using UPGMA and PCA, and (2) for the varieties. All analyses recovered three major groups coincident with (1) var. altissima, (2) var. longifolia, and (3) all other varieties. These results, together with geographical and habitat information, were taken as evidence of three separate metapopulation lineages recognized here as three distinct species. Nomenclatural adjustments, including reclassifying formerly misapplied types, are proposed.

  19. Morphological analyses suggest a new taxonomic circumscription for Hymenaea courbaril L. (Leguminosae, Caesalpinioideae)

    PubMed Central

    Souza, Isys Mascarenhas; Funch, Ligia Silveira; de Queiroz, Luciano Paganucci

    2014-01-01

    Abstract Hymenaea is a genus of the Resin-producing Clade of the tribe Detarieae (Leguminosae: Caesalpinioideae) with 14 species. Hymenaea courbaril is the most widespread species of the genus, ranging from southern Mexico to southeastern Brazil. As currently circumscribed, Hymenaea courbaril is a polytypic species with six varieties: var. altissima, var. courbaril, var. longifolia, var. stilbocarpa, var. subsessilis, and var. villosa. These varieties are distinguishable mostly by traits related to leaflet shape and indumentation, and calyx indumentation. We carried out morphometric analyses of 14 quantitative (continuous) leaf characters in order to assess the taxonomy of Hymenaea courbaril under the Unified Species Concept framework. Cluster analysis used the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) based on Bray-Curtis dissimilarity matrices. Principal Component Analyses (PCA) were carried out based on the same morphometric matrix. Two sets of Analyses of Similarity and Non Parametric Multivariate Analysis of Variance were carried out to evaluate statistical support (1) for the major groups recovered using UPGMA and PCA, and (2) for the varieties. All analyses recovered three major groups coincident with (1) var. altissima, (2) var. longifolia, and (3) all other varieties. These results, together with geographical and habitat information, were taken as evidence of three separate metapopulation lineages recognized here as three distinct species. Nomenclatural adjustments, including reclassifying formerly misapplied types, are proposed. PMID:25009440

  20. The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data.

    PubMed

    Duchêne, Sebastián; Duchêne, David; Holmes, Edward C; Ho, Simon Y W

    2015-07-01

    Rates and timescales of viral evolution can be estimated using phylogenetic analyses of time-structured molecular sequences. This involves the use of molecular-clock methods, calibrated by the sampling times of the viral sequences. However, the spread of these sampling times is not always sufficient to allow the substitution rate to be estimated accurately. We conducted Bayesian phylogenetic analyses of simulated virus data to evaluate the performance of the date-randomization test, which is sometimes used to investigate whether time-structured data sets have temporal signal. An estimate of the substitution rate passes this test if its mean does not fall within the 95% credible intervals of rate estimates obtained using replicate data sets in which the sampling times have been randomized. We find that the test sometimes fails to detect rate estimates from data with no temporal signal. This error can be minimized by using a more conservative criterion, whereby the 95% credible interval of the estimate with correct sampling times should not overlap with those obtained with randomized sampling times. We also investigated the behavior of the test when the sampling times are not uniformly distributed throughout the tree, which sometimes occurs in empirical data sets. The test performs poorly in these circumstances, such that a modification to the randomization scheme is needed. Finally, we illustrate the behavior of the test in analyses of nucleotide sequences of cereal yellow dwarf virus. Our results validate the use of the date-randomization test and allow us to propose guidelines for interpretation of its results.

  1. Triparental origin of triploid onion, Allium × cornutum (Clementi ex Visiani, 1842), as evidenced by molecular, phylogenetic and cytogenetic analyses

    PubMed Central

    2014-01-01

    Background Reconstruction of the parental origins of cultivated plants from wild relatives, especially after long periods of domestication, is not a trivial task. However, recent advances in molecular phylogenetics, among other approaches, have proved to be very informative in analyses of the origin and evolution of polyploid genomes. An established minor garden crop, triploid onion Allium × cornutum (Clementi ex Visiani, 1842) (2n = 3x = 24), is widespread in southeastern Asia and Europe. Our previous cytogenetic analyses confirmed its highly heterozygous karyotype and indicated its possible complex triparental genome origin. Allium cepa L. and Allium roylei Stearn were suggested as two putative parental species of A. × cornutum, whereas the third parental species remained hitherto unknown. Results Here we report the phylogenetic analyses of the internal transcribed spacers ITS1-5.8S-ITS2 of 35S rDNA and the non-transcribed spacer (NTS) region of 5S rDNA of A. × cornutum and its relatives of the section Cepa. Both ITS and NTS sequence data revealed intra-individual variation in triploid onion, and these data clustered into the three main clades, each with high sequence homology to one of three other species of section Cepa: A. cepa, A. roylei, and unexpectedly, the wild Asian species Allium pskemense B. Fedtsh. Allium pskemense is therefore inferred to be the third, so far unknown, putative parental species of triploid onion Allium × cornutum. The 35S and 5S rRNA genes were found to be localised on somatic chromosomes of A. × cornutum and its putative parental species by double fluorescent in situ hybridisation (FISH). The localisation of 35S and 5S rDNA in A. × cornutum chromosomes corresponded to their respective positions in the three putative parental species, A. cepa, A. pskemense, and A. roylei. GISH (genomic in situ hybridisation) using DNA of the three putative parental diploids corroborated the results of the phylogenetic study

  2. Geometric morphometric analyses of hominid proximal femora: taxonomic and phylogenetic considerations.

    PubMed

    Holliday, T W; Hutchinson, Vance T; Morrow, Melissa M B; Livesay, Glen A

    2010-02-01

    The proximal femur has long been used to distinguish fossil hominin taxa. Specifically, the genus Homo is said to be characterized by larger femoral heads, shorter femoral necks, and more lateral flare of the greater trochanter than are members of the genera Australopithecus or Paranthropus. Here, a digitizing arm was used to collect landmark data on recent human (n=82), chimpanzee (n=16), and gorilla (n=20) femora and casts of six fossil hominin femora in order to test whether one can discriminate extant and fossil hominid (sensu lato) femora into different taxa using three-dimensional (3D) geometric morphometric analyses. Twenty proximal femoral landmarks were chosen to best quantify the shape differences between hominin genera. These data were first subjected to Procrustes analysis. The resultant fitted coordinate values were then subjected to PCA. PC scores were used to compute a dissimilarity matrix that was subjected to cluster analyses. Results indicate that one can easily distinguish Homo, Pan, and Gorilla from each other based on proximal femur shape, and one can distinguish Pliocene and Early Pleistocene hominin femora from those of recent Homo. It is more difficult to distinguish Early Pleistocene Homo proximal femora from those of Australopithecus or Paranthropus, but cluster analyses appear to separate the fossil hominins into four groups: an early australopith cluster that is an outlier from other fossil hominins; and two clusters that are sister taxa to each other: a late australopith/Paranthropus group and an early Homo group. PMID:20096410

  3. Phylogenetic Analyses of Armillaria Reveal at Least 15 Phylogenetic Lineages in China, Seven of Which Are Associated with Cultivated Gastrodia elata

    PubMed Central

    Guo, Ting; Wang, Han Chen; Xue, Wan Qiu; Zhao, Jun; Yang, Zhu L.

    2016-01-01

    Fungal species of Armillaria, which can act as plant pathogens and/or symbionts of the Chinese traditional medicinal herb Gastrodia elata (“Tianma”), are ecologically and economically important and have consequently attracted the attention of mycologists. However, their taxonomy has been highly dependent on morphological characterization and mating tests. In this study, we phylogenetically analyzed Chinese Armillaria samples using the sequences of the internal transcribed spacer region, translation elongation factor-1 alpha gene and beta-tubulin gene. Our data revealed at least 15 phylogenetic lineages of Armillaria from China, of which seven were newly discovered and two were recorded from China for the first time. Fourteen Chinese biological species of Armillaria, which were previously defined based on mating tests, could be assigned to the 15 phylogenetic lineages identified herein. Seven of the 15 phylogenetic lineages were found to be disjunctively distributed in different continents of the Northern Hemisphere, while eight were revealed to be endemic to certain continents. In addition, we found that seven phylogenetic lineages of Armillaria were used for the cultivation of Tianma, only two of which had been recorded to be associated with Tianma previously. We also illustrated that G. elata f. glauca (“Brown Tianma”) and G. elata f. elata (“Red Tianma”), two cultivars of Tianma grown in different regions of China, form symbiotic relationships with different phylogenetic lineages of Armillaria. These findings should aid the development of Tianma cultivation in China. PMID:27138686

  4. Phylogenetic Analyses of Armillaria Reveal at Least 15 Phylogenetic Lineages in China, Seven of Which Are Associated with Cultivated Gastrodia elata.

    PubMed

    Guo, Ting; Wang, Han Chen; Xue, Wan Qiu; Zhao, Jun; Yang, Zhu L

    2016-01-01

    Fungal species of Armillaria, which can act as plant pathogens and/or symbionts of the Chinese traditional medicinal herb Gastrodia elata ("Tianma"), are ecologically and economically important and have consequently attracted the attention of mycologists. However, their taxonomy has been highly dependent on morphological characterization and mating tests. In this study, we phylogenetically analyzed Chinese Armillaria samples using the sequences of the internal transcribed spacer region, translation elongation factor-1 alpha gene and beta-tubulin gene. Our data revealed at least 15 phylogenetic lineages of Armillaria from China, of which seven were newly discovered and two were recorded from China for the first time. Fourteen Chinese biological species of Armillaria, which were previously defined based on mating tests, could be assigned to the 15 phylogenetic lineages identified herein. Seven of the 15 phylogenetic lineages were found to be disjunctively distributed in different continents of the Northern Hemisphere, while eight were revealed to be endemic to certain continents. In addition, we found that seven phylogenetic lineages of Armillaria were used for the cultivation of Tianma, only two of which had been recorded to be associated with Tianma previously. We also illustrated that G. elata f. glauca ("Brown Tianma") and G. elata f. elata ("Red Tianma"), two cultivars of Tianma grown in different regions of China, form symbiotic relationships with different phylogenetic lineages of Armillaria. These findings should aid the development of Tianma cultivation in China. PMID:27138686

  5. Phylogenetic Relationships and Morphological Character Evolution of Photosynthetic Euglenids (Excavata) Inferred from Taxon-rich Analyses of Five Genes.

    PubMed

    Karnkowska, Anna; Bennett, Matthew S; Watza, Donovan; Kim, Jong Im; Zakryś, Bożena; Triemer, Richard E

    2015-01-01

    Photosynthetic euglenids acquired chloroplasts by secondary endosymbiosis, which resulted in changes to their mode of nutrition and affected the evolution of their morphological characters. Mapping morphological characters onto a reliable molecular tree could elucidate major trends of those changes. We analyzed nucleotide sequence data from regions of three nuclear-encoded genes (nSSU, nLSU, hsp90), one chloroplast-encoded gene (cpSSU) and one nuclear-encoded chloroplast gene (psbO) to estimate phylogenetic relationships among 59 photosynthetic euglenid species. Our results were consistent with previous works; most genera were monophyletic, except for the polyphyletic genus Euglena, and the paraphyletic genus Phacus. We also analyzed character evolution in photosynthetic euglenids using our phylogenetic tree and eight morphological traits commonly used for generic and species diagnoses, including: characters corresponding to well-defined clades, apomorphies like presence of lorica and mucilaginous stalks, and homoplastic characters like rigid cells and presence of large paramylon grains. This research indicated that pyrenoids were lost twice during the evolution of phototrophic euglenids, and that mucocysts, which only occur in the genus Euglena, evolved independently at least twice. In contrast, the evolution of cell shape and chloroplast morphology was difficult to elucidate, and could not be unambiguously reconstructed in our analyses.

  6. Phylogenetic Relationships among the Cryptophyta: Analyses of Nuclear-Encoded SSU rRNA Sequences Support the Monophyly of Extant Plastid-Containing Lineages.

    PubMed

    Marin, B; Klingberg, M; Melkonian, M

    1998-09-01

    The Cryptophyta comprise photoautotrophic protists with complex plastids which harbor a remnant eukaryotic nucleus (nucleomorph) and a few heterotrophic taxa which either lack a plastid (Goniomonas) or contain a complex plastid devoid of pigments (Ieucoplast; Chilomonas). To resolve the phylogenetic relationships between photosynthetic, leucoplast-containing and aplastidial taxa, we determined complete nuclear-encoded SSU rRNA-sequences from 12 cryptophyte taxa representing the genera Cryptomonas, Chilomonas, Rhodomonas, Chroomonas, Hemiselmis, Proteomonas and Teleaulax and, as an outgroup taxon, Cyanoptyche gloeocystis (Glaucocystophyta). Phylogenetic analyses of SSU rRNA sequences from a total of 24 cryptophyte taxa rooted with 4 glaucocystophyte taxa using distance, parsimony and likelihood methods as well as LogDet transformations invariably position the aplastidial genus Goniomonas as a sister taxon to a monophyletic lineage consisting of all plastid containing cryptophytes including Chilomonas. Among the plastid-containing taxa, we identify six major clades each supported by high bootstrap values: clade I (Cryptomonas and Chilomonas), clade II (Rhodomonas, Pyrenomonas, Rhinomonas and Storeatula), clade III (Guillardia and the 'unidentified cryptophyte' strain CCMP 325), clade IV (Teleaulax and Geminigera), clade V (Proteomonas) and clade VI (Hemiselmis, Chroomonas and Komma). Clade I (Cryptomonas and Chilomonas) represents a sister group to clades II-VI which together form a monophyletic lineage; the phylogenetic relationships between clades II-VI remain largely unresolved. Chilomonas is positioned within the Cryptomonas clade and thus presumably evolved from a photosynthetic taxon of this genus. In our analysis the characters blue and red pigmentation do not correspond with a basal subdivision of the phylum, thus rejecting this character for higher-level classification of cryptophytes. However, different spectroscopic subtypes of phycoerythrin (PE I-III) and

  7. Phylogenetic Relationships among the Cryptophyta: Analyses of Nuclear-Encoded SSU rRNA Sequences Support the Monophyly of Extant Plastid-Containing Lineages.

    PubMed

    Marin, B; Klingberg, M; Melkonian, M

    1998-09-01

    The Cryptophyta comprise photoautotrophic protists with complex plastids which harbor a remnant eukaryotic nucleus (nucleomorph) and a few heterotrophic taxa which either lack a plastid (Goniomonas) or contain a complex plastid devoid of pigments (Ieucoplast; Chilomonas). To resolve the phylogenetic relationships between photosynthetic, leucoplast-containing and aplastidial taxa, we determined complete nuclear-encoded SSU rRNA-sequences from 12 cryptophyte taxa representing the genera Cryptomonas, Chilomonas, Rhodomonas, Chroomonas, Hemiselmis, Proteomonas and Teleaulax and, as an outgroup taxon, Cyanoptyche gloeocystis (Glaucocystophyta). Phylogenetic analyses of SSU rRNA sequences from a total of 24 cryptophyte taxa rooted with 4 glaucocystophyte taxa using distance, parsimony and likelihood methods as well as LogDet transformations invariably position the aplastidial genus Goniomonas as a sister taxon to a monophyletic lineage consisting of all plastid containing cryptophytes including Chilomonas. Among the plastid-containing taxa, we identify six major clades each supported by high bootstrap values: clade I (Cryptomonas and Chilomonas), clade II (Rhodomonas, Pyrenomonas, Rhinomonas and Storeatula), clade III (Guillardia and the 'unidentified cryptophyte' strain CCMP 325), clade IV (Teleaulax and Geminigera), clade V (Proteomonas) and clade VI (Hemiselmis, Chroomonas and Komma). Clade I (Cryptomonas and Chilomonas) represents a sister group to clades II-VI which together form a monophyletic lineage; the phylogenetic relationships between clades II-VI remain largely unresolved. Chilomonas is positioned within the Cryptomonas clade and thus presumably evolved from a photosynthetic taxon of this genus. In our analysis the characters blue and red pigmentation do not correspond with a basal subdivision of the phylum, thus rejecting this character for higher-level classification of cryptophytes. However, different spectroscopic subtypes of phycoerythrin (PE I-III) and

  8. Evolutionary Analyses Suggest a Function of MxB Immunity Proteins Beyond Lentivirus Restriction

    PubMed Central

    Mitchell, Patrick S.; Young, Janet M.; Emerman, Michael; Malik, Harmit S.

    2015-01-01

    Viruses impose diverse and dynamic challenges on host defenses. Diversifying selection of codons and gene copy number variation are two hallmarks of genetic innovation in antiviral genes engaged in host-virus genetic conflicts. The myxovirus resistance (Mx) genes encode interferon-inducible GTPases that constitute a major arm of the cell-autonomous defense against viral infection. Unlike the broad antiviral activity of MxA, primate MxB was recently shown to specifically inhibit lentiviruses including HIV-1. We carried out detailed evolutionary analyses to investigate whether genetic conflict with lentiviruses has shaped MxB evolution in primates. We found strong evidence for diversifying selection in the MxB N-terminal tail, which contains molecular determinants of MxB anti-lentivirus specificity. However, we found no overlap between previously-mapped residues that dictate lentiviral restriction and those that have evolved under diversifying selection. Instead, our findings are consistent with MxB having a long-standing and important role in the interferon response to viral infection against a broader range of pathogens than is currently appreciated. Despite its critical role in host innate immunity, we also uncovered multiple functional losses of MxB during mammalian evolution, either by pseudogenization or by gene conversion from MxA genes. Thus, although the majority of mammalian genomes encode two Mx genes, this apparent stasis masks the dramatic effects that recombination and diversifying selection have played in shaping the evolutionary history of Mx genes. Discrepancies between our study and previous publications highlight the need to account for recombination in analyses of positive selection, as well as the importance of using sequence datasets with appropriate depth of divergence. Our study also illustrates that evolutionary analyses of antiviral gene families are critical towards understanding molecular principles that govern host-virus interactions and

  9. Evolutionary Analyses Suggest a Function of MxB Immunity Proteins Beyond Lentivirus Restriction.

    PubMed

    Mitchell, Patrick S; Young, Janet M; Emerman, Michael; Malik, Harmit S

    2015-12-01

    Viruses impose diverse and dynamic challenges on host defenses. Diversifying selection of codons and gene copy number variation are two hallmarks of genetic innovation in antiviral genes engaged in host-virus genetic conflicts. The myxovirus resistance (Mx) genes encode interferon-inducible GTPases that constitute a major arm of the cell-autonomous defense against viral infection. Unlike the broad antiviral activity of MxA, primate MxB was recently shown to specifically inhibit lentiviruses including HIV-1. We carried out detailed evolutionary analyses to investigate whether genetic conflict with lentiviruses has shaped MxB evolution in primates. We found strong evidence for diversifying selection in the MxB N-terminal tail, which contains molecular determinants of MxB anti-lentivirus specificity. However, we found no overlap between previously-mapped residues that dictate lentiviral restriction and those that have evolved under diversifying selection. Instead, our findings are consistent with MxB having a long-standing and important role in the interferon response to viral infection against a broader range of pathogens than is currently appreciated. Despite its critical role in host innate immunity, we also uncovered multiple functional losses of MxB during mammalian evolution, either by pseudogenization or by gene conversion from MxA genes. Thus, although the majority of mammalian genomes encode two Mx genes, this apparent stasis masks the dramatic effects that recombination and diversifying selection have played in shaping the evolutionary history of Mx genes. Discrepancies between our study and previous publications highlight the need to account for recombination in analyses of positive selection, as well as the importance of using sequence datasets with appropriate depth of divergence. Our study also illustrates that evolutionary analyses of antiviral gene families are critical towards understanding molecular principles that govern host-virus interactions and

  10. Analyses of soft tissue from Tyrannosaurus rex suggest the presence of protein.

    PubMed

    Schweitzer, Mary Higby; Suo, Zhiyong; Avci, Recep; Asara, John M; Allen, Mark A; Arce, Fernando Teran; Horner, John R

    2007-04-13

    We performed multiple analyses of Tyrannosaurus rex (specimen MOR 1125) fibrous cortical and medullary tissues remaining after demineralization. The results indicate that collagen I, the main organic component of bone, has been preserved in low concentrations in these tissues. The findings were independently confirmed by mass spectrometry. We propose a possible chemical pathway that may contribute to this preservation. The presence of endogenous protein in dinosaur bone may validate hypotheses about evolutionary relationships, rates, and patterns of molecular change and degradation, as well as the chemical stability of molecules over time.

  11. Genome-Wide Identification, Phylogenetic and Expression Analyses of the Ubiquitin-Conjugating Enzyme Gene Family in Maize

    PubMed Central

    Jue, Dengwei; Sang, Xuelian; Lu, Shengqiao; Dong, Chen; Zhao, Qiufang; Chen, Hongliang; Jia, Liqiang

    2015-01-01

    Background Ubiquitination is a post-translation modification where ubiquitin is attached to a substrate. Ubiquitin-conjugating enzymes (E2s) play a major role in the ubiquitin transfer pathway, as well as a variety of functions in plant biological processes. To date, no genome-wide characterization of this gene family has been conducted in maize (Zea mays). Methodology/Principal Findings In the present study, a total of 75 putative ZmUBC genes have been identified and located in the maize genome. Phylogenetic analysis revealed that ZmUBC proteins could be divided into 15 subfamilies, which include 13 ubiquitin-conjugating enzymes (ZmE2s) and two independent ubiquitin-conjugating enzyme variant (UEV) groups. The predicted ZmUBC genes were distributed across 10 chromosomes at different densities. In addition, analysis of exon-intron junctions and sequence motifs in each candidate gene has revealed high levels of conservation within and between phylogenetic groups. Tissue expression analysis indicated that most ZmUBC genes were expressed in at least one of the tissues, indicating that these are involved in various physiological and developmental processes in maize. Moreover, expression profile analyses of ZmUBC genes under different stress treatments (4°C, 20% PEG6000, and 200 mM NaCl) and various expression patterns indicated that these may play crucial roles in the response of plants to stress. Conclusions Genome-wide identification, chromosome organization, gene structure, evolutionary and expression analyses of ZmUBC genes have facilitated in the characterization of this gene family, as well as determined its potential involvement in growth, development, and stress responses. This study provides valuable information for better understanding the classification and putative functions of the UBC-encoding genes of maize. PMID:26606743

  12. Revisiting the Clinal Concept of Evolution and Dispersal for the Tick-Borne Flaviviruses by Using Phylogenetic and Biogeographic Analyses

    PubMed Central

    Heinze, D. M.; Gould, E. A.

    2012-01-01

    Tick-borne flaviviruses (TBF) are widely dispersed across Africa, Europe, Asia, Oceania, and North America, and some present a significant threat to human health. Seminal studies on tick-borne encephalitis viruses (TBEV), based on partial envelope gene sequences, predicted a westward clinal pattern of evolution and dispersal across northern Eurasia, terminating in the British Isles. We tested this hypothesis using all available full-length open reading frame (ORF) TBF sequences. Phylogenetic analysis was consistent with current reports. However, linear and nonlinear regression analysis of genetic versus geographic distance combined with BEAST analysis identified two separate clines, suggesting that TBEV spread both east and west from a central point. In addition, BEAST analysis suggested that TBF emerged and dispersed more than 16,000 years ago, significantly earlier than previously predicted. Thus, climatic and ecological changes may have played a greater role in TBF dispersal than humans. PMID:22674986

  13. Phylogenetic and phylogeographic analyses of porcine circovirus type 2 among pig farms in Vietnam.

    PubMed

    Huynh, T M L; Nguyen, B H; Nguyen, V G; Dang, H A; Mai, T N; Tran, T H G; Ngo, M H; Le, V T; Vu, T N; Ta, T K C; Vo, V H; Kim, H K; Park, B K

    2014-12-01

    This study demonstrated the prevalence of Porcine circovirus type 2 (PCV2) among pig farms in Vietnam. Analyses of the genome, capsid protein and phylogeny classified all 30 Vietnamese PCV2 strains as the PCV2b genotype, belonging to the clusters of 1A, 1B, 1C and recombinant forms. Each viral genome was 1767 nucleotides long and shared 96.0-100% nucleotide sequence identity. The amino acid substitutions in the capsid protein of the Vietnamese PCV2 strains were in immunodominant regions, and the majority of strains (24/30) contained a lysine extension at the C-terminus. Bayesian phylogeographic analysis revealed epidemic links of the PCV2 recombinant cluster within and among countries, which supports a circulating recombinant form of PCV2. Further analysis by the Jameson-Wolf antigenic index indicated antigenic alterations at important sites in the capsid protein (sites 131-133) among the recombinant cluster and the other clusters of PCV2b. PMID:23414511

  14. The analysis of core and symbiotic genes of rhizobia nodulating Vicia from different continents reveals their common phylogenetic origin and suggests the distribution of Rhizobium leguminosarum strains together with Vicia seeds.

    PubMed

    Alvarez-Martínez, Estela R; Valverde, Angel; Ramírez-Bahena, Martha Helena; García-Fraile, Paula; Tejedor, Carmen; Mateos, Pedro F; Santillana, Nery; Zúñiga, Doris; Peix, Alvaro; Velázquez, Encarna

    2009-08-01

    In this work, we analysed the core and symbiotic genes of rhizobial strains isolated from Vicia sativa in three soils from the Northwest of Spain, and compared them with other Vicia endosymbionts isolated in other geographical locations. The analysis of rrs, recA and atpD genes and 16S-23S rRNA intergenic spacer showed that the Spanish strains nodulating V. sativa are phylogenetically close to those isolated from V. sativa and V. faba in different European, American and Asian countries forming a group related to Rhizobium leguminosarum. The analysis of the nodC gene of strains nodulating V. sativa and V. faba in different continents showed they belong to a phylogenetically compact group indicating that these legumes are restrictive hosts. The results of the nodC gene analysis allow the delineation of the biovar viciae showing a common phylogenetic origin of V. sativa and V. faba endosymbionts in several continents. Since these two legume species are indigenous from Europe, our results suggest a world distribution of strains from R. leguminosarum together with the V. sativa and V. faba seeds and a close coevolution among chromosome, symbiotic genes and legume host in this Rhizobium-Vicia symbiosis.

  15. Multivariate and phylogenetic analyses assessing the response of bacterial mat communities from an ancient oligotrophic aquatic ecosystem to different scenarios of long-term environmental disturbance.

    PubMed

    Pajares, Silvia; Souza, Valeria; Eguiarte, Luis E

    2015-01-01

    Understanding the response of bacterial communities to environmental change is extremely important in predicting the effect of biogeochemical modifications in ecosystem functioning. The Cuatro Cienegas Basin is an ancient oasis in the Mexican Chihuahuan desert that hosts a wide diversity of microbial mats and stromatolites that have survived in extremely oligotrophic pools with nearly constant conditions. However, thus far, the response of these unique microbial communities to long-term environmental disturbances remains unexplored. We therefore studied the compositional stability of these bacterial mat communities by using a replicated (3x) mesocosm experiment: a) Control; b) Fluct: fluctuating temperature; c) 40C: increase to 40 ºC; d) UVplus: artificial increase in UV radiation; and f) UVmin: UV radiation protection. In order to observe the changes in biodiversity, we obtained 16S rRNA gene clone libraries from microbial mats at the end of the experiment (eight months) and analyzed them using multivariate and phylogenetic tools. Sequences were assigned to 13 major lineages, among which Cyanobacteria (38.8%) and Alphaproteobacteria (25.5%) were the most abundant. The less extreme treatments (Control and UVmin) had a more similar composition and distribution of the phylogenetic groups with the natural pools than the most extreme treatments (Fluct, 40C, and UVplus), which showed drastic changes in the community composition and structure, indicating a different community response to each environmental disturbance. An increase in bacterial diversity was found in the UVmin treatment, suggesting that protected environments promote the establishment of complex bacterial communities, while stressful environments reduce diversity and increase the dominance of a few Cyanobacterial OTUs (mainly Leptolyngbya sp) through environmental filtering. Mesocosm experiments using complex bacterial communities, along with multivariate and phylogenetic analyses of molecular data, can

  16. Multivariate and Phylogenetic Analyses Assessing the Response of Bacterial Mat Communities from an Ancient Oligotrophic Aquatic Ecosystem to Different Scenarios of Long-Term Environmental Disturbance

    PubMed Central

    Pajares, Silvia; Souza, Valeria; Eguiarte, Luis E.

    2015-01-01

    Understanding the response of bacterial communities to environmental change is extremely important in predicting the effect of biogeochemical modifications in ecosystem functioning. The Cuatro Cienegas Basin is an ancient oasis in the Mexican Chihuahuan desert that hosts a wide diversity of microbial mats and stromatolites that have survived in extremely oligotrophic pools with nearly constant conditions. However, thus far, the response of these unique microbial communities to long-term environmental disturbances remains unexplored. We therefore studied the compositional stability of these bacterial mat communities by using a replicated (3x) mesocosm experiment: a) Control; b) Fluct: fluctuating temperature; c) 40C: increase to 40 ºC; d) UVplus: artificial increase in UV radiation; and f) UVmin: UV radiation protection. In order to observe the changes in biodiversity, we obtained 16S rRNA gene clone libraries from microbial mats at the end of the experiment (eight months) and analyzed them using multivariate and phylogenetic tools. Sequences were assigned to 13 major lineages, among which Cyanobacteria (38.8%) and Alphaproteobacteria (25.5%) were the most abundant. The less extreme treatments (Control and UVmin) had a more similar composition and distribution of the phylogenetic groups with the natural pools than the most extreme treatments (Fluct, 40C, and UVplus), which showed drastic changes in the community composition and structure, indicating a different community response to each environmental disturbance. An increase in bacterial diversity was found in the UVmin treatment, suggesting that protected environments promote the establishment of complex bacterial communities, while stressful environments reduce diversity and increase the dominance of a few Cyanobacterial OTUs (mainly Leptolyngbya sp) through environmental filtering. Mesocosm experiments using complex bacterial communities, along with multivariate and phylogenetic analyses of molecular data, can

  17. Phylogenetic distribution of intron positions in alpha-amylase genes of bilateria suggests numerous gains and losses.

    PubMed

    Da Lage, Jean-Luc; Maczkowiak, Frédérique; Cariou, Marie-Louise

    2011-01-01

    Most eukaryotes have at least some genes interrupted by introns. While it is well accepted that introns were already present at moderate density in the last eukaryote common ancestor, the conspicuous diversity of intron density among genomes suggests a complex evolutionary history, with marked differences between phyla. The question of the rates of intron gains and loss in the course of evolution and factors influencing them remains controversial. We have investigated a single gene family, alpha-amylase, in 55 species covering a variety of animal phyla. Comparison of intron positions across phyla suggests a complex history, with a likely ancestral intronless gene undergoing frequent intron loss and gain, leading to extant intron/exon structures that are highly variable, even among species from the same phylum. Because introns are known to play no regulatory role in this gene and there is no alternative splicing, the structural differences may be interpreted more easily: intron positions, sizes, losses or gains may be more likely related to factors linked to splicing mechanisms and requirements, and to recognition of introns and exons, or to more extrinsic factors, such as life cycle and population size. We have shown that intron losses outnumbered gains in recent periods, but that "resets" of intron positions occurred at the origin of several phyla, including vertebrates. Rates of gain and loss appear to be positively correlated. No phase preference was found. We also found evidence for parallel gains and for intron sliding. Presence of introns at given positions was correlated to a strong protosplice consensus sequence AG/G, which was much weaker in the absence of intron. In contrast, recent intron insertions were not associated with a specific sequence. In animal Amy genes, population size and generation time seem to have played only minor roles in shaping gene structures.

  18. The importance of retaining a phylogenetic perspective in traits-based community analyses

    SciTech Connect

    Poteat, Monica D.; Buchwalter, David B.; Jacobus, Luke M.

    2015-04-08

    1) Many environmental stressors manifest their effects via physiological processes (traits) that can differ significantly among species and species groups. We compiled available data for three traits related to the bioconcentration of the toxic metal cadmium (Cd) from 42 aquatic insect species representing orders Ephemeroptera (mayfly), Plecoptera (stonefly), and Trichoptera (caddisfly). These traits included the propensity to take up Cd from water (uptake rate constant, ku), the ability to excrete Cd (efflux rate constant, ke), and the net result of these two processes (bioconcentration factor, BCF). 2) Ranges in these Cd bioaccumulation traits varied in magnitude across lineages (some lineages had a greater tendency to bioaccumulate Cd than others). Overlap in the ranges of trait values among different lineages was common and highlights situations where species from different lineages can share a similar trait state, but represent the high end of possible physiological values for one lineage and the low end for another. 3) Variance around the mean trait state differed widely across clades, suggesting that some groups (e.g., Ephemerellidae) are inherently more variable than others (e.g., Perlidae). Thus, trait variability/lability is at least partially a function of lineage. 4) Akaike information criterion (AIC) comparisons of statistical models were more often driven by clade than by other potential biological or ecological explanation tested. Clade-driven models generally improved with increasing taxonomic resolution. 5) Altogether, these findings suggest that lineage provides context for the analysis of species traits, and that failure to consider lineage in community-based analysis of traits may obscure important patterns of species responses to environmental change.

  19. The importance of retaining a phylogenetic perspective in traits-based community analyses

    DOE PAGESBeta

    Poteat, Monica D.; Buchwalter, David B.; Jacobus, Luke M.

    2015-04-08

    1) Many environmental stressors manifest their effects via physiological processes (traits) that can differ significantly among species and species groups. We compiled available data for three traits related to the bioconcentration of the toxic metal cadmium (Cd) from 42 aquatic insect species representing orders Ephemeroptera (mayfly), Plecoptera (stonefly), and Trichoptera (caddisfly). These traits included the propensity to take up Cd from water (uptake rate constant, ku), the ability to excrete Cd (efflux rate constant, ke), and the net result of these two processes (bioconcentration factor, BCF). 2) Ranges in these Cd bioaccumulation traits varied in magnitude across lineages (some lineagesmore » had a greater tendency to bioaccumulate Cd than others). Overlap in the ranges of trait values among different lineages was common and highlights situations where species from different lineages can share a similar trait state, but represent the high end of possible physiological values for one lineage and the low end for another. 3) Variance around the mean trait state differed widely across clades, suggesting that some groups (e.g., Ephemerellidae) are inherently more variable than others (e.g., Perlidae). Thus, trait variability/lability is at least partially a function of lineage. 4) Akaike information criterion (AIC) comparisons of statistical models were more often driven by clade than by other potential biological or ecological explanation tested. Clade-driven models generally improved with increasing taxonomic resolution. 5) Altogether, these findings suggest that lineage provides context for the analysis of species traits, and that failure to consider lineage in community-based analysis of traits may obscure important patterns of species responses to environmental change.« less

  20. Full-length cloning and phylogenetic analyses of translationally controlled tumour protein and ferritin genes from the Indian white prawn, Fenneropenaeus indicus (H. Milne Edwards).

    PubMed

    Nayak, S; Ramaiah, N; Meena, R M; Sreepada, R A

    2014-02-01

    Elucidation, through molecular analyses, of bacterial afflictions in commercially important aquaculture-reared shrimps is pivotal for the prevention and/or control of disease outbreaks. In this study, we examined the phylogenetic relatedness and compared the possible immune-related functional roles of both translationally controlled tumour protein (TCTP) and ferritin genes with previous studies. Both TCTP and ferritin genes were substantially upregulated in the Indian white prawn, Fenneropenaeus indicus (H. Milne Edwards), post-larvae following bath challenge with the virulent strain of bacteria, Vibrio harveyi D3. Full-length cloning of these genes by rapid amplification of complementary DNA ends -polymerase chain reaction (RACE-PCR) yielded 727-base pair (bp)-long TCTP and 1212-bp-long ferritin gene sequences. Their open reading frames (ORFs) were 507 and 510 bp, respectively. The TCTP-ORF coded for 168 amino acids with three substitutions at positions 37, 141, 155, and the ferritin ORF coded for 170 amino acids with no species-specific substitutions. Phylogenetic analysis suggested the closest relatedness of both TCTP and ferritin from F. indicus to Chinese white prawn, Fenneropenaeus chinensis (Osbeck). In addition to reporting the full-length sequences of these immune-relevant genes, this study highlighted their conserved natures, which perhaps make them important defence-related proteins in the innate immune system of F. indicus.

  1. The first internal transcribed spacer (ITS-1) of ribosomal DNA as a molecular marker for phylogenetic and population analyses in crustacea.

    PubMed

    Chu, K H; Li, C P; Ho, H Y

    2001-07-01

    The objective of the present study is to explore the feasibility of using the first internal transcribed spacer (ITS-1) of ribosomal DNA as a molecular marker for studying the interspecific and intraspecific genetic variations among crustaceans. We designed primers that could amplify ITS-1 from a majority of taxonomic groups of crustaceans. The gene was found to exhibit a high degree of length polymorphism among different groups, ranging from 182 bp in the barnacle Balanus amphitrite to approximately 820 bp in the spiny lobster Panulirus japonicus. With respect to differences between congeneric species, it was found that the ITS-1 sequences of 3 mitten crabs, Eriocheir sinensis, Eriocheir leptognathus, and Eriocheir formosa, exhibit 5.4% to 16.3% nucleotide divergence, suggesting that ITS-1 is informative for phylogenetic analysis at the species level. Yet there are extensive (0.9%-2.3%) variations within individual E. formosa, so that phylogenetic analyses could be obscured. ITS-1 was found to vary between 2 geographical populations of the shrimp Penaeus japonicus. The variations involved substitutions as well as insertions/deletions between shrimp from Australia and South China Sea. These results show that ITS-1 is highly divergent among different crustaceans and could be an appropriate marker for molecular systematic studies at the species and population levels, although the presence of intragenomic variation needs to be taken into consideration.

  2. Microarray and bioinformatic analyses suggest models for carbon metabolism in the autotroph Acidithiobacillus ferrooxidans

    SciTech Connect

    C. Appia-ayme; R. Quatrini; Y. Denis; F. Denizot; S. Silver; F. Roberto; F. Veloso; J. Valdes; J. P. Cardenas; M. Esparza; O. Orellana; E. Jedlicki; V. Bonnefoy; D. Holmes

    2006-09-01

    Acidithiobacillus ferrooxidans is a chemolithoautotrophic bacterium that uses iron or sulfur as an energy and electron source. Bioinformatic analysis was used to identify putative genes and potential metabolic pathways involved in CO2 fixation, 2P-glycolate detoxification, carboxysome formation and glycogen utilization in At. ferrooxidans. Microarray transcript profiling was carried out to compare the relative expression of the predicted genes of these pathways when the microorganism was grown in the presence of iron versus sulfur. Several gene expression patterns were confirmed by real-time PCR. Genes for each of the above predicted pathways were found to be organized into discrete clusters. Clusters exhibited differential gene expression depending on the presence of iron or sulfur in the medium. Concordance of gene expression within each cluster, suggested that they are operons Most notably, clusters of genes predicted to be involved in CO2 fixation, carboxysome formation, 2P-glycolate detoxification and glycogen biosynthesis were up-regulated in sulfur medium, whereas genes involved in glycogen utilization were preferentially expressed in iron medium. These results can be explained in terms of models of gene regulation that suggest how A. ferrooxidans can adjust its central carbon management to respond to changing environmental conditions.

  3. Comparative analyses suggest that information transfer promoted sociality in male bats in the temperate zone.

    PubMed

    Safi, Kamran; Kerth, Gerald

    2007-09-01

    The evolution of sociality is a central theme in evolutionary biology. The vast majority of bats are social, which has been explained in terms of the benefits of communal breeding. However, the causes for segregated male groups remain unknown. In a comparative study, we tested whether diet and morphological adaptations to specific foraging styles, two factors known to influence the occurrence of information transfer, can predict male sociality. Our results suggest that the species most likely to benefit from information transfer--namely, those preying on ephemeral insects and with morphological adaptations to feeding in open habitat--are more likely to form male groups. Our findings also indicate that solitary life was the ancestral state of males and sociality evolved in several lineages. Beyond their significance for explaining the existence of male groups in bats, our findings highlight the importance of information transfer in the evolution of animal sociality.

  4. Pseudomonas community structure and antagonistic potential in the rhizosphere: insights gained by combining phylogenetic and functional gene-based analyses.

    PubMed

    Costa, Rodrigo; Gomes, Newton C M; Krögerrecklenfort, Ellen; Opelt, Katja; Berg, Gabriele; Smalla, Kornelia

    2007-09-01

    The Pseudomonas community structure and antagonistic potential in the rhizospheres of strawberry and oilseed rape (host plants of the fungal phytopathogen Verticillium dahliae) were assessed. The use of a new PCR-DGGE system, designed to target Pseudomonas-specific gacA gene fragments in environmental DNA, circumvented common biases of 16S rRNA gene-based DGGE analyses and proved to be a reliable tool to unravel the diversity of uncultured Pseudomonas in bulk and rhizosphere soils. Pseudomonas-specific gacA fingerprints of total-community (TC) rhizosphere DNA were surprisingly diverse, plant-specific and differed markedly from those of the corresponding bulk soils. By combining multiple culture-dependent and independent surveys, a group of Pseudomonas isolates antagonistic towards V. dahliae was shown to be genotypically conserved, to carry the phlD biosynthetic locus (involved in the biosynthesis of 2,4-diacetylphloroglucinol - 2,4-DAPG), and to correspond to a dominant and highly frequent Pseudomonas population in the rhizosphere of field-grown strawberries planted at three sites in Germany which have different land use histories. This population belongs to the Pseudomonas fluorescens phylogenetic lineage and showed closest relatedness to P. fluorescens strain F113 (97% gacA gene sequence identity in 492-bp sequences), a biocontrol agent and 2,4-DAPG producer. Partial gacA gene sequences derived from isolates, clones of the strawberry rhizosphere and DGGE bands retrieved in this study represent previously undescribed Pseudomonas gacA gene clusters as revealed by phylogenetic analysis.

  5. Phylogenetic analyses of small subunit ribosomal RNA coding regions reveal a monophyletic lineage of euglyphid testate amoebae (Order Euglyphida).

    PubMed

    Wylezich, Claudia; Meisterfeld, Ralf; Meisterfeld, Susanne; Schlegel, Martin

    2002-01-01

    The Testaceafilosia includes amoebae with filopodia and with a proteinaceous, agglutinated or siliceous test. To explore the deeper phylogeny of this group, we sequenced the small subunit ribosomal RNA coding region of 13 species, including the first sequence of an amoeba with an agglutinated test, Pseudodifflugia sp. Phylogenetic analyses using maximum parsimony and maximum likelihood methods as well as neighbor joining method yielded the following results: the order Euglyphida forms a monophyletic lineage with the sarcomonads as sister group. The next related taxa are the Chlorarachnea and the unidentified filose strain N-Por. In agreement with the previous studies the Phytomyxea branch off at the base of this lineage. The Monadofilosa (Testaceafilosia and Sarcomonadea) appear monophyletic. The Testaceafilosia are polyphyletic, because Pseudodifflugia sp. is positioned as the sister taxon to the sarcomonads. Within the order Euglyphida Paulinella branches off first, together with Cyphoderia followed by Tracheleuglypha. In maximum likelihood and neighbor joining analyses, the genus Euglypha is monophyletic. The branching pattern within the order Euglyphida reflects the evolution of shell morphology from simple to complex built test.

  6. Sequence analyses of herpesviral enzymes suggest an ancient origin for human sexual behavior.

    PubMed Central

    Gentry, G A; Lowe, M; Alford, G; Nevins, R

    1988-01-01

    Comparison of the amino acid sequences of the deoxythymidine kinases of herpes simplex (HSV) and of marmoset herpes viruses (MHV) suggests a divergence time of 8 to 10 million years ago for HSV-1 and -2. Like MHV, HSV-1 and -2 cause local infections in their natural hosts, and direct contact between two individuals during the brief period of infectivity is needed for transmission. Because B virus, a nearer relative of HSV, depends on both oral and genital routes of transmission, we postulate that ancestral HSV (aHSV) was similar, and that for HSV-1 and -2 to diverge, genital and oral sites had to become microbiologically somewhat isolated from each other, while oral--oral and genital--genital contact had to be facilitated to maintain both aHSV strains. We propose that acquisition of continual sexual attractiveness by the ancestral human female and the adoption of close face-to-face mating, two hallmarks of human sexual behavior, provided the conditions for the divergence. PMID:3128793

  7. Sampling strategies for improving tree accuracy and phylogenetic analyses: a case study in ciliate protists, with notes on the genus Paramecium.

    PubMed

    Yi, Zhenzhen; Strüder-Kypke, Michaela; Hu, Xiaozhong; Lin, Xiaofeng; Song, Weibo

    2014-02-01

    In order to assess how dataset-selection for multi-gene analyses affects the accuracy of inferred phylogenetic trees in ciliates, we chose five genes and the genus Paramecium, one of the most widely used model protist genera, and compared tree topologies of the single- and multi-gene analyses. Our empirical study shows that: (1) Using multiple genes improves phylogenetic accuracy, even when their one-gene topologies are in conflict with each other. (2) The impact of missing data on phylogenetic accuracy is ambiguous: resolution power and topological similarity, but not number of represented taxa, are the most important criteria of a dataset for inclusion in concatenated analyses. (3) As an example, we tested the three classification models of the genus Paramecium with a multi-gene based approach, and only the monophyly of the subgenus Paramecium is supported.

  8. Autosomal STR analyses in native Amazonian tribes suggest a population structure driven by isolation by distance.

    PubMed

    Dos Santos, Sidney E B; Ribeiro-Rodrigues, Elzemar M; Ribeiro-Dos-Santos, Andrea K C; Hutz, Mara H; Tovo-Rodrigues, Luciana; Salzano, Francisco M; Callegari-Jacques, Sidia M

    2009-02-01

    Eleven short tandem repeat loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, TH01, and TPOX) were investigated in 232 individuals from 6 Amazonian native tribes (Tiriyó, Waiãpi, Zoé, Urubu-Kaapor, Awa-Guajá, and Parakanã). We added the new data to a database that included five previously typed native populations from the same area (Wai Wai, Gavião, Zoró, Suruí, and Xavante). The results presented here concern this new data set, which accounts for 526 individuals in total. We tested whether major geographic or linguistic barriers to gene flow exist among such human groups and tried to find a possible anthropological or ethnological explanation for such patterns. We measured the average heterozygosity (H) and the number of alleles (N(A) ) and found that both are lower than values observed in populations of different ethnic backgrounds, such as European or African descendants. Despite such a result, we found high between-population variation; lower H and/or N(A) values were obtained from four isolated tribes that came into contact with external nonnative populations in recent times (1921-1989). By applying analysis of molecular variance, generalized hierarchical modeling, and the Structure Bayesian analysis, we were not able to detect any significant geographic or linguistic barrier to gene flow. Geographic autocorrelation analysis suggests that the genetic structure of native Amazonian tribes is better explained by isolation by distance because the level of genetic similarity decreases according to linear geographic distance, reaching null or negative values at a scale of 300 km.

  9. Genome analyses suggest the presence of polyploidy and recent human-driven expansions in eight global populations of the honeybee pathogen Nosema ceranae.

    PubMed

    Pelin, Adrian; Selman, Mohammed; Aris-Brosou, Stéphane; Farinelli, Laurent; Corradi, Nicolas

    2015-11-01

    Nosema ceranae is a microsporidian pathogen whose infections have been associated with recent global declines in the populations of western honeybees (Apis mellifera). Despite the outstanding economic and ecological threat that N. ceranae may represent for honeybees worldwide, many aspects of its biology, including its mode of reproduction, propagation and ploidy, are either very unclear or unknown. In the present study, we set to gain knowledge in these biological aspects by re-sequencing the genome of eight isolates (i.e. a population of spores isolated from one single beehive) of this species harvested from eight geographically distant beehives, and by investigating their level of polymorphism. Consistent with previous analyses performed using single gene sequences, our analyses uncovered the presence of very high genetic diversity within each isolate, but also very little hive-specific polymorphism. Surprisingly, the nature, location and distribution of this genetic variation suggest that beehives around the globe are infected by a population of N. ceranae cells that may be polyploid (4n or more), and possibly clonal. Lastly, phylogenetic analyses based on genome-wide single-nucleotide polymorphism data extracted from these parasites and mitochondrial sequences from their hosts all failed to support the current geographical structure of our isolates.

  10. Cloning, characterization and phylogenetic analyses of members of three major venom families from a single specimen of Walterinnesia aegyptia.

    PubMed

    Tsai, Hsin-Yu; Wang, Ying Ming; Tsai, Inn-Ho

    2008-06-01

    Walterinnesia aegyptia is a monotypic elapid snake inhabiting in Africa and Mideast. Although its envenoming is known to cause rapid deaths and paralysis, structural data of its venom proteins are rather limited. Using gel filtration and reverse-phase HPLC, phospholipases A(2) (PLAs), three-fingered toxins (3FTxs), and Kunitz-type protease inhibitors (KIns) were purified from the venom of a single specimen of this species caught in northern Egypt. In addition, specific primers were designed and PCR was carried out to amplify the cDNAs encoding members of the three venom families, respectively, using total cDNA prepared from its venom glands. Complete amino acid sequences of two acidic PLAs, three short chain 3FTxs, and four KIns of this venom species were thus deduced after their cDNAs were cloned and sequenced. They are all novel sequences and match the mass data of purified proteins. For members of each toxin family, protein sequences were aligned and subjected to molecular phylogenetic analyses. The results indicated that the PLAs and a Kunitz inhibitor of W. aegyptia are most similar to those of king cobra venom, and its 3FTxs belongs to either Type I alpha-neurotoxins or weak toxins of orphan-II subtype. It is remarkable that both king cobra and W. aegyptia cause rapid deaths of the victims, and a close evolutionary relationship between them is speculated. PMID:18405934

  11. Phylogenetic and Morphologic Analyses of a Coastal Fish Reveals a Marine Biogeographic Break of Terrestrial Origin in the Southern Caribbean

    PubMed Central

    Betancur-R, Ricardo; Acero P., Arturo; Duque-Caro, Hermann; Santos, Scott R.

    2010-01-01

    Background Marine allopatric speciation involves interplay between intrinsic organismal properties and extrinsic factors. However, the relative contribution of each depends on the taxon under study and its geographic context. Utilizing sea catfishes in the Cathorops mapale species group, this study tests the hypothesis that both reproductive strategies conferring limited dispersal opportunities and an apparent geomorphologic barrier in the Southern Caribbean have promoted speciation in this group from a little studied area of the world. Methodology/Principal Findings Mitochondrial gene sequences were obtained from representatives of the Cathorops mapale species group across its distributional range from Colombia to Venezuela. Morphometric and meristic analyses were also done to assess morphologic variation. Along a ∼2000 km transect, two major lineages, Cathorops sp. and C. mapale, were identified by levels of genetic differentiation, phylogenetic reconstructions, and morphological analyses. The lineages are separated by ∼150 km at the Santa Marta Massif (SMM) in Colombia. The northward displacement of the SMM into the Caribbean in the early Pleistocene altered the geomorphology of the continental margin, ultimately disrupting the natural habitat of C. mapale. The estimated ∼0.86 my divergence of the lineages from a common ancestor coincides with the timing of the SMM displacement at ∼0.78 my. Main Conclusions/Significance Results presented here support the hypothesis that organismal properties as well as extrinsic factors lead to diversification of the Cathorops mapale group along the northern coast of South America. While a lack of pelagic larval stages and ecological specialization are forces impacting this process, the identification of the SMM as contributing to allopatric speciation in marine organisms adds to the list of recognized barriers in the Caribbean. Comparative examination of additional Southern Caribbean taxa, particularly those with

  12. Assembly and variation analyses of Clarias batrachus mitogenome retrieved from WGS data and its phylogenetic relationship with other catfishes

    PubMed Central

    Kushwaha, Basdeo; Kumar, Ravindra; Agarwal, Suyash; Pandey, Manmohan; Nagpure, N.S.; Singh, Mahender; Srivastava, Shreya; Joshi, C.G.; Das, P.; Sahoo, L.; Jayasankar, P.; Meher, P.K.; Shah, T.M.; Patel, A.B.; Patel, Namrata; Koringa, P.; Das, Sofia Priyadarsani; Patnaik, Siddhi; Bit, Amrita; Sarika; Iquebal, M.A.; Kumar, Dinesh; Jena, J.K.

    2015-01-01

    Whole genome sequencing (WGS) using next generation sequencing technologies paves the way to sequence the mitochondrial genomes with greater ease and lesser time. Here, we used the WGS data of Clarias batrachus, generated from Roche 454 and Ion Torrent sequencing platforms, to assemble the complete mitogenome using both de novo and reference based approaches. Both the methods yielded almost similar results and the best assembled mitogenome was of 16,510 bp size (GenBank Acc. No. KM259918). The mitogenome annotation resulted in 13 coding genes, 22 tRNA genes, 2 rRNA genes and one control region, and the gene order was found to be identical with other catfishes. Variation analyses between assembled and the reference (GenBank Acc. No. NC_023923) mitogenome revealed 51 variations. The phylogenetic analysis of coding DNA sequences and tRNA supports the monophyly of catfishes. Two SSRs were identified in C. batrachus mitogenome, out of which one was unique to this species. Based on the relative rate of gene evolution, protein coding mitochondrial genes were found to evolve at a much faster pace than the d-loop, which in turn are followed by the rRNAs; the tRNAs showed wide variability in the rate of sequence evolution, and on average evolve the slowest. Among the coding genes, ND2 evolves most rapidly. The variations present in the coding regions of the mitogenome and their comparative analyses with other catfish species may be useful in species conservation and management programs. PMID:26137446

  13. Binding of phylogenetically distant Bacillus thuringiensis cry toxins to a Bombyx mori aminopeptidase N suggests importance of Cry toxin's conserved structure in receptor binding.

    PubMed

    Shinkawa, A; Yaoi, K; Kadotani, T; Imamura, M; Koizumi, N; Iwahana, H; Sato, R

    1999-07-01

    We investigated the binding proteins for three Cry toxins, Cry1Aa, Cry1Ac, and the phylogenetically distant Cry9Da, in the midgut cell membrane of the silkworm. In a ligand blot experiment, Cry1Ac and Cry9Da bound to the same 120-kDa aminopeptidase N (APN) as Cry1Aa. A competition experiment with the ligand blot indicated that the three toxins share the same binding site on several proteins. The values of the dissociation constants of the three Cry toxins and 120-kDa APN are as low as the case of other Cry toxins and receptors. These results suggest that distantly related Cry toxins bind to the same site on the same proteins, especially with APN. We propose that the conserved structure in these three toxins includes the receptor-binding site. PMID:10387111

  14. Sequence, secondary structure, and phylogenetic analyses of the ribosomal internal transcribed spacer 2 (ITS2) in members of the North American Signifera Group of Orthopodomyia (Diptera: Culicidae).

    PubMed

    Byrd, Brian D; Harrison, Bruce A; Zavortink, Thomas J; Wesson, Dawn M

    2012-11-01

    Mosquitoes of the genus Orthopodomyia (Diptera: Culicidae) are little known and of uncertain epidemiological importance. In the United States, there are three Orthopodomyia species (i.e., Or. signifera (Coquillett), Or. alba Baker, and Or. kummi Edwards); they are all members of the Signifera Group based on the current morphological taxonomy. In the course of identifying recently collected specimens, a problem was found with the current key morphological characters for separating the fourth instar larvae of Or. signifera and Or. kummi. Internal transcribed spacer two sequences of the rDNA were obtained to resolve the identities. The Orthopodomyia internal transcribed spacer two ranged in size from 193 (Or. kummi) to 244 bp (Or. signifera) (mean = 218 bp) and were slightly Adenine/Thymine enriched (44.7% Guanine/Cytosine on average). Putative secondary structures reveal structural homologies (four domains) consistent between species that also feature conserved sequences specific to mosquitoes (e.g., a conserved motif on the 3' aspect of the longest helix: GARTACATCC). Sequence analyses suggest that in certain areas of southwestern North America, hybridization may occur between Or. kummi and Or. signifera. Furthermore, our analyses confirm that Or. californica (a junior synonym of Or. signifera) is indeed Or. signifera. To our knowledge, this is the first sequence-based phylogenetic and molecular analysis of the Orthopodomyia.

  15. Genetic diversity of Trypanosoma cruzi in bats, and multilocus phylogenetic and phylogeographical analyses supporting Tcbat as an independent DTU (discrete typing unit).

    PubMed

    Lima, Luciana; Espinosa-Álvarez, Oneida; Ortiz, Paola A; Trejo-Varón, Javier A; Carranza, Julio C; Pinto, C Miguel; Serrano, Myrna G; Buck, Gregory A; Camargo, Erney P; Teixeira, Marta M G

    2015-11-01

    Trypanosoma cruzi is a complex of phenotypically and genetically diverse isolates distributed in six discrete typing units (DTUs) designated as TcI-TcVI. Five years ago, T. cruzi isolates from Brazilian bats showing unique patterns of traditional ribosomal and spliced leader PCRs not clustering into any of the six DTUs were designated as the Tcbat genotype. In the present study, phylogenies inferred using SSU rRNA (small subunit of ribosomal rRNA), gGAPDH (glycosomal glyceraldehyde 3-phosphate dehydrogenase) and Cytb (cytochrome b) genes strongly supported Tcbat as a monophyletic lineage prevalent in Brazil, Panama and Colombia. Providing strong support for Tcbat, sequences from 37 of 47 nuclear and 12 mitochondrial genes (retrieved from a draft genome of Tcbat) and reference strains of all DTUs available in databanks corroborated Tcbat as an independent DTU. Consistent with previous studies, multilocus analysis of most nuclear genes corroborated the evolution of T. cruzi from bat trypanosomes its divergence into two main phylogenetic lineages: the basal TcII; and the lineage clustering TcIV, the clade comprising TcIII and the sister groups TcI-Tcbat. Most likely, the common ancestor of Tcbat and TcI was a bat trypanosome. However, the results of the present analysis did not support Tcbat as the ancestor of all DTUs. Despite the insights provided by reports of TcIII, TcIV and TcII in bats, including Amazonian bats harbouring TcII, further studies are necessary to understand the roles played by bats in the diversification of all DTUs. We also demonstrated that in addition to value as molecular markers for DTU assignment, Cytb, ITS rDNA and the spliced leader (SL) polymorphic sequences suggest spatially structured populations of Tcbat. Phylogenetic and phylogeographical analyses, multiple molecular markers specific to Tcbat, and the degrees of sequence divergence between Tcbat and the accepted DTUs strongly support the definitive classification of Tcbat as a new DTU.

  16. Genome-Scale Phylogenetic Analyses of Chikungunya Virus Reveal Independent Emergences of Recent Epidemics and Various Evolutionary Rates▿ ‡

    PubMed Central

    Volk, Sara M.; Chen, Rubing; Tsetsarkin, Konstantin A.; Adams, A. Paige; Garcia, Tzintzuni I.; Sall, Amadou A.; Nasar, Farooq; Schuh, Amy J.; Holmes, Edward C.; Higgs, Stephen; Maharaj, Payal D.; Brault, Aaron C.; Weaver, Scott C.

    2010-01-01

    Chikungunya virus (CHIKV), a mosquito-borne alphavirus, has traditionally circulated in Africa and Asia, causing human febrile illness accompanied by severe, chronic joint pain. In Africa, epidemic emergence of CHIKV involves the transition from an enzootic, sylvatic cycle involving arboreal mosquito vectors and nonhuman primates, into an urban cycle where peridomestic mosquitoes transmit among humans. In Asia, however, CHIKV appears to circulate only in the endemic, urban cycle. Recently, CHIKV emerged into the Indian Ocean and the Indian subcontinent to cause major epidemics. To examine patterns of CHIKV evolution and the origins of these outbreaks, as well as to examine whether evolutionary rates that vary between enzootic and epidemic transmission, we sequenced the genomes of 40 CHIKV strains and performed a phylogenetic analysis representing the most comprehensive study of its kind to date. We inferred that extant CHIKV strains evolved from an ancestor that existed within the last 500 years and that some geographic overlap exists between two main enzootic lineages previously thought to be geographically separated within Africa. We estimated that CHIKV was introduced from Africa into Asia 70 to 90 years ago. The recent Indian Ocean and Indian subcontinent epidemics appear to have emerged independently from the mainland of East Africa. This finding underscores the importance of surveillance to rapidly detect and control African outbreaks before exportation can occur. Significantly higher rates of nucleotide substitution appear to occur during urban than during enzootic transmission. These results suggest fundamental differences in transmission modes and/or dynamics in these two transmission cycles. PMID:20410280

  17. Genetic and Phylogenetic Analyses of Influenza A H1N1pdm Virus in Buenos Aires, Argentina ▿ †

    PubMed Central

    Barrero, P. R.; Viegas, M.; Valinotto, L. E.; Mistchenko, A. S.

    2011-01-01

    An influenza pandemic caused by swine-origin influenza virus A/H1N1 (H1N1pdm) spread worldwide in 2009, with 12,080 confirmed cases and 626 deaths occurring in Argentina. A total of 330 H1N1pdm viruses were detected from May to August 2009, and phylogenetic and genetic analyses of 21 complete genome sequences from both mild and fatal cases were achieved with reference to concatenated whole genomes. In addition, the analysis of another 16 hemagglutinin (HA), neuraminidase (NA), and matrix (M) gene sequences of Argentinean isolates was performed. The microevolution timeline was assessed and resistance monitoring of an NA fragment from 228 samples throughout the 2009 pandemic peak was performed by sequencing and pyrosequencing. We also assessed the viral growth kinetics for samples with replacements at the genomic level or special clinical features. In this study, we found by Bayesian inference that the Argentinean complete genome sequences clustered with globally distributed clade 7 sequences. The HA sequences were related to samples from the northern hemisphere autumn-winter from September to December 2009. The NA of Argentinean sequences belonged to the New York group. The N-4 fragment as well as the hierarchical clustering of samples showed that a consensus sequence prevailed in time but also that different variants, including five H275Y oseltamivir-resistant strains, arose from May to August 2009. Fatal and oseltamivir-resistant isolates had impaired growth and a small plaque phenotype compared to oseltamivir-sensitive and consensus strains. Although these strains might not be fit enough to spread in the entire population, molecular surveillance proved to be essential to monitor resistance and viral dynamics in our country. PMID:21047959

  18. Combined Genotypic, Phylogenetic, and Epidemiologic Analyses of Mycobacterium tuberculosis Genetic Diversity in the Rhône Alpes Region, France

    PubMed Central

    Pichat, Catherine; Couvin, David; Carret, Gérard; Frédénucci, Isabelle; Jacomo, Véronique; Carricajo, Anne; Boisset, Sandrine; Dumitrescu, Oana; Flandrois, Jean-Pierre; Lina, Gérard; Rastogi, Nalin

    2016-01-01

    Background The present work relates to identification and a deep molecular characterization of circulating Mycobacterium tuberculosis complex (MTBC) strains in the Rhône-Alpes region, France from 2000 to 2010. It aimed to provide with a first snapshot of MTBC genetic diversity in conjunction with bacterial drug resistance, type of disease and available demographic and epidemiologic characteristics over an eleven-year period, in the south-east of France. Methods Mycobacterium tuberculosis complex (MTBC) strains isolated in the Rhône-Alpes region, France (n = 2257, 1 isolate per patient) between 2000 and 2010 were analyzed by spoligotyping. MIRU-VNTR typing was applied on n = 1698 strains (with full results available for 974 strains). The data obtained were compared with the SITVIT2 database, followed by detailed genotyping, phylogenetic, and epidemiologic analyses in correlation with anonymized data on available demographic, and epidemiologic characteristics, and location of disease (pulmonary or extrapulmonary TB). Results The most predominant spoligotyping clusters were SIT53/T1 (n = 346, 15.3%) > SIT50/H3 (n = 166, 7.35%) > SIT42/LAM9 (n = 125, 5.5%) > SIT1/Beijing (n = 72, 3.2%) > SIT47/H1 (n = 71, 3.1%). Evolutionary-recent strains belonging to the Principal Genetic Group (PGG) 2/3, or Euro-American lineages (T, LAM, Haarlem, X, S) were predominant and represented 1768 or 78.33% of all isolates. For strains having drug resistance information (n = 1119), any drug resistance accounted for 14.83% cases vs. 1.52% for multidrug resistance (MDR); and was significantly more associated with age group 21–40 years (p-value<0.001). Extra-pulmonary TB was more common among female patients while pulmonary TB predominated among men (p-value<0.001; OR = 2.16 95%CI [1.69; 2.77]). Also, BOV and CAS lineages were significantly well represented in patients affected by extra-pulmonary TB (p-value<0.001). The origin was known for 927/2257 patients: 376 (40.6%) being French

  19. Phylogenetic position of Rhynchopus sp. and Diplonema ambulator as indicated by analyses of euglenozoan small subunit ribosomal DNA.

    PubMed

    Busse, I; Preisfeld, Angelika

    2002-02-01

    The taxa Rhynchopus Skuja and Diplonema Griessmann were first described as remarkable protists with euglenid affinities. Later on, the placement of Diplonema within the Euglenozoa was confirmed by molecular data. For this study two new sequences were added to the euglenozoan data set. The uncertainly placed Rhynchopus can be identified as a close relative to Diplonema by small subunit ribosomal DNA (SSU rDNA) analysis. The new sequence of Diplonema ambulator is in close relationship to two other Diplonema species. Our molecular analyses clearly support the monophyly of the diplonemids comprising Rhynchopus and Diplonema. Yet the topology at the base of the euglenozoan tree remains unresolved, and especially the monophyly of the euglenids is arguable. SSU rDNA sequence analyses suggest that significantly different GC contents, high mutational saturation in the euglenids, and different evolutionary rates in the euglenozoan clades make it difficult to identify any sister group to the diplonemids.

  20. Phylogenetic Relationships among the Colobine Monkeys Revisited: New Insights from Analyses of Complete mt Genomes and 44 Nuclear Non-Coding Markers

    PubMed Central

    Roos, Christian; Ting, Nelson; Chen, Cui Ping; Wang, Jing; Zhang, Ya Ping

    2012-01-01

    Background Phylogenetic relationships among Asian and African colobine genera have been disputed and are not yet well established. In the present study, we revisit the contentious relationships within the Asian and African Colobinae by analyzing 44 nuclear non-coding genes (>23 kb) and mitochondrial (mt) genome sequences from 14 colobine and 4 non-colobine primates. Principal Findings The combined nuclear gene and the mt genome as well as the combined nuclear and mt gene analyses yielded different phylogenetic relationships among colobine genera with the exception of a monophyletic ‘odd-nosed’ group consisting of Rhinopithecus, Pygathrix and Nasalis, and a monophyletic African group consisting of Colobus and Piliocolobus. The combined nuclear data analyses supported a sister-grouping between Semnopithecus and Trachypithecus, and between Presbytis and the odd-nosed monkey group, as well as a sister-taxon association of Pygathrix and Rhinopithecus within the odd-nosed monkey group. In contrast, mt genome data analyses revealed that Semnopithecus diverged earliest among the Asian colobines and that the odd-nosed monkey group is sister to a Presbytis and Trachypithecus clade, as well as a close association of Pygathrix with Nasalis. The relationships among these genera inferred from the analyses of combined nuclear and mt genes, however, varied with the tree-building methods used. Another remarkable finding of the present study is that all of our analyses rejected the recently proposed African colobine paraphyly and hybridization hypothesis and supported reciprocal monophyly of the African and Asian groups. Significance The phylogenetic utility of large-scale new non-coding genes was assessed using the Colobinae as a model, We found that these markers were useful for distinguishing nodes resulting from rapid radiation episodes such as the Asian colobine radiation. None of these markers here have previously been used for colobine phylogenetic reconstruction

  1. Phylogenetic and biogeographic analyses of the Sino-Himalayan endemic genus Cyananthus (Campanulaceae) and implications for the evolution of its sexual system.

    PubMed

    Zhou, Zhuo; Hong, Deyuan; Niu, Yang; Li, Guodong; Nie, Zelong; Wen, Jun; Sun, Hang

    2013-09-01

    Cyananthus (Campanulaceae) is a small genus consisting of ca. 20 species endemic to the Sino-Himalayan region. Based on phylogenetic analysis using nuclear ribosomal ITS and four plastid markers (matK, rbcL, psbA-trnH and trnG-S), our results strongly support the monophyly of Cyananthus and its close relationship with the Codonopsis clade of the platycodonoids. Three major clades are supported, corresponding to the three sections of the genus, with sect. Cyananthus, which mainly occurs in the Himalayas, being a sister to the clade comprising the other two sections (sect. Stenolobi and sect. Annui) distributed primarily in the Hengduan Mountain region. We also observed that Cyananthus exhibits variation in its sexual system, possessing both hermaphroditic and gynodioecious species. Character evolution analyses using Mesquite suggest that gynodioecy evolved from hermaphroditism only once in sect. Stenolobi, but that there is a reversal in C. formosus. Molecular dating and biogeographic analysis with LAGRANGE support dispersal from the Himalayas to the Hengduan Mountains during the early evolution of Cyananthus. The extensive uplift of the Qinghai-Tibetan Plateau and the Hengduan Mountains played an important role in the subsequent diversification of the genus.

  2. Phylogenetic and transcriptomic analyses reveal the evolution of bioluminescence and light detection in marine deep-sea shrimps of the family Oplophoridae (Crustacea: Decapoda).

    PubMed

    Wong, Juliet M; Pérez-Moreno, Jorge L; Chan, Tin-Yam; Frank, Tamara M; Bracken-Grissom, Heather D

    2015-02-01

    Bioluminescence is essential to the survival of many organisms, particularly in the deep sea where light is limited. Shrimp of the family Oplophoridae exhibit a remarkable mechanism of bioluminescence in the form of a secretion used for predatory defense. Three of the ten genera possess an additional mode of bioluminescence in the form of light-emitting organs called photophores. Phylogenetic analyses can be useful for tracing the evolution of bioluminescence, however, the few studies that have attempted to reconcile the relationships within Oplophoridae have generated trees with low-resolution. We present the most comprehensive phylogeny of Oplophoridae to date, with 90% genera coverage using seven genes (mitochondrial and nuclear) across 30 oplophorid species. We use our resulting topology to trace the evolution of bioluminescence within Oplophoridae. Previous studies have suggested that oplophorid visual systems may be tuned to differentiate the separate modes of bioluminescence. While all oplophorid shrimp possess a visual pigment sensitive to blue-green light, only those bearing photophores have an additional pigment sensitive to near-ultraviolet light. We attempt to characterize opsins, visual pigment proteins essential to light detection, in two photophore-bearing species (Systellaspis debilis and Oplophorus gracilirostris) and make inferences regarding their function and evolutionary significance.

  3. A well-sampled phylogenetic analysis of the polystichoid ferns (Dryopteridaceae) suggests a complex biogeographical history involving both boreotropical migrations and recent transoceanic dispersals.

    PubMed

    Le Péchon, Timothée; Zhang, Liang; He, Hai; Zhou, Xin-Mao; Bytebier, Benny; Gao, Xin-Fen; Zhang, Li-Bing

    2016-05-01

    Intercontinental disjunctions in ferns have often been considered as the result of long-distance dispersal (LDD) events rather than of vicariance. However, in many leptosporangiate groups, both processes appear to have played a major role in shaping current geographical distribution. In this study, we reconstructed the phylogenetic relationships and inferred the ancestral distribution areas of the polystichoid ferns (Cyrtomium, Phanerophlebia, and Polystichum), to evaluate the relative impact of vicariance and LDD on the biogeography of this group. We used a molecular dataset including 3346 characters from five plastid loci. With 190 accessions our taxon coverage was about three times as large as any previous worldwide sampling. Biogeographical analyses were performed using S-DIVA and S-DEC and divergence times were estimated by integrating fossil and secondary calibrations. The polystichoid ferns are a monophyletic clade that may have originated in East Asia during the Eocene, an age much younger than previously estimated. Three transoceanic disjunctions between East Asia and New World were identified in the Paleogene: one for Phanerophlebia during late Eocene (34Ma, 19-51Ma), and two in Polystichum at the Eocene-Oligocene boundary (30Ma, 18-43Ma; 28Ma, 19-39Ma respectively). During the Neogene, further range expansions took place from Asia to Africa, Hawaii, and the Southwestern Indian Ocean region. Our results indicate that early transfers between the Old and the New World are compatible with a boreotropical migration scenario. After evolving in Asia during the Eocene, the polystichoid ferns reached the New World in independent migrations at the Eocene-Oligocene boundary through the boreotropical belt. However, although less likely, the alternative hypothesis of independent transoceanic dispersals from the Old to the New World cannot be ruled out. Further range expansion during the Neogene was most likely the result of long-distance dispersal (LDD). PMID

  4. A well-sampled phylogenetic analysis of the polystichoid ferns (Dryopteridaceae) suggests a complex biogeographical history involving both boreotropical migrations and recent transoceanic dispersals.

    PubMed

    Le Péchon, Timothée; Zhang, Liang; He, Hai; Zhou, Xin-Mao; Bytebier, Benny; Gao, Xin-Fen; Zhang, Li-Bing

    2016-05-01

    Intercontinental disjunctions in ferns have often been considered as the result of long-distance dispersal (LDD) events rather than of vicariance. However, in many leptosporangiate groups, both processes appear to have played a major role in shaping current geographical distribution. In this study, we reconstructed the phylogenetic relationships and inferred the ancestral distribution areas of the polystichoid ferns (Cyrtomium, Phanerophlebia, and Polystichum), to evaluate the relative impact of vicariance and LDD on the biogeography of this group. We used a molecular dataset including 3346 characters from five plastid loci. With 190 accessions our taxon coverage was about three times as large as any previous worldwide sampling. Biogeographical analyses were performed using S-DIVA and S-DEC and divergence times were estimated by integrating fossil and secondary calibrations. The polystichoid ferns are a monophyletic clade that may have originated in East Asia during the Eocene, an age much younger than previously estimated. Three transoceanic disjunctions between East Asia and New World were identified in the Paleogene: one for Phanerophlebia during late Eocene (34Ma, 19-51Ma), and two in Polystichum at the Eocene-Oligocene boundary (30Ma, 18-43Ma; 28Ma, 19-39Ma respectively). During the Neogene, further range expansions took place from Asia to Africa, Hawaii, and the Southwestern Indian Ocean region. Our results indicate that early transfers between the Old and the New World are compatible with a boreotropical migration scenario. After evolving in Asia during the Eocene, the polystichoid ferns reached the New World in independent migrations at the Eocene-Oligocene boundary through the boreotropical belt. However, although less likely, the alternative hypothesis of independent transoceanic dispersals from the Old to the New World cannot be ruled out. Further range expansion during the Neogene was most likely the result of long-distance dispersal (LDD).

  5. Disentangling the complex evolutionary history of the Western Palearctic blue tits (Cyanistes spp.) - phylogenomic analyses suggest radiation by multiple colonization events and subsequent isolation.

    PubMed

    Stervander, Martin; Illera, Juan Carlos; Kvist, Laura; Barbosa, Pedro; Keehnen, Naomi P; Pruisscher, Peter; Bensch, Staffan; Hansson, Bengt

    2015-05-01

    Isolated islands and their often unique biota continue to play key roles for understanding the importance of drift, genetic variation and adaptation in the process of population differentiation and speciation. One island system that has inspired and intrigued evolutionary biologists is the blue tit complex (Cyanistes spp.) in Europe and Africa, in particular the complex evolutionary history of the multiple genetically distinct taxa of the Canary Islands. Understanding Afrocanarian colonization events is of particular importance because of recent unconventional suggestions that these island populations acted as source of the widespread population in mainland Africa. We investigated the relationship between mainland and island blue tits using a combination of Sanger sequencing at a population level (20 loci; 12 500 nucleotides) and next-generation sequencing of single population representatives (>3 200 000 nucleotides), analysed in coalescence and phylogenetic frameworks. We found (i) that Afrocanarian blue tits are monophyletic and represent four major clades, (ii) that the blue tit complex has a continental origin and that the Canary Islands were colonized three times, (iii) that all island populations have low genetic variation, indicating low long-term effective population sizes and (iv) that populations on La Palma and in Libya represent relicts of an ancestral North African population. Further, demographic reconstructions revealed (v) that the Canary Islands, conforming to traditional views, hold sink populations, which have not served as source for back colonization of the African mainland. Our study demonstrates the importance of complete taxon sampling and an extensive multimarker study design to obtain robust phylogeographical inferences.

  6. Paleogenetic Analyses Reveal Unsuspected Phylogenetic Affinities between Mice and the Extinct Malpaisomys insularis, an Endemic Rodent of the Canaries

    PubMed Central

    Gros-Balthazard, Muriel; Hughes, Sandrine; Alcover, Josep Antoni; Hutterer, Rainer; Rando, Juan Carlos; Michaux, Jacques; Hänni, Catherine

    2012-01-01

    Background The lava mouse, Malpaisomys insularis, was endemic to the Eastern Canary islands and became extinct at the beginning of the 14th century when the Europeans reached the archipelago. Studies to determine Malpaisomys' phylogenetic affinities, based on morphological characters, remained inconclusive because morphological changes experienced by this insular rodent make phylogenetic investigations a real challenge. Over 20 years since its first description, Malpaisomys' phylogenetic position remains enigmatic. Methodology/Principal Findings In this study, we resolved this issue using molecular characters. Mitochondrial and nuclear markers were successfully amplified from subfossils of three lava mouse samples. Molecular phylogenetic reconstructions revealed, without any ambiguity, unsuspected relationships between Malpaisomys and extant mice (genus Mus, Murinae). Moreover, through molecular dating we estimated the origin of the Malpaisomys/mouse clade at 6.9 Ma, corresponding to the maximal age at which the archipelago was colonised by the Malpaisomys ancestor via natural rafting. Conclusion/Significance This study reconsiders the derived morphological characters of Malpaisomys in light of this unexpected molecular finding. To reconcile molecular and morphological data, we propose to consider Malpaisomys insularis as an insular lineage of mouse. PMID:22363563

  7. The Phylogenetic Diversity of Metagenomes

    PubMed Central

    Kembel, Steven W.; Eisen, Jonathan A.; Pollard, Katherine S.; Green, Jessica L.

    2011-01-01

    Phylogenetic diversity—patterns of phylogenetic relatedness among organisms in ecological communities—provides important insights into the mechanisms underlying community assembly. Studies that measure phylogenetic diversity in microbial communities have primarily been limited to a single marker gene approach, using the small subunit of the rRNA gene (SSU-rRNA) to quantify phylogenetic relationships among microbial taxa. In this study, we present an approach for inferring phylogenetic relationships among microorganisms based on the random metagenomic sequencing of DNA fragments. To overcome challenges caused by the fragmentary nature of metagenomic data, we leveraged fully sequenced bacterial genomes as a scaffold to enable inference of phylogenetic relationships among metagenomic sequences from multiple phylogenetic marker gene families. The resulting metagenomic phylogeny can be used to quantify the phylogenetic diversity of microbial communities based on metagenomic data sets. We applied this method to understand patterns of microbial phylogenetic diversity and community assembly along an oceanic depth gradient, and compared our findings to previous studies of this gradient using SSU-rRNA gene and metagenomic analyses. Bacterial phylogenetic diversity was highest at intermediate depths beneath the ocean surface, whereas taxonomic diversity (diversity measured by binning sequences into taxonomically similar groups) showed no relationship with depth. Phylogenetic diversity estimates based on the SSU-rRNA gene and the multi-gene metagenomic phylogeny were broadly concordant, suggesting that our approach will be applicable to other metagenomic data sets for which corresponding SSU-rRNA gene sequences are unavailable. Our approach opens up the possibility of using metagenomic data to study microbial diversity in a phylogenetic context. PMID:21912589

  8. Expertly Validated Models and Phylogenetically-Controlled Analysis Suggests Responses to Climate Change Are Related to Species Traits in the Order Lagomorpha

    PubMed Central

    Leach, Katie; Kelly, Ruth; Cameron, Alison; Montgomery, W. Ian; Reid, Neil

    2015-01-01

    Climate change during the past five decades has impacted significantly on natural ecosystems, and the rate of current climate change is of great concern among conservation biologists. Species Distribution Models (SDMs) have been used widely to project changes in species’ bioclimatic envelopes under future climate scenarios. Here, we aimed to advance this technique by assessing future changes in the bioclimatic envelopes of an entire mammalian order, the Lagomorpha, using a novel framework for model validation based jointly on subjective expert evaluation and objective model evaluation statistics. SDMs were built using climatic, topographical, and habitat variables for all 87 lagomorph species under past and current climate scenarios. Expert evaluation and Kappa values were used to validate past and current models and only those deemed ‘modellable’ within our framework were projected under future climate scenarios (58 species). Phylogenetically-controlled regressions were used to test whether species traits correlated with predicted responses to climate change. Climate change is likely to impact more than two-thirds of lagomorph species, with leporids (rabbits, hares, and jackrabbits) likely to undertake poleward shifts with little overall change in range extent, whilst pikas are likely to show extreme shifts to higher altitudes associated with marked range declines, including the likely extinction of Kozlov’s Pika (Ochotona koslowi). Smaller-bodied species were more likely to exhibit range contractions and elevational increases, but showing little poleward movement, and fecund species were more likely to shift latitudinally and elevationally. Our results suggest that species traits may be important indicators of future climate change and we believe multi-species approaches, as demonstrated here, are likely to lead to more effective mitigation measures and conservation management. We strongly advocate studies minimising data gaps in our knowledge of the

  9. Expertly validated models and phylogenetically-controlled analysis suggests responses to climate change are related to species traits in the order lagomorpha.

    PubMed

    Leach, Katie; Kelly, Ruth; Cameron, Alison; Montgomery, W Ian; Reid, Neil

    2015-01-01

    Climate change during the past five decades has impacted significantly on natural ecosystems, and the rate of current climate change is of great concern among conservation biologists. Species Distribution Models (SDMs) have been used widely to project changes in species' bioclimatic envelopes under future climate scenarios. Here, we aimed to advance this technique by assessing future changes in the bioclimatic envelopes of an entire mammalian order, the Lagomorpha, using a novel framework for model validation based jointly on subjective expert evaluation and objective model evaluation statistics. SDMs were built using climatic, topographical, and habitat variables for all 87 lagomorph species under past and current climate scenarios. Expert evaluation and Kappa values were used to validate past and current models and only those deemed 'modellable' within our framework were projected under future climate scenarios (58 species). Phylogenetically-controlled regressions were used to test whether species traits correlated with predicted responses to climate change. Climate change is likely to impact more than two-thirds of lagomorph species, with leporids (rabbits, hares, and jackrabbits) likely to undertake poleward shifts with little overall change in range extent, whilst pikas are likely to show extreme shifts to higher altitudes associated with marked range declines, including the likely extinction of Kozlov's Pika (Ochotona koslowi). Smaller-bodied species were more likely to exhibit range contractions and elevational increases, but showing little poleward movement, and fecund species were more likely to shift latitudinally and elevationally. Our results suggest that species traits may be important indicators of future climate change and we believe multi-species approaches, as demonstrated here, are likely to lead to more effective mitigation measures and conservation management. We strongly advocate studies minimising data gaps in our knowledge of the Order

  10. Genetic and resistance phenotypic subtyping of Salmonella Saintpaul isolates from various food sources and humans: Phylogenetic concordance in combinatory analyses.

    PubMed

    Hayford, Alice E; Brown, Eric W; Zhao, Shaohua; Mammel, Mark K; Gangiredla, Jayanthi; Abbott, Jason W; Friedman, Sharon L; Ayers, Sherry L; Lewis, Jada L; Lacher, David W; McDermott, Patrick; Elkins, Christopher A

    2015-12-01

    Bacterial pathogen subtyping for public health traceback of foodborne outbreaks has increasingly produced a number of disparate molecular techniques of varying resolution. Here, we bridge the molecular divide across three methodologies, transform data types for cross-comparison, and test phylogenetic concordance. Single nucleotide polymorphism (SNP) discovery was combined with pulsed-field gel electrophoresis (PFGE) and antimicrobial susceptibility profiles for identifying and differentiating 183 strains of closely related Salmonella enterica serovar Saintpaul isolates from retail meats, produce-associated outbreaks, and clinical sources. Fifty-six SNPs across 30 different genes were identified by comparative genomic analysis. These SNPs stratified general, monophyletic S. Saintpaul serovar specific signatures down to informative strain-specific markers. This SNP panel resulted in 17 distinct genotypes that, in concert with standard PFGE profiling, generated additional discriminatory power among clonal swarms of isolates when the data were transformed into a cross-comparable binary format. In a limited number of cases, antimicrobial susceptibility profiles (ASP) provided additional attributes for some strains when combined similarly. However, as expected from presumably acquired elements, resistant and susceptible populations produced some conflicting signals in most clonal complexes but they remained largely undisruptive to the general concordance. Taken in concert together, the three datasets (SNPs, PFGE,ASP) yielded a matrix of 156 independent phylogenetic characters that were statistically evaluated and found to be largely congruent, resulting in a consistently structured, non-homoplastic, phylogenetic signal and tree topology. PMID:26299886

  11. Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov.

    PubMed

    Drancourt, M; Bollet, C; Carta, A; Rousselier, P

    2001-05-01

    The phylogenetic relationships of the type strains of 9 Klebsiella species and 20 species from 11 genera of the family Enterobacteriaceae were investigated by performing a comparative analysis of the sequences of the 16S rRNA and rpoB genes. The sequence data were phylogenetically analysed by the neighbourjoining and parsimony methods. The phylogenetic inference of the sequence comparison confirmed that the genus Klebsiella is heterogeneous and composed of species which form three clusters that also included members of other genera, including Enterobacter aerogenes, Erwinia clusters I and II and Tatumella. Cluster I contained the type strains of Klebsiella pneumoniae subsp. pneumoniae, Klebsiella pneumoniae subsp. rhinoscleromatis and Klebsiella pneumoniae subsp. ozaenae. Cluster II contained Klebsiella ornithinolytica, Klebsiella planticola, Klebsiella trevisanii and Klebsiella terrigena, organisms characterized by growth at 10 degrees C and utilization of L-sorbose as carbon source. Cluster III contained Klebsiella oxytoca. The data from the sequence analyses along with previously reported biochemical and DNA-DNA hybridization data support the division of the genus Klebsiella into two genera and one genogroup. The name Raoultella is proposed as a genus name for species of cluster II and emended definitions of Klebsiella species are proposed.

  12. Phylogenetic relationships of Hepatozoon (Haemogregarina) boigae, Hepatozoon sp., Haemogregarina clelandi and Haemoproteus chelodina from Australian reptiles to other Apicomplexa based on cladistic analyses of ultrastructural and life-cycle characters.

    PubMed

    Jakes, K; O'Donoghue, P J; Cameron, S L

    2003-06-01

    The phylogeny of representative haemozoan species of the phylum Apicomplexa was reconstructed by cladistic analyses of ultrastructural and life-cycle characteristics. The analysis incorporated 4 apicomplexans previously not included in phylogenetic reconstructions: Haemogregarina clelandi from the Brisbane River tortoise (Emydura signata), Hepatozoon sp. from the slaty grey snake (Stegonotus cucullatus), Hepatozoon (Haemogregarina) boigae from the brown tree snake (Boiga irregularis), and Haemoproteus chelodina from the saw-shelled tortoise (Elseya latisternum). There was no apparent correlation between parasite phylogeny and that of their vertebrate hosts, but there appeared to be some relationship between parasites and their intermediate hosts, suggestive of parasite/vector co-evolution. PMID:12866793

  13. Phylogenetically resolving epidemiologic linkage

    DOE PAGESBeta

    Romero-Severson, Ethan O.; Bulla, Ingo; Leitner, Thomas

    2016-02-22

    The use of phylogenetic trees in epidemiological investigations has become commonplace, but their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the truemore » transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals’ HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. Moreover, we confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results.« less

  14. Phylogenetically resolving epidemiologic linkage.

    PubMed

    Romero-Severson, Ethan O; Bulla, Ingo; Leitner, Thomas

    2016-03-01

    Although the use of phylogenetic trees in epidemiological investigations has become commonplace, their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the true transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals' HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. We confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results. PMID:26903617

  15. Phylogenetically resolving epidemiologic linkage

    PubMed Central

    Romero-Severson, Ethan O.; Bulla, Ingo; Leitner, Thomas

    2016-01-01

    Although the use of phylogenetic trees in epidemiological investigations has become commonplace, their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the true transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals’ HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. We confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results. PMID:26903617

  16. Transmembrane molecules for phylogenetic analyses of pathogenic protists: Leishmania-specific informative sites in hydrophilic loops of trans- endoplasmic reticulum N-acetylglucosamine-1-phosphate transferase.

    PubMed

    Waki, Kayoko; Dutta, Sujoy; Ray, Debalina; Kolli, Bala Krishna; Akman, Leyla; Kawazu, Shin-Ichiro; Lin, Chung-Ping; Chang, Kwang-Poo

    2007-02-01

    A sequence database was created for the Leishmania N-acetylglucosamine-1-phosphate transferase (nagt) gene from 193 independent isolates. PCR products of this single-copy gene were analyzed for restriction fragment length polymorphism based on seven nagt sequences initially available. We subsequently sequenced 77 samples and found 19 new variants (genotypes). Alignment of all 26 nagt sequences is gap free, except for a single codon addition or deletion. Phylogenetic analyses of the sequences allow grouping the isolates into three subgenera, each consisting of recognized species complexes, i.e., subgenus Leishmania (L. amazonensis-L. mexicana, L. donovani-L. infantum, L. tropica, L. major, and L. turanica-L. gerbilli), subgenus Viannia (L. braziliensis, L. panamensis), and one unclassified (L. enriettii) species. This hierarchy of grouping is also supported by sequence analyses of selected samples for additional single-copy genes present on different chromosomes. Intraspecies divergence of nagt varies considerably with different species complexes. Interestingly, species complexes with less subspecies divergence are more widely distributed than those that are more divergent. The relevance of this to Leishmania evolutionary adaptation is discussed. Heterozygosity of subspecies variants contributes to intraspecies diversity, which is prominent in L. tropica but not in L. donovani-L. infantum. This disparity is thought to result from the genetic recombination of the respective species at different times as a rare event during their predominantly clonal evolution. Phylogenetically useful sites of nagt are restricted largely to several extended hydrophilic loops predicted from hypothetical models of Leishmania NAGT as an endoplasmic reticulum transmembrane protein. In silico analyses of nagt from fungi and other protozoa further illustrate the potential value of this and, perhaps, other similar transmembrane molecules for phylogenetic analyses of single-cell eukaryotes.

  17. Transmembrane Molecules for Phylogenetic Analyses of Pathogenic Protists: Leishmania-Specific Informative Sites in Hydrophilic Loops of Trans- Endoplasmic Reticulum N-Acetylglucosamine-1-Phosphate Transferase▿ †

    PubMed Central

    Waki, Kayoko; Dutta, Sujoy; Ray, Debalina; Kolli, Bala Krishna; Akman, Leyla; Kawazu, Shin-Ichiro; Lin, Chung-Ping; Chang, Kwang-Poo

    2007-01-01

    A sequence database was created for the Leishmania N-acetylglucosamine-1-phosphate transferase (nagt) gene from 193 independent isolates. PCR products of this single-copy gene were analyzed for restriction fragment length polymorphism based on seven nagt sequences initially available. We subsequently sequenced 77 samples and found 19 new variants (genotypes). Alignment of all 26 nagt sequences is gap free, except for a single codon addition or deletion. Phylogenetic analyses of the sequences allow grouping the isolates into three subgenera, each consisting of recognized species complexes, i.e., subgenus Leishmania (L. amazonensis-L. mexicana, L. donovani-L. infantum, L. tropica, L. major, and L. turanica-L. gerbilli), subgenus Viannia (L. braziliensis, L. panamensis), and one unclassified (L. enriettii) species. This hierarchy of grouping is also supported by sequence analyses of selected samples for additional single-copy genes present on different chromosomes. Intraspecies divergence of nagt varies considerably with different species complexes. Interestingly, species complexes with less subspecies divergence are more widely distributed than those that are more divergent. The relevance of this to Leishmania evolutionary adaptation is discussed. Heterozygosity of subspecies variants contributes to intraspecies diversity, which is prominent in L. tropica but not in L. donovani-L. infantum. This disparity is thought to result from the genetic recombination of the respective species at different times as a rare event during their predominantly clonal evolution. Phylogenetically useful sites of nagt are restricted largely to several extended hydrophilic loops predicted from hypothetical models of Leishmania NAGT as an endoplasmic reticulum transmembrane protein. In silico analyses of nagt from fungi and other protozoa further illustrate the potential value of this and, perhaps, other similar transmembrane molecules for phylogenetic analyses of single-cell eukaryotes

  18. Multiplex cytokine analyses in dogs with pyometra suggest involvement of KC-like chemokine in canine bacterial sepsis.

    PubMed

    Karlsson, Iulia; Hagman, Ragnvi; Johannisson, Anders; Wang, Liya; Södersten, Fredrik; Wernersson, Sara

    2016-02-01

    Clinical diagnostic criteria for sepsis (systemic inflammatory response syndrome caused by infection) are unspecific and, therefore, biomarkers for sepsis diagnosis are needed for appropriate treatment and patient survival. Pyometra, a common disease caused by bacterial infection of the uterus, results in sepsis in nearly 60% of cases in dogs. We used dogs with pyometra as a natural model for sepsis and collected serum samples from 39 dogs, of which 22 with pyometra and 17 healthy controls. Dogs with pyometra were further grouped into dogs with sepsis (n=18) and without sepsis (n=4). Serum concentrations of a panel of cytokines, including keratinocyte-derived chemokine (KC)-like, granulocyte-macrophages colony stimulating factor (GM-CSF), interleukin (IL)-2, IL-4, IL-6, IL-7, IL-8, IL-10, IL-15, IL-18, chemokine C-X-C motif ligand (CXCL)10 and tumor necrosis factor (TNF)-α, were measured using multiplex analyses. Serum C-reactive protein (CRP) levels were determined using an automated immunoturbidimetric assay. In addition to physical examination hematological and serum biochemical analyses were performed to evaluate the overall status of the dogs. Significantly higher concentrations of KC-like (757 vs 304 pg/ml) were detected in dogs with pyometra as compared to healthy dogs. Within the pyometra group, dogs with sepsis compared to dogs without sepsis had a higher KC-like concentration (873 vs 300 pg/ml). Hemoglobin levels were significantly lower in dogs with pyometra compared to healthy dogs, regardless of the presence or absence of sepsis, and correlated negatively with KC-like. KC-like concentrations correlated positively with CRP, number of hospitalization days, number of monocytes, concentrations of IL-8, and percentage band neutrophils. Our data suggest that bacterial infection triggers the expression of KC-like and further studies are warranted of KC-like as a possible biomarker for diagnosing sepsis and uterine bacterial infection in dogs. PMID:26837616

  19. Disentangling the complex evolutionary history of the Western Palearctic blue tits (Cyanistes spp.) - phylogenomic analyses suggest radiation by multiple colonization events and subsequent isolation.

    PubMed

    Stervander, Martin; Illera, Juan Carlos; Kvist, Laura; Barbosa, Pedro; Keehnen, Naomi P; Pruisscher, Peter; Bensch, Staffan; Hansson, Bengt

    2015-05-01

    Isolated islands and their often unique biota continue to play key roles for understanding the importance of drift, genetic variation and adaptation in the process of population differentiation and speciation. One island system that has inspired and intrigued evolutionary biologists is the blue tit complex (Cyanistes spp.) in Europe and Africa, in particular the complex evolutionary history of the multiple genetically distinct taxa of the Canary Islands. Understanding Afrocanarian colonization events is of particular importance because of recent unconventional suggestions that these island populations acted as source of the widespread population in mainland Africa. We investigated the relationship between mainland and island blue tits using a combination of Sanger sequencing at a population level (20 loci; 12 500 nucleotides) and next-generation sequencing of single population representatives (>3 200 000 nucleotides), analysed in coalescence and phylogenetic frameworks. We found (i) that Afrocanarian blue tits are monophyletic and represent four major clades, (ii) that the blue tit complex has a continental origin and that the Canary Islands were colonized three times, (iii) that all island populations have low genetic variation, indicating low long-term effective population sizes and (iv) that populations on La Palma and in Libya represent relicts of an ancestral North African population. Further, demographic reconstructions revealed (v) that the Canary Islands, conforming to traditional views, hold sink populations, which have not served as source for back colonization of the African mainland. Our study demonstrates the importance of complete taxon sampling and an extensive multimarker study design to obtain robust phylogeographical inferences. PMID:25753616

  20. Genome-Wide Analyses Suggest Mechanisms Involving Early B-Cell Development in Canine IgA Deficiency

    PubMed Central

    Frankowiack, Marcel; Kierczak, Marcin; Bergvall, Kerstin; Axelsson, Erik; Tintle, Linda; Marti, Eliane; Roosje, Petra; Leeb, Tosso; Hedhammar, Åke; Hammarström, Lennart; Lindblad-Toh, Kerstin

    2015-01-01

    Immunoglobulin A deficiency (IgAD) is the most common primary immune deficiency disorder in both humans and dogs, characterized by recurrent mucosal tract infections and a predisposition for allergic and other immune mediated diseases. In several dog breeds, low IgA levels have been observed at a high frequency and with a clinical resemblance to human IgAD. In this study, we used genome-wide association studies (GWAS) to identify genomic regions associated with low IgA levels in dogs as a comparative model for human IgAD. We used a novel percentile groups-approach to establish breed-specific cut-offs and to perform analyses in a close to continuous manner. GWAS performed in four breeds prone to low IgA levels (German shepherd, Golden retriever, Labrador retriever and Shar-Pei) identified 35 genomic loci suggestively associated (p <0.0005) to IgA levels. In German shepherd, three genomic regions (candidate genes include KIRREL3 and SERPINA9) were genome-wide significantly associated (p <0.0002) with IgA levels. A ~20kb long haplotype on CFA28, significantly associated (p = 0.0005) to IgA levels in Shar-Pei, was positioned within the first intron of the gene SLIT1. Both KIRREL3 and SLIT1 are highly expressed in the central nervous system and in bone marrow and are potentially important during B-cell development. SERPINA9 expression is restricted to B-cells and peaks at the time-point when B-cells proliferate into antibody-producing plasma cells. The suggestively associated regions were enriched for genes in Gene Ontology gene sets involving inflammation and early immune cell development. PMID:26225558

  1. Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette Syndrome and Obsessive-Compulsive Disorder

    PubMed Central

    Yu, Dongmei; Mathews, Carol A.; Scharf, Jeremiah M.; Neale, Benjamin M.; Davis, Lea K.; Gamazon, Eric R.; Derks, Eske M.; Evans, Patrick; Edlund, Christopher K.; Crane, Jacquelyn; Fagerness, Jesen A.; Osiecki, Lisa; Gallagher, Patience; Gerber, Gloria; Haddad, Stephen; Illmann, Cornelia; McGrath, Lauren M.; Mayerfeld, Catherine; Arepalli, Sampath; Barlassina, Cristina; Barr, Cathy L.; Bellodi, Laura; Benarroch, Fortu; Berrió, Gabriel Bedoya; Bienvenu, O. Joseph; Black, Donald; Bloch, Michael H.; Brentani, Helena; Bruun, Ruth D.; Budman, Cathy L.; Camarena, Beatriz; Campbell, Desmond D.; Cappi, Carolina; Cardona Silgado, Julio C.; Cavallini, Maria C.; Chavira, Denise A.; Chouinard, Sylvain; Cook, Edwin H.; Cookson, M. R.; Coric, Vladimir; Cullen, Bernadette; Cusi, Daniele; Delorme, Richard; Denys, Damiaan; Dion, Yves; Eapen, Valsama; Egberts, Karin; Falkai, Peter; Fernandez, Thomas; Fournier, Eduardo; Garrido, Helena; Geller, Daniel; Gilbert, Donald; Girard, Simon L.; Grabe, Hans J.; Grados, Marco A.; Greenberg, Benjamin D.; Gross-Tsur, Varda; Grünblatt, Edna; Hardy, John; Heiman, Gary A.; Hemmings, Sian M.J.; Herrera, Luis D.; Hezel, Dianne M.; Hoekstra, Pieter J.; Jankovic, Joseph; Kennedy, James L.; King, Robert A.; Konkashbaev, Anuar I.; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F.; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L.; Lupoli, Sara; Macciardi, Fabio; Maier, Wolfgang; Manunta, Paolo; Marconi, Maurizio; McCracken, James T.; Mesa Restrepo, Sandra C.; Moessner, Rainald; Moorjani, Priya; Morgan, Jubel; Muller, Heike; Murphy, Dennis L.; Naarden, Allan L.; Ochoa, William Cornejo; Ophoff, Roel A.; Pakstis, Andrew J.; Pato, Michele T.; Pato, Carlos N.; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L.; Renner, Tobias; Reus, Victor I.; Richter, Margaret A.; Riddle, Mark A.; Robertson, Mary M.; Romero, Roxana; Rosário, Maria C.; Rosenberg, David; Ruhrmann, Stephan; Sabatti, Chiara; Salvi, Erika; Sampaio, Aline S.; Samuels, Jack; Sandor, Paul; Service, Susan K.; Sheppard, Brooke; Singer, Harvey S.; Smit, Jan H.; Stein, Dan J.; Strengman, Eric; Tischfield, Jay A.; Turiel, Maurizio; Valencia Duarte, Ana V.; Vallada, Homero; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Walkup, John; Wang, Ying; Weale, Mike; Weiss, Robert; Wendland, Jens R.; Westenberg, Herman G.M.; Yao, Yin; Hounie, Ana G.; Miguel, Euripedes C.; Nicolini, Humberto; Wagner, Michael; Ruiz-Linares, Andres; Cath, Danielle C.; McMahon, William; Posthuma, Danielle; Oostra, Ben A.; Nestadt, Gerald; Rouleau, Guy A.; Purcell, Shaun; Jenike, Michael A.; Heutink, Peter; Hanna, Gregory L.; Conti, David V.; Arnold, Paul D.; Freimer, Nelson; Stewart, S. Evelyn; Knowles, James A.; Cox, Nancy J.; Pauls, David L.

    2014-01-01

    Obsessive-compulsive disorder (OCD) and Tourette Syndrome (TS) are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. Here, we report a combined genome-wide association study (GWAS) of TS and OCD in 2723 cases (1310 with OCD, 834 with TS, 579 with OCD plus TS/chronic tics (CT)), 5667 ancestry-matched controls, and 290 OCD parent-child trios. Although no individual single nucleotide polymorphisms (SNPs) achieved genome-wide significance, the GWAS signals were enriched for SNPs strongly associated with variations in brain gene expression levels, i.e. expression quantitative loci (eQTLs), suggesting the presence of true functional variants that contribute to risk of these disorders. Polygenic score analyses identified a significant polygenic component for OCD (p=2×10−4), predicting 3.2% of the phenotypic variance in an independent data set. In contrast, TS had a smaller, non-significant polygenic component, predicting only 0.6% of the phenotypic variance (p=0.06). No significant polygenic signal was detected across the two disorders, although the sample is likely underpowered to detect a modest shared signal. Furthermore, the OCD polygenic signal was significantly attenuated when cases with both OCD and TS/CT were included in the analysis (p=0.01). Previous work has shown that TS and OCD have some degree of shared genetic variation. However, the data from this study suggest that there are also distinct components to the genetic architectures of TS and OCD. Furthermore, OCD with co-occurring TS/CT may have different underlying genetic susceptibility compared to OCD alone. PMID:25158072

  2. Phylogenetic systematics and biogeography of hummingbirds: Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy.

    PubMed

    McGuire, Jimmy A; Witt, Christopher C; Altshuler, Douglas L; Remsen, J V

    2007-10-01

    Hummingbirds are an important model system in avian biology, but to date the group has been the subject of remarkably few phylogenetic investigations. Here we present partitioned Bayesian and maximum likelihood phylogenetic analyses for 151 of approximately 330 species of hummingbirds and 12 outgroup taxa based on two protein-coding mitochondrial genes (ND2 and ND4), flanking tRNAs, and two nuclear introns (AK1 and BFib). We analyzed these data under several partitioning strategies ranging between unpartitioned and a maximum of nine partitions. In order to select a statistically justified partitioning strategy following partitioned Bayesian analysis, we considered four alternative criteria including Bayes factors, modified versions of the Akaike information criterion for small sample sizes (AIC(c)), Bayesian information criterion (BIC), and a decision-theoretic methodology (DT). Following partitioned maximum likelihood analyses, we selected a best-fitting strategy using hierarchical likelihood ratio tests (hLRTS), the conventional AICc, BIC, and DT, concluding that the most stringent criterion, the performance-based DT, was the most appropriate methodology for selecting amongst partitioning strategies. In the context of our well-resolved and well-supported phylogenetic estimate, we consider the historical biogeography of hummingbirds using ancestral state reconstructions of (1) primary geographic region of occurrence (i.e., South America, Central America, North America, Greater Antilles, Lesser Antilles), (2) Andean or non-Andean geographic distribution, and (3) minimum elevational occurrence. These analyses indicate that the basal hummingbird assemblages originated in the lowlands of South America, that most of the principle clades of hummingbirds (all but Mountain Gems and possibly Bees) originated on this continent, and that there have been many (at least 30) independent invasions of other primary landmasses, especially Central America.

  3. Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA

    PubMed Central

    Molak, Martyna; Suchard, Marc A.; Ho, Simon Y. W.; Beilman, David W.; Shapiro, Beth

    2014-01-01

    Studies of DNA from ancient samples provide a valuable opportunity to gain insight into past evolutionary and demographic processes. Bayesian phylogenetic methods can estimate evolutionary rates and timescales from ancient DNA sequences, with the ages of the samples acting as calibrations for the molecular clock. Sample ages are often estimated using radiocarbon dating, but the associated measurement error is rarely taken into account. In addition, the total uncertainty quantified by converting radiocarbon dates to calendar dates is typically ignored. Here we present a tool for incorporating both of these sources of uncertainty into Bayesian phylogenetic analyses of ancient DNA. This empirical calibrated radiocarbon sampler (ECRS) integrates the age uncertainty for each ancient sequence over the calibrated probability density function estimated for its radiocarbon date and associated error. We use the ECRS to analyse three ancient DNA data sets. Accounting for radiocarbon-dating and calibration error appeared to have little impact on estimates of evolutionary rates and related parameters for these data sets. However, analyses of other data sets, particularly those with few or only very old radiocarbon dates, might be more sensitive to using artificially precise sample ages and should benefit from use of the ECRS. PMID:24964386

  4. Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA.

    PubMed

    Molak, Martyna; Suchard, Marc A; Ho, Simon Y W; Beilman, David W; Shapiro, Beth

    2015-01-01

    Studies of DNA from ancient samples provide a valuable opportunity to gain insight into past evolutionary and demographic processes. Bayesian phylogenetic methods can estimate evolutionary rates and timescales from ancient DNA sequences, with the ages of the samples acting as calibrations for the molecular clock. Sample ages are often estimated using radiocarbon dating, but the associated measurement error is rarely taken into account. In addition, the total uncertainty quantified by converting radiocarbon dates to calendar dates is typically ignored. Here, we present a tool for incorporating both of these sources of uncertainty into Bayesian phylogenetic analyses of ancient DNA. This empirical calibrated radiocarbon sampler (ECRS) integrates the age uncertainty for each ancient sequence over the calibrated probability density function estimated for its radiocarbon date and associated error. We use the ECRS to analyse three ancient DNA data sets. Accounting for radiocarbon-dating and calibration error appeared to have little impact on estimates of evolutionary rates and related parameters for these data sets. However, analyses of other data sets, particularly those with few or only very old radiocarbon dates, might be more sensitive to using artificially precise sample ages and should benefit from use of the ECRS.

  5. The evolution of eukaryotic cells from the perspective of peroxisomes: phylogenetic analyses of peroxisomal beta-oxidation enzymes support mitochondria-first models of eukaryotic cell evolution.

    PubMed

    Bolte, Kathrin; Rensing, Stefan A; Maier, Uwe-G

    2015-02-01

    Beta-oxidation of fatty acids and detoxification of reactive oxygen species are generally accepted as being fundamental functions of peroxisomes. Additionally, these pathways might have been the driving force favoring the selection of this compartment during eukaryotic evolution. Here we performed phylogenetic analyses of enzymes involved in beta-oxidation of fatty acids in Bacteria, Eukaryota, and Archaea. These imply an alpha-proteobacterial origin for three out of four enzymes. By integrating the enzymes' history into the contrasting models on the origin of eukaryotic cells, we conclude that peroxisomes most likely evolved non-symbiotically and subsequent to the acquisition of mitochondria in an archaeal host cell.

  6. Phylogenetic distance of Thelohania butleri Johnston, Vernick, and Sprague, 1978 (Microsporidia; Thelohaniidae), a parasite of the smooth pink shrimp Pandalus jordani, from its congeners suggests need for major revision of the genus Thelohania Henneguy, 1892.

    PubMed

    Brown, Amanda M V; Adamson, Martin L

    2006-01-01

    Thelohania butleri, a microsporidian that causes mortality and commercial losses in the smooth pink shrimp Pandalus jordani, is of taxonomic interest as a species resembling the poorly studied type species, Thelohania giardi, of the large, polyphyletic genus Thelohania. We examined the ultrastructure of T. butleri to confirm its identity and reconstructed phylogenies using ribosomal DNA to find the relationship of T. butleri with other Thelohania species in crayfish and ants. Light and transmission electron microscopy from specimens collected from the type locality, the Pacific coast of Canada, confirmed the identity and demonstrated a development similar to that of T. giardi, involving a series of binary fissions without formation of a plasmodium. Phylogenetic analyses consistently showed T. butleri to be distantly related to other Thelohania species, and closely related to species from marine decapods within a larger fish-parasitic clade. Together, features such as host group and habitat, developmental morphology, and phylogeny suggest T. butleri may be a closer relative to T. giardi than any other Thelohania species represented by DNA data so far, and thus imply species from crayfish and ants may not belong in this genus. Results also confirm that genus Thelohania and family Thelohanidae are in need of revision. PMID:17123408

  7. Taxonomic relationships among Turkish water frogs as revealed by phylogenetic analyses using mtDNA gene sequences.

    PubMed

    Bülbül, Ufuk; Matsui, Masafumi; Kutrup, Bilal; Eto, Koshiro

    2011-12-01

    We assessed taxonomic relationships among Turkish water frogs through estimation of phylogenetic relationships among 62 adult specimens from 44 distinct populations inhabiting seven main geographical regions of Turkey using 2897 bp sequences of the mitochondrial Cytb, 12S rRNA and 16S rRNA genes with equally-weighted parsimony, likelihood, and Bayesian methods of inference. Monophyletic clade (Clade A) of the northwesternmost (Thrace) samples is identified as Pelophylax ridibundus. The other clade (Clade B) consisted of two monophyletic subclades. One of these contains specimens from southernmost populations that are regarded as an unnamed species. The other subclade consists of two lineages, of which one corresponds to P. caralitanus and another to P. bedriagae. Taxonomic relationships of these two species are discussed and recognition of P. caralitanus as a subspecies of P. bedriagae is proposed.

  8. Revisiting the phylogeny of Bombacoideae (Malvaceae): Novel relationships, morphologically cohesive clades, and a new tribal classification based on multilocus phylogenetic analyses.

    PubMed

    Carvalho-Sobrinho, Jefferson G; Alverson, William S; Alcantara, Suzana; Queiroz, Luciano P; Mota, Aline C; Baum, David A

    2016-08-01

    Bombacoideae (Malvaceae) is a clade of deciduous trees with a marked dominance in many forests, especially in the Neotropics. The historical lack of a well-resolved phylogenetic framework for Bombacoideae hinders studies in this ecologically important group. We reexamined phylogenetic relationships in this clade based on a matrix of 6465 nuclear (ETS, ITS) and plastid (matK, trnL-trnF, trnS-trnG) DNA characters. We used maximum parsimony, maximum likelihood, and Bayesian inference to infer relationships among 108 species (∼70% of the total number of known species). We analyzed the evolution of selected morphological traits: trunk or branch prickles, calyx shape, endocarp type, seed shape, and seed number per fruit, using ML reconstructions of their ancestral states to identify possible synapomorphies for major clades. Novel phylogenetic relationships emerged from our analyses, including three major lineages marked by fruit or seed traits: the winged-seed clade (Bernoullia, Gyranthera, and Huberodendron), the spongy endocarp clade (Adansonia, Aguiaria, Catostemma, Cavanillesia, and Scleronema), and the Kapok clade (Bombax, Ceiba, Eriotheca, Neobuchia, Pachira, Pseudobombax, Rhodognaphalon, and Spirotheca). The Kapok clade, the most diverse lineage of the subfamily, includes sister relationships (i) between Pseudobombax and "Pochota fendleri" a historically incertae sedis taxon, and (ii) between the Paleotropical genera Bombax and Rhodognaphalon, implying just two bombacoid dispersals to the Old World, the other one involving Adansonia. This new phylogenetic framework offers new insights and a promising avenue for further evolutionary studies. In view of this information, we present a new tribal classification of the subfamily, accompanied by an identification key.

  9. Revisiting the phylogeny of Bombacoideae (Malvaceae): Novel relationships, morphologically cohesive clades, and a new tribal classification based on multilocus phylogenetic analyses.

    PubMed

    Carvalho-Sobrinho, Jefferson G; Alverson, William S; Alcantara, Suzana; Queiroz, Luciano P; Mota, Aline C; Baum, David A

    2016-08-01

    Bombacoideae (Malvaceae) is a clade of deciduous trees with a marked dominance in many forests, especially in the Neotropics. The historical lack of a well-resolved phylogenetic framework for Bombacoideae hinders studies in this ecologically important group. We reexamined phylogenetic relationships in this clade based on a matrix of 6465 nuclear (ETS, ITS) and plastid (matK, trnL-trnF, trnS-trnG) DNA characters. We used maximum parsimony, maximum likelihood, and Bayesian inference to infer relationships among 108 species (∼70% of the total number of known species). We analyzed the evolution of selected morphological traits: trunk or branch prickles, calyx shape, endocarp type, seed shape, and seed number per fruit, using ML reconstructions of their ancestral states to identify possible synapomorphies for major clades. Novel phylogenetic relationships emerged from our analyses, including three major lineages marked by fruit or seed traits: the winged-seed clade (Bernoullia, Gyranthera, and Huberodendron), the spongy endocarp clade (Adansonia, Aguiaria, Catostemma, Cavanillesia, and Scleronema), and the Kapok clade (Bombax, Ceiba, Eriotheca, Neobuchia, Pachira, Pseudobombax, Rhodognaphalon, and Spirotheca). The Kapok clade, the most diverse lineage of the subfamily, includes sister relationships (i) between Pseudobombax and "Pochota fendleri" a historically incertae sedis taxon, and (ii) between the Paleotropical genera Bombax and Rhodognaphalon, implying just two bombacoid dispersals to the Old World, the other one involving Adansonia. This new phylogenetic framework offers new insights and a promising avenue for further evolutionary studies. In view of this information, we present a new tribal classification of the subfamily, accompanied by an identification key. PMID:27154210

  10. Pathogenesis and Phylogenetic Analyses of Two Avian Influenza H7N1 Viruses Isolated from Wild Birds.

    PubMed

    Jin, Hongmei; Wang, Deli; Sun, Jing; Cui, Yanfang; Chen, Guang; Zhang, Xiaolin; Zhang, Jiajie; Li, Xiang; Chai, Hongliang; Gao, Yuwei; Li, Yanbing; Hua, Yuping

    2016-01-01

    The emergence of human infections with a novel H7N9 influenza strain has raised global concerns about a potential human pandemic. To further understand the character of other influenza viruses of the H7 subtype, we selected two H7N1 avian influenza viruses (AIVs) isolated from wild birds during routine surveillance in China: A/Baer's Pochard/Hunan/414/2010 (BP/HuN/414/10) (H7N1) and A/Common Pochard/Xianghai/420/2010 (CP/XH/420/10) (H7N1). To better understand the molecular characteristics of these two isolated H7N1 viruses, we sequenced and phylogenetically analyzed their entire genomes. The results showed that the two H7N1 strains belonged to a Eurasian branch, originating from a common ancestor. Phylogenetic analysis of their hemagglutinin (HA) genes showed that BP/HuN/414/10 and CP/XH/420/10 have a more distant genetic relationship with A/Shanghai/13/2013 (H7N9), with similarities of 91.6 and 91.4%, respectively. To assess the replication and pathogenicity of these viruses in different hosts, they were inoculated in chickens, ducks and mice. Although, both CP/XH/420/10 and BP/HuN/414/10 can infect chickens, ducks and mice, they exhibited different replication capacities in these animals. The results of this study demonstrated that two low pathogenic avian influenza (LPAI) H7N1 viruses of the Eurasian branch could infect mammals and may even have the potential to infect humans. Therefore, it is important to monitor H7 viruses in both domestic and wild birds.

  11. Pathogenesis and Phylogenetic Analyses of Two Avian Influenza H7N1 Viruses Isolated from Wild Birds.

    PubMed

    Jin, Hongmei; Wang, Deli; Sun, Jing; Cui, Yanfang; Chen, Guang; Zhang, Xiaolin; Zhang, Jiajie; Li, Xiang; Chai, Hongliang; Gao, Yuwei; Li, Yanbing; Hua, Yuping

    2016-01-01

    The emergence of human infections with a novel H7N9 influenza strain has raised global concerns about a potential human pandemic. To further understand the character of other influenza viruses of the H7 subtype, we selected two H7N1 avian influenza viruses (AIVs) isolated from wild birds during routine surveillance in China: A/Baer's Pochard/Hunan/414/2010 (BP/HuN/414/10) (H7N1) and A/Common Pochard/Xianghai/420/2010 (CP/XH/420/10) (H7N1). To better understand the molecular characteristics of these two isolated H7N1 viruses, we sequenced and phylogenetically analyzed their entire genomes. The results showed that the two H7N1 strains belonged to a Eurasian branch, originating from a common ancestor. Phylogenetic analysis of their hemagglutinin (HA) genes showed that BP/HuN/414/10 and CP/XH/420/10 have a more distant genetic relationship with A/Shanghai/13/2013 (H7N9), with similarities of 91.6 and 91.4%, respectively. To assess the replication and pathogenicity of these viruses in different hosts, they were inoculated in chickens, ducks and mice. Although, both CP/XH/420/10 and BP/HuN/414/10 can infect chickens, ducks and mice, they exhibited different replication capacities in these animals. The results of this study demonstrated that two low pathogenic avian influenza (LPAI) H7N1 viruses of the Eurasian branch could infect mammals and may even have the potential to infect humans. Therefore, it is important to monitor H7 viruses in both domestic and wild birds. PMID:27458455

  12. Pathogenesis and Phylogenetic Analyses of Two Avian Influenza H7N1 Viruses Isolated from Wild Birds

    PubMed Central

    Jin, Hongmei; Wang, Deli; Sun, Jing; Cui, Yanfang; Chen, Guang; Zhang, Xiaolin; Zhang, Jiajie; Li, Xiang; Chai, Hongliang; Gao, Yuwei; Li, Yanbing; Hua, Yuping

    2016-01-01

    The emergence of human infections with a novel H7N9 influenza strain has raised global concerns about a potential human pandemic. To further understand the character of other influenza viruses of the H7 subtype, we selected two H7N1 avian influenza viruses (AIVs) isolated from wild birds during routine surveillance in China: A/Baer's Pochard/Hunan/414/2010 (BP/HuN/414/10) (H7N1) and A/Common Pochard/Xianghai/420/2010 (CP/XH/420/10) (H7N1). To better understand the molecular characteristics of these two isolated H7N1 viruses, we sequenced and phylogenetically analyzed their entire genomes. The results showed that the two H7N1 strains belonged to a Eurasian branch, originating from a common ancestor. Phylogenetic analysis of their hemagglutinin (HA) genes showed that BP/HuN/414/10 and CP/XH/420/10 have a more distant genetic relationship with A/Shanghai/13/2013 (H7N9), with similarities of 91.6 and 91.4%, respectively. To assess the replication and pathogenicity of these viruses in different hosts, they were inoculated in chickens, ducks and mice. Although, both CP/XH/420/10 and BP/HuN/414/10 can infect chickens, ducks and mice, they exhibited different replication capacities in these animals. The results of this study demonstrated that two low pathogenic avian influenza (LPAI) H7N1 viruses of the Eurasian branch could infect mammals and may even have the potential to infect humans. Therefore, it is important to monitor H7 viruses in both domestic and wild birds. PMID:27458455

  13. Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites.

    PubMed

    Saghaï, Aurélien; Zivanovic, Yvan; Zeyen, Nina; Moreira, David; Benzerara, Karim; Deschamps, Philippe; Bertolino, Paola; Ragon, Marie; Tavera, Rosaluz; López-Archilla, Ana I; López-García, Purificación

    2015-01-01

    Cyanobacteria are thought to play a key role in carbonate formation due to their metabolic activity, but other organisms carrying out oxygenic photosynthesis (photosynthetic eukaryotes) or other metabolisms (e.g., anoxygenic photosynthesis, sulfate reduction), may also contribute to carbonate formation. To obtain more quantitative information than that provided by more classical PCR-dependent methods, we studied the microbial diversity of microbialites from the Alchichica crater lake (Mexico) by mining for 16S/18S rRNA genes in metagenomes obtained by direct sequencing of environmental DNA. We studied samples collected at the Western (AL-W) and Northern (AL-N) shores of the lake and, at the latter site, along a depth gradient (1, 5, 10, and 15 m depth). The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible. Eukaryotes composed a relatively minor fraction dominated by photosynthetic lineages, diatoms in AL-W, influenced by Si-rich seepage waters, and green algae in AL-N samples. Members of the Gammaproteobacteria and Alphaproteobacteria classes of Proteobacteria, Cyanobacteria, and Bacteroidetes were the most abundant bacterial taxa, followed by Planctomycetes, Deltaproteobacteria (Proteobacteria), Verrucomicrobia, Actinobacteria, Firmicutes, and Chloroflexi. Community composition varied among sites and with depth. Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant. Cyanobacteria affiliated to Pleurocapsales largely increased with depth. Scanning electron microscopy (SEM) observations showed considerable areas of aragonite-encrusted Pleurocapsa-like cyanobacteria at microscale. Multivariate statistical analyses showed a strong positive correlation of Pleurocapsales and Chroococcales with aragonite formation at

  14. Genome-wide analyses suggest parallel selection for universal traits may eclipse local environmental selection in a highly mobile carnivore.

    PubMed

    Stronen, Astrid Vik; Jędrzejewska, Bogumiła; Pertoldi, Cino; Demontis, Ditte; Randi, Ettore; Niedziałkowska, Magdalena; Borowik, Tomasz; Sidorovich, Vadim E; Kusak, Josip; Kojola, Ilpo; Karamanlidis, Alexandros A; Ozolins, Janis; Dumenko, Vitalii; Czarnomska, Sylwia D

    2015-10-01

    Ecological and environmental heterogeneity can produce genetic differentiation in highly mobile species. Accordingly, local adaptation may be expected across comparatively short distances in the presence of marked environmental gradients. Within the European continent, wolves (Canis lupus) exhibit distinct north-south population differentiation. We investigated more than 67-K single nucleotide polymorphism (SNP) loci for signatures of local adaptation in 59 unrelated wolves from four previously identified population clusters (northcentral Europe n = 32, Carpathian Mountains n = 7, Dinaric-Balkan n = 9, Ukrainian Steppe n = 11). Our analyses combined identification of outlier loci with findings from genome-wide association study of individual genomic profiles and 12 environmental variables. We identified 353 candidate SNP loci. We examined the SNP position and neighboring megabase (1 Mb, one million bases) regions in the dog (C. lupus familiaris) genome for genes potentially under selection, including homologue genes in other vertebrates. These regions included functional genes for, for example, temperature regulation that may indicate local adaptation and genes controlling for functions universally important for wolves, including olfaction, hearing, vision, and cognitive functions. We also observed strong outliers not associated with any of the investigated variables, which could suggest selective pressures associated with other unmeasured environmental variables and/or demographic factors. These patterns are further supported by the examination of spatial distributions of the SNPs associated with universally important traits, which typically show marked differences in allele frequencies among population clusters. Accordingly, parallel selection for features important to all wolves may eclipse local environmental selection and implies long-term separation among population clusters. PMID:26664688

  15. Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites

    PubMed Central

    Saghaï, Aurélien; Zivanovic, Yvan; Zeyen, Nina; Moreira, David; Benzerara, Karim; Deschamps, Philippe; Bertolino, Paola; Ragon, Marie; Tavera, Rosaluz; López-Archilla, Ana I.; López-García, Purificación

    2015-01-01

    Cyanobacteria are thought to play a key role in carbonate formation due to their metabolic activity, but other organisms carrying out oxygenic photosynthesis (photosynthetic eukaryotes) or other metabolisms (e.g., anoxygenic photosynthesis, sulfate reduction), may also contribute to carbonate formation. To obtain more quantitative information than that provided by more classical PCR-dependent methods, we studied the microbial diversity of microbialites from the Alchichica crater lake (Mexico) by mining for 16S/18S rRNA genes in metagenomes obtained by direct sequencing of environmental DNA. We studied samples collected at the Western (AL-W) and Northern (AL-N) shores of the lake and, at the latter site, along a depth gradient (1, 5, 10, and 15 m depth). The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible. Eukaryotes composed a relatively minor fraction dominated by photosynthetic lineages, diatoms in AL-W, influenced by Si-rich seepage waters, and green algae in AL-N samples. Members of the Gammaproteobacteria and Alphaproteobacteria classes of Proteobacteria, Cyanobacteria, and Bacteroidetes were the most abundant bacterial taxa, followed by Planctomycetes, Deltaproteobacteria (Proteobacteria), Verrucomicrobia, Actinobacteria, Firmicutes, and Chloroflexi. Community composition varied among sites and with depth. Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant. Cyanobacteria affiliated to Pleurocapsales largely increased with depth. Scanning electron microscopy (SEM) observations showed considerable areas of aragonite-encrusted Pleurocapsa-like cyanobacteria at microscale. Multivariate statistical analyses showed a strong positive correlation of Pleurocapsales and Chroococcales with aragonite formation at

  16. The Different Potential of Sponge Bacterial Symbionts in N2 Release Indicated by the Phylogenetic Diversity and Abundance Analyses of Denitrification Genes, nirK and nosZ

    PubMed Central

    Zhang, Xia; He, Liming; Zhang, Fengli; Sun, Wei; Li, Zhiyong

    2013-01-01

    Nitrogen cycle is a critical biogeochemical process of the oceans. The nitrogen fixation by sponge cyanobacteria was early observed. Until recently, sponges were found to be able to release nitrogen gas. However the gene-level evidence for the role of bacterial symbionts from different species sponges in nitrogen gas release is limited. And meanwhile, the quanitative analysis of nitrogen cycle-related genes of sponge microbial symbionts is relatively lacking. The nirK gene encoding nitrite reductase which catalyzes soluble nitrite into gas NO and nosZ gene encoding nitrous oxide reductase which catalyzes N2O into N2 are two key functional genes in the complete denitrification pathway. In this study, using nirK and nosZ genes as markers, the potential of bacterial symbionts in six species of sponges in the release of N2 was investigated by phylogenetic analysis and real-time qPCR. As a result, totally, 2 OTUs of nirK and 5 OTUs of nosZ genes were detected by gene library-based saturated sequencing. Difference phylogenetic diversity of nirK and nosZ genes were observed at OTU level in sponges. Meanwhile, real-time qPCR analysis showed that Xestospongia testudinaria had the highest abundance of nosZ gene, while Cinachyrella sp. had the greatest abundance of nirK gene. Phylogenetic analysis showed that the nirK and nosZ genes were probably of Alpha-, Beta-, and Gammaproteobacteria origin. The results from this study suggest that the denitrification potential of bacteria varies among sponges because of the different phylogenetic diversity and relative abundance of nosZ and nirK genes in sponges. Totally, both the qualitative and quantitative analyses of nirK and nosZ genes indicated the different potential of sponge bacterial symbionts in the release of nitrogen gas. PMID:23762300

  17. Analyses of the radiation of birnaviruses from diverse host phyla and of their evolutionary affinities with other double-stranded RNA and positive strand RNA viruses using robust structure-based multiple sequence alignments and advanced phylogenetic methods

    PubMed Central

    2013-01-01

    Background Birnaviruses form a distinct family of double-stranded RNA viruses infecting animals as different as vertebrates, mollusks, insects and rotifers. With such a wide host range, they constitute a good model for studying the adaptation to the host. Additionally, several lines of evidence link birnaviruses to positive strand RNA viruses and suggest that phylogenetic analyses may provide clues about transition. Results We characterized the genome of a birnavirus from the rotifer Branchionus plicalitis. We used X-ray structures of RNA-dependent RNA polymerases and capsid proteins to obtain multiple structure alignments that allowed us to obtain reliable multiple sequence alignments and we employed “advanced” phylogenetic methods to study the evolutionary relationships between some positive strand and double-stranded RNA viruses. We showed that the rotifer birnavirus genome exhibited an organization remarkably similar to other birnaviruses. As this host was phylogenetically very distant from the other known species targeted by birnaviruses, we revisited the evolutionary pathways within the Birnaviridae family using phylogenetic reconstruction methods. We also applied a number of phylogenetic approaches based on structurally conserved domains/regions of the capsid and RNA-dependent RNA polymerase proteins to study the evolutionary relationships between birnaviruses, other double-stranded RNA viruses and positive strand RNA viruses. Conclusions We show that there is a good correlation between the phylogeny of the birnaviruses and that of their hosts at the phylum level using the RNA-dependent RNA polymerase (genomic segment B) on the one hand and a concatenation of the capsid protein, protease and ribonucleoprotein (genomic segment A) on the other hand. This correlation tends to vanish within phyla. The use of advanced phylogenetic methods and robust structure-based multiple sequence alignments allowed us to obtain a more accurate picture (in terms of

  18. Construction of an infectious clone of simian foamy virus of Japanese macaque (SFVjm) and phylogenetic analyses of SFVjm isolates.

    PubMed

    Yoshikawa, Rokusuke; Nakagawa, So; Okamoto, Munehiro; Miyazawa, Takayuki

    2014-09-10

    Foamy viruses belong to the genus Spumavirus of the family Retroviridae and have been isolated from many mammalian species. It was reported that simian foamy viruses (SFVs) have co-evolved with host species. In this study, we isolated four strains (WK1, WK2, AR1 and AR2) of SFV (named SFVjm) from Japanese macaques (Macaca fuscata) in main island Honshu of Japan. We constructed an infectious molecular clone of SFVjm strain WK1, termed pJM356. The virus derived from the clone replicated and induced syncytia in human (human embryonic kidney 293T cells), African green monkey (Vero cells) and mouse cell lines (Mus dunni tail fibroblast cells). Phylogenetic analysis also revealed that these four SFVjm strains formed two distinct SFVjm clusters. SFVjm strains WK1 and WK2 and SFV isolated from Taiwanese macaques (Macaca cyclopis) formed one cluster, whereas strains AR1 and AR2 formed the other cluster with SFV isolated from a rhesus macaque (Macaca mulatta).

  19. Phylogenetic Analysis of Bolivian Bat Trypanosomes of the Subgenus Schizotrypanum Based on Cytochrome b Sequence and Minicircle Analyses

    PubMed Central

    García, Lineth; Ortiz, Sylvia; Osorio, Gonzalo; Torrico, Mary Cruz; Torrico, Faustino; Solari, Aldo

    2012-01-01

    The aim of this study was to establish the phylogenetic relationships of trypanosomes present in blood samples of Bolivian Carollia bats. Eighteen cloned stocks were isolated from 115 bats belonging to Carollia perspicillata (Phyllostomidae) from three Amazonian areas of the Chapare Province of Bolivia and studied by xenodiagnosis using the vectors Rhodnius robustus and Triatoma infestans (Trypanosoma cruzi marenkellei) or haemoculture (Trypanosoma dionisii). The PCR DNA amplified was analyzed by nucleotide sequences of maxicircles encoding cytochrome b and by means of the molecular size of hyper variable regions of minicircles. Ten samples were classified as Trypanosoma cruzi marinkellei and 8 samples as Trypanosoma dionisii. The two species have a different molecular size profile with respect to the amplified regions of minicircles and also with respect to Trypanosoma cruzi and Trypanosoma rangeli used for comparative purpose. We conclude the presence of two species of bat trypanosomes in these samples, which can clearly be identified by the methods used in this study. The presence of these trypanosomes in Amazonian bats is discussed. PMID:22590570

  20. Large-scale phylogenetic analyses reveal multiple gains of actinorhizal nitrogen-fixing symbioses in angiosperms associated with climate change.

    PubMed

    Li, Hong-Lei; Wang, Wei; Mortimer, Peter E; Li, Rui-Qi; Li, De-Zhu; Hyde, Kevin D; Xu, Jian-Chu; Soltis, Douglas E; Chen, Zhi-Duan

    2015-09-10

    Nitrogen is fundamental to all life forms and is also one of the most limiting of nutrients for plant growth. Several clades of angiosperms have developed symbiotic relationships with actinorhizal bacteria that fix atmospheric nitrogen and increase access to this nutrient. However, the evolutionary patterns of actinorhizal nitrogen-fixing symbioses remain unclear to date. Furthermore the underlying environmental pressures that led to the gain of symbiotic actinorhizal nitrogen fixation have never been investigated. Here, we present the most comprehensive genus-level phylogenetic analysis of the nitrogen-fixing angiosperms based on three plastid loci. We found that actinorhizal nitrogen-fixing species are distributed in nine distinct lineages. By dating the branching events, we determined that seven actinorhizal nitrogen-fixing lineages originated during the Late Cretaceous, and two more emerged during the Eocene. We put forward a hypothesis that multiple gains of actinorhizal nitrogen-fixing symbioses in angiosperms may have been associated with increased global temperatures and high levels of atmospheric carbon dioxide during these two time periods, as well as the availability of open habitats with high light conditions. Our nearly complete genus-level time-tree for the nitrogen-fixing clade is a significant advance in understanding the evolutionary and ecological background of this important symbiosis between plants and bacteria.

  1. Large-scale phylogenetic analyses reveal multiple gains of actinorhizal nitrogen-fixing symbioses in angiosperms associated with climate change

    PubMed Central

    Li, Hong-Lei; Wang, Wei; Mortimer, Peter E.; Li, Rui-Qi; Li, De-Zhu; Hyde, Kevin D.; Xu, Jian-Chu; Soltis, Douglas E.; Chen, Zhi-Duan

    2015-01-01

    Nitrogen is fundamental to all life forms and is also one of the most limiting of nutrients for plant growth. Several clades of angiosperms have developed symbiotic relationships with actinorhizal bacteria that fix atmospheric nitrogen and increase access to this nutrient. However, the evolutionary patterns of actinorhizal nitrogen-fixing symbioses remain unclear to date. Furthermore the underlying environmental pressures that led to the gain of symbiotic actinorhizal nitrogen fixation have never been investigated. Here, we present the most comprehensive genus-level phylogenetic analysis of the nitrogen-fixing angiosperms based on three plastid loci. We found that actinorhizal nitrogen-fixing species are distributed in nine distinct lineages. By dating the branching events, we determined that seven actinorhizal nitrogen-fixing lineages originated during the Late Cretaceous, and two more emerged during the Eocene. We put forward a hypothesis that multiple gains of actinorhizal nitrogen-fixing symbioses in angiosperms may have been associated with increased global temperatures and high levels of atmospheric carbon dioxide during these two time periods, as well as the availability of open habitats with high light conditions. Our nearly complete genus-level time-tree for the nitrogen-fixing clade is a significant advance in understanding the evolutionary and ecological background of this important symbiosis between plants and bacteria. PMID:26354898

  2. Large-scale phylogenetic analyses reveal multiple gains of actinorhizal nitrogen-fixing symbioses in angiosperms associated with climate change.

    PubMed

    Li, Hong-Lei; Wang, Wei; Mortimer, Peter E; Li, Rui-Qi; Li, De-Zhu; Hyde, Kevin D; Xu, Jian-Chu; Soltis, Douglas E; Chen, Zhi-Duan

    2015-01-01

    Nitrogen is fundamental to all life forms and is also one of the most limiting of nutrients for plant growth. Several clades of angiosperms have developed symbiotic relationships with actinorhizal bacteria that fix atmospheric nitrogen and increase access to this nutrient. However, the evolutionary patterns of actinorhizal nitrogen-fixing symbioses remain unclear to date. Furthermore the underlying environmental pressures that led to the gain of symbiotic actinorhizal nitrogen fixation have never been investigated. Here, we present the most comprehensive genus-level phylogenetic analysis of the nitrogen-fixing angiosperms based on three plastid loci. We found that actinorhizal nitrogen-fixing species are distributed in nine distinct lineages. By dating the branching events, we determined that seven actinorhizal nitrogen-fixing lineages originated during the Late Cretaceous, and two more emerged during the Eocene. We put forward a hypothesis that multiple gains of actinorhizal nitrogen-fixing symbioses in angiosperms may have been associated with increased global temperatures and high levels of atmospheric carbon dioxide during these two time periods, as well as the availability of open habitats with high light conditions. Our nearly complete genus-level time-tree for the nitrogen-fixing clade is a significant advance in understanding the evolutionary and ecological background of this important symbiosis between plants and bacteria. PMID:26354898

  3. Multilocus analyses of seven candidate genes suggest interacting pathways for obesity-related traits in Brazilian populations.

    PubMed

    Angeli, Cláudia B; Kimura, Lilian; Auricchio, Maria T; Vicente, João P; Mattevi, Vanessa S; Zembrzuski, Verônica M; Hutz, Mara H; Pereira, Alexandre C; Pereira, Tiago V; Mingroni-Netto, Regina C

    2011-06-01

    We investigated whether variants in major candidate genes for food intake and body weight regulation contribute to obesity-related traits under a multilocus perspective. We studied 375 Brazilian subjects from partially isolated African-derived populations (quilombos). Seven variants displaying conflicting results in previous reports and supposedly implicated in the susceptibility of obesity-related phenotypes were investigated: β2-adrenergic receptor (ADRB2) (Arg16Gly), insulin induced gene 2 (INSIG2) (rs7566605), leptin (LEP) (A19G), LEP receptor (LEPR) (Gln223Arg), perilipin (PLIN) (6209T > C), peroxisome proliferator-activated receptor-γ (PPARG) (Pro12Ala), and resistin (RETN) (-420 C > G). Regression models as well as generalized multifactor dimensionality reduction (GMDR) were employed to test the contribution of individual effects and higher-order interactions to BMI and waist-hip ratio (WHR) variation and risk of overweight/obesity. The best multilocus association signal identified in the quilombos was further examined in an independent sample of 334 Brazilian subjects of European ancestry. In quilombos, only the PPARG polymorphism displayed significant individual effects (WHR variation, P = 0.028). No association was observed either with the risk of overweight/obesity (BMI ≥ 25 kg/m2), risk of obesity alone (BMI ≥ 30 kg/m2) or BMI variation. However, GMDR analyses revealed an interaction between the LEPR and ADRB2 polymorphisms (P = 0.009) as well as a third-order effect involving the latter two variants plus INSIG2 (P = 0.034) with overweight/obesity. Assessment of the LEPR-ADRB2 interaction in the second sample indicated a marginally significant association (P = 0.0724), which was further verified to be limited to men (P = 0.0118). Together, our findings suggest evidence for a two-locus interaction between the LEPR Gln223Arg and ADRB2 Arg16Gly variants in the risk of overweight/obesity, and highlight further the importance of multilocus effects in

  4. Phylogenetic analyses of Lapita decoration do not support branching evolution or regional population structure during colonization of Remote Oceania.

    PubMed

    Cochrane, Ethan E; Lipo, Carl P

    2010-12-12

    Intricately decorated Lapita pottery (3100-2700 BP) was made and deposited by the prehistoric colonizers of Pacific islands, east of the main Solomon's chain. For decades, analyses of this pottery have focused on the ancestor-descendant relationships of populations and the relative degree of interaction across the region to explain similarities in Lapita decoration. Cladistic analyses, increasingly used to examine the evolutionary relationships of material culture assemblages, have not been conducted on Lapita artefacts. Here, we present the first cladistic analysis of Lapita pottery and note the difficulties in using cladistics to investigate datasets where a high degree of horizontal transmission and non-branching evolution may explain observed variation. We additionally present NeighborNet and phenetic distance network analyses to generate hypotheses that may account for Lapita decorative similarity. PMID:21041213

  5. Nucleotide and phylogenetic analyses of the Chlamydia trachomatis ompA gene indicates it is a hotspot for mutation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Serovars of the human pathogen Chlamydia trachomatis occupy one of three specific tissue niches. Genomic analyses indicate that the serovars have a phylogeny congruent with their pathobiology and have an average substitution rate of less than one nucleotide per kilobase. The ompA gene, h...

  6. Reprint of "Sequence and phylogenetic analyses of novel totivirus-like double-stranded RNAs from field-collected powdery mildew fungi".

    PubMed

    Kondo, Hideki; Hisano, Sakae; Chiba, Sotaro; Maruyama, Kazuyuki; Andika, Ida Bagus; Toyoda, Kazuhiro; Fujimori, Fumihiro; Suzuki, Nobuhiro

    2016-07-01

    The identification of mycoviruses contributes greatly to understanding of the diversity and evolutionary aspects of viruses. Powdery mildew fungi are important and widely studied obligate phytopathogenic agents, but there has been no report on mycoviruses infecting these fungi. In this study, we used a deep sequencing approach to analyze the double-stranded RNA (dsRNA) segments isolated from field-collected samples of powdery mildew fungus-infected red clover plants in Japan. Database searches identified the presence of at least ten totivirus (genus Totivirus)-like sequences, termed red clover powdery mildew-associated totiviruses (RPaTVs). The majority of these sequences shared moderate amino acid sequence identity with each other (<44%) and with other known totiviruses (<59%). Nine of these identified sequences (RPaTV1a, 1b and 2-8) resembled the genome of the prototype totivirus, Saccharomyces cerevisiae virus-L-A (ScV-L-A) in that they contained two overlapping open reading frames (ORFs) encoding a putative coat protein (CP) and an RNA dependent RNA polymerase (RdRp), while one sequence (RPaTV9) showed similarity to another totivirus, Ustilago maydis virus H1 (UmV-H1) that encodes a single polyprotein (CP-RdRp fusion). Similar to yeast totiviruses, each ScV-L-A-like RPaTV contains a -1 ribosomal frameshift site downstream of a predicted pseudoknot structure in the overlapping region of these ORFs, suggesting that the RdRp is translated as a CP-RdRp fusion. Moreover, several ScV-L-A-like sequences were also found by searches of the transcriptome shotgun assembly (TSA) libraries from rust fungi, plants and insects. Phylogenetic analyses show that nine ScV-L-A-like RPaTVs along with ScV-L-A-like sequences derived from TSA libraries are clustered with most established members of the genus Totivirus, while one RPaTV forms a new distinct clade with UmV-H1, possibly establishing an additional genus in the family. Taken together, our results indicate the presence of

  7. Southeast Asian mouth-brooding Betta fighting fish (Teleostei: Perciformes) species and their phylogenetic relationships based on mitochondrial COI and nuclear ITS1 DNA sequences and analyses.

    PubMed

    Panijpan, Bhinyo; Kowasupat, Chanon; Laosinchai, Parames; Ruenwongsa, Pintip; Phongdara, Amornrat; Senapin, Saengchan; Wanna, Warapond; Phiwsaiya, Kornsunee; Kühne, Jens; Fasquel, Frédéric

    2014-12-01

    Fighting fish species in the genus Betta are found in several Southeast Asian countries. Depending on the mode of paternal care for fertilized eggs and hatchlings, various species of the betta fish are classified as mouth brooders or nest builders whose members in turn have been grouped according to their similarities mainly in morphology. The mouth brooders as well as some nest builders involved in the present study include fishes discovered and identified subsequent to previous reports on species groupings and their positions on phylogenetic trees based on DNA sequences that differ from those used by us in this study. From the mitochondrial COI gene and nuclear ITS1 gene sequences and more accurate analyses we conclude that the following members of the mouth-brooding pairs, named differently previously, are virtually identical, viz the Betta prima-Betta pallida pair and Betta ferox-Betta apollon pair. The Betta simplex, hitherto believed to be one species, could possibly be genetically split into 2 distinct species. In addition, several other established type-locality fishes could harbor cryptic species as judged by genetic differences. Assignments of fish species to groups reported earlier may have to be altered somewhat by the present genetic findings. We propose here a new Betta fish phylogenetic tree which, albeit being similar to the previous ones, is clearly different from them. Our gene-based evidence also leads to assignments of some fishes to new species groups and alters the positions of some species on the new phylogenetic tree, thus implying different ancestral relationships.

  8. Southeast Asian mouth-brooding Betta fighting fish (Teleostei: Perciformes) species and their phylogenetic relationships based on mitochondrial COI and nuclear ITS1 DNA sequences and analyses

    PubMed Central

    Panijpan, Bhinyo; Kowasupat, Chanon; Laosinchai, Parames; Ruenwongsa, Pintip; Phongdara, Amornrat; Senapin, Saengchan; Wanna, Warapond; Phiwsaiya, Kornsunee; Kühne, Jens; Fasquel, Frédéric

    2014-01-01

    Fighting fish species in the genus Betta are found in several Southeast Asian countries. Depending on the mode of paternal care for fertilized eggs and hatchlings, various species of the betta fish are classified as mouth brooders or nest builders whose members in turn have been grouped according to their similarities mainly in morphology. The mouth brooders as well as some nest builders involved in the present study include fishes discovered and identified subsequent to previous reports on species groupings and their positions on phylogenetic trees based on DNA sequences that differ from those used by us in this study. From the mitochondrial COI gene and nuclear ITS1 gene sequences and more accurate analyses we conclude that the following members of the mouth-brooding pairs, named differently previously, are virtually identical, viz the Betta prima–Betta pallida pair and Betta ferox–Betta apollon pair. The Betta simplex, hitherto believed to be one species, could possibly be genetically split into 2 distinct species. In addition, several other established type-locality fishes could harbor cryptic species as judged by genetic differences. Assignments of fish species to groups reported earlier may have to be altered somewhat by the present genetic findings. We propose here a new Betta fish phylogenetic tree which, albeit being similar to the previous ones, is clearly different from them. Our gene-based evidence also leads to assignments of some fishes to new species groups and alters the positions of some species on the new phylogenetic tree, thus implying different ancestral relationships. PMID:25606468

  9. Phylogenetic analyses of influenza A (H1N1)pdm09 hemagglutinin gene during and after the pandemic event in Brazil.

    PubMed

    Resende, Paola Cristina; Motta, Fernando Couto; Born, Priscila Silva; Machado, Daniela; Caetano, Braulia Costa; Brown, David; Siqueira, Marilda Mendonça

    2015-12-01

    Pandemic influenza A H1N1 [A(H1N1)pdm09] was first detected in Brazil in May 2009, and spread extensively throughout the country causing a peak of infection during June to August 2009. Since then, it has continued to circulate with a seasonal pattern, causing high rates of morbidity and mortality. Over this period, the virus has continually evolved with the accumulation of new mutations. In this study we analyze the phylogenetic relationship in a collection of 220 A(H1N1)pdm09 hemagglutinin (HA) gene sequences collected during and after the pandemic period (2009 to 2014) in Brazil. In addition, we have looked for evidence of viral polymorphisms associated with severe disease and compared the range of viral variants with the vaccine strain (A/California/7/2009) used throughout this period. The phylogenetic analyses in this study revealed the circulation of at least eight genetic groups in Brazil. Two (G6-pdm and G7-pdm) co-circulated during the pandemic period, showing an early pattern of viral diversification with a low genetic distance from vaccine strain. Other phylogenetic groups, G5, G6 (including 6B, 6C and 6D subgroups), and G7 were found in the subsequent epidemic seasons from 2011 to 2014. These viruses exhibited more amino acid differences from the vaccine strain with several substitutions at the antigenic sites. This is associated with a theoretical decrease in the vaccine efficacy. Furthermore, we observed that the presence of any polymorphism at residue 222 of the HA gene was significantly associated with severe/fatal cases, reinforcing previous reports that described this residue as a potential virulence marker. This study provides new information about the circulation of some viral variants in Brazil, follows up potential genetic markers associated with virulence and allows infer if the efficacy of the current vaccine against more recent A(H1N1)pdm09 strains may be reduced.

  10. Southeast Asian mouth-brooding Betta fighting fish (Teleostei: Perciformes) species and their phylogenetic relationships based on mitochondrial COI and nuclear ITS1 DNA sequences and analyses.

    PubMed

    Panijpan, Bhinyo; Kowasupat, Chanon; Laosinchai, Parames; Ruenwongsa, Pintip; Phongdara, Amornrat; Senapin, Saengchan; Wanna, Warapond; Phiwsaiya, Kornsunee; Kühne, Jens; Fasquel, Frédéric

    2014-12-01

    Fighting fish species in the genus Betta are found in several Southeast Asian countries. Depending on the mode of paternal care for fertilized eggs and hatchlings, various species of the betta fish are classified as mouth brooders or nest builders whose members in turn have been grouped according to their similarities mainly in morphology. The mouth brooders as well as some nest builders involved in the present study include fishes discovered and identified subsequent to previous reports on species groupings and their positions on phylogenetic trees based on DNA sequences that differ from those used by us in this study. From the mitochondrial COI gene and nuclear ITS1 gene sequences and more accurate analyses we conclude that the following members of the mouth-brooding pairs, named differently previously, are virtually identical, viz the Betta prima-Betta pallida pair and Betta ferox-Betta apollon pair. The Betta simplex, hitherto believed to be one species, could possibly be genetically split into 2 distinct species. In addition, several other established type-locality fishes could harbor cryptic species as judged by genetic differences. Assignments of fish species to groups reported earlier may have to be altered somewhat by the present genetic findings. We propose here a new Betta fish phylogenetic tree which, albeit being similar to the previous ones, is clearly different from them. Our gene-based evidence also leads to assignments of some fishes to new species groups and alters the positions of some species on the new phylogenetic tree, thus implying different ancestral relationships. PMID:25606468

  11. Phylogenetic analyses and nitrate-reducing activity of fungal cultures isolated from the permanent, oceanic oxygen minimum zone of the Arabian Sea.

    PubMed

    Manohar, Cathrine Sumathi; Menezes, Larissa Danielle; Ramasamy, Kesava Priyan; Meena, Ram M

    2015-03-01

    Reports on the active role of fungi as denitrifiers in terrestrial ecosystems have stimulated an interest in the study of the role of fungi in oxygen-deficient marine systems. In this study, the culturable diversity of fungi was investigated from 4 stations within the permanent, oceanic, oxygen minimum zone of the Arabian Sea. The isolated cultures grouped within the 2 major fungal phyla Ascomycota and Basidiomycota; diversity estimates in the stations sampled indicated that the diversity of the oxygen-depleted environments is less than that of mangrove regions and deep-sea habitats. Phylogenetic analyses of 18S rRNA sequences revealed a few divergent isolates that clustered with environmental sequences previously obtained by others. This is significant, as these isolates represent phylotypes that so far were known only from metagenomic studies and are of phylogenetic importance. Nitrate reduction activity, the first step in the denitrification process, was recorded for isolates under simulated anoxic, deep-sea conditions showing ecological significance of fungi in the oxygen-depleted habitats. This report increases our understanding of fungal diversity in unique, poorly studied habitats and underlines the importance of fungi in the oxygen-depleted environments.

  12. Phylogenetic analyses and nitrate-reducing activity of fungal cultures isolated from the permanent, oceanic oxygen minimum zone of the Arabian Sea.

    PubMed

    Manohar, Cathrine Sumathi; Menezes, Larissa Danielle; Ramasamy, Kesava Priyan; Meena, Ram M

    2015-03-01

    Reports on the active role of fungi as denitrifiers in terrestrial ecosystems have stimulated an interest in the study of the role of fungi in oxygen-deficient marine systems. In this study, the culturable diversity of fungi was investigated from 4 stations within the permanent, oceanic, oxygen minimum zone of the Arabian Sea. The isolated cultures grouped within the 2 major fungal phyla Ascomycota and Basidiomycota; diversity estimates in the stations sampled indicated that the diversity of the oxygen-depleted environments is less than that of mangrove regions and deep-sea habitats. Phylogenetic analyses of 18S rRNA sequences revealed a few divergent isolates that clustered with environmental sequences previously obtained by others. This is significant, as these isolates represent phylotypes that so far were known only from metagenomic studies and are of phylogenetic importance. Nitrate reduction activity, the first step in the denitrification process, was recorded for isolates under simulated anoxic, deep-sea conditions showing ecological significance of fungi in the oxygen-depleted habitats. This report increases our understanding of fungal diversity in unique, poorly studied habitats and underlines the importance of fungi in the oxygen-depleted environments. PMID:25688692

  13. Assessment of fecal pollution sources in a small northern-plains watershed using PCR and phylogenetic analyses of Bacteroidetes 16S rRNA gene

    USGS Publications Warehouse

    Lamendella, R.; Domingo, J.W.S.; Oerther, D.B.; Vogel, J.R.; Stoeckel, D.M.

    2007-01-01

    We evaluated the efficacy, sensitivity, host-specificity, and spatial/temporal dynamics of human- and ruminant-specific 16S rRNA gene Bacteroidetes markers used to assess the sources of fecal pollution in a fecally impacted watershed. Phylogenetic analyses of 1271 fecal and environmental 16S rRNA gene clones were also performed to study the diversity of Bacteroidetes in this watershed. The host-specific assays indicated that ruminant feces were present in 28-54% of the water samples and in all sampling seasons, with increasing frequency in downstream sites. The human-targeted assays indicated that only 3-5% of the water samples were positive for human fecal signals, although a higher percentage of human-associated signals (19-24%) were detected in sediment samples. Phylogenetic analysis indicated that 57% of all water clones clustered with yet-to-be-cultured Bacteroidetes species associated with sequences obtained from ruminant feces, further supporting the prevalence of ruminant contamination in this watershed. However, since several clusters contained sequences from multiple sources, future studies need to consider the potential cosmopolitan nature of these bacterial populations when assessing fecal pollution sources using Bacteroidetes markers. Moreover, additional data is needed in order to understand the distribution of Bacteroidetes host-specific markers and their relationship to water quality regulatory standards. ?? 2006 Federation of European Microbiological Societies.

  14. Phylogenetic Analysis of Multiple FISH Markers in Oral Tongue Squamous Cell Carcinoma Suggests that a Diverse Distribution of Copy Number Changes Is Associated with Poor Prognosis

    PubMed Central

    Wangsa, Darawalee; Chowdhury, Salim Akhter; Ryott, Michael; Gertz, E. Michael; Elmberger, Göran; Auer, Gert; Lundqvist, Elisabeth Åvall; Küffer, Stefan; Ströbel, Philipp; Schäffer, Alejandro A.; Schwartz, Russell; Munck-Wikland, Eva; Ried, Thomas; Heselmeyer-Haddad, Kerstin

    2016-01-01

    Oral tongue squamous cell carcinoma (OTSCC) is associated with poor prognosis. To improve prognostication, we analyzed four gene probes (TERC, CCND1, EGFR, and TP53) and the centromere probe CEP4 as a marker of chromosomal instability, using fluorescence in situ hybridization (FISH) in single cells from the tumors of sixty-five OTSCC patients (Stage I, n=15; Stage II, n=30; Stage III, n=7; Stage IV, n=13). Unsupervised hierarchical clustering of the FISH data distinguished three clusters related to smoking status. Copy number increases of all five markers were found to be correlated to non-smoking habits, while smokers in this cohort had low-level copy number gains. Using the phylogenetic modeling software FISHtrees, we constructed models of tumor progression for each patient based on the four gene probes. Then, we derived test statistics on the models that are significant predictors of disease-free and overall survival, independent of tumor stage and smoking status in multivariate analysis. The patients whose tumors were modeled as progressing by a more diverse distribution of copy number changes across the four genes have poorer prognosis. This is consistent with the view that multiple genetic pathways need to become deregulated in order for cancer to progress. PMID:26175310

  15. Analysis of genetic diversity in banana cultivars (Musa cvs.) from the South of Oman using AFLP markers and classification by phylogenetic, hierarchical clustering and principal component analyses*

    PubMed Central

    Opara, Umezuruike Linus; Jacobson, Dan; Al-Saady, Nadiya Abubakar

    2010-01-01

    Banana is an important crop grown in Oman and there is a dearth of information on its genetic diversity to assist in crop breeding and improvement programs. This study employed amplified fragment length polymorphism (AFLP) to investigate the genetic variation in local banana cultivars from the southern region of Oman. Using 12 primer combinations, a total of 1094 bands were scored, of which 1012 were polymorphic. Eighty-two unique markers were identified, which revealed the distinct separation of the seven cultivars. The results obtained show that AFLP can be used to differentiate the banana cultivars. Further classification by phylogenetic, hierarchical clustering and principal component analyses showed significant differences between the clusters found with molecular markers and those clusters created by previous studies using morphological analysis. Based on the analytical results, a consensus dendrogram of the banana cultivars is presented. PMID:20443211

  16. Suggested protocol for collecting, handling and preparing peat cores and peat samples for physical, chemical, mineralogical and isotopic analyses.

    PubMed

    Givelet, Nicolas; Le Roux, Gaël; Cheburkin, Andriy; Chen, Bin; Frank, Jutta; Goodsite, Michael E; Kempter, Heike; Krachler, Michael; Noernberg, Tommy; Rausch, Nicole; Rheinberger, Stefan; Roos-Barraclough, Fiona; Sapkota, Atindra; Scholz, Christian; Shotyk, William

    2004-05-01

    For detailed reconstructions of atmospheric metal deposition using peat cores from bogs, a comprehensive protocol for working with peat cores is proposed. The first step is to locate and determine suitable sampling sites in accordance with the principal goal of the study, the period of time of interest and the precision required. Using the state of the art procedures and field equipment, peat cores are collected in such a way as to provide high quality records for paleoenvironmental study. Pertinent field observations gathered during the fieldwork are recorded in a field report. Cores are kept frozen at -18 degree C until they can be prepared in the laboratory. Frozen peat cores are precisely cut into 1 cm slices using a stainless steel band saw with stainless steel blades. The outside edges of each slice are removed using a titanium knife to avoid any possible contamination which might have occurred during the sampling and handling stage. Each slice is split, with one-half kept frozen for future studies (archived), and the other half further subdivided for physical, chemical, and mineralogical analyses. Physical parameters such as ash and water contents, the bulk density and the degree of decomposition of the peat are determined using established methods. A subsample is dried overnight at 105 degree C in a drying oven and milled in a centrifugal mill with titanium sieve. Prior to any expensive and time consuming chemical procedures and analyses, the resulting powdered samples, after manual homogenisation, are measured for more than twenty-two major and trace elements using non-destructive X-Ray fluorescence (XRF) methods. This approach provides lots of valuable geochemical data which documents the natural geochemical processes which occur in the peat profiles and their possible effect on the trace metal profiles. The development, evaluation and use of peat cores from bogs as archives of high-resolution records of atmospheric deposition of mineral dust and trace

  17. Suggested protocol for collecting, handling and preparing peat cores and peat samples for physical, chemical, mineralogical and isotopic analyses.

    PubMed

    Givelet, Nicolas; Le Roux, Gaël; Cheburkin, Andriy; Chen, Bin; Frank, Jutta; Goodsite, Michael E; Kempter, Heike; Krachler, Michael; Noernberg, Tommy; Rausch, Nicole; Rheinberger, Stefan; Roos-Barraclough, Fiona; Sapkota, Atindra; Scholz, Christian; Shotyk, William

    2004-05-01

    For detailed reconstructions of atmospheric metal deposition using peat cores from bogs, a comprehensive protocol for working with peat cores is proposed. The first step is to locate and determine suitable sampling sites in accordance with the principal goal of the study, the period of time of interest and the precision required. Using the state of the art procedures and field equipment, peat cores are collected in such a way as to provide high quality records for paleoenvironmental study. Pertinent field observations gathered during the fieldwork are recorded in a field report. Cores are kept frozen at -18 degree C until they can be prepared in the laboratory. Frozen peat cores are precisely cut into 1 cm slices using a stainless steel band saw with stainless steel blades. The outside edges of each slice are removed using a titanium knife to avoid any possible contamination which might have occurred during the sampling and handling stage. Each slice is split, with one-half kept frozen for future studies (archived), and the other half further subdivided for physical, chemical, and mineralogical analyses. Physical parameters such as ash and water contents, the bulk density and the degree of decomposition of the peat are determined using established methods. A subsample is dried overnight at 105 degree C in a drying oven and milled in a centrifugal mill with titanium sieve. Prior to any expensive and time consuming chemical procedures and analyses, the resulting powdered samples, after manual homogenisation, are measured for more than twenty-two major and trace elements using non-destructive X-Ray fluorescence (XRF) methods. This approach provides lots of valuable geochemical data which documents the natural geochemical processes which occur in the peat profiles and their possible effect on the trace metal profiles. The development, evaluation and use of peat cores from bogs as archives of high-resolution records of atmospheric deposition of mineral dust and trace

  18. The interrelationships of metazoan parasites: a review of phylum-and higher-level hypotheses from recent morphological and molecular phylogenetic analyses.

    PubMed

    Zrzavý, J

    2001-01-01

    Phylogeny of seven groups of metazoan parasitic groups is reviewed, based on both morphological and molecular data. The Myxozoa (=Malacosporea + Myxosporea) are most probably related to the egg-parasitic cnidarian Polypodium (Hydrozoa?: Polypodiozoa); the other phylogenetic hypotheses are discussed and the possible non-monophyly of the Cnidaria (with the Polypodiozoa-Myxozoa clade closest to the Triploblastica) is suggested. The Mesozoa is a monophyletic group, possibly closely related to the (monophyletic) Acoelomorpha; whether the Acoelomorpha and Mesozoa represent the basalmost triploblast clade(s) or a derived platyhelminth subclade may depend on rooting the tree of the Triploblastica. Position of the monophyletic Neodermata (=Trematoda + Cercomeromorpha) within the rhabditophoran flatworms is discussed, with two major alternative hypotheses about the neodermatan sister-group relationships (viz., the "neoophoran" and "revertospermatan"). The Myzostomida are not annelids but belong among the Platyzoa, possibly to the clade of animals with anterior sperm flagella (=Prosomastigozoa). The Acanthocephala represent derived syndermates ("rotifers"), possibly related to Seison (the name Pararotatoria comb. n. is proposed for Seisonida + Acanthocephala). The crustacean origin of the Pentastomida based on spermatological and molecular evidence (Pentastomida + Branchiura = Ichthyostraca) is confronted with palaeontological views favouring the pre-arthropod derivation of the pentastomids. Phylogenetic position of the nematodes within the Ecdysozoa and evolution of nematode parasitism are discussed, and the lack of relevant information about the enigmatic ectoproctan parasite Buddenbrockia is emphasised.

  19. Expression and Functional Analyses of the Plastid Lipid-Associated Protein CHRC Suggest Its Role in Chromoplastogenesis and Stress1

    PubMed Central

    Leitner-Dagan, Yael; Ovadis, Marianna; Shklarman, Elena; Elad, Yigal; Rav David, Dalia; Vainstein, Alexander

    2006-01-01

    Chromoplastogenesis during flower development and fruit ripening involves the dramatic overaccumulation of carotenoids sequestered into structures containing lipids and proteins called plastid lipid-associated proteins (PAPs). CHRC, a cucumber (Cucumis sativus) PAP, has been suggested to be transcriptionally activated in carotenoid-accumulating flowers by gibberellin (GA). Mybys, a MYB-like trans-activator identified here, may represent a chromoplastogenesis-related factor: Its expression is flower specific and parallels that of ChrC during flower development; moreover, as revealed by stable ectopic and transient-expression assays, it specifically trans-activates ChrC promoter in flowers accumulating carotenoids and flavonoids. A detailed dissection of ChrC promoter revealed a GA-responsive element, gacCTCcaa, the mutation of which abolished ChrC activation by GA. This cis-element is different from the GARE motif and is involved in ChrC activation probably via negative regulation, similar to other GA-responsive systems. The GA responsiveness and MYBYS floral activation of the ChrC promoter do not overlap with respect to cis-elements. To study the functionality of CHRC, which is activated in vegetative tissues similar to other PAPs by various biotic and abiotic stresses, we employed a tomato (Lycopersicon esculentum) plant system and generated RNAi-transgenic lines with suppressed LeCHRC. Transgenic flowers accumulated approximately 30% less carotenoids per unit protein than controls, indicating an interrelationship between PAPs and flower-specific carotenoid accumulation in chromoplasts. Moreover, the transgenic LeCHRC-suppressed plants were significantly more susceptible to Botrytis cinerea infection, suggesting CHRC's involvement in plant protection under stress conditions and supporting the general, evolutionarily preserved role of PAPs. PMID:16815957

  20. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data.

    PubMed

    Hamady, Micah; Lozupone, Catherine; Knight, Rob

    2010-01-01

    Next-generation sequencing techniques, and PhyloChip, have made simultaneous phylogenetic analyses of hundreds of microbial communities possible. Insight into community structure has been limited by the inability to integrate and visualize such vast datasets. Fast UniFrac overcomes these issues, allowing integration of larger numbers of sequences and samples into a single analysis. Its new array-based implementation offers orders of magnitude improvements over the original version. New 3D visualization of principal coordinates analysis results, with the option to view multiple coordinate axes simultaneously, provides a powerful way to quickly identify patterns that relate vast numbers of microbial communities. We show the potential of Fast UniFrac using examples from three data types: Sanger-sequencing studies of diverse free-living and animal-associated bacterial assemblages and from the gut of obese humans as they diet, pyrosequencing data integrated from studies of the human hand and gut, and PhyloChip data from a study of citrus pathogens. We show that a Fast UniFrac analysis using a reference tree recaptures patterns that could not be detected without considering phylogenetic relationships and that Fast UniFrac, coupled with BLAST-based sequence assignment, can be used to quickly analyze pyrosequencing runs containing hundreds of thousands of sequences, showing patterns relating human and gut samples. Finally, we show that the application of Fast UniFrac to PhyloChip data could identify well-defined subcategories associated with infection. Together, these case studies point the way toward a broad range of applications and show some of the new features of Fast UniFrac.

  1. Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

    PubMed Central

    Hamady, Micah; Lozupone, Catherine; Knight, Rob

    2009-01-01

    Next-generation sequencing techniques, and PhyloChip, have made simultaneous phylogenetic analyses of hundreds of microbial communities possible. Insight into community structure has been limited by the inability to integrate and visualize such vast datasets. Fast UniFrac overcomes these issues, allowing integration of larger numbers of sequences and samples into a single analysis. Its new array-based implementation offers orders of magnitude improvements over the original version. New 3D visualization of principal coordinates analysis (PCoA) results, with the option to view multiple coordinate axes simultaneously, provides a powerful way to quickly identify patterns that relate vast numbers of microbial communities. We demonstrate the potential of Fast UniFrac using examples from three data types: Sanger-sequencing studies of diverse free-living and animal-associated bacterial assemblages and from the gut of obese humans as they diet, pyrosequencing data integrated from studies of the human hand and gut, and PhyloChip data from a study of citrus pathogens. We show that a Fast UniFrac analysis using a reference tree recaptures patterns that could not be detected without considering phylogenetic relationships and that Fast UniFrac, coupled with BLAST-based sequence assignment, can be used to quickly analyze pyrosequencing runs containing hundreds of thousands of sequences, revealing patterns relating human and gut samples. Finally, we show that the application of Fast UniFrac to PhyloChip data could identify well-defined subcategories associated with infection. Together, these case studies point the way towards a broad range of applications and demonstrate some of the new features of Fast UniFrac. PMID:19710709

  2. Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation.

    PubMed

    Pettengill, Emily A; Pettengill, James B; Binet, Rachel

    2015-01-01

    As a leading cause of bacterial dysentery, Shigella represents a significant threat to public health and food safety. Related, but often overlooked, enteroinvasive Escherichia coli (EIEC) can also cause dysentery. Current typing methods have limited ability to identify and differentiate between these pathogens despite the need for rapid and accurate identification of pathogens for clinical treatment and outbreak response. We present a comprehensive phylogeny of Shigella and EIEC using whole genome sequencing of 169 samples, constituting unparalleled strain diversity, and observe a lack of monophyly between Shigella and EIEC and among Shigella taxonomic groups. The evolutionary relationships in the phylogeny are supported by analyses of population structure and hierarchical clustering patterns of translated gene homolog abundance. Lastly, we identified a panel of 404 single nucleotide polymorphism (SNP) markers specific to each phylogenetic cluster for more accurate identification of Shigella and EIEC. Our findings show that Shigella and EIEC are not distinct evolutionary groups within the E. coli genus and, thus, EIEC as a group is not the ancestor to Shigella. The multiple analyses presented provide evidence for reconsidering the taxonomic placement of Shigella. The SNP markers offer more discriminatory power to molecular epidemiological typing methods involving these bacterial pathogens. PMID:26834722

  3. Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation

    PubMed Central

    Pettengill, Emily A.; Pettengill, James B.; Binet, Rachel

    2016-01-01

    As a leading cause of bacterial dysentery, Shigella represents a significant threat to public health and food safety. Related, but often overlooked, enteroinvasive Escherichia coli (EIEC) can also cause dysentery. Current typing methods have limited ability to identify and differentiate between these pathogens despite the need for rapid and accurate identification of pathogens for clinical treatment and outbreak response. We present a comprehensive phylogeny of Shigella and EIEC using whole genome sequencing of 169 samples, constituting unparalleled strain diversity, and observe a lack of monophyly between Shigella and EIEC and among Shigella taxonomic groups. The evolutionary relationships in the phylogeny are supported by analyses of population structure and hierarchical clustering patterns of translated gene homolog abundance. Lastly, we identified a panel of 404 single nucleotide polymorphism (SNP) markers specific to each phylogenetic cluster for more accurate identification of Shigella and EIEC. Our findings show that Shigella and EIEC are not distinct evolutionary groups within the E. coli genus and, thus, EIEC as a group is not the ancestor to Shigella. The multiple analyses presented provide evidence for reconsidering the taxonomic placement of Shigella. The SNP markers offer more discriminatory power to molecular epidemiological typing methods involving these bacterial pathogens. PMID:26834722

  4. Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation.

    PubMed

    Pettengill, Emily A; Pettengill, James B; Binet, Rachel

    2015-01-01

    As a leading cause of bacterial dysentery, Shigella represents a significant threat to public health and food safety. Related, but often overlooked, enteroinvasive Escherichia coli (EIEC) can also cause dysentery. Current typing methods have limited ability to identify and differentiate between these pathogens despite the need for rapid and accurate identification of pathogens for clinical treatment and outbreak response. We present a comprehensive phylogeny of Shigella and EIEC using whole genome sequencing of 169 samples, constituting unparalleled strain diversity, and observe a lack of monophyly between Shigella and EIEC and among Shigella taxonomic groups. The evolutionary relationships in the phylogeny are supported by analyses of population structure and hierarchical clustering patterns of translated gene homolog abundance. Lastly, we identified a panel of 404 single nucleotide polymorphism (SNP) markers specific to each phylogenetic cluster for more accurate identification of Shigella and EIEC. Our findings show that Shigella and EIEC are not distinct evolutionary groups within the E. coli genus and, thus, EIEC as a group is not the ancestor to Shigella. The multiple analyses presented provide evidence for reconsidering the taxonomic placement of Shigella. The SNP markers offer more discriminatory power to molecular epidemiological typing methods involving these bacterial pathogens.

  5. Mutational analyses of HAMP helices suggest a dynamic bundle model of input-output signalling in chemoreceptors.

    PubMed

    Zhou, Qin; Ames, Peter; Parkinson, John S

    2009-09-01

    To test the gearbox model of HAMP signalling in the Escherichia coli serine receptor, Tsr, we generated a series of amino acid replacements at each residue of the AS1 and AS2 helices. The residues most critical for Tsr function defined hydrophobic packing faces consistent with a four-helix bundle. Suppression patterns of helix lesions conformed to the predicted packing layers in the bundle. Although the properties and patterns of most AS1 and AS2 lesions were consistent with both proposed gearbox structures, some mutational features specifically indicate the functional importance of an x-da bundle over an alternative a-d bundle. These genetic data suggest that HAMP signalling could simply involve changes in the stability of its x-da bundle. We propose that Tsr HAMP controls output signals by modulating destabilizing phase clashes between the AS2 helices and the adjoining kinase control helices. Our model further proposes that chemoeffectors regulate HAMP bundle stability through a control cable connection between the transmembrane segments and AS1 helices. Attractant stimuli, which cause inward piston displacements in chemoreceptors, should reduce cable tension, thereby stabilizing the HAMP bundle. This study shows how transmembrane signalling and HAMP input-output control could occur without the helix rotations central to the gearbox model.

  6. A new mechanism to ensure integration during LINE retrotransposition: a suggestion from analyses of the 5' extra nucleotides.

    PubMed

    Kajikawa, Masaki; Yamaguchi, Katsumi; Okada, Norihiro

    2012-09-01

    Long interspersed elements (LINEs) are transposable elements that exist in the chromosomal DNA of most eukaryotes; as such, they have a large impact on the genome evolution of their hosts. LINEs mobilize by a mechanism called retrotransposition in which the LINE RNA is reverse-transcribed into DNA and then integrated into the host chromosome. The integration of the 3' end of the LINE element simultaneously occurs with the initiation of reverse transcription; this process is called target-primed reverse transcription and is one of the important characteristics of LINEs. However, the molecular mechanism of the integration of the 5' end is not well understood. Here, we show that, in cultured cells, the integrants of the zebrafish ZfL2-2 LINE produce extra nucleotides at their 5' ends, and the extra nucleotides originate from their flanking sequences. We also found that, in cultured cells, some integrants of the human L1 LINE and, in their native hosts, some endogenous elements of two other LINEs also contain 5' extra nucleotides of similar origin, suggesting that the mechanism for generation of the 5' extra nucleotides is universal among various LINEs. From these data, we propose a general mechanism for 5' integration in LINE retrotransposition.

  7. A new mechanism to ensure integration during LINE retrotransposition: a suggestion from analyses of the 5' extra nucleotides.

    PubMed

    Kajikawa, Masaki; Yamaguchi, Katsumi; Okada, Norihiro

    2012-09-01

    Long interspersed elements (LINEs) are transposable elements that exist in the chromosomal DNA of most eukaryotes; as such, they have a large impact on the genome evolution of their hosts. LINEs mobilize by a mechanism called retrotransposition in which the LINE RNA is reverse-transcribed into DNA and then integrated into the host chromosome. The integration of the 3' end of the LINE element simultaneously occurs with the initiation of reverse transcription; this process is called target-primed reverse transcription and is one of the important characteristics of LINEs. However, the molecular mechanism of the integration of the 5' end is not well understood. Here, we show that, in cultured cells, the integrants of the zebrafish ZfL2-2 LINE produce extra nucleotides at their 5' ends, and the extra nucleotides originate from their flanking sequences. We also found that, in cultured cells, some integrants of the human L1 LINE and, in their native hosts, some endogenous elements of two other LINEs also contain 5' extra nucleotides of similar origin, suggesting that the mechanism for generation of the 5' extra nucleotides is universal among various LINEs. From these data, we propose a general mechanism for 5' integration in LINE retrotransposition. PMID:22405943

  8. Comparative Transcriptome Analyses Reveal Core Parasitism Genes and Suggest Gene Duplication and Repurposing as Sources of Structural Novelty

    PubMed Central

    Yang, Zhenzhen; Wafula, Eric K.; Honaas, Loren A.; Zhang, Huiting; Das, Malay; Fernandez-Aparicio, Monica; Huang, Kan; Bandaranayake, Pradeepa C.G.; Wu, Biao; Der, Joshua P.; Clarke, Christopher R.; Ralph, Paula E.; Landherr, Lena; Altman, Naomi S.; Timko, Michael P.; Yoder, John I.; Westwood, James H.; dePamphilis, Claude W.

    2015-01-01

    The origin of novel traits is recognized as an important process underlying many major evolutionary radiations. We studied the genetic basis for the evolution of haustoria, the novel feeding organs of parasitic flowering plants, using comparative transcriptome sequencing in three species of Orobanchaceae. Around 180 genes are upregulated during haustorial development following host attachment in at least two species, and these are enriched in proteases, cell wall modifying enzymes, and extracellular secretion proteins. Additionally, about 100 shared genes are upregulated in response to haustorium inducing factors prior to host attachment. Collectively, we refer to these newly identified genes as putative “parasitism genes.” Most of these parasitism genes are derived from gene duplications in a common ancestor of Orobanchaceae and Mimulus guttatus, a related nonparasitic plant. Additionally, the signature of relaxed purifying selection and/or adaptive evolution at specific sites was detected in many haustorial genes, and may play an important role in parasite evolution. Comparative analysis of gene expression patterns in parasitic and nonparasitic angiosperms suggests that parasitism genes are derived primarily from root and floral tissues, but with some genes co-opted from other tissues. Gene duplication, often taking place in a nonparasitic ancestor of Orobanchaceae, followed by regulatory neofunctionalization, was an important process in the origin of parasitic haustoria. PMID:25534030

  9. Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty.

    PubMed

    Yang, Zhenzhen; Wafula, Eric K; Honaas, Loren A; Zhang, Huiting; Das, Malay; Fernandez-Aparicio, Monica; Huang, Kan; Bandaranayake, Pradeepa C G; Wu, Biao; Der, Joshua P; Clarke, Christopher R; Ralph, Paula E; Landherr, Lena; Altman, Naomi S; Timko, Michael P; Yoder, John I; Westwood, James H; dePamphilis, Claude W

    2015-03-01

    The origin of novel traits is recognized as an important process underlying many major evolutionary radiations. We studied the genetic basis for the evolution of haustoria, the novel feeding organs of parasitic flowering plants, using comparative transcriptome sequencing in three species of Orobanchaceae. Around 180 genes are upregulated during haustorial development following host attachment in at least two species, and these are enriched in proteases, cell wall modifying enzymes, and extracellular secretion proteins. Additionally, about 100 shared genes are upregulated in response to haustorium inducing factors prior to host attachment. Collectively, we refer to these newly identified genes as putative "parasitism genes." Most of these parasitism genes are derived from gene duplications in a common ancestor of Orobanchaceae and Mimulus guttatus, a related nonparasitic plant. Additionally, the signature of relaxed purifying selection and/or adaptive evolution at specific sites was detected in many haustorial genes, and may play an important role in parasite evolution. Comparative analysis of gene expression patterns in parasitic and nonparasitic angiosperms suggests that parasitism genes are derived primarily from root and floral tissues, but with some genes co-opted from other tissues. Gene duplication, often taking place in a nonparasitic ancestor of Orobanchaceae, followed by regulatory neofunctionalization, was an important process in the origin of parasitic haustoria.

  10. Phylogeographic Analyses of American Black Bears (Ursus americanus) Suggest Four Glacial Refugia and Complex Patterns of Postglacial Admixture.

    PubMed

    Puckett, Emily E; Etter, Paul D; Johnson, Eric A; Eggert, Lori S

    2015-09-01

    Studies of species with continental distributions continue to identify intraspecific lineages despite continuous habitat. Lineages may form due to isolation by distance, adaptation, divergence across barriers, or genetic drift following range expansion. We investigated lineage diversification and admixture within American black bears (Ursus americanus) across their range using 22 k single nucleotide polymorphisms and mitochondrial DNA sequences. We identified three subcontinental nuclear clusters which we further divided into nine geographic regions: Alaskan (Alaska-East), eastern (Central Interior Highlands, Great Lakes, Northeast, Southeast), and western (Alaska-West, West, Pacific Coast, Southwest). We estimated that the western cluster diverged 67 ka, before eastern and Alaskan divergence 31 ka; these divergence dates contrasted with those from the mitochondrial genome where clades A and B diverged 1.07 Ma, and clades A-east and A-west diverged 169 ka. We combined estimates of divergence timing with hindcast species distribution models to infer glacial refugia for the species in Beringia, Pacific Northwest, Southwest, and Southeast. Our results show a complex arrangement of admixture due to expansion out of multiple refugia. The delineation of the genomic population clusters was inconsistent with the ranges for 16 previously described subspecies. Ranges for U. a. pugnax and U. a. cinnamomum were concordant with admixed clusters, calling into question how to order taxa below the species level. Additionally, our finding that U. a. floridanus has not diverged from U. a. americanus also suggests that morphology and genetics should be reanalyzed to assess taxonomic designations relevant to the conservation management of the species. PMID:25989983

  11. Phylogeographic Analyses of American Black Bears (Ursus americanus) Suggest Four Glacial Refugia and Complex Patterns of Postglacial Admixture.

    PubMed

    Puckett, Emily E; Etter, Paul D; Johnson, Eric A; Eggert, Lori S

    2015-09-01

    Studies of species with continental distributions continue to identify intraspecific lineages despite continuous habitat. Lineages may form due to isolation by distance, adaptation, divergence across barriers, or genetic drift following range expansion. We investigated lineage diversification and admixture within American black bears (Ursus americanus) across their range using 22 k single nucleotide polymorphisms and mitochondrial DNA sequences. We identified three subcontinental nuclear clusters which we further divided into nine geographic regions: Alaskan (Alaska-East), eastern (Central Interior Highlands, Great Lakes, Northeast, Southeast), and western (Alaska-West, West, Pacific Coast, Southwest). We estimated that the western cluster diverged 67 ka, before eastern and Alaskan divergence 31 ka; these divergence dates contrasted with those from the mitochondrial genome where clades A and B diverged 1.07 Ma, and clades A-east and A-west diverged 169 ka. We combined estimates of divergence timing with hindcast species distribution models to infer glacial refugia for the species in Beringia, Pacific Northwest, Southwest, and Southeast. Our results show a complex arrangement of admixture due to expansion out of multiple refugia. The delineation of the genomic population clusters was inconsistent with the ranges for 16 previously described subspecies. Ranges for U. a. pugnax and U. a. cinnamomum were concordant with admixed clusters, calling into question how to order taxa below the species level. Additionally, our finding that U. a. floridanus has not diverged from U. a. americanus also suggests that morphology and genetics should be reanalyzed to assess taxonomic designations relevant to the conservation management of the species.

  12. Structure-function analyses involving palindromic analogs of tritrypticin suggest autonomy of anti-endotoxin and antibacterial activities.

    PubMed

    Kaur, Kanwal J; Sarkar, Pampi; Nagpal, Sushma; Khan, Tarique; Salunke, Dinakar M

    2008-03-01

    Neutralization of invading pathogens by gene-encoded peptide antibiotics has been suggested to manifest in a variety of different modes. Some of these modes require internalization of the peptide through a pathway that involves LPS-mediated uptake of the peptide antibiotics. Many proline/tryptophan-rich cationic peptides for which this mode has been invoked do, indeed, show LPS (endotoxin) binding. If the mechanism of antibiotic action involves the LPS-mediated pathway, a positive correlation ought to manifest between the binding to LPS, its neutralization, and the bacterial killing. No such correlation was evident based on our studies involving minimal active analogs of tritrypticin. The anti-endotoxin activities of these analogs appear not to relate directly to their antibiotic potential. The two palindromic analogs of tritrypticin, NT7 (RRFPWWW) and CT7 (WWWPFRR), showed comparable antibacterial activities. However, while NT7 exhibited anti-endotoxin activity, CT7 did not. The LPS binding of two tritrypticin analogs correlated with their corresponding structures, but the antibacterial activities did not. Further structure-function analysis indicated specific structural implications of the antibacterial activity at the molecular level. Studies involving designed analogs of NT7 incorporating either rigid or flexible linkers between the specifically distanced hydrophobic and cationic clusters modulate the LPS binding. On the other hand, not knowing the target receptor for antibacterial activity is a drawback since the precise epitope for antibacterial activity is not definable. It is apparent that the anti-endotoxin and antibacterial activities represent two independent functions of tritrypticin, consistent with the emerging multifunctionality in the nature of cathelicidins.

  13. CNMS: The preferred genic markers for comparative genomic, molecular phylogenetic, functional genetic diversity and differential gene regulatory expression analyses in chickpea.

    PubMed

    Bajaj, Deepak; Das, Shouvik; Parida, Swarup K

    2015-09-01

    The intra/inter-genomic comparative mapping-based phylogenetic footprinting identified 5 paralogous and 656 orthologous genome-wide CNMS markers in the upstream sequences of chickpea genes. These CNMS markers revealed a high-degree of gene-based syntenic relationship between chickpea and Medicago genomes while minimum between chickpea and Vitis genomes. The time of divergence and duplication estimated using CNMS markers highlight the expected phylogenetic relationships between chickpea and six dicot (legume) species as well as occurrence of ancient genome (approximately 53 Mya) with small-scale recent segmental (approximately 10 Mya) duplication events in chickpea. A wider level of functional molecular diversity (14 to 88 percent) and admixed population genetic structure was detected among desi, kabuli and wild genotypes by genic CNMS markers at a genome-wide scale suggesting their utility in large-scale genetic analysis in chickpea. The subfunctionalization at the cis-regulatory element region and TFBS (transcription factor binding site) motif levels in the upstream sequences of CNMS marker-associated orthologous genes than the paralogues was predominant. Functional constraint might have considerable effect on these CNMScontaining regulatory elements controlling consistent orthologous gene expression in dicots. A rapid subfunctionalization based on diverge differential expression of paralogous CNMS marker-associated genes particularly those that underwent recent small-scale segmental duplication events in chickpea was apparent. The differential regulation of expression and subfunctionalization potential of Ultra CNMS marker-associated genes suggest their utility in deciphering the complex gene regulatory function as well as identification and targeted mapping of potential genes/QTLs governing vital agronomic traits in chickpea. The gene-based CNMS markers with desirable inherent genetic attributes like higher degree of comparative genome mapping, functional

  14. Co-orthology of Pax4 and Pax6 to the fly eyeless gene: molecular phylogenetic, comparative genomic, and embryological analyses.

    PubMed

    Manousaki, Tereza; Feiner, Nathalie; Begemann, Gerrit; Meyer, Axel; Kuraku, Shigehiro

    2011-01-01

    The functional equivalence of Pax6/eyeless genes across distantly related animal phyla has been one of central findings on which evo-devo studies is based. In this study, we show that Pax4, in addition to Pax6, is a vertebrate ortholog of the fly eyeless gene (and its duplicate, twin of eyeless [toy] gene, unique to Insecta). Molecular phylogenetic trees published to date placed the Pax4 gene outside the Pax6/eyeless subgroup as if the Pax4 gene originated from a gene duplication before the origin of bilaterians. However, Pax4 genes had only been reported for mammals. Our molecular phylogenetic analysis, including previously unidentified teleost fish pax4 genes, equally supported two scenarios: one with the Pax4-Pax6 duplication early in vertebrate evolution and the other with this duplication before the bilaterian radiation. We then investigated gene compositions in the genomic regions containing Pax4 and Pax6, and identified (1) conserved synteny between these two regions, suggesting that the Pax4-Pax6 split was caused by a large-scale duplication and (2) its timing within early vertebrate evolution based on the duplication timing of the members of neighboring gene families. Our results are consistent with the so-called two-round genome duplications in early vertebrates. Overall, the Pax6/eyeless ortholog is merely part of a 2:2 orthology relationship between vertebrates (with Pax4 and Pax6) and the fly (with eyeless and toy). In this context, evolution of transcriptional regulation associated with the Pax4-Pax6 split is also discussed in light of the zebrafish pax4 expression pattern that is analyzed here for the first time. PMID:23016906

  15. Phylogenetic and Evolutionary Analyses of the Frizzled Gene Family in Common Carp (Cyprinus carpio) Provide Insights into Gene Expansion from Whole-Genome Duplications.

    PubMed

    Dong, Chuanju; Jiang, Likun; Peng, Wenzhu; Xu, Jian; Mahboob, Shahid; Al-Ghanim, Khalid A; Sun, Xiaowen; Xu, Peng

    2015-01-01

    In humans, the frizzled (FZD) gene family encodes 10 homologous proteins that commonly localize to the plasma membrane. Besides being associated with three main signaling pathways for cell development, most FZDs have different physiological effects and are major determinants in the development process of vertebrates and. Here, we identified and annotated the FZD genes in the whole-genome of common carp (Cyprinus carpio), a teleost fish, and determined their phylogenetic relationships to FZDs in other vertebrates. Our analyses revealed extensive gene duplications in the common carp that have led to the 26 FZD genes that we detected in the common carp genome. All 26 FZD genes were assigned orthology to the 10 FZD genes of on-land vertebrates, with none of genes being specific to the fish lineage. We postulated that the expansion of the FZD gene family in common carp was the result of an additional whole genome duplication event and that the FZD gene family in other teleosts has been lost in their evolution history with the reason that the functions of genes are redundant and conservation. Through the expression profiling of FZD genes in common carp, we speculate that the ancestral gene was likely capable of performing all functions and was expressed broadly, while some descendant duplicate genes only performed partial functions and were specifically expressed at certain stages of development. PMID:26675214

  16. Phylogenetic and molecular analyses of human parainfluenza type 3 virus in Buenos Aires, Argentina, between 2009 and 2013: The emergence of new genetic lineages.

    PubMed

    Goya, Stephanie; Mistchenko, Alicia Susana; Viegas, Mariana

    2016-04-01

    Despite that human parainfluenza type 3 viruses (HPIV3) are one of the leading causes of acute lower respiratory tract infections in children under five, there is no licensed vaccine and there is limited current information on the molecular characteristics of regional and global circulating strains. The aim of this study was to describe the molecular characterization of HPIV3 circulating in Buenos Aires. We performed a genetic and phylogenetic analysis of the HN glycoprotein gene. Between 2009 and 2013, 124 HPIV3-positive samples taken from hospitalized pediatric patients were analyzed. Four new genetic lineages were described. Among them, C1c and C3d lineages showed local circulation patterns, whereas C3e and C3f comprised sequences from very distant countries. Despite the diversity of the described genotypes, C3a and C3d predominated over the others, the latter was present during the first years of the study and it was progressively replaced by C3a. Molecular analyses showed 28 non-synonymous substitutions; of these, 13 were located in potentially predicted B-cell epitopes. Taken together, the emergence of genetic lineages and the information of the molecular characteristics of HN protein may contribute to the general knowledge of HPIV3 molecular epidemiology for future vaccine development and antiviral therapies. PMID:26780643

  17. Genomic and phylogenetic analyses of an adenovirus isolated from a corn snake (Elaphe guttata) imply a common origin with members of the proposed new genus Atadenovirus.

    PubMed

    Farkas, Szilvia L; Benko, Mária; Elo, Péter; Ursu, Krisztina; Dán, Adám; Ahne, Winfried; Harrach, Balázs

    2002-10-01

    Approximately 60% of the genome of an adenovirus isolated from a corn snake (Elaphe guttata) was cloned and sequenced. The results of homology searches showed that the genes of the corn snake adenovirus (SnAdV-1) were closest to their counterparts in members of the recently proposed new genus ATADENOVIRUS: In phylogenetic analyses of the complete hexon and protease genes, SnAdV-1 indeed clustered together with the atadenoviruses. The characteristic features in the genome organization of SnAdV-1 included the presence of a gene homologous to that for protein p32K, the lack of structural proteins V and IX and the absence of homologues of the E1A and E3 regions. These characteristics are in accordance with the genus-defining markers of atadenoviruses. Comparison of the cleavage sites of the viral protease in core protein pVII also confirmed SnAdV-1 as a candidate member of the genus ATADENOVIRUS: Thus, the hypothesis on the possible reptilian origin of atadenoviruses (Harrach, Acta Veterinaria Hungarica 48, 484-490, 2000) seems to be supported. However, the base composition of DNA sequence (>18 kb) determined from the SnAdV-1 genome showed an equilibrated GC content of 51%, which is unusual for an atadenovirus.

  18. The complete mitochondrial genome sequence of the network pipefish (Corythoichthys flavofasciatus) and the analyses of phylogenetic relationships within the Syngnathidae species.

    PubMed

    Zhang, Huixian; Zhang, Yanhong; Qin, Geng; Lin, Qiang

    2015-02-01

    This study determined the mitochondrial genome sequence of the network pipefish (Corythoichthys flavofasciatus) (Gasterosteiformes: Syngnathidae). The mitogenome was a circular molecule consisting of 16,961 nucleotides, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a control region. The nucleotide composition of the genome was biased toward A+T content at 59.3%. All tRNA genes had typical cloverleaf secondary structure except for tRNA(Ser (AGY)), in which the dihydrouridine arm was missing. The C. flavofasciatus control region of 1130 bp contained several features common to other teleost, including conserved sequence blocks. We also performed comparative analysis of the network pipefish mitogenome to the available mitogenome sequences of other Syngnathidae species, and phylogenetic relationship of the Syngnathidae species was constructed based on the data sets including all the concatenated nucleotide sequences of the mitogenomes except the third codon positions. Partitioned Bayesian inference and maximum likelihood analyses showed that all seahorse species formed a monophyletic group of Hippocampus with 100% PPs and BPs, but the pipefish species did not form a monophyletic group. Corythoichthys flavofasciatus was placed as a sister relationship to the Hippocampus clade by strong node-supporting values. The availability of mitogenome of the network pipefish will shed light on the molecular systematics, biogeography and genetic differentiation in this species.

  19. Phylogenetic and coalescent analysis of three loci suggest that the Water Rail is divisible into two species, Rallus aquaticus and R. indicus

    PubMed Central

    2010-01-01

    Background Water Rails (Rallus aquaticus) inhabit fragmented freshwater wetlands across their Palearctic distribution. Disjunct populations are now thought to be morphologically similar over their vast geographic range, though four subspecies had been recognized previously. The fossil record suggests that Water Rails (R. aquaticus) were already spread across the Palearctic by the Pleistocene ~2 million years ago, and the oldest fossil remains thought to be closely related to the common ancestor of water rails date from the Pliocene. Results To investigate population structure in Water Rails at the genetic level we sequenced three independent loci: 686 base pairs (bp) of the mitochondrial DNA COI barcode; 618 bp of the intron ADH5; and 746 bp of the exon PTPN12. Phylogeographic analysis revealed that Water Rails breeding in eastern Asia (R. a. indicus, also known as the Brown-cheeked Rail) are strongly differentiated from the Water Rails in Western and Middle Asia and Europe (R. a. aquaticus and R. a. korejewi). The Kimura 3-parameter plus Gamma COI genetic distance between these two geographic groups was > 3%, and they differed by 18 diagnostic substitutions commensurate with differences between recently diverged sister species of birds. In spite of the low number of variable sites, the two nuclear loci supported this split. We estimated the split of the Brown-cheeked Rail and the Water Rail to have occurred ~534,000 years ago (95% CI 275,000-990,000 years ago). Fragmentation of the widespread ancestral population and eventual speciation of water rails is likely attributable to vicariance by a barrier formed by glacial cycles, continuous uplift of the Tibetan Plateau and increased sedimentation in deserts in southern Asia that originated in the Miocene. Conclusions Water Rails from East Asia were genetically differentiated from the ones breeding in Europe and Western to Middle Asia. Most of the genetic signal was from mitochondrial COI, and was corroborated by

  20. A case study for effects of operational taxonomic units from intracellular endoparasites and ciliates on the eukaryotic phylogeny: phylogenetic position of the haptophyta in analyses of multiple slowly evolving genes.

    PubMed

    Nozaki, Hisayoshi; Yang, Yi; Maruyama, Shinichiro; Suzaki, Toshinobu

    2012-01-01

    Recent multigene phylogenetic analyses have contributed much to our understanding of eukaryotic phylogeny. However, the phylogenetic positions of various lineages within the eukaryotes have remained unresolved or in conflict between different phylogenetic studies. These phylogenetic ambiguities might have resulted from mixtures or integration from various factors including limited taxon sampling, missing data in the alignment, saturations of rapidly evolving genes, mixed analyses of short- and long-branched operational taxonomic units (OTUs), intracellular endoparasite and ciliate OTUs with unusual substitution etc. In order to evaluate the effects from intracellular endoparasite and ciliate OTUs co-analyzed on the eukaryotic phylogeny and simplify the results, we here used two different sets of data matrices of multiple slowly evolving genes with small amounts of missing data and examined the phylogenetic position of the secondary photosynthetic chromalveolates Haptophyta, one of the most abundant groups of oceanic phytoplankton and significant primary producers. In both sets, a robust sister relationship between Haptophyta and SAR (stramenopiles, alveolates, rhizarians, or SA [stramenopiles and alveolates]) was resolved when intracellular endoparasite/ciliate OTUs were excluded, but not in their presence. Based on comparisons of character optimizations on a fixed tree (with a clade composed of haptophytes and SAR or SA), disruption of the monophyly between haptophytes and SAR (or SA) in the presence of intracellular endoparasite/ciliate OTUs can be considered to be a result of multiple evolutionary reversals of character positions that supported the synapomorphy of the haptophyte and SAR (or SA) clade in the absence of intracellular endoparasite/ciliate OTUs.

  1. Cloning and characterization of a pectin lyase gene from Colletotrichum lindemuthianum and comparative phylogenetic/structural analyses with genes from phytopathogenic and saprophytic/opportunistic microorganisms

    PubMed Central

    2011-01-01

    Background Microorganisms produce cell-wall-degrading enzymes as part of their strategies for plant invasion/nutrition. Among these, pectin lyases (PNLs) catalyze the depolymerization of esterified pectin by a β-elimination mechanism. PNLs are grouped together with pectate lyases (PL) in Family 1 of the polysaccharide lyases, as they share a conserved structure in a parallel β-helix. The best-characterized fungal pectin lyases are obtained from saprophytic/opportunistic fungi in the genera Aspergillus and Penicillium and from some pathogens such as Colletotrichum gloeosporioides. The organism used in the present study, Colletotrichum lindemuthianum, is a phytopathogenic fungus that can be subdivided into different physiological races with different capacities to infect its host, Phaseolus vulgaris. These include the non-pathogenic and pathogenic strains known as races 0 and 1472, respectively. Results Here we report the isolation and sequence analysis of the Clpnl2 gene, which encodes the pectin lyase 2 of C. lindemuthianum, and its expression in pathogenic and non-pathogenic races of C. lindemuthianum grown on different carbon sources. In addition, we performed a phylogenetic analysis of the deduced amino acid sequence of Clpnl2 based on reported sequences of PNLs from other sources and compared the three-dimensional structure of Clpnl2, as predicted by homology modeling, with those of other organisms. Both analyses revealed an early separation of bacterial pectin lyases from those found in fungi and oomycetes. Furthermore, two groups could be distinguished among the enzymes from fungi and oomycetes: one comprising enzymes from mostly saprophytic/opportunistic fungi and the other formed mainly by enzymes from pathogenic fungi and oomycetes. Clpnl2 was found in the latter group and was grouped together with the pectin lyase from C. gloeosporioides. Conclusions The Clpnl2 gene of C. lindemuthianum shares the characteristic elements of genes coding for pectin

  2. Proteomics computational analyses suggest that hepatitis C virus E1 and pestivirus E2 envelope glycoproteins are truncated class II fusion proteins.

    PubMed

    Garry, Robert F; Dash, Srikanta

    2003-03-15

    Class II fusion proteins encoded by tick-borne encephalitis virus (TBEV), dengue virus, and Semliki Forest virus have a fusion peptide located at the end of a rod-like molecule comprised of three antiparallel beta sheet domains. Proteomics computational analyses suggest that hepatitis C virus (HCV) envelope glycoprotein E1 and pestivirus envelope glycoprotein E2 are truncated class II fusion proteins. Similarities were also detected between the receptor-binding portion of TBEV E and HCV E2, and between TBEV small membrane protein precursor prM and pestivirus E1. The proposed models of Flaviviridae envelope proteins can facilitate drug and vaccine development.

  3. Integrated network-diversity analyses suggest suppressive effect of Hodgkin’s lymphoma and slightly relieving effect of chemotherapy on human milk microbiome

    PubMed Central

    Ma, Zhanshan (Sam); Li, Lianwei; Li, Wendy; Li, Jie; Chen, Hongju

    2016-01-01

    We aim to investigate the effects of Hodgkin’s lymphoma and the chemotherapy for treating the disease on the human milk microbiome through integrated network and community diversity analyses. Our analyses suggest that Hodgkin’s lymphoma seems to have a suppressing effect on the milk microbiome by lowering the milk microbial community diversity, as measured by the Hill numbers profiles. Although the diversity analysis did not reveal an effect of chemotherapy on community diversity, bacterial species interaction network analysis shows that chemotherapy may help to slightly restore the milk microbiome impacted by Hodgkin’s lymphoma through its influence on the interactions among species (or OTUs). We further constructed diversity-metabolites network, which suggests that the milk microbial diversity is positively correlated with some beneficial milk metabolites such as DHA (DocosaHexaenoic Acid), and that the diversity is negatively correlated with some potentially harmful metabolites such as Butanal. We hence postulate that higher milk microbial diversity should be a signature of healthy mothers and beneficial to infants. Finally, we constructed metabolites OTU correlation networks, from which we identified some special OTUs. These OTUs deserve further investigations given their apparent involvements in regulating the levels of critical milk metabolites such as DHA, Inositol and Butanal. PMID:27386954

  4. Intricate patterns of phylogenetic relationships in the olive family as inferred from multi-locus plastid and nuclear DNA sequence analyses: a close-up on Chionanthus and Noronhia (Oleaceae).

    PubMed

    Hong-Wa, Cynthia; Besnard, Guillaume

    2013-05-01

    Noronhia represents the most successful radiation of the olive family (Oleaceae) in Madagascar with more than 40 named endemic species distributed in all ecoregions from sea level to high mountains. Its position within the subtribe Oleinae has, however, been largely unresolved and its evolutionary history has remained unexplored. In this study, we generated a dataset of plastid (trnL-F, trnT-L, trnS-G, trnK-matK) and nuclear (internal transcribed spacer [ITS]) DNA sequences to infer phylogenetic relationships within Oleinae and to examine evolutionary patterns within Noronhia. Our sample included most species of Noronhia and representatives of the ten other extant genera within the subtribe with an emphasis on Chionanthus. Bayesian inferences and maximum likelihood analyses of plastid and nuclear data indicated several instances of paraphyly and polyphyly within Oleinae, with some geographic signal. Both plastid and ITS data showed a polyphyletic Noronhia that included Indian Ocean species of Chionanthus. They also found close relationships between Noronhia and African Chionanthus. However, the plastid data showed little clear differentiation between Noronhia and the African Chionanthus whereas relationships suggested by the nuclear ITS data were more consistent with taxonomy and geography. We used molecular dating to discriminate between hybridization and lineage sorting/gene duplication as alternative explanations for these topological discordances and to infer the biogeographic history of Noronhia. Hybridization between African Chionanthus and Noronhia could not be ruled out. However, Noronhia has long been established in Madagascar after a likely Cenozoic dispersal from Africa, suggesting any hybridization between representatives of African and Malagasy taxa was ancient. In any case, the African and Indian Ocean Chionanthus and Noronhia together formed a strongly supported monophyletic clade distinct and distant from other Chionanthus, which calls for a revised

  5. Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world.

    PubMed

    Parenicová, Lucie; de Folter, Stefan; Kieffer, Martin; Horner, David S; Favalli, Cristina; Busscher, Jacqueline; Cook, Holly E; Ingram, Richard M; Kater, Martin M; Davies, Brendan; Angenent, Gerco C; Colombo, Lucia

    2003-07-01

    MADS-box transcription factors are key regulators of several plant development processes. Analysis of the complete Arabidopsis genome sequence revealed 107 genes encoding MADS-box proteins, of which 84% are of unknown function. Here, we provide a complete overview of this family, describing the gene structure, gene expression, genome localization, protein motif organization, and phylogenetic relationship of each member. We have divided this transcription factor family into five groups (named MIKC, Malpha, Mbeta, Mgamma, and Mdelta) based on the phylogenetic relationships of the conserved MADS-box domain. This study provides a solid base for functional genomics studies into this important family of plant regulatory genes, including the poorly characterized group of M-type MADS-box proteins. MADS-box genes also constitute an excellent system with which to study the evolution of complex gene families in higher plants. PMID:12837945

  6. Morphology and life history of Brachypeplus glaber LeConte(Coleoptera: Nitidulidae), with a discussion of multiple life stage data for phylogenetic analyses.

    PubMed

    Cline, Andrew R; Skelley, Paul E; Audisio, Paolo

    2013-01-01

    A detailed description of the sap beetle Brachypeplus glaber LeConte (Nitidulidae) is provided, including egg, larval, pupal and adult stages. Rearing and DNA barcoding were used to confirm life stage identifications. This is the first New World Brachypeplus species for which larval and pupal descriptions are available. Characters and character states for larvae, pupae, and adults are discussed at the species and generic levels within the context of phylogenetic revisions at different hierarchical levels.

  7. Re-Evaluation of Phylogenetic Relationships among Species of the Mangrove Genus Avicennia from Indo-West Pacific Based on Multilocus Analyses

    PubMed Central

    Li, Xinnian; Duke, Norman C.; Yang, Yuchen; Huang, Lishi; Zhu, Yuxiang; Zhang, Zhang; Zhou, Renchao; Zhong, Cairong; Huang, Yelin; Shi, Suhua

    2016-01-01

    Avicennia L. (Avicenniaceae), one of the most diverse mangrove genera, is distributed widely in tropical and subtropical intertidal zones worldwide. Five species of Avicennia in the Indo-West Pacific region have been previously described. However, their phylogenetic relationships were determined based on morphological and allozyme data. To enhance our understanding of evolutionary patterns in the clade, we carried out a molecular phylogenetic study using wide sampling and multiple loci. Our results support two monophyletic clades across all species worldwide in Avicennia: an Atlantic-East Pacific (AEP) lineage and an Indo-West Pacific (IWP) lineage. This split is in line with biogeographic distribution of the clade. Focusing on the IWP branch, we reconstructed a detailed phylogenetic tree based on sequences from 25 nuclear genes. The results identified three distinct subclades, (1) A. rumphiana and A. alba, (2) A. officinalis and A. integra, and (3) the A. marina complex, with high bootstrap support. The results strongly corresponded to two morphological traits in floral structure: stigma position in relation to the anthers and style length. Using Bayesian dating methods we estimated diversification of the IWP lineage was dated to late Miocene (c. 6.0 million years ago) and may have been driven largely by the fluctuating sea levels since that time. PMID:27716800

  8. A close relationship between Cercozoa and Foraminifera supported by phylogenetic analyses based on combined amino acid sequences of three cytoskeletal proteins (actin, alpha-tubulin, and beta-tubulin).

    PubMed

    Takishita, Kiyotaka; Inagaki, Yuji; Tsuchiya, Masashi; Sakaguchi, Miako; Maruyama, Tadashi

    2005-12-01

    Recently, there has been increasing molecular evidence of phylogenetic affinity between Cercozoa and Foraminifera in the eukaryotic lineage. We performed phylogenetic analyses based on the combined (concatenated) amino acid sequence data of actin, alpha-tubulin, and beta-tubulin from a wide variety of eukaryotes, including the foraminifers Planoglabratella opercularis and Reticulomyxa filosa, as well as cercomonad and chlorarachniophyte members of Cercozoa. A monophyletic lineage composed of two foraminiferan species branched with the centroheliozoan species Raphidiophrys contractilis was reconstructed in both Bayesian and maximum-likelihood (ML) analyses under 'linked' models, enforcing a single set of the parameters (the parameter for among-site rate variation and branch lengths) on the entire combined alignment. Considering the extremely divergent nature of Foraminifera and Raphidiophyrs tubulins, the union of these lineages recovered is most probably a long-branch attraction artifact due to ignoring gene-specific evolutionary processes. On the other hand, the foraminiferan lineage was within the radiation of Cercozoa in Bayesian analyses under 'unlinked' model conditions, accommodating differences in evolutionary processes across the three genes in the combined alignment. The Foraminifera+Cercozoa affinity recovered in the latter multi-gene analyses is most likely genuine, and thus our data presented here provide further support for the close relationship between these two protist lineages.

  9. Phylogenetic Co-Occurrence of ExoR, ExoS, and ChvI, Components of the RSI Bacterial Invasion Switch, Suggests a Key Adaptive Mechanism Regulating the Transition between Free-Living and Host-Invading Phases in Rhizobiales

    PubMed Central

    Heavner, Mary Ellen; Qiu, Wei-Gang; Cheng, Hai-Ping

    2015-01-01

    Both bacterial symbionts and pathogens rely on their host-sensing mechanisms to activate the biosynthetic pathways necessary for their invasion into host cells. The Gram-negative bacterium Sinorhizobium meliloti relies on its RSI (ExoR-ExoS-ChvI) Invasion Switch to turn on the production of succinoglycan, an exopolysaccharide required for its host invasion. Recent whole-genome sequencing efforts have uncovered putative components of RSI-like invasion switches in many other symbiotic and pathogenic bacteria. To explore the possibility of the existence of a common invasion switch, we have conducted a phylogenomic survey of orthologous ExoR, ExoS, and ChvI tripartite sets in more than ninety proteobacterial genomes. Our analyses suggest that functional orthologs of the RSI invasion switch co-exist in Rhizobiales, an order characterized by numerous invasive species, but not in the order’s close relatives. Phylogenomic analyses and reconstruction of orthologous sets of the three proteins in Alphaproteobacteria confirm Rhizobiales-specific gene synteny and congruent RSI evolutionary histories. Evolutionary analyses further revealed site-specific substitutions correlated specifically to either animal-bacteria or plant-bacteria associations. Lineage restricted conservation of any one specialized gene is in itself an indication of species adaptation. However, the orthologous phylogenetic co-occurrence of all interacting partners within this single signaling pathway strongly suggests that the development of the RSI switch was a key adaptive mechanism. The RSI invasion switch, originally found in S. meliloti, is a characteristic of the Rhizobiales, and potentially a conserved crucial activation step that may be targeted to control host invasion by pathogenic bacterial species. PMID:26309130

  10. Relaxed Phylogenetics and Dating with Confidence

    PubMed Central

    Ho, Simon Y. W; Phillips, Matthew J

    2006-01-01

    In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution. PMID:16683862

  11. Characterizations and expression analyses of NF-κB and Rel genes in the Yesso scallop (Patinopecten yessoensis) suggest specific response patterns against Gram-negative infection in bivalves.

    PubMed

    Li, Ruojiao; Zhang, Ru; Zhang, Lu; Zou, Jiajun; Xing, Qiang; Dou, Huaiqian; Hu, Xiaoli; Zhang, Lingling; Wang, Ruijia; Bao, Zhenmin

    2015-06-01

    Rel/NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) genes are evolutionarily conserved and play a pivotal role in several physiological events. They have been extensively studied from various species, including both vertebrates and invertebrates. However, the Rel/NF-κB genes have not been systematically characterized in bivalves. In this study, we identified and characterized PyNF-κB and PyRel in the Yesso scallop (Patinopecten yessoensis). Phylogenetic and protein structural analyses were conducted to determine the identities and evolutionary relationships of Rel/NF-κB genes in Yesso scallop. Compared with the Rel/NF-κB genes from vertebrate species, the PyNF-κB and PyRel are relatively conserved in their structural features, but there were no paralogs found in P. yessoensis or other invertebrates. To gain insights into the roles of Rel/NF-κB genes during the innate immune response in scallop, quantitative real-time PCR was used to investigate the expression profiles of these genes at different developmental stages, in healthy adult tissues and in the hemolymph after bacterial infection with Micrococcus luteus and Vibrio anguillarum. The real-time PCR results indicated the abundance of PyNF-κB in the first four embryonic stages, including oocytes, fertilized eggs, morulae and blastulae. By contrast, PyRel was abundantly expressed in blastulae, trochophores and D-shaped larvae. In adult scallops, PyNF-κB and PyRel were ubiquitously expressed in most healthy tissues and highly expressed in most of the immune related tissues. Both genes were significantly up-regulated during the acute phase (3 h) after infection with Gram-positive (M. luteus) and negative (V. anguillarum) bacteria, while the much higher expression level of PyNF-κB suggested the involvement of the extra immune deficiency (IMD)-like pathway against the Gram-negative bacterial infection. The complex pattern of Rel/NF-κB induced expression suggested that PyNF-κB and

  12. Analyses of the Distribution Patterns of Burkholderia pseudomallei and Associated Phages in Soil Samples in Thailand Suggest That Phage Presence Reduces the Frequency of Bacterial Isolation

    PubMed Central

    Withatanung, Patoo; Chantratita, Narisara; Muangsombut, Veerachat; Saiprom, Natnaree; Lertmemongkolchai, Ganjana; Klumpp, Jochen; Clokie, Martha R. J.; Galyov, Edouard E.

    2016-01-01

    Background Burkholderia pseudomallei is a soil saprophytic bacterium that causes melioidosis. The infection occurs through cutaneous inoculation, inhalation or ingestion. Bacteriophages (phages) in the same ecosystem may significantly impact the biology of this bacterium in the environment, and in their culturability in the laboratory. Methods/Principal Findings The soil samples were analysed for the presence of bacteria using culture methods, and for phages using plaque assays on B. pseudomallei strain 1106a lawns. Of the 86 soil samples collected from northeastern Thailand, B. pseudomallei was cultured from 23 (26.7%) samples; no phage capable of infecting B. pseudomallei was detected in these samples. In contrast, phages capable of infecting B. pseudomallei, but no bacteria, were present in 10 (11.6%) samples. B. pseudomallei and their phages were co-isolated from only 3 (3.5%) of soil samples. Since phage capable of infecting B. pseudomallei could not have appeared in the samples without the prior presence of bacteria, or exposure to bacteria nearby, our data suggest that all phage-positive/bacteria-negative samples have had B. pseudomallei in or in a close proximity to them. Taken together, these findings indicate that the presence of phages may influence the success of B. pseudomallei isolation. Transmission electron microscopy revealed that the isolated phages are podoviruses. The temperate phages residing in soil-isolated strains of B. pseudomallei that were resistant to the dominant soil borne phages could be induced by mitomycin C. These induced-temperate phages were closely related, but not identical, to the more dominant soil-isolated phage type. Conclusion/Significance The presence of podoviruses capable of infecting B. pseudomallei may affect the success of the pathogen isolation from the soil. The currently used culture-based methods of B. pseudomallei isolation appear to under-estimate the bacterial abundance. The detection of phage capable of

  13. Isopentenyltransferase-1 (IPT1) knockout in Physcomitrella together with phylogenetic analyses of IPTs provide insights into evolution of plant cytokinin biosynthesis

    PubMed Central

    von Schwartzenberg, Klaus

    2014-01-01

    The moss Physcomitrella patens is part of an early divergent clade of land plants utilizing the plant hormone cytokinin for growth control. The rate-limiting step of cytokinin biosynthesis is mediated by isopentenyltransferases (IPTs), found in land plants either as adenylate-IPTs or as tRNA-IPTs. Although a dominant part of cytokinins in flowering plants are synthesized by adenylate-IPTs, the Physcomitrella genome only encodes homologues of tRNA-IPTs. This study therefore looked into the question of whether cytokinins in moss derive from tRNA exclusively. Targeted gene knockout of ipt1 (d|ipt1) along with localization studies revealed that the chloroplast-bound IPT1 was almost exclusively responsible for the A37 prenylation of tRNA in Physcomitrella. Ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS)-based cytokinin profiling demonstrated that the total amount of all free cytokinins in tissue was almost unaffected. However, the knockout plants showed increased levels of the N 6-isopentenyladenine (iP)- and trans-zeatin (tZ)-type cytokinins, considered to provide active forms, while cis-zeatin (cZ)-type cytokinins were reduced. The data provide evidence for an additional and unexpected tRNA-independent cytokinin biosynthetic pathway in moss. Comprehensive phylogenetic analysis indicates a diversification of tRNA-IPT-like genes in bryophytes probably related to additional functions. PMID:24692654

  14. Phylogenetic and genome-wide deep-sequencing analyses of canine parvovirus reveal co-infection with field variants and emergence of a recent recombinant strain.

    PubMed

    Pérez, Ruben; Calleros, Lucía; Marandino, Ana; Sarute, Nicolás; Iraola, Gregorio; Grecco, Sofia; Blanc, Hervé; Vignuzzi, Marco; Isakov, Ofer; Shomron, Noam; Carrau, Lucía; Hernández, Martín; Francia, Lourdes; Sosa, Katia; Tomás, Gonzalo; Panzera, Yanina

    2014-01-01

    Canine parvovirus (CPV), a fast-evolving single-stranded DNA virus, comprises three antigenic variants (2a, 2b, and 2c) with different frequencies and genetic variability among countries. The contribution of co-infection and recombination to the genetic variability of CPV is far from being fully elucidated. Here we took advantage of a natural CPV population, recently formed by the convergence of divergent CPV-2c and CPV-2a strains, to study co-infection and recombination. Complete sequences of the viral coding region of CPV-2a and CPV-2c strains from 40 samples were generated and analyzed using phylogenetic tools. Two samples showed co-infection and were further analyzed by deep sequencing. The sequence profile of one of the samples revealed the presence of CPV-2c and CPV-2a strains that differed at 29 nucleotides. The other sample included a minor CPV-2a strain (13.3% of the viral population) and a major recombinant strain (86.7%). The recombinant strain arose from inter-genotypic recombination between CPV-2c and CPV-2a strains within the VP1/VP2 gene boundary. Our findings highlight the importance of deep-sequencing analysis to provide a better understanding of CPV molecular diversity.

  15. Phylogenetic and pathogenic analyses of three H5N1 avian influenza viruses (clade 2.3.2.1) isolated from wild birds in Northeast China.

    PubMed

    Fan, Zhaobin; Ci, Yanpeng; Liu, Liling; Ma, Yixin; Jia, Ying; Wang, Deli; Guan, Yuntao; Tian, Guobin; Ma, Jianzhang; Li, Yanbing; Chen, Hualan

    2015-01-01

    From April to September 2012, periodic surveillance of avian influenza H5N1 viruses from different wild bird species was conducted in Northeast China. Three highly pathogenic avian influenza (HPAI) H5N1 viruses were isolated from a yellow-browed warbler, common shoveler, and mallard. To trace the genetic lineage of the isolates, nucleotide sequences of all eight gene segments were determined and phylogenetically analyzed. The data indicated that three viruses belonged to the same antigenic virus group: clade 2.3.2.1. To investigate the pathogenicity of these three viruses in different hosts, chickens, ducks, and mice were inoculated. The results showed that chickens were susceptible to each of the three HPAI H5N1 viruses, resulting in 100% mortality within 2-6 days after infection, whereas the three isolates exhibited distinctly different virulence in ducks and mice. The results of this study demonstrated that HPAI H5N1 viruses of clade 2.3.2.1 are still circulating in wild birds through overlapping migratory flyways. Therefore, continuous monitoring of H5N1 in both domestic and wild birds is necessary to prevent a potentially wider outbreak.

  16. Cnidarian phylogenetic relationships as revealed by mitogenomics

    PubMed Central

    2013-01-01

    Background Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia + Octocorallia) – cnidarians with a reproductive polyp and the absence of a medusa stage – and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) – cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution. Results We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia + Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae + Coronatae], Acraspeda [Cubozoa + Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans. Conclusions Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that

  17. Comparative genomic and phylogenetic analyses of Gammaproteobacterial glg genes traced the origin of the Escherichia coli glycogen glgBXCAP operon to the last common ancestor of the sister orders Enterobacteriales and Pasteurellales.

    PubMed

    Almagro, Goizeder; Viale, Alejandro M; Montero, Manuel; Rahimpour, Mehdi; Muñoz, Francisco José; Baroja-Fernández, Edurne; Bahaji, Abdellatif; Zúñiga, Manuel; González-Candelas, Fernando; Pozueta-Romero, Javier

    2015-01-01

    Production of branched α-glucan, glycogen-like polymers is widely spread in the Bacteria domain. The glycogen pathway of synthesis and degradation has been fairly well characterized in the model enterobacterial species Escherichia coli (order Enterobacteriales, class Gammaproteobacteria), in which the cognate genes (branching enzyme glgB, debranching enzyme glgX, ADP-glucose pyrophosphorylase glgC, glycogen synthase glgA, and glycogen phosphorylase glgP) are clustered in a glgBXCAP operon arrangement. However, the evolutionary origin of this particular arrangement and of its constituent genes is unknown. Here, by using 265 complete gammaproteobacterial genomes we have carried out a comparative analysis of the presence, copy number and arrangement of glg genes in all lineages of the Gammaproteobacteria. These analyses revealed large variations in glg gene presence, copy number and arrangements among different gammaproteobacterial lineages. However, the glgBXCAP arrangement was remarkably conserved in all glg-possessing species of the orders Enterobacteriales and Pasteurellales (the E/P group). Subsequent phylogenetic analyses of glg genes present in the Gammaproteobacteria and in other main bacterial groups indicated that glg genes have undergone a complex evolutionary history in which horizontal gene transfer may have played an important role. These analyses also revealed that the E/P glgBXCAP genes (a) share a common evolutionary origin, (b) were vertically transmitted within the E/P group, and (c) are closely related to glg genes of some phylogenetically distant betaproteobacterial species. The overall data allowed tracing the origin of the E. coli glgBXCAP operon to the last common ancestor of the E/P group, and also to uncover a likely glgBXCAP transfer event from the E/P group to particular lineages of the Betaproteobacteria.

  18. Comparative Genomic and Phylogenetic Analyses of Gammaproteobacterial glg Genes Traced the Origin of the Escherichia coli Glycogen glgBXCAP Operon to the Last Common Ancestor of the Sister Orders Enterobacteriales and Pasteurellales

    PubMed Central

    Almagro, Goizeder; Viale, Alejandro M.; Montero, Manuel; Rahimpour, Mehdi; Muñoz, Francisco José; Baroja-Fernández, Edurne; Bahaji, Abdellatif; Zúñiga, Manuel; González-Candelas, Fernando; Pozueta-Romero, Javier

    2015-01-01

    Production of branched α-glucan, glycogen-like polymers is widely spread in the Bacteria domain. The glycogen pathway of synthesis and degradation has been fairly well characterized in the model enterobacterial species Escherichia coli (order Enterobacteriales, class Gammaproteobacteria), in which the cognate genes (branching enzyme glgB, debranching enzyme glgX, ADP-glucose pyrophosphorylase glgC, glycogen synthase glgA, and glycogen phosphorylase glgP) are clustered in a glgBXCAP operon arrangement. However, the evolutionary origin of this particular arrangement and of its constituent genes is unknown. Here, by using 265 complete gammaproteobacterial genomes we have carried out a comparative analysis of the presence, copy number and arrangement of glg genes in all lineages of the Gammaproteobacteria. These analyses revealed large variations in glg gene presence, copy number and arrangements among different gammaproteobacterial lineages. However, the glgBXCAP arrangement was remarkably conserved in all glg-possessing species of the orders Enterobacteriales and Pasteurellales (the E/P group). Subsequent phylogenetic analyses of glg genes present in the Gammaproteobacteria and in other main bacterial groups indicated that glg genes have undergone a complex evolutionary history in which horizontal gene transfer may have played an important role. These analyses also revealed that the E/P glgBXCAP genes (a) share a common evolutionary origin, (b) were vertically transmitted within the E/P group, and (c) are closely related to glg genes of some phylogenetically distant betaproteobacterial species. The overall data allowed tracing the origin of the E. coli glgBXCAP operon to the last common ancestor of the E/P group, and also to uncover a likely glgBXCAP transfer event from the E/P group to particular lineages of the Betaproteobacteria. PMID:25607991

  19. Bayesian phylogenetic estimation of fossil ages

    PubMed Central

    Drummond, Alexei J.; Stadler, Tanja

    2016-01-01

    Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth–death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the ‘morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses. This article is part of the themed issue ‘Dating species divergences

  20. Bayesian phylogenetic estimation of fossil ages.

    PubMed

    Drummond, Alexei J; Stadler, Tanja

    2016-07-19

    Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth-death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the 'morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue 'Dating species divergences using

  1. Bayesian phylogenetic estimation of fossil ages.

    PubMed

    Drummond, Alexei J; Stadler, Tanja

    2016-07-19

    Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth-death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the 'morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue 'Dating species divergences using

  2. Morphometric study of phylogenetic and ecologic signals in procyonid (mammalia: carnivora) endocasts.

    PubMed

    Ahrens, Heather E

    2014-12-01

    Endocasts provide a proxy for brain morphology but are rarely incorporated in phylogenetic analyses despite the potential for new suites of characters. The phylogeny of Procyonidae, a carnivoran family with relatively limited taxonomic diversity, is not well resolved because morphological and molecular data yield conflicting topologies. The presence of phylogenetic and ecologic signals in the endocasts of procyonids will be determined using three-dimensional geometric morphometrics. Endocasts of seven ingroup species and four outgroup species were digitally rendered and 21 landmarks were collected from the endocast surface. Two phylogenetic hypotheses of Procyonidae will be examined using methods testing for phylogenetic signal in morphometric data. In analyses of all taxa, there is significant phylogenetic signal in brain shape for both the morphological and molecular topologies. However, the analyses of ingroup taxa recover a significant phylogenetic signal for the morphological topology only. These results indicate support for the molecular outgroup topology, but not the ingroup topology given the brain shape data. Further examination of brain shape using principal components analysis and wireframe comparisons suggests procyonids possess more developed areas of the brain associated with motor control, spatial perception, and balance relative to the basal musteloid condition. Within Procyonidae, similar patterns of variation are present, and may be associated with increased arboreality in certain taxa. Thus, brain shape derived from endocasts may be used to test for phylogenetic signal and preliminary analyses suggest an association with behavior and ecology.

  3. Morphometric study of phylogenetic and ecologic signals in procyonid (mammalia: carnivora) endocasts.

    PubMed

    Ahrens, Heather E

    2014-12-01

    Endocasts provide a proxy for brain morphology but are rarely incorporated in phylogenetic analyses despite the potential for new suites of characters. The phylogeny of Procyonidae, a carnivoran family with relatively limited taxonomic diversity, is not well resolved because morphological and molecular data yield conflicting topologies. The presence of phylogenetic and ecologic signals in the endocasts of procyonids will be determined using three-dimensional geometric morphometrics. Endocasts of seven ingroup species and four outgroup species were digitally rendered and 21 landmarks were collected from the endocast surface. Two phylogenetic hypotheses of Procyonidae will be examined using methods testing for phylogenetic signal in morphometric data. In analyses of all taxa, there is significant phylogenetic signal in brain shape for both the morphological and molecular topologies. However, the analyses of ingroup taxa recover a significant phylogenetic signal for the morphological topology only. These results indicate support for the molecular outgroup topology, but not the ingroup topology given the brain shape data. Further examination of brain shape using principal components analysis and wireframe comparisons suggests procyonids possess more developed areas of the brain associated with motor control, spatial perception, and balance relative to the basal musteloid condition. Within Procyonidae, similar patterns of variation are present, and may be associated with increased arboreality in certain taxa. Thus, brain shape derived from endocasts may be used to test for phylogenetic signal and preliminary analyses suggest an association with behavior and ecology. PMID:25066912

  4. A phylogenetic re-appraisal of the family Liagoraceae sensu lato (Nemaliales, Rhodophyta) based on sequence analyses of two plastid genes and postfertilization development.

    PubMed

    Lin, Showe-Mei; Rodríguez-Prieto, Conxi; Huisman, John M; Guiry, Michael D; Payri, Claude; Nelson, Wendy A; Liu, Shao-Lun

    2015-06-01

    The marine red algal family Liagoraceae sensu lato is shown to be polyphyletic based on analyses of a combined rbcL and psaA data set and the pattern of carposporophyte development. Fifteen of eighteen genera analyzed formed a monophyletic lineage that included the genus Liagora. Nemalion did not cluster with Liagoraceae sensu stricto, and Nemaliaceae is reinstated, characterized morphologically by the formation of the primary gonimolobes by longitudinal divisions of the gonimoblast initial. Yamadaella and Liagoropsis, previously placed in the Dermonemataceae, are shown to be independent lineages and are recognized as two new families Yamadaellaceae and Liagoropsidaceae. Yamadaellaceae is characterized by two gonimoblast initials cut off bilaterally from the fertilized carpogonium and diffusely spreading gonimoblast filaments. Liagoropsidaceae is characterized by at least three gonimoblast initials cut off by longitudinal septa from the fertilized carpogonium. In contrast, Liagoraceae sensu stricto is characterized by a single gonimoblast initial cut off transversely or diagonally from the fertilized carpogonium. Reproductive features, such as diffuse gonimoblasts and unfused carpogonial branches following postfertilization, appear to have evolved on more than one occasion in the Nemaliales and are therefore not taxonomically diagnostic at the family level, although they may be useful in recognizing genera. PMID:26986669

  5. A phylogenetic re-appraisal of the family Liagoraceae sensu lato (Nemaliales, Rhodophyta) based on sequence analyses of two plastid genes and postfertilization development.

    PubMed

    Lin, Showe-Mei; Rodríguez-Prieto, Conxi; Huisman, John M; Guiry, Michael D; Payri, Claude; Nelson, Wendy A; Liu, Shao-Lun

    2015-06-01

    The marine red algal family Liagoraceae sensu lato is shown to be polyphyletic based on analyses of a combined rbcL and psaA data set and the pattern of carposporophyte development. Fifteen of eighteen genera analyzed formed a monophyletic lineage that included the genus Liagora. Nemalion did not cluster with Liagoraceae sensu stricto, and Nemaliaceae is reinstated, characterized morphologically by the formation of the primary gonimolobes by longitudinal divisions of the gonimoblast initial. Yamadaella and Liagoropsis, previously placed in the Dermonemataceae, are shown to be independent lineages and are recognized as two new families Yamadaellaceae and Liagoropsidaceae. Yamadaellaceae is characterized by two gonimoblast initials cut off bilaterally from the fertilized carpogonium and diffusely spreading gonimoblast filaments. Liagoropsidaceae is characterized by at least three gonimoblast initials cut off by longitudinal septa from the fertilized carpogonium. In contrast, Liagoraceae sensu stricto is characterized by a single gonimoblast initial cut off transversely or diagonally from the fertilized carpogonium. Reproductive features, such as diffuse gonimoblasts and unfused carpogonial branches following postfertilization, appear to have evolved on more than one occasion in the Nemaliales and are therefore not taxonomically diagnostic at the family level, although they may be useful in recognizing genera.

  6. Morphology and morphogenesis of a novel mangrove ciliate, Sterkiella subtropica sp. nov. (Protozoa, Ciliophora, Hypotrichia), with phylogenetic analyses based on small-subunit rDNA sequence data.

    PubMed

    Chen, Xumiao; Gao, Feng; Al-Farraj, Saleh A; Al-Rasheid, Khaled A S; Xu, Kuidong; Song, Weibo; Song, Weibo

    2015-07-01

    A novel marine hypotrichous ciliate, Sterkiella subtropica sp. nov., was recently isolated from a mangrove wetland in Hong Kong. Its morphology, morphogenesis and systematic position have been investigated. The novel species is diagnosed by combined features of morphology, ciliature and nuclear apparatus, while its ontogenetic events present a stable pattern: (i) the six streaks of the undulating membrane (UM) and cirral anlagen are segmented in a 1 : 3 : 3 : 3 : 4 : 4 pattern from left to right, and form three frontal, four frontoventral, one buccal, five ventral and five transverse cirri; (ii) the dorsal structure is similar to most other oxytrichids; that is, in a '4+2' pattern with three caudal cirri being formed. Based on the small-subunit rDNA sequence, the novel species is different from its congeners by between 21 and 35 bp, with sequence identities from 0.978 to 0.987. All molecular trees exhibited a similar topology: the monophyly of species of the genus Sterkiella is not completely supported in our analyses, and approximately unbiased tests (both including and excluding the novel species) also reject the possibility that Sterkiella is a monophyletic lineage, as indicated by the morphology-based classification. PMID:25872955

  7. Geologic Insights and Suggestions on Mineral Potential Based on Analyses of Geophysical Data of the Southern Toquima Range, Nye County, Nevada

    USGS Publications Warehouse

    Shawe, D.R.; Kucks, R.P.; Hildenbrand, T.G.

    2004-01-01

    Aeromagnetic and gravity data provide confirmation of major structural and lithologic units in the southern Toquima Range, Nevada. These units include Cretaceous granite plutons and Tertiary calderas. In addition, the geophysical maps pinpoint numerous faults and lesser intrusions, and they suggest locations of several inferred subsurface intrusions. They also corroborate a system of northwesterly and northeasterly conjugate structures that probably are fundamental to the structural framework of the Toquima Range. A combination of geophysical, geochemical, and geologic data available for the widely mineralized and productive area suggests additional mineral resource potential, especially in and (or) adjacent to the Round Mountain, Jefferson, Manhattan, and Belmont mining districts. Also, evidence for mineral potential exists for areas near the Flower mercury mine south of Mount Jefferson caldera, and in the Bald Mountain Canyon belt of gold-quartz veins in the Manhattan caldera. A few other areas also show potential for mineral resources. The various geologic environments indicated within the map area suggest base- and precious-metal potential in porphyry deposits as well as in quartz-vein and skarn deposits associated with intrusive stocks.

  8. Seed plant phylogenetic diversity and species richness in conservation planning within a global biodiversity hotspot in eastern Asia.

    PubMed

    Li, Rong; Kraft, Nathan J B; Yu, Haiying; Li, Heng

    2015-12-01

    One of the main goals of conservation biology is to understand the factors shaping variation in biodiversity across the planet. This understanding is critical for conservation planners to be able to develop effective conservation strategies. Although many studies have focused on species richness and the protection of rare and endemic species, less attention has been paid to the protection of the phylogenetic dimension of biodiversity. We explored how phylogenetic diversity, species richness, and phylogenetic community structure vary in seed plant communities along an elevational gradient in a relatively understudied high mountain region, the Dulong Valley, in southeastern Tibet, China. As expected, phylogenetic diversity was well correlated with species richness among the elevational bands and among communities. At the community level, evergreen broad-leaved forests had the highest levels of species richness and phylogenetic diversity. Using null model analyses, we found evidence of nonrandom phylogenetic structure across the region. Evergreen broad-leaved forests were phylogenetically overdispersed, whereas other vegetation types tended to be phylogenetically clustered. We suggest that communities with high species richness or overdispersed phylogenetic structure should be a focus for biodiversity conservation within the Dulong Valley because these areas may help maximize the potential of this flora to respond to future global change. In biodiversity hotspots worldwide, we suggest that the phylogenetic structure of a community may serve as a useful measure of phylogenetic diversity in the context of conservation planning.

  9. Analyses of MbtB, MbtE, and MbtF Suggest Revisions to the Mycobactin Biosynthesis Pathway in Mycobacterium tuberculosis

    PubMed Central

    McMahon, Matthew D.; Rush, Jason S.

    2012-01-01

    The production of mycobactin (MBT) by Mycobacterium tuberculosis is essential for this bacterium to access iron when it is in an infected host. Due to this essential function, there is considerable interest in deciphering the mechanism of MBT assembly, with the goal of targeting select biosynthetic steps for antituberculosis drug development. The proposed scheme for MBT biosynthesis involves assembly of the MBT backbone by a hybrid nonribosomal peptide synthetase (NRPS)/polyketide synthase (PKS) megasynthase followed by the tailoring of this backbone by N6 acylation of the central l-Lys residue and subsequent N6-hydroxylation of the central N6-acyl-l-Lys and the terminal caprolactam. A complete testing of this hypothesis has been hindered by the inability to heterologously produce soluble megasynthase components. Here we show that soluble forms of the NRPS components MbtB, MbtE, and MbtF are obtained when these enzymes are coproduced with MbtH. Using these soluble enzymes we determined the amino acid specificity of each adenylation (A) domain. These results suggest that the proposed tailoring enzymes are actually involved in precursor biosynthesis since the A domains of MbtE and MbtF are specific for N6-acyl-N6-hydroxy-l-Lys and N6-hydroxy-l-Lys, respectively. Furthermore, the preference of the A domain of MbtB for l-Thr over l-Ser suggests that the megasynthase produces MBT derivatives with β-methyl oxazoline rings. Since the most prominent form of MBT produced by M. tuberculosis lacks this β-methyl group, a mechanism for demethylation remains to be discovered. These results suggest revisions to the MBT biosynthesis pathway while also identifying new targets for antituberculosis drug development. PMID:22447909

  10. Analyses of MbtB, MbtE, and MbtF suggest revisions to the mycobactin biosynthesis pathway in Mycobacterium tuberculosis.

    PubMed

    McMahon, Matthew D; Rush, Jason S; Thomas, Michael G

    2012-06-01

    The production of mycobactin (MBT) by Mycobacterium tuberculosis is essential for this bacterium to access iron when it is in an infected host. Due to this essential function, there is considerable interest in deciphering the mechanism of MBT assembly, with the goal of targeting select biosynthetic steps for antituberculosis drug development. The proposed scheme for MBT biosynthesis involves assembly of the MBT backbone by a hybrid nonribosomal peptide synthetase (NRPS)/polyketide synthase (PKS) megasynthase followed by the tailoring of this backbone by N(6) acylation of the central l-Lys residue and subsequent N(6)-hydroxylation of the central N(6)-acyl-l-Lys and the terminal caprolactam. A complete testing of this hypothesis has been hindered by the inability to heterologously produce soluble megasynthase components. Here we show that soluble forms of the NRPS components MbtB, MbtE, and MbtF are obtained when these enzymes are coproduced with MbtH. Using these soluble enzymes we determined the amino acid specificity of each adenylation (A) domain. These results suggest that the proposed tailoring enzymes are actually involved in precursor biosynthesis since the A domains of MbtE and MbtF are specific for N(6)-acyl-N(6)-hydroxy-l-Lys and N(6)-hydroxy-l-Lys, respectively. Furthermore, the preference of the A domain of MbtB for l-Thr over l-Ser suggests that the megasynthase produces MBT derivatives with β-methyl oxazoline rings. Since the most prominent form of MBT produced by M. tuberculosis lacks this β-methyl group, a mechanism for demethylation remains to be discovered. These results suggest revisions to the MBT biosynthesis pathway while also identifying new targets for antituberculosis drug development.

  11. Biophysical and Functional Analyses Suggest That Adenovirus E4-ORF3 Protein Requires Higher-order Multimerization to Function against Promyelocytic Leukemia Protein Nuclear Bodies*

    PubMed Central

    Patsalo, Vadim; Yondola, Mark A.; Luan, Bowu; Shoshani, Ilana; Kisker, Caroline; Green, David F.; Raleigh, Daniel P.; Hearing, Patrick

    2012-01-01

    The early region 4 open reading frame 3 protein (E4-ORF3; UniProt ID P04489) is the most highly conserved of all adenovirus-encoded gene products at the amino acid level. A conserved attribute of the E4-ORF3 proteins of different human adenoviruses is the ability to disrupt PML nuclear bodies from their normally punctate appearance into heterogeneous filamentous structures. This E4-ORF3 activity correlates with the inhibition of PML-mediated antiviral activity. The mechanism of E4-ORF3-mediated reorganization of PML nuclear bodies is unknown. Biophysical analysis of the purified WT E4-ORF3 protein revealed an ordered secondary/tertiary structure and the ability to form heterogeneous higher-order multimers in solution. Importantly, a nonfunctional E4-ORF3 mutant protein, L103A, forms a stable dimer with WT secondary structure content. Because the L103A mutant is incapable of PML reorganization, this result suggests that higher-order multimerization of E4-ORF3 may be required for the activity of the protein. In support of this hypothesis, we demonstrate that the E4-ORF3 L103A mutant protein acts as a dominant-negative effector when coexpressed with the WT E4-ORF3 in mammalian cells. It prevents WT E4-ORF3-mediated PML track formation presumably by binding to the WT protein and inhibiting the formation of higher-order multimers. In vitro protein binding studies support this conclusion as demonstrated by copurification of coexpressed WT and L103A proteins in Escherichia coli and coimmunoprecipitation of WT·L103A E4-ORF3 complexes in mammalian cells. These results provide new insight into the properties of the Ad E4-ORF3 protein and suggest that higher-order protein multimerization is essential for E4-ORF3 activity. PMID:22573317

  12. Analyses of GA20ox- and GID1-over-expressing aspen suggest that gibberellins play two distinct roles in wood formation.

    PubMed

    Mauriat, Mélanie; Moritz, Thomas

    2009-06-01

    Gibberellins (GAs) are involved in many aspects of plant development, including shoot growth, flowering and wood formation. Increased levels of bioactive GAs are known to induce xylogenesis and xylem fiber elongation in aspen. However, there is currently little information on the response pathway(s) that mediate GA effects on wood formation. Here we characterize an important element of the GA pathway in hybrid aspen: the GA receptor, GID1. Four orthologs of GID1 were identified in Populus tremula x P. tremuloides (PttGID1.1-1.4). These were functional when expressed in Arabidopsis thaliana, and appear to present a degree of sub-functionalization in hybrid aspen. PttGID1.1 and PttGID1.3 were over-expressed in independent lines of hybrid aspen using either the 35S promoter or a xylem-specific promoter (LMX5). The 35S:PttGID1 over-expressors shared several phenotypic traits previously described in 35S:AtGA20ox1 over-expressors, including rapid growth, increased elongation, and increased xylogenesis. However, their xylem fibers were not elongated, unlike those of 35S:AtGA20ox1 plants. Similar differences in the xylem fiber phenotype were observed when PttGID1.1, PttGID1.3 or AtGA20ox1 were expressed under the control of the LMX5 promoter, suggesting either that PttGID1.1 and PttGID1.3 play no role in fiber elongation or that GA homeostasis is strongly controlled when GA signaling is altered. Our data suggest that GAs are required in two distinct wood-formation processes that have tissue-specific signaling pathways: xylogenesis, as mediated by GA signaling in the cambium, and fiber elongation in the developing xylem.

  13. MeV-ion microprobe analyses of whole Drosophila suggest that zinc and copper accumulation is regulated storage not deposit excretion.

    PubMed

    Schofield, R M; Postlethwait, J H; Lefevre, H W

    1997-12-01

    We examined Drosophila spp. using a penetrative ion microprobe technique that allows us to quantify element contents in whole organs and organisms. Comparatively non-penetrative techniques, such as electron microscopy, could not have been used to make many of these measurements because material is lost during sectioning. We found that zinc was accumulated predominantly within a single organ: in the main segments of both the anterior and posterior Malpighian tubules. In contrast to zinc, iron and copper were more generally distributed throughout the body. Zinc concentrations as high as 2.8 % of dry mass were measured in cell-sized volumes of the Malpighian tubules. The large quantities of zinc (approximately 2x10(-8) g in 8-day-old male adults) were sequestered by an unidentified mechanism. We found less than 1 % of the estimated amount of consumed zinc and copper in the abdomen of flies fed food containing several hundred parts per million dry mass of these metals. Our results are inconsistent with the detoxification hypothesis that predicts that a large proportion of the heavy metals passing through the gut are absorbed and stored permanently. We found for both zinc and copper that the quantity in the abdomen was not proportional to the concentration of these metals in the consumed food but was, instead, relatively invariant. For these reasons, we suggest that regulated biological availability, not detoxification, may be the primary benefit of zinc and copper storage.

  14. MeV-ion microprobe analyses of whole Drosophila suggest that zinc and copper accumulation is regulated storage not deposit excretion.

    PubMed

    Schofield, R M; Postlethwait, J H; Lefevre, H W

    1997-12-01

    We examined Drosophila spp. using a penetrative ion microprobe technique that allows us to quantify element contents in whole organs and organisms. Comparatively non-penetrative techniques, such as electron microscopy, could not have been used to make many of these measurements because material is lost during sectioning. We found that zinc was accumulated predominantly within a single organ: in the main segments of both the anterior and posterior Malpighian tubules. In contrast to zinc, iron and copper were more generally distributed throughout the body. Zinc concentrations as high as 2.8 % of dry mass were measured in cell-sized volumes of the Malpighian tubules. The large quantities of zinc (approximately 2x10(-8) g in 8-day-old male adults) were sequestered by an unidentified mechanism. We found less than 1 % of the estimated amount of consumed zinc and copper in the abdomen of flies fed food containing several hundred parts per million dry mass of these metals. Our results are inconsistent with the detoxification hypothesis that predicts that a large proportion of the heavy metals passing through the gut are absorbed and stored permanently. We found for both zinc and copper that the quantity in the abdomen was not proportional to the concentration of these metals in the consumed food but was, instead, relatively invariant. For these reasons, we suggest that regulated biological availability, not detoxification, may be the primary benefit of zinc and copper storage. PMID:9364029

  15. Analyses of loss-of-function mutations of the MITF gene suggest that haploinsufficiency is a cause of Waardenburg syndrome type 2A

    SciTech Connect

    Nobukuni, Yoshitaka; Watanabe, A.; Takeda, Kazushisa; Skarka, Hana; Tachibana, Masayoshi

    1996-07-01

    Waardenburg syndrome type 2 (WS2) is a dominantly inherited disorder characterized by a pigmentation anomaly and hearing impairment due to lack of melanocyte. Previous work has linked a subset of families with WS2 (WS2A) to the MITF gene that encodes a transcription factor with a basic-helix-loop-helix-leucine zipper (bHLH-Zip) motif and that is involved in melanocyte differentiation. Several splice-site and missense mutations have been reported in individuals affected with WS2A. In this report, we have identified two novel point mutations in the MITF gene in affected individuals from two different families with WS2A. The two mutations (C760{r_arrow}T and C895{r_arrow}T) create stop codons in exons 7 and 8, respectively. Corresponding mutant alleles predict the truncated proteins lacking HLH-Zip or Zip structure. To understand how these mutations cause WS2 in heterozygotes, we generated mutant MITF cDNAs and used them for DNA-binding and luciferase reporter assays. The mutated MITF proteins lose the DNA-binding activity and fail to transactivate the promoter of tyrosinase, a melanocyte-specific enzyme. However, these mutated proteins do not appear to interfere with the activity of wild-type MITF protein in these assays, indicating that they do not show a dominant-negative effect. These findings suggest that the phenotypes of the two families with WS2A in the present study are caused by loss-of-function mutations in one of the two alleles of the MITF gene, resulting in haploinsufficiency of the MITF protein, the protein necessary for normal development of melanocytes. 37 refs., 4 figs.

  16. Structural mapping of the coiled-coil domain of a bacterial condensin and comparative analyses across all domains of life suggest conserved features of SMC proteins.

    PubMed

    Waldman, Vincent M; Stanage, Tyler H; Mims, Alexandra; Norden, Ian S; Oakley, Martha G

    2015-06-01

    The structural maintenance of chromosomes (SMC) proteins form the cores of multisubunit complexes that are required for the segregation and global organization of chromosomes in all domains of life. These proteins share a common domain structure in which N- and C- terminal regions pack against one another to form a globular ATPase domain. This "head" domain is connected to a central, globular, "hinge" or dimerization domain by a long, antiparallel coiled coil. To date, most efforts for structural characterization of SMC proteins have focused on the globular domains. Recently, however, we developed a method to map interstrand interactions in the 50-nm coiled-coil domain of MukB, the divergent SMC protein found in γ-proteobacteria. Here, we apply that technique to map the structure of the Bacillus subtilis SMC (BsSMC) coiled-coil domain. We find that, in contrast to the relatively complicated coiled-coil domain of MukB, the BsSMC domain is nearly continuous, with only two detectable coiled-coil interruptions. Near the middle of the domain is a break in coiled-coil structure in which there are three more residues on the C-terminal strand than on the N-terminal strand. Close to the head domain, there is a second break with a significantly longer insertion on the same strand. These results provide an experience base that allows an informed interpretation of the output of coiled-coil prediction algorithms for this family of proteins. A comparison of such predictions suggests that these coiled-coil deviations are highly conserved across SMC types in a wide variety of organisms, including humans.

  17. Comparative Transcriptome Analyses between a Spontaneous Late-Ripening Sweet Orange Mutant and Its Wild Type Suggest the Functions of ABA, Sucrose and JA during Citrus Fruit Ripening

    PubMed Central

    Zhang, Ya-Jian; Wang, Xing-Jian; Wu, Ju-Xun; Chen, Shan-Yan; Chen, Hong; Chai, Li-Jun; Yi, Hua-Lin

    2014-01-01

    A spontaneous late-ripening mutant of ‘Jincheng’ (C. sinensis L. Osbeck) sweet orange exhibited a delay of fruit pigmentation and harvesting. In this work, we studied the processes of orange fruit ripening through the comparative analysis between the Jincheng mutant and its wild type. This study revealed that the fruit quality began to differ on 166th days after anthesis. At this stage, fruits were subjected to transcriptome analysis by RNA sequencing. 13,412 differentially expressed unigenes (DEGs) were found. Of these unigenes, 75.8% were down-regulated in the wild type, suggesting that the transcription level of wild type was lower than that of the mutant during this stage. These DEGs were mainly clustered into five pathways: metabolic pathways, plant-pathogen interaction, spliceosome, biosynthesis of plant hormones and biosynthesis of phenylpropanoids. Therefore, the expression profiles of the genes that are involved in abscisic acid, sucrose, and jasmonic acid metabolism and signal transduction pathways were analyzed during the six fruit ripening stages. The results revealed the regulation mechanism of sweet orange fruit ripening metabolism in the following four aspects: First, the more mature orange fruits were, the lower the transcription levels were. Second, the expression level of PME boosted with the maturity of the citrus fruit. Therefore, the expression level of PME might represent the degree of the orange fruit ripeness. Third, the interaction of PP2C, PYR/PYL, and SnRK2 was peculiar to the orange fruit ripening process. Fourth, abscisic acid, sucrose, and jasmonic acid all took part in orange fruit ripening process and might interact with each other. These findings provide an insight into the intricate process of sweet orange fruit ripening. PMID:25551568

  18. Structure-function analyses of isochorismate-pyruvate lyase from Pseudomonas aeruginosa suggest differing catalytic mechanisms for the two pericyclic reactions of this bifunctional enzyme.

    PubMed

    Luo, Qianyi; Olucha, Jose; Lamb, Audrey L

    2009-06-16

    The isochorismate-pyruvate lyase from Pseudomonas aeruginosa (PchB) catalyzes two pericyclic reactions in a single active site. PchB physiologically produces salicylate and pyruvate from isochorismate for ultimate incorporation of the salicylate into the siderophore pyochelin. PchB also produces prephenate from chorismate, most likely due to structural homology to the Escherchia coli chorismate mutase. The molecular basis of catalysis among enzymatic pericyclic reactions is a matter of debate, one view holding that catalysis may be derived from electrostatic transition state stabilization and the opposing view that catalysis is derived from the generation of a reactive substrate conformation. Mutant forms of PchB were generated by site-directed mutagenesis at the site (K42) hypothesized to be key for electrostatic transition state stabilization (K42A, K42Q, K42E, and K42H). The loop containing K42 is mobile, and a mutant to slow loop dynamics was also designed (A43P). Finally, a previously characterized mutation (I87T) was also produced. Circular dichroism was used to assess the overall effect on secondary structure as a result of the mutations, and X-ray crystallographic structures are reported for K42A with salicylate and pyruvate bound and for apo-I87T. The data illustrate that the active site architecture is maintained in K42A-PchB, which indicates that differences in activity are not caused by secondary structural changes or by differences in active site loop conformation but rather by the chemical nature of this key residue. In contrast, the I87T structure demonstrates considerable mobility, suggesting that loop dynamics and conformational plasticity may be important for efficient catalysis. Finally, the mutational effects on k(cat) provide evidence that the two activities of PchB are not covariant and that a single hypothesis may not provide a sufficient explanation for catalysis. PMID:19432488

  19. Marine turtle mitogenome phylogenetics and evolution.

    PubMed

    Duchene, Sebastián; Frey, Amy; Alfaro-Núñez, Alonzo; Dutton, Peter H; Thomas P Gilbert, M; Morin, Phillip A

    2012-10-01

    The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phylogeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1 Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution. PMID:22750111

  20. Whole genome sequence and phylogenetic analyses reveal human rotavirus G3P[3] strains Ro1845 and HCR3A are examples of direct virion transmission of canine/feline rotaviruses to humans.

    PubMed

    Tsugawa, Takeshi; Hoshino, Yasutaka

    2008-10-25

    Rotaviruses, the major causative agents of infantile diarrhea worldwide, are, in general, highly species-specific. Interspecies virus transmission is thought to be one of the important contributors involved in the evolution and diversity of rotaviruses in nature. Human rotavirus (HRV) G3P[3] strains Ro1845 and HCR3A have been reported to be closely related genetically to certain canine and feline rotaviruses (RVs). Whole genome sequence and phylogenetic analyses of each of these 2 HRVs as well as 3 canine RVs (CU-1, K9 and A79-10, each with G3P[3] specificity) and 2 feline RVs (Cat97 with G3P[3] specificity and Cat2 with G3P[9] specificity) revealed that (i) each of 11 genes of the Ro1845 and HCR3A was of canine/feline origin; (ii) canine and feline rotaviruses with G3P[3] specificity bore highly conserved species-specific genomes; and (iii) the Cat2 strain may have evolved via multiple reassortment events involving canine, feline, human and bovine rotaviruses. PMID:18789808

  1. Phylogenetic and biogeographic implications inferred by mitochondrial intergenic region analyses and ITS1-5.8S-ITS2 of the entomopathogenic fungi Beauveria bassiana and B. brongniartii

    PubMed Central

    2010-01-01

    Background The entomopathogenic fungi of the genus Beauveria are cosmopolitan with a variety of different insect hosts. The two most important species, B. bassiana and B. brongniartii, have already been used as biological control agents of pests in agriculture and as models for the study of insect host - pathogen interactions. Mitochondrial (mt) genomes, due to their properties to evolve faster than the nuclear DNA, to contain introns and mobile elements and to exhibit extended polymorphisms, are ideal tools to examine genetic diversity within fungal populations and genetically identify a species or a particular isolate. Moreover, mt intergenic region can provide valuable phylogenetic information to study the biogeography of the fungus. Results The complete mt genomes of B. bassiana (32,263 bp) and B. brongniartii (33,920 bp) were fully analysed. Apart from a typical gene content and organization, the Beauveria mt genomes contained several introns and had longer intergenic regions when compared with their close relatives. The phylogenetic diversity of a population of 84 Beauveria strains -mainly B. bassiana (n = 76) - isolated from temperate, sub-tropical and tropical habitats was examined by analyzing the nucleotide sequences of two mt intergenic regions (atp6-rns and nad3-atp9) and the nuclear ITS1-5.8S-ITS2 domain. Mt sequences allowed better differentiation of strains than the ITS region. Based on mt and the concatenated dataset of all genes, the B. bassiana strains were placed into two main clades: (a) the B. bassiana s. l. and (b) the "pseudobassiana". The combination of molecular phylogeny with criteria of geographic and climatic origin showed for the first time in entomopathogenic fungi, that the B. bassiana s. l. can be subdivided into seven clusters with common climate characteristics. Conclusions This study indicates that mt genomes and in particular intergenic regions provide molecular phylogeny tools that combined with criteria of geographic and

  2. Phylogenetic Codivergence Supports Coevolution of Mimetic Heliconius Butterflies

    PubMed Central

    Hoyal Cuthill, Jennifer; Charleston, Michael

    2012-01-01

    The unpalatable and warning-patterned butterflies Heliconius erato and Heliconius melpomene provide the best studied example of mutualistic Müllerian mimicry, thought–but rarely demonstrated–to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of H. erato and H. melpomene, and this was initially hailed as one of the most striking known cases of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence) that argued against codivergence. We present the first explicit cophylogenetic test of codivergence between mimetic populations of H. erato and H. melpomene, and re-examine the timing of these radiations. We find statistically significant topological congruence between multilocus coalescent population phylogenies of H. erato and H. melpomene. Cophylogenetic historical reconstructions support repeated codivergence of mimetic populations, from the base of the sampled radiations. Pairwise distance correlation tests, based on our coalescent analyses plus recently published AFLP and wing colour pattern gene data, also suggest that the phylogenies of H. erato and H. melpomene show significant topological congruence. Divergence time estimates, based on a Bayesian coalescent model, suggest that the evolutionary radiations of H. erato and H. melpomene occurred over the same time period, and are compatible with a series of temporally congruent codivergence events. Our results suggest that differences in within-species genetic divergence are the result of a greater overall effective population size for H. erato relative to H. melpomene and do not imply incongruence in the timing of their phylogenetic radiations. Repeated codivergence between M

  3. Phylogenetic codivergence supports coevolution of mimetic Heliconius butterflies.

    PubMed

    Cuthill, Jennifer Hoyal; Charleston, Michael

    2012-01-01

    The unpalatable and warning-patterned butterflies Heliconius erato and Heliconius melpomene provide the best studied example of mutualistic Müllerian mimicry, thought-but rarely demonstrated-to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of H. erato and H. melpomene, and this was initially hailed as one of the most striking known cases of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence) that argued against codivergence. We present the first explicit cophylogenetic test of codivergence between mimetic populations of H. erato and H. melpomene, and re-examine the timing of these radiations. We find statistically significant topological congruence between multilocus coalescent population phylogenies of H. erato and H. melpomene. Cophylogenetic historical reconstructions support repeated codivergence of mimetic populations, from the base of the sampled radiations. Pairwise distance correlation tests, based on our coalescent analyses plus recently published AFLP and wing colour pattern gene data, also suggest that the phylogenies of H. erato and H. melpomene show significant topological congruence. Divergence time estimates, based on a Bayesian coalescent model, suggest that the evolutionary radiations of H. erato and H. melpomene occurred over the same time period, and are compatible with a series of temporally congruent codivergence events. Our results suggest that differences in within-species genetic divergence are the result of a greater overall effective population size for H. erato relative to H. melpomene and do not imply incongruence in the timing of their phylogenetic radiations. Repeated codivergence between Müllerian co

  4. Structural analysis of the CD11b gene and phylogenetic analysis of the [alpha]-integrin gene family demonstrate remarkable conservation of genomic organization and suggest early diversification during evolution

    SciTech Connect

    Fleming, J.C.; Gonzalez, D.A.; Tenen, D.G. ); Pahl, H.L. Harvard Medical School, Boston, MA ); Smith, T.F. )

    1993-01-15

    CD11b is a member of the [beta]2 subfamily of the human leukocyte integrins. Its expression is limited to mature myeloid and NK cells and is up-regulated during the course of granulocytic and monocytic differentiation. The CD11b/CD18 (Mo1) heterodimer promotes adhesion of granulocytes and monocytes to C3bi-coated bacteria and endothelial cells. In an attempt to relate the exon structure to the known functional domains, as well as to identify and study cis-acting elements that are involved in its tissue-specific expression, the authors have isolated genomic clones encoding CD11b, deduced the exon/intron organization, and determined the transcriptional start site. The CD11b gene spans 55 kb and is encoded by 30 exons. Its structure closely resembles that of CD11c, another of the three leukocyte integrin [alpha]-chains, and suggests that these two genes arose by a gene duplication event. Furthermore, comparison of the CD11b gene structure with that of platelet glycoprotein llb and Drosophila PS2 suggest how the human leukocyte integrins evolved and dispersed during the course of evolution. 67 refs., 5 figs., 2 tabs.

  5. Phylogenetic fields of species: cross-species patterns of phylogenetic structure and geographical coexistence.

    PubMed

    Villalobos, Fabricio; Rangel, Thiago F; Diniz-Filho, José Alexandre F

    2013-04-01

    Differential coexistence among species underlies geographical patterns of biodiversity. Understanding such patterns has relied either on ecological or historical approaches applied separately. Recently, macroecology and community phylogenetics have tried to integrate both ecological and historical approaches. However, macroecology is mostly non-phylogenetic, whereas community phylogenetics is largely focused on local scales. Here, we propose a conceptual framework to link macroecology and community phylogenetics by exploring the evolutionary context of large-scale species coexistence, introducing the phylogenetic field concept. This is defined as the phylogenetic structure of species co-occurrence within a focal species' geographical range. We developed concepts and methods for analysing phylogenetic fields and applied them to study coexistence patterns of the bat family Phyllostomidae. Our analyses showed that phyllostomid bats coexist mostly with closely related species, revealing a north-south gradient from overdispersed to clustered phylogenetic fields. Patterns at different phylogenetic levels (i.e. all species versus close relatives only) presented the same gradient. Results support the tropical niche conservatism hypothesis, potentially mediated by higher speciation rates in the region of origin coupled with shared environmental preferences among species. The phylogenetic field approach enables species-based community phylogenetics, instead of those that are site-based, allowing the description of historical processes at more appropriate macroecological and biogeographic scales.

  6. Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.

    PubMed

    Tárraga, Joaquín; Medina, Ignacio; Arbiza, Leonardo; Huerta-Cepas, Jaime; Gabaldón, Toni; Dopazo, Joaquín; Dopazo, Hernán

    2007-07-01

    Phylemon is an online platform for phylogenetic and evolutionary analyses of molecular sequence data. It has been developed as a web server that integrates a suite of different tools selected among the most popular stand-alone programs in phylogenetic and evolutionary analysis. It has been conceived as a natural response to the increasing demand of data analysis of many experimental scientists wishing to add a molecular evolution and phylogenetics insight into their research. Tools included in Phylemon cover a wide yet selected range of programs: from the most basic for multiple sequence alignment to elaborate statistical methods of phylogenetic reconstruction including methods for evolutionary rates analyses and molecular adaptation. Phylemon has several features that differentiates it from other resources: (i) It offers an integrated environment that enables the direct concatenation of evolutionary analyses, the storage of results and handles required data format conversions, (ii) Once an outfile is produced, Phylemon suggests the next possible analyses, thus guiding the user and facilitating the integration of multi-step analyses, and (iii) users can define and save complete pipelines for specific phylogenetic analysis to be automatically used on many genes in subsequent sessions or multiple genes in a single session (phylogenomics). The Phylemon web server is available at http://phylemon.bioinfo.cipf.es.

  7. Geometric morphometric character suites as phylogenetic data: extracting phylogenetic signal from gastropod shells.

    PubMed

    Smith, Ursula E; Hendricks, Jonathan R

    2013-05-01

    Despite being the objects of numerous macroevolutionary studies, many of the best represented constituents of the fossil record-including diverse examples such as foraminifera, brachiopods, and mollusks-have mineralized skeletons with limited discrete characteristics, making morphological phylogenies difficult to construct. In contrast to their paucity of phylogenetic characters, the mineralized structures (tests and shells) of these fossil groups frequently have distinctive shapes that have long proved useful for their classification. The recent introduction of methodologies for including continuous data directly in a phylogenetic analysis has increased the number of available characters, making it possible to produce phylogenies based, in whole or part, on continuous character data collected from such taxa. Geometric morphometric methods provide tools for accurately characterizing shape variation and can produce quantitative data that can therefore now be included in a phylogenetic matrix in a nonarbitrary manner. Here, the marine gastropod genus Conus is used to evaluate the ability of continuous characters-generated from a geometric morphometric analysis of shell shape-to contribute to a total evidence phylogenetic hypothesis constructed using molecular and morphological data. Furthermore, the ability of continuous characters derived from geometric morphometric analyses to place fossil taxa with limited discrete characters into a phylogeny with their extant relatives was tested by simulating the inclusion of fossil taxa. This was done by removing the molecular partition of individual extant species to produce a "cladistic pseudofossil" with only the geometric morphometric derived characters coded. The phylogenetic position of each cladistic pseudofossil taxon was then compared with its placement in the total evidence tree and a symmetric resampling tree to evaluate the degree to which morphometric characters alone can correctly place simulated fossil species

  8. Phylogenetically-informed priorities for amphibian conservation.

    PubMed

    Isaac, Nick J B; Redding, David W; Meredith, Helen M; Safi, Kamran

    2012-01-01

    The amphibian decline and extinction crisis demands urgent action to prevent further large numbers of species extinctions. Lists of priority species for conservation, based on a combination of species' threat status and unique contribution to phylogenetic diversity, are one tool for the direction and catalyzation of conservation action. We describe the construction of a near-complete species-level phylogeny of 5713 amphibian species, which we use to create a list of evolutionarily distinct and globally endangered species (EDGE list) for the entire class Amphibia. We present sensitivity analyses to test the robustness of our priority list to uncertainty in species' phylogenetic position and threat status. We find that both sources of uncertainty have only minor impacts on our 'top 100' list of priority species, indicating the robustness of the approach. By contrast, our analyses suggest that a large number of Data Deficient species are likely to be high priorities for conservation action from the perspective of their contribution to the evolutionary history.

  9. Phylogenetic signal in diatom ecology: perspectives for aquatic ecosystems biomonitoring.

    PubMed

    Keck, François; Rimet, Frédéric; Franc, Alain; Bouchez, Agnés

    2016-04-01

    Diatoms include a great diversity of taxa and are recognized as powerful bioindicators in rivers. However using diatoms for monitoring programs is costly and time consuming because most of the methodologies necessitate species-level identification. This raises the question of the optimal trade-off between taxonomic resolution and bioassessment quality. Phylogenetic tools may form the bases of new, more efficient approaches for biomonitoring if relationships between ecology and phylogeny can be demonstrated. We estimated the ecological optima of 127 diatom species for 19 environmental parameters using count data from 2119 diatom communities sampled during eight years in eastern France. Using uni- and multivariate analyses, we explored the relationships between freshwater diatom phylogeny and ecology (i.e., the phylogenetic signal). We found a significant phylogenetic signal for many of the ecological optima that were tested, but the strength of the signal varied significantly from one trait to another. Multivariate analysis also showed that the multidimensional ecological niche of diatoms can be strongly related to phylogeny. The presence of clades containing species that exhibit homogeneous ecology suggests that phylogenetic information can be useful for aquatic biomonitoring. This study highlights the presence of significant patterns of ecological optima for freshwater diatoms in relation to their phylogeny. These results suggest the presence of a signal above the species level, which is encouraging for the development of simplified methods for biomonitoring survey. PMID:27411256

  10. The phylogenetic position and diversity of the enigmatic mongrel frog Nothophryne Poynton, 1963 (Amphibia, Anura).

    PubMed

    Bittencourt-Silva, Gabriela B; Conradie, Werner; Siu-Ting, Karen; Tolley, Krystal A; Channing, Alan; Cunningham, Michael; Farooq, Harith M; Menegon, Michele; Loader, Simon P

    2016-06-01

    The phylogenetic relationships of the African mongrel frog genus Nothophryne are poorly understood. We provide the first molecular assessment of the phylogenetic position of, and diversity within, this monotypic genus from across its range-the Afromontane regions of Malawi and Mozambique. Our analysis using a two-tiered phylogenetic approach allowed us to place the genus in Pyxicephalidae. Within the family, Nothophryne grouped with Tomopterna, a hypothesis judged significantly better than alternative hypotheses proposed based on morphology. Our analyses of populations across the range of Nothophryne suggest the presence of several cryptic species, at least one species per mountain. Formal recognition of these species is pending but there is a major conservation concern for these narrowly distributed populations in an area impacted by major habitat change. The phylogenetic tree of pyxicephalids is used to examine evolution of life history, ancestral habitat, and biogeography of this group. PMID:27001603

  11. The phylogenetic position and diversity of the enigmatic mongrel frog Nothophryne Poynton, 1963 (Amphibia, Anura).

    PubMed

    Bittencourt-Silva, Gabriela B; Conradie, Werner; Siu-Ting, Karen; Tolley, Krystal A; Channing, Alan; Cunningham, Michael; Farooq, Harith M; Menegon, Michele; Loader, Simon P

    2016-06-01

    The phylogenetic relationships of the African mongrel frog genus Nothophryne are poorly understood. We provide the first molecular assessment of the phylogenetic position of, and diversity within, this monotypic genus from across its range-the Afromontane regions of Malawi and Mozambique. Our analysis using a two-tiered phylogenetic approach allowed us to place the genus in Pyxicephalidae. Within the family, Nothophryne grouped with Tomopterna, a hypothesis judged significantly better than alternative hypotheses proposed based on morphology. Our analyses of populations across the range of Nothophryne suggest the presence of several cryptic species, at least one species per mountain. Formal recognition of these species is pending but there is a major conservation concern for these narrowly distributed populations in an area impacted by major habitat change. The phylogenetic tree of pyxicephalids is used to examine evolution of life history, ancestral habitat, and biogeography of this group.

  12. Characterizing the Phylogenetic Tree Community Structure of a Protected Tropical Rain Forest Area in Cameroon

    PubMed Central

    Munoz, François; Couteron, Pierre; Hardy, Olivier J.; Sonké, Bonaventure

    2014-01-01

    Tropical rain forests, the richest terrestrial ecosystems in biodiversity on Earth are highly threatened by global changes. This paper aims to infer the mechanisms governing species tree assemblages by characterizing the phylogenetic structure of a tropical rain forest in a protected area of the Congo Basin, the Dja Faunal Reserve (Cameroon). We re-analyzed a dataset of 11538 individuals belonging to 372 taxa found along nine transects spanning five habitat types. We generated a dated phylogenetic tree including all sampled taxa to partition the phylogenetic diversity of the nine transects into alpha and beta components at the level of the transects and of the habitat types. The variation in phylogenetic composition among transects did not deviate from a random pattern at the scale of the Dja Faunal Reserve, probably due to a common history and weak environmental variation across the park. This lack of phylogenetic structure combined with an isolation-by-distance pattern of taxonomic diversity suggests that neutral dispersal limitation is a major driver of community assembly in the Dja. To assess any lack of sensitivity to the variation in habitat types, we restricted the analyses of transects to the terra firme primary forest and found results consistent with those of the whole dataset at the level of the transects. Additionally to previous analyses, we detected a weak but significant phylogenetic turnover among habitat types, suggesting that species sort in varying environments, even though it is not predominating on the overall phylogenetic structure. Finer analyses of clades indicated a signal of clustering for species from the Annonaceae family, while species from the Apocynaceae family indicated overdispersion. These results can contribute to the conservation of the park by improving our understanding of the processes dictating community assembly in these hyperdiverse but threatened regions of the world. PMID:24936786

  13. Characterizing the phylogenetic tree community structure of a protected tropical rain forest area in Cameroon.

    PubMed

    Manel, Stéphanie; Couvreur, Thomas L P; Munoz, François; Couteron, Pierre; Hardy, Olivier J; Sonké, Bonaventure

    2014-01-01

    Tropical rain forests, the richest terrestrial ecosystems in biodiversity on Earth are highly threatened by global changes. This paper aims to infer the mechanisms governing species tree assemblages by characterizing the phylogenetic structure of a tropical rain forest in a protected area of the Congo Basin, the Dja Faunal Reserve (Cameroon). We re-analyzed a dataset of 11538 individuals belonging to 372 taxa found along nine transects spanning five habitat types. We generated a dated phylogenetic tree including all sampled taxa to partition the phylogenetic diversity of the nine transects into alpha and beta components at the level of the transects and of the habitat types. The variation in phylogenetic composition among transects did not deviate from a random pattern at the scale of the Dja Faunal Reserve, probably due to a common history and weak environmental variation across the park. This lack of phylogenetic structure combined with an isolation-by-distance pattern of taxonomic diversity suggests that neutral dispersal limitation is a major driver of community assembly in the Dja. To assess any lack of sensitivity to the variation in habitat types, we restricted the analyses of transects to the terra firme primary forest and found results consistent with those of the whole dataset at the level of the transects. Additionally to previous analyses, we detected a weak but significant phylogenetic turnover among habitat types, suggesting that species sort in varying environments, even though it is not predominating on the overall phylogenetic structure. Finer analyses of clades indicated a signal of clustering for species from the Annonaceae family, while species from the Apocynaceae family indicated overdispersion. These results can contribute to the conservation of the park by improving our understanding of the processes dictating community assembly in these hyperdiverse but threatened regions of the world.

  14. Phylogenetic Analyses of Three Genes of Pedinomonas noctilucae, the Green Endosymbiont of the Marine Dinoflagellate Noctiluca scintillans, Reveal its Affiliation to the Order Marsupiomonadales (Chlorophyta, Pedinophyceae) under the Reinstated Name Protoeuglena noctilucae.

    PubMed

    Wang, Lu; Lin, Xin; Goes, Joaquim I; Lin, Senjie

    2016-04-01

    In the last decade, field studies in the northern Arabian Sea showed a drastic shift from diatom-dominated phytoplankton blooms to thick and widespread blooms of the green dinoflagellate, Noctiluca scintillans. Unlike the exclusively heterotrophic red form, which occurs widely in tropical to temperate coastal waters, the green Noctiluca contains a large number of endosymbiotic algal cells that can perform photosynthesis. These symbiotic microalgae were first described under the genus Protoeuglena Subrahmanyan and further transferred to Pedinomonas as P. noctilucae Sweeney. In this study, we used the 18S rDNA, rbcL and chloroplast 16S rDNA as gene markers, in combination with the previously reported morphological features, to re-examine the phylogenetic position of this endosymbiotic algal species. Phylogenetic trees inferred from these genes consistently indicated that P. noctilucae is distantly related to the type species of Pedinomonas. The sequences formed a monophyletic clade sister to the clade of Marsupiomonas necessitating the placement of the algal symbionts as an independent genus within the family Marsupiomonadaceae. Based on the phylogenetic affiliation and ecological characteristics of this alga as well as the priority rule of nomenclature, we reinstate the genus Protoeuglena and reclassify the endosymbiont as Protoeuglena noctilucae. PMID:27033730

  15. Estimating phylogenetic trees from genome-scale data.

    PubMed

    Liu, Liang; Xi, Zhenxiang; Wu, Shaoyuan; Davis, Charles C; Edwards, Scott V

    2015-12-01

    The heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. Phylogenetic methods known as "species tree" methods have been proposed to directly address one important source of gene tree heterogeneity, namely the incomplete lineage sorting that occurs when evolving lineages radiate rapidly, resulting in a diversity of gene trees from a single underlying species tree. Here we review theory and empirical examples that help clarify conflicts between species tree and concatenation methods, and misconceptions in the literature about the performance of species tree methods. Considering concatenation as a special case of the multispecies coalescent model helps explain differences in the behavior of the two methods on phylogenomic data sets. Recent work suggests that species tree methods are more robust than concatenation approaches to some of the classic challenges of phylogenetic analysis, including rapidly evolving sites in DNA sequences and long-branch attraction. We show that approaches, such as binning, designed to augment the signal in species tree analyses can distort the distribution of gene trees and are inconsistent. Computationally efficient species tree methods incorporating biological realism are a key to phylogenetic analysis of whole-genome data. PMID:25873435

  16. Phylogenetic plant community structure along elevation is lineage specific.

    PubMed

    Ndiribe, Charlotte; Pellissier, Loïc; Antonelli, Silvia; Dubuis, Anne; Pottier, Julien; Vittoz, Pascal; Guisan, Antoine; Salamin, Nicolas

    2013-12-01

    The trend of closely related taxa to retain similar environmental preferences mediated by inherited traits suggests that several patterns observed at the community scale originate from longer evolutionary processes. While the effects of phylogenetic relatedness have been previously studied within a single genus or family, lineage-specific effects on the ecological processes governing community assembly have rarely been studied for entire communities or flora. Here, we measured how community phylogenetic structure varies across a wide elevation gradient for plant lineages represented by 35 families, using a co-occurrence index and net relatedness index (NRI). We propose a framework that analyses each lineage separately and reveals the trend of ecological assembly at tree nodes. We found prevailing phylogenetic clustering for more ancient nodes and overdispersion in more recent tree nodes. Closely related species may thus rapidly evolve new environmental tolerances to radiate into distinct communities, while older lineages likely retain inherent environmental tolerances to occupy communities in similar environments, either through efficient dispersal mechanisms or the exclusion of older lineages with more divergent environmental tolerances. Our study illustrates the importance of disentangling the patterns of community assembly among lineages to better interpret the ecological role of traits. It also sheds light on studies reporting absence of phylogenetic signal, and opens new perspectives on the analysis of niche and trait conservatism across lineages.

  17. Phylogenetic plant community structure along elevation is lineage specific

    PubMed Central

    Ndiribe, Charlotte; Pellissier, Loïc; Antonelli, Silvia; Dubuis, Anne; Pottier, Julien; Vittoz, Pascal; Guisan, Antoine; Salamin, Nicolas

    2013-01-01

    The trend of closely related taxa to retain similar environmental preferences mediated by inherited traits suggests that several patterns observed at the community scale originate from longer evolutionary processes. While the effects of phylogenetic relatedness have been previously studied within a single genus or family, lineage-specific effects on the ecological processes governing community assembly have rarely been studied for entire communities or flora. Here, we measured how community phylogenetic structure varies across a wide elevation gradient for plant lineages represented by 35 families, using a co-occurrence index and net relatedness index (NRI). We propose a framework that analyses each lineage separately and reveals the trend of ecological assembly at tree nodes. We found prevailing phylogenetic clustering for more ancient nodes and overdispersion in more recent tree nodes. Closely related species may thus rapidly evolve new environmental tolerances to radiate into distinct communities, while older lineages likely retain inherent environmental tolerances to occupy communities in similar environments, either through efficient dispersal mechanisms or the exclusion of older lineages with more divergent environmental tolerances. Our study illustrates the importance of disentangling the patterns of community assembly among lineages to better interpret the ecological role of traits. It also sheds light on studies reporting absence of phylogenetic signal, and opens new perspectives on the analysis of niche and trait conservatism across lineages. PMID:24455126

  18. The anatomy, affinity, and phylogenetic significance of Markuelia.

    PubMed

    Dong, Xi-Ping; Donoghue, Philip C J; Cunningham, John A; Liu, Jian-Bo; Cheng, Hong

    2005-01-01

    The fossil record provides a paucity of data on the development of extinct organisms, particularly for their embryology. The recovery of fossilized embryos heralds new insight into the evolution of development but advances are limited by an almost complete absence of phylogenetic constraint. Markuelia is an exception to this, known from cleavage and pre-hatchling stages as a vermiform and profusely annulated direct-developing bilaterian with terminal circumoral and posterior radial arrays of spines. Phylogenetic analyses have hitherto suggested assignment to stem-Scalidophora (phyla Kinorhyncha, Loricifera, Priapulida). We test this assumption with additional data and through the inclusion of additional taxa. The available evidence supports stem-Scalidophora affinity, leading to the conclusion that scalidophorans, cyclonerualians, and ecdysozoans are primitive direct developers, and the likelihood that scalidophorans are primitively metameric. PMID:16174039

  19. The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis.

    PubMed

    Perseke, Marleen; Hankeln, Thomas; Weich, Bettina; Fritzsch, Guido; Stadler, Peter F; Israelsson, Olle; Bernhard, Detlef; Schlegel, Martin

    2007-08-01

    The phylogenetic position of Xenoturbella bocki has been a matter of controversy since its description in 1949. We sequenced a second complete mitochondrial genome of this species and performed phylogenetic analyses based on the amino acid sequences of all 13 mitochondrial protein-coding genes and on its gene order. Our results confirm the deuterostome relationship of Xenoturbella. However, in contrast to a recently published study (Bourlat et al. in Nature 444:85-88, 2006), our data analysis suggests a more basal branching of Xenoturbella within the deuterostomes, rather than a sister-group relationship to the Ambulacraria (Hemichordata and Echinodermata). PMID:18087755

  20. The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis.

    PubMed

    Perseke, Marleen; Hankeln, Thomas; Weich, Bettina; Fritzsch, Guido; Stadler, Peter F; Israelsson, Olle; Bernhard, Detlef; Schlegel, Martin

    2007-08-01

    The phylogenetic position of Xenoturbella bocki has been a matter of controversy since its description in 1949. We sequenced a second complete mitochondrial genome of this species and performed phylogenetic analyses based on the amino acid sequences of all 13 mitochondrial protein-coding genes and on its gene order. Our results confirm the deuterostome relationship of Xenoturbella. However, in contrast to a recently published study (Bourlat et al. in Nature 444:85-88, 2006), our data analysis suggests a more basal branching of Xenoturbella within the deuterostomes, rather than a sister-group relationship to the Ambulacraria (Hemichordata and Echinodermata).

  1. Phylogenetic effective sample size.

    PubMed

    Bartoszek, Krzysztof

    2016-10-21

    In this paper I address the question-how large is a phylogenetic sample? I propose a definition of a phylogenetic effective sample size for Brownian motion and Ornstein-Uhlenbeck processes-the regression effective sample size. I discuss how mutual information can be used to define an effective sample size in the non-normal process case and compare these two definitions to an already present concept of effective sample size (the mean effective sample size). Through a simulation study I find that the AICc is robust if one corrects for the number of species or effective number of species. Lastly I discuss how the concept of the phylogenetic effective sample size can be useful for biodiversity quantification, identification of interesting clades and deciding on the importance of phylogenetic correlations. PMID:27343033

  2. Phylogenetic lineages in Entomophthoromycota

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Entomophthoromycota Humber is one of five major phylogenetic lineages among the former phylum Zygomycota. These early terrestrial fungi share evolutionarily ancestral characters such as coenocytic mycelium and gametangiogamy as a sexual process resulting in zygospore formation. Previous molecular st...

  3. Soft-tissue anatomy of the primates: phylogenetic analyses based on the muscles of the head, neck, pectoral region and upper limb, with notes on the evolution of these muscles.

    PubMed

    Diogo, R; Wood, B

    2011-09-01

    Apart from molecular data, nearly all the evidence used to study primate relationships comes from hard tissues. Here, we provide details of the first parsimony and Bayesian cladistic analyses of the order Primates based exclusively on muscle data. The most parsimonious tree obtained from the cladistic analysis of 166 characters taken from the head, neck, pectoral and upper limb musculature is fully congruent with the most recent evolutionary molecular tree of Primates. That is, this tree recovers not only the relationships among the major groups of primates, i.e. Strepsirrhini {Tarsiiformes [Platyrrhini (Cercopithecidae, Hominoidea)]}, but it also recovers the relationships within each of these inclusive groups. Of the 301 character state changes occurring in this tree, ca. 30% are non-homoplasic evolutionary transitions; within the 220 changes that are unambiguously optimized in the tree, ca. 15% are reversions. The trees obtained by using characters derived from the muscles of the head and neck are more similar to the most recent evolutionary molecular tree than are the trees obtained by using characters derived from the pectoral and upper limb muscles. It was recently argued that since the Pan/Homo split, chimpanzees accumulated more phenotypic adaptations than humans, but our results indicate that modern humans accumulated more muscle character state changes than chimpanzees, and that both these taxa accumulated more changes than gorillas. This overview of the evolution of the primate head, neck, pectoral and upper limb musculature suggests that the only muscle groups for which modern humans have more muscles than most other extant primates are the muscles of the face, larynx and forearm.

  4. Soft-tissue anatomy of the primates: phylogenetic analyses based on the muscles of the head, neck, pectoral region and upper limb, with notes on the evolution of these muscles

    PubMed Central

    Diogo, R; Wood, B

    2011-01-01

    Apart from molecular data, nearly all the evidence used to study primate relationships comes from hard tissues. Here, we provide details of the first parsimony and Bayesian cladistic analyses of the order Primates based exclusively on muscle data. The most parsimonious tree obtained from the cladistic analysis of 166 characters taken from the head, neck, pectoral and upper limb musculature is fully congruent with the most recent evolutionary molecular tree of Primates. That is, this tree recovers not only the relationships among the major groups of primates, i.e. Strepsirrhini {Tarsiiformes [Platyrrhini (Cercopithecidae, Hominoidea)]}, but it also recovers the relationships within each of these inclusive groups. Of the 301 character state changes occurring in this tree, ca. 30% are non-homoplasic evolutionary transitions; within the 220 changes that are unambiguously optimized in the tree, ca. 15% are reversions. The trees obtained by using characters derived from the muscles of the head and neck are more similar to the most recent evolutionary molecular tree than are the trees obtained by using characters derived from the pectoral and upper limb muscles. It was recently argued that since the Pan/Homo split, chimpanzees accumulated more phenotypic adaptations than humans, but our results indicate that modern humans accumulated more muscle character state changes than chimpanzees, and that both these taxa accumulated more changes than gorillas. This overview of the evolution of the primate head, neck, pectoral and upper limb musculature suggests that the only muscle groups for which modern humans have more muscles than most other extant primates are the muscles of the face, larynx and forearm. PMID:21689100

  5. Phylogenetic Signal Dissection Identifies the Root of Starfishes

    PubMed Central

    Feuda, Roberto; Smith, Andrew B.

    2015-01-01

    Relationships within the class Asteroidea have remained controversial for almost 100 years and, despite many attempts to resolve this problem using molecular data, no consensus has yet emerged. Using two nuclear genes and a taxon sampling covering the major asteroid clades we show that non-phylogenetic signal created by three factors - Long Branch Attraction, compositional heterogeneity and the use of poorly fitting models of evolution – have confounded accurate estimation of phylogenetic relationships. To overcome the effect of this non-phylogenetic signal we analyse the data using non-homogeneous models, site stripping and the creation of subpartitions aimed to reduce or amplify the systematic error, and calculate Bayes Factor support for a selection of previously suggested topological arrangements of asteroid orders. We show that most of the previous alternative hypotheses are not supported in the most reliable data partitions, including the previously suggested placement of either Forcipulatida or Paxillosida as sister group to the other major branches. The best-supported solution places Velatida as the sister group to other asteroids, and the implications of this finding for the morphological evolution of asteroids are presented. PMID:25955729

  6. Phylogenetic signal dissection identifies the root of starfishes.

    PubMed

    Feuda, Roberto; Smith, Andrew B

    2015-01-01

    Relationships within the class Asteroidea have remained controversial for almost 100 years and, despite many attempts to resolve this problem using molecular data, no consensus has yet emerged. Using two nuclear genes and a taxon sampling covering the major asteroid clades we show that non-phylogenetic signal created by three factors--Long Branch Attraction, compositional heterogeneity and the use of poorly fitting models of evolution--have confounded accurate estimation of phylogenetic relationships. To overcome the effect of this non-phylogenetic signal we analyse the data using non-homogeneous models, site stripping and the creation of subpartitions aimed to reduce or amplify the systematic error, and calculate Bayes Factor support for a selection of previously suggested topological arrangements of asteroid orders. We show that most of the previous alternative hypotheses are not supported in the most reliable data partitions, including the previously suggested placement of either Forcipulatida or Paxillosida as sister group to the other major branches. The best-supported solution places Velatida as the sister group to other asteroids, and the implications of this finding for the morphological evolution of asteroids are presented.

  7. Phylogenetic signal dissection identifies the root of starfishes.

    PubMed

    Feuda, Roberto; Smith, Andrew B

    2015-01-01

    Relationships within the class Asteroidea have remained controversial for almost 100 years and, despite many attempts to resolve this problem using molecular data, no consensus has yet emerged. Using two nuclear genes and a taxon sampling covering the major asteroid clades we show that non-phylogenetic signal created by three factors--Long Branch Attraction, compositional heterogeneity and the use of poorly fitting models of evolution--have confounded accurate estimation of phylogenetic relationships. To overcome the effect of this non-phylogenetic signal we analyse the data using non-homogeneous models, site stripping and the creation of subpartitions aimed to reduce or amplify the systematic error, and calculate Bayes Factor support for a selection of previously suggested topological arrangements of asteroid orders. We show that most of the previous alternative hypotheses are not supported in the most reliable data partitions, including the previously suggested placement of either Forcipulatida or Paxillosida as sister group to the other major branches. The best-supported solution places Velatida as the sister group to other asteroids, and the implications of this finding for the morphological evolution of asteroids are presented. PMID:25955729

  8. Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics

    PubMed Central

    van Hazel, Ilke; Santini, Francesco; Müller, Johannes; Chang, Belinda SW

    2006-01-01

    Background Vertebrate SWS1 visual pigments mediate visual transduction in response to light at short wavelengths. Due to their importance in vision, SWS1 genes have been isolated from a surprisingly wide range of vertebrates, including lampreys, teleosts, amphibians, reptiles, birds, and mammals. The SWS1 genes exhibit many of the characteristics of genes typically targeted for phylogenetic analyses. This study investigates both the utility of SWS1 as a marker for inferring vertebrate phylogenetic relationships, and the characteristics of the gene that contribute to its phylogenetic utility. Results Phylogenetic analyses of vertebrate SWS1 genes produced topologies that were remarkably congruent with generally accepted hypotheses of vertebrate evolution at both higher and lower taxonomic levels. The few exceptions were generally associated with areas of poor taxonomic sampling, or relationships that have been difficult to resolve using other molecular markers. The SWS1 data set was characterized by a substantial amount of among-site rate variation, and a relatively unskewed substitution rate matrix, even when the data were partitioned into different codon sites and individual taxonomic groups. Although there were nucleotide biases in some groups at third positions, these biases were not convergent across different taxonomic groups. Conclusion Our results suggest that SWS1 may be a good marker for vertebrate phylogenetics due to the variable yet consistent patterns of sequence evolution exhibited across fairly wide taxonomic groups. This may result from constraints imposed by the functional role of SWS1 pigments in visual transduction. PMID:17107620

  9. Molecular systematics of the Amazonian genus Aldina, a phylogenetically enigmatic ectomycorrhizal lineage of papilionoid legumes.

    PubMed

    Ramos, Gustavo; de Lima, Haroldo Cavalcante; Prenner, Gerhard; de Queiroz, Luciano Paganucci; Zartman, Charles E; Cardoso, Domingos

    2016-04-01

    Aldina (Leguminosae) is among the very few ecologically successful ectomycorrhizal lineages in a family largely marked by the evolution of nodulating symbiosis. The genus comprises 20 species predominantly distributed in Amazonia and has been traditionally classified in the tribe Swartzieae because of its radial flowers with an entire calyx and numerous free stamens. The taxonomy of Aldina is complicated due to its poor representation in herbaria and the lack of a robust phylogenetic hypothesis of relationship. Recent phylogenetic analyses of matK and trnL sequences confirmed the placement of Aldina in the 50-kb inversion clade, although the genus remained phylogenetically isolated or unresolved in the context of the evolutionary history of the main early-branching papilionoid lineages. We performed maximum likelihood and Bayesian analyses of combined chloroplast datasets (matK, rbcL, and trnL) and explored the effect of incomplete taxa or missing data in order to shed light on the enigmatic phylogenetic position of Aldina. Unexpectedly, a sister relationship of Aldina with the Andira clade (Andira and Hymenolobium) is revealed. We suggest that a new tribal phylogenetic classification of the papilionoid legumes should place Aldina along with Andira and Hymenolobium. These results highlight yet another example of the independent evolution of radial floral symmetry within the early-branching Papilionoideae, a large collection of florally heterogeneous lineages dominated by papilionate or bilaterally symmetric flower morphology. PMID:26748266

  10. Molecular systematics of the Amazonian genus Aldina, a phylogenetically enigmatic ectomycorrhizal lineage of papilionoid legumes.

    PubMed

    Ramos, Gustavo; de Lima, Haroldo Cavalcante; Prenner, Gerhard; de Queiroz, Luciano Paganucci; Zartman, Charles E; Cardoso, Domingos

    2016-04-01

    Aldina (Leguminosae) is among the very few ecologically successful ectomycorrhizal lineages in a family largely marked by the evolution of nodulating symbiosis. The genus comprises 20 species predominantly distributed in Amazonia and has been traditionally classified in the tribe Swartzieae because of its radial flowers with an entire calyx and numerous free stamens. The taxonomy of Aldina is complicated due to its poor representation in herbaria and the lack of a robust phylogenetic hypothesis of relationship. Recent phylogenetic analyses of matK and trnL sequences confirmed the placement of Aldina in the 50-kb inversion clade, although the genus remained phylogenetically isolated or unresolved in the context of the evolutionary history of the main early-branching papilionoid lineages. We performed maximum likelihood and Bayesian analyses of combined chloroplast datasets (matK, rbcL, and trnL) and explored the effect of incomplete taxa or missing data in order to shed light on the enigmatic phylogenetic position of Aldina. Unexpectedly, a sister relationship of Aldina with the Andira clade (Andira and Hymenolobium) is revealed. We suggest that a new tribal phylogenetic classification of the papilionoid legumes should place Aldina along with Andira and Hymenolobium. These results highlight yet another example of the independent evolution of radial floral symmetry within the early-branching Papilionoideae, a large collection of florally heterogeneous lineages dominated by papilionate or bilaterally symmetric flower morphology.

  11. The phylogenetic relationships of cynopterine fruit bats (Chiroptera: Pteropodidae: Cynopterinae).

    PubMed

    Almeida, Francisca C; Giannini, Norberto P; DeSalle, Rob; Simmons, Nancy B

    2009-12-01

    The subfamily Cynopterinae comprises ca. 24 species of pteropodid bats (Family Pteropodidae) distributed exclusively in South and Southeast Asia. Although some studies have supported monophyly of the subfamily, molecular analyses have produced contradictory results and there has been little agreement on relationships of cynopterines to other megabat groups. However, no previous studies have included a complete sampling of cynopterine genera. Here we describe a phylogenetic analysis of Cynopterinae based on more than 6000 bp from six different genes sampled in representatives of all 14 recognized genera. Our results support the monophyly of Cynopterinae but refute a close relationship of cynopterines with Nyctimeninae. Within Cynopterinae, our analyses consistently recovered two monophyletic clades, which we recommend be recognized formally as tribes: Cynopterini and Balionycterini. Biogeographic analyses indicate a Sundaland origin of the Cynopterinae and divergence date estimates suggest different timing of diversification of the two major cynopterine clades.

  12. Influence of tree shape and evolutionary time-scale on phylogenetic diversity metrics

    PubMed Central

    Mazel, F.; Davies, T.J; Gallien, L.; Renaud, J.; Groussin, M.; Münkemüller, T.; Thuiller, W.

    2016-01-01

    During the last decades, describing, analysing and understanding the phylogenetic structure of species assemblages has been a central theme in both community ecology and macro-ecology. Among the wide variety of phylogenetic structure metrics, three have been predominant in the literature: Faith’s phylogenetic diversity (PDFaith), which represents the sum of the branch lengths of the phylogenetic tree linking all species of a particular assemblage, the mean pairwise distance between all species in an assemblage (MPD) and the pairwise distance between the closest relatives in an assemblage (MNTD). Comparisons between studies using one or several of these metrics are difficult because there has been no comprehensive evaluation of the phylogenetic properties each metric captures. In particular it is unknown how PDFaith relates to MDP and MNTD. Consequently, it is possible that apparently opposing patterns in different studies might simply reflect differences in metric properties. Here, we aim to fill this gap by comparing these metrics using simulations and empirical data. We first used simulation experiments to test the influence of community structure and size on the mismatch between metrics whilst varying the shape and size of the phylogenetic tree of the species pool. Second we investigated the mismatch between metrics for two empirical datasets (gut microbes and global carnivoran assemblages). We show that MNTD and PDFaith provide similar information on phylogenetic structure, and respond similarly to variation in species richness and assemblage structure. However, MPD demonstrate a very different behaviour, and is highly sensitive to deep branching structure. We suggest that by combining complementary metrics that are sensitive to processes operating at different phylogenetic depths (i.e. MPD and MNTD or PDFaith) we can obtain a better understanding of assemblage structure. PMID:27713599

  13. Phylogenetic patterns of climatic, habitat and trophic niches in a European avian assemblage

    PubMed Central

    Pearman, Peter B; Lavergne, Sébastien; Roquet, Cristina; Wüest, Rafael; Zimmermann, Niklaus E; Thuiller, Wilfried

    2014-01-01

    Aim The origins of ecological diversity in continental species assemblages have long intrigued biogeographers. We apply phylogenetic comparative analyses to disentangle the evolutionary patterns of ecological niches in an assemblage of European birds. We compare phylogenetic patterns in trophic, habitat and climatic niche components. Location Europe. Methods From polygon range maps and handbook data we inferred the realized climatic, habitat and trophic niches of 405 species of breeding birds in Europe. We fitted Pagel's lambda and kappa statistics, and conducted analyses of disparity through time to compare temporal patterns of ecological diversification on all niche axes together. All observed patterns were compared with expectations based on neutral (Brownian) models of niche divergence. Results In this assemblage, patterns of phylogenetic signal (lambda) suggest that related species resemble each other less in regard to their climatic and habitat niches than they do in their trophic niche. Kappa estimates show that ecological divergence does not gradually increase with divergence time, and that this punctualism is stronger in climatic niches than in habitat and trophic niches. Observed niche disparity markedly exceeds levels expected from a Brownian model of ecological diversification, thus providing no evidence for past phylogenetic niche conservatism in these multivariate niches. Levels of multivariate disparity are greatest for the climatic niche, followed by disparity of the habitat and the trophic niches. Main conclusions Phylogenetic patterns in the three niche components differ within this avian assemblage. Variation in evolutionary rates (degree of gradualism, constancy through the tree) and/or non-random macroecological sampling probably lead here to differences in the phylogenetic structure of niche components. Testing hypotheses on the origin of these patterns requires more complete phylogenetic trees of the birds, and extended ecological data on

  14. Phylogenetic analysis of otospiralin protein

    PubMed Central

    Torktaz, Ibrahim; Behjati, Mohaddeseh; Rostami, Amin

    2016-01-01

    Background: Fibrocyte-specific protein, otospiralin, is a small protein, widely expressed in the central nervous system as neuronal cell bodies and glia. The increased expression of otospiralin in reactive astrocytes implicates its role in signaling pathways and reparative mechanisms subsequent to injury. Indeed, otospiralin is considered to be essential for the survival of fibrocytes of the mesenchymal nonsensory regions of the cochlea. It seems that other functions of this protein are not yet completely understood. Materials and Methods: Amino acid sequences of otospiralin from 12 vertebrates were derived from National Center for Biotechnology Information database. Phylogenetic analysis and phylogeny estimation were performed using MEGA 5.0.5 program, and neighbor-joining tree was constructed by this software. Results: In this computational study, the phylogenetic tree of otospiralin has been investigated. Therefore, dendrograms of otospiralin were depicted. Alignment performed in MUSCLE method by UPGMB algorithm. Also, entropy plot determined for a better illustration of amino acid variations in this protein. Conclusion: In the present study, we used otospiralin sequence of 12 different species and by constructing phylogenetic tree, we suggested out group for some related species. PMID:27099854

  15. Ultrafast approximation for phylogenetic bootstrap.

    PubMed

    Minh, Bui Quang; Nguyen, Minh Anh Thi; von Haeseler, Arndt

    2013-05-01

    Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the clade support of phylogenetic trees. However, with the rapidly growing amount of data, this task remains a computational bottleneck. Recently, approximation methods such as the RAxML rapid bootstrap (RBS) and the Shimodaira-Hasegawa-like approximate likelihood ratio test have been introduced to speed up the bootstrap. Here, we suggest an ultrafast bootstrap approximation approach (UFBoot) to compute the support of phylogenetic groups in maximum likelihood (ML) based trees. To achieve this, we combine the resampling estimated log-likelihood method with a simple but effective collection scheme of candidate trees. We also propose a stopping rule that assesses the convergence of branch support values to automatically determine when to stop collecting candidate trees. UFBoot achieves a median speed up of 3.1 (range: 0.66-33.3) to 10.2 (range: 1.32-41.4) compared with RAxML RBS for real DNA and amino acid alignments, respectively. Moreover, our extensive simulations show that UFBoot is robust against moderate model violations and the support values obtained appear to be relatively unbiased compared with the conservative standard bootstrap. This provides a more direct interpretation of the bootstrap support. We offer an efficient and easy-to-use software (available at http://www.cibiv.at/software/iqtree) to perform the UFBoot analysis with ML tree inference.

  16. Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer

    PubMed Central

    Nickrent, Daniel L; Blarer, Albert; Qiu, Yin-Long; Vidal-Russell, Romina; Anderson, Frank E

    2004-01-01

    Background The phylogenetic relationships among the holoparasites of Rafflesiales have remained enigmatic for over a century. Recent molecular phylogenetic studies using the mitochondrial matR gene placed Rafflesia, Rhizanthes and Sapria (Rafflesiaceae s. str.) in the angiosperm order Malpighiales and Mitrastema (Mitrastemonaceae) in Ericales. These phylogenetic studies did not, however, sample two additional groups traditionally classified within Rafflesiales (Apodantheaceae and Cytinaceae). Here we provide molecular phylogenetic evidence using DNA sequence data from mitochondrial and nuclear genes for representatives of all genera in Rafflesiales. Results Our analyses indicate that the phylogenetic affinities of the large-flowered clade and Mitrastema, ascertained using mitochondrial matR, are congruent with results from nuclear SSU rDNA when these data are analyzed using maximum likelihood and Bayesian methods. The relationship of Cytinaceae to Malvales was recovered in all analyses. Relationships between Apodanthaceae and photosynthetic angiosperms varied depending upon the data partition: Malvales (3-gene), Cucurbitales (matR) or Fabales (atp1). The latter incongruencies suggest that horizontal gene transfer (HGT) may be affecting the mitochondrial gene topologies. The lack of association between Mitrastema and Ericales using atp1 is suggestive of HGT, but greater sampling within eudicots is needed to test this hypothesis further. Conclusions Rafflesiales are not monophyletic but composed of three or four independent lineages (families): Rafflesiaceae, Mitrastemonaceae, Apodanthaceae and Cytinaceae. Long-branch attraction appears to be misleading parsimony analyses of nuclear small-subunit rDNA data, but model-based methods (maximum likelihood and Bayesian analyses) recover a topology that is congruent with the mitochondrial matR gene tree, thus providing compelling evidence for organismal relationships. Horizontal gene transfer appears to be influencing only

  17. Phylogenetic analyses among octocorals (Cnidaria): mitochondrial and nuclear DNA sequences (lsu-rRNA, 16S and ssu-rRNA, 18S) support two convergent clades of branching gorgonians.

    PubMed

    Armando Sánchez, Juan; Lasker, Howard R; Taylor, Derek J

    2003-10-01

    Gorgonian octocorals lack corroborated hypotheses of phylogeny. This study reconstructs genealogical relationships among some octocoral species based on published DNA sequences from the large ribosomal subunit of the mitochondrial RNA (lsu-rRNA, 16S: 524bp and 21 species) and the small subunit of the nuclear RNA (ssu-rRNA, 18S: 1815bp and 13 spp) using information from insertions-deletions (INDELS) and the predicted secondary structure of the lsu-rRNA (16S). There were seven short (3-10bp) INDELS in the 18S with consistent phylogenetic information. The INDELS in the 16S corresponded to informative signature sequences homologous to the G13 helix found in Escherichia coli. We found two main groups of gorgonian octocorals using a maximum parsimony analysis of the two genes. One group corresponds to deep-water taxa including species from the suborders Calcaxonia and Scleraxonia characterized by an enlargement of the G13 helix. The second group has species from Alcyoniina, Holaxonia and again Scleraxonia characterized by insertions in the 18S. Gorgonian corals, branching colonies with a gorgonin-containing flexible multilayered axis (Holaxonia and Calcaxonia), do not form a monophyletic group. These corroborated results from maternally inherited (16S) and biparentally inherited (18S) genes support a hypothesis of independent evolution of branching in the two octocoral clades.

  18. Genomic Repeat Abundances Contain Phylogenetic Signal

    PubMed Central

    Dodsworth, Steven; Chase, Mark W.; Kelly, Laura J.; Leitch, Ilia J.; Macas, Jiří; Novák, Petr; Piednoël, Mathieu; Weiss-Schneeweiss, Hanna; Leitch, Andrew R.

    2015-01-01

    A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution. PMID:25261464

  19. Genomic repeat abundances contain phylogenetic signal.

    PubMed

    Dodsworth, Steven; Chase, Mark W; Kelly, Laura J; Leitch, Ilia J; Macas, Jiří; Novák, Petr; Piednoël, Mathieu; Weiss-Schneeweiss, Hanna; Leitch, Andrew R

    2015-01-01

    A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.

  20. The phylogenetic likelihood library.

    PubMed

    Flouri, T; Izquierdo-Carrasco, F; Darriba, D; Aberer, A J; Nguyen, L-T; Minh, B Q; Von Haeseler, A; Stamatakis, A

    2015-03-01

    We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implementation of the phylogenetic likelihood function and a thorough documentation provide a framework for rapid development of scalable parallel phylogenetic software. By example of two likelihood-based phylogenetic codes we show that the PLL improves the sequential performance of current software by a factor of 2-10 while requiring only 1 month of programming time for integration. We show that, when numerical scaling for preventing floating point underflow is enabled, the double precision likelihood calculations in the PLL are up to 1.9 times faster than those in BEAGLE. On an empirical DNA dataset with 2000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling enabled and required). The PLL is available at http://www.libpll.org under the GNU General Public License (GPL).

  1. Phylogenetic niche conservatism in C4 grasses.

    PubMed

    Liu, Hui; Edwards, Erika J; Freckleton, Robert P; Osborne, Colin P

    2012-11-01

    Photosynthetic pathway is used widely to discriminate plant functional types in studies of global change. However, independent evolutionary lineages of C(4) grasses with different variants of C(4) photosynthesis show different biogeographical relationships with mean annual precipitation, suggesting phylogenetic niche conservatism (PNC). To investigate how phylogeny and photosynthetic type differentiate C(4) grasses, we compiled a dataset of morphological and habitat information of 185 genera belonging to two monophyletic subfamilies, Chloridoideae and Panicoideae, which together account for 90 % of the world's C(4) grass species. We evaluated evolutionary variance and covariance of morphological and habitat traits. Strong phylogenetic signals were found in both morphological and habitat traits, arising mainly from the divergence of the two subfamilies. Genera in Chloridoideae had significantly smaller culm heights, leaf widths, 1,000-seed weights and stomata; they also appeared more in dry, open or saline habitats than those of Panicoideae. Controlling for phylogenetic structure showed significant covariation among morphological traits, supporting the hypothesis of phylogenetically independent scaling effects. However, associations between morphological and habitat traits showed limited phylogenetic covariance. Subfamily was a better explanation than photosynthetic type for the variance in most morphological traits. Morphology, habitat water availability, shading, and productivity are therefore all involved in the PNC of C(4) grass lineages. This study emphasized the importance of phylogenetic history in the ecology and biogeography of C(4) grasses, suggesting that divergent lineages need to be considered to fully understand the impacts of global change on plant distributions. PMID:22569558

  2. Phylogenetic lineages in Pseudocercospora

    PubMed Central

    Crous, P.W.; Braun, U.; Hunter, G.C.; Wingfield, M.J.; Verkley, G.J.M.; Shin, H.-D.; Nakashima, C.; Groenewald, J.Z.

    2013-01-01

    Pseudocercospora is a large cosmopolitan genus of plant pathogenic fungi that are commonly associated with leaf and fruit spots as well as blights on a wide range of plant hosts. They occur in arid as well as wet environments and in a wide range of climates including cool temperate, sub-tropical and tropical regions. Pseudocercospora is now treated as a genus in its own right, although formerly recognised as either an anamorphic state of Mycosphaerella or having mycosphaerella-like teleomorphs. The aim of this study was to sequence the partial 28S nuclear ribosomal RNA gene of a selected set of isolates to resolve phylogenetic generic limits within the Pseudocercospora complex. From these data, 14 clades are recognised, six of which cluster in Mycosphaerellaceae. Pseudocercospora s. str. represents a distinct clade, sister to Passalora eucalypti, and a clade representing the genera Scolecostigmina, Trochophora and Pallidocercospora gen. nov., taxa formerly accommodated in the Mycosphaerella heimii complex and characterised by smooth, pale brown conidia, as well as the formation of red crystals in agar media. Other clades in Mycosphaerellaceae include Sonderhenia, Microcyclosporella, and Paracercospora. Pseudocercosporella resides in a large clade along with Phloeospora, Miuraea, Cercospora and Septoria. Additional clades represent Dissoconiaceae, Teratosphaeriaceae, Cladosporiaceae, and the genera Xenostigmina, Strelitziana, Cyphellophora and Thedgonia. The genus Phaeomycocentrospora is introduced to accommodate Mycocentrospora cantuariensis, primarily distinguished from Pseudocercospora based on its hyaline hyphae, broad conidiogenous loci and hila. Host specificity was considered for 146 species of Pseudocercospora occurring on 115 host genera from 33 countries. Partial nucleotide sequence data for three gene loci, ITS, EF-1α, and ACT suggest that the majority of these species are host specific. Species identified on the basis of host, symptomatology and general

  3. Phylogenetic analysis with the iPlant discovery environment.

    PubMed

    Matasci, Naim; McKay, Sheldon

    2013-06-01

    The iPlant Collaborative's Discovery Environment is a unified Web portal to many bioinformatics applications and analytical workflows, including various methods of phylogenetic analysis. This unit describes example protocols for phylogenetic analyses, starting at sequence retrieval from the GenBank sequence database, through to multiple sequence alignment inference and visualization of phylogenetic trees. Methods for extracting smaller sub-trees from very large phylogenies, and the comparative method of continuous ancestral character state reconstruction based on observed morphology of extant species related to their phylogenetic relationships, are also presented.

  4. Phylogenetic and Evolutionary Patterns in Microbial Carotenoid Biosynthesis Are Revealed by Comparative Genomics

    PubMed Central

    Klassen, Jonathan L.

    2010-01-01

    Background Carotenoids are multifunctional, taxonomically widespread and biotechnologically important pigments. Their biosynthesis serves as a model system for understanding the evolution of secondary metabolism. Microbial carotenoid diversity and evolution has hitherto been analyzed primarily from structural and biosynthetic perspectives, with the few phylogenetic analyses of microbial carotenoid biosynthetic proteins using either used limited datasets or lacking methodological rigor. Given the recent accumulation of microbial genome sequences, a reappraisal of microbial carotenoid biosynthetic diversity and evolution from the perspective of comparative genomics is warranted to validate and complement models of microbial carotenoid diversity and evolution based upon structural and biosynthetic data. Methodology/Principal Findings Comparative genomics were used to identify and analyze in silico microbial carotenoid biosynthetic pathways. Four major phylogenetic lineages of carotenoid biosynthesis are suggested composed of: (i) Proteobacteria; (ii) Firmicutes; (iii) Chlorobi, Cyanobacteria and photosynthetic eukaryotes; and (iv) Archaea, Bacteroidetes and two separate sub-lineages of Actinobacteria. Using this phylogenetic framework, specific evolutionary mechanisms are proposed for carotenoid desaturase CrtI-family enzymes and carotenoid cyclases. Several phylogenetic lineage-specific evolutionary mechanisms are also suggested, including: (i) horizontal gene transfer; (ii) gene acquisition followed by differential gene loss; (iii) co-evolution with other biochemical structures such as proteorhodopsins; and (iv) positive selection. Conclusions/Significance Comparative genomics analyses of microbial carotenoid biosynthetic proteins indicate a much greater taxonomic diversity then that identified based on structural and biosynthetic data, and divides microbial carotenoid biosynthesis into several, well-supported phylogenetic lineages not evident previously. This

  5. A Universal Phylogenetic Tree.

    ERIC Educational Resources Information Center

    Offner, Susan

    2001-01-01

    Presents a universal phylogenetic tree suitable for use in high school and college-level biology classrooms. Illustrates the antiquity of life and that all life is related, even if it dates back 3.5 billion years. Reflects important evolutionary relationships and provides an exciting way to learn about the history of life. (SAH)

  6. Phylogenetic Inference From Conserved sites Alignments

    SciTech Connect

    grundy, W.N.; Naylor, G.J.P.

    1999-08-15

    Molecular sequences provide a rich source of data for inferring the phylogenetic relationships among species. However, recent work indicates that even an accurate multiple alignment of a large sequence set may yield an incorrect phylogeny and that the quality of the phylogenetic tree improves when the input consists only of the highly conserved, motif regions of the alignment. This work introduces two methods of producing multiple alignments that include only the conserved regions of the initial alignment. The first method retains conserved motifs, whereas the second retains individual conserved sites in the initial alignment. Using parsimony analysis on a mitochondrial data set containing 19 species among which the phylogenetic relationships are widely accepted, both conserved alignment methods produce better phylogenetic trees than the complete alignment. Unlike any of the 19 inference methods used before to analyze this data, both methods produce trees that are completely consistent with the known phylogeny. The motif-based method employs far fewer alignment sites for comparable error rates. For a larger data set containing mitochondrial sequences from 39 species, the site-based method produces a phylogenetic tree that is largely consistent with known phylogenetic relationships and suggests several novel placements.

  7. Phylogenetic clustering and overdispersion in bacterial communities.

    PubMed

    Horner-Devine, M Claire; Bohannan, Brendan J M

    2006-07-01

    Very little is known about the structure of microbial communities, despite their abundance and importance to ecosystem processes. Recent work suggests that bacterial biodiversity might exhibit patterns similar to those of plants and animals. However, relative to our knowledge about the diversity of macro-organisms, we know little about patterns of relatedness in free-living bacterial communities, and relatively few studies have quantitatively examined community structure in a phylogenetic framework. Here we apply phylogenetic tools to bacterial diversity data to determine whether bacterial communities are phylogenetically structured. We find that bacterial communities tend to contain lower taxonomic diversity and are more likely to be phylogenetically clustered than expected by chance. Such phylogenetic clustering may indicate the importance of habitat filtering (where a group of closely related species shares a trait, or suite of traits, that allow them to persist in a given habitat) in the assembly of bacterial communities. Microbial communities are especially accessible for phylogenetic analysis and thus have the potential to figure prominently in the integration of evolutionary biology and community ecology.

  8. Estimating Bayesian Phylogenetic Information Content

    PubMed Central

    Lewis, Paul O.; Chen, Ming-Hui; Kuo, Lynn; Lewis, Louise A.; Fučíková, Karolina; Neupane, Suman; Wang, Yu-Bo; Shi, Daoyuan

    2016-01-01

    Measuring the phylogenetic information content of data has a long history in systematics. Here we explore a Bayesian approach to information content estimation. The entropy of the posterior distribution compared with the entropy of the prior distribution provides a natural way to measure information content. If the data have no information relevant to ranking tree topologies beyond the information supplied by the prior, the posterior and prior will be identical. Information in data discourages consideration of some hypotheses allowed by the prior, resulting in a posterior distribution that is more concentrated (has lower entropy) than the prior. We focus on measuring information about tree topology using marginal posterior distributions of tree topologies. We show that both the accuracy and the computational efficiency of topological information content estimation improve with use of the conditional clade distribution, which also allows topological information content to be partitioned by clade. We explore two important applications of our method: providing a compelling definition of saturation and detecting conflict among data partitions that can negatively affect analyses of concatenated data. [Bayesian; concatenation; conditional clade distribution; entropy; information; phylogenetics; saturation.] PMID:27155008

  9. Phylogenetic conservatism of extinctions in marine bivalves.

    PubMed

    Roy, Kaustuv; Hunt, Gene; Jablonski, David

    2009-08-01

    Evolutionary histories of species and lineages can influence their vulnerabilities to extinction, but the importance of this effect remains poorly explored for extinctions in the geologic past. When analyzed using a standardized taxonomy within a phylogenetic framework, extinction rates of marine bivalves estimated from the fossil record for the last approximately 200 million years show conservatism at multiple levels of evolutionary divergence, both within individual families and among related families. The strength of such phylogenetic clustering varies over time and is influenced by earlier extinction history, especially by the demise of volatile taxa in the end-Cretaceous mass extinction. Analyses of the evolutionary roles of ancient extinctions and predictive models of vulnerability of taxa to future natural and anthropogenic stressors should take phylogenetic relationships and extinction history into account.

  10. A phylogenetic analysis of macroevolutionary patterns in fermentative yeasts.

    PubMed

    Paleo-López, Rocío; Quintero-Galvis, Julian F; Solano-Iguaran, Jaiber J; Sanchez-Salazar, Angela M; Gaitan-Espitia, Juan D; Nespolo, Roberto F

    2016-06-01

    When novel sources of ecological opportunity are available, physiological innovations can trigger adaptive radiations. This could be the case of yeasts (Saccharomycotina), in which an evolutionary novelty is represented by the capacity to exploit simple sugars from fruits (fermentation). During adaptive radiations, diversification and morphological evolution are predicted to slow-down after early bursts of diversification. Here, we performed the first comparative phylogenetic analysis in yeasts, testing the "early burst" prediction on species diversification and also on traits of putative ecological relevance (cell-size and fermentation versatility). We found that speciation rates are constant during the time-range we considered (ca., 150 millions of years). Phylogenetic signal of both traits was significant (but lower for cell-size), suggesting that lineages resemble each other in trait-values. Disparity analysis suggested accelerated evolution (diversification in trait values above Brownian Motion expectations) in cell-size. We also found a significant phylogenetic regression between cell-size and fermentation versatility (R (2) = 0.10), which suggests correlated evolution between both traits. Overall, our results do not support the early burst prediction both in species and traits, but suggest a number of interesting evolutionary patterns, that warrant further exploration. For instance, we show that the Whole Genomic Duplication that affected a whole clade of yeasts, does not seems to have a statistically detectable phenotypic effect at our level of analysis. In this regard, further studies of fermentation under common-garden conditions combined with comparative analyses are warranted. PMID:27516851

  11. On the origin of and phylogenetic relationships among living amphibians

    PubMed Central

    Zardoya, Rafael; Meyer, Axel

    2001-01-01

    The phylogenetic relationships among the three orders of modern amphibians (Caudata, Gymnophiona, and Anura) have been estimated based on both morphological and molecular evidence. Most morphological and paleontological studies of living and fossil amphibians support the hypothesis that salamanders and frogs are sister lineages (the Batrachia hypothesis) and that caecilians are more distantly related. Previous interpretations of molecular data based on nuclear and mitochondrial rRNA sequences suggested that salamanders and caecilians are sister groups to the exclusion of frogs. In an attempt to resolve this apparent conflict, the complete mitochondrial genomes of a salamander (Mertensiella luschani) and a caecilian (Typhlonectes natans) were determined (16,656 and 17,005 bp, respectively) and compared with previously published sequences from a frog (Xenopus laevis) and several other groups of vertebrates. Phylogenetic analyses of the mitochondrial data supported with high bootstrap values the monophyly of living amphibians with respect to other living groups of tetrapods, and a sister group relationship of salamanders and frogs. The lack of phylogenetically informative sites in the previous rRNA data sets (because of its shorter size and higher among-site rate variation) likely explains the discrepancy between our results and those based on previous molecular data. Strong support of the Batrachia hypothesis from both molecule- and morphology-based studies provides a robust phylogenetic framework that will be helpful to comparative studies among the three living orders of amphibians and will permit better understanding of the considerably divergent vertebral, brain, and digit developmental patterns found in frogs and salamanders. PMID:11390961

  12. On the origin of and phylogenetic relationships among living amphibians.

    PubMed

    Zardoya, R; Meyer, A

    2001-06-19

    The phylogenetic relationships among the three orders of modern amphibians (Caudata, Gymnophiona, and Anura) have been estimated based on both morphological and molecular evidence. Most morphological and paleontological studies of living and fossil amphibians support the hypothesis that salamanders and frogs are sister lineages (the Batrachia hypothesis) and that caecilians are more distantly related. Previous interpretations of molecular data based on nuclear and mitochondrial rRNA sequences suggested that salamanders and caecilians are sister groups to the exclusion of frogs. In an attempt to resolve this apparent conflict, the complete mitochondrial genomes of a salamander (Mertensiella luschani) and a caecilian (Typhlonectes natans) were determined (16,656 and 17,005 bp, respectively) and compared with previously published sequences from a frog (Xenopus laevis) and several other groups of vertebrates. Phylogenetic analyses of the mitochondrial data supported with high bootstrap values the monophyly of living amphibians with respect to other living groups of tetrapods, and a sister group relationship of salamanders and frogs. The lack of phylogenetically informative sites in the previous rRNA data sets (because of its shorter size and higher among-site rate variation) likely explains the discrepancy between our results and those based on previous molecular data. Strong support of the Batrachia hypothesis from both molecule- and morphology-based studies provides a robust phylogenetic framework that will be helpful to comparative studies among the three living orders of amphibians and will permit better understanding of the considerably divergent vertebral, brain, and digit developmental patterns found in frogs and salamanders.

  13. On the origin of and phylogenetic relationships among living amphibians.

    PubMed

    Zardoya, R; Meyer, A

    2001-06-19

    The phylogenetic relationships among the three orders of modern amphibians (Caudata, Gymnophiona, and Anura) have been estimated based on both morphological and molecular evidence. Most morphological and paleontological studies of living and fossil amphibians support the hypothesis that salamanders and frogs are sister lineages (the Batrachia hypothesis) and that caecilians are more distantly related. Previous interpretations of molecular data based on nuclear and mitochondrial rRNA sequences suggested that salamanders and caecilians are sister groups to the exclusion of frogs. In an attempt to resolve this apparent conflict, the complete mitochondrial genomes of a salamander (Mertensiella luschani) and a caecilian (Typhlonectes natans) were determined (16,656 and 17,005 bp, respectively) and compared with previously published sequences from a frog (Xenopus laevis) and several other groups of vertebrates. Phylogenetic analyses of the mitochondrial data supported with high bootstrap values the monophyly of living amphibians with respect to other living groups of tetrapods, and a sister group relationship of salamanders and frogs. The lack of phylogenetically informative sites in the previous rRNA data sets (because of its shorter size and higher among-site rate variation) likely explains the discrepancy between our results and those based on previous molecular data. Strong support of the Batrachia hypothesis from both molecule- and morphology-based studies provides a robust phylogenetic framework that will be helpful to comparative studies among the three living orders of amphibians and will permit better understanding of the considerably divergent vertebral, brain, and digit developmental patterns found in frogs and salamanders. PMID:11390961

  14. Evolution of specialization: a phylogenetic study of host range in the red milkweed beetle (Tetraopes tetraophthalmus).

    PubMed

    Rasmann, Sergio; Agrawal, Anurag A

    2011-06-01

    Specialization is common in most lineages of insect herbivores, one of the most diverse groups of organisms on earth. To address how and why specialization is maintained over evolutionary time, we hypothesized that plant defense and other ecological attributes of potential host plants would predict the performance of a specialist root-feeding herbivore (the red milkweed beetle, Tetraopes tetraophthalmus). Using a comparative phylogenetic and functional trait approach, we assessed the determinants of insect host range across 18 species of Asclepias. Larval survivorship decreased with increasing phylogenetic distance from the true host, Asclepias syriaca, suggesting that adaptation to plant traits drives specialization. Among several root traits measured, only cardenolides (toxic defense chemicals) correlated with larval survival, and cardenolides also explained the phylogenetic distance effect in phylogenetically controlled multiple regression analyses. Additionally, milkweed species having a known association with other Tetraopes beetles were better hosts than species lacking Tetraopes herbivores, and milkweeds with specific leaf area values (a trait related to leaf function and habitat affiliation) similar to those of A. syriaca were better hosts than species having divergent values. We thus conclude that phylogenetic distance is an integrated measure of phenotypic and ecological attributes of Asclepias species, especially defensive cardenolides, which can be used to explain specialization and constraints on host shifts over evolutionary time. PMID:21597250

  15. Worldwide phylogenetic relationship of avian poxviruses

    USGS Publications Warehouse

    Gyuranecz, Miklós; Foster, Jeffrey T.; Dán, Ádám; Ip, Hon S.; Egstad, Kristina F.; Parker, Patricia G.; Higashiguchi, Jenni M.; Skinner, Michael A.; Höfle, Ursula; Kreizinger, Zsuzsa; Dorrestein, Gerry M.; Solt, Szabolcs; Sós, Endre; Kim, Young Jun; Uhart, Marcela; Pereda, Ariel; González-Hein, Gisela; Hidalgo, Hector; Blanco, Juan-Manuel; Erdélyi, Károly

    2013-01-01

    Poxvirus infections have been found in 230 species of wild and domestic birds worldwide in both terrestrial and marine environments. This ubiquity raises the question of how infection has been transmitted and globally dispersed. We present a comprehensive global phylogeny of 111 novel poxvirus isolates in addition to all available sequences from GenBank. Phylogenetic analysis of Avipoxvirus genus has traditionally relied on one gene region (4b core protein). In this study we have expanded the analyses to include a second locus (DNA polymerase gene), allowing for a more robust phylogenetic framework, finer genetic resolution within specific groups and the detection of potential recombination. Our phylogenetic results reveal several major features of avipoxvirus evolution and ecology and propose an updated avipoxvirus taxonomy, including three novel subclades. The characterization of poxviruses from 57 species of birds in this study extends the current knowledge of their host range and provides the first evidence of the phylogenetic effect of genetic recombination of avipoxviruses. The repeated occurrence of avian family or order-specific grouping within certain clades (e.g. starling poxvirus, falcon poxvirus, raptor poxvirus, etc.) indicates a marked role of host adaptation, while the sharing of poxvirus species within prey-predator systems emphasizes the capacity for cross-species infection and limited host adaptation. Our study provides a broad and comprehensive phylogenetic analysis of the Avipoxvirus genus, an ecologically and environmentally important viral group, to formulate a genome sequencing strategy that will clarify avipoxvirus taxonomy.

  16. Worldwide Phylogenetic Relationship of Avian Poxviruses

    PubMed Central

    Foster, Jeffrey T.; Dán, Ádám; Ip, Hon S.; Egstad, Kristina F.; Parker, Patricia G.; Higashiguchi, Jenni M.; Skinner, Michael A.; Höfle, Ursula; Kreizinger, Zsuzsa; Dorrestein, Gerry M.; Solt, Szabolcs; Sós, Endre; Kim, Young Jun; Uhart, Marcela; Pereda, Ariel; González-Hein, Gisela; Hidalgo, Hector; Blanco, Juan-Manuel; Erdélyi, Károly

    2013-01-01

    Poxvirus infections have been found in 230 species of wild and domestic birds worldwide in both terrestrial and marine environments. This ubiquity raises the question of how infection has been transmitted and globally dispersed. We present a comprehensive global phylogeny of 111 novel poxvirus isolates in addition to all available sequences from GenBank. Phylogenetic analysis of the Avipoxvirus genus has traditionally relied on one gene region (4b core protein). In this study we expanded the analyses to include a second locus (DNA polymerase gene), allowing for a more robust phylogenetic framework, finer genetic resolution within specific groups, and the detection of potential recombination. Our phylogenetic results reveal several major features of avipoxvirus evolution and ecology and propose an updated avipoxvirus taxonomy, including three novel subclades. The characterization of poxviruses from 57 species of birds in this study extends the current knowledge of their host range and provides the first evidence of the phylogenetic effect of genetic recombination of avipoxviruses. The repeated occurrence of avian family or order-specific grouping within certain clades (e.g., starling poxvirus, falcon poxvirus, raptor poxvirus, etc.) indicates a marked role of host adaptation, while the sharing of poxvirus species within prey-predator systems emphasizes the capacity for cross-species infection and limited host adaptation. Our study provides a broad and comprehensive phylogenetic analysis of the Avipoxvirus genus, an ecologically and environmentally important viral group, to formulate a genome sequencing strategy that will clarify avipoxvirus taxonomy. PMID:23408635

  17. Continental scale patterns and predictors of fern richness and phylogenetic diversity.

    PubMed

    Nagalingum, Nathalie S; Knerr, Nunzio; Laffan, Shawn W; González-Orozco, Carlos E; Thornhill, Andrew H; Miller, Joseph T; Mishler, Brent D

    2015-01-01

    Because ferns have a wide range of habitat preferences and are widely distributed, they are an ideal group for understanding how diversity is distributed. Here we examine fern diversity on a broad-scale using standard and corrected richness measures as well as phylogenetic indices; in addition we determine the environmental predictors of each diversity metric. Using the combined records of Australian herbaria, a dataset of over 60,000 records was obtained for 89 genera to infer richness. A molecular phylogeny of all the genera was constructed and combined with the herbarium records to obtain phylogenetic diversity patterns. A hotspot of both taxic and phylogenetic diversity occurs in the Wet Tropics of northeastern Australia. Although considerable diversity is distributed along the eastern coast, some important regions of diversity are identified only after sample-standardization of richness and through the phylogenetic metric. Of all of the metrics, annual precipitation was identified as the most explanatory variable, in part, in agreement with global and regional fern studies. However, precipitation was combined with a different variable for each different metric. For corrected richness, precipitation was combined with temperature seasonality, while correlation of phylogenetic diversity to precipitation plus radiation indicated support for the species-energy hypothesis. Significantly high and significantly low phylogenetic diversity were found in geographically separate areas. These separate areas correlated with different climatic conditions such as seasonality in precipitation. The phylogenetic metrics identified additional areas of significant diversity, some of which have not been revealed using traditional taxonomic analyses, suggesting that different ecological and evolutionary processes have operated over the continent. Our study demonstrates that it is possible and vital to incorporate evolutionary metrics when inferring biodiversity hotspots from large

  18. Continental scale patterns and predictors of fern richness and phylogenetic diversity

    PubMed Central

    Nagalingum, Nathalie S.; Knerr, Nunzio; Laffan, Shawn W.; González-Orozco, Carlos E.; Thornhill, Andrew H.; Miller, Joseph T.; Mishler, Brent D.

    2015-01-01

    Because ferns have a wide range of habitat preferences and are widely distributed, they are an ideal group for understanding how diversity is distributed. Here we examine fern diversity on a broad-scale using standard and corrected richness measures as well as phylogenetic indices; in addition we determine the environmental predictors of each diversity metric. Using the combined records of Australian herbaria, a dataset of over 60,000 records was obtained for 89 genera to infer richness. A molecular phylogeny of all the genera was constructed and combined with the herbarium records to obtain phylogenetic diversity patterns. A hotspot of both taxic and phylogenetic diversity occurs in the Wet Tropics of northeastern Australia. Although considerable diversity is distributed along the eastern coast, some important regions of diversity are identified only after sample-standardization of richness and through the phylogenetic metric. Of all of the metrics, annual precipitation was identified as the most explanatory variable, in part, in agreement with global and regional fern studies. However, precipitation was combined with a different variable for each different metric. For corrected richness, precipitation was combined with temperature seasonality, while correlation of phylogenetic diversity to precipitation plus radiation indicated support for the species-energy hypothesis. Significantly high and significantly low phylogenetic diversity were found in geographically separate areas. These separate areas correlated with different climatic conditions such as seasonality in precipitation. The phylogenetic metrics identified additional areas of significant diversity, some of which have not been revealed using traditional taxonomic analyses, suggesting that different ecological and evolutionary processes have operated over the continent. Our study demonstrates that it is possible and vital to incorporate evolutionary metrics when inferring biodiversity hotspots from large

  19. Phylogenetic system and zoogeography of the Plecoptera.

    PubMed

    Zwick, P

    2000-01-01

    Information about the phylogenetic relationships of Plecoptera is summarized. The few characters supporting monophyly of the order are outlined. Several characters of possible significance for the search for the closest relatives of the stoneflies are discussed, but the sister-group of the order remains unknown. Numerous characters supporting the presently recognized phylogenetic system of Plecoptera are presented, alternative classifications are discussed, and suggestions for future studies are made. Notes on zoogeography are appended. The order as such is old (Permian fossils), but phylogenetic relationships and global distribution patterns suggest that evolution of the extant suborders started with the breakup of Pangaea. There is evidence of extensive recent speciation in all parts of the world.

  20. Suitability of cuticular pores and sensilla for harpacticoid copepod species delineation and phylogenetic reconstruction.

    PubMed

    Karanovic, Tomislav; Kim, Kichoon

    2014-11-01

    Cuticular organs have not been described systematically in harpacticoids until recently, and they haven ever been used as characters for reconstructing phylogenetic relationships in any crustacean group. We survey cuticular pores and sensilla on somites in ten Miraciidae species, belonging to six genera, from Korea, Australia, and Russia. Nine species belong to the subfamily Stenheliinae, while the outgroup belongs to the subfamily Diosaccinae. We aim to compare phylogenetic trees reconstructed for these harpactioids based on: 1) cuticular organs (with 76 characters scored, 71% of them phylogenetically informative); 2) traditionally used macro-morphological characters (66 scored, 77% of them informative);and 3) mtCOI DNA data. All analyses suggest that cuticular organs are useful characters for harpacticoid species delineation, although not as sensitive as some fast-evolving molecular markers. Reconstructed cladograms based on all three datasets show very high bootstrap values for clades representing distinct genera, suggesting that cuticular organs are suitable characters for studying phylogenetic relationships. Bootstrap values for the more basal nodes differ among the different cladograms,as do the sister-group relationships they suggest, indicating that cuticular organs probably have different evolutionary constraints from macro-morphological characters. Cuticular organs could be quite useful in the study of old museum specimens and fossil crustaceans. PMID:25264078

  1. Understanding phylogenetic incongruence: lessons from phyllostomid bats

    PubMed Central

    Dávalos, Liliana M; Cirranello, Andrea L; Geisler, Jonathan H; Simmons, Nancy B

    2012-01-01

    All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive

  2. Phylogenetic lineages in Pseudocercospora

    PubMed Central

    Crous, P.W.; Braun, U.; Hunter, G.C.; Wingfield, M.J.; Verkley, G.J.M.; Shin, H.-D.; Nakashima, C.; Groenewald, J.Z.

    2013-01-01

    Pseudocercospora is a large cosmopolitan genus of plant pathogenic fungi that are commonly associated with leaf and fruit spots as well as blights on a wide range of plant hosts. They occur in arid as well as wet environments and in a wide range of climates including cool temperate, sub-tropical and tropical regions. Pseudocercospora is now treated as a genus in its own right, although formerly recognised as either an anamorphic state of Mycosphaerella or having mycosphaerella-like teleomorphs. The aim of this study was to sequence the partial 28S nuclear ribosomal RNA gene of a selected set of isolates to resolve phylogenetic generic limits within the Pseudocercospora complex. From these data, 14 clades are recognised, six of which cluster in Mycosphaerellaceae. Pseudocercospora s. str. represents a distinct clade, sister to Passalora eucalypti, and a clade representing the genera Scolecostigmina, Trochophora and Pallidocercospora gen. nov., taxa formerly accommodated in the Mycosphaerella heimii complex and characterised by smooth, pale brown conidia, as well as the formation of red crystals in agar media. Other clades in Mycosphaerellaceae include Sonderhenia, Microcyclosporella, and Paracercospora. Pseudocercosporella resides in a large clade along with Phloeospora, Miuraea, Cercospora and Septoria. Additional clades represent Dissoconiaceae, Teratosphaeriaceae, Cladosporiaceae, and the genera Xenostigmina, Strelitziana, Cyphellophora and Thedgonia. The genus Phaeomycocentrospora is introduced to accommodate Mycocentrospora cantuariensis, primarily distinguished from Pseudocercospora based on its hyaline hyphae, broad conidiogenous loci and hila. Host specificity was considered for 146 species of Pseudocercospora occurring on 115 host genera from 33 countries. Partial nucleotide sequence data for three gene loci, ITS, EF-1α, and ACT suggest that the majority of these species are host specific. Species identified on the basis of host, symptomatology and general

  3. Neurogenesis suggests independent evolution of opercula in serpulid polychaetes

    PubMed Central

    2009-01-01

    Background The internal phylogenetic relationships of Annelida, one of the key lophotrochozoan lineages, are still heavily debated. Recent molecular analyses suggest that morphologically distinct groups, such as the polychaetes, are paraphyletic assemblages, thus questioning the homology of a number of polychaete morphological characters. Serpulid polychaetes are typically recognized by having fused anterior ends bearing a tentacular crown and an operculum. The latter is commonly viewed as a modified tentacle (= radiole) and is often used as an important diagnostic character in serpulid systematics. Results By reconstructing the developmental neuroanatomy of the serpulid polychaete Spirorbis cf. spirorbis (Spirorbinae), we found striking differences in the overall neural architecture, the innervation pattern, and the ontogenetic establishment of the nervous supply of the operculum and the radioles in this species. Accordingly, the spirorbin operculum might not be homologous to the radioles or to the opercula of other serpulid taxa such as Serpula and Pomatoceros and is thus probably not a part of the tentacular crown. Conclusion We demonstrate that common morphological traits such as the prostomial appendages may have evolved independently in respective serpulid sublineages and therefore require reassessment before being used in phylogenetic analyses. Our findings corroborate recent molecular studies that argue for a revision of serpulid systematics. In addition, our data on Spirorbis neurogenesis provide a novel set of characters that highlight the developmental plasticity of the segmented annelid nervous system. PMID:19930667

  4. Phylogenetic Origins of Brain Organisers

    PubMed Central

    Robertshaw, Ellen; Kiecker, Clemens

    2012-01-01

    The regionalisation of the nervous system begins early in embryogenesis, concomitant with the establishment of the anteroposterior (AP) and dorsoventral (DV) body axes. The molecular mechanisms that drive axis induction appear to be conserved throughout the animal kingdom and may be phylogenetically older than the emergence of bilateral symmetry. As a result of this process, groups of patterning genes that are equally well conserved are expressed at specific AP and DV coordinates of the embryo. In the emerging nervous system of vertebrate embryos, this initial pattern is refined by local signalling centres, secondary organisers, that regulate patterning, proliferation, and axonal pathfinding in adjacent neuroepithelium. The main secondary organisers for the AP neuraxis are the midbrain-hindbrain boundary, zona limitans intrathalamica, and anterior neural ridge and for the DV neuraxis the notochord, floor plate, and roof plate. A search for homologous secondary organisers in nonvertebrate lineages has led to controversy over their phylogenetic origins. Based on a recent study in hemichordates, it has been suggested that the AP secondary organisers evolved at the base of the deuterostome superphylum, earlier than previously thought. According to this view, the lack of signalling centres in some deuterostome lineages is likely to reflect a secondary loss due to adaptive processes. We propose that the relative evolutionary flexibility of secondary organisers has contributed to a broader morphological complexity of nervous systems in different clades. PMID:24278699

  5. Phylogenetic Conservatism in Plant Phenology

    NASA Technical Reports Server (NTRS)

    Davies, T. Jonathan; Wolkovich, Elizabeth M.; Kraft, Nathan J. B.; Salamin, Nicolas; Allen, Jenica M.; Ault, Toby R.; Betancourt, Julio L.; Bolmgren, Kjell; Cleland, Elsa E.; Cook, Benjamin I.; Crimmins, Theresa M.; Mazer, Susan J.; McCabe, Gregory J.; Pau, Stephanie; Regetz, Jim; Schwartz, Mark D.; Travers, Steven E.

    2013-01-01

    Phenological events defined points in the life cycle of a plant or animal have been regarded as highly plastic traits, reflecting flexible responses to various environmental cues. The ability of a species to track, via shifts in phenological events, the abiotic environment through time might dictate its vulnerability to future climate change. Understanding the predictors and drivers of phenological change is therefore critical. Here, we evaluated evidence for phylogenetic conservatism the tendency for closely related species to share similar ecological and biological attributes in phenological traits across flowering plants. We aggregated published and unpublished data on timing of first flower and first leaf, encompassing 4000 species at 23 sites across the Northern Hemisphere. We reconstructed the phylogeny for the set of included species, first, using the software program Phylomatic, and second, from DNA data. We then quantified phylogenetic conservatism in plant phenology within and across sites. We show that more closely related species tend to flower and leaf at similar times. By contrasting mean flowering times within and across sites, however, we illustrate that it is not the time of year that is conserved, but rather the phenological responses to a common set of abiotic cues. Our findings suggest that species cannot be treated as statistically independent when modelling phenological responses.Closely related species tend to resemble each other in the timing of their life-history events, a likely product of evolutionarily conserved responses to environmental cues. The search for the underlying drivers of phenology must therefore account for species' shared evolutionary histories.

  6. High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae)

    PubMed Central

    Li, De-Zhu

    2011-01-01

    Background Bambusoideae is the only subfamily that contains woody members in the grass family, Poaceae. In phylogenetic analyses, Bambusoideae, Pooideae and Ehrhartoideae formed the BEP clade, yet the internal relationships of this clade are controversial. The distinctive life history (infrequent flowering and predominance of asexual reproduction) of woody bamboos makes them an interesting but taxonomically difficult group. Phylogenetic analyses based on large DNA fragments could only provide a moderate resolution of woody bamboo relationships, although a robust phylogenetic tree is needed to elucidate their evolutionary history. Phylogenomics is an alternative choice for resolving difficult phylogenies. Methodology/Principal Findings Here we present the complete nucleotide sequences of six woody bamboo chloroplast (cp) genomes using Illumina sequencing. These genomes are similar to those of other grasses and rather conservative in evolution. We constructed a phylogeny of Poaceae from 24 complete cp genomes including 21 grass species. Within the BEP clade, we found strong support for a sister relationship between Bambusoideae and Pooideae. In a substantial improvement over prior studies, all six nodes within Bambusoideae were supported with ≥0.95 posterior probability from Bayesian inference and 5/6 nodes resolved with 100% bootstrap support in maximum parsimony and maximum likelihood analyses. We found that repeats in the cp genome could provide phylogenetic information, while caution is needed when using indels in phylogenetic analyses based on few selected genes. We also identified relatively rapidly evolving cp genome regions that have the potential to be used for further phylogenetic study in Bambusoideae. Conclusions/Significance The cp genome of Bambusoideae evolved slowly, and phylogenomics based on whole cp genome could be used to resolve major relationships within the subfamily. The difficulty in resolving the diversification among three clades of

  7. Phylogenetic utility of indels within ribosomal DNA and beta-tubulin sequences from fungi in the Rhizoctonia solani species complex.

    PubMed

    González, Dolores; Cubeta, Marc A; Vilgalys, Rytas

    2006-08-01

    The genus Rhizoctonia consists of a diverse assemblage of anamorphic fungi frequently associated with plants and soil throughout the world. Some anamorphs are related with teleomorphs (sexual stage) in different taxonomic classes, orders, and families. The fungus may exist as pathogen, saprophyte, or mycorrhizal symbiont and shows extensive variation in characteristics such as geographic location, morphology, host specificity, and pathogenicity. In this study, phylogenetic analyses were performed in the Rhizoctonia solani species complex with individual and combined data sets from three gene partitions (ITS, LSU rDNA, and beta-tubulin). To explore whether indels were a source of phylogenetically informative characters, single-site indels were treated as a new state, while indels greater than one contiguous nucleotide were analyzed by including them as ambiguous data (Coding A); excluding them from the analyses (Coding B), and with three distinct codes: multistate for different sequence (Coding C); multistate for different length (Coding D) and different characters for each distinct sequence (Coding E). Results suggest that indels in noncoding regions contain phylogenetic information and support the fact that the R. solani species complex is not monophyletic. Six clades within R. solani (teleomorph=Thanatephorus) representing distinct anastomosis groups and five clades within binucleate Rhizoctonia (teleomorph=Ceratobasidium) were well supported in all analyses. The data suggest that clades with representatives of R. solani fungi belonging to anastomosis groups 1, 4, 6, and 8 should be recognized as phylogenetic species.

  8. Ecomorphology and phylogenetic risk: Implications for habitat reconstruction using fossil bovids.

    PubMed

    Scott, Robert S; Barr, W Andrew

    2014-08-01

    Reconstructions of paleohabitats are necessary aids in understanding hominin evolution. The morphology of species from relevant sites, understood in terms of functional relationships to habitat (termed ecomorphology), offers a direct link to habitat. Bovids are a speciose radiation that includes many habitat specialists and are abundant in the fossil record. Thus, bovids are extremely common in ecomorphological analyses. However, bovid phylogeny and habitat preference are related, which raises the possibility that analyses linking habitat with morphology are not 'taxon free' but 'taxon-dependent.' Here we analyze eight relative dimensions and one shape index of the metatarsal for a sample of 72 bovid species and one antilocaprid. The selected variables have been previously shown to have strong associations with habitat and to have functional explanations for these associations. Phylogenetic generalized least squares analyses of these variables, including habitat and size, resulted in estimates for the parameter lambda (used to model phylogenetic signal) varying from zero to one. Thus, while phylogeny, morphology, and habitat all march together among the bovids, the odds that phylogeny confounds ecomorphological analyses may vary depending on particular morphological characteristics. While large values of lambda do not necessarily indicate that habitat differences are unimportant drivers of morphology, we consider the low value of lambda for relative metatarsal width suggestive that conclusions about habitat built on observations of this particular morphology carry with them less 'phylogenetic risk.' We suggest that the way forward for ecomorphology is grounded in functionally relevant observations and careful consideration of phylogeny designed to bracket probable habitat preferences appropriately. Separate consideration of different morphological variables may help to determine the level of 'phylogenetic risk' attached to conclusions linking habitat and morphology.

  9. The phylogenetic position of the Critically Endangered Saint Croix ground lizard Ameiva polops: revisiting molecular systematics of West Indian Ameiva.

    PubMed

    Hurtado, Luis A; Santamaria, Carlos A; Fitzgerald, Lee A

    2014-01-01

    The phylogenetic position of the critically endangered Saint Croix ground lizard Ameiva polops is presently unknown and several hypotheses have been proposed. We investigated the phylogenetic position of this species using molecular phylogenetic methods. We obtained sequences of DNA fragments of the mitochondrial ribosomal genes 12S rDNA and 16S rDNA for this species. We aligned these sequences with published sequences of other Ameiva species, which include most of the Ameiva species from the West Indies, three Ameiva species from Central America and South America, and one from the teiid lizard Tupinambis teguixin, which was used as outgroup. We conducted Maximum Likelihood and Bayesian phylogenetic analyses. The phylogenetic reconstructions among the different methods were very similar, supporting the monophyly of West Indian Ameiva and showing within this lineage, a basal polytomy of four clades that are separated geographically. Ameiva polops grouped in a cluster that included the other two Ameiva species found in the Puerto Rican Bank: A. wetmorei and A. exsul. A sister relationship between A. polops and A. wetmorei is suggested by our analyses. We compare our results with a previous study on molecular systematics of West Indian Ameiva.  PMID:24870322

  10. Molecular tests of phylogenetic taxonomies: a general procedure and example using four subfamilies of the lizard family Iguanidae.

    PubMed

    Schulte, J A; Macey, J R; Larson, A; Papenfuss, T J

    1998-12-01

    A general procedure is described for examining when results of molecular phylogenetic analyses warrant formal revision of taxonomies constructed using morphological characters. We illustrate this procedure with tests of monophyly for four subfamilies in the lizard family Iguanidae using 1561 aligned base positions (838 phylogenetically informative) of mitochondrial DNA sequences, representing coding regions for eight tRNAs, ND2, and portions of ND1 and COI. Ten new sequences ranging in length from 1732 to 1751 bases are compared with 12 previously reported sequences and 67 morphological characters (54 phylogenetically informative) from the literature. New morphological character states are provided for Sator. Phylogenies derived from the molecular and combined data are in agreement but both conflict with phylogenetic inferences from the morphological data alone. Strong support is found for the monophyly of the subfamilies Crotaphytinae and Phrynosomatinae. Monophyly of the Iguaninae is weakly supported in each analysis. All analyses suggest that the Tropidurinae is not monophyletic but the hypothesis of monophyly cannot be rejected. A phylogenetic taxonomy is proposed in which the Tropidurinae* is maintained as a metataxon (denoted with an asterisk), for which monophyly has not been demonstrated. Within the Phrynosomatinae, the close relationship of Sator and Sceloporus is questioned and an alternative hypothesis in which Sator is the sister taxon to a clade comprising Petrosaurus, Sceloporus, and Urosaurus is presented. Statistical tests of monophyly provide a powerful way to evaluate support for taxonomic groupings. Use of the metataxon prevents premature taxonomic rearrangements where support is lacking.

  11. A phylogenetic analysis of Aquifex pyrophilus

    NASA Technical Reports Server (NTRS)

    Burggraf, S.; Olsen, G. J.; Stetter, K. O.; Woese, C. R.

    1992-01-01

    The 16S rRNA of the bacterion Aquifex pyrophilus, a microaerophilic, oxygen-reducing hyperthermophile, has been sequenced directly from the the PCR amplified gene. Phylogenetic analyses show the Aq. pyrophilus lineage to be probably the deepest (earliest) in the (eu)bacterial tree. The addition of this deep branching to the bacterial tree further supports the argument that the Bacteria are of thermophilic ancestry.

  12. Prioritizing populations for conservation using phylogenetic networks.

    PubMed

    Volkmann, Logan; Martyn, Iain; Moulton, Vincent; Spillner, Andreas; Mooers, Arne O

    2014-01-01

    In the face of inevitable future losses to biodiversity, ranking species by conservation priority seems more than prudent. Setting conservation priorities within species (i.e., at the population level) may be critical as species ranges become fragmented and connectivity declines. However, existing approaches to prioritization (e.g., scoring organisms by their expected genetic contribution) are based on phylogenetic trees, which may be poor representations of differentiation below the species level. In this paper we extend evolutionary isolation indices used in conservation planning from phylogenetic trees to phylogenetic networks. Such networks better represent population differentiation, and our extension allows populations to be ranked in order of their expected contribution to the set. We illustrate the approach using data from two imperiled species: the spotted owl Strix occidentalis in North America and the mountain pygmy-possum Burramys parvus in Australia. Using previously published mitochondrial and microsatellite data, we construct phylogenetic networks and score each population by its relative genetic distinctiveness. In both cases, our phylogenetic networks capture the geographic structure of each species: geographically peripheral populations harbor less-redundant genetic information, increasing their conservation rankings. We note that our approach can be used with all conservation-relevant distances (e.g., those based on whole-genome, ecological, or adaptive variation) and suggest it be added to the assortment of tools available to wildlife managers for allocating effort among threatened populations. PMID:24586451

  13. Prioritizing Populations for Conservation Using Phylogenetic Networks

    PubMed Central

    Volkmann, Logan; Martyn, Iain; Moulton, Vincent; Spillner, Andreas; Mooers, Arne O.

    2014-01-01

    In the face of inevitable future losses to biodiversity, ranking species by conservation priority seems more than prudent. Setting conservation priorities within species (i.e., at the population level) may be critical as species ranges become fragmented and connectivity declines. However, existing approaches to prioritization (e.g., scoring organisms by their expected genetic contribution) are based on phylogenetic trees, which may be poor representations of differentiation below the species level. In this paper we extend evolutionary isolation indices used in conservation planning from phylogenetic trees to phylogenetic networks. Such networks better represent population differentiation, and our extension allows populations to be ranked in order of their expected contribution to the set. We illustrate the approach using data from two imperiled species: the spotted owl Strix occidentalis in North America and the mountain pygmy-possum Burramys parvus in Australia. Using previously published mitochondrial and microsatellite data, we construct phylogenetic networks and score each population by its relative genetic distinctiveness. In both cases, our phylogenetic networks capture the geographic structure of each species: geographically peripheral populations harbor less-redundant genetic information, increasing their conservation rankings. We note that our approach can be used with all conservation-relevant distances (e.g., those based on whole-genome, ecological, or adaptive variation) and suggest it be added to the assortment of tools available to wildlife managers for allocating effort among threatened populations. PMID:24586451

  14. Phylogenetic relationships within Cornus (Cornaceae) based on 26S rDNA sequences.

    PubMed

    Fan, C

    2001-06-01

    Phylogenetic relationships within the dogwood genus Cornus have been highly controversial due to the great morphological heterogeneity. Earlier phylogenetic analyses of Cornus using chloroplast DNA (cpDNA) data (including rbcL and matK sequences, as well as restriction sites) and morphological characters suggested incongruent relationships within the genus. The present study generated sequence data from the nuclear gene 26S rDNA for Cornus to test the phylogenetic hypotheses based on cpDNA and morphological data. The 26S rDNA sequence data obtained represent 16 species, 13 from Cornus and three from outgroups, having an aligned length of 3380 bp. Both parsimony and maximum likelihood analyses of these sequences were conducted. Trees resulting from these analyses suggest relationships among subgroups of Cornus consistent with those inferred from cpDNA data. That is, the dwarf dogwood (subg. Arctocrania) and the big-bracted dogwood (subg. Cynoxylon and subg. Syncarpea) clades are sisters, which are, in turn, sister to the cornelian cherries (subg. Cornus and subg. Afrocrania). This red-fruited clade is sister to the blue- or white-fruited dogwoods (subg. Mesomora, subg. Kraniopsis, and subg. Yinquania). Within the blue- or white-fruited clade, C. oblonga (subg. Yinquania) is sister to the remainder, and subg. Mesomora is sister to subg. Kraniopsis. These relationships were also suggested by the combined 26S rDNA and cpDNA data, but with higher bootstrap and Bremer support in the combined analysis. The 26S rDNA sequence data of Cornus consist of 12 expansion segments spanning 1034 bp. These expansion segments evolve approximately four times as fast as the conserved core regions. The study provides an example of phylogenetic utility of 26S rDNA sequences below the genus level. PMID:11410478

  15. Phylogenetic Analysis and Epidemic History of Hepatitis C Virus Genotype 2 in Tunisia, North Africa

    PubMed Central

    Rajhi, Mouna; Ghedira, Kais; Chouikha, Anissa; Djebbi, Ahlem; Cheikh, Imed; Ben Yahia, Ahlem; Sadraoui, Amel; Hammami, Walid; Azouz, Msaddek; Ben Mami, Nabil; Triki, Henda

    2016-01-01

    HCV genotype 2 (HCV-2) has a worldwide distribution with prevalence rates that vary from country to country. High genetic diversity and long-term endemicity were suggested in West African countries. A global dispersal of HCV-2 would have occurred during the 20th century, especially in European countries. In Tunisia, genotype 2 was the second prevalent genotype after genotype 1 and most isolates belong to subtypes 2c and 2k. In this study, phylogenetic analyses based on the NS5B genomic sequences of 113 Tunisian HCV isolates from subtypes 2c and 2k were carried out. A Bayesian coalescent-based framework was used to estimate the origin and the spread of these subtypes circulating in Tunisia. Phylogenetic analyses of HCV-2c sequences suggest the absence of country-specific or time-specific variants. In contrast, the phylogenetic grouping of HCV-2k sequences shows the existence of two major genetic clusters that may represent two distinct circulating variants. Coalescent analysis indicated a most recent common ancestor (tMRCA) of Tunisian HCV-2c around 1886 (1869–1902) before the introduction of HCV-2k in 1901 (1867–1931). Our findings suggest that the introduction of HCV-2c in Tunisia is possibly a result of population movements between Tunisia and European population following the French colonization. PMID:27100294

  16. Phylogenetic Analysis and Epidemic History of Hepatitis C Virus Genotype 2 in Tunisia, North Africa.

    PubMed

    Rajhi, Mouna; Ghedira, Kais; Chouikha, Anissa; Djebbi, Ahlem; Cheikh, Imed; Ben Yahia, Ahlem; Sadraoui, Amel; Hammami, Walid; Azouz, Msaddek; Ben Mami, Nabil; Triki, Henda

    2016-01-01

    HCV genotype 2 (HCV-2) has a worldwide distribution with prevalence rates that vary from country to country. High genetic diversity and long-term endemicity were suggested in West African countries. A global dispersal of HCV-2 would have occurred during the 20th century, especially in European countries. In Tunisia, genotype 2 was the second prevalent genotype after genotype 1 and most isolates belong to subtypes 2c and 2k. In this study, phylogenetic analyses based on the NS5B genomic sequences of 113 Tunisian HCV isolates from subtypes 2c and 2k were carried out. A Bayesian coalescent-based framework was used to estimate the origin and the spread of these subtypes circulating in Tunisia. Phylogenetic analyses of HCV-2c sequences suggest the absence of country-specific or time-specific variants. In contrast, the phylogenetic grouping of HCV-2k sequences shows the existence of two major genetic clusters that may represent two distinct circulating variants. Coalescent analysis indicated a most recent common ancestor (tMRCA) of Tunisian HCV-2c around 1886 (1869-1902) before the introduction of HCV-2k in 1901 (1867-1931). Our findings suggest that the introduction of HCV-2c in Tunisia is possibly a result of population movements between Tunisia and European population following the French colonization.

  17. Phylogenetic Analysis and Epidemic History of Hepatitis C Virus Genotype 2 in Tunisia, North Africa.

    PubMed

    Rajhi, Mouna; Ghedira, Kais; Chouikha, Anissa; Djebbi, Ahlem; Cheikh, Imed; Ben Yahia, Ahlem; Sadraoui, Amel; Hammami, Walid; Azouz, Msaddek; Ben Mami, Nabil; Triki, Henda

    2016-01-01

    HCV genotype 2 (HCV-2) has a worldwide distribution with prevalence rates that vary from country to country. High genetic diversity and long-term endemicity were suggested in West African countries. A global dispersal of HCV-2 would have occurred during the 20th century, especially in European countries. In Tunisia, genotype 2 was the second prevalent genotype after genotype 1 and most isolates belong to subtypes 2c and 2k. In this study, phylogenetic analyses based on the NS5B genomic sequences of 113 Tunisian HCV isolates from subtypes 2c and 2k were carried out. A Bayesian coalescent-based framework was used to estimate the origin and the spread of these subtypes circulating in Tunisia. Phylogenetic analyses of HCV-2c sequences suggest the absence of country-specific or time-specific variants. In contrast, the phylogenetic grouping of HCV-2k sequences shows the existence of two major genetic clusters that may represent two distinct circulating variants. Coalescent analysis indicated a most recent common ancestor (tMRCA) of Tunisian HCV-2c around 1886 (1869-1902) before the introduction of HCV-2k in 1901 (1867-1931). Our findings suggest that the introduction of HCV-2c in Tunisia is possibly a result of population movements between Tunisia and European population following the French colonization. PMID:27100294

  18. Investigation of glycan evolution based on a comprehensive analysis of glycosyltransferases using phylogenetic profiling

    PubMed Central

    Tomono, Takayoshi; Kojima, Hisao; Fukuchi, Satoshi; Tohsato, Yukako; Ito, Masahiro

    2015-01-01

    Glycans play important roles in such cell-cell interactions as signaling and adhesion, including processes involved in pathogenic infections, cancers, and neurological diseases. Glycans are biosynthesized by multiple glycosyltransferases (GTs), which function sequentially. Excluding mucin-type O-glycosylation, the non-reducing terminus of glycans is biosynthesized in the Golgi apparatus after the reducing terminus is biosynthesized in the ER. In the present study, we performed genome-wide analyses of human GTs by investigating the degree of conservation of homologues in other organisms, as well as by elucidating the phylogenetic relationship between cephalochordates and urochordates, which has long been controversial in deuterostome phylogeny. We analyzed 173 human GTs and functionally linked glycan synthesis enzymes by phylogenetic profiling and clustering, compiled orthologous genes from the genomes of other organisms, and converted them into a binary sequence based on the presence (1) or absence (0) of orthologous genes in the genomes. Our results suggest that the non-reducing terminus of glycans is biosynthesized by newly evolved GTs. According to our analysis, the phylogenetic profiles of GTs resemble the phylogenetic tree of life, where deuterostomes, metazoans, and eukaryotes are resolved into separate branches. Lineage-specific GTs appear to play essential roles in the divergence of these particular lineages. We suggest that urochordates lose several genes that are conserved among metazoans, such as those expressing sialyltransferases, and that the Golgi apparatus acquires the ability to synthesize glycans after the ER acquires this function. PMID:27493855

  19. Phylogenetic analysis of the spirochetes.

    PubMed Central

    Paster, B J; Dewhirst, F E; Weisburg, W G; Tordoff, L A; Fraser, G J; Hespell, R B; Stanton, T B; Zablen, L; Mandelco, L; Woese, C R

    1991-01-01

    , Leptospira biflexa, and Leptospira interrogans formed the sixth and most deeply branching group. The average similarity within this group was 83.2%. This study represents the first demonstration that pathogenic and saprophytic Leptospira species are phylogenetically related. The division of the spirochetes into six major phylogenetic clusters was defined also by sequence signature elements. These signature analyses supported the conclusion that the spirochetes represent a monophylectic bacterial phylum. PMID:1917844

  20. Phylogenetic placement of Trichonympha.

    PubMed

    Dacks, J B; Redfield, R J

    1998-01-01

    Flagellated protists of the Class Hypermastigida have previously been classified on morphology alone, since no molecular sequences have been available. We have isolated DNA from 350 cells of the hypermastigote Trichonympha, manually collected from the hindgut of Zootermopsis angusticollis, and used this DNA as template for polymerase chain reaction amplification of the small-subunit ribosomal RNA gene. The DNA sequence of the amplified fragment is closely related to that of a previously-unidentified gut symbiont from the termite Reticulitermes flavipes, and phylogenetic analysis places both sequences as a sister group to the known trichomonads, in agreement with the morphological classification.

  1. Phylogenetic Comparative Assembly

    NASA Astrophysics Data System (ADS)

    Husemann, Peter; Stoye, Jens

    Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers successfully merge the overlapping reads, often several contigs remain which cannot be assembled any further. It is still costly and time consuming to close all the gaps in order to acquire the whole genomic sequence. Here we propose an algorithm that takes several related genomes and their phylogenetic relationships into account to create a contig adjacency graph. From this a layout graph can be computed which indicates putative adjacencies of the contigs in order to aid biologists in finishing the complete genomic sequence.

  2. Molecular modeling and computational analyses suggests that the Sinorhizobium meliloti periplasmic regulator protein ExoR adopts a superhelical fold and is controlled by a unique mechanism of proteolysis

    PubMed Central

    Wiech, Eliza M; Cheng, Hai-Ping; Singh, Shaneen M

    2015-01-01

    The Sinorhizobium meliloti periplasmic ExoR protein and the ExoS/ChvI two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. In the absence of crystal structures, understanding the molecular mechanism of interaction between ExoR and the ExoS sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. In this study, we present a theoretical structural model of the active form of ExoR protein, ExoRm, generated using computational methods. Our model suggests that ExoR possesses a super-helical fold comprising 12 α-helices forming six Sel1-like repeats, including two that were unidentified in previous studies. This fold is highly conducive to mediating protein–protein interactions and this is corroborated by the identification of putative protein binding sites on the surface of the ExoRm protein. Our studies reveal two novel insights: (a) an extended conformation of the third Sel1-like repeat that might be important for ExoR regulatory function and (b) a buried proteolytic site that implies a unique proteolytic mechanism. This study provides new and interesting insights into the structure of S. meliloti ExoR, lays the groundwork for elaborating the molecular mechanism of ExoRm cleavage, ExoRm–ExoS interactions, and studies of ExoR homologs in other bacterial host interactions. PMID:25492513

  3. Octocoral Mitochondrial Genomes Provide Insights into the Phylogenetic History of Gene Order Rearrangements, Order Reversals, and Cnidarian Phylogenetics

    PubMed Central

    Figueroa, Diego F.; Baco, Amy R.

    2015-01-01

    We use full mitochondrial genomes to test the robustness of the phylogeny of the Octocorallia, to determine the evolutionary pathway for the five known mitochondrial gene rearrangements in octocorals, and to test the suitability of using mitochondrial genomes for higher taxonomic-level phylogenetic reconstructions. Our phylogeny supports three major divisions within the Octocorallia and show that Paragorgiidae is paraphyletic, with Sibogagorgia forming a sister branch to the Coralliidae. Furthermore, Sibogagorgia cauliflora has what is presumed to be the ancestral gene order in octocorals, but the presence of a pair of inverted repeat sequences suggest that this gene order was not conserved but rather evolved back to this apparent ancestral state. Based on this we recommend the resurrection of the family Sibogagorgiidae to fix the paraphyly of the Paragorgiidae. This is the first study to show that in the Octocorallia, mitochondrial gene orders have evolved back to an ancestral state after going through a gene rearrangement, with at least one of the gene orders evolving independently in different lineages. A number of studies have used gene boundaries to determine the type of mitochondrial gene arrangement present. However, our findings suggest that this method known as gene junction screening may miss evolutionary reversals. Additionally, substitution saturation analysis demonstrates that while whole mitochondrial genomes can be used effectively for phylogenetic analyses within Octocorallia, their utility at higher taxonomic levels within Cnidaria is inadequate. Therefore for phylogenetic reconstruction at taxonomic levels higher than subclass within the Cnidaria, nuclear genes will be required, even when whole mitochondrial genomes are available. PMID:25539723

  4. Phylogenetic trees in bioinformatics

    SciTech Connect

    Burr, Tom L

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  5. Entanglement, Invariants, and Phylogenetics

    NASA Astrophysics Data System (ADS)

    Sumner, J. G.

    2007-10-01

    This thesis develops and expands upon known techniques of mathematical physics relevant to the analysis of the popular Markov model of phylogenetic trees required in biology to reconstruct the evolutionary relationships of taxonomic units from biomolecular sequence data. The techniques of mathematical physics are plethora and have been developed for some time. The Markov model of phylogenetics and its analysis is a relatively new technique where most progress to date has been achieved by using discrete mathematics. This thesis takes a group theoretical approach to the problem by beginning with a remarkable mathematical parallel to the process of scattering in particle physics. This is shown to equate to branching events in the evolutionary history of molecular units. The major technical result of this thesis is the derivation of existence proofs and computational techniques for calculating polynomial group invariant functions on a multi-linear space where the group action is that relevant to a Markovian time evolution. The practical results of this thesis are an extended analysis of the use of invariant functions in distance based methods and the presentation of a new reconstruction technique for quartet trees which is consistent with the most general Markov model of sequence evolution.

  6. Patterns of taxonomic, phylogenetic diversity during a long-term succession of forest on the Loess Plateau, China: insights into assembly process

    PubMed Central

    Chai, Yongfu; Yue, Ming; Liu, Xiao; Guo, Yaoxin; Wang, Mao; Xu, Jinshi; Zhang, Chenguang; Chen, Yu; Zhang, Lixia; Zhang, Ruichang

    2016-01-01

    Quantifying the drivers underlying the distribution of biodiversity during succession is a critical issue in ecology and conservation, and also can provide insights into the mechanisms of community assembly. Ninety plots were established in the Loess Plateau region of northern Shaanxi in China. The taxonomic and phylogenetic (alpha and beta) diversity were quantified within six succession stages. Null models were used to test whether phylogenetic distance observed differed from random expectations. Taxonomic beta diversity did not show a regular pattern, while phylogenetic beta diversity decreased throughout succession. The shrub stage occurred as a transition from phylogenetic overdispersion to clustering either for NRI (Net Relatedness Index) or betaNRI. The betaNTI (Nearest Taxon Index) values for early stages were on average phylogenetically random, but for the betaNRI analyses, these stages were phylogenetically overdispersed. Assembly of woody plants differed from that of herbaceous plants during late community succession. We suggest that deterministic and stochastic processes respectively play a role in different aspects of community phylogenetic structure for early succession stage, and that community composition of late succession stage is governed by a deterministic process. In conclusion, the long-lasting evolutionary imprints on the present-day composition of communities arrayed along the succession gradient. PMID:27272407

  7. Patterns of taxonomic, phylogenetic diversity during a long-term succession of forest on the Loess Plateau, China: insights into assembly process.

    PubMed

    Chai, Yongfu; Yue, Ming; Liu, Xiao; Guo, Yaoxin; Wang, Mao; Xu, Jinshi; Zhang, Chenguang; Chen, Yu; Zhang, Lixia; Zhang, Ruichang

    2016-01-01

    Quantifying the drivers underlying the distribution of biodiversity during succession is a critical issue in ecology and conservation, and also can provide insights into the mechanisms of community assembly. Ninety plots were established in the Loess Plateau region of northern Shaanxi in China. The taxonomic and phylogenetic (alpha and beta) diversity were quantified within six succession stages. Null models were used to test whether phylogenetic distance observed differed from random expectations. Taxonomic beta diversity did not show a regular pattern, while phylogenetic beta diversity decreased throughout succession. The shrub stage occurred as a transition from phylogenetic overdispersion to clustering either for NRI (Net Relatedness Index) or betaNRI. The betaNTI (Nearest Taxon Index) values for early stages were on average phylogenetically random, but for the betaNRI analyses, these stages were phylogenetically overdispersed. Assembly of woody plants differed from that of herbaceous plants during late community succession. We suggest that deterministic and stochastic processes respectively play a role in different aspects of community phylogenetic structure for early succession stage, and that community composition of late succession stage is governed by a deterministic process. In conclusion, the long-lasting evolutionary imprints on the present-day composition of communities arrayed along the succession gradient. PMID:27272407

  8. Patterns of taxonomic, phylogenetic diversity during a long-term succession of forest on the Loess Plateau, China: insights into assembly process.

    PubMed

    Chai, Yongfu; Yue, Ming; Liu, Xiao; Guo, Yaoxin; Wang, Mao; Xu, Jinshi; Zhang, Chenguang; Chen, Yu; Zhang, Lixia; Zhang, Ruichang

    2016-01-01

    Quantifying the drivers underlying the distribution of biodiversity during succession is a critical issue in ecology and conservation, and also can provide insights into the mechanisms of community assembly. Ninety plots were established in the Loess Plateau region of northern Shaanxi in China. The taxonomic and phylogenetic (alpha and beta) diversity were quantified within six succession stages. Null models were used to test whether phylogenetic distance observed differed from random expectations. Taxonomic beta diversity did not show a regular pattern, while phylogenetic beta diversity decreased throughout succession. The shrub stage occurred as a transition from phylogenetic overdispersion to clustering either for NRI (Net Relatedness Index) or betaNRI. The betaNTI (Nearest Taxon Index) values for early stages were on average phylogenetically random, but for the betaNRI analyses, these stages were phylogenetically overdispersed. Assembly of woody plants differed from that of herbaceous plants during late community succession. We suggest that deterministic and stochastic processes respectively play a role in different aspects of community phylogenetic structure for early succession stage, and that community composition of late succession stage is governed by a deterministic process. In conclusion, the long-lasting evolutionary imprints on the present-day composition of communities arrayed along the succession gradient.

  9. Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.

    PubMed

    Sánchez, Rubén; Serra, François; Tárraga, Joaquín; Medina, Ignacio; Carbonell, José; Pulido, Luis; de María, Alejandro; Capella-Gutíerrez, Salvador; Huerta-Cepas, Jaime; Gabaldón, Toni; Dopazo, Joaquín; Dopazo, Hernán

    2011-07-01

    Phylemon 2.0 is a new release of the suite of web tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It has been designed as a response to the increasing demand of molecular sequence analyses for experts and non-expert users. Phylemon 2.0 has several unique features that differentiates it from other similar web resources: (i) it offers an integrated environment that enables evolutionary analyses, format conversion, file storage and edition of results; (ii) it suggests further analyses, thereby guiding the users through the web server; and (iii) it allows users to design and save phylogenetic pipelines to be used over multiple genes (phylogenomics). Altogether, Phylemon 2.0 integrates a suite of 30 tools covering sequence alignment reconstruction and trimming; tree reconstruction, visualization and manipulation; and evolutionary hypotheses testing.

  10. The relationship between global and regional distribution diminishes among phylogenetically basal species.

    PubMed

    Prinzing, Andreas; Ozinga, Wim A; Durka, Walter

    2004-12-01

    Phylogenetic legacy and phylogenetic trends affect the ecology of species-except, apparently, for the width of their distribution. As a result, "macroecological" patterns of species distributions emerge constantly in phylogenetically very distinct species assemblages. The width of the global distribution of species, for instance, constantly correlates positively to the width of their regional distribution. However, such patterns primarily reflect the phylogenetically derived species that dominate most assemblages. Basal species, in contrast, might show different macroecological patterns. We tested the hypothesis that the correlation between global and regional distributions of species diminishes among the phylogenetically basal species. We considered central European higher plants and defined global distribution as the occupancy of global floristic zones, regional distribution as the grid occupancy in Eastern Germany, and phylogenetic position as the rank distance to tree base. We also took into account a number of confounding variables. We found that, across all lineages, the global/regional correlation diminished among basal species. We then reanalyzed 19 lineages separately and always found the same pattern. The pattern reflected both increases in global distributions and decreases in regional distributions among basal species. The results indicate that many basal species face a risk of global or at least regional extinction, but have escaped the downward spiral of mutually reinforcing extinction risks at multiple scales. We suggest that many basal species had much time to expand their global ranges but are presently displaced locally by more derived species. Overall, the study shows that macroecological patterns may not be static and universal, but may undergo macroevolutionary trends. Analyses of macroecological patterns across a phylogeny may thus provide insights into macroevolutionary processes.

  11. Hypnosis, suggestion, and suggestibility: an integrative model.

    PubMed

    Lynn, Steven Jay; Laurence, Jean-Roch; Kirsch, Irving

    2015-01-01

    This article elucidates an integrative model of hypnosis that integrates social, cultural, cognitive, and neurophysiological variables at play both in and out of hypnosis and considers their dynamic interaction as determinants of the multifaceted experience of hypnosis. The roles of these variables are examined in the induction and suggestion stages of hypnosis, including how they are related to the experience of involuntariness, one of the hallmarks of hypnosis. It is suggested that studies of the modification of hypnotic suggestibility; cognitive flexibility; response sets and expectancies; the default-mode network; and the search for the neurophysiological correlates of hypnosis, more broadly, in conjunction with research on social psychological variables, hold much promise to further understanding of hypnosis.

  12. Disentangling the phylogenetic and ecological components of spider phenotypic variation.

    PubMed

    Gonçalves-Souza, Thiago; Diniz-Filho, José Alexandre Felizola; Romero, Gustavo Quevedo

    2014-01-01

    An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial to inferring the mechanisms governing the assembly of communities. We evaluated the relative importance of spider phylogenetic relationships and ecological niche (plant morphological variables) to the variation in spider body size and shape by comparing spiders at different scales: (i) between bromeliads and dicot plants (i.e., habitat scale) and (ii) among bromeliads with distinct architectural features (i.e., microhabitat scale). We partitioned the interspecific variation in body size and shape into phylogenetic (that express trait values as expected by phylogenetic relationships among species) and ecological components (that express trait values independent of phylogenetic relationships). At the habitat scale, bromeliad spiders were larger and flatter than spiders associated with the surrounding dicots. At this scale, plant morphology sorted out close related spiders. Our results showed that spider flatness is phylogenetically clustered at the habitat scale, whereas it is phylogenetically overdispersed at the microhabitat scale, although phylogenic signal is present in both scales. Taken together, these results suggest that whereas at the habitat scale selective colonization affect spider body size and shape, at fine scales both selective colonization and adaptive evolution determine spider body shape. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape. We also discussed the relevance in considering multiple scales when studying phylogenetic community structure.

  13. Mitochondrial phylogenetics and evolution of mysticete whales.

    PubMed

    Sasaki, Takeshi; Nikaido, Masato; Hamilton, Healy; Goto, Mutsuo; Kato, Hidehiro; Kanda, Naohisa; Pastene, Luis; Cao, Ying; Fordyce, R; Hasegawa, Masami; Okada, Norihiro

    2005-02-01

    The phylogenetic relationships among baleen whales (Order: Cetacea) remain uncertain despite extensive research in cetacean molecular phylogenetics and a potential morphological sample size of over 2 million animals harvested. Questions remain regarding the number of species and the monophyly of genera, as well as higher order relationships. Here, we approach mysticete phylogeny with complete mitochondrial genome sequence analysis. We determined complete mtDNA sequences of 10 extant Mysticeti species, inferred their phylogenetic relationships, and estimated node divergence times. The mtDNA sequence analysis concurs with previous molecular studies in the ordering of the principal branches, with Balaenidae (right whales) as sister to all other mysticetes base, followed by Neobalaenidae (pygmy right whale), Eschrichtiidae (gray whale), and finally Balaenopteridae (rorquals + humpback whale). The mtDNA analysis further suggests that four lineages exist within the clade of Eschrichtiidae + Balaenopteridae, including a sister relationship between the humpback and fin whales, and a monophyletic group formed by the blue, sei, and Bryde's whales, each of which represents a newly recognized phylogenetic relationship in Mysticeti. We also estimated the divergence times of all extant mysticete species, accounting for evolutionary rate heterogeneity among lineages. When the mtDNA divergence estimates are compared with the mysticete fossil record, several lineages have molecular divergence estimates strikingly older than indicated by paleontological data. We suggest this discrepancy reflects both a large amount of ancestral polymorphism and long generation times of ancestral baleen whale populations.

  14. Phylogenetic conservatism of functional traits in microorganisms.

    PubMed

    Martiny, Adam C; Treseder, Kathleen; Pusch, Gordon

    2013-04-01

    A central question in biology is how biodiversity influences ecosystem functioning. Underlying this is the relationship between organismal phylogeny and the presence of specific functional traits. The relationship is complicated by gene loss and convergent evolution, resulting in the polyphyletic distribution of many traits. In microorganisms, lateral gene transfer can further distort the linkage between phylogeny and the presence of specific functional traits. To identify the phylogenetic conservation of specific traits in microorganisms, we developed a new phylogenetic metric-consenTRAIT-to estimate the clade depth where organisms share a trait. We then analyzed the distribution of 89 functional traits across a broad range of Bacteria and Archaea using genotypic and phenotypic data. A total of 93% of the traits were significantly non-randomly distributed, which suggested that vertical inheritance was generally important for the phylogenetic dispersion of functional traits in microorganisms. Further, traits in microbes were associated with a continuum of trait depths (τD), ranging from a few deep to many shallow clades (average τD: 0.101-0.0011 rRNA sequence dissimilarity). Next, we demonstrated that the dispersion and the depth of clades that contain a trait is correlated with the trait's complexity. Specifically, complex traits encoded by many genes like photosynthesis and methanogenesis were found in a few deep clusters, whereas the ability to use simple carbon substrates was highly phylogenetically dispersed. On the basis of these results, we propose a framework for predicting the phylogenetic conservatism of functional traits depending on the complexity of the trait. This framework enables predicting how variation in microbial composition may affect microbially-mediated ecosystem processes as well as linking phylogenetic and trait-based patterns of biogeography.

  15. PhyloBLAST: facilitating phylogenetic analysis of BLAST results.

    PubMed

    Brinkman, F S; Wan, I; Hancock, R E; Rose, A M; Jones, S J

    2001-04-01

    PhyloBLAST is an internet-accessed application based on CGI/Perl programming that compares a users protein sequence to a SwissProt/TREMBL database using BLAST2 and then allows phylogenetic analyses to be performed on selected sequences from the BLAST output. Flexible features such as ability to input your own multiple sequence alignment and use PHYLIP program options provide additional web-based phylogenetic analysis functionality beyond the analysis of a BLAST result.

  16. Inferring the phylogenetic position of Boa constrictor among the Boinae.

    PubMed

    Burbrink, Frank T

    2005-01-01

    Snakes of the subfamily Boinae are found in Madagascar, the Papuan-Pacific Islands, and the Neotropics. It has been suggested that genera within each of these particular areas do not form monophyletic groups. Further, it was proposed that the New World Boa constrictor is more closely related to boine genera in Madagascar than to boines in the Neotropics. Along with inferring the relationship of all boine genera using data from the cytochrome b gene and morphology, the placement of Boa was also examined. Phylogenetic inferences using maximum likelihood and Bayesian (BI) methods for combined data analyses and separate analyses of DNA sequence and morphological data were conducted. Priors, parametric bootstraps, and the Shimodaira-Hasegawa test were used to examine the previously proposed placement of Boa with Madagascan taxa using these DNA data. DNA data and combined data analyses strongly reject the hypothesis that Boa is more closely related to Old World genera than to other New World genera. Additionally, strong tree support suggests that all species within Madagascar, the Papuan-Pacific Islands, and the Neotropics each form a monophyletic group with respect to their geographic region.

  17. Phylogenetic relationships within the lophophorate lineages (Ectoprocta, Brachiopoda and Phoronida).

    PubMed

    Hausdorf, Bernhard; Helmkampf, Martin; Nesnidal, Maximilian P; Bruchhaus, Iris

    2010-06-01

    We produced two new EST datasets of so far uncovered clades of ectoprocts to investigate the phylogenetic relationships within the lophophorate lineages, Ectoprocta, Brachiopoda and Phoronida. Maximum-likelihood analyses based on 78 ribosomal proteins of 62 metazoan taxa support the monophyly of Ectoprocta and a sister group relationship of Phylactolaemata living in freshwater and the mainly marine Gymnolaemata. Hypotheses suggesting that Ectoprocta is diphyletic with phylactolaemates forming a clade with phoronids or paraphyletic with respect to Entoprocta could be rejected by topology tests. The hypotheses that Stenolaemata are the sister group of all other ectoprocts, that Stenolaemata constitutes a monophyletic group with Cheilostomata, and that Phylactolaemata have been derived from Ctenostomata could also be excluded. However, the hypothesis that Phylactolaemata and Stenolaemata form a monophyletic group could not be rejected. Brachiopoda and Phoronida constitute a monophylum, Brachiozoa. The hypotheses that phoronids are the sister group of articulate or inarticulate brachiopods could be rejected by topology tests, thus confirming the monophyly of Brachiopoda.

  18. Detecting Network Communities: An Application to Phylogenetic Analysis

    PubMed Central

    Andrade, Roberto F. S.; Rocha-Neto, Ivan C.; Santos, Leonardo B. L.; de Santana, Charles N.; Diniz, Marcelo V. C.; Lobão, Thierry Petit; Goés-Neto, Aristóteles; Pinho, Suani T. R.; El-Hani, Charbel N.

    2011-01-01

    This paper proposes a new method to identify communities in generally weighted complex networks and apply it to phylogenetic analysis. In this case, weights correspond to the similarity indexes among protein sequences, which can be used for network construction so that the network structure can be analyzed to recover phylogenetically useful information from its properties. The analyses discussed here are mainly based on the modular character of protein similarity networks, explored through the Newman-Girvan algorithm, with the help of the neighborhood matrix . The most relevant networks are found when the network topology changes abruptly revealing distinct modules related to the sets of organisms to which the proteins belong. Sound biological information can be retrieved by the computational routines used in the network approach, without using biological assumptions other than those incorporated by BLAST. Usually, all the main bacterial phyla and, in some cases, also some bacterial classes corresponded totally (100%) or to a great extent (>70%) to the modules. We checked for internal consistency in the obtained results, and we scored close to 84% of matches for community pertinence when comparisons between the results were performed. To illustrate how to use the network-based method, we employed data for enzymes involved in the chitin metabolic pathway that are present in more than 100 organisms from an original data set containing 1,695 organisms, downloaded from GenBank on May 19, 2007. A preliminary comparison between the outcomes of the network-based method and the results of methods based on Bayesian, distance, likelihood, and parsimony criteria suggests that the former is as reliable as these commonly used methods. We conclude that the network-based method can be used as a powerful tool for retrieving modularity information from weighted networks, which is useful for phylogenetic analysis. PMID:21573202

  19. A phylogenetic approach to disentangling the role of competition and habitat filtering in community assembly of Neotropical forest birds.

    PubMed

    Gómez, Juan Pablo; Bravo, Gustavo A; Brumfield, Robb T; Tello, José G; Cadena, Carlos Daniel

    2010-11-01

    1. Methods that assess patterns of phylogenetic relatedness, as well as character distribution and evolution, allow one to infer the ecological processes involved in community assembly. Assuming niche conservatism, assemblages should shift from phylogenetic clustering to evenness with decreasing geographic scale because the relative importance of mechanisms that shape assemblages is hypothesized to be scale-dependent. Whereas habitat filtering is more likely to act at regional scales because of increased habitat heterogeneity that allows sorting of ecologically similar species in contrasting environments, competition is more likely to act at local scales because low habitat heterogeneity provides few opportunities for niche partitioning. 2. We used species lists to assess assemblage composition, data on ecologically-relevant traits, and a molecular phylogeny, to examine the phylogenetic structure of antbird (Thamnophilidae) assemblages at three different geographical scales: regional (ecoregions), intermediate (100-ha plots) and local (mixed-flocks). In addition, we used patterns of phylogenetic beta diversity and beta diversity to separate the factors that structure antbird assemblages at regional scales. 3. Contrary to previous findings, we found a shift from phylogenetic evenness to clustering with decreasing geographical scale. We argue that this does not reject the hypothesis that habitat filtering is the predominant force in regional community assembly, because analyses of trait evolution and structure indicated a lack of niche conservatism in antbirds. 4. In some cases, phylogenetic evenness at regional scales can be an effect of historical biogeographic processes instead of niche-based processes. However, regional patterns of beta diversity and phylogenetic beta diversity suggested that phylogenetic structure in our study cannot be explained by the history of speciation and dispersal of antbirds, further supporting the habitat-filtering hypothesis. 5. Our

  20. The Independent Evolution Method Is Not a Viable Phylogenetic Comparative Method

    PubMed Central

    2015-01-01

    Phylogenetic comparative methods (PCMs) use data on species traits and phylogenetic relationships to shed light on evolutionary questions. Recently, Smaers and Vinicius suggested a new PCM, Independent Evolution (IE), which purportedly employs a novel model of evolution based on Felsenstein’s Adaptive Peak Model. The authors found that IE improves upon previous PCMs by producing more accurate estimates of ancestral states, as well as separate estimates of evolutionary rates for each branch of a phylogenetic tree. Here, we document substantial theoretical and computational issues with IE. When data are simulated under a simple Brownian motion model of evolution, IE produces severely biased estimates of ancestral states and changes along individual branches. We show that these branch-specific changes are essentially ancestor-descendant or “directional” contrasts, and draw parallels between IE and previous PCMs such as “minimum evolution”. Additionally, while comparisons of branch-specific changes between variables have been interpreted as reflecting the relative strength of selection on those traits, we demonstrate through simulations that regressing IE estimated branch-specific changes against one another gives a biased estimate of the scaling relationship between these variables, and provides no advantages or insights beyond established PCMs such as phylogenetically independent contrasts. In light of our findings, we discuss the results of previous papers that employed IE. We conclude that Independent Evolution is not a viable PCM, and should not be used in comparative analyses. PMID:26683838

  1. From symmetry to asymmetry: Phylogenetic patterns of asymmetry variation in animals and their evolutionary significance

    PubMed Central

    Palmer, A. Richard

    1996-01-01

    Phylogenetic analyses of asymmetry variation offer a powerful tool for exploring the interplay between ontogeny and evolution because (i) conspicuous asymmetries exist in many higher metazoans with widely varying modes of development, (ii) patterns of bilateral variation within species may identify genetically and environmentally triggered asymmetries, and (iii) asymmetries arising at different times during development may be more sensitive to internal cytoplasmic inhomogeneities compared to external environmental stimuli. Using four broadly comparable asymmetry states (symmetry, antisymmetry, dextral, and sinistral), and two stages at which asymmetry appears developmentally (larval and postlarval), I evaluated relations between ontogenetic and phylogenetic patterns of asymmetry variation. Among 140 inferred phylogenetic transitions between asymmetry states, recorded from 11 classes in five phyla, directional asymmetry (dextral or sinistral) evolved directly from symmetrical ancestors proportionally more frequently among larval asymmetries. In contrast, antisymmetry, either as an end state or as a transitional stage preceding directional asymmetry, was confined primarily to postlarval asymmetries. The ontogenetic origin of asymmetry thus significantly influences its subsequent evolution. Furthermore, because antisymmetry typically signals an environmentally triggered asymmetry, the phylogenetic transition from antisymmetry to directional asymmetry suggests that many cases of laterally fixed asymmetries evolved via genetic assimilation. PMID:8962039

  2. Phylogenetic origins of Lophocereus (Cactaceae) and the senita cactus-senita moth pollination mutualism.

    PubMed

    Hartmann, Stefanie; Nason, John D; Bhattacharya, Debashish

    2002-07-01

    Recent ecological research has revealed that the Sonoran Desert columnar cactus Lophocereus and the pyralid moth Upiga virescens form an obligate pollination mutualism, a rare but important case of coevolution. To investigate the phylogenetic origins of this unusual pollination system, we used molecular sequence data to reconstruct the phylogeny of the four taxa within the genus Lophocereus and to determine the phylogenetic position of Lophocereus within the North American columnar cacti (tribe Pachycereeae). Our analysis included Lophocereus, six Pachycereus species, Carnegiea gigantea, and Neobuxbaumia tetetzo within the subtribe Pachycereinae, and Stenocereus thurberi as an outgroup within the Stenocereinae. Extensive screening of chloroplast and mitochondrial genomes failed to reveal sequence variation within Lophocereus. At a deeper phylogenetic level, however, we found strong support for the placement of Lophocereus within Pachycereus as sister group to the hummingbird-pollinated P. marginatus. We discuss possible hypotheses that may explain the transition from bat pollination (ancestral) to moth and hummingbird pollination in Lophocereus and P. marginatus, respectively. Additional phylogenetic analyses suggest that the genus Pachycereus should be expanded to include Lophocereus, Carnegiea, Neobuxbaumia, and perhaps other species, whereas P. hollianus may need to be excluded from this clade. Future study will be needed to test taxonomic distinctions within Lophocereus, to test for parallel cladogenesis between phylogroups within Lophocereus and Upiga, and to fully delineate the genus Pachycereus and relationships among genera in the Pachycereinae.

  3. Phylogenetic Information Content of Copepoda Ribosomal DNA Repeat Units: ITS1 and ITS2 Impact

    PubMed Central

    Zagoskin, Maxim V.; Lazareva, Valentina I.; Grishanin, Andrey K.; Mukha, Dmitry V.

    2014-01-01

    The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that the Mesocyclops, Thermocyclops, and Macrocyclops genera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals. PMID:25215300

  4. A molecular phylogenetic analysis of strombid gastropod morphological diversity.

    PubMed

    Latiolais, Jared M; Taylor, Michael S; Roy, Kaustuv; Hellberg, Michael E

    2006-11-01

    The shells of strombid gastropods show a wide variety of forms, ranging from small and fusiform to large and elaborately ornamented with a strongly flared outer lip. Here, we present the first species-level molecular phylogeny for strombids and use the resulting phylogenetic framework to explore relationships between species richness and morphological diversity. We use portions of one nuclear (325 bp of histone H3) and one mitochondrial (640 bp of cytochrome oxidase I, COI) gene to infer relationships within the two most species-rich genera in the Strombidae: Strombus and Lambis. We include 32 species of Strombus, representing 10 of 11 extant subgenera, and 3 of the 9 species of Lambis, representing 2 of 3 extant subgenera. Maximum likelihood and Bayesian analyses of COI and of H3 and COI combined suggest Lambis is nested within a paraphyletic Strombus. Eastern Pacific and western Atlantic species of Strombus form a relatively recent monophyletic radiation within an older, paraphyletic Indo-West Pacific grade. Morphological diversity of subclades scales positively with species richness but does not show evidence of strong phylogenetic constraints. PMID:16839783

  5. Phylogenetic position of Guihaiothamnus (Rubiaceae): its evolutionary and ecological implications.

    PubMed

    Xie, Peiwu; Tu, Tieyao; Razafimandimbison, Sylvain G; Zhu, Chengjie; Zhang, Dianxiang

    2014-09-01

    Guihaiothamnus (Rubiaceae) is an enigmatic, monotypic genus endemic to southwestern China. Its generic status has never been doubted because it is morphologically unique by having rosette habit, showy, long-corolla-tubed flowers, and multi-seeded indehiscent berry-like fruits. The genus has been postulated to be a relict in the broad-leaved forests of China, and to be related to the genus Wendlandia, which was placed in the subfamily Cinchonoideae and recently classified in the tribe Augusteae of the subfamily Dialypetalanthoideae. Using combined evidence from palynology, cytology, and DNA sequences of nuclear ITS and four plastid markers (rps16, trnT-F, ndhF, rbcL), we assessed the phylogenetic position of Guihaiothamnus in Rubiaceae. Our molecular phylogenetic analyses placed the genus deeply nested within Wendlandia. This relationship is corroborated by evidence from palynology and cytology. Using a relaxed molecular clock method based on five fossil records, we dated the stem age of Wendlandia to be 17.46 my and, the split between G. acaulis and related Wendlandia species in southwestern China to be 2.11mya. This young age, coupled with the derived position in Wendlandia, suggests an evolutionary derivation rather than an evolutionary relict of G. acaulis. Its rosette habit and large showy flowers, which are very distinctive from other Wendlandias, are interpreted as a result of recent rapid adaptation to rock and cliff habitats.

  6. Phylogenetic position of Multicilia marina and the evolution of Amoebozoa.

    PubMed

    Nikolaev, Sergey I; Berney, Cédric; Petrov, Nikolai B; Mylnikov, Alexandre P; Fahrni, José F; Pawlowski, Jan

    2006-06-01

    Recent molecular phylogenetic studies have led to the erection of the phylum Amoebozoa, uniting naked and testate lobose amoebae, the mycetozoan slime moulds and amitochondriate amoeboid protists (Archamoebae). Molecular data together with ultrastructural evidence have suggested a close relationship between Mycetozoa and Archamoebae, classified together in the Conosea, which was named after the cone of microtubules that, when present, is characteristic of their kinetids. However, the relationships of conoseans to other amoebozoans remain unclear. Here, we obtained the complete small-subunit (SSU) rRNA gene sequence (2746 bp) of the enigmatic, multiflagellated protist Multicilia marina, which has formerly been classified either in a distinct phylum, Multiflagellata, or among lobose amoebae. Our study clearly shows that Multicilia marina belongs to the Amoebozoa. Phylogenetic analyses including 60 amoebozoan SSU rRNA gene sequences revealed that Multicilia marina branches at the base of the Conosea, together with another flagellated amoebozoan, Phalansterium solitarium, as well as with Gephyramoeba sp., Filamoeba nolandi and two unidentified amoebae. This is the first report showing strong support for a clade containing all flagellated amoebozoans and we discuss the position of the root of the phylum Amoebozoa in the light of this result. PMID:16738126

  7. Phylogenetic analysis of burkholderia species by multilocus sequence analysis.

    PubMed

    Estrada-de los Santos, Paulina; Vinuesa, Pablo; Martínez-Aguilar, Lourdes; Hirsch, Ann M; Caballero-Mellado, Jesús

    2013-07-01

    Burkholderia comprises more than 60 species of environmental, clinical, and agro-biotechnological relevance. Previous phylogenetic analyses of 16S rRNA, recA, gyrB, rpoB, and acdS gene sequences as well as genome sequence comparisons of different Burkholderia species have revealed two major species clusters. In this study, we undertook a multilocus sequence analysis of 77 type and reference strains of Burkholderia using atpD, gltB, lepA, and recA genes in combination with the 16S rRNA gene sequence and employed maximum likelihood and neighbor-joining criteria to test this further. The phylogenetic analysis revealed, with high supporting values, distinct lineages within the genus Burkholderia. The two large groups were named A and B, whereas the B. rhizoxinica/B. endofungorum, and B. andropogonis groups consisted of two and one species, respectively. The group A encompasses several plant-associated and saprophytic bacterial species. The group B comprises the B. cepacia complex (opportunistic human pathogens), the B. pseudomallei subgroup, which includes both human and animal pathogens, and an assemblage of plant pathogenic species. The distinct lineages present in Burkholderia suggest that each group might represent a different genus. However, it will be necessary to analyze the full set of Burkholderia species and explore whether enough phenotypic features exist among the different clusters to propose that these groups should be considered separate genera.

  8. Phylogenetic position of Multicilia marina and the evolution of Amoebozoa.

    PubMed

    Nikolaev, Sergey I; Berney, Cédric; Petrov, Nikolai B; Mylnikov, Alexandre P; Fahrni, José F; Pawlowski, Jan

    2006-06-01

    Recent molecular phylogenetic studies have led to the erection of the phylum Amoebozoa, uniting naked and testate lobose amoebae, the mycetozoan slime moulds and amitochondriate amoeboid protists (Archamoebae). Molecular data together with ultrastructural evidence have suggested a close relationship between Mycetozoa and Archamoebae, classified together in the Conosea, which was named after the cone of microtubules that, when present, is characteristic of their kinetids. However, the relationships of conoseans to other amoebozoans remain unclear. Here, we obtained the complete small-subunit (SSU) rRNA gene sequence (2746 bp) of the enigmatic, multiflagellated protist Multicilia marina, which has formerly been classified either in a distinct phylum, Multiflagellata, or among lobose amoebae. Our study clearly shows that Multicilia marina belongs to the Amoebozoa. Phylogenetic analyses including 60 amoebozoan SSU rRNA gene sequences revealed that Multicilia marina branches at the base of the Conosea, together with another flagellated amoebozoan, Phalansterium solitarium, as well as with Gephyramoeba sp., Filamoeba nolandi and two unidentified amoebae. This is the first report showing strong support for a clade containing all flagellated amoebozoans and we discuss the position of the root of the phylum Amoebozoa in the light of this result.

  9. Phylogenetic analysis of the formin homology 2 domain.

    PubMed

    Higgs, Henry N; Peterson, Kevin J

    2005-01-01

    Formin proteins are key regulators of eukaryotic actin filament assembly and elongation, and many species possess multiple formin isoforms. A nomenclature system based on fundamental features would be desirable, to aid the rapid identification and characterization of novel formins. In this article, we attempt to systematize the formin family by performing phylogenetic analyses of the formin homology 2 (FH2) domain, an independently folding region common to all formins, which alone can influence actin dynamics. Through database searches, we identify 101 FH2 domains from 26 eukaryotic species, including 15 in mice. Sequence alignments reveal a highly conserved yeast-specific insert in the "knob loop" region of the FH2 domain, with unknown functional consequences. Phylogenetic analysis using minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML) algorithms strongly supports the existence of seven metazoan groups. Yeast FH2 domains segregate from all other eukaryotes, including metazoans, other fungi, plants, and protists. Sequence comparisons of non-FH2 regions support relationships between three metazoan groups (Dia, DAAM, and FRL) and examine previously identified coiled-coil and Diaphanous auto-regulatory domain sequences. This analysis allows for a formin nomenclature system based on sequence relationships, as well as suggesting strategies for the determination of biochemical and cellular activities of these proteins.

  10. Homologous recombination in bovine pestiviruses. Phylogenetic and statistic evidence.

    PubMed

    Jones, Leandro Roberto; Weber, E Laura

    2004-12-01

    Bovine pestiviruses (Bovine Viral Diarrea Virus 1 (BVDV 1) and Bovine Viral Diarrea Virus 2 (BVDV 2)) belong to the genus Pestivirus (Flaviviridae), which is composed of positive stranded RNA viruses causing significant economic losses world-wide. We used phylogenetic and bootstrap analyses to systematically scan alignments of previously sequenced genomes in order to explore further the evolutionary mechanisms responsible for variation in the virus. Previously published data suggested that homologous crossover might be one of the mechanisms responsible for the genomic rearrangements observed in cytopathic (cp) strains of bovine pestiviruses. Nevertheless, homologous recombination involves not just homologous crossovers, but also replacement of a homologous region of the acceptor RNA. Furthermore, cytopathic strains represent dead paths in evolution, since they are isolated exclusively from the fatal cases of mucosal disease. Herein, we report evidence of homologous inter-genotype recombination in the genome of a non-cytopathic (ncp) strain of Bovine Viral Diarrea Virus 1, the type species of the genus Pestivirus. We also show that intra-genotype homologous recombination might be a common phenomenon in both species of Pestivirus. This evidence demonstrates that homologous recombination contribute to the diversification of bovine pestiviruses in nature. Implications for virus evolution, taxonomy and phylogenetics are discussed.

  11. Reconstructing phylogenetic networks using maximum parsimony.

    PubMed

    Nakhleh, Luay; Jin, Guohua; Zhao, Fengmei; Mellor-Crummey, John

    2005-01-01

    Phylogenies - the evolutionary histories of groups of organisms - are one of the most widely used tools throughout the life sciences, as well as objects of research within systematics, evolutionary biology, epidemiology, etc. Almost every tool devised to date to reconstruct phylogenies produces trees; yet it is widely understood and accepted that trees oversimplify the evolutionary histories of many groups of organims, most prominently bacteria (because of horizontal gene transfer) and plants (because of hybrid speciation). Various methods and criteria have been introduced for phylogenetic tree reconstruction. Parsimony is one of the most widely used and studied criteria, and various accurate and efficient heuristics for reconstructing trees based on parsimony have been devised. Jotun Hein suggested a straightforward extension of the parsimony criterion to phylogenetic networks. In this paper we formalize this concept, and provide the first experimental study of the quality of parsimony as a criterion for constructing and evaluating phylogenetic networks. Our results show that, when extended to phylogenetic networks, the parsimony criterion produces promising results. In a great majority of the cases in our experiments, the parsimony criterion accurately predicts the numbers and placements of non-tree events.

  12. Phylogenomic Analyses Support Traditional Relationships within Cnidaria.

    PubMed

    Zapata, Felipe; Goetz, Freya E; Smith, Stephen A; Howison, Mark; Siebert, Stefan; Church, Samuel H; Sanders, Steven M; Ames, Cheryl Lewis; McFadden, Catherine S; France, Scott C; Daly, Marymegan; Collins, Allen G; Haddock, Steven H D; Dunn, Casey W; Cartwright, Paulyn

    2015-01-01

    Cnidaria, the sister group to Bilateria, is a highly diverse group of animals in terms of morphology, lifecycles, ecology, and development. How this diversity originated and evolved is not well understood because phylogenetic relationships among major cnidarian lineages are unclear, and recent studies present contrasting phylogenetic hypotheses. Here, we use transcriptome data from 15 newly-sequenced species in combination with 26 publicly available genomes and transcriptomes to assess phylogenetic relationships among major cnidarian lineages. Phylogenetic analyses using different partition schemes and models of molecular evolution, as well as topology tests for alternative phylogenetic relationships, support the monophyly of Medusozoa, Anthozoa, Octocorallia, Hydrozoa, and a clade consisting of Staurozoa, Cubozoa, and Scyphozoa. Support for the monophyly of Hexacorallia is weak due to the equivocal position of Ceriantharia. Taken together, these results further resolve deep cnidarian relationships, largely support traditional phylogenetic views on relationships, and provide a historical framework for studying the evolutionary processes involved in one of the most ancient animal radiations.

  13. Quartets and unrooted phylogenetic networks.

    PubMed

    Gambette, Philippe; Berry, Vincent; Paul, Christophe

    2012-08-01

    Phylogenetic networks were introduced to describe evolution in the presence of exchanges of genetic material between coexisting species or individuals. Split networks in particular were introduced as a special kind of abstract network to visualize conflicts between phylogenetic trees which may correspond to such exchanges. More recently, methods were designed to reconstruct explicit phylogenetic networks (whose vertices can be interpreted as biological events) from triplet data. In this article, we link abstract and explicit networks through their combinatorial properties, by introducing the unrooted analog of level-k networks. In particular, we give an equivalence theorem between circular split systems and unrooted level-1 networks. We also show how to adapt to quartets some existing results on triplets, in order to reconstruct unrooted level-k phylogenetic networks. These results give an interesting perspective on the combinatorics of phylogenetic networks and also raise algorithmic and combinatorial questions.

  14. Quartets and unrooted phylogenetic networks.

    PubMed

    Gambette, Philippe; Berry, Vincent; Paul, Christophe

    2012-08-01

    Phylogenetic networks were introduced to describe evolution in the presence of exchanges of genetic material between coexisting species or individuals. Split networks in particular were introduced as a special kind of abstract network to visualize conflicts between phylogenetic trees which may correspond to such exchanges. More recently, methods were designed to reconstruct explicit phylogenetic networks (whose vertices can be interpreted as biological events) from triplet data. In this article, we link abstract and explicit networks through their combinatorial properties, by introducing the unrooted analog of level-k networks. In particular, we give an equivalence theorem between circular split systems and unrooted level-1 networks. We also show how to adapt to quartets some existing results on triplets, in order to reconstruct unrooted level-k phylogenetic networks. These results give an interesting perspective on the combinatorics of phylogenetic networks and also raise algorithmic and combinatorial questions. PMID:22809417

  15. Possible sister groups and phylogenetic relationships among selected North Pacific and North Atlantic Rhodophyta

    NASA Astrophysics Data System (ADS)

    Lindstrom, Sandra C.

    1987-09-01

    Although the cool temperate (boreal) waters of the N. Pacific and N. Atlantic share many similar if not identical species, there have been few studies to test the identity of these species pairs. Whereas such tests are important from a taxonomic perspective, they tell us little if anything about biogeographic relationships. A more useful approach is one employing phylogenetic systematics (cladistics). The interpretation of phylogenetic diagrams (cladograms) in terms of biogeographic area relationships is explained. It is argued that cladistic analyses of taxa occurring in the cool temperate waters of the northern oceans can provide biogeographic tracks, which in turn can suggest the origins and migrations of species and possibly even floras. A number of cool temperate taxa that appear particularly amenable to this approach are discussed, including genera in the Palmariaceae, Corallinaceae, Dumontiaceae, Solieriaceae, Petrocelidaceae, Ceramiaceae and Rhodomelaceae.

  16. Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach.

    PubMed

    Erickson, David L; Jones, Frank A; Swenson, Nathan G; Pei, Nancai; Bourg, Norman A; Chen, Wenna; Davies, Stuart J; Ge, Xue-Jun; Hao, Zhanqing; Howe, Robert W; Huang, Chun-Lin; Larson, Andrew J; Lum, Shawn K Y; Lutz, James A; Ma, Keping; Meegaskumbura, Madhava; Mi, Xiangcheng; Parker, John D; Fang-Sun, I; Wright, S Joseph; Wolf, Amy T; Ye, W; Xing, Dingliang; Zimmerman, Jess K; Kress, W John

    2014-01-01

    phylogenetic diversity in the mega-phylogeny were more consistent, thereby removing a potential source of bias at the plot-level, and demonstrating the value of assessing phylogenetic relationships simultaneously within a mega-phylogeny. An unexpected result of the comparisons among plots based on the mega-phylogeny was that the communities in the ForestGEO plots in general appear to be assemblages of more closely related species than expected by chance, and that differentiation among communities is very low, suggesting deep floristic connections among communities and new avenues for future analyses in community ecology. PMID:25414723

  17. Open to Suggestion.

    ERIC Educational Resources Information Center

    Journal of Reading, 1987

    1987-01-01

    Offers (1) suggestions for improving college students' study skills; (2) a system for keeping track of parent, teacher, and community contacts; (3) suggestions for motivating students using tic tac toe; (4) suggestions for using etymology to improve word retention; (5) a word search grid; and (6) suggestions for using postcards in remedial reading…

  18. Are Victoria West cores "proto-Levallois"? A phylogenetic assessment.

    PubMed

    Lycett, Stephen J

    2009-02-01

    Cores from South Africa assigned to the "Victoria West" industry have long been purported as a "proto-Levallois" core form, and thus regarded as ancestral to the Levallois prepared core technologies of the Middle Paleolithic and African Middle Stone Age. Similarities in form between Victoria West cores, in terms of surface morphology and the removal of large flakes from a prepared surface, led to hypothesized schemes of technological evolution from Victoria West cores through to fully developed Levallois cores. However, the phylogenetic basis of this Victoria West "proto-Levallois" hypothesis, and the assumptions of phylogenetic homology upon which it rests, have never been tested formally. In recent years, archaeologists have begun to use phylogenetic methods drawn from biology to test hypotheses of technological and cultural evolution. Here, the phylogenetic assumptions of the Victoria West "proto-Levallois" hypothesis are tested directly using a cladistic (maximum parsimony) protocol. The cladistic analyses indicate that Victoria West cores are not the basal sister taxon of a Levallois clade, as predicted by the proto-Levallois hypothesis. Moreover, character analyses demonstrate that several characters relating to core surfaces and flake scar morphology are not phylogenetically homologous, but result from convergent technological evolution within the Acheulean techno-complex. Post hoc analyses further determine that these results are not confounded by choice of outgroup or raw material factors. The results were also shown to be robust on the basis of the ensemble retention index statistic, bootstrap analyses, and permutation tests. Hence, it is concluded that Victoria West cores do not represent a "proto-Levallois" core form, and that the term "para-Levallois" should more correctly be applied on phylogenetic grounds. It is further argued that even in cases where different technologies are found to share phylogenetically homologous features, use of the term

  19. Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum Cnidaria

    PubMed Central

    2008-01-01

    Background Polypodium hydriforme is a parasite with an unusual life cycle and peculiar morphology, both of which have made its systematic position uncertain. Polypodium has traditionally been considered a cnidarian because it possesses nematocysts, the stinging structures characteristic of this phylum. However, recent molecular phylogenetic studies using 18S rDNA sequence data have challenged this interpretation, and have shown that Polypodium is a close relative to myxozoans and together they share a closer affinity to bilaterians than cnidarians. Due to the variable rates of 18S rDNA sequences, these results have been suggested to be an artifact of long-branch attraction (LBA). A recent study, using multiple protein coding markers, shows that the myxozoan Buddenbrockia, is nested within cnidarians. Polypodium was not included in this study. To further investigate the phylogenetic placement of Polypodium, we have performed phylogenetic analyses of metazoans with 18S and partial 28S rDNA sequences in a large dataset that includes Polypodium and a comprehensive sampling of cnidarian taxa. Results Analyses of a combined dataset of 18S and partial 28S sequences, and partial 28S alone, support the placement of Polypodium within Cnidaria. Removal of the long-branched myxozoans from the 18S dataset also results in Polypodium being nested within Cnidaria. These results suggest that previous reports showing that Polypodium and Myxozoa form a sister group to Bilateria were an artifact of long-branch attraction. Conclusion By including 28S rDNA sequences and a comprehensive sampling of cnidarian taxa, we demonstrate that previously conflicting hypotheses concerning the phylogenetic placement of Polypodium can be reconciled. Specifically, the data presented provide evidence that Polypodium is indeed a cnidarian and is either the sister taxon to Hydrozoa, or part of the hydrozoan clade, Leptothecata. The former hypothesis is consistent with the traditional view that Polypodium

  20. Neogastropod phylogenetic relationships based on entire mitochondrial genomes

    PubMed Central

    Cunha, Regina L; Grande, Cristina; Zardoya, Rafael

    2009-01-01

    Background The Neogastropoda is a highly diversified group of predatory marine snails (Gastropoda: Caenogastropoda). Traditionally, its monophyly has been widely accepted based on several morphological synapomorphies mostly related with the digestive system. However, recent molecular phylogenetic studies challenged the monophyly of Neogastropoda due to the inclusion of representatives of other caenogastropod lineages (e.g. Littorinimorpha) within the group. Neogastropoda has been classified into up to six superfamilies including Buccinoidea, Muricoidea, Olivoidea, Pseudolivoidea, Conoidea, and Cancellarioidea. Phylogenetic relationships among neogastropod superfamilies remain unresolved. Results The complete mitochondrial (mt) genomes of seven Neogastropoda (Bolinus brandaris, Cancellaria cancellata, Conus borgesi, Cymbium olla, Fusiturris similis, Nassarius reticulatus, and Terebra dimidiata) and of the tonnoidean Cymatium parthenopeum (Littorinimorpha), a putative sister group to Neogastropoda, were sequenced. In addition, the partial sequence of the mitochondrial genome of the calyptraeoidean Calyptraea chinensis (Littorinimorpha) was also determined. All sequenced neogastropod mt genomes shared a highly conserved gene order with only two instances of tRNA gene translocation. Phylogenetic relationships of Neogastropoda were inferred based on the 13 mt protein coding genes (both at the amino acid and nucleotide level) of all available caenogastropod mitochondrial genomes. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic analyses failed to recover the monophyly of Neogastropoda due to the inclusion of the tonnoidean Cymatium parthenopeum within the group. At the superfamily level, all phylogenetic analyses questioned the taxonomic validity of Muricoidea, whereas the monophyly of Conoidea was supported by most phylogenetic analyses, albeit weakly. All analyzed families were recovered as monophyletic except Turridae due to the inclusion of Terebridae

  1. Species names in phylogenetic nomenclature.

    PubMed

    Cantino, P D; Bryant, H N; de Queiroz, K; Donoghue, M J; Eriksson, T; Hillis, D M; Lee, M S

    1999-12-01

    Linnaean binomial nomenclature is logically incompatible with the phylogenetic nomenclature of de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449-480): The former is based on the concept of genus, thus making this rank mandatory, while the latter is based on phylogenetic definitions and requires the abandonment of mandatory ranks. Thus, if species are to receive names under phylogenetic nomenclature, a different method must be devised to name them. Here, 13 methods for naming species in the context of phylogenetic nomenclature are contrasted with each other and with Linnaean binomials. A fundamental dichotomy among the proposed methods distinguishes those that retain the entire binomial of a preexisting species name from those that retain only the specific epithet. Other relevant issues include the stability, uniqueness, and ease of pronunciation of species names; their capacity to convey phylogenetic information; and the distinguishability of species names that are governed by a code of phylogenetic nomenclature both from clade names and from species names governed by the current codes. No method is ideal. Each has advantages and drawbacks, and preference for one option over another will be influenced by one's evaluation of the relative importance of the pros and cons for each. Moreover, sometimes the same feature is viewed as an advantage by some and a drawback by others. Nevertheless, all of the proposed methods for naming species in the context of phylogenetic nomenclature provide names that are more stable than Linnaean binomials. PMID:12066299

  2. Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution.

    PubMed

    Khang, Tsung Fei; Soo, Oi Yoon Michelle; Tan, Wooi Boon; Lim, Lee Hong Susan

    2016-01-01

    Background. Anchors are one of the important attachment appendages for monogenean parasites. Common descent and evolutionary processes have left their mark on anchor morphometry, in the form of patterns of shape and size variation useful for systematic and evolutionary studies. When combined with morphological and molecular data, analysis of anchor morphometry can potentially answer a wide range of biological questions. Materials and Methods. We used data from anchor morphometry, body size and morphology of 13 Ligophorus (Monogenea: Ancyrocephalidae) species infecting two marine mugilid (Teleostei: Mugilidae) fish hosts: Moolgarda buchanani (Bleeker) and Liza subviridis (Valenciennes) from Malaysia. Anchor shape and size data (n = 530) were generated using methods of geometric morphometrics. We used 28S rRNA, 18S rRNA, and ITS1 sequence data to infer a maximum likelihood phylogeny. We discriminated species using principal component and cluster analysis of shape data. Adams's K mult was used to detect phylogenetic signal in anchor shape. Phylogeny-correlated size and shape changes were investigated using continuous character mapping and directional statistics, respectively. We assessed morphological constraints in anchor morphometry using phylogenetic regression of anchor shape against body size and anchor size. Anchor morphological integration was studied using partial least squares method. The association between copulatory organ morphology and anchor shape and size in phylomorphospace was used to test the Rohde-Hobbs hypothesis. We created monogeneaGM, a new R package that integrates analyses of monogenean anchor geometric morphometric data with morphological and phylogenetic data. Results. We discriminated 12 of the 13 Ligophorus species using anchor shape data. Significant phylogenetic signal was detected in anchor shape. Thus, we discovered new morphological characters based on anchor shaft shape, the length between the inner root point and the outer root

  3. Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution

    PubMed Central

    Soo, Oi Yoon Michelle; Tan, Wooi Boon; Lim, Lee Hong Susan

    2016-01-01

    Background. Anchors are one of the important attachment appendages for monogenean parasites. Common descent and evolutionary processes have left their mark on anchor morphometry, in the form of patterns of shape and size variation useful for systematic and evolutionary studies. When combined with morphological and molecular data, analysis of anchor morphometry can potentially answer a wide range of biological questions. Materials and Methods. We used data from anchor morphometry, body size and morphology of 13 Ligophorus (Monogenea: Ancyrocephalidae) species infecting two marine mugilid (Teleostei: Mugilidae) fish hosts: Moolgarda buchanani (Bleeker) and Liza subviridis (Valenciennes) from Malaysia. Anchor shape and size data (n = 530) were generated using methods of geometric morphometrics. We used 28S rRNA, 18S rRNA, and ITS1 sequence data to infer a maximum likelihood phylogeny. We discriminated species using principal component and cluster analysis of shape data. Adams’s Kmult was used to detect phylogenetic signal in anchor shape. Phylogeny-correlated size and shape changes were investigated using continuous character mapping and directional statistics, respectively. We assessed morphological constraints in anchor morphometry using phylogenetic regression of anchor shape against body size and anchor size. Anchor morphological integration was studied using partial least squares method. The association between copulatory organ morphology and anchor shape and size in phylomorphospace was used to test the Rohde-Hobbs hypothesis. We created monogeneaGM, a new R package that integrates analyses of monogenean anchor geometric morphometric data with morphological and phylogenetic data. Results. We discriminated 12 of the 13 Ligophorus species using anchor shape data. Significant phylogenetic signal was detected in anchor shape. Thus, we discovered new morphological characters based on anchor shaft shape, the length between the inner root point and the outer root

  4. Towards a better understanding of Apis mellifera and Varroa destructor microbiomes: introducing 'phyloh' as a novel phylogenetic diversity analysis tool.

    PubMed

    Sandionigi, A; Vicario, S; Prosdocimi, E M; Galimberti, A; Ferri, E; Bruno, A; Balech, B; Mezzasalma, V; Casiraghi, M

    2015-07-01

    The study of diversity in biological communities is an intriguing field. Huge amount of data are nowadays available (provided by the innovative DNA sequencing techniques), and management, analysis and display of results are not trivial. Here, we propose for the first time the use of phylogenetic entropy as a measure of bacterial diversity in studies of microbial community structure. We then compared our new method (i.e. the web tool phyloh) for partitioning phylogenetic diversity with the traditional approach in diversity analyses of bacteria communities. We tested phyloh to characterize microbiome in the honeybee (Apis mellifera, Insecta: Hymenoptera) and its parasitic mite varroa (Varroa destructor, Arachnida: Parasitiformes). The rationale is that the comparative analysis of honeybee and varroa microbiomes could open new perspectives concerning the role of the parasites on honeybee colonies health. Our results showed a dramatic change of the honeybee microbiome when varroa occurs, suggesting that this parasite is able to influence host microbiome. Among the different approaches used, only the entropy method, in conjunction with phylogenetic constraint as implemented in phyloh, was able to discriminate varroa microbiome from that of parasitized honeybees. In conclusion, we foresee that the use of phylogenetic entropy could become a new standard in the analyses of community structure, in particular to prove the contribution of each biological entity to the overall diversity.

  5. Genome-wide analysis of the cyclin family in Arabidopsis and comparative phylogenetic analysis of plant cyclin-like proteins.

    PubMed

    Wang, Guanfang; Kong, Hongzhi; Sun, Yujin; Zhang, Xiaohong; Zhang, Wei; Altman, Naomi; DePamphilis, Claude W; Ma, Hong

    2004-06-01

    Cyclins are primary regulators of the activity of cyclin-dependent kinases, which are known to play critical roles in controlling eukaryotic cell cycle progression. While there has been extensive research on cell cycle mechanisms and cyclin function in animals and yeasts, only a small number of plant cyclins have been characterized functionally. In this paper, we describe an exhaustive search for cyclin genes in the Arabidopsis genome and among available sequences from other vascular plants. Based on phylogenetic analysis, we define 10 classes of plant cyclins, four of which are plant-specific, and a fifth is shared between plants and protists but not animals. Microarray and reverse transcriptase-polymerase chain reaction analyses further provide expression profiles of cyclin genes in different tissues of wild-type Arabidopsis plants. Comparative phylogenetic studies of 174 plant cyclins were also performed. The phylogenetic results imply that the cyclin gene family in plants has experienced more gene duplication events than in animals. Expression patterns and phylogenetic analyses of Arabidopsis cyclin genes suggest potential gene redundancy among members belonging to the same group. We discuss possible divergence and conservation of some plant cyclins. Our study provides an opportunity to rapidly assess the position of plant cyclin genes in terms of evolution and classification, serving as a guide for further functional study of plant cyclins.

  6. Posterior Predictive Bayesian Phylogenetic Model Selection

    PubMed Central

    Lewis, Paul O.; Xie, Wangang; Chen, Ming-Hui; Fan, Yu; Kuo, Lynn

    2014-01-01

    We present two distinctly different posterior predictive approaches to Bayesian phylogenetic model selection and illustrate these methods using examples from green algal protein-coding cpDNA sequences and flowering plant rDNA sequences. The Gelfand–Ghosh (GG) approach allows dissection of an overall measure of model fit into components due to posterior predictive variance (GGp) and goodness-of-fit (GGg), which distinguishes this method from the posterior predictive P-value approach. The conditional predictive ordinate (CPO) method provides a site-specific measure of model fit useful for exploratory analyses and can be combined over sites yielding the log pseudomarginal likelihood (LPML) which is useful as an overall measure of model fit. CPO provides a useful cross-validation approach that is computationally efficient, requiring only a sample from the posterior distribution (no additional simulation is required). Both GG and CPO add new perspectives to Bayesian phylogenetic model selection based on the predictive abilities of models and complement the perspective provided by the marginal likelihood (including Bayes Factor comparisons) based solely on the fit of competing models to observed data. [Bayesian; conditional predictive ordinate; CPO; L-measure; LPML; model selection; phylogenetics; posterior predictive.] PMID:24193892

  7. PAML 4: phylogenetic analysis by maximum likelihood.

    PubMed

    Yang, Ziheng

    2007-08-01

    PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html).

  8. Modularized evolution in archaeal methanogens phylogenetic forest.

    PubMed

    Li, Jun; Wong, Chi-Fat; Wong, Mabel Ting; Huang, He; Leung, Frederick C

    2014-12-09

    Methanogens are methane-producing archaea that plays a key role in the global carbon cycle. To date, the evolutionary history of methanogens and closely related nonmethanogen species remains unresolved among studies conducted upon different genetic markers, attributing to horizontal gene transfers (HGTs). With an effort to decipher both congruent and conflicting evolutionary events, reconstruction of coevolved gene clusters and hierarchical structure in the archaeal methanogen phylogenetic forest, comprehensive evolution, and network analyses were performed upon 3,694 gene families from 41 methanogens and 33 closely related archaea. Our results show that 1) greater than 50% of genes are in topological dissonance with others; 2) the prevalent interorder HGTs, even for core genes, in methanogen genomes led to their scrambled phylogenetic relationships; 3) most methanogenesis-related genes have experienced at least one HGT; 4) greater than 20% of the genes in methanogen genomes were transferred horizontally from other archaea, with genes involved in cell-wall synthesis and defense system having been transferred most frequently; 5) the coevolution network contains seven statistically robust modules, wherein the central module has the highest average node strength and comprises a majority of the core genes; 6) different coevolutionary module genes boomed in different time and evolutionary lineage, constructing diversified pan-genome structures; 7) the modularized evolution is also closely related to the vertical evolution signals and the HGT rate of the genes. Overall, this study presented a modularized phylogenetic forest that describes a combination of complicated vertical and nonvertical evolutionary processes for methanogenic archaeal species.

  9. The evolution of HIV: Inferences using phylogenetics

    PubMed Central

    Castro-Nallar, Eduardo; Pérez-Losada, Marcos; Burton, Gregory F.; Crandall, Keith A.

    2011-01-01

    Molecular phylogenetics has revolutionized the study of not only evolution but also disparate fields such as genomics, bioinformatics, epidemiology, ecology, microbiology, molecular biology and biochemistry. Particularly significant are its achievements in population genetics as a result of the development of coalescent theory, which have contributed to more accurate model-based parameter estimation and explicit hypothesis testing. The study of the evolution of many microorganisms, and HIV in particular, have benefited from these new methodologies. HIV is well suited for such sophisticated population analyses because of its large population sizes, short generation times, high substitution rates and relatively small genomes. All these factors make HIV an ideal and fascinating model to study molecular evolution in real time. Here we review the significant advances made in HIV evolution through the application of phylogenetic approaches. We first examine the relative roles of mutation and recombination on the molecular evolution of HIV and its adaptive response to drug therapy and tissue allocation. We then review some of the fundamental questions in HIV evolution in relation to its origin and diversification and describe some of the insights gained using phylogenies. Finally, we show how phylogenetic analysis has advanced our knowledge of HIV dynamics (i.e., phylodynamics). PMID:22138161

  10. Complete mitochondrial genomes elucidate phylogenetic relationships of the deep-sea octocoral families Coralliidae and Paragorgiidae

    NASA Astrophysics Data System (ADS)

    Figueroa, Diego F.; Baco, Amy R.

    2014-01-01

    In the past decade, molecular phylogenetic analyses of octocorals have shown that the current morphological taxonomic classification of these organisms needs to be revised. The latest phylogenetic analyses show that most octocorals can be divided into three main clades. One of these clades contains the families Coralliidae and Paragorgiidae. These families share several taxonomically important characters and it has been suggested that they may not be monophyletic; with the possibility of the Coralliidae being a derived branch of the Paragorgiidae. Uncertainty exists not only in the relationship of these two families, but also in the classification of the two genera that make up the Coralliidae, Corallium and Paracorallium. Molecular analyses suggest that the genus Corallium is paraphyletic, and it can be divided into two main clades, with the Paracorallium as members of one of these clades. In this study we sequenced the whole mitochondrial genome of five species of Paragorgia and of five species of Corallium to use in a phylogenetic analysis to achieve two main objectives; the first to elucidate the phylogenetic relationship between the Paragorgiidae and Coralliidae and the second to determine whether the genera Corallium and Paracorallium are monophyletic. Our results show that other members of the Coralliidae share the two novel mitochondrial gene arrangements found in a previous study in Corallium konojoi and Paracorallium japonicum; and that the Corallium konojoi arrangement is also found in the Paragorgiidae. Our phylogenetic reconstruction based on all the protein coding genes and ribosomal RNAs of the mitochondrial genome suggest that the Coralliidae are not a derived branch of the Paragorgiidae, but rather a monophyletic sister branch to the Paragorgiidae. While our manuscript was in review a study was published using morphological data and several fragments from mitochondrial genes to redefine the taxonomy of the Coralliidae. Paracorallium was subsumed

  11. Phylogenetics and the Human Microbiome

    PubMed Central

    Matsen, Frederick A.

    2015-01-01

    The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this article, I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work. PMID:25102857

  12. The Life of Suggestions

    ERIC Educational Resources Information Center

    Pearce, Cathie

    2010-01-01

    Using the notion of a suggestion, or rather charting the life of suggestions, this article considers the happenings of chance and embodiment as the "problems that got away." The life of suggestions helps us to ask how connectivities are made, how desire functions, and how "immanence" rather than "transcendence" can open up the politics and ethics…

  13. [Foundations of the new phylogenetics].

    PubMed

    Pavlinov, I Ia

    2004-01-01

    Evolutionary idea is the core of the modern biology. Due to this, phylogenetics dealing with historical reconstructions in biology takes a priority position among biological disciplines. The second half of the 20th century witnessed growth of a great interest to phylogenetic reconstructions at macrotaxonomic level which replaced microevolutionary studies dominating during the 30s-60s. This meant shift from population thinking to phylogenetic one but it was not revival of the classical phylogenetics; rather, a new approach emerged that was baptized The New Phylogenetics. It arose as a result of merging of three disciplines which were developing independently during 60s-70s, namely cladistics, numerical phyletics, and molecular phylogenetics (now basically genophyletics). Thus, the new phylogenetics could be defined as a branch of evolutionary biology aimed at elaboration of "parsimonious" cladistic hypotheses by means of numerical methods on the basis of mostly molecular data. Classical phylogenetics, as a historical predecessor of the new one, emerged on the basis of the naturphilosophical worldview which included a superorganismal idea of biota. Accordingly to that view, historical development (the phylogeny) was thought an analogy of individual one (the ontogeny) so its most basical features were progressive parallel developments of "parts" (taxa), supplemented with Darwinian concept of monophyly. Two predominating traditions were diverged within classical phylogenetics according to a particular interpretation of relation between these concepts. One of them (Cope, Severtzow) belittled monophyly and paid most attention to progressive parallel developments of morphological traits. Such an attitude turned this kind of phylogenetics to be rather the semogenetics dealing primarily with evolution of structures and not of taxa. Another tradition (Haeckel) considered both monophyletic and parallel origins of taxa jointly: in the middle of 20th century it was split into

  14. Evolutionary history and phylogenetic relationship between Auxis thazard and Auxis rochei inferred from COI sequences of mtDNA.

    PubMed

    Kumar, Girish; Kunal, Swaraj Priyaranjan; Shyama, S K

    2013-01-01

    Tunas of the genus Auxis are cosmopolitan species and the smallest members of the tribe Thunnini, the true tunas. In the present study, COI sequences of mtDNA were employed to examine the evolutionary history and phylogenetic relationship between A. thazard and A. rochei. A total of 29 COI sequences were retrieved from NCBI. Historic demographic analyses of sequence data showed that A. thazard has undergone sudden population expansion in the past while population size of A. rochei has been remain constant for long period. Non-significant value of Tajimas's D (P = 0.22400) and Fu's FS (P = 0.21400) test fail to reject the null hypothesis of neutral evolution for A. rochei. Phylogenetic analyses of nucleotide sequences demonstrated separate clusters for both species and are strongly supported by 98% bootstrap value. The results of the present study suggest the recent founding of A. thazard in world ocean while A. rochei represents the ancestral species. PMID:24084241

  15. Exploration of phylogenetic data using a global sequence analysis method

    PubMed Central

    Chapus, Charles; Dufraigne, Christine; Edwards, Scott; Giron, Alain; Fertil, Bernard; Deschavanne, Patrick

    2005-01-01

    Background Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets. Results Here we explore the phylogenetic signal present in molecular data by genomic signatures, defined as the set of frequencies of short oligonucleotides present in DNA sequences. Although violating many of the standard assumptions of traditional phylogenetic analyses – in particular explicit statements of homology inherent in character matrices – the use of the signature does permit the analysis of very long sequences, even those that are unalignable, and is therefore most useful in cases where alignment is questionable. We compare the results obtained by traditional phylogenetic methods to those inferred by the signature method for two genes: RAG1, which is easily alignable, and 18S RNA, where alignments are often ambiguous for some regions. We also apply this method to a multigene data set of 33 genes for 9 bacteria and one archea species as well as to the whole genome of a set of 16 γ-proteobacteria. In addition to delivering phylogenetic results comparable to traditional methods, the comparison of signatures for the sequences involved in the bacterial example identified putative candidates for horizontal gene transfers. Conclusion The signature method is therefore a fast tool for exploring phylogenetic data, providing not only a pretreatment for discovering new sequence relationships, but also for identifying cases of sequence evolution that could confound traditional phylogenetic analysis. PMID:16280081

  16. Methods for analyzing the evolutionary relationship of NF-κB proteins using free, web-driven bioinformatics and phylogenetic tools.

    PubMed

    Finnerty, John R; Gilmore, Thomas D

    2015-01-01

    Phylogenetic analysis enables one to reconstruct the functional evolution of proteins. Current understanding of NF-κB signaling derives primarily from studies of a relatively small number of laboratory models-mainly vertebrates and insects-that represent a tiny fraction of animal evolution. As such, NF-κB has been the subject of limited phylogenetic analysis. The recent discovery of NF-κB proteins in "basal" marine animals (e.g., sponges, sea anemones, corals) and NF-κB-like proteins in non-metazoan lineages extends the origin of NF-κB signaling by several hundred million years and provides the opportunity to investigate the early evolution of this pathway using phylogenetic approaches. Here, we describe a combination of bioinformatic and phylogenetic analyses based on menu-driven, open-source computer programs that are readily accessible to molecular biologists without formal training in phylogenetic methods. These phylogenetically based comparisons of NF-κB proteins are powerful in that they reveal deep conservation and repeated instances of parallel evolution in the sequence and structure of NF-κB in distant animal groups, which suggest that important functional constraints limit the evolution of this protein.

  17. A phylogenetic comparative study of flowering phenology along an elevational gradient in the Canadian subarctic

    NASA Astrophysics Data System (ADS)

    Lessard-Therrien, Malie; Davies, T. Jonathan; Bolmgren, Kjell

    2014-05-01

    Climate change is affecting high-altitude and high-latitude communities in significant ways. In the short growing season of subarctic habitats, it is essential that the timing and duration of phenological phases match favorable environmental conditions. We explored the time of the first appearance of flowers (first flowering day, FFD) and flowering duration across subarctic species composing different communities, from boreal forest to tundra, along an elevational gradient (600-800 m). The study was conducted on Mount Irony (856 m), North-East Canada (54°90'N, 67°16'W) during summer 2012. First, we quantified phylogenetic signal in FFD at different spatial scales. Second, we used phylogenetic comparative methods to explore the relationship between FFD, flowering duration, and elevation. We found that the phylogenetic signal for FFD was stronger at finer spatial scales and at lower elevations, indicating that closely related species tend to flower at similar times when the local environment is less harsh. The comparatively weaker phylogenetic signal at higher elevation may be indicative of convergent evolution for FFD. Flowering duration was correlated significantly with mean FFD, with later-flowering species having a longer flowering duration, but only at the lowest elevation. Our results indicate significant evolutionary conservatism in responses to phenological cues, but high phenotypic plasticity in flowering times. We suggest that phylogenetic relationships should be considered in the search for predictions and drivers of flowering time in comparative analyses, because species cannot be considered as statistically independent. Further, phenological drivers should be measured at spatial scales such that variation in flowering matches variation in environment.

  18. Phylogenetic analyses of the genus Glaciecola: emended description of the genus Glaciecola, transfer of Glaciecola mesophila, G. agarilytica, G. aquimarina, G. arctica, G. chathamensis, G. polaris and G. psychrophila to the genus Paraglaciecola gen. nov. as Paraglaciecola mesophila comb. nov., P. agarilytica comb. nov., P. aquimarina comb. nov., P. arctica comb. nov., P. chathamensis comb. nov., P. polaris comb. nov. and P. psychrophila comb. nov., and description of Paraglaciecola oceanifecundans sp. nov., isolated from the Southern Ocean.

    PubMed

    Shivaji, Sisinthy; Reddy, Gundlapally Sathyanarayana

    2014-09-01

    Phylogenetic analyses of the genus Glaciecola were performed using the sequences of the 16S rRNA gene and the GyrB protein to establish its taxonomic status. The results indicated a consistent clustering of the genus Glaciecola into two clades, with significant bootstrap values, with all the phylogenetic methods employed. Clade 1 was represented by seven species, Glaciecola agarilytica, G. aquimarina, G. arctica, G. chathamensis, G. mesophila, G. polaris and G. psychrophila, while clade 2 consisted of only three species, Glaciecola nitratireducens, G. pallidula and G. punicea. Evolutionary distances between species of clades 1 and 2, based on 16S rRNA gene and GyrB protein sequences, ranged from 93.0 to 95.0 % and 69.0 to 73.0 %, respectively. In addition, clades 1 and 2 possessed 18 unique signature nucleotides, at positions 132, 184 : 193, 185 : 192, 230, 616 : 624, 631, 632, 633, 738, 829, 1257, 1265, 1281, 1356 and 1366, in the 16S rRNA gene sequence and can be differentiated by the occurrence of a 15 nt signature motif 5'-CAAATCAGAATGTTG at positions 1354-1368 in members of clade 2. Robust clustering of the genus Glaciecola into two clades based on analysis of 16S rRNA gene and GyrB protein sequences, 16S rRNA gene sequence similarity of ≤95.0 % and the occurrence of signature nucleotides and signature motifs in the 16S rRNA gene suggested that the genus should be split into two genera. The genus Paraglaciecola gen. nov. is therefore created to accommodate the seven species of clade 1, while the name Glaciecola sensu stricto is retained to represent species of clade 2. The species of clade 1 are transferred to the genus Paraglaciecola as Paraglaciecola mesophila comb. nov. (type strain DSM 15026(T) = KMM 241(T)), P. agarilytica comb. nov. (type strain NO2(T) = KCTC 12755(T) = LMG 23762(T)), P. aquimarina comb. nov. (type strain GGW-M5(T) = KCTC 32108(T) = CCUG 62918(T)), P. arctica comb. nov. (type strain BSs20135(T

  19. Phylogenetic analyses of the genus Glaciecola: emended description of the genus Glaciecola, transfer of Glaciecola mesophila, G. agarilytica, G. aquimarina, G. arctica, G. chathamensis, G. polaris and G. psychrophila to the genus Paraglaciecola gen. nov. as Paraglaciecola mesophila comb. nov., P. agarilytica comb. nov., P. aquimarina comb. nov., P. arctica comb. nov., P. chathamensis comb. nov., P. polaris comb. nov. and P. psychrophila comb. nov., and description of Paraglaciecola oceanifecundans sp. nov., isolated from the Southern Ocean.

    PubMed

    Shivaji, Sisinthy; Reddy, Gundlapally Sathyanarayana

    2014-09-01

    Phylogenetic analyses of the genus Glaciecola were performed using the sequences of the 16S rRNA gene and the GyrB protein to establish its taxonomic status. The results indicated a consistent clustering of the genus Glaciecola into two clades, with significant bootstrap values, with all the phylogenetic methods employed. Clade 1 was represented by seven species, Glaciecola agarilytica, G. aquimarina, G. arctica, G. chathamensis, G. mesophila, G. polaris and G. psychrophila, while clade 2 consisted of only three species, Glaciecola nitratireducens, G. pallidula and G. punicea. Evolutionary distances between species of clades 1 and 2, based on 16S rRNA gene and GyrB protein sequences, ranged from 93.0 to 95.0 % and 69.0 to 73.0 %, respectively. In addition, clades 1 and 2 possessed 18 unique signature nucleotides, at positions 132, 184 : 193, 185 : 192, 230, 616 : 624, 631, 632, 633, 738, 829, 1257, 1265, 1281, 1356 and 1366, in the 16S rRNA gene sequence and can be differentiated by the occurrence of a 15 nt signature motif 5'-CAAATCAGAATGTTG at positions 1354-1368 in members of clade 2. Robust clustering of the genus Glaciecola into two clades based on analysis of 16S rRNA gene and GyrB protein sequences, 16S rRNA gene sequence similarity of ≤95.0 % and the occurrence of signature nucleotides and signature motifs in the 16S rRNA gene suggested that the genus should be split into two genera. The genus Paraglaciecola gen. nov. is therefore created to accommodate the seven species of clade 1, while the name Glaciecola sensu stricto is retained to represent species of clade 2. The species of clade 1 are transferred to the genus Paraglaciecola as Paraglaciecola mesophila comb. nov. (type strain DSM 15026(T) = KMM 241(T)), P. agarilytica comb. nov. (type strain NO2(T) = KCTC 12755(T) = LMG 23762(T)), P. aquimarina comb. nov. (type strain GGW-M5(T) = KCTC 32108(T) = CCUG 62918(T)), P. arctica comb. nov. (type strain BSs20135(T

  20. The phylogenetic affinities of the extinct glyptodonts.

    PubMed

    Delsuc, Frédéric; Gibb, Gillian C; Kuch, Melanie; Billet, Guillaume; Hautier, Lionel; Southon, John; Rouillard, Jean-Marie; Fernicola, Juan Carlos; Vizcaíno, Sergio F; MacPhee, Ross D E; Poinar, Hendrik N

    2016-02-22

    Among the fossils of hitherto unknown mammals that Darwin collected in South America between 1832 and 1833 during the Beagle expedition were examples of the large, heavily armored herbivores later known as glyptodonts. Ever since, glyptodonts have fascinated evolutionary biologists because of their remarkable skeletal adaptations and seemingly isolated phylogenetic position even within their natural group, the cingulate xenarthrans (armadillos and their allies). In possessing a carapace comprised of fused osteoderms, the glyptodonts were clearly related to other cingulates, but their precise phylogenetic position as suggested by morphology remains unresolved. To provide a molecular perspective on this issue, we designed sequence-capture baits using in silico reconstructed ancestral sequences and successfully assembled the complete mitochondrial genome of Doedicurus sp., one of the largest glyptodonts. Our phylogenetic reconstructions establish that glyptodonts are in fact deeply nested within the armadillo crown-group, representing a distinct subfamily (Glyptodontinae) within family Chlamyphoridae. Molecular dating suggests that glyptodonts diverged no earlier than around 35 million years ago, in good agreement with their fossil record. Our results highlight the derived nature of the glyptodont morphotype, one aspect of which is a spectacular increase in body size until their extinction at the end of the last ice age. PMID:26906483

  1. The phylogenetic affinities of the extinct glyptodonts.

    PubMed

    Delsuc, Frédéric; Gibb, Gillian C; Kuch, Melanie; Billet, Guillaume; Hautier, Lionel; Southon, John; Rouillard, Jean-Marie; Fernicola, Juan Carlos; Vizcaíno, Sergio F; MacPhee, Ross D E; Poinar, Hendrik N

    2016-02-22

    Among the fossils of hitherto unknown mammals that Darwin collected in South America between 1832 and 1833 during the Beagle expedition were examples of the large, heavily armored herbivores later known as glyptodonts. Ever since, glyptodonts have fascinated evolutionary biologists because of their remarkable skeletal adaptations and seemingly isolated phylogenetic position even within their natural group, the cingulate xenarthrans (armadillos and their allies). In possessing a carapace comprised of fused osteoderms, the glyptodonts were clearly related to other cingulates, but their precise phylogenetic position as suggested by morphology remains unresolved. To provide a molecular perspective on this issue, we designed sequence-capture baits using in silico reconstructed ancestral sequences and successfully assembled the complete mitochondrial genome of Doedicurus sp., one of the largest glyptodonts. Our phylogenetic reconstructions establish that glyptodonts are in fact deeply nested within the armadillo crown-group, representing a distinct subfamily (Glyptodontinae) within family Chlamyphoridae. Molecular dating suggests that glyptodonts diverged no earlier than around 35 million years ago, in good agreement with their fossil record. Our results highlight the derived nature of the glyptodont morphotype, one aspect of which is a spectacular increase in body size until their extinction at the end of the last ice age.

  2. Phylogenetic conservatism of environmental niches in mammals.

    PubMed

    Cooper, Natalie; Freckleton, Rob P; Jetz, Walter

    2011-08-01

    Phylogenetic niche conservatism is the pattern where close relatives occupy similar niches, whereas distant relatives are more dissimilar. We suggest that niche conservatism will vary across clades in relation to their characteristics. Specifically, we investigate how conservatism of environmental niches varies among mammals according to their latitude, range size, body size and specialization. We use the Brownian rate parameter, σ(2), to measure the rate of evolution in key variables related to the ecological niche and define the more conserved group as the one with the slower rate of evolution. We find that tropical, small-ranged and specialized mammals have more conserved thermal niches than temperate, large-ranged or generalized mammals. Partitioning niche conservatism into its spatial and phylogenetic components, we find that spatial effects on niche variables are generally greater than phylogenetic effects. This suggests that recent evolution and dispersal have more influence on species' niches than more distant evolutionary events. These results have implications for our understanding of the role of niche conservatism in species richness patterns and for gauging the potential for species to adapt to global change.

  3. Dentition of eight species of Mediterranean Sea Gobiidae: do dentition characters of gobies reflect phylogenetic relationships?

    PubMed

    Kramer, A; Kovačić, M; Patzner, R A

    2012-01-01

    Oral and pharyngeal dentition was analysed in eight Mediterranean species of five different genera using scanning electron microscopy (SEM). Number, position, shape and size of teeth in the jaws and the pharyngeal tooth plates were used as a basis for comparison among taxa. Three different groups could be established based on the dental morphology among the species investigated and homoplasy due to feeding ecology cannot be considered the reason for similarity among them. The established groups are suggested to reflect phylogenetic relationships and correspond with the scarce published data on the topic.

  4. A phylogenetic analysis of the phylum Fibrobacteres.

    PubMed

    Jewell, Kelsea A; Scott, Jarrod J; Adams, Sandra M; Suen, Garret

    2013-09-01

    Members of the phylum Fibrobacteres are highly efficient cellulolytic bacteria, best known for their role in rumen function and as potential sources of novel enzymes for bioenergy applications. Despite being key members of ruminants and other digestive microbial communities, our knowledge of this phylum remains incomplete, as much of our understanding is focused on two recognized species, Fibrobacter succinogenes and F. intestinalis. As a result, we lack insights regarding the environmental niche, host range, and phylogenetic organization of this phylum. Here, we analyzed over 1000 16S rRNA Fibrobacteres sequences available from public databases to establish a phylogenetic framework for this phylum. We identify both species- and genus-level clades that are suggestive of previously unknown taxonomic relationships between Fibrobacteres in addition to their putative lifestyles as host-associated or free-living. Our results shed light on this poorly understood phylum and will be useful for elucidating the function, distribution, and diversity of these bacteria in their niches.

  5. Molecular phylogenetics of mastodon and Tyrannosaurus rex.

    PubMed

    Organ, Chris L; Schweitzer, Mary H; Zheng, Wenxia; Freimark, Lisa M; Cantley, Lewis C; Asara, John M

    2008-04-25

    We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen alpha1(I) and alpha2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for T. rex. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable.

  6. Update of phylogenetic and genetic diversity of Sporothrix schenckii sensu lato.

    PubMed

    Rangel-Gamboa, Lucía; Martínez-Hernandez, Fernando; Maravilla, Pablo; Arenas-Guzmán, Roberto; Flisser, Ana

    2016-03-01

    Sporothrix schenckii sensu lato causes subcutaneous mycosis. In this article we analysed its phylogeny and genetic diversity using calmodulin DNA sequences deposited in GenBank database. Population genetics indices were calculated, plus phylogenetic and haplotype network trees were built. Five clades with high values of posterior probability, 47 haplotypes and high diversity in the complex were found. Analysis of partial calmodulin sequences alignment revealed conserved and polymorphic regions that could be used as reference for taxonomic identification. The use of population genetics analysis allowed understanding the phylogenetic proximity of S. schenckii s. str. and S. brasiliensis; scarce genetic flow among them with low migration index and high ancestry coefficient was found. Similarly, S. globosa, S. mexicana and S. pallida sequences showed highly differentiated species with no genetic exchange. The phylogenetic tree suggests that S. mexicana shared a common ancestor with S. pallida; while S. globosa and S. brasiliensis are more related to S. schenckii s. str. and showed less haplotype diversity and restrictions in geographic distribution. In the haplotype network tree S. schenckii s. str. species displayed worldwide distribution without dispersion centres; while S. brasiliensis and S. globosa, exhibited Brazil and Euro-Asia as dispersion centres, respectively. Our data suggest that S. schenckii complex has been submitted to a divergent evolution process, probably due to the pressure of the environment and of the host. In contrast, S. brasiliensis could have been submitted to purifying selection or expansion process.

  7. The morphological state space revisited: what do phylogenetic patterns in homoplasy tell us about the number of possible character states?

    PubMed

    Hoyal Cuthill, Jennifer F

    2015-12-01

    Biological variety and major evolutionary transitions suggest that the space of possible morphologies may have varied among lineages and through time. However, most models of phylogenetic character evolution assume that the potential state space is finite. Here, I explore what the morphological state space might be like, by analysing trends in homoplasy (repeated derivation of the same character state). Analyses of ten published character matrices are compared against computer simulations with different state space models: infinite states, finite states, ordered states and an 'inertial' model, simulating phylogenetic constraints. Of these, only the infinite states model results in evolution without homoplasy, a prediction which is not generally met by real phylogenies. Many authors have interpreted the ubiquity of homoplasy as evidence that the number of evolutionary alternatives is finite. However, homoplasy is also predicted by phylogenetic constraints on the morphological distance that can be traversed between ancestor and descendent. Phylogenetic rarefaction (sub-sampling) shows that finite and inertial state spaces do produce contrasting trends in the distribution of homoplasy. Two clades show trends characteristic of phylogenetic inertia, with decreasing homoplasy (increasing consistency index) as we sub-sample more distantly related taxa. One clade shows increasing homoplasy, suggesting exhaustion of finite states. Different clades may, therefore, show different patterns of character evolution. However, when parsimony uninformative characters are excluded (which may occur without documentation in cladistic studies), it may no longer be possible to distinguish inertial and finite state spaces. Interestingly, inertial models predict that homoplasy should be clustered among comparatively close relatives (parallel evolution), whereas finite state models do not. If morphological evolution is often inertial in nature, then homoplasy (false homology) may primarily

  8. The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms.

    PubMed

    Raman, Gurusamy; Park, SeonJoo

    2016-01-01

    Ampelopsis brevipedunculata is an economically important plant that belongs to the Vitaceae family of angiosperms. The phylogenetic placement of Vitaceae is still unresolved. Recent phylogenetic studies suggested that it should be placed in various alternative families including Caryophyllaceae, asteraceae, Saxifragaceae, Dilleniaceae, or with the rest of the rosid families. However, these analyses provided weak supportive results because they were based on only one of several genes. Accordingly, complete chloroplast genome sequences are required to resolve the phylogenetic relationships among angiosperms. Recent phylogenetic analyses based on the complete chloroplast genome sequence suggested strong support for the position of Vitaceae as the earliest diverging lineage of rosids and placed it as a sister to the remaining rosids. These studies also revealed relationships among several major lineages of angiosperms; however, they highlighted the significance of taxon sampling for obtaining accurate phylogenies. In the present study, we sequenced the complete chloroplast genome of A. brevipedunculata and used these data to assess the relationships among 32 angiosperms, including 18 taxa of rosids. The Ampelopsis chloroplast genome is 161,090 bp in length, and includes a pair of inverted repeats of 26,394 bp that are separated by small and large single copy regions of 19,036 bp and 89,266 bp, respectively. The gene content and order of Ampelopsis is identical to many other unrearranged angiosperm chloroplast genomes, including Vitis and tobacco. A phylogenetic tree constructed based on 70 protein-coding genes of 33 angiosperms showed that both Saxifragales and Vitaceae diverged from the rosid clade and formed two clades with 100% bootstrap value. The position of the Vitaceae is sister to Saxifragales, and both are the basal and earliest diverging lineages. Moreover, Saxifragales forms a sister clade to Vitaceae of rosids. Overall, the results of this study will

  9. The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms.

    PubMed

    Raman, Gurusamy; Park, SeonJoo

    2016-01-01

    Ampelopsis brevipedunculata is an economically important plant that belongs to the Vitaceae family of angiosperms. The phylogenetic placement of Vitaceae is still unresolved. Recent phylogenetic studies suggested that it should be placed in various alternative families including Caryophyllaceae, asteraceae, Saxifragaceae, Dilleniaceae, or with the rest of the rosid families. However, these analyses provided weak supportive results because they were based on only one of several genes. Accordingly, complete chloroplast genome sequences are required to resolve the phylogenetic relationships among angiosperms. Recent phylogenetic analyses based on the complete chloroplast genome sequence suggested strong support for the position of Vitaceae as the earliest diverging lineage of rosids and placed it as a sister to the remaining rosids. These studies also revealed relationships among several major lineages of angiosperms; however, they highlighted the significance of taxon sampling for obtaining accurate phylogenies. In the present study, we sequenced the complete chloroplast genome of A. brevipedunculata and used these data to assess the relationships among 32 angiosperms, including 18 taxa of rosids. The Ampelopsis chloroplast genome is 161,090 bp in length, and includes a pair of inverted repeats of 26,394 bp that are separated by small and large single copy regions of 19,036 bp and 89,266 bp, respectively. The gene content and order of Ampelopsis is identical to many other unrearranged angiosperm chloroplast genomes, including Vitis and tobacco. A phylogenetic tree constructed based on 70 protein-coding genes of 33 angiosperms showed that both Saxifragales and Vitaceae diverged from the rosid clade and formed two clades with 100% bootstrap value. The position of the Vitaceae is sister to Saxifragales, and both are the basal and earliest diverging lineages. Moreover, Saxifragales forms a sister clade to Vitaceae of rosids. Overall, the results of this study will

  10. The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms

    PubMed Central

    Raman, Gurusamy; Park, SeonJoo

    2016-01-01

    Ampelopsis brevipedunculata is an economically important plant that belongs to the Vitaceae family of angiosperms. The phylogenetic placement of Vitaceae is still unresolved. Recent phylogenetic studies suggested that it should be placed in various alternative families including Caryophyllaceae, asteraceae, Saxifragaceae, Dilleniaceae, or with the rest of the rosid families. However, these analyses provided weak supportive results because they were based on only one of several genes. Accordingly, complete chloroplast genome sequences are required to resolve the phylogenetic relationships among angiosperms. Recent phylogenetic analyses based on the complete chloroplast genome sequence suggested strong support for the position of Vitaceae as the earliest diverging lineage of rosids and placed it as a sister to the remaining rosids. These studies also revealed relationships among several major lineages of angiosperms; however, they highlighted the significance of taxon sampling for obtaining accurate phylogenies. In the present study, we sequenced the complete chloroplast genome of A. brevipedunculata and used these data to assess the relationships among 32 angiosperms, including 18 taxa of rosids. The Ampelopsis chloroplast genome is 161,090 bp in length, and includes a pair of inverted repeats of 26,394 bp that are separated by small and large single copy regions of 19,036 bp and 89,266 bp, respectively. The gene content and order of Ampelopsis is identical to many other unrearranged angiosperm chloroplast genomes, including Vitis and tobacco. A phylogenetic tree constructed based on 70 protein-coding genes of 33 angiosperms showed that both Saxifragales and Vitaceae diverged from the rosid clade and formed two clades with 100% bootstrap value. The position of the Vitaceae is sister to Saxifragales, and both are the basal and earliest diverging lineages. Moreover, Saxifragales forms a sister clade to Vitaceae of rosids. Overall, the results of this study will

  11. Testing for Divergent Transmission Histories among Cultural Characters: A Study Using Bayesian Phylogenetic Methods and Iranian Tribal Textile Data

    PubMed Central

    Matthews, Luke J.; Tehrani, Jamie J.; Jordan, Fiona M.; Collard, Mark; Nunn, Charles L.

    2011-01-01

    Background Archaeologists and anthropologists have long recognized that different cultural complexes may have distinct descent histories, but they have lacked analytical techniques capable of easily identifying such incongruence. Here, we show how Bayesian phylogenetic analysis can be used to identify incongruent cultural histories. We employ the approach to investigate Iranian tribal textile traditions. Methods We used Bayes factor comparisons in a phylogenetic framework to test two models of cultural evolution: the hierarchically integrated system hypothesis and the multiple coherent units hypothesis. In the hierarchically integrated system hypothesis, a core tradition of characters evolves through descent with modification and characters peripheral to the core are exchanged among contemporaneous populations. In the multiple coherent units hypothesis, a core tradition does not exist. Rather, there are several cultural units consisting of sets of characters that have different histories of descent. Results For the Iranian textiles, the Bayesian phylogenetic analyses supported the multiple coherent units hypothesis over the hierarchically integrated system hypothesis. Our analyses suggest that pile-weave designs represent a distinct cultural unit that has a different phylogenetic history compared to other textile characters. Conclusions The results from the Iranian textiles are consistent with the available ethnographic evidence, which suggests that the commercial rug market has influenced pile-rug designs but not the techniques or designs incorporated in the other textiles produced by the tribes. We anticipate that Bayesian phylogenetic tests for inferring cultural units will be of great value for researchers interested in studying the evolution of cultural traits including language, behavior, and material culture. PMID:21559083

  12. Chemistry Curricula. Course Suggestions.

    ERIC Educational Resources Information Center

    American Chemical Society, Washington, DC.

    Listings of suggested topics aimed at helping university and college faculties plan courses in the main areas of the chemistry curricula are provided. The suggestions were originally offered as appendices to the American Chemical Society's (ACS) Committee on Professional Training's 1983 guidelines for ACS-approved schools. The course data included…

  13. Phylogenetic relationships and the evolution of BMP4 in triggerfishes and filefishes (Balistoidea).

    PubMed

    McCord, Charlene L; Westneat, Mark W

    2016-01-01

    The triggerfishes (family Balistidae) and filefishes (family Monacanthidae) comprise a charismatic superfamily (Balistoidea) within the diverse order Tetraodontiformes. This group of largely marine fishes occupies an impressive ecological range across the world's oceans, and is well known for its locomotor and feeding diversity, unusual body shapes, small genome size, and ecological and economic importance. In order to investigate the evolutionary history of these important fish families, we used multiple phylogenetic methods to analyze molecular data from 86 species spanning the extant biodiversity of Balistidae and Monacanthidae. In addition to three gene regions that have been used extensively in phylogenetic analyses, we include sequence data for two mitochondrial regions, two nuclear markers, and the growth factor gene bmp4, which is involved with cranial development. Phylogenetic analyses strongly support the monophyly of the superfamily Balistoidea, the sister-family relationship of Balistidae and Monacanthidae, as well as three triggerfish and four filefish clades that are well resolved. A new classification for the Balistidae is proposed based on phylogenetic groups. Bayesian topology, as well as the timing of major cladogenesis events, is largely congruent with previous hypotheses of balistid phylogeny. However, we present a novel topology for major clades in the filefish family that illustrate the genera Aluterus and Stephanolepis are more closely related than previously posited. Molecular rates suggest a Miocene and Oligocene origin for the families Balistidae and Monacanthidae, respectively, and significant divergence of species in both families within the past 5 million years. A second key finding of this study is that, relative to the other protein-coding gene regions in our DNA supermatrix, bmp4 shows a rapid accumulation of both synonymous and non-synonymous substitutions, especially within the family Monacanthidae. Overall substitution patterns in

  14. One Tree to Link Them All: A Phylogenetic Dataset for the European Tetrapoda

    PubMed Central

    Roquet, Cristina; Lavergne, Sébastien; Thuiller, Wilfried

    2014-01-01

    Since the ever-increasing availability of phylogenetic informative data, the last decade has seen an upsurge of ecological studies incorporating information on evolutionary relationships among species. However, detailed species-level phylogenies are still lacking for many large groups and regions, which are necessary for comprehensive large-scale eco-phylogenetic analyses. Here, we provide a dataset of 100 dated phylogenetic trees for all European tetrapods based on a mixture of supermatrix and supertree approaches. Phylogenetic inference was performed separately for each of the main Tetrapoda groups of Europe except mammals (i.e. amphibians, birds, squamates and turtles) by means of maximum likelihood (ML) analyses of supermatrix applying a tree constraint at the family (amphibians and squamates) or order (birds and turtles) levels based on consensus knowledge. For each group, we inferred 100 ML trees to be able to provide a phylogenetic dataset that accounts for phylogenetic uncertainty, and assessed node support with bootstrap analyses. Each tree was dated using penalized-likelihood and fossil calibration. The trees obtained were well-supported by existing knowledge and previous phylogenetic studies. For mammals, we modified the most complete supertree dataset available on the literature to include a recent update of the Carnivora clade. As a final step, we merged the phylogenetic trees of all groups to obtain a set of 100 phylogenetic trees for all European Tetrapoda species for which data was available (91%). We provide this phylogenetic dataset (100 chronograms) for the purpose of comparative analyses, macro-ecological or community ecology studies aiming to incorporate phylogenetic information while accounting for phylogenetic uncertainty. PMID:25685620

  15. Investigating the performance of AIC in selecting phylogenetic models.

    PubMed

    Jhwueng, Dwueng-Chwuan; Huzurbazar, Snehalata; O'Meara, Brian C; Liu, Liang

    2014-08-01

    The popular likelihood-based model selection criterion, Akaike's Information Criterion (AIC), is a breakthrough mathematical result derived from information theory. AIC is an approximation to Kullback-Leibler (KL) divergence with the derivation relying on the assumption that the likelihood function has finite second derivatives. However, for phylogenetic estimation, given that tree space is discrete with respect to tree topology, the assumption of a continuous likelihood function with finite second derivatives is violated. In this paper, we investigate the relationship between the expected log likelihood of a candidate model, and the expected KL divergence in the context of phylogenetic tree estimation. We find that given the tree topology, AIC is an unbiased estimator of the expected KL divergence. However, when the tree topology is unknown, AIC tends to underestimate the expected KL divergence for phylogenetic models. Simulation results suggest that the degree of underestimation varies across phylogenetic models so that even for large sample sizes, the bias of AIC can result in selecting a wrong model. As the choice of phylogenetic models is essential for statistical phylogenetic inference, it is important to improve the accuracy of model selection criteria in the context of phylogenetics. PMID:24867284

  16. Open to Suggestion.

    ERIC Educational Resources Information Center

    Journal of Reading, 1984

    1984-01-01

    Contributors offer suggestions concerning parents as reading stimulators, book discussions, a test bank for the secondary school/college reading lab, standardized reading tests, television reading, plagiarism, vocabulary development, and book reports. (FL)

  17. [Therapy and suggestion].

    PubMed

    Barrucand, D; Paille, F

    1986-12-01

    Therapy and suggestion are closely related. That is clear for the ancient time: primitive medicine gives a good place to the Word. In plant, animal or mineral remedies, the suggestion is clearly preponderant. Towards the end of the 19th century, the "Ecole de Nancy" sets up a real theory of the suggestion, and Bernheim, its leader, bases hypnosis, then psychotherapy on this concept. Thereafter Coué will bring up the "conscious autosuggestion". Today, despite the progress of scientific medicine, the part of suggestion is still very important in medical therapy (with or without drugs), or in chirurgical therapy; this part is also very important in psychotherapies, whatever has been said in this field. This has to be known and used consciously in the doctor-patient relation, which is always essential in the therapeutic effectiveness.

  18. Origin, evolution, and biogeography of Juglans: a phylogenetic perspective

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phylogenetic analyses of extant Juglans (Juglandaceae) using five cpDNA intergenic spacer (IGS) sequences (trnT-trnF, psbA-trnH, atpB-rbcL, trnV-16S rRNA, and trnS-trnfM) were performed to elucidate the origin, diversification, historical biogeography, and evolutionary relationships within the genus...

  19. Bootstrap estimation and comparison of an index of phylogenetic correlation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A common objective of bioinformatic analyses is to assess the similarity of species, given a biological trait or characteristic. Phylogenetic correlation is one means to achieve this objective. Such measures provide a means to evaluate evolutionary models and history as well as having potential appl...

  20. Disentangling the Phylogenetic and Ecological Components of Spider Phenotypic Variation

    PubMed Central

    Gonçalves-Souza, Thiago; Diniz-Filho, José Alexandre Felizola; Romero, Gustavo Quevedo

    2014-01-01

    An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial to inferring the mechanisms governing the assembly of communities. We evaluated the relative importance of spider phylogenetic relationships and ecological niche (plant morphological variables) to the variation in spider body size and shape by comparing spiders at different scales: (i) between bromeliads and dicot plants (i.e., habitat scale) and (ii) among bromeliads with distinct architectural features (i.e., microhabitat scale). We partitioned the interspecific variation in body size and shape into phylogenetic (that express trait values as expected by phylogenetic relationships among species) and ecological components (that express trait values independent of phylogenetic relationships). At the habitat scale, bromeliad spiders were larger and flatter than spiders associated with the surrounding dicots. At this scale, plant morphology sorted out close related spiders. Our results showed that spider flatness is phylogenetically clustered at the habitat scale, whereas it is phylogenetically overdispersed at the microhab