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Sample records for addition phylogenetic analyses

  1. Which Phylogenetic Networks are Merely Trees with Additional Arcs?

    PubMed Central

    Francis, Andrew R.; Steel, Mike

    2015-01-01

    A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on “2-SAT”) that efficiently determines whether or not any given network can be realized in this way. Moreover, the proof provides a polynomial-time algorithm for finding one or more trees (when they exist) on which the network can be based. A number of interesting consequences are presented as corollaries; these lead to some further relevant questions and observations, which we outline in the conclusion. PMID:26070685

  2. Which Phylogenetic Networks are Merely Trees with Additional Arcs?

    PubMed

    Francis, Andrew R; Steel, Mike

    2015-09-01

    A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on "2-SAT") that efficiently determines whether or not any given network can be realized in this way. Moreover, the proof provides a polynomial-time algorithm for finding one or more trees (when they exist) on which the network can be based. A number of interesting consequences are presented as corollaries; these lead to some further relevant questions and observations, which we outline in the conclusion.

  3. [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

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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).

  14. 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

  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. 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

  18. 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

  19. 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

  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. 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

  4. 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.

  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.

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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

  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. PMID:26800782

  18. 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.

  19. 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

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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.

  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. 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

  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. 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.

  19. 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.

  20. 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

  1. 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

  2. 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....

  3. 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

  4. 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

  5. Cucumis monosomic alien addition lines: morphological, cytological, and genotypic analyses.

    PubMed

    Chen, Jin-Feng; Luo, Xiang-Dong; Qian, Chun-Tao; Jahn, Molly M; Staub, Jack E; Zhuang, Fei-Yun; Lou, Qun-Feng; Ren, Gang

    2004-05-01

    Cucumis hystrix Chakr. (HH, 2n=24), a wild relative of the cultivated cucumber, possesses several potentially valuable disease-resistance and abiotic stress-tolerance traits for cucumber ( C. sativus L., CC, 2n=14) improvement. Numerous attempts have been made to transfer desirable traits since the successful interspecific hybridization between C. hystrix and C. sativus, one of which resulted in the production of an allotriploid (HCC, 2n=26: one genome of C. hystrix and two of C. sativus). When this genotype was treated with colchicine to induce polyploidy, two monosomic alien addition lines (MAALs) (plant nos. 87 and 517: 14 CC+1 H, 2n=15) were recovered among 252 viable plants. Each of these plants was morphologically distinct from allotriploids and cultivated cucumbers. Cytogenetic and molecular marker analyses were performed to confirm the genetic constitution and further characterize these two MAALs. Chromosome counts made from at least 30 meristematic cells from each plant confirmed 15 nuclear chromosomes. In pollen mother cells of plant nos. 87 and 517, seven bivalents and one univalent were observed at diakinesis and metaphase I; the frequency of trivalent formation was low (about 4-5%). At anaphase I and II, stochastic and asymmetric division led to the formation of two gamete classes: n=7 and n=8; however, pollen fertility was relatively high. Pollen stainability in plant no. 87 was 86.7% and in plant no. 517 was 93.2%. Random amplified polymorphic DNA analysis was performed using 100 random 10-base primers. Genotypes obtained with eight primers (A-9, A-11, AH-13, AI-19, AJ-18, AJ-20, E-19, and N-20) showed a band common to the two MAAL plants and C. hystrix that was absent in C. sativus, confirming that the alien chromosomes present in the MAALs were derived from C. hystrix. Morphological differences and differences in banding patterns were also observed between plant nos. 87 and 517 after amplification with primers AI-5, AJ-13, N-12, and N-20

  6. 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.

  7. 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

  8. 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

  9. Shifts in the phylogenetic structure of arbuscular mycorrhizal fungi in response to experimental nitrogen and carbon dioxide additions.

    PubMed

    Mueller, Rebecca C; Bohannan, Brendan J M

    2015-09-01

    Global N inputs and atmospheric CO2 concentrations have increased as a result of human activities, and are predicted to increase along with population growth, with potentially negative effects on biodiversity. Using taxonomic and phylogenetic measures, we examined the response of arbuscular mycorrhizal fungi (AMF) to experimental manipulations of N and CO2 at the Jasper Ridge Global Change Experiment. No significant interactions between N and CO2 were observed, but individual effects of N and CO2 were found. Elevated CO2 resulted in changes in phylogenetic similarity, and a shift to phylogenetic clustering of AMF communities. N addition resulted in higher phylogenetic diversity and evenness, with no shifts in community composition and no significant signal for phylogenetic clustering. N addition resulted in an increase in both available N and the N:P ratio in N-amended plots, which suggests that changing patterns of nutrient limitation could have lead to altered species interactions. These findings suggest that elevated levels of N and CO2 altered patterns of AMF community assembly, with potential effects on ecosystem function. PMID:25990297

  10. 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

  11. 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.

  12. 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

  13. 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

  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. 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.

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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

  9. Multigene phylogenetic reconstruction of the Tubulinea (Amoebozoa) corroborates four of the six major lineages, while additionally revealing that shell composition does not predict phylogeny in the Arcellinida.

    PubMed

    Lahr, Daniel J G; Grant, Jessica R; Katz, Laura A

    2013-05-01

    Tubulinea is a phylogenetically stable higher-level taxon within Amoebozoa, morphologically characterized by monoaxially streaming and cylindrical pseudopods. Contemporary phylogenetic reconstructions have largely relied on SSU rDNA, and to a lesser extent, on actin genes to reveal the relationships among these organisms. Additionally, the test (shell) forming Arcellinida, one of the most species-rich amoebozoan groups, is nested within Tubulinea and suffers from substantial under-sampling of taxa. Here, we increase taxonomic and gene sampling within the Tubulinea, characterizing molecular data for 22 taxa and six genes (SSU rDNA, actin, α- and β-tubulin, elongation factor 2 and the 14-3-3 regulatory protein). We perform concatenated phylogenetic analyses using these genes as well as approximately unbiased tests to assess evolutionary relationships within the Tubulinea. We confirm the monophyly of Tubulinea and four of the six included lineages (Echinamoeboidea, Leptomyxida, Amoebida and Poseidonida). Arcellinida and Hartmanellidae, the remaining lineages, are not monophyletic in our reconstructions, although statistical testing does not allow rejection of either group. We further investigate more fine-grained morphological evolution of previously defined groups, concluding that relationships within Arcellinida are more consistent with general test and aperture shape than with test composition. We also discuss the implications of this phylogeny for interpretations of the Precambrian fossil record of testate amoebae. PMID:23499265

  10. Nitrogen addition, not initial phylogenetic diversity, increases litter decomposition by fungal communities.

    PubMed

    Amend, Anthony S; Matulich, Kristin L; Martiny, Jennifer B H

    2015-01-01

    Fungi play a critical role in the degradation of organic matter. Because different combinations of fungi result in different rates of decomposition, determining how climate change will affect microbial composition and function is fundamental to predicting future environments. Fungal response to global change is patterned by genetic relatedness, resulting in communities with comparatively low phylogenetic diversity (PD). This may have important implications for the functional capacity of disturbed communities if lineages sensitive to disturbance also contain unique traits important for litter decomposition. Here we tested the relationship between PD and decomposition rates. Leaf litter fungi were isolated from the field and deployed in microcosms as mock communities along a gradient of initial PD, while species richness was held constant. Replicate communities were subject to nitrogen fertilization comparable to anthropogenic deposition levels. Carbon mineralization rates were measured over the course of 66 days. We found that nitrogen fertilization increased cumulative respiration by 24.8%, and that differences in respiration between fertilized and ambient communities diminished over the course of the experiment. Initial PD failed to predict respiration rates or their change in response to nitrogen fertilization, and there was no correlation between community similarity and respiration rates. Last, we detected no phylogenetic signal in the contributions of individual isolates to respiration rates. Our results suggest that the degree to which PD predicts ecosystem function will depend on environmental context. PMID:25741330

  11. Nitrogen addition, not initial phylogenetic diversity, increases litter decomposition by fungal communities

    PubMed Central

    Amend, Anthony S.; Matulich, Kristin L.; Martiny, Jennifer B. H.

    2015-01-01

    Fungi play a critical role in the degradation of organic matter. Because different combinations of fungi result in different rates of decomposition, determining how climate change will affect microbial composition and function is fundamental to predicting future environments. Fungal response to global change is patterned by genetic relatedness, resulting in communities with comparatively low phylogenetic diversity (PD). This may have important implications for the functional capacity of disturbed communities if lineages sensitive to disturbance also contain unique traits important for litter decomposition. Here we tested the relationship between PD and decomposition rates. Leaf litter fungi were isolated from the field and deployed in microcosms as mock communities along a gradient of initial PD, while species richness was held constant. Replicate communities were subject to nitrogen fertilization comparable to anthropogenic deposition levels. Carbon mineralization rates were measured over the course of 66 days. We found that nitrogen fertilization increased cumulative respiration by 24.8%, and that differences in respiration between fertilized and ambient communities diminished over the course of the experiment. Initial PD failed to predict respiration rates or their change in response to nitrogen fertilization, and there was no correlation between community similarity and respiration rates. Last, we detected no phylogenetic signal in the contributions of individual isolates to respiration rates. Our results suggest that the degree to which PD predicts ecosystem function will depend on environmental context. PMID:25741330

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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

  7. 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.

  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

    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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  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. Phylogenetically resolving epidemiologic linkage

    DOE PAGES

    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

  13. 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

  14. 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

  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. 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.

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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

  7. ADDITIONAL STRESS AND FRACTURE MECHANICS ANALYSES OF PRESSURIZED WATER REACTOR PRESSURE VESSEL NOZZLES

    SciTech Connect

    Walter, Matthew; Yin, Shengjun; Stevens, Gary; Sommerville, Daniel; Palm, Nathan; Heinecke, Carol

    2012-01-01

    In past years, the authors have undertaken various studies of nozzles in both boiling water reactors (BWRs) and pressurized water reactors (PWRs) located in the reactor pressure vessel (RPV) adjacent to the core beltline region. Those studies described stress and fracture mechanics analyses performed to assess various RPV nozzle geometries, which were selected based on their proximity to the core beltline region, i.e., those nozzle configurations that are located close enough to the core region such that they may receive sufficient fluence prior to end-of-life (EOL) to require evaluation of embrittlement as part of the RPV analyses associated with pressure-temperature (P-T) limits. In this paper, additional stress and fracture analyses are summarized that were performed for additional PWR nozzles with the following objectives: To expand the population of PWR nozzle configurations evaluated, which was limited in the previous work to just two nozzles (one inlet and one outlet nozzle). To model and understand differences in stress results obtained for an internal pressure load case using a two-dimensional (2-D) axi-symmetric finite element model (FEM) vs. a three-dimensional (3-D) FEM for these PWR nozzles. In particular, the ovalization (stress concentration) effect of two intersecting cylinders, which is typical of RPV nozzle configurations, was investigated. To investigate the applicability of previously recommended linear elastic fracture mechanics (LEFM) hand solutions for calculating the Mode I stress intensity factor for a postulated nozzle corner crack for pressure loading for these PWR nozzles. These analyses were performed to further expand earlier work completed to support potential revision and refinement of Title 10 to the U.S. Code of Federal Regulations (CFR), Part 50, Appendix G, Fracture Toughness Requirements, and are intended to supplement similar evaluation of nozzles presented at the 2008, 2009, and 2011 Pressure Vessels and Piping (PVP

  8. 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

  9. 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).

  10. 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

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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

  16. Additional Measurements and Analyses of H217O and H218O

    NASA Astrophysics Data System (ADS)

    Pearson, John; Yu, Shanshan; Walters, Adam; Daly, Adam M.

    2015-06-01

    Historically the analysis of the spectrum of water has been a balance between the quality of the data set and the applicability of the Hamiltonian to a highly non-rigid molecule. Recently, a number of different non-rigid analysis approaches have successfully been applied to 16O water resulting in a self-consistent set of transitions and energy levels to high J which allowed the spectrum to be modeled to experimental precision. The data set for 17O and 18O water was previously reviewed and many of the problematic measurements identified, but Hamiltonian modeling of the remaining data resulted in significantly poorer quality fits than that for the 16O parent. As a result, we have made additional microwave measurements and modeled the existing 17O and 18O data sets with an Euler series model. This effort has illuminated a number of additional problematic measurements in the previous data sets and has resulted in analyses of 17O and 18O water that are of similar quality to the 16O analysis. We report the new lines, the analyses and make recommendations on the quality of the experimental data sets. SS. Yu, J.C. Pearson, B.J. Drouin et al. J. Mol. Spectrosc. 279,~16-25 (2012) J. Tennyson, P.F. Bernath, L.R. Brown et al. J. Quant. Spectrosc. Rad. Trans. 117, 29-58 (2013) J. Tennyson, P.F. Bernath, L.R. Brown et al. J. Quant. Spectrosc. Rad. Trans. 110, 573-596 (2009) H.M. Pickett, J.C. Pearson, C.E. Miller J. Mol. Spectrosc. 233, 174-179 (2005)

  17. 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...

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. Using Additional Analyses to Clarify the Functions of Problem Behavior: An Analysis of Two Cases

    ERIC Educational Resources Information Center

    Payne, Steven W.; Dozier, Claudia L.; Neidert, Pamela L.; Jowett, Erica S.; Newquist, Matthew H.

    2014-01-01

    Functional analyses (FA) have proven useful for identifying contingencies that influence problem behavior. Research has shown that some problem behavior may only occur in specific contexts or be influenced by multiple or idiosyncratic variables. When these contexts or sources of influence are not assessed in an FA, further assessment may be…

  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. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. Metagenomic analyses of the late Pleistocene permafrost - additional tools for reconstruction of environmental conditions

    NASA Astrophysics Data System (ADS)

    Rivkina, Elizaveta; Petrovskaya, Lada; Vishnivetskaya, Tatiana; Krivushin, Kirill; Shmakova, Lyubov; Tutukina, Maria; Meyers, Arthur; Kondrashov, Fyodor

    2016-04-01

    A comparative analysis of the metagenomes from two 30 000-year-old permafrost samples, one of lake-alluvial origin and the other from late Pleistocene Ice Complex sediments, revealed significant differences within microbial communities. The late Pleistocene Ice Complex sediments (which have been characterized by the absence of methane with lower values of redox potential and Fe2+ content) showed a low abundance of methanogenic archaea and enzymes from both the carbon and nitrogen cycles, but a higher abundance of enzymes associated with the sulfur cycle. The metagenomic and geochemical analyses described in the paper provide evidence that the formation of the sampled late Pleistocene Ice Complex sediments likely took place under much more aerobic conditions than lake-alluvial sediments.

  2. 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.

  3. Additional Development and Systems Analyses of Pneumatic Technology for High Speed Civil Transport Aircraft

    NASA Technical Reports Server (NTRS)

    Englar, Robert J.; Willie, F. Scott; Lee, Warren J.

    1999-01-01

    In the Task I portion of this NASA research grant, configuration development and experimental investigations have been conducted on a series of pneumatic high-lift and control surface devices applied to a generic High Speed Civil Transport (HSCT) model configuration to determine their potential for improved aerodynamic performance, plus stability and control of higher performance aircraft. These investigations were intended to optimize pneumatic lift and drag performance; provide adequate control and longitudinal stability; reduce separation flowfields at high angle of attack; increase takeoff/climbout lift-to-drag ratios; and reduce system complexity and weight. Experimental aerodynamic evaluations were performed on a semi-span HSCT generic model with improved fuselage fineness ratio and with interchangeable plain flaps, blown flaps, pneumatic Circulation Control Wing (CCW) high-lift configurations, plain and blown canards, a novel Circulation Control (CC) cylinder blown canard, and a clean cruise wing for reference. Conventional tail power was also investigated for longitudinal trim capability. Also evaluated was unsteady pulsed blowing of the wing high-lift system to determine if reduced pulsed mass flow rates and blowing requirements could be made to yield the same lift as that resulting from steady-state blowing. Depending on the pulsing frequency applied, reduced mass flow rates were indeed found able to provide lift augmentation at lesser blowing values than for the steady conditions. Significant improvements in the aerodynamic characteristics leading to improved performance and stability/control were identified, and the various components were compared to evaluate the pneumatic potential of each. Aerodynamic results were provided to the Georgia Tech Aerospace System Design Lab. to conduct the companion system analyses and feasibility study (Task 2) of theses concepts applied to an operational advanced HSCT aircraft. Results and conclusions from these

  4. Reprocessing the Southern Hemisphere ADditional OZonesondes (SHADOZ) Database for Long-Term Trend Analyses

    NASA Astrophysics Data System (ADS)

    Witte, J. C.; Thompson, A. M.; Coetzee, G.; Fujiwara, M.; Johnson, B. J.; Sterling, C. W.; Cullis, P.; Ashburn, C. E.; Jordan, A. F.

    2015-12-01

    SHADOZ is a large archive of tropical balloon-bone ozonesonde data at NASA/Goddard Space Flight Center with data from 14 tropical and subtropical stations provided by collaborators in Europe, Asia, Latin America and Africa . The SHADOZ time series began in 1998, using electrochemical concentration cell (ECC) ozonesondes. Like many long-term sounding stations, SHADOZ is characterized by variations in operating procedures, launch protocols, and data processing such that biases within a data record and among sites appear. In addition, over time, the radiosonde and ozonesonde instruments and data processing protocols have changed, adding to the measurement uncertainties at individual stations and limiting the reliability of ozone profile trends and continuous satellite validation. Currently, the ozonesonde community is engaged in reprocessing ECC data, with an emphasis on homogenization of the records to compensate for the variations in instrumentation and technique. The goals are to improve the information and integrity of each measurement record and to support calculation of more reliable trends. We illustrate the reprocessing activity of SHADOZ with selected stations. We will (1) show reprocessing steps based on the recent WMO report that provides post-processing guidelines for ozonesondes; (2) characterize uncertainties in various parts of the ECC conditioning process; and (3) compare original and reprocessed data to co-located ground and satellite measurements of column ozone.

  5. Phylogenetic analysis of a gene cluster encoding an additional, rhizobial-like type III secretion system that is narrowly distributed among Pseudomonas syringae strains

    PubMed Central

    2012-01-01

    Background The central role of Type III secretion systems (T3SS) in bacteria-plant interactions is well established, yet unexpected findings are being uncovered through bacterial genome sequencing. Some Pseudomonas syringae strains possess an uncharacterized cluster of genes encoding putative components of a second T3SS (T3SS-2) in addition to the well characterized Hrc1 T3SS which is associated with disease lesions in host plants and with the triggering of hypersensitive response in non-host plants. The aim of this study is to perform an in silico analysis of T3SS-2, and to compare it with other known T3SSs. Results Based on phylogenetic analysis and gene organization comparisons, the T3SS-2 cluster of the P. syringae pv. phaseolicola strain is grouped with a second T3SS found in the pNGR234b plasmid of Rhizobium sp. These additional T3SS gene clusters define a subgroup within the Rhizobium T3SS family. Although, T3SS-2 is not distributed as widely as the Hrc1 T3SS in P. syringae strains, it was found to be constitutively expressed in P. syringae pv phaseolicola through RT-PCR experiments. Conclusions The relatedness of the P. syringae T3SS-2 to a second T3SS from the pNGR234b plasmid of Rhizobium sp., member of subgroup II of the rhizobial T3SS family, indicates common ancestry and/or possible horizontal transfer events between these species. Functional analysis and genome sequencing of more rhizobia and P. syringae pathovars may shed light into why these bacteria maintain a second T3SS gene cluster in their genome. PMID:22937899

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  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. 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

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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

  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. 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.

  9. 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

  10. 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

  11. Analyses of microbial community within a composter operated using household garbage with special reference to the addition of soybean oil.

    PubMed

    Aoshima, M; Pedro, M S; Haruta, S; Ding, L; Fukada, T; Kigawa, A; Kodama, T; Ishii, M; Igarashi, Y

    2001-01-01

    A commercially available composter was operated using fixed composition of garbage with or without the addition of soybean oil. The composter was operated without adding seed microorganisms or bulking materials. Microflora within the composter were analyzed by denaturing gradient gel electrophoresis (DGGE) in the case of oil addition, or by 16/18 S rRNA gene sequencing of the isolated microorganisms in the case of no oil addition. The results showed that, irrespective of the addition of oil, the bacteria identified were all gram positive, and that lactobacilli seemed to be the key microorganisms. Based on the results, suitable microflora for use in a household composter are discussed.

  12. 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

  13. 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

  14. 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.

  15. 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

  16. Biochemical analyses of the antioxidative activity and chemical ingredients in eight different Allium alien monosomic addition lines.

    PubMed

    Yaguchi, Shigenori; Matsumoto, Misato; Date, Rie; Harada, Kazuki; Maeda, Toshimichi; Yamauchi, Naoki; Shigyo, Masayoshi

    2013-01-01

    We measured the antioxidant contents and antioxidative activities in eight Allium fistulosum-shallot monosomic addition lines (MAL; FF+1A-FF+8A). The high antioxidative activity lines (FF+2A and FF+6A) showed high polyphenol accumulation. These additional chromosomes (2A and 6A) would therefore have anonymous genes related to the upregulation of polyphenol production, the antioxidative activities consequently being increased in these MALs. PMID:24317054

  17. 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

  18. Towards an integrated phylogenetic classification of the Tremellomycetes

    PubMed Central

    Liu, X.-Z.; Wang, Q.-M.; Göker, M.; Groenewald, M.; Kachalkin, A.V.; Lumbsch, H.T.; Millanes, A.M.; Wedin, M.; Yurkov, A.M.; Boekhout, T.; Bai, F.-Y.

    2016-01-01

    Families and genera assigned to Tremellomycetes have been mainly circumscribed by morphology and for the yeasts also by biochemical and physiological characteristics. This phenotype-based classification is largely in conflict with molecular phylogenetic analyses. Here a phylogenetic classification framework for the Tremellomycetes is proposed based on the results of phylogenetic analyses from a seven-genes dataset covering the majority of tremellomycetous yeasts and closely related filamentous taxa. Circumscriptions of the taxonomic units at the order, family and genus levels recognised were quantitatively assessed using the phylogenetic rank boundary optimisation (PRBO) and modified general mixed Yule coalescent (GMYC) tests. In addition, a comprehensive phylogenetic analysis on an expanded LSU rRNA (D1/D2 domains) gene sequence dataset covering as many as available teleomorphic and filamentous taxa within Tremellomycetes was performed to investigate the relationships between yeasts and filamentous taxa and to examine the stability of undersampled clades. Based on the results inferred from molecular data and morphological and physiochemical features, we propose an updated classification for the Tremellomycetes. We accept five orders, 17 families and 54 genera, including seven new families and 18 new genera. In addition, seven families and 17 genera are emended and one new species name and 185 new combinations are proposed. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the species names that are temporarily maintained. PMID:26955199

  19. Towards an integrated phylogenetic classification of the Tremellomycetes.

    PubMed

    Liu, X-Z; Wang, Q-M; Göker, M; Groenewald, M; Kachalkin, A V; Lumbsch, H T; Millanes, A M; Wedin, M; Yurkov, A M; Boekhout, T; Bai, F-Y

    2015-06-01

    Families and genera assigned to Tremellomycetes have been mainly circumscribed by morphology and for the yeasts also by biochemical and physiological characteristics. This phenotype-based classification is largely in conflict with molecular phylogenetic analyses. Here a phylogenetic classification framework for the Tremellomycetes is proposed based on the results of phylogenetic analyses from a seven-genes dataset covering the majority of tremellomycetous yeasts and closely related filamentous taxa. Circumscriptions of the taxonomic units at the order, family and genus levels recognised were quantitatively assessed using the phylogenetic rank boundary optimisation (PRBO) and modified general mixed Yule coalescent (GMYC) tests. In addition, a comprehensive phylogenetic analysis on an expanded LSU rRNA (D1/D2 domains) gene sequence dataset covering as many as available teleomorphic and filamentous taxa within Tremellomycetes was performed to investigate the relationships between yeasts and filamentous taxa and to examine the stability of undersampled clades. Based on the results inferred from molecular data and morphological and physiochemical features, we propose an updated classification for the Tremellomycetes. We accept five orders, 17 families and 54 genera, including seven new families and 18 new genera. In addition, seven families and 17 genera are emended and one new species name and 185 new combinations are proposed. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the species names that are temporarily maintained.

  20. Towards an integrated phylogenetic classification of the Tremellomycetes.

    PubMed

    Liu, X-Z; Wang, Q-M; Göker, M; Groenewald, M; Kachalkin, A V; Lumbsch, H T; Millanes, A M; Wedin, M; Yurkov, A M; Boekhout, T; Bai, F-Y

    2015-06-01

    Families and genera assigned to Tremellomycetes have been mainly circumscribed by morphology and for the yeasts also by biochemical and physiological characteristics. This phenotype-based classification is largely in conflict with molecular phylogenetic analyses. Here a phylogenetic classification framework for the Tremellomycetes is proposed based on the results of phylogenetic analyses from a seven-genes dataset covering the majority of tremellomycetous yeasts and closely related filamentous taxa. Circumscriptions of the taxonomic units at the order, family and genus levels recognised were quantitatively assessed using the phylogenetic rank boundary optimisation (PRBO) and modified general mixed Yule coalescent (GMYC) tests. In addition, a comprehensive phylogenetic analysis on an expanded LSU rRNA (D1/D2 domains) gene sequence dataset covering as many as available teleomorphic and filamentous taxa within Tremellomycetes was performed to investigate the relationships between yeasts and filamentous taxa and to examine the stability of undersampled clades. Based on the results inferred from molecular data and morphological and physiochemical features, we propose an updated classification for the Tremellomycetes. We accept five orders, 17 families and 54 genera, including seven new families and 18 new genera. In addition, seven families and 17 genera are emended and one new species name and 185 new combinations are proposed. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the species names that are temporarily maintained. PMID:26955199

  1. The more, the better: the use of multiple landmark configurations to solve the phylogenetic relationships in musteloids.

    PubMed

    Catalano, Santiago A; Ercoli, Marcos D; Prevosti, Francisco J

    2015-03-01

    Although the use of landmark data to study shape changes along a phylogenetic tree has become a common practice in evolutionary studies, the role of this sort of data for the inference of phylogenetic relationships remains under debate. Theoretical issues aside, the very existence of historical information in landmark data has been challenged, since phylogenetic analyses have often shown little congruence with alternative sources of evidence. However, most analyses conducted in the past were based upon a single landmark configuration, leaving it unsettled whether the incorporation of multiple configurations may improve the rather poor performance of this data source in most previous phylogenetic analyses. In the present study, we present a phylogenetic analysis of landmark data that combines information derived from several skeletal structures to derive a phylogenetic tree for musteloids. The analysis includes nine configurations representing different skeletal structures for 24 species. The resulting tree presents several notable concordances with phylogenetic hypotheses derived from molecular data. In particular, Mephitidae, Procyonidae, and Lutrinae plus the genera Martes, Mustela, Galictis, and Procyon were retrieved as monophyletic. In addition, other groupings were in agreement with molecular phylogenies or presented only minor discordances. Complementary analyses have also indicated that the results improve substantially when an increasing number of landmark configurations are included in the analysis. The results presented here thus highlight the importance of combining information from multiple structures to derive phylogenetic hypotheses from landmark data. PMID:25516268

  2. 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

  3. Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata.

    PubMed

    Fong, Jonathan J; Fujita, Matthew K

    2011-11-01

    As a resource for vertebrate phylogenetics, we developed 75 new protein-coding genes using a combination of expressed sequence tags (ESTs) available in Genbank, and targeted amplification of complementary DNA (cDNA). In addition, we performed three additional analyses in order to assess the utility of our approach. First, we profiled the phylogenetic informativeness of these new markers using the online program PhyDesign. Next, we compared the utility of four different data-types used in phylogenetics: nucleotides (NUCL), amino acids (AA), 1st and 2nd codon positions only (N12), and modified sequences to account for codon degeneracy (DEGEN1; Regier et al., 2010). Lastly, we use these new markers to construct a vertebrate phylogeny and address the uncertain relationship between higher-level mammal groups: monotremes, marsupials, and placentals. Our results show that phylogenetic informativeness of the 75 new markers varies, both in the amount of phylogenetic signal and optimal timescale. When comparing the four data-types, we find that the NUCL data-type, due to the high level of phylogenetic signal, performs the best across all divergence times. The remaining three data-types (AA, N12, DEGEN1) are less subject to homoplasy, but have greatly reduced levels of phylogenetic signal relative to NUCL. Our phylogenetic inference supports the Theria hypothesis of mammalian relationships, with marsupials and placentals being sister groups.

  4. 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

  5. Application of the phylogenetic informativeness method to chloroplast markers: a test case of closely related species in tribe Hydrangeeae (Hydrangeaceae).

    PubMed

    Granados Mendoza, Carolina; Wanke, Stefan; Salomo, Karsten; Goetghebeur, Paul; Samain, Marie-Stéphanie

    2013-01-01

    In evolutionary biology appropriate marker selection for the reconstruction of solid phylogenetic hypotheses is fundamental. One of the most challenging tasks addresses the appropriate choice of genomic regions in studies of closely related species. Robust phylogenetic frameworks are central to studies dealing with questions ranging from evolutionary and conservation biology, biogeography to plant breeding. Phylogenetic informativeness profiles provide a quantitative measure of the phylogenetic signal in markers and therefore a method for locus prioritization. The present work profiles phylogenetic informativeness of mostly non-coding chloroplast regions in an angiosperm lineage of closely related species: the popular ornamental tribe Hydrangeeae (Hydrangeaceae, Cornales, Asterids). A recent phylogenetic study denoted a case of resolution contrast between the two strongly supported clades within tribe Hydrangeeae. We evaluate the phylogenetic signal of 13 highly variable plastid markers for estimating relationships within and among the currently recognized monophyletic groups of this tribe. A selection of combined loci based on their phylogenetic informativeness retrieved more robust phylogenetic hypotheses than simply combining individual markers performing best with respect to resolution, nodal support and accuracy or those presenting the highest number of parsimony informative characters. We propose the rpl32-ndhF intergenic spacer (IGS), trnV-ndhC IGS, trnL-rpl32 IGS, psbT-petB region and ndhA intron as the best candidates for future phylogenetic studies in Hydrangeeae and potentially in other Asterids. We also contrasted the phylogenetic informativeness of coded indels against substitutions concluding that, despite their low phylogenetic informativeness, coded indels provide additional phylogenetic signal that is nearly free of noise. Phylogenetic relationships obtained from our total combined analyses showed improved resolution and nodal support with respect

  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. 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.

  8. 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

  9. 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.

  10. Phylogenetic analysis of ruminant Theileria spp. from China based on 28S ribosomal RNA gene.

    PubMed

    Gou, Huitian; Guan, Guiquan; Ma, Miling; Liu, Aihong; Liu, Zhijie; Xu, Zongke; Ren, Qiaoyun; Li, Youquan; Yang, Jifei; Chen, Ze; Yin, Hong; Luo, Jianxun

    2013-10-01

    Species identification using DNA sequences is the basis for DNA taxonomy. In this study, we sequenced the ribosomal large-subunit RNA gene sequences (3,037-3,061 bp) in length of 13 Chinese Theileria stocks that were infective to cattle and sheep. The complete 28S rRNA gene is relatively difficult to amplify and its conserved region is not important for phylogenetic study. Therefore, we selected the D2-D3 region from the complete 28S rRNA sequences for phylogenetic analysis. Our analyses of 28S rRNA gene sequences showed that the 28S rRNA was useful as a phylogenetic marker for analyzing the relationships among Theileria spp. in ruminants. In addition, the D2-D3 region was a short segment that could be used instead of the whole 28S rRNA sequence during the phylogenetic analysis of Theileria, and it may be an ideal DNA barcode.

  11. 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

  12. 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

  13. New algorithms for reconstructing phylogenetic trees

    SciTech Connect

    Dress, A.

    1994-12-31

    Since the time of Linne, classification of living beings into subspecies, species, orders, families etc. has been an important task in biology. With the advent of molecular biology, many more data have become available which can be exploited for this purpose using comparative sequence analysis, while the sheer amount of these data stored presently in biomolecular data bases make automated classification procedures unavoidable. Consequently, many algorithms have been developed in the last 25 years to support this task. In the lecture, an amazingly successful polynomial algorithm for analysing all sorts of distance data derived from sequence analysis (or elsewhere) will be presented which simultaneously highlights phylogenetic similarity and similarity caused by convergent evolution. In addition to sketching the mathematics on which the algorithm is based and discussing its implementation (including some interesting computer graphics aspects), various proper biological examples will be presented which stretch from the analysis of data relating to the origin of life and the first bifurcations into the various {open_quote}kingdoms of life{close_quote} to the analysis of data relating to, say, the phylogenetic history of mammals or that of the AIDS or the Influenca virus family.

  14. Posterior predictive Bayesian phylogenetic model selection.

    PubMed

    Lewis, Paul O; Xie, Wangang; Chen, Ming-Hui; Fan, Yu; Kuo, Lynn

    2014-05-01

    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. PMID:24193892

  15. Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

    PubMed Central

    Meusemann, Karen; Meyer, Benjamin; Borner, Janus; Petersen, Malte; Aberer, Andre J.; Stamatakis, Alexandros; Walzl, Manfred G.; Minh, Bui Quang; von Haeseler, Arndt; Ebersberger, Ingo; Pass, Günther; Misof, Bernhard

    2014-01-01

    Phylogenetic relationships of the primarily wingless insects are still considered unresolved. Even the most comprehensive phylogenomic studies that addressed this question did not yield congruent results. To get a grip on these problems, we here analyzed the sources of incongruence in these phylogenomic studies by using an extended transcriptome data set. Our analyses showed that unevenly distributed missing data can be severely misleading by inflating node support despite the absence of phylogenetic signal. In consequence, only decisive data sets should be used which exclusively comprise data blocks containing all taxa whose relationships are addressed. Additionally, we used Four-cluster Likelihood Mapping (FcLM) to measure the degree of congruence among genes of a data set, as a measure of support alternative to bootstrap. FcLM showed incongruent signal among genes, which in our case is correlated neither with functional class assignment of these genes nor with model misspecification due to unpartitioned analyses. The herein analyzed data set is the currently largest data set covering primarily wingless insects, but failed to elucidate their interordinal phylogenetic relationships. Although this is unsatisfying from a phylogenetic perspective, we try to show that the analyses of structure and signal within phylogenomic data can protect us from biased phylogenetic inferences due to analytical artifacts. PMID:24140757

  16. 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

  17. 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.

  18. Analysing spatio-temporal patterns of the global NO2-distribution retrieved from GOME satellite observations using a generalized additive model

    NASA Astrophysics Data System (ADS)

    Hayn, M.; Beirle, S.; Hamprecht, F. A.; Platt, U.; Menze, B. H.; Wagner, T.

    2009-09-01

    With the increasing availability of observational data from different sources at a global level, joint analysis of these data is becoming especially attractive. For such an analysis - oftentimes with little prior knowledge about local and global interactions between the different observational variables at hand - an exploratory, data-driven analysis of the data may be of particular relevance. In the present work we used generalized additive models (GAM) in an exemplary study of spatio-temporal patterns in the tropospheric NO2-distribution derived from GOME satellite observations (1996 to 2001) at global scale. We focused on identifying correlations between NO2 and local wind fields, a quantity which is of particular interest in the analysis of spatio-temporal interactions. Formulating general functional, parametric relationships between the observed NO2 distribution and local wind fields, however, is difficult - if not impossible. So, rather than following a model-based analysis testing the data for predefined hypotheses (assuming, for example, sinusoidal seasonal trends), we used a GAM with non-parametric model terms to learn this functional relationship between NO2 and wind directly from the data. The NO2 observations showed to be affected by wind-dominated processes over large areas. We estimated the extent of areas affected by specific NO2 emission sources, and were able to highlight likely atmospheric transport "pathways". General temporal trends which were also part of our model - weekly, seasonal and linear changes - showed to be in good agreement with previous studies and alternative ways of analysing the time series. Overall, using a non-parametric model provided favorable means for a rapid inspection of this large spatio-temporal NO2 data set, with less bias than parametric approaches, and allowing to visualize dynamical processes of the NO2 distribution at a global scale.

  19. Impact of enzalutamide on quality of life in men with metastatic castration-resistant prostate cancer after chemotherapy: additional analyses from the AFFIRM randomized clinical trial

    PubMed Central

    Cella, D.; Ivanescu, C.; Holmstrom, S.; Bui, C. N.; Spalding, J.; Fizazi, K.

    2015-01-01

    Background To present longitudinal changes in Functional Assessment of Cancer Therapy-Prostate (FACT-P) scores during 25-week treatment with enzalutamide or placebo in men with progressive metastatic castration-resistant prostate cancer (mCRPC) after chemotherapy in the AFFIRM trial. Patients and methods Patients were randomly assigned to enzalutamide 160 mg/day or placebo. FACT-P was completed before randomization, at weeks 13, 17, 21, and 25, and every 12 weeks thereafter while on study treatment. Longitudinal changes in FACT-P scores from baseline to 25 weeks were analyzed using a mixed effects model for repeated measures (MMRM), with a pattern mixture model (PMM) applied as secondary analysis to address non-ignorable missing data. Cumulative distribution function (CDF) plots were generated and different methodological approaches and models for handling missing data were applied. Due to the exploratory nature of the analyses, adjustments for multiple comparisons were not made. AFFIRM is registered with ClinicalTrials.gov, number NCT00974311. Results The intention-to-treat FACT-P population included 938 patients (enzalutamide, n = 674; placebo n = 264) with evaluable FACT-P assessments at baseline and ≥1 post-baseline assessment. After 25 weeks, the mean FACT-P total score decreased by 1.52 points with enzalutamide compared with 13.73 points with placebo (P < 0.001). In addition, significant treatment differences at week 25 favoring enzalutamide were evident for all FACT-P subscales and indices, whether analyzed by MMRM or PMM. CDF plots revealed differences favoring enzalutamide compared with placebo across the full range of possible response levels for FACT-P total and all disease- and symptom-specific subscales/indices. Conclusion In men with progressive mCRPC after docetaxel-based chemotherapy, enzalutamide is superior to placebo in health-related quality-of-life outcomes, regardless of analysis model or threshold selected for meaningful response. Clinical

  20. On Tree-Based Phylogenetic Networks.

    PubMed

    Zhang, Louxin

    2016-07-01

    A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree-based networks. We present a simple necessary and sufficient condition for tree-based networks and prove that a universal tree-based network exists for any number of taxa that contains as its base every phylogenetic tree on the same set of taxa. This answers two problems posted by Francis and Steel recently. A byproduct is a computer program for generating random binary phylogenetic networks under the uniform distribution model.

  1. Terraces in phylogenetic tree space.

    PubMed

    Sanderson, Michael J; McMahon, Michelle M; Steel, Mike

    2011-07-22

    A key step in assembling the tree of life is the construction of species-rich phylogenies from multilocus--but often incomplete--sequence data sets. We describe previously unknown structure in the landscape of solutions to the tree reconstruction problem, comprising sometimes vast "terraces" of trees with identical quality, arranged on islands of phylogenetically similar trees. Phylogenetic ambiguity within a terrace can be characterized efficiently and then ameliorated by new algorithms for obtaining a terrace's maximum-agreement subtree or by identifying the smallest set of new targets for additional sequencing. Algorithms to find optimal trees or estimate Bayesian posterior tree distributions may need to navigate strategically in the neighborhood of large terraces in tree space.

  2. 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

  3. 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...

  4. Maximum Parsimony on Phylogenetic networks

    PubMed Central

    2012-01-01

    Background Phylogenetic networks are generalizations of phylogenetic trees, that are used to model evolutionary events in various contexts. Several different methods and criteria have been introduced for reconstructing phylogenetic trees. Maximum Parsimony is a character-based approach that infers a phylogenetic tree by minimizing the total number of evolutionary steps required to explain a given set of data assigned on the leaves. Exact solutions for optimizing parsimony scores on phylogenetic trees have been introduced in the past. Results In this paper, we define the parsimony score on networks as the sum of the substitution costs along all the edges of the network; and show that certain well-known algorithms that calculate the optimum parsimony score on trees, such as Sankoff and Fitch algorithms extend naturally for networks, barring conflicting assignments at the reticulate vertices. We provide heuristics for finding the optimum parsimony scores on networks. Our algorithms can be applied for any cost matrix that may contain unequal substitution costs of transforming between different characters along different edges of the network. We analyzed this for experimental data on 10 leaves or fewer with at most 2 reticulations and found that for almost all networks, the bounds returned by the heuristics matched with the exhaustively determined optimum parsimony scores. Conclusion The parsimony score we define here does not directly reflect the cost of the best tree in the network that displays the evolution of the character. However, when searching for the most parsimonious network that describes a collection of characters, it becomes necessary to add additional cost considerations to prefer simpler structures, such as trees over networks. The parsimony score on a network that we describe here takes into account the substitution costs along the additional edges incident on each reticulate vertex, in addition to the substitution costs along the other edges which are

  5. Phylogenetic analysis of adenovirus sequences.

    PubMed

    Harrach, Balázs; Benko, Mária

    2007-01-01

    Members of the family Adenoviridae have been isolated from a large variety of hosts, including representatives from every major vertebrate class from fish to mammals. The high prevalence, together with the fairly conserved organization of the central part of their genomes, make the adenoviruses one of (if not the) best models for studying viral evolution on a larger time scale. Phylogenetic calculation can infer the evolutionary distance among adenovirus strains on serotype, species, and genus levels, thus helping the establishment of a correct taxonomy on the one hand, and speeding up the process of typing new isolates on the other. Initially, four major lineages corresponding to four genera were recognized. Later, the demarcation criteria of lower taxon levels, such as species or types, could also be defined with phylogenetic calculations. A limited number of possible host switches have been hypothesized and convincingly supported. Application of the web-based BLAST and MultAlin programs and the freely available PHYLIP package, along with the TreeView program, enables everyone to make correct calculations. In addition to step-by-step instruction on how to perform phylogenetic analysis, critical points where typical mistakes or misinterpretation of the results might occur will be identified and hints for their avoidance will be provided. PMID:17656792

  6. Phylogenetic analysis of adenovirus sequences.

    PubMed

    Harrach, Balázs; Benko, Mária

    2007-01-01

    Members of the family Adenoviridae have been isolated from a large variety of hosts, including representatives from every major vertebrate class from fish to mammals. The high prevalence, together with the fairly conserved organization of the central part of their genomes, make the adenoviruses one of (if not the) best models for studying viral evolution on a larger time scale. Phylogenetic calculation can infer the evolutionary distance among adenovirus strains on serotype, species, and genus levels, thus helping the establishment of a correct taxonomy on the one hand, and speeding up the process of typing new isolates on the other. Initially, four major lineages corresponding to four genera were recognized. Later, the demarcation criteria of lower taxon levels, such as species or types, could also be defined with phylogenetic calculations. A limited number of possible host switches have been hypothesized and convincingly supported. Application of the web-based BLAST and MultAlin programs and the freely available PHYLIP package, along with the TreeView program, enables everyone to make correct calculations. In addition to step-by-step instruction on how to perform phylogenetic analysis, critical points where typical mistakes or misinterpretation of the results might occur will be identified and hints for their avoidance will be provided.

  7. 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

  8. 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

  9. 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.

  10. 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).

  11. 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

  12. 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.

  13. Maximizing the phylogenetic diversity of seed banks.

    PubMed

    Griffiths, Kate E; Balding, Sharon T; Dickie, John B; Lewis, Gwilym P; Pearce, Tim R; Grenyer, Richard

    2015-04-01

    Ex situ conservation efforts such as those of zoos, botanical gardens, and seed banks will form a vital complement to in situ conservation actions over the coming decades. It is therefore necessary to pay the same attention to the biological diversity represented in ex situ conservation facilities as is often paid to protected-area networks. Building the phylogenetic diversity of ex situ collections will strengthen our capacity to respond to biodiversity loss. Since 2000, the Millennium Seed Bank Partnership has banked seed from 14% of the world's plant species. We assessed the taxonomic, geographic, and phylogenetic diversity of the Millennium Seed Bank collection of legumes (Leguminosae). We compared the collection with all known legume genera, their known geographic range (at country and regional levels), and a genus-level phylogeny of the legume family constructed for this study. Over half the phylogenetic diversity of legumes at the genus level was represented in the Millennium Seed Bank. However, pragmatic prioritization of species of economic importance and endangerment has led to the banking of a less-than-optimal phylogenetic diversity and prioritization of range-restricted species risks an underdispersed collection. The current state of the phylogenetic diversity of legumes in the Millennium Seed Bank could be substantially improved through the strategic banking of relatively few additional taxa. Our method draws on tools that are widely applied to in situ conservation planning, and it can be used to evaluate and improve the phylogenetic diversity of ex situ collections.

  14. Maximizing the phylogenetic diversity of seed banks.

    PubMed

    Griffiths, Kate E; Balding, Sharon T; Dickie, John B; Lewis, Gwilym P; Pearce, Tim R; Grenyer, Richard

    2015-04-01

    Ex situ conservation efforts such as those of zoos, botanical gardens, and seed banks will form a vital complement to in situ conservation actions over the coming decades. It is therefore necessary to pay the same attention to the biological diversity represented in ex situ conservation facilities as is often paid to protected-area networks. Building the phylogenetic diversity of ex situ collections will strengthen our capacity to respond to biodiversity loss. Since 2000, the Millennium Seed Bank Partnership has banked seed from 14% of the world's plant species. We assessed the taxonomic, geographic, and phylogenetic diversity of the Millennium Seed Bank collection of legumes (Leguminosae). We compared the collection with all known legume genera, their known geographic range (at country and regional levels), and a genus-level phylogeny of the legume family constructed for this study. Over half the phylogenetic diversity of legumes at the genus level was represented in the Millennium Seed Bank. However, pragmatic prioritization of species of economic importance and endangerment has led to the banking of a less-than-optimal phylogenetic diversity and prioritization of range-restricted species risks an underdispersed collection. The current state of the phylogenetic diversity of legumes in the Millennium Seed Bank could be substantially improved through the strategic banking of relatively few additional taxa. Our method draws on tools that are widely applied to in situ conservation planning, and it can be used to evaluate and improve the phylogenetic diversity of ex situ collections. PMID:25196170

  15. 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)

  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. 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

  18. 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

  19. Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing

    PubMed Central

    Pearson, Talima; Busch, Joseph D.; Ravel, Jacques; Read, Timothy D.; Rhoton, Shane D.; U'Ren, Jana M.; Simonson, Tatum S.; Kachur, Sergey M.; Leadem, Rebecca R.; Cardon, Michelle L.; Van Ert, Matthew N.; Huynh, Lynn Y.; Fraser, Claire M.; Keim, Paul

    2004-01-01

    Phylogenetic reconstruction using molecular data is often subject to homoplasy, leading to inaccurate conclusions about phylogenetic relationships among operational taxonomic units. Compared with other molecular markers, single-nucleotide polymorphisms (SNPs) exhibit extremely low mutation rates, making them rare in recently emerged pathogens, but they are less prone to homoplasy and thus extremely valuable for phylogenetic analyses. Despite their phylogenetic potential, ascertainment bias occurs when SNP characters are discovered through biased taxonomic sampling; by using whole-genome comparisons of five diverse strains of Bacillus anthracis to facilitate SNP discovery, we show that only polymorphisms lying along the evolutionary pathway between reference strains will be observed. We illustrate this in theoretical and simulated data sets in which complex phylogenetic topologies are reduced to linear evolutionary models. Using a set of 990 SNP markers, we also show how divergent branches in our topologies collapse to single points but provide accurate information on internodal distances and points of origin for ancestral clades. These data allowed us to determine the ancestral root of B. anthracis, showing that it lies closer to a newly described “C” branch than to either of two previously described “A” or “B” branches. In addition, subclade rooting of the C branch revealed unequal evolutionary rates that seem to be correlated with ecological parameters and strain attributes. Our use of nonhomoplastic whole-genome SNP characters allows branch points and clade membership to be estimated with great precision, providing greater insight into epidemiological, ecological, and forensic questions. PMID:15347815

  20. 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.

  1. Additive-dominance genetic model analyses for late-maturity alpha-amylase activity in a bread wheat factorial crossing population.

    PubMed

    Rasul, Golam; Glover, Karl D; Krishnan, Padmanaban G; Wu, Jixiang; Berzonsky, William A; Ibrahim, Amir M H

    2015-12-01

    Elevated level of late maturity α-amylase activity (LMAA) can result in low falling number scores, reduced grain quality, and downgrade of wheat (Triticum aestivum L.) class. A mating population was developed by crossing parents with different levels of LMAA. The F2 and F3 hybrids and their parents were evaluated for LMAA, and data were analyzed using the R software package 'qgtools' integrated with an additive-dominance genetic model and a mixed linear model approach. Simulated results showed high testing powers for additive and additive × environment variances, and comparatively low powers for dominance and dominance × environment variances. All variance components and their proportions to the phenotypic variance for the parents and hybrids were significant except for the dominance × environment variance. The estimated narrow-sense heritability and broad-sense heritability for LMAA were 14 and 54%, respectively. High significant negative additive effects for parents suggest that spring wheat cultivars 'Lancer' and 'Chester' can serve as good general combiners, and that 'Kinsman' and 'Seri-82' had negative specific combining ability in some hybrids despite of their own significant positive additive effects, suggesting they can be used as parents to reduce LMAA levels. Seri-82 showed very good general combining ability effect when used as a male parent, indicating the importance of reciprocal effects. High significant negative dominance effects and high-parent heterosis for hybrids demonstrated that the specific hybrid combinations; Chester × Kinsman, 'Lerma52' × Lancer, Lerma52 × 'LoSprout' and 'Janz' × Seri-82 could be generated to produce cultivars with significantly reduced LMAA level.

  2. Deep sequencing increases hepatitis C virus phylogenetic cluster detection compared to Sanger sequencing.

    PubMed

    Montoya, Vincent; Olmstead, Andrea; Tang, Patrick; Cook, Darrel; Janjua, Naveed; Grebely, Jason; Jacka, Brendan; Poon, Art F Y; Krajden, Mel

    2016-09-01

    Effective surveillance and treatment strategies are required to control the hepatitis C virus (HCV) epidemic. Phylogenetic analyses are powerful tools for reconstructing the evolutionary history of viral outbreaks and identifying transmission clusters. These studies often rely on Sanger sequencing which typically generates a single consensus sequence for each infected individual. For rapidly mutating viruses such as HCV, consensus sequencing underestimates the complexity of the viral quasispecies population and could therefore generate different phylogenetic tree topologies. Although deep sequencing provides a more detailed quasispecies characterization, in-depth phylogenetic analyses are challenging due to dataset complexity and computational limitations. Here, we apply deep sequencing to a characterized population to assess its ability to identify phylogenetic clusters compared with consensus Sanger sequencing. For deep sequencing, a sample specific threshold determined by the 50th percentile of the patristic distance distribution for all variants within each individual was used to identify clusters. Among seven patristic distance thresholds tested for the Sanger sequence phylogeny ranging from 0.005-0.06, a threshold of 0.03 was found to provide the maximum balance between positive agreement (samples in a cluster) and negative agreement (samples not in a cluster) relative to the deep sequencing dataset. From 77 HCV seroconverters, 10 individuals were identified in phylogenetic clusters using both methods. Deep sequencing analysis identified an additional 4 individuals and excluded 8 other individuals relative to Sanger sequencing. The application of this deep sequencing approach could be a more effective tool to understand onward HCV transmission dynamics compared with Sanger sequencing, since the incorporation of minority sequence variants improves the discrimination of phylogenetically linked clusters.

  3. Novel Flow Cytometry Analyses of Boar Sperm Viability: Can the Addition of Whole Sperm-Rich Fraction Seminal Plasma to Frozen-Thawed Boar Sperm Affect It?

    PubMed Central

    Díaz, Rommy; Boguen, Rodrigo; Martins, Simone Maria Massami Kitamura; Ravagnani, Gisele Mouro; Leal, Diego Feitosa; Oliveira, Melissa de Lima; Muro, Bruno Bracco Donatelli; Parra, Beatriz Martins; Meirelles, Flávio Vieira; Papa, Frederico Ozanan; Dell’Aqua, José Antônio; Alvarenga, Marco Antônio; Moretti, Aníbal de Sant’Anna; Sepúlveda, Néstor

    2016-01-01

    Boar semen cryopreservation remains a challenge due to the extension of cold shock damage. Thus, many alternatives have emerged to improve the quality of frozen-thawed boar sperm. Although the use of seminal plasma arising from boar sperm-rich fraction (SP-SRF) has shown good efficacy; however, the majority of actual sperm evaluation techniques include a single or dual sperm parameter analysis, which overrates the real sperm viability. Within this context, this work was performed to introduce a sperm flow cytometry fourfold stain technique for simultaneous evaluation of plasma and acrosomal membrane integrity and mitochondrial membrane potential. We then used the sperm flow cytometry fourfold stain technique to study the effect of SP-SRF on frozen-thawed boar sperm and further evaluated the effect of this treatment on sperm movement, tyrosine phosphorylation and fertility rate (FR). The sperm fourfold stain technique is accurate (R2 = 0.9356, p > 0.01) for simultaneous evaluation of plasma and acrosomal membrane integrity and mitochondrial membrane potential (IPIAH cells). Centrifugation pre-cryopreservation was not deleterious (p > 0.05) for any analyzed variables. Addition of SP-SRF after cryopreservation was able to improve total and progressive motility (p < 0.05) when boar semen was cryopreserved without SP-SRF; however, it was not able to decrease tyrosine phosphorylation (p > 0.05) or improve IPIAH cells (p > 0.05). FR was not (p > 0.05) statistically increased by the addition of seminal plasma, though females inseminated with frozen-thawed boar semen plus SP-SRF did perform better than those inseminated with sperm lacking seminal plasma. Thus, we conclude that sperm fourfold stain can be used to simultaneously evaluate plasma and acrosomal membrane integrity and mitochondrial membrane potential, and the addition of SP-SRF at thawed boar semen cryopreserved in absence of SP-SRF improve its total and progressive motility. PMID:27529819

  4. Diversity of Clonostachys species assessed by molecular phylogenetics and MALDI-TOF mass spectrometry.

    PubMed

    Abreu, Lucas M; Moreira, Gláucia M; Ferreira, Douglas; Rodrigues-Filho, Edson; Pfenning, Ludwig H

    2014-12-01

    We assessed the species diversity among 45 strains of Clonostachys from different substrates and localities in Brazil using molecular phylogenetics, and compared the results with the phenotypic classification of strains obtained from matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Phylogenetic analyses were based on beta tubulin (Tub), ITS-LSU rDNA, and a combined Tub-ITS DNA dataset. MALDI-TOF MS analyses were performed using intact conidia and conidiophores of strains cultivated on oatmeal agar and 4% malt extract agar. Six known species were identified: Clonostachys byssicola, Clonostachys candelabrum, Clonostachys pseudochroleuca, Clonostachys rhizophaga, Clonostachys rogersoniana, and Clonostachys rosea. Two clades and two singleton lineages did not correspond to known species represented in the reference DNA dataset and were identified as Clonostachys sp. 1-4. Multivariate cluster analyses of MALDI-TOF MS data classified the strains into eight clusters and three singletons, corresponding to the ten identified species plus one additional cluster containing two strains of C. rogersoniana that split from the other co-specific strains. The consistent results of MALDI-TOF MS supported the identification of strains assigned to C. byssicola and C. pseudochroleuca, which did not form well supported clades in all phylogenetic analyses, but formed distinct clusters in the MALDI-TOF dendrograms. PMID:25457948

  5. Merging and comparing three mitochondrial markers for phylogenetic studies of Eurasian reindeer (Rangifer tarandus).

    PubMed

    Kvie, Kjersti S; Heggenes, Jan; Røed, Knut H

    2016-07-01

    Phylogenetic analyses provide information that can be useful in the conservation of genetic variation by identifying intraspecific genetic structure. Reconstruction of phylogenetic relationships requires the use of markers with the appropriate amount of variation relative to the timeframe and purpose of the study. Here, genetic structure and clustering are inferred from comparative analyses of three widely used mitochondrial markers, the CR, cytb and the COI region, merged and separately, using Eurasian reindeer as a model. A Bayesian phylogeny and a MJ network, both based on the merged dataset, indicate several distinct maternal haplotype clusters within Eurasian reindeer. In addition to confirm previously described clusters, two new subclusters were found. When comparing the results from the merged dataset with the results from analyses of the three markers separately, similar clustering was found in the CR and COI phylogenies, whereas the cytb region showed poor resolution. Phylogenetic analyses of the merged dataset and the CR revealed congruent results, implying that single sequencing analysis of the CR is an applicable method for studying the haplotype structure in Eurasian reindeer.

  6. Merging and comparing three mitochondrial markers for phylogenetic studies of Eurasian reindeer (Rangifer tarandus).

    PubMed

    Kvie, Kjersti S; Heggenes, Jan; Røed, Knut H

    2016-07-01

    Phylogenetic analyses provide information that can be useful in the conservation of genetic variation by identifying intraspecific genetic structure. Reconstruction of phylogenetic relationships requires the use of markers with the appropriate amount of variation relative to the timeframe and purpose of the study. Here, genetic structure and clustering are inferred from comparative analyses of three widely used mitochondrial markers, the CR, cytb and the COI region, merged and separately, using Eurasian reindeer as a model. A Bayesian phylogeny and a MJ network, both based on the merged dataset, indicate several distinct maternal haplotype clusters within Eurasian reindeer. In addition to confirm previously described clusters, two new subclusters were found. When comparing the results from the merged dataset with the results from analyses of the three markers separately, similar clustering was found in the CR and COI phylogenies, whereas the cytb region showed poor resolution. Phylogenetic analyses of the merged dataset and the CR revealed congruent results, implying that single sequencing analysis of the CR is an applicable method for studying the haplotype structure in Eurasian reindeer. PMID:27386080

  7. Phylogenetic perspectives of nitrogen-fixing actinobacteria.

    PubMed

    Gtari, Maher; Ghodhbane-Gtari, Faten; Nouioui, Imen; Beauchemin, Nicholas; Tisa, Louis S

    2012-01-01

    It was assumed for a long time that the ability to catalyze atmospheric nitrogen (diazotrophy) has a narrow distribution among actinobacteria being limited to the genus Frankia. Recently, the number of nitrogen fixation (nifH) genes identified in other non-Frankia actinobacteria has dramatically increased and has opened investigation on the origin and emergence of diazotrophy among actinobacteria. During the last decade, Mycobacterium flavum, Corynebacterium autotrophicum and a fluorescent Arthrobacter sp. have been reported to have nitrogenase activity, but these studies have not been further verified. Additional reports of nitrogen fixation by Agromyces, Microbacterium, Corynebacterium and Micromonospora isolated from root nodules of leguminous and actinorhizal plants have increased. For several actinobacteria, nitrogen fixation was demonstrated by the ability to grow on nitrogen-free medium, acetylene reduction activity, 15N isotope dilution analysis and identification of a nifH gene via PCR amplification. Moreover, the analyses of draft genome sequences of actinobacteria including Slackia exigua, Rothia mucilaginosa and Gordonibacter pamelaeae have also revealed the presence of nifH-like sequences. Whether these nifH sequences are associated with effective nitrogen fixation in these actinobacteria taxa has not yet been demonstrated. These genes may be vertically or horizontally transferred and be silent sequences. These ideas merit further investigation. This minireview presents a phylogenetic comparison of nitrogen fixation gene (nifH) with the aim of elucidating the processes underlying the evolutionary history of this catalytic ability among actinobacteria.

  8. 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

  9. 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

  10. Phylogenomic analyses and improved resolution of Cetartiodactyla.

    PubMed

    Zhou, Xuming; Xu, Shixia; Yang, Yunxia; Zhou, Kaiya; Yang, Guang

    2011-11-01

    The remarkable antiquity, diversity, and significance in the ecology and evolution of Cetartiodactyla have inspired numerous attempts to resolve their phylogenetic relationships. However, previous analyses based on limited samples of nuclear genes or mitochondrial DNA sequences have generated results that were either inconsistent with one another, weakly supported, or highly sensitive to analytical conditions. Here, we present strongly supported results based upon over 1.4 Mb of an aligned DNA sequence matrix from 110 single-copy nuclear protein-coding genes of 21 Cetartiodactyla species, which represent major Cetartiodactyla lineages, and three species of Perissodactyla and Carnivora as outgroups. Phylogenetic analysis of this newly developed genomic sequence data using a codon-based model and recently developed models of the rate autocorrelation resolved the phylogenetic relationships of the major cetartiodactylan lineages and of those lineages with a high degree of confidence. Cetacea was found to nest within Artiodactyla as the sister group of Hippopotamidae, and Tylopoda was corroborated as the sole base clade of Cetartiodactyla. Within Cetacea, the monophyletic status of Odontoceti relative to Mysticeti, the basal position of Physeteroidea in Odontoceti, the non-monophyly of the river dolphins, and the sister relationship between Delphinidae and Monodontidae+Phocoenidae were strongly supported. In particular, the groups of Tursiops (bottlenose dolphins) and Stenella (spotted dolphins) were validated as unnatural groups. Additionally, a very narrow time frame of ∼3 My (million years) was found for the rapid diversification of delphinids in the late Miocene, which made it difficult to resolve the phylogenetic relationships within the Delphinidae, especially for previous studies with limited data sets. The present study provides a statistically well-supported phylogenetic framework of Cetartiodactyla, which represents an important step toward ending some of

  11. The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation

    PubMed Central

    Roger, Andrew J; Hug, Laura A

    2006-01-01

    Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes. Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods

  12. 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.

  13. 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

  14. Analysing spatio-temporal patterns of the global NO2-distribution retrieved from GOME satellite observations using a generalized additive model

    NASA Astrophysics Data System (ADS)

    Hayn, M.; Beirle, S.; Hamprecht, F. A.; Platt, U.; Menze, B. H.; Wagner, T.

    2009-04-01

    With the increasing availability of observations from different space-borne sensors, the joint analysis of observational data from multiple sources becomes more and more attractive. For such an analysis - oftentimes with little prior knowledge about local and global interactions between the different observational variables available - an explorative data-driven analysis of the remote sensing data may be of particular relevance. In the present work we used generalized additive models (GAM) in this task, in an exemplary study of spatio-temporal patterns in the tropospheric NO2-distribution derived from GOME satellite observations (1996 to 2001) at global scale. We modelled different temporal trends in the time series of the observed NO2, but focused on identifying correlations between NO2 and local wind fields. Here, our nonparametric modelling approach had several advantages over standard parametric models: While the model-based analysis allowed to test predefined hypotheses (assuming, for example, sinusoidal seasonal trends) only, the GAM allowed to learn functional relations between different observational variables directly from the data. This was of particular interest in the present task, as little was known about relations between the observed NO2 distribution and transport processes by local wind fields, and the formulation of general functional relationships to be tested remained difficult. We found the observed temporal trends - weekly, seasonal and linear changes - to be in overall good agreement with previous studies and alternative ways of data analysis. However, NO2 observations showed to be affected by wind-dominated processes over several areas, world wide. Here we were able to estimate the extent of areas affected by specific NO2 emission sources, and to highlight likely atmospheric transport pathways. Overall, using a nonparametric model provided favourable means for a rapid inspection of this large spatio-temporal data set,with less bias than

  15. 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

  16. 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.

  17. 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.

  18. Ancient phylogenetic relationships.

    PubMed

    Gribaldo, Simonetta; Philippe, Hervé

    2002-06-01

    Traditional views on deep evolutionary events have been seriously challenged over the last few years, following the identification of major pitfalls affecting molecular phylogeny reconstruction. Here we describe the principally encountered artifacts, notably long branch attraction, and their causes (i.e., difference in evolutionary rates, mutational saturation, compositional biases). Additional difficulties due to phenomena of biological nature (i.e., lateral gene transfer, recombination, hidden paralogy) are also discussed. Moreover, contrary to common beliefs, we show that the use of rare genomic events can also be misleading and should be treated with the same caution as standard molecular phylogeny. The universal tree of life, as described in most textbooks, is partly affected by tree reconstruction artifacts, e.g. (i) the bacterial rooting of the universal tree of life; (ii) the early emergence of amitochondriate lineages in eukaryotic phylogenies; and (iii) the position of hyperthermophilic taxa in bacterial phylogenies. We present an alternative view of this tree, based on recent evidence obtained from reanalyses of ancient data sets and from novel analyses of large combination of genes.

  19. 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.

  20. Trinets encode tree-child and level-2 phylogenetic networks.

    PubMed

    van Iersel, Leo; Moulton, Vincent

    2014-06-01

    Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. Recently, there has been great interest in trying to develop methods to construct rooted phylogenetic networks from triplets, that is rooted trees on three species. However, although triplets determine or encode rooted phylogenetic trees, they do not in general encode rooted phylogenetic networks, which is a potential issue for any such method. Motivated by this fact, Huber and Moulton recently introduced trinets as a natural extension of rooted triplets to networks. In particular, they showed that [Formula: see text] phylogenetic networks are encoded by their trinets, and also conjectured that all "recoverable" rooted phylogenetic networks are encoded by their trinets. Here we prove that recoverable binary level-2 networks and binary tree-child networks are also encoded by their trinets. To do this we prove two decomposition theorems based on trinets which hold for all recoverable binary rooted phylogenetic networks. Our results provide some additional evidence in support of the conjecture that trinets encode all recoverable rooted phylogenetic networks, and could also lead to new approaches to construct phylogenetic networks from trinets.

  1. Multigene analysis of phylogenetic relationships and divergence times of primate sucking lice (Phthiraptera: Anoplura).

    PubMed

    Light, Jessica E; Reed, David L

    2009-02-01

    Cospeciation between hosts and parasites offers a unique opportunity to use information from parasites to infer events in host evolutionary history. Although lice (Insecta: Phthiraptera) are known to cospeciate with their hosts and have frequently served as important markers to infer host evolutionary history, most molecular studies are based on only one or two markers. Resulting phylogenies may, therefore, represent gene histories (rather than species histories), and analyses of multiple molecular markers are needed to increase confidence in the results of phylogenetic analyses. Herein, we phylogenetically examine nine molecular markers in primate sucking lice (Phthiraptera: Anoplura) and we use these markers to estimate divergence times among louse lineages. Individual and combined analyses of these nine markers are, for the most part, congruent, supporting relationships hypothesized in previous studies. Only one marker, the nuclear protein-coding gene Histone 3, has a significantly different tree topology compared to the other markers. The disparate evolutionary history of this marker, however, has no significant effect on topology or nodal support in the combined phylogenetic analyses. Therefore, phylogenetic results from the combined data set likely represent a solid hypothesis of species relationships. Additionally, we find that simultaneous use of multiple markers and calibration points provides the most reliable estimates of louse divergence times, in agreement with previous studies estimating divergences among species. Estimates of phylogenies and divergence times also allow us to verify the results of [Reed, D.L., Light, J.E., Allen, J.M., Kirchman, J.J., 2007. Pair of lice lost or parasites regained: the evolutionary history of anthropoid primate lice. BMC Biol. 5, 7.]; there was probable contact between gorilla and archaic hominids roughly 3 Ma resulting in a host switch of Pthirus lice from gorillas to archaic hominids. Thus, these results provide

  2. 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

  3. 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

  4. 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

  5. Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots.

    PubMed

    Barrett, Craig F; Baker, William J; Comer, Jason R; Conran, John G; Lahmeyer, Sean C; Leebens-Mack, James H; Li, Jeff; Lim, Gwynne S; Mayfield-Jones, Dustin R; Perez, Leticia; Medina, Jesus; Pires, J Chris; Santos, Cristian; Wm Stevenson, Dennis; Zomlefer, Wendy B; Davis, Jerrold I

    2016-01-01

    Despite progress based on multilocus, phylogenetic studies of the palms (order Arecales, family Arecaceae), uncertainty remains in resolution/support among major clades and for the placement of the palms among the commelinid monocots. Palms and related commelinids represent a classic case of substitution rate heterogeneity that has not been investigated in the genomic era. To address questions of relationships, support and rate variation among palms and commelinid relatives, 39 plastomes representing the palms and related family Dasypogonaceae were generated via genome skimming and integrated within a monocot-wide matrix for phylogenetic and molecular evolutionary analyses. Support was strong for 'deep' relationships among the commelinid orders, among the five palm subfamilies, and among tribes of the subfamily Coryphoideae. Additionally, there was extreme heterogeneity in the plastid substitution rates across the commelinid orders indicated by model based analyses, with c. 22 rate shifts, and significant departure from a global clock. To date, this study represents the most comprehensively sampled matrix of plastomes assembled for monocot angiosperms, providing genome-scale support for phylogenetic relationships of monocot angiosperms, and lays the phylogenetic groundwork for comparative analyses of the drivers and correlates of such drastic differences in substitution rates across a diverse and significant clade. PMID:26350789

  6. Phylogenetic utility of ribosomal genes for reconstructing the phylogeny of five Chinese satyrine tribes (Lepidoptera, Nymphalidae)

    PubMed Central

    Yang, Mingsheng; Zhang, Yalin

    2015-01-01

    Abstract Satyrinae is one of twelve subfamilies of the butterfly family Nymphalidae, which currently includes nine tribes. However, phylogenetic relationships among them remain largely unresolved, though different researches have been conducted based on both morphological and molecular data. However, ribosomal genes have never been used in tribe level phylogenetic analyses of Satyrinae. In this study we investigate for the first time the phylogenetic relationships among the tribes Elymniini, Amathusiini, Zetherini and Melanitini which are indicated to be a monophyletic group, and the Satyrini, using two ribosomal genes (28s rDNA and 16s rDNA) and four protein-coding genes (EF-1α, COI, COII and Cytb). We mainly aim to assess the phylogenetic informativeness of the ribosomal genes as well as clarify the relationships among different tribes. Our results show the two ribosomal genes generally have the same high phylogenetic informativeness compared with EF-1α; and we infer the 28s rDNA would show better informativeness if the 28s rDNA sequence data for each sampling taxon are obtained in this study. The placement of the monotypic genus Callarge Leech in Zetherini is confirmed for the first time based on molecular evidence. In addition, our maximum likelihood (ML) and Bayesian inference (BI) trees consistently show that the involved Satyrinae including the Amathusiini is monophyletic with high support values. Although the relationships among the five tribes are identical among ML and BI analyses and are mostly strongly-supported in BI analysis, those in ML analysis are lowly- or moderately- supported. Therefore, the relationships among the related five tribes recovered herein need further verification based on more sampling taxa. PMID:25878526

  7. 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

  8. 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.

  9. Phylogenetic Relationships Matter: Antifungal Susceptibility among Clinically Relevant Yeasts

    PubMed Central

    Schmalreck, A. F.; Becker, K.; Fegeler, W.; Czaika, V.; Ulmer, H.; Lass-Flörl, C.

    2014-01-01

    The objective of this study was 2-fold: to evaluate whether phylogenetically closely related yeasts share common antifungal susceptibility profiles (ASPs) and whether these ASPs can be predicted from phylogeny. To address this question, 9,627 yeast strains were collected and tested for their antifungal susceptibility. Isolates were reidentified by considering recent changes in taxonomy and nomenclature. A phylogenetic (PHYLO) code based on the results of multilocus sequence analyses (large-subunit rRNA, small-subunit rRNA, translation elongation factor 1α, RNA polymerase II subunits 1 and 2) and the classification of the cellular neutral sugar composition of coenzyme Q and 18S ribosomal DNA was created to group related yeasts into PHYLO groups. The ASPs were determined for fluconazole, itraconazole, and voriconazole in each PHYLO group. The majority (95%) of the yeast strains were Ascomycetes. After reclassification, a total of 23 genera and 54 species were identified, resulting in an increase of 64% of genera and a decrease of 5% of species compared with the initial identification. These taxa were assigned to 17 distinct PHYLO groups (Ascomycota, n = 13; Basidiomycota, n = 4). ASPs for azoles were similar among members of the same PHYLO group and different between the various PHYLO groups. Yeast phylogeny may be an additional tool to significantly enhance the assessment of MIC values and to predict antifungal susceptibility, thereby more rapidly initiating appropriate patient management. PMID:24366735

  10. 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

  11. 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

  12. 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

  13. 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

  14. Probabilistic phylogenetic inference with insertions and deletions.

    PubMed

    Rivas, Elena; Eddy, Sean R

    2008-01-01

    A fundamental task in sequence analysis is to calculate the probability of a multiple alignment given a phylogenetic tree relating the sequences and an evolutionary model describing how sequences change over time. However, the most widely used phylogenetic models only account for residue substitution events. We describe a probabilistic model of a multiple sequence alignment that accounts for insertion and deletion events in addition to substitutions, given a phylogenetic tree, using a rate matrix augmented by the gap character. Starting from a continuous Markov process, we construct a non-reversible generative (birth-death) evolutionary model for insertions and deletions. The model assumes that insertion and deletion events occur one residue at a time. We apply this model to phylogenetic tree inference by extending the program dnaml in phylip. Using standard benchmarking methods on simulated data and a new "concordance test" benchmark on real ribosomal RNA alignments, we show that the extended program dnamlepsilon improves accuracy relative to the usual approach of ignoring gaps, while retaining the computational efficiency of the Felsenstein peeling algorithm. PMID:18787703

  15. 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.

  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

    Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of

  17. 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.

  18. 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

  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. 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

  1. 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.

  2. Phylogenetic analysis of HIV type 1 CRF02_AG in multiple genes in Italian and African patients living in Italy.

    PubMed

    Paolucci, Stefania; Piralla, Antonio; Fiorina, Loretta; Gulminetti, Roberto; Novati, Stefano; Lai, Alessia; Baldanti, Fausto

    2014-08-01

    Human immunodeficiency virus type 1 (HIV-1) circulating recombinant form (CRF) 02_AG is a major recombinant variant in different geographic areas and is predominant in West and Central Africa. Of particular interest is the increased frequency of CRF02_AG in patients living in Italy. In the present study, phylogenetic analyses were performed on gag, pol (integrase), and env (gp120 and gp41) gene sequences from 34 CRF02_AG-infected patients living in Italy. Thirty out of 34 (89.4%) patients were from western Africa, 3/34 (8.8%) were born in Italy, and 1/34 (2.9%) was from Cuba. Phylogenetic analysis revealed the presence of a well-supported clade (aLRT score>0.75) of sequences only in gp120 and gp41 trees. Evolutionary rate estimation showed a faster evolution for the gp120 gene with respect to the gag, integrase, and gp41 genes. This finding was confirmed by the analysis of interpatient variability. Intrapatient variability was greater in gp120 gene sequences; 10/19 (52.6%; p<0.001) patients had a ratio of dN/dS>1 as compared with gag, integrase, and gp41 gene sequences with dN/dS ratios<1. In summary, phylogenetic analyses of CRF02_AG strains offer a perspective on intrapatient and interpatient variability among CRF02_AG-infected patients living in Italy. In addition, divergent phylogenetic relationships were observed among different genomic regions.

  3. 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

  4. A phylogenetic perspective on the evolution of Mediterranean teleost fishes.

    PubMed

    Meynard, Christine N; Mouillot, David; Mouquet, Nicolas; Douzery, Emmanuel J P

    2012-01-01

    The Mediterranean Sea is a highly diverse, highly studied, and highly impacted biogeographic region, yet no phylogenetic reconstruction of fish diversity in this area has been published to date. Here, we infer the timing and geographic origins of Mediterranean teleost species diversity using nucleotide sequences collected from GenBank. We assembled a DNA supermatrix composed of four mitochondrial genes (12S ribosomal DNA, 16S ribosomal DNA, cytochrome c oxidase subunit I and cytochrome b) and two nuclear genes (rhodopsin and recombination activating gene I), including 62% of Mediterranean teleost species plus 9 outgroups. Maximum likelihood and Bayesian phylogenetic and dating analyses were calibrated using 20 fossil constraints. An additional 124 species were grafted onto the chronogram according to their taxonomic affinity, checking for the effects of taxonomic coverage in subsequent diversification analyses. We then interpreted the time-line of teleost diversification in light of Mediterranean historical biogeography, distinguishing non-endemic natives, endemics and exotic species. Results show that the major Mediterranean orders are of Cretaceous origin, specifically ~100-80 Mya, and most Perciformes families originated 80-50 Mya. Two important clade origin events were detected. The first at 100-80 Mya, affected native and exotic species, and reflects a global diversification period at a time when the Mediterranean Sea did not yet exist. The second occurred during the last 50 Mya, and is noticeable among endemic and native species, but not among exotic species. This period corresponds to isolation of the Mediterranean from Indo-Pacific waters before the Messinian salinity crisis. The Mediterranean fish fauna illustrates well the assembly of regional faunas through origination and immigration, where dispersal and isolation have shaped the emergence of a biodiversity hotspot. PMID:22590545

  5. 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).

  6. 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.

  7. 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

  8. 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

  9. A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families

    PubMed Central

    Miadlikowska, Jolanta; Kauff, Frank; Högnabba, Filip; Oliver, Jeffrey C.; Molnár, Katalin; Fraker, Emily; Gaya, Ester; Hafellner, Josef; Hofstetter, Valérie; Gueidan, Cécile; Otálora, Mónica A.G.; Hodkinson, Brendan; Kukwa, Martin; Lücking, Robert; Björk, Curtis; Sipman, Harrie J.M.; Burgaz, Ana Rosa; Thell, Arne; Passo, Alfredo; Myllys, Leena; Goward, Trevor; Fernández-Brime, Samantha; Hestmark, Geir; Lendemer, James; Lumbsch, H. Thorsten; Schmull, Michaela; Schoch, Conrad; Sérusiaux, Emmanuël; Maddison, David R.; Arnold, A. Elizabeth; Lutzoni, François; Stenroos, Soili

    2014-01-01

    The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, ‘Candelariomycetidae’). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed

  10. [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

  11. A phylogenetic analysis of the brassicales clade based on an alignment-free sequence comparison method.

    PubMed

    Hatje, Klas; Kollmar, Martin

    2012-01-01

    Phylogenetic analyses reveal the evolutionary derivation of species. A phylogenetic tree can be inferred from multiple sequence alignments of proteins or genes. The alignment of whole genome sequences of higher eukaryotes is a computational intensive and ambitious task as is the computation of phylogenetic trees based on these alignments. To overcome these limitations, we here used an alignment-free method to compare genomes of the Brassicales clade. For each nucleotide sequence a Chaos Game Representation (CGR) can be computed, which represents each nucleotide of the sequence as a point in a square defined by the four nucleotides as vertices. Each CGR is therefore a unique fingerprint of the underlying sequence. If the CGRs are divided by grid lines each grid square denotes the occurrence of oligonucleotides of a specific length in the sequence (Frequency Chaos Game Representation, FCGR). Here, we used distance measures between FCGRs to infer phylogenetic trees of Brassicales species. Three types of data were analyzed because of their different characteristics: (A) Whole genome assemblies as far as available for species belonging to the Malvidae taxon. (B) EST data of species of the Brassicales clade. (C) Mitochondrial genomes of the Rosids branch, a supergroup of the Malvidae. The trees reconstructed based on the Euclidean distance method are in general agreement with single gene trees. The Fitch-Margoliash and Neighbor joining algorithms resulted in similar to identical trees. Here, for the first time we have applied the bootstrap re-sampling concept to trees based on FCGRs to determine the support of the branchings. FCGRs have the advantage that they are fast to calculate, and can be used as additional information to alignment based data and morphological characteristics to improve the phylogenetic classification of species in ambiguous cases.

  12. Solid and Aqueous Geochemical Controls on Phylogenetic Diversity and Abundance of Microbial Biofilms

    NASA Astrophysics Data System (ADS)

    Jones, A. A.; Bennett, P. C.

    2015-12-01

    In the subsurface, the vast majority of microorganisms are found in biofilms attached to mineral surfaces. The fickle nature of these environments (chemically and physically) likely causes dynamic ecological shifts in these microbial communities. We used laboratory biofilm reactors (inoculated with a diverse subsurface community) to explore the role of mineralogy as part of a microbe-mineral-water ecosystem under variable pressures (mineralogy, pH, carbon, phosphate). Following multivariate analyses, pH was identified as the key physicochemical property associated with variation in both phylogenetic and taxonomic diversity as well as overall community structure (P<0.05). In particular, the ability of minerals, media, or a combination of the two to buffer metabolically generated acidity impacted community structure under oligotrophic and eutrophic conditions. Additionally, we found that media phosphate limitations were significantly correlated to greater biofilm accumulation (P<0.002), but lower species richness (P<0.001) and Shannon diversity (P<0.001); while mineral-bound phosphate limitations were significantly correlated to lesser biofilm accumulation (P<0.05) but not to species richness or diversity. Carbon (as acetate, lactate, or formate) added to the media was correlated with a significant increase in biofilm accumulation (P<0.04), and overall Shannon diversity (P<0.006), but not significantly correlated with overall species richness. Although variable in magnitude, the effect of surface chemistry on microbial diversity (both phylogenetic and taxonomic) was statistically significant, in all reactors, regardless of environmental pressures. Phylogenetically, surface type (carbonate, silicate, or Al-silicate) controlled ~70-90%, meaning that organisms attached to similar surfaces were significantly more genetically similar. Taxonomy and proportional abundance was significantly sensitive to variations in media chemistry with consistent patterns emerging among

  13. 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.

  14. Phylogenetic relationships among subsurface microorganisms

    SciTech Connect

    Nierzwicki-Bauer, S.A.

    1991-01-01

    This report summarizes the progress made from 6/90--3/91 toward completion of our project, Phylogenetic Relationships among subsurface microorganisms. 16S rRNA was sequenced, and based on the sequence the SMCC isolates were assigned to preliminary groups. Microorganisms were obtained at various depths at the Savannah River Site, including the Surface (0 m), Congaree (91 m), and Middendorf (244 m, 259 m, 265 m). Sequence data from four isolates from the Congaree formation indicate these microorganisms can be divided into Pseudomonas spp. or Acinetobacter spp. Three 16S rRNA probes were synthesized based on sequence data. The synthesized probes were tested through in situ hybridization. Optimal conditions for in situ hybridization were determined. Because stability of RNA-DNA hybrids is dependent on hybridization stringency, related organisms can be differentiated using a single probe under different strigencies. The results of these hybridizations agree with results obtained by Balkwill and Reeves using restriction fragment length polymorphism analysis. The RNA content of a cell reflects its metabolic state. Cells which are starved for four days are not detectable with the homologous 16S rRNA probe. However, within 15 minutes of refeeding, detectable rRNA appeared. This suggests that organisms which are undetectable in environmental samples due to starvation may be detectable after addition of nutrients. Stepwise addition of specific nutrients could indicate which nutrients are rate limiting for growth. Preliminary experiments with soil samples from the Hanford Site indicate indigenous microorganisms can be detected by oligionucleotide probes. Further, using multiple probes based on universal sequences increases the number of organisms detected. Double label experiments, using a rhodamine-labelled oligionucleotide probe with free coumarin succinimidyl ester will allow simultaneous detection of total bacteria and specific 16S rRNA containing bacteria. 4 tabs. (MHB)

  15. 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

  16. Comparative sequence analyses of sixteen reptilian paramyxoviruses

    USGS Publications Warehouse

    Ahne, W.; Batts, W.N.; Kurath, G.; Winton, J.R.

    1999-01-01

    Viral genomic RNA of Fer-de-Lance virus (FDLV), a paramyxovirus highly pathogenic for reptiles, was reverse transcribed and cloned. Plasmids with significant sequence similarities to the hemagglutinin-neuraminidase (HN) and polymerase (L) genes of mammalian paramyxoviruses were identified by BLAST search. Partial sequences of the FDLV genes were used to design primers for amplification by nested polymerase chain reaction (PCR) and sequencing of 518-bp L gene and 352-bp HN gene fragments from a collection of 15 previously uncharacterized reptilian paramyxoviruses. Phylogenetic analyses of the partial L and HN sequences produced similar trees in which there were two distinct subgroups of isolates that were supported with maximum bootstrap values, and several intermediate isolates. Within each subgroup the nucleotide divergence values were less than 2.5%, while the divergence between the two subgroups was 20-22%. This indicated that the two subgroups represent distinct virus species containing multiple virus strains. The five intermediate isolates had nucleotide divergence values of 11-20% and may represent additional distinct species. In addition to establishing diversity among reptilian paramyxoviruses, the phylogenetic groupings showed some correlation with geographic location, and clearly demonstrated a low level of host species-specificity within these viruses. Copyright (C) 1999 Elsevier Science B.V.

  17. 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

  18. 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.

  19. A reassessment of the phylogenetic utility of genus-level morphological characters in the family Bogidiellidae (Crustacea, Amphipoda), with description of a new species of Eobogidiella Karaman, 1981

    PubMed Central

    Sidorov, Dmitry A.; Katz, Aron D.; Taylor, Steven J.; Chertoprud, Mikhail V.

    2016-01-01

    Abstract Bogidiellidae is the most diverse and cosmopolitan family of stygobiotic amphipods, and inhabits a variety of subterranean biotopes, especially interstitial habitats. While the family is characterized by considerable sexual dimorphism, this dimorphism has adversely affected our understanding of the systematics of the group. Most species have restricted geographic ranges and occur in difficult to sample habitats, so it is common for individual species descriptions to be based on a single sex. In this work we revisit an analysis of morphological characters in an attempt to clarify their phylogenetic utility in resolving taxonomic relationships among genera by introducing a new species, two additional characters, and phylogenetic statistical support values. Eobogidiella venkataramani sp. n., from a spring fed brook in the Shirawati River basin along the escarpment of the Western Ghats (Karnataka, India) differs from the only known congener, Eobogidiella purmamarcensis, from Argentina, in the structure of mouthparts, the shape and ornamentation on gnathopods and characters of the telson. Our phylogenetic analyses indicate that the available morphological characters are not sufficient to resolve phylogenetic relationships within Bogidiellidae, thus these characters alone cannot be used to determine the phylogenetic placement of Eobogidiella venkataramani sp. n. within the family. Nevertheless, Eobogidiella venkataramani sp. n. shares diagnostic characters with Eobogidiella, supporting placement of the new species in this genus. Our findings point towards a critical need to resolve relationships within the family using molecular approaches, along with the development of a suite of additional morphological characters for Bogidiellidae. This is the third species of Bogidiellidae from southern India. PMID:27587976

  20. A reassessment of the phylogenetic utility of genus-level morphological characters in the family Bogidiellidae (Crustacea, Amphipoda), with description of a new species of Eobogidiella Karaman, 1981.

    PubMed

    Sidorov, Dmitry A; Katz, Aron D; Taylor, Steven J; Chertoprud, Mikhail V

    2016-01-01

    Bogidiellidae is the most diverse and cosmopolitan family of stygobiotic amphipods, and inhabits a variety of subterranean biotopes, especially interstitial habitats. While the family is characterized by considerable sexual dimorphism, this dimorphism has adversely affected our understanding of the systematics of the group. Most species have restricted geographic ranges and occur in difficult to sample habitats, so it is common for individual species descriptions to be based on a single sex. In this work we revisit an analysis of morphological characters in an attempt to clarify their phylogenetic utility in resolving taxonomic relationships among genera by introducing a new species, two additional characters, and phylogenetic statistical support values. Eobogidiella venkataramani sp. n., from a spring fed brook in the Shirawati River basin along the escarpment of the Western Ghats (Karnataka, India) differs from the only known congener, Eobogidiella purmamarcensis, from Argentina, in the structure of mouthparts, the shape and ornamentation on gnathopods and characters of the telson. Our phylogenetic analyses indicate that the available morphological characters are not sufficient to resolve phylogenetic relationships within Bogidiellidae, thus these characters alone cannot be used to determine the phylogenetic placement of Eobogidiella venkataramani sp. n. within the family. Nevertheless, Eobogidiella venkataramani sp. n. shares diagnostic characters with Eobogidiella, supporting placement of the new species in this genus. Our findings point towards a critical need to resolve relationships within the family using molecular approaches, along with the development of a suite of additional morphological characters for Bogidiellidae. This is the third species of Bogidiellidae from southern India. PMID:27587976

  1. Multi-locus phylogenetic inference among New World Vultures (Aves: Cathartidae).

    PubMed

    Johnson, Jeff A; Brown, Joseph W; Fuchs, Jérôme; Mindell, David P

    2016-12-01

    New World Vultures are large-bodied carrion feeding birds in the family Cathartidae, currently consisting of seven species from five genera with geographic distributions in North and South America. No study to date has included all cathartid species in a single phylogenetic analysis. In this study, we investigated the phylogenetic relationships among all cathartid species using five nuclear (nuc; 4060bp) and two mitochondrial (mt; 2165bp) DNA loci with fossil calibrated gene tree (27 outgroup taxa) and coalescent-based species tree (2 outgroup taxa) analyses. We also included an additional four nuclear loci (2578bp) for the species tree analysis to explore changes in nodal support values. Although the stem lineage is inferred to have originated ∼69 million years ago (Ma; 74.5-64.9 credible interval), a more recent basal split within Cathartidae was recovered at ∼14Ma (17.1-11.1 credible interval). Two primary clades were identified: (1) Black Vulture (Coragyps atratus) together with the three Cathartes species (Lesser C. burrovianus and Greater C. melambrotus Yellow-headed Vultures, and Turkey Vulture C. aura), and (2) King Vulture (Sarcoramphus papa), California (Gymnogyps californianus) and Andean (Vultur gryphus) Condors. Support for taxon relationships within the two basal clades were inconsistent between analyses with the exception of Black Vulture sister to a monophyletic Cathartes clade. Increased support for a yellow-headed vulture clade was recovered in the species tree analysis using the four additional nuclear loci. Overall, these results are in agreement with cathartid life history (e.g. olfaction ability and behavior) and contrasting habitat affinities among sister taxa with overlapping geographic distributions. More research is needed using additional molecular loci to further resolve the phylogenetic relationships within the two basal cathartid clades, as speciation appeared to have occurred in a relatively short period of time.

  2. Multi-locus phylogenetic inference among New World Vultures (Aves: Cathartidae).

    PubMed

    Johnson, Jeff A; Brown, Joseph W; Fuchs, Jérôme; Mindell, David P

    2016-12-01

    New World Vultures are large-bodied carrion feeding birds in the family Cathartidae, currently consisting of seven species from five genera with geographic distributions in North and South America. No study to date has included all cathartid species in a single phylogenetic analysis. In this study, we investigated the phylogenetic relationships among all cathartid species using five nuclear (nuc; 4060bp) and two mitochondrial (mt; 2165bp) DNA loci with fossil calibrated gene tree (27 outgroup taxa) and coalescent-based species tree (2 outgroup taxa) analyses. We also included an additional four nuclear loci (2578bp) for the species tree analysis to explore changes in nodal support values. Although the stem lineage is inferred to have originated ∼69 million years ago (Ma; 74.5-64.9 credible interval), a more recent basal split within Cathartidae was recovered at ∼14Ma (17.1-11.1 credible interval). Two primary clades were identified: (1) Black Vulture (Coragyps atratus) together with the three Cathartes species (Lesser C. burrovianus and Greater C. melambrotus Yellow-headed Vultures, and Turkey Vulture C. aura), and (2) King Vulture (Sarcoramphus papa), California (Gymnogyps californianus) and Andean (Vultur gryphus) Condors. Support for taxon relationships within the two basal clades were inconsistent between analyses with the exception of Black Vulture sister to a monophyletic Cathartes clade. Increased support for a yellow-headed vulture clade was recovered in the species tree analysis using the four additional nuclear loci. Overall, these results are in agreement with cathartid life history (e.g. olfaction ability and behavior) and contrasting habitat affinities among sister taxa with overlapping geographic distributions. More research is needed using additional molecular loci to further resolve the phylogenetic relationships within the two basal cathartid clades, as speciation appeared to have occurred in a relatively short period of time. PMID:27601346

  3. Photobiont Relationships and Phylogenetic History of Dermatocarpon luridum var. luridum and Related Dermatocarpon Species

    PubMed Central

    Fontaine, Kyle M.; Beck, Andreas; Stocker-Wörgötter, Elfie; Piercey-Normore, Michele D.

    2012-01-01

    Members of the genus Dermatocarpon are widespread throughout the Northern Hemisphere along the edge of lakes, rivers and streams, and are subject to abiotic conditions reflecting both aquatic and terrestrial environments. Little is known about the evolutionary relationships within the genus and between continents. Investigation of the photobiont(s) associated with sub-aquatic and terrestrial Dermatocarpon species may reveal habitat requirements of the photobiont and the ability for fungal species to share the same photobiont species under different habitat conditions. The focus of our study was todetermine the relationship between Canadian and Austrian Dermatocarpon luridum var. luridum along with three additional sub-aquatic Dermatocarpon species, and to determine the species of photobionts that associate with D. luridum var. luridum. Culture experiments were performed to identify the photobionts. In addition, the question of the algal sharing potential regarding different species of Dermatocarpon was addressed. Specimens were collected from four lakes in northwestern Manitoba, Canada and three streams in Austria. Three Canadian and four Austrian thalli of D. luridum var. luridum were selected for algal culturing. The nuclear Internal Transcribed Spacer (ITS) rDNA gene of the fungal partner along with the algal ITS rDNA gene was sequenced to confirm the identity of the lichen/photobiont and afterwards the same data sets were used in phylogenetic analyses to assess algal sharing. The green algal photobiont was identified as Diplosphaera chodatii (Trebouxiophyceae). The phylogenetic analyses of Canadian and Austrian D. luridum var. luridum revealed that ITS sequences are identical despite the vast geographic distance. Phylogenetic placement of D. luridum var. decipiens and D. arnoldianum suggested that a re-examination of the species status might be necessary. This study concluded that additional photobiont culture experiments should be conducted to answer the

  4. 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

  5. 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...

  6. 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...

  7. Mitogenome Phylogenetics: The Impact of Using Single Regions and Partitioning Schemes on Topology, Substitution Rate and Divergence Time Estimation

    PubMed Central

    Duchêne, Sebastián; Archer, Frederick I.; Vilstrup, Julia; Caballero, Susana; Morin, Phillip A.

    2011-01-01

    The availability of mitochondrial genome sequences is growing as a result of recent technological advances in molecular biology. In phylogenetic analyses, the complete mitogenome is increasingly becoming the marker of choice, usually providing better phylogenetic resolution and precision relative to traditional markers such as cytochrome b (CYTB) and the control region (CR). In some cases, the differences in phylogenetic estimates between mitogenomic and single-gene markers have yielded incongruent conclusions. By comparing phylogenetic estimates made from different genes, we identified the most informative mitochondrial regions and evaluated the minimum amount of data necessary to reproduce the same results as the mitogenome. We compared results among individual genes and the mitogenome for recently published complete mitogenome datasets of selected delphinids (Delphinidae) and killer whales (genus Orcinus). Using Bayesian phylogenetic methods, we investigated differences in estimation of topologies, divergence dates, and clock-like behavior among genes for both datasets. Although the most informative regions were not the same for each taxonomic group (COX1, CYTB, ND3 and ATP6 for Orcinus, and ND1, COX1 and ND4 for Delphinidae), in both cases they were equivalent to less than a quarter of the complete mitogenome. This suggests that gene information content can vary among groups, but can be adequately represented by a portion of the complete sequence. Although our results indicate that complete mitogenomes provide the highest phylogenetic resolution and most precise date estimates, a minimum amount of data can be selected using our approach when the complete sequence is unavailable. Studies based on single genes can benefit from the addition of a few more mitochondrial markers, producing topologies and date estimates similar to those obtained using the entire mitogenome. PMID:22073275

  8. Mitogenome phylogenetics: the impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation.

    PubMed

    Duchêne, Sebastián; Archer, Frederick I; Vilstrup, Julia; Caballero, Susana; Morin, Phillip A

    2011-01-01

    The availability of mitochondrial genome sequences is growing as a result of recent technological advances in molecular biology. In phylogenetic analyses, the complete mitogenome is increasingly becoming the marker of choice, usually providing better phylogenetic resolution and precision relative to traditional markers such as cytochrome b (CYTB) and the control region (CR). In some cases, the differences in phylogenetic estimates between mitogenomic and single-gene markers have yielded incongruent conclusions. By comparing phylogenetic estimates made from different genes, we identified the most informative mitochondrial regions and evaluated the minimum amount of data necessary to reproduce the same results as the mitogenome. We compared results among individual genes and the mitogenome for recently published complete mitogenome datasets of selected delphinids (Delphinidae) and killer whales (genus Orcinus). Using Bayesian phylogenetic methods, we investigated differences in estimation of topologies, divergence dates, and clock-like behavior among genes for both datasets. Although the most informative regions were not the same for each taxonomic group (COX1, CYTB, ND3 and ATP6 for Orcinus, and ND1, COX1 and ND4 for Delphinidae), in both cases they were equivalent to less than a quarter of the complete mitogenome. This suggests that gene information content can vary among groups, but can be adequately represented by a portion of the complete sequence. Although our results indicate that complete mitogenomes provide the highest phylogenetic resolution and most precise date estimates, a minimum amount of data can be selected using our approach when the complete sequence is unavailable. Studies based on single genes can benefit from the addition of a few more mitochondrial markers, producing topologies and date estimates similar to those obtained using the entire mitogenome.

  9. Reassessing the phylogenetic position of the epizoic earwigs (Insecta: Dermaptera).

    PubMed

    Naegle, Michael A; Mugleston, Joseph D; Bybee, Seth M; Whiting, Michael F

    2016-07-01

    Dermaptera is a relatively small order of free-living insects that typically feed on detritus and other plant material. However, two earwig lineages - Arixeniidae and Hemimeridae - are epizoic on Cheiromeles bats and Beamys and Cricetomys rats respectively. Both of these epizoic families are comprised of viviparous species. The monophyly of these epizoic lineages and their placement within dermapteran phylogeny has remained unclear. A phylogenetic analyses was performed on a diverse sample of 47 earwig taxa for five loci (18S rDNA, 28S rDNA, COI, Histone 3, and Tubulin Alpha I). Our results support two independent origins of the epizoic lifestyle within Dermaptera, with Hemimeridae and Arixeniidae each derived from a different lineage of Spongiphoridae. Our analyses places Marava, a genus of spongiphorids that includes free-living but viviparous earwigs, as sister group to Arixeniidae, suggesting that viviparity evolved prior to the shift to the epizoic lifestyle. Additionally, our results support the monophyly of Forficulidae and Chelisochidae and the paraphyly of Labiduridae, Pygidicranidae, Spongiphoridae, and Anisolabididae. PMID:27033951

  10. Phylogenetic analysis of vertically transmitted psyllid endosymbionts (Candidatus Carsonella ruddii) based on atpAGD and rpoC: comparisons with 16S-23S rDNA-derived phylogeny.

    PubMed

    Thao, M L; Clark, M A; Burckhardt, D H; Moran, N A; Baumann, P

    2001-06-01

    Psyllids are insects that harbor endosymbionts (Candidatuus Carsonella ruddii) within specialized cells found in the insect's body cavity. Previous phylogenetic analyses based on endosymbiont 16S-23S ribosomal DNA and a host gene were concordant (M.L. Thao, et al., Appl. Env. Microbiol. 66:2898, 2000). Additional analyses with atpAGD and rpoBC gave similar trees showing the agreement expected from organisms that evolve through vertical transmission with no gene exchange.

  11. Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals.

    PubMed

    Heydari, Mahdi; Marashi, Sayed-Amir; Tusserkani, Ruzbeh; Sadeghi, Mehdi

    2014-10-01

    One of the fundamental problems in bioinformatics is phylogenetic tree reconstruction, which can be used for classifying living organisms into different taxonomic clades. The classical approach to this problem is based on a marker such as 16S ribosomal RNA. Since evolutionary events like genomic rearrangements are not included in reconstructions of phylogenetic trees based on single genes, much effort has been made to find other characteristics for phylogenetic reconstruction in recent years. With the increasing availability of completely sequenced genomes, gene order can be considered as a new solution for this problem. In the present work, we applied maximal common intervals (MCIs) in two or more genomes to infer their distance and to reconstruct their evolutionary relationship. Additionally, measures based on uncommon segments (UCS's), i.e., those genomic segments which are not detected as part of any of the MCIs, are also used for phylogenetic tree reconstruction. We applied these two types of measures for reconstructing the phylogenetic tree of 63 prokaryotes with known COG (clusters of orthologous groups) families. Similarity between the MCI-based (resp. UCS-based) reconstructed phylogenetic trees and the phylogenetic tree obtained from NCBI taxonomy browser is as high as 93.1% (resp. 94.9%). We show that in the case of this diverse dataset of prokaryotes, tree reconstruction based on MCI and UCS outperforms most of the currently available methods based on gene orders, including breakpoint distance and DCJ. We additionally tested our new measures on a dataset of 13 closely-related bacteria from the genus Prochlorococcus. In this case, distances like rearrangement distance, breakpoint distance and DCJ proved to be useful, while our new measures are still appropriate for phylogenetic reconstruction.

  12. The phylogenetic problem of Huia (Amphibia: Ranidae).

    PubMed

    Stuart, Bryan L

    2008-01-01

    A taxonomic consensus for the diverse and pan-global frog family Ranidae is lacking. A recently proposed classification of living amphibians [Frost, D.R., Grant, T., Faivovich, J., Bain, R. H., Haas, A., Haddad, C.F.B., de Sá, R.O., Channing, A., Wilkinson, M., Donnellan, S.C., Raxworthy, C.J., Campbell, J.A., Blotto, B.L., Moler, P., Drewes, R.C., Nussbaum, R.A., Lynch, J.D., Green, D.M., Wheeler, W.C., 2006. The amphibian tree of life. B. Am. Mus. Nat. Hist. 297, 1-370] included expansion of the Southeast Asian ranid frog genus Huia from seven to 47 species, but without having studied the type species of Huia. This study tested the monophyly of this concept of Huia by sampling the type species and putative members of Huia. Molecular phylogenetic analyses consistently recovered the type species H. cavitympanum as the sister taxon to other Bornean-endemic species in the genus Meristogenys, rendering all previously published concepts of Huia as polyphyletic. Members of Huia sensu [Frost, D.R., Grant, T., Faivovich, J., Bain, R. H., Haas, A., Haddad, C.F.B., de Sá, R.O., Channing, A., Wilkinson, M., Donnellan, S.C., Raxworthy, C.J., Campbell, J.A., Blotto, B.L., Moler, P., Drewes, R.C., Nussbaum, R.A., Lynch, J.D., Green, D.M., Wheeler, W.C., 2006. The amphibian tree of life. B. Am. Mus. Nat. Hist. 297, 1-370.] appear in four places within the family Ranidae. A clade containing the type species of Odorrana is phylogenetically unrelated to the type species of Huia, and Odorrana is removed from synonymy with Huia. These findings underscore the need to include relevant type species in phylogenetic studies before proposing sweeping taxonomic changes. The molecular phylogenetic analyses revealed a high degree of homoplasy in larval and adult morphology of Asian ranid frogs. Detailed studies are needed to identify morphological synapomorphies that unite members in these major clades of ranid frogs.

  13. Geographic distribution of phylogenetically-distinct legume pod borer, Maruca vitrata (Lepidoptera: Pyraloidea: Crambidae).

    PubMed

    Margam, Venu M; Coates, Brad S; Ba, Malick N; Sun, Weilin; Binso-Dabire, Clementine L; Baoua, Ibrahim; Ishiyaku, Mohammad F; Shukle, John T; Hellmich, Richard L; Covas, Fernando G; Ramasamy, Srinivasan; Armstrong, Joel; Pittendrigh, Barry R; Murdock, Larry L

    2011-02-01

    Maruca vitrata Fabricius is a pantropical lepidopteran pest of legumes. Phylogenetic analysis of a mitochondrial cytochrome c oxidase-I gene (cox1) fragment indicates that three Maruca sp. mitochondrial lineages have unique geographic distributions [lineages 1 and 2: Australia, Taiwan, and West Africa (Niger, Nigeria, and Burkina Faso), and lineage 3: Puerto Rico]. The haplotype (T30, T114) is specific to lineages 1&2 and was assayed by NsiI and SacI polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) within population samples; it was not observed in the Puerto Rican samples, but was nearly fixed among samples from West Africa, Australia and Taiwan (85.5-100%). Re-sequencing and phylogenetic analyses of PCR-RFLP defined cox1 haplotypes indicate that nucleotide diversity is highest among samples from West Africa. Phylogenetic reconstruction based upon ribosomal DNA (rDNA) internal transcribed spacer-2 (ITS-2) sequences provided additional evidence for three Maruca sp. clades. These data suggest that multiple unique Maruca species or subspecies are present worldwide, which has implications for the management of this pest species-complex.

  14. Application of the Ribosomal DNA ITS2 Region of Physalis (Solanaceae): DNA Barcoding and Phylogenetic Study

    PubMed Central

    Feng, Shangguo; Jiang, Mengying; Shi, Yujun; Jiao, Kaili; Shen, Chenjia; Lu, Jiangjie; Ying, Qicai; Wang, Huizhong

    2016-01-01

    Recently, commercial interest in Physalis species has grown worldwide due to their high nutritional value, edible fruit, and potential medicinal properties. However, many Physalis species have similar shapes and are easily confused, and consequently the phylogenetic relationships between Physalis species are poorly understood. This hinders their safe utilization and genetic resource conservation. In this study, the nuclear ribosomal ITS2 region was used to identify species and phylogenetically examine Physalis. Eighty-six ITS2 regions from 45 Physalis species were analyzed. The ITS2 sequences were aligned using Clustal W and genetic distances were calculated using MEGA V6.0. The results showed that ITS2 regions have significant intra- and inter-specific divergences, obvious barcoding gaps, and higher species discrimination rates (82.2% for both the BLASTA1 and nearest distance methods). In addition, the secondary structure of ITS2 provided another way to differentiate species. Cluster analysis based on ITS2 regions largely concurred with the relationships among Physalis species established by many previous molecular analyses, and showed that most sections of Physalis appear to be polyphyletic. Our results demonstrated that ITS2 can be used as an efficient and powerful marker in the identification and phylogenetic study of Physalis species. The technique provides a scientific basis for the conservation of Physalis plants and for utilization of resources. PMID:27486467

  15. Phylogenetic relationships within mammalian order Carnivora indicated by sequences of two nuclear DNA genes.

    PubMed

    Yu, Li; Li, Qing-wei; Ryder, O A; Zhang, Ya-ping

    2004-12-01

    Phylogenetic relationships among 37 living species of order Carnivora spanning a relatively broad range of divergence times and taxonomic levels were examined using nuclear sequence data from exon 1 of the IRBP gene (approximately 1.3 kb) and first intron of the TTR gene (approximately 1 kb). These data were used to analyze carnivoran phylogeny at the family and generic level as well as the interspecific relationships within recently derived Felidae. Phylogenetic results using a combined IRBP+TTR dataset strongly supported within the superfamily Califormia, the red panda as the closest lineage to procyonid-mustelid (i.e., Musteloidea) clade followed by pinnipeds (Otariidae and Phocidae), Ursidae (including the giant panda), and Canidae. Four feliform families, namely the monophyletic Herpestidae, Hyaenidae, and Felidae, as well as the paraphyletic Viverridae were consistently recovered convincingly. The utilities of these two gene segments for the phylogenetic analyses were extensively explored and both were found to be fairly informative for higher-group associations within the order Carnivora, but not for those of low level divergence at the species level. Therefore, there is a need to find additional genetic markers with more rapid mutation rates that would be diagnostic at deciphering relatively recent relationships within the Carnivora.

  16. Phylogenetic analysis of New Zealand earthworms (Oligochaeta: Megascolecidae) reveals ancient clades and cryptic taxonomic diversity.

    PubMed

    Buckley, Thomas R; James, Sam; Allwood, Julia; Bartlam, Scott; Howitt, Robyn; Prada, Diana

    2011-01-01

    We have constructed the first ever phylogeny for the New Zealand earthworm fauna (Megascolecinae and Acanthodrilinae) including representatives from other major continental regions. Bayesian and maximum likelihood phylogenetic trees were constructed from 427 base pairs from the mitochondrial large subunit (16S) rRNA gene and 661 base pairs from the nuclear large subunit (28S) rRNA gene. Within the Acanthodrilinae we were able to identify a number of well-supported clades that were restricted to continental landmasses. Estimates of nodal support for these major clades were generally high, but relationships among clades were poorly resolved. The phylogenetic analyses revealed several independent lineages in New Zealand, some of which had a comparable phylogenetic depth to monophyletic groups sampled from Madagascar, Africa, North America and Australia. These results are consistent with at least some of these clades having inhabited New Zealand since rifting from Gondwana in the Late Cretaceous. Within the New Zealand Acanthodrilinae, major clades tended to be restricted to specific regions of New Zealand, with the central North Island and Cook Strait representing major biogeographic boundaries. Our field surveys of New Zealand and subsequent identification has also revealed extensive cryptic taxonomic diversity with approximately 48 new species sampled in addition to the 199 species recognized by previous authors. Our results indicate that further survey and taxonomic work is required to establish a foundation for future biogeographic and ecological research on this vitally important component of the New Zealand biota.

  17. The complete mitogenome of the snakehead Channa argus (Perciformes: Channoidei): genome characterization and phylogenetic implications.

    PubMed

    Wang, Jialian; Yang, Guang

    2011-08-01

    To better understand the phylogenetic status of the snakehead, Channa argus, we determined its complete mitogenome sequence using long-polymerase chain reaction and the direct sequencing method. The complete mitogenome sequence was 16,559 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region (D-loop), the gene composition/order of which was identical to that observed in most other vertebrates. This was the first report of the mitogenome sequence in suborder Channoidei. Phylogenetic relationships of 14 perciform suborders based on mitogenome sequences were reconstructed using Bayesian inference and maximum likelihood methods. The results strongly supported the monophyly of Perciformes and the snakehead, as a representative species of suborder Channoidei, formed the most basal branch having sister relationship with the clade containing all other analyzed perciform fishes. The further phylogenetic analyses of six channid species, based on cytochrome b gene, suggested that two channid genera constituted reciprocally monophyletic clades. In addition, the relaxed molecular clock method was used to estimate divergence dates among major suborders of Perciformes and major species in Channoidei.

  18. Application of the Ribosomal DNA ITS2 Region of Physalis (Solanaceae): DNA Barcoding and Phylogenetic Study.

    PubMed

    Feng, Shangguo; Jiang, Mengying; Shi, Yujun; Jiao, Kaili; Shen, Chenjia; Lu, Jiangjie; Ying, Qicai; Wang, Huizhong

    2016-01-01

    Recently, commercial interest in Physalis species has grown worldwide due to their high nutritional value, edible fruit, and potential medicinal properties. However, many Physalis species have similar shapes and are easily confused, and consequently the phylogenetic relationships between Physalis species are poorly understood. This hinders their safe utilization and genetic resource conservation. In this study, the nuclear ribosomal ITS2 region was used to identify species and phylogenetically examine Physalis. Eighty-six ITS2 regions from 45 Physalis species were analyzed. The ITS2 sequences were aligned using Clustal W and genetic distances were calculated using MEGA V6.0. The results showed that ITS2 regions have significant intra- and inter-specific divergences, obvious barcoding gaps, and higher species discrimination rates (82.2% for both the BLASTA1 and nearest distance methods). In addition, the secondary structure of ITS2 provided another way to differentiate species. Cluster analysis based on ITS2 regions largely concurred with the relationships among Physalis species established by many previous molecular analyses, and showed that most sections of Physalis appear to be polyphyletic. Our results demonstrated that ITS2 can be used as an efficient and powerful marker in the identification and phylogenetic study of Physalis species. The technique provides a scientific basis for the conservation of Physalis plants and for utilization of resources. PMID:27486467

  19. [Phylogenetic analysis of Pleurotus species].

    PubMed

    Shnyreva, A A; Shnyreva, A V

    2015-02-01

    We performed phylogenetic analysis for ten Pleurotus species, based on internal transcribed spacer (ITS) sequences of rDNA. A phylogenetic tree was constructed on the basis of 31 oyster fungi strains of different origin and 10 reference sequences from GenBank. Our analysis demonstrates that the tested Pleurotus species are of monophyletic origin. We evaluated the evolutionary distances between these species. Classic genetic analysis of sexual compatibility based on monocaryon (mon)-mon crosses showed no reproductive barriers within the P. cornucopiae-P. euosmus species complex. Thus, despite the divergence (subclustering) between commercial strains and natural isolates of P. ostreatus revealed by phylogenetic analysis, there is no reproductive isolation between these groups. A common allele of the matB locus was identified for the commercial strains Sommer and L/4, supporting the common origin of these strains. PMID:25966583

  20. Charles Darwin, beetles and phylogenetics.

    PubMed

    Beutel, Rolf G; Friedrich, Frank; Leschen, Richard A B

    2009-11-01

    Here, we review Charles Darwin's relation to beetles and developments in coleopteran systematics in the last two centuries. Darwin was an enthusiastic beetle collector. He used beetles to illustrate different evolutionary phenomena in his major works, and astonishingly, an entire sub-chapter is dedicated to beetles in "The Descent of Man". During his voyage on the Beagle, Darwin was impressed by the high diversity of beetles in the tropics, and he remarked that, to his surprise, the majority of species were small and inconspicuous. However, despite his obvious interest in the group, he did not get involved in beetle taxonomy, and his theoretical work had little immediate impact on beetle classification. The development of taxonomy and classification in the late nineteenth and earlier twentieth century was mainly characterised by the exploration of new character systems (e.g. larval features and wing venation). In the mid-twentieth century, Hennig's new methodology to group lineages by derived characters revolutionised systematics of Coleoptera and other organisms. As envisioned by Darwin and Ernst Haeckel, the new Hennigian approach enabled systematists to establish classifications truly reflecting evolution. Roy A. Crowson and Howard E. Hinton, who both made tremendous contributions to coleopterology, had an ambivalent attitude towards the Hennigian ideas. The Mickoleit school combined detailed anatomical work with a classical Hennigian character evaluation, with stepwise tree building, comparatively few characters and a priori polarity assessment without explicit use of the outgroup comparison method. The rise of cladistic methods in the 1970s had a strong impact on beetle systematics. Cladistic computer programs facilitated parsimony analyses of large data matrices, mostly morphological characters not requiring detailed anatomical investigations. Molecular studies on beetle phylogeny started in the 1990s with modest taxon sampling and limited DNA data. This has

  1. Charles Darwin, beetles and phylogenetics

    NASA Astrophysics Data System (ADS)

    Beutel, Rolf G.; Friedrich, Frank; Leschen, Richard A. B.

    2009-11-01

    Here, we review Charles Darwin’s relation to beetles and developments in coleopteran systematics in the last two centuries. Darwin was an enthusiastic beetle collector. He used beetles to illustrate different evolutionary phenomena in his major works, and astonishingly, an entire sub-chapter is dedicated to beetles in “The Descent of Man”. During his voyage on the Beagle, Darwin was impressed by the high diversity of beetles in the tropics, and he remarked that, to his surprise, the majority of species were small and inconspicuous. However, despite his obvious interest in the group, he did not get involved in beetle taxonomy, and his theoretical work had little immediate impact on beetle classification. The development of taxonomy and classification in the late nineteenth and earlier twentieth century was mainly characterised by the exploration of new character systems (e.g. larval features and wing venation). In the mid-twentieth century, Hennig’s new methodology to group lineages by derived characters revolutionised systematics of Coleoptera and other organisms. As envisioned by Darwin and Ernst Haeckel, the new Hennigian approach enabled systematists to establish classifications truly reflecting evolution. Roy A. Crowson and Howard E. Hinton, who both made tremendous contributions to coleopterology, had an ambivalent attitude towards the Hennigian ideas. The Mickoleit school combined detailed anatomical work with a classical Hennigian character evaluation, with stepwise tree building, comparatively few characters and a priori polarity assessment without explicit use of the outgroup comparison method. The rise of cladistic methods in the 1970s had a strong impact on beetle systematics. Cladistic computer programs facilitated parsimony analyses of large data matrices, mostly morphological characters not requiring detailed anatomical investigations. Molecular studies on beetle phylogeny started in the 1990s with modest taxon sampling and limited DNA data

  2. Charles Darwin, beetles and phylogenetics.

    PubMed

    Beutel, Rolf G; Friedrich, Frank; Leschen, Richard A B

    2009-11-01

    Here, we review Charles Darwin's relation to beetles and developments in coleopteran systematics in the last two centuries. Darwin was an enthusiastic beetle collector. He used beetles to illustrate different evolutionary phenomena in his major works, and astonishingly, an entire sub-chapter is dedicated to beetles in "The Descent of Man". During his voyage on the Beagle, Darwin was impressed by the high diversity of beetles in the tropics, and he remarked that, to his surprise, the majority of species were small and inconspicuous. However, despite his obvious interest in the group, he did not get involved in beetle taxonomy, and his theoretical work had little immediate impact on beetle classification. The development of taxonomy and classification in the late nineteenth and earlier twentieth century was mainly characterised by the exploration of new character systems (e.g. larval features and wing venation). In the mid-twentieth century, Hennig's new methodology to group lineages by derived characters revolutionised systematics of Coleoptera and other organisms. As envisioned by Darwin and Ernst Haeckel, the new Hennigian approach enabled systematists to establish classifications truly reflecting evolution. Roy A. Crowson and Howard E. Hinton, who both made tremendous contributions to coleopterology, had an ambivalent attitude towards the Hennigian ideas. The Mickoleit school combined detailed anatomical work with a classical Hennigian character evaluation, with stepwise tree building, comparatively few characters and a priori polarity assessment without explicit use of the outgroup comparison method. The rise of cladistic methods in the 1970s had a strong impact on beetle systematics. Cladistic computer programs facilitated parsimony analyses of large data matrices, mostly morphological characters not requiring detailed anatomical investigations. Molecular studies on beetle phylogeny started in the 1990s with modest taxon sampling and limited DNA data. This has

  3. Interpreting the universal phylogenetic tree

    NASA Technical Reports Server (NTRS)

    Woese, C. R.

    2000-01-01

    The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist.

  4. Phylogenetic relationships of Malaysia's pig-tailed macaque Macaca nemestrina based on D-loop region sequences

    NASA Astrophysics Data System (ADS)

    Abdul-Latiff M. A., B.; Ampeng, A.; Yaakop, S.; Md-Zain B., M.

    2014-09-01

    Phylogenetic relationships among Malaysian pig-tailed macaques have never been established even though the data are crucial in aiding conservation plan for the species. The aims of this study is to establish the phylogenetic relationships of Macaca nemestrina in Malaysia. A total of 21 genetic samples of M. nemestrina yielding 458 bp of D-loop sequences were used in phylogenetic analyses, in addition to one sample of M. fascicularis which was used as an outgroup. Sequence character analysis revealed that D-loop locus contains 23% parsimony informative character detected among the ingroups. Further analysis indicated a clear separation between populations originating from different regions; the Malay Peninsula populations are separated from Borneo Insular population; and Perak population formed a distinctive clade within Peninsular Malaysia populations. Phylogenetic trees (NJ, MP and Bayesian) portray a consistent clustering paradigm as Borneo population was distinguished from Peninsula population (100% bootstrap value in the NJ, MP, 1.00 posterior probability in Bayesian trees). Perak's population was separated from other Peninsula populations (100% in NJ, 99% in MP and 1.00 in Bayesian). D-loop region of mtDNA is proven to be a suitable locus in studying the separation of M. nemestrina at population level. These findings are crucial in aiding the conservation management and translocation process of M. fascicularis populations in Malaysia.

  5. Small RNA pathway genes identified by patterns of phylogenetic conservation and divergence

    PubMed Central

    Tabach, Yuval; Billi, Allison C.; Hayes, Gabriel D.; Newman, Martin A.; Zuk, Or; Gabel, Harrison; Kamath, Ravi; Yacoby, Keren; Chapman, Brad; Garcia, Susana M.; Borowsky, Mark; Kim, John K.; Ruvkun, Gary

    2013-01-01

    Genetic and biochemical analyses of RNA interference (RNAi) and microRNA (miRNA) pathways have revealed proteins such as Argonaute/PIWI and Dicer that process and present small RNAs to their targets. Well validated small RNA pathway cofactors, such as the Argonaute/PIWI proteins show distinctive patterns of conservation or divergence in particular animal, plant, fungal, and protist species. We compared 86 divergent eukaryotic genome sequences to discern sets of proteins that show similar phylogenetic profiles with known small RNA cofactors. A large set of additional candidate small RNA cofactors have emerged from functional genomic screens for defects in miRNA- or siRNA-mediated repression in C. elegans and D. melanogaster1,2 and from proteomic analyses of proteins co-purifying with validated small RNA pathway proteins3,4. The phylogenetic profiles of many of these candidate small RNA pathway proteins are similar to those of known small RNA cofactor proteins. We used a Bayesian approach to integrate the phylogenetic profile analysis with predictions from diverse transcriptional coregulation and proteome interaction datasets to assign a probability for each protein for a role in a small RNA pathway. Testing high-confidence candidates from this analysis for defects in RNAi silencing, we found that about half of the predicted small RNA cofactors are required for RNAi silencing. Many of the newly identified small RNA pathway proteins are orthologues of proteins implicated in RNA splicing. In support of a deep connection between the mechanism of RNA splicing and small RNA-mediated gene silencing, the presence of the Argonaute proteins and other small RNA components in the many species analysed strongly correlates with the number of introns in that species. PMID:23364702

  6. Seasonal and genotypic changes in escherichia coli phylogenetic groups in the Yeongsan River basin of South Korea.

    PubMed

    Jang, Jeonghwan; Di, Doris Y W; Lee, Anna; Unno, Tatsuya; Sadowsky, Michael J; Hur, Hor-Gil

    2014-01-01

    With 3,480 E. coli strains isolated from the Yeongsan River basin, South Korea, correlations between phylogenetic groups and horizontal fluorophore enhanced rep-PCR (HFERP) genotypes were examined, and environmental factors affecting E. coli phylogenetic groups in the river water were determined. Interestingly, multidimentional scaling (MDS) analyses based on HFERP DNA fingerprint data indicated that E. coli in phylogenetic groups A and B1 were uniquely clustered. Results of self-organized maps (SOMs) analyses also indicated that E. coli phylogenetic groups were seasonally affected by water temperature, with greater occurrences of phylogenetic groups A and B1 in low and high temperature seasons, respectively. The presence of E. coli in phylogenetic groups A and B1 were inversely related. Furthermore, redundancy analysis (RDA) revealed that phylogenetic group B1 correlated positively with temperature, strain diversity, and biochemical oxygen demand (BOD) but negatively with phylogenetic group A. Results of this study indicated that while E. coli strains could be clustered based on their genotypes and environment conditions, their phylogenetic groups did not change in relation to the same conditions. The distributional differences of phylogenetic groups among E. coli populations in different environments may be caused by different genomic adaptability and plasticity of E. coli strains belonging to each phylogenetic group. Although several previous studies have reported different E. coli ecological structures depending on their origins, this study is a first description of the specific environmental factors affecting E. coli phylogenetic groups in river water. PMID:24999864

  7. Seasonal and Genotypic Changes in Escherichia coli Phylogenetic Groups in the Yeongsan River Basin of South Korea

    PubMed Central

    Jang, Jeonghwan; Di, Doris Y. W.; Lee, Anna; Unno, Tatsuya; Sadowsky, Michael J.; Hur, Hor-Gil

    2014-01-01

    With 3,480 E. coli strains isolated from the Yeongsan River basin, South Korea, correlations between phylogenetic groups and horizontal fluorophore enhanced rep-PCR (HFERP) genotypes were examined, and environmental factors affecting E. coli phylogenetic groups in the river water were determined. Interestingly, multidimentional scaling (MDS) analyses based on HFERP DNA fingerprint data indicated that E. coli in phylogenetic groups A and B1 were uniquely clustered. Results of self-organized maps (SOMs) analyses also indicated that E. coli phylogenetic groups were seasonally affected by water temperature, with greater occurrences of phylogenetic groups A and B1 in low and high temperature seasons, respectively. The presence of E. coli in phylogenetic groups A and B1 were inversely related. Furthermore, redundancy analysis (RDA) revealed that phylogenetic group B1 correlated positively with temperature, strain diversity, and biochemical oxygen demand (BOD) but negatively with phylogenetic group A. Results of this study indicated that while E. coli strains could be clustered based on their genotypes and environment conditions, their phylogenetic groups did not change in relation to the same conditions. The distributional differences of phylogenetic groups among E. coli populations in different environments may be caused by different genomic adaptability and plasticity of E. coli strains belonging to each phylogenetic group. Although several previous studies have reported different E. coli ecological structures depending on their origins, this study is a first description of the specific environmental factors affecting E. coli phylogenetic groups in river water. PMID:24999864

  8. Phyloproteomics: What Phylogenetic Analysis Reveals about Serum Proteomics

    PubMed Central

    Abu-Asab, Mones; Chaouchi, Mohamed; Amri, Hakima

    2008-01-01

    Phyloproteomics is a novel analytical tool that solves the issue of comparability between proteomic analyses, utilizes a total spectrum-parsing algorithm, and produces biologically meaningful classification of specimens. Phyloproteomics employs two algorithms: a new parsing algorithm (UNIPAL) and a phylogenetic algorithm (MIX). By outgroup comparison, the parsing algorithm identifies novel or vanished MS peaks and peaks signifying up or down regulated proteins and scores them as derived or ancestral. The phylogenetic algorithm uses the latter scores to produce a biologically meaningful classification of the specimens. PMID:16944935

  9. The phylogenetic structure of plant-pollinator networks increases with habitat size and isolation.

    PubMed

    Aizen, Marcelo A; Gleiser, Gabriela; Sabatino, Malena; Gilarranz, Luis J; Bascompte, Jordi; Verdú, Miguel

    2016-01-01

    Similarity among species in traits related to ecological interactions is frequently associated with common ancestry. Thus, closely related species usually interact with ecologically similar partners, which can be reinforced by diverse co-evolutionary processes. The effect of habitat fragmentation on the phylogenetic signal in interspecific interactions and correspondence between plant and animal phylogenies is, however, unknown. Here, we address to what extent phylogenetic signal and co-phylogenetic congruence of plant-animal interactions depend on habitat size and isolation by analysing the phylogenetic structure of 12 pollination webs from isolated Pampean hills. Phylogenetic signal in interspecific interactions differed among webs, being stronger for flower-visiting insects than plants. Phylogenetic signal and overall co-phylogenetic congruence increased independently with hill size and isolation. We propose that habitat fragmentation would erode the phylogenetic structure of interaction webs. A decrease in phylogenetic signal and co-phylogenetic correspondence in plant-pollinator interactions could be associated with less reliable mutualism and erratic co-evolutionary change.

  10. In situ sulfur isotopes (δ(34)S and δ(33)S) analyses in sulfides and elemental sulfur using high sensitivity cones combined with the addition of nitrogen by laser ablation MC-ICP-MS.

    PubMed

    Fu, Jiali; Hu, Zhaochu; Zhang, Wen; Yang, Lu; Liu, Yongsheng; Li, Ming; Zong, Keqing; Gao, Shan; Hu, Shenghong

    2016-03-10

    The sulfur isotope is an important geochemical tracer in diverse fields of geosciences. In this study, the effects of three different cone combinations with the addition of N2 on the performance of in situ S isotope analyses were investigated in detail. The signal intensities of S isotopes were improved by a factor of 2.3 and 3.6 using the X skimmer cone combined with the standard sample cone or the Jet sample cone, respectively, compared with the standard arrangement (H skimmer cone combined with the standard sample cone). This signal enhancement is important for the improvement of the precision and accuracy of in situ S isotope analysis at high spatial resolution. Different cone combinations have a significant effect on the mass bias and mass bias stability for S isotopes. Poor precisions of S isotope ratios were obtained using the Jet and X cones combination at their corresponding optimum makeup gas flow when using Ar plasma only. The addition of 4-8 ml min(-1) nitrogen to the central gas flow in laser ablation MC-ICP-MS was found to significantly enlarge the mass bias stability zone at their corresponding optimum makeup gas flow in these three different cone combinations. The polyatomic interferences of OO, SH, OOH were also significantly reduced, and the interference free plateaus of sulfur isotopes became broader and flatter in the nitrogen mode (N2 = 4 ml min(-1)). However, the signal intensity of S was not increased by the addition of nitrogen in this study. The laser fluence and ablation mode had significant effects on sulfur isotope fractionation during the analysis of sulfides and elemental sulfur by laser ablation MC-ICP-MS. The matrix effect among different sulfides and elemental sulfur was observed, but could be significantly reduced by line scan ablation in preference to single spot ablation under the optimized fluence. It is recommended that the d90 values of the particles in pressed powder pellets for accurate and precise S isotope analysis

  11. In situ sulfur isotopes (δ(34)S and δ(33)S) analyses in sulfides and elemental sulfur using high sensitivity cones combined with the addition of nitrogen by laser ablation MC-ICP-MS.

    PubMed

    Fu, Jiali; Hu, Zhaochu; Zhang, Wen; Yang, Lu; Liu, Yongsheng; Li, Ming; Zong, Keqing; Gao, Shan; Hu, Shenghong

    2016-03-10

    The sulfur isotope is an important geochemical tracer in diverse fields of geosciences. In this study, the effects of three different cone combinations with the addition of N2 on the performance of in situ S isotope analyses were investigated in detail. The signal intensities of S isotopes were improved by a factor of 2.3 and 3.6 using the X skimmer cone combined with the standard sample cone or the Jet sample cone, respectively, compared with the standard arrangement (H skimmer cone combined with the standard sample cone). This signal enhancement is important for the improvement of the precision and accuracy of in situ S isotope analysis at high spatial resolution. Different cone combinations have a significant effect on the mass bias and mass bias stability for S isotopes. Poor precisions of S isotope ratios were obtained using the Jet and X cones combination at their corresponding optimum makeup gas flow when using Ar plasma only. The addition of 4-8 ml min(-1) nitrogen to the central gas flow in laser ablation MC-ICP-MS was found to significantly enlarge the mass bias stability zone at their corresponding optimum makeup gas flow in these three different cone combinations. The polyatomic interferences of OO, SH, OOH were also significantly reduced, and the interference free plateaus of sulfur isotopes became broader and flatter in the nitrogen mode (N2 = 4 ml min(-1)). However, the signal intensity of S was not increased by the addition of nitrogen in this study. The laser fluence and ablation mode had significant effects on sulfur isotope fractionation during the analysis of sulfides and elemental sulfur by laser ablation MC-ICP-MS. The matrix effect among different sulfides and elemental sulfur was observed, but could be significantly reduced by line scan ablation in preference to single spot ablation under the optimized fluence. It is recommended that the d90 values of the particles in pressed powder pellets for accurate and precise S isotope analysis

  12. A Distance Measure for Genome Phylogenetic Analysis

    NASA Astrophysics Data System (ADS)

    Cao, Minh Duc; Allison, Lloyd; Dix, Trevor

    Phylogenetic analyses of species based on single genes or parts of the genomes are often inconsistent because of factors such as variable rates of evolution and horizontal gene transfer. The availability of more and more sequenced genomes allows phylogeny construction from complete genomes that is less sensitive to such inconsistency. For such long sequences, construction methods like maximum parsimony and maximum likelihood are often not possible due to their intensive computational requirement. Another class of tree construction methods, namely distance-based methods, require a measure of distances between any two genomes. Some measures such as evolutionary edit distance of gene order and gene content are computational expensive or do not perform well when the gene content of the organisms are similar. This study presents an information theoretic measure of genetic distances between genomes based on the biological compression algorithm expert model. We demonstrate that our distance measure can be applied to reconstruct the consensus phylogenetic tree of a number of Plasmodium parasites from their genomes, the statistical bias of which would mislead conventional analysis methods. Our approach is also used to successfully construct a plausible evolutionary tree for the γ-Proteobacteria group whose genomes are known to contain many horizontally transferred genes.

  13. Phylogenetic Species Identification in Rattus Highlights Rapid Radiation and Morphological Similarity of New Guinean Species

    PubMed Central

    Robins, Judith H.; Tintinger, Vernon; Aplin, Ken P.; Hingston, Melanie; Matisoo-Smith, Elizabeth; Penny, David; Lavery, Shane D.

    2014-01-01

    The genus Rattus is highly speciose, the taxonomy is complex, and individuals are often difficult to identify to the species level. Previous studies have demonstrated the usefulness of phylogenetic approaches to identification in Rattus but some species, especially among the endemics of the New Guinean region, showed poor resolution. Possible reasons for this are simple misidentification, incomplete gene lineage sorting, hybridization, and phylogenetically distinct lineages that are unrecognised taxonomically. To assess these explanations we analysed 217 samples, representing nominally 25 Rattus species, collected in New Guinea, Asia, Australia and the Pacific. To reduce misidentification problems we sequenced museum specimens from earlier morphological studies and recently collected tissues from samples with associated voucher specimens. We also reassessed vouchers from previously sequenced specimens. We inferred combined and separate phylogenies from two mitochondrial DNA regions comprising 550 base pair D-loop sequences and both long (655 base pair) and short (150 base pair) cytochrome oxidase I sequences. Our phylogenetic species identification for 17 species was consistent with morphological designations and current taxonomy thus reinforcing the usefulness of this approach. We reduced misidentifications and consequently the number of polyphyletic species in our phylogenies but the New Guinean Rattus clades still exhibited considerable complexity. Only three of our eight New Guinean species were monophyletic. We found good evidence for either incomplete mitochondrial lineage sorting or hybridization between species within two pairs, R. leucopus/R. cf. verecundus and R. steini/R. praetor. Additionally, our results showed that R. praetor, R. niobe and R. verecundus each likely encompass more than one species. Our study clearly points to the need for a revised taxonomy of the rats of New Guinea, based on broader sampling and informed by both morphology and

  14. Biological pattern and transcriptomic exploration and phylogenetic analysis in the odd floral architecture tree: Helwingia willd

    PubMed Central

    2014-01-01

    Background Odd traits in few of plant species usually implicate potential biology significances in plant evolutions. The genus Helwingia Willd, a dioecious medical shrub in Aquifoliales order, has an odd floral architecture-epiphyllous inflorescence. The potential significances and possible evolutionary origin of this specie are not well understood due to poorly available data of biological and genetic studies. In addition, the advent of genomics-based technologies has widely revolutionized plant species with unknown genomic information. Results Morphological and biological pattern were detailed via anatomical and pollination analyses. An RNA sequencing based transcriptomic analysis were undertaken and a high-resolution phylogenetic analysis was conducted based on single-copy genes in more than 80 species of seed plants, including H. japonica. It is verified that a potential fusion of rachis to the leaf midvein facilitates insect pollination. RNA sequencing yielded a total of 111450 unigenes; half of them had significant similarity with proteins in the public database, and 20281 unigenes were mapped to 119 pathways. Deduced from the phylogenetic analysis based on single-copy genes, the group of Helwingia is closer with Euasterids II and rather than Euasterids, congruent with previous reports using plastid sequences. Conclusions The odd flower architecture make H. Willd adapt to insect pollination by hosting those insects larger than the flower in size via leave, which has little common character that other insect pollination plants hold. Further the present transcriptome greatly riches genomics information of Helwingia species and nucleus genes based phylogenetic analysis also greatly improve the resolution and robustness of phylogenetic reconstruction in H. japonica. PMID:24969969

  15. Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

    PubMed Central

    Gao, Beile

    2012-01-01

    Summary: The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades (viz., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria. The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria. PMID:22390973

  16. Genetic and phylogenetic characterization of novel bocaparvovirus infecting chimpanzee.

    PubMed

    Brožová, Kristýna; Hrazdilová, Kristýna; Slaninková, Eva; Modrý, David; Černý, Jiří; Celer, Vladimír

    2016-01-01

    Primate bocaparvoviruses were first described in 2005, since then further human and gorilla bocaparvoviruses have been identified. To uncover diversity of non-human primates' bocaparvoviruses, their phylogenetic relationship and potential to cross the host species barrier, we tested 153 fecal samples from 17 captive primate species. The only one captive female of central chimpanzee (coded CPZh2) has been identified as bocaparvovirus positive. Based on the full genome phylogenetic analyses, CPZh2 strain shows close relationship to HBoV3 and GBoV. Further recombination analysis confirmed expected mosaic origin of CPZh2 strain. According the phylogenetic position, following the ICTV recommendations, we propose a novel genotype within the Primate bocaparvovirus 1 species infecting chimpanzee.

  17. Genetic and phylogenetic characterization of novel bocaparvovirus infecting chimpanzee.

    PubMed

    Brožová, Kristýna; Hrazdilová, Kristýna; Slaninková, Eva; Modrý, David; Černý, Jiří; Celer, Vladimír

    2016-01-01

    Primate bocaparvoviruses were first described in 2005, since then further human and gorilla bocaparvoviruses have been identified. To uncover diversity of non-human primates' bocaparvoviruses, their phylogenetic relationship and potential to cross the host species barrier, we tested 153 fecal samples from 17 captive primate species. The only one captive female of central chimpanzee (coded CPZh2) has been identified as bocaparvovirus positive. Based on the full genome phylogenetic analyses, CPZh2 strain shows close relationship to HBoV3 and GBoV. Further recombination analysis confirmed expected mosaic origin of CPZh2 strain. According the phylogenetic position, following the ICTV recommendations, we propose a novel genotype within the Primate bocaparvovirus 1 species infecting chimpanzee. PMID:26616676

  18. Phylogenomic Analyses of Echinodermata Support the Sister Groups of Asterozoa and Echinozoa

    PubMed Central

    Reich, Adrian; Dunn, Casey; Akasaka, Koji; Wessel, Gary

    2015-01-01

    Echinoderms (sea urchins, sea stars, brittle stars, sea lilies and sea cucumbers) are a group of diverse organisms, second in number within deuterostome species to only the chordates. Echinoderms serve as excellent model systems for developmental biology due to their diverse developmental mechanisms, tractable laboratory use, and close phylogenetic distance to chordates. In addition, echinoderms are very well represented in the fossil record, including some larval features, making echinoderms a valuable system for studying evolutionary development. The internal relationships of Echinodermata have not been consistently supported across phylogenetic analyses, however, and this has hindered the study of other aspects of their biology. In order to test echinoderm phylogenetic relationships, we sequenced 23 de novo transcriptomes from all five clades of echinoderms. Using multiple phylogenetic methods at a variety of sampling depths we have constructed a well-supported phylogenetic tree of Echinodermata, including support for the sister groups of Asterozoa (sea stars and brittle stars) and Echinozoa (sea urchins and sea cucumbers). These results will help inform developmental and evolutionary studies specifically in echinoderms and deuterostomes in general. PMID:25794146

  19. Phylogenomic analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa.

    PubMed

    Reich, Adrian; Dunn, Casey; Akasaka, Koji; Wessel, Gary

    2015-01-01

    Echinoderms (sea urchins, sea stars, brittle stars, sea lilies and sea cucumbers) are a group of diverse organisms, second in number within deuterostome species to only the chordates. Echinoderms serve as excellent model systems for developmental biology due to their diverse developmental mechanisms, tractable laboratory use, and close phylogenetic distance to chordates. In addition, echinoderms are very well represented in the fossil record, including some larval features, making echinoderms a valuable system for studying evolutionary development. The internal relationships of Echinodermata have not been consistently supported across phylogenetic analyses, however, and this has hindered the study of other aspects of their biology. In order to test echinoderm phylogenetic relationships, we sequenced 23 de novo transcriptomes from all five clades of echinoderms. Using multiple phylogenetic methods at a variety of sampling depths we have constructed a well-supported phylogenetic tree of Echinodermata, including support for the sister groups of Asterozoa (sea stars and brittle stars) and Echinozoa (sea urchins and sea cucumbers). These results will help inform developmental and evolutionary studies specifically in echinoderms and deuterostomes in general.

  20. Molecular Identification of Dendrobium Species (Orchidaceae) Based on the DNA Barcode ITS2 Region and Its Application for Phylogenetic Study

    PubMed Central

    Feng, Shangguo; Jiang, Yan; Wang, Shang; Jiang, Mengying; Chen, Zhe; Ying, Qicai; Wang, Huizhong

    2015-01-01

    The over-collection and habitat destruction of natural Dendrobium populations for their commercial medicinal value has led to these plants being under severe threat of extinction. In addition, many Dendrobium plants are similarly shaped and easily confused during the absence of flowering stages. In the present study, we examined the application of the ITS2 region in barcoding and phylogenetic analyses of Dendrobium species (Orchidaceae). For barcoding, ITS2 regions of 43 samples in Dendrobium were amplified. In combination with sequences from GenBank, the sequences were aligned using Clustal W and genetic distances were computed using MEGA V5.1. The success rate of PCR amplification and sequencing was 100%. There was a significant divergence between the inter- and intra-specific genetic distances of ITS2 regions, while the presence of a barcoding gap was obvious. Based on the BLAST1, nearest distance and TaxonGAP methods, our results showed that the ITS2 regions could successfully identify the species of most Dendrobium samples examined; Second, we used ITS2 as a DNA marker to infer phylogenetic relationships of 64 Dendrobium species. The results showed that cluster analysis using the ITS2 region mainly supported the relationship between the species of Dendrobium established by traditional morphological methods and many previous molecular analyses. To sum up, the ITS2 region can not only be used as an efficient barcode to identify Dendrobium species, but also has the potential to contribute to the phylogenetic analysis of the genus Dendrobium. PMID:26378526

  1. 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.

  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. PMID:25066912

  3. Using tree diversity to compare phylogenetic heuristics

    PubMed Central

    Sul, Seung-Jin; Matthews, Suzanne; Williams, Tiffani L

    2009-01-01

    Background Evolutionary trees are family trees that represent the relationships between a group of organisms. Phylogenetic heuristics are used to search stochastically for the best-scoring trees in tree space. Given that better tree scores are believed to be better approximations of the true phylogeny, traditional evaluation techniques have used tree scores to determine the heuristics that find the best scores in the fastest time. We develop new techniques to evaluate phylogenetic heuristics based on both tree scores and topologies to compare Pauprat and Rec-I-DCM3, two popular Maximum Parsimony search algorithms. Results Our results show that although Pauprat and Rec-I-DCM3 find the trees with the same best scores, topologically these trees are quite different. Furthermore, the Rec-I-DCM3 trees cluster distinctly from the Pauprat trees. In addition to our heatmap visualizations of using parsimony scores and the Robinson-Foulds distance to compare best-scoring trees found by the two heuristics, we also develop entropy-based methods to show the diversity of the trees found. Overall, Pauprat identifies more diverse trees than Rec-I-DCM3. Conclusion Overall, our work shows that there is value to comparing heuristics beyond the parsimony scores that they find. Pauprat is a slower heuristic than Rec-I-DCM3. However, our work shows that there is tremendous value in using Pauprat to reconstruct trees—especially since it finds identical scoring but topologically distinct trees. Hence, instead of discounting Pauprat, effort should go in improving its implementation. Ultimately, improved performance measures lead to better phylogenetic heuristics and will result in better approximations of the true evolutionary history of the organisms of interest. PMID:19426451

  4. Friends or Relatives? Phylogenetics and Species Delimitation in the Controversial European Orchid Genus Ophrys

    PubMed Central

    Devey, Dion S.; Bateman, Richard M.; Fay, Michael F.; Hawkins, Julie A.

    2008-01-01

    Background and Aims Highly variable, yet possibly convergent, morphology and lack of sequence variation have severely hindered production of a robust phylogenetic framework for the genus Ophrys. The aim of this study is to produce this framework as a basis for more rigorous species delimitation and conservation recommendations. Methods Nuclear and plastid DNA sequencing and amplified fragment length polymorphism (AFLP) were performed on 85 accessions of Ophrys, spanning the full range of species aggregates currently recognized. Data were analysed using a combination of parsimony and Bayesian tree-building techniques and by principal co-ordinates analysis. Key Results Complementary phylogenetic analyses and ordinations using nuclear, plastid and AFLP datasets identify ten genetically distinct groups (six robust) within the genus that may in turn be grouped into three sections (treated as subgenera by some authors). Additionally, genetic evidence is provided for a close relationship between the O. tenthredinifera, O. bombyliflora and O. speculum groups. The combination of these analytical techniques provides new insights into Ophrys systematics, notably recognition of the novel O. umbilicata group. Conclusions Heterogeneous copies of the nuclear ITS region show that some putative Ophrys species arose through hybridization rather than divergent speciation. The supposedly highly specific pseudocopulatory pollination syndrome of Ophrys is demonstrably ‘leaky’, suggesting that the genus has been substantially over-divided at the species level. PMID:18184645

  5. Morphologic, Phylogenetic and Chemical Characterization of a Brackish Colonial Picocyanobacterium (Coelosphaeriaceae) with Bioactive Properties.

    PubMed

    Häggqvist, Kerstin; Toruńska-Sitarz, Anna; Błaszczyk, Agata; Mazur-Marzec, Hanna; Meriluoto, Jussi

    2016-04-01

    Despite their cosmopolitan distribution, knowledge on cyanobacteria in the family Coelosphaeriaceae is limited. In this study, a single species culture of a coelosphaeran cyanobacterium isolated from a brackish rock pool in the Baltic Sea was established. The strain was characterized by morphological features, partial 16S rRNA sequence and nonribosomal oligopeptide profile. The bioactivity of fractionated extracts against several serine proteases, as well as protein-serine/threonine phosphatases was studied. Phylogenetic analyses of the strain suggested a close relationship with Snowella litoralis, but its morphology resembled Woronichinia compacta. The controversial morphologic and phylogenetic results demonstrated remaining uncertainties regarding species division in this cyanobacteria family. Chemical analyses of the strain indicated production of nonribosomal oligopeptides. In fractionated extracts, masses and ion fragmentation spectra of seven possible anabaenopeptins were identified. Additionally, fragmentation spectra of cyanopeptolin-like peptides were collected in several of the fractions. The nonribosomal oligopeptide profile adds another potential identification criterion in future inter- and intraspecies comparisons of coelosphaeran cyanobacteria. The fractionated extracts showed significant activity against carboxypeptidase A and trypsin. Inhibition of these important metabolic enzymes might have impacts at the ecosystem level in aquatic habitats with high cyanobacteria densities. PMID:27077885

  6. Morphologic, Phylogenetic and Chemical Characterization of a Brackish Colonial Picocyanobacterium (Coelosphaeriaceae) with Bioactive Properties

    PubMed Central

    Häggqvist, Kerstin; Toruńska-Sitarz, Anna; Błaszczyk, Agata; Mazur-Marzec, Hanna; Meriluoto, Jussi

    2016-01-01

    Despite their cosmopolitan distribution, knowledge on cyanobacteria in the family Coelosphaeriaceae is limited. In this study, a single species culture of a coelosphaeran cyanobacterium isolated from a brackish rock pool in the Baltic Sea was established. The strain was characterized by morphological features, partial 16S rRNA sequence and nonribosomal oligopeptide profile. The bioactivity of fractionated extracts against several serine proteases, as well as protein-serine/threonine phosphatases was studied. Phylogenetic analyses of the strain suggested a close relationship with Snowella litoralis, but its morphology resembled Woronichinia compacta. The controversial morphologic and phylogenetic results demonstrated remaining uncertainties regarding species division in this cyanobacteria family. Chemical analyses of the strain indicated production of nonribosomal oligopeptides. In fractionated extracts, masses and ion fragmentation spectra of seven possible anabaenopeptins were identified. Additionally, fragmentation spectra of cyanopeptolin-like peptides were collected in several of the fractions. The nonribosomal oligopeptide profile adds another potential identification criterion in future inter- and intraspecies comparisons of coelosphaeran cyanobacteria. The fractionated extracts showed significant activity against carboxypeptidase A and trypsin. Inhibition of these important metabolic enzymes might have impacts at the ecosystem level in aquatic habitats with high cyanobacteria densities. PMID:27077885

  7. Cleaning up the biogeography of Labroides dimidiatus using phylogenetics and morphometrics

    NASA Astrophysics Data System (ADS)

    Sims, C. A.; Riginos, C.; Blomberg, S. P.; Huelsken, T.; Drew, J.; Grutter, A. S.

    2014-03-01

    Cleaner fishes are some of the most conspicuous organisms on coral reefs due to their behaviour and prominent body pattern, consisting of a lateral stripe and blue/yellow colouration. All obligate cleaner fishes share this body stripe pattern, which is an important signal for attracting client fishes. However, variability in the cleaning signal of the cleaner fish Labroides dimidiatus has been documented across its range. Here, we investigate the geographic distribution of cleaner signal polymorphisms in L. dimidiatus and contrast this to phylogeographic variation in mitochondrial (mt) DNA. We used samples from 12 sites for genetic analyses, encompassing much of L. dimidiatus' range from the Red Sea to Fiji. We obtained morphometric measures of the cleaner signal body stripe width from individuals among six of the sites and qualitatively grouped tail stripe shape. mtDNA control region sequences were used for phylogenetic and population genetic analyses. We found that body stripe width was significantly correlated with tail stripe shape and geographical location, with Indian Ocean populations differing in morphology from western Pacific populations. L. dimidiatus haplotypes formed two reciprocally monophyletic clades, although in contrast to morphology, Japanese cleaner fish fell within the same clade as Indian Ocean cleaner fish and both clade types were sympatric in Papua New Guinea. An additional novel finding of our research was that the inclusion of two closely related cleaner fish species, Labroides pectoralis and Labroides bicolor, in the phylogenetic analysis rendered L. dimidiatus polyphyletic. Overall, the findings suggest the diversity within L. dimidiatus is underestimated.

  8. Range size: disentangling current traits and phylogenetic and biogeographic factors.

    PubMed

    Böhning-Gaese, Katrin; Caprano, Tanja; van Ewijk, Karin; Veith, Michael

    2006-04-01

    The range size of a species can be determined by its current traits and by phylogenetic and biogeographic factors. However, only rarely have these factors been studied in combination. We use data on the geographic range sizes of all 26 Sylvia warblers to explicitly test whether range size was determined by current species-specific traits (e.g., body size, dispersal ability), phylogenetic factors (e.g., age of the lineage), or environmental, biogeographic factors (e.g., latitudinal position of the range). The results demonstrated that current traits and phylogenetic and biogeographic factors were interrelated. While a number of factors were significant in simple regression analyses, only one factor determined range size in the multiple regression analyses--dispersal ability. Species with better dispersal ability had larger ranges than species with poorer dispersal ability. Apparent increases of range size with latitude or with the age of the species resulted from correlations with dispersal ability. While the most significant factor that influences the range size of a group of species might differ from one group to the next, these results demonstrate that studies that focus only on a single, for example, phylogenetic, factor might yield misleading results.

  9. Addition of docetaxel or bisphosphonates to standard of care in men with localised or metastatic, hormone-sensitive prostate cancer: a systematic review and meta-analyses of aggregate data

    PubMed Central

    Vale, Claire L; Burdett, Sarah; Rydzewska, Larysa H M; Albiges, Laurence; Clarke, Noel W; Fisher, David; Fizazi, Karim; Gravis, Gwenaelle; James, Nicholas D; Mason, Malcolm D; Parmar, Mahesh K B; Sweeney, Christopher J; Sydes, Matthew R; Tombal, Bertrand; Tierney, Jayne F

    2016-01-01

    docetaxel for men with locally advanced disease (M0). Survival results from three (GETUG-12, RTOG 0521, STAMPEDE) of these trials (2121 [53%] of 3978 men) showed no evidence of a benefit from the addition of docetaxel (HR 0·87 [95% CI 0·69–1·09]; p=0·218), whereas failure-free survival data from four (GETUG-12, RTOG 0521, STAMPEDE, TAX 3501) of these trials (2348 [59%] of 3978 men) showed that docetaxel improved failure-free survival (0·70 [0·61–0·81]; p<0·0001), which translates into a reduced absolute 4-year failure rate of 8% (5–10). We identified seven eligible randomised controlled trials of bisphosphonates for men with M1 disease. Survival results from three of these trials (2740 [88%] of 3109 men) showed that addition of bisphosphonates improved survival (0·88 [0·79–0·98]; p=0·025), which translates to 5% (1–8) absolute improvement, but this result was influenced by the positive result of one trial of sodium clodronate, and we found no evidence of a benefit from the addition of zoledronic acid (0·94 [0·83–1·07]; p=0·323), which translates to an absolute improvement in survival of 2% (−3 to 7). Of 17 trials of bisphosphonates for men with M0 disease, survival results from four trials (4079 [66%] of 6220 men) showed no evidence of benefit from the addition of bisphosphonates (1·03 [0·89–1·18]; p=0·724) or zoledronic acid (0·98 [0·82–1·16]; p=0·782). Failure-free survival definitions were too inconsistent for formal meta-analyses for the bisphosphonate trials. Interpretation The addition of docetaxel to standard of care should be considered standard care for men with M1 hormone-sensitive prostate cancer who are starting treatment for the first time. More evidence on the effects of docetaxel on survival is needed in the M0 disease setting. No evidence exists to suggest that zoledronic acid improves survival in men with

  10. Addition of docetaxel or bisphosphonates to standard of care in men with localised or metastatic, hormone-sensitive prostate cancer: a systematic review and meta-analyses of aggregate data

    PubMed Central

    Vale, Claire L; Burdett, Sarah; Rydzewska, Larysa H M; Albiges, Laurence; Clarke, Noel W; Fisher, David; Fizazi, Karim; Gravis, Gwenaelle; James, Nicholas D; Mason, Malcolm D; Parmar, Mahesh K B; Sweeney, Christopher J; Sydes, Matthew R; Tombal, Bertrand; Tierney, Jayne F

    2016-01-01

    docetaxel for men with locally advanced disease (M0). Survival results from three (GETUG-12, RTOG 0521, STAMPEDE) of these trials (2121 [53%] of 3978 men) showed no evidence of a benefit from the addition of docetaxel (HR 0·87 [95% CI 0·69–1·09]; p=0·218), whereas failure-free survival data from four (GETUG-12, RTOG 0521, STAMPEDE, TAX 3501) of these trials (2348 [59%] of 3978 men) showed that docetaxel improved failure-free survival (0·70 [0·61–0·81]; p<0·0001), which translates into a reduced absolute 4-year failure rate of 8% (5–10). We identified seven eligible randomised controlled trials of bisphosphonates for men with M1 disease. Survival results from three of these trials (2740 [88%] of 3109 men) showed that addition of bisphosphonates improved survival (0·88 [0·79–0·98]; p=0·025), which translates to 5% (1–8) absolute improvement, but this result was influenced by the positive result of one trial of sodium clodronate, and we found no evidence of a benefit from the addition of zoledronic acid (0·94 [0·83–1·07]; p=0·323), which translates to an absolute improvement in survival of 2% (−3 to 7). Of 17 trials of bisphosphonates for men with M0 disease, survival results from four trials (4079 [66%] of 6220 men) showed no evidence of benefit from the addition of bisphosphonates (1·03 [0·89–1·18]; p=0·724) or zoledronic acid (0·98 [0·82–1·16]; p=0·782). Failure-free survival definitions were too inconsistent for formal meta-analyses for the bisphosphonate trials. Interpretation The addition of docetaxel to standard of care should be considered standard care for men with M1 hormone-sensitive prostate cancer who are starting treatment for the first time. More evidence on the effects of docetaxel on survival is needed in the M0 disease setting. No evidence exists to suggest that zoledronic acid improves survival in men with M1 or M0 disease, and any potential benefit is probably small. Funding Medical Research Council UK. PMID

  11. Phylogenetic methods in drug discovery.

    PubMed

    Ashton, John C

    2013-12-01

    In recent decades, growth of computing power has facilitated powerful techniques for reconstructing evolutionary relationships from online genetic and proteomic databases. These methods are useful tools for pharmacologists for analyzing relationships between receptors and associated enzymes. Phylogenetic analysis can help generate hypotheses and leads for experimentation. Reconstruction of molecular phylogenies for the nonspecialist is described in this article using the example of the orphaned g protein coupled receptor GPR18.

  12. Phylogenetic Analysis of Fusarium solani Associated with the Asian Longhorned Beetle, Anoplophora glabripennis

    PubMed Central

    Geib, Scott M.; Scully, Erin D.; Jimenez-Gasco, Maria del Mar; Carlson, John E.; Tien, Ming; Hoover, Kelli

    2012-01-01

    Culture-independent analysis of the gut of a wood-boring insect, Anoplophora glabripennis (Coleoptera: Cerambycidae), revealed a consistent association between members of the fungal Fusarium solani species complex and the larval stage of both colony-derived and wild A. glabripennis populations. Using the translation elongation factor 1-alpha region for culture-independent phylogenetic and operational taxonomic unit (OTU)-based analyses, only two OTUs were detected, suggesting that genetic variance at this locus was low among A. glabripennis-associated isolates. To better survey the genetic variation of F. solani associated with A. glabripennis, and establish its phylogenetic relationship with other members of the F. solani species complex, single spore isolates were created from different populations and multi-locus phylogenetic analysis was performed using a combination of the translation elongation factor alpha-1, internal transcribed spacer, and large subunit rDNA regions. These analyses revealed that colony-derived larvae reared in three different tree species or on artificial diet, as well as larvae from wild populations collected from three additional tree species in New York City and from a single tree species in Worcester, MA, consistently harbored F. solani within their guts. While there is some genetic variation in the F. solani carried between populations, within-population variation is low. We speculate that F. solani is able to fill a broad niche in the A. glabripennis gut, providing it with fungal lignocellulases to allow the larvae to grow and develop on woody tissue. However, it is likely that many F. solani genotypes could potentially fill this niche, so the relationship may not be limited to a single member of the F. solani species complex. While little is known about the role of filamentous fungi and their symbiotic associations with insects, this report suggests that larval A. glabripennis has developed an intimate relationship with F. solani

  13. A molecular assessment of phylogenetic relationships and lineage accumulation rates within the family Salamandridae (Amphibia, Caudata).

    PubMed

    Weisrock, David W; Papenfuss, Theodore J; Macey, J Robert; Litvinchuk, Spartak N; Polymeni, Rosa; Ugurtas, Ismail H; Zhao, Ermi; Jowkar, Houman; Larson, Allan

    2006-11-01

    We examine phylogenetic relationships among salamanders of the family Salamandridae using approximately 2700 bases of new mtDNA sequence data (the tRNALeu, ND1, tRNAIle, tRNAGln, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and COI genes and the origin for light-strand replication) collected from 96 individuals representing 61 of the 66 recognized salamandrid species and outgroups. Phylogenetic analyses using maximum parsimony and Bayesian analysis are performed on the new data alone and combined with previously reported sequences from other parts of the mitochondrial genome. The basal phylogenetic split is a polytomy of lineages ancestral to (1) the Italian newt Salamandrina terdigitata, (2) a strongly supported clade comprising the "true" salamanders (genera Chioglossa, Mertensiella, Lyciasalamandra, and Salamandra), and (3) a strongly supported clade comprising all newts except S. terdigitata. Strongly supported clades within the true salamanders include monophyly of each genus and grouping Chioglossa and Mertensiella as the sister taxon to a clade comprising Lyciasalamandra and Salamandra. Among newts, genera Echinotriton, Pleurodeles, and Tylototriton form a strongly supported clade whose sister taxon comprises the genera Calotriton, Cynops, Euproctus, Neurergus, Notophthalmus, Pachytriton, Paramesotriton, Taricha, and Triturus. Our results strongly support monophyly of all polytypic newt genera except Paramesotriton and Triturus, which appear paraphyletic, and Calotriton, for which only one of the two species is sampled. Other well-supported clades within newts include (1) Asian genera Cynops, Pachytriton, and Paramesotriton, (2) North American genera Notophthalmus and Taricha, (3) the Triturus vulgaris species group, and (4) the Triturus cristatus species group; some additional groupings appear strong in Bayesian but not parsimony analyses. Rates of lineage accumulation through time are evaluated using this nearly comprehensive sampling of

  14. Phylogenetic relationship among genera of Polymorphidae (Acanthocephala), inferred from nuclear and mitochondrial gene sequences.

    PubMed

    García-Varela, Martín; Pérez-Ponce de León, Gerardo; Aznar, Francisco J; Nadler, Steven A

    2013-08-01

    Acanthocephalans of the family Polymorphidae Meyer, 1931 are obligate endoparasites with complex life cycles. These worms use vertebrates (marine mammals, fish-eating birds and waterfowl) as definitive hosts and invertebrates (amphipods, decapods and euphausiids) as intermediate hosts to complete their life cycle. Polymorphidae has a wordwide distribution, containing 12 genera, with approximately 127 species. The family is diagnosed by having a spinose trunk, bulbose proboscis, double-walled proboscis receptacle, and usually four to eight tubular cement glands. To conduct a phylogenetic analysis, in the current study sequences of the small (18S) and large-subunit (28S) ribosomal RNA, and cytochrome c oxidase subunit 1 (cox 1) were generated for 27 taxa representing 10 of 12 genera of Polymorphidae, plus three additional species of acanthocephalans that were used as outgroups. Maximum likelihood (ML), maximum parsimony (MP), and Bayesian analyses were conducted on a combined nuclear rRNA (18S+28S) data set and on a concatenated dataset of nuclear plus one mitochondrial gene (18S+28S+cox 1). Phylogenetic analyses inferred with the concatenated dataset of three genes support the monophyly of nine genera (Andracantha, Corynosoma, Bolbosoma, Profilicollis, Pseudocorynosoma, Southwellina, Arhythmorhynchus, Hexaglandula and Ibirhynchus). However, the four sampled species of Polymorphus were nested within several clades, indicating that these species do not share a common ancestor, requiring further taxonomic revision using phylogenetic systematics, and reexamination of morphological and ecological data. By mapping definitive and intermediate host association onto the resulting cladogram, we observe that aquatic birds were the ancestral definitive hosts for the family with a secondary colonization and diversification to marine mammals. Whereas amphipods were ancestral intermediate hosts and that the association with decapods represent episodes of secondary colonization

  15. Phylogenetic diversity of Rhizobium strains nodulating diverse legume species growing in Ethiopia.

    PubMed

    Degefu, Tulu; Wolde-meskel, Endalkachew; Frostegård, Åsa

    2013-06-01

    The taxonomic diversity of thirty-seven Rhizobium strains, isolated from nodules of leguminous trees and herbs growing in Ethiopia, was studied using multilocus sequence analyses (MLSA) of six core and two symbiosis-related genes. Phylogenetic analysis based on the 16S rRNA gene grouped them into five clusters related to nine Rhizobium reference species (99-100% sequence similarity). In addition, two test strains occupied their own independent branches on the phylogenetic tree (AC86a2 along with R. tibeticum; 99.1% similarity and AC100b along with R. multihospitium; 99.5% similarity). One strain from Milletia ferruginea was closely related (>99%) to the genus Shinella, further corroborating earlier findings that nitrogen-fixing bacteria are distributed among phylogenetically unrelated taxa. Sequence analyses of five housekeeping genes also separated the strains into five well-supported clusters, three of which grouped with previously studied Ethiopian common bean rhizobia. Three of the five clusters could potentially be described into new species. Based on the nifH genes, most of the test strains from crop legumes were closely related to several strains of Ethiopian common bean rhizobia and other symbionts of bean plants (R. etli and R. gallicum sv. phaseoli). The grouping of the test strains based on the symbiosis-related genes was not in agreement with the housekeeping genes, signifying differences in their evolutionary history. Our earlier studies revealing a large diversity of Mesorhizobium and Ensifer microsymbionts isolated from Ethiopian legumes, together with the results from the present analysis of Rhizobium strains, suggest that this region might be a potential hotspot for rhizobial biodiversity. PMID:23643092

  16. 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

  17. 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.

  18. Phylogenetic analysis of trophic associations.

    PubMed

    Ives, A R; Godfray, H C J

    2006-07-01

    Ecologists frequently collect data on the patterns of association between adjacent trophic levels in the form of binary or quantitative food webs. Here, we develop statistical methods to estimate the roles of consumer and resource phylogenies in explaining patterns of consumer-resource association. We use these methods to ask whether closely related consumer species are more likely to attack the same resource species and whether closely related resource species are more likely to be attacked by the same consumer species. We then show how to use estimates of phylogenetic signals to predict novel consumer-resource associations solely from the phylogenetic position of species for which no other (or only partial) data are available. Finally, we show how to combine phylogenetic information with information about species' ecological characteristics and life-history traits to estimate the effects of species traits on consumer-resource associations while accounting for phylogenies. We illustrate these techniques using a food web comprising species of parasitoids, leaf-mining moths, and their host plants.

  19. Phylogenetic patterns and phenotypic plasticity of molluscan sexual systems.

    PubMed

    Collin, Rachel

    2013-10-01

    Molluscs show a wide diversity of sexual systems and strategies. There are both gastropod and bivalve families that are each primarily dioecious, simultaneous hermaphrodites, or sequential hermaphrodites, and other families in which almost every sexual strategy occurs. The multiple evolutionary transitions of sexual systems within molluscs would allow comparative analyses of the associated ecological factors, but data on all but a few groups are too sparse to draw many solid conclusions. The phylogenetic distribution of sexual systems in the Mollusca shows that gastropods and bivalves demonstrate different patterns, possibly associated with the presence/absence of copulation. The distribution of change of sex suggests that, in gastropods, sequential hermaphrodites do not evolve from simultaneous hermaphrodites, and that sex reversal (flip-flopping) occurs in free-spawners but not in copulators. Three well-studied protandrous gastropod groups (calyptraeids, coralliophilids, and patellogastropods) show similar responses to environmental conditions and associations with conspecifics. They all have the following attributes: (1) they are sedentary, (2) they live in groups, patches, or aggregates, and (3) size at sex change varies among sites and among aggregates. In addition the available experimental evidence suggests that (4) the presence of females or large individuals represses growth and sex change of males, and (5) behavior seems to mediate the repressive influence of large females. Available data from other species tend to support these patterns. Finally, the repression of growth of males by females in protandry likely facilitates the evolution of dwarf males.

  20. Studies of morphological and molecular phylogenetic divergence in spiders (Araneae: Homalonychus) from the American southwest, including divergence along the Baja California Peninsula.

    PubMed

    Crews, Sarah C; Hedin, Marshal

    2006-02-01

    Comparative phylogenetic and phylogeographic analyses have revealed a pervasive midpeninsular divergence in the mitochondrial genealogies of numerous vertebrate taxa distributed on the Baja California Peninsula. In this study, we extend the investigation of regional vicariance in Baja California to an arthropod taxon by examining patterns of phylogenetic and morphological divergence in the spider genus Homalonychus (Araneae, Homalonychidae). We analyzed data from two mtDNA genes (16S rRNA and NADH dehydrogenase subunit (1) and a nuclear gene (28S rRNA) using maximum parsimony and Bayesian phylogenetic analyses, and also conducted geometric morphometric analyses employing landmark data on male and female genitalia. Genes and morphology both reveal a deep split across the Colorado River and Gulf of California, separating Homalonychus selenopoides on the east side of river from its congener Homalonychus theologus on the west side of the river, including the Baja California Peninsula. Along the north-south axis of the Baja Peninsula, an apparently more recent midpeninsular phylogenetic break is evident within H. theologus in the mitochondrial genome and in female genitalia. However, there is no measurable divergence between northern and southern populations in either nuclear DNA or male genitalia. We suggest that this discordance between datasets reflects either a difference in rates of evolution between male versus female systems, or that male-based nuclear gene flow is obscuring a phylogenetic split that is fixed in the female-based systems. Our findings provide additional support for a midpeninsular Baja divergence event, although the timing and geological evidence for such an event remain elusive.

  1. On phylogenetic tests of irreversible evolution.

    PubMed

    Goldberg, Emma E; Igić, Boris

    2008-11-01

    "Dollo's law" states that, following loss, a complex trait cannot reevolve in an identical manner. Although the law has previously fallen into disrepute, it has only recently been challenged with statistical phylogenetic methods. We employ simulation studies of an irreversible binary character to show that rejections of Dollo's law based on likelihood-ratio tests of transition rate constraints or on reconstructions of ancestral states are frequently incorrect. We identify two major causes of errors: incorrect assignment of root state frequencies, and neglect of the effect of the character state on rates of speciation and extinction. Our findings do not necessarily overturn the conclusions of phylogenetic studies claiming reversals, but we demonstrate devastating flaws in the methods that are the foundation of all such studies. Furthermore, we show that false rejections of Dollo's law can be reduced by the use of appropriate existing models and model selection procedures. More powerful tests of irreversibility require data beyond phylogenies and character states of extant taxa, and we highlight empirical work that incorporates additional information.

  2. Sociopolitical Analyses.

    ERIC Educational Resources Information Center

    Van Galen, Jane, Ed.; And Others

    1992-01-01

    This theme issue of the serial "Educational Foundations" contains four articles devoted to the topic of "Sociopolitical Analyses." In "An Interview with Peter L. McLaren," Mary Leach presented the views of Peter L. McLaren on topics of local and national discourses, values, and the politics of difference. Landon E. Beyer's "Educational Studies and…

  3. Comparative Sequence Analyses of La Crosse Virus Strain Isolated from Patient with Fatal Encephalitis, Tennessee, USA

    PubMed Central

    Fryxell, Rebecca Trout; Freyman, Kimberly; Ulloa, Armando; Velez, Jason O.; Paulsen, Dave; Lanciotti, Robert S.; Moncayo, Abelardo

    2015-01-01

    We characterized a La Crosse virus (LACV) isolate from the brain of a child who died of encephalitis-associated complications in eastern Tennessee, USA, during summer 2012. We compared the isolate with LACV sequences from mosquitoes collected near the child’s home just after his postmortem diagnosis. In addition, we conducted phylogenetic analyses of these and other sequences derived from LACV strains representing varied temporal, geographic, and ecologic origins. Consistent with historical findings, results of these analyses indicate that a limited range of LACV lineage I genotypes is associated with severe clinical outcomes. PMID:25898269

  4. Community structure of a microbial mat: The phylogenetic dimension

    USGS Publications Warehouse

    Risatti, J.B.; Capman, W.C.; Stahl, D.A.

    1994-01-01

    Traditional studies of microbial communities are incomplete because of the inability to identify and quantify all contributing populations. In the present study, we directly determine the abundance and distribution of sulfate-reducing bacterial populations in a microbial mat community by using hybridization probes complementary to the 16S-like rRNAs of major phylogenetic groups. Most of the major groups were found in this single community, distributed for the most part in nonoverlapping depth intervals of the mat. The reflection of the phylogenetic structure in the community structure suggests that those species making up the major phylogenetic groups perform specific interrelated metabolic functions in the community. Comparison of population profiles to previously observed rates of sulfate reduction suggests there are additional populations of sulfate-reducing bacteria both within the photooxic zone and deeper in the mat.

  5. Transforming phylogenetic networks: Moving beyond tree space.

    PubMed

    Huber, Katharina T; Moulton, Vincent; Wu, Taoyang

    2016-09-01

    Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees. In this paper we define two operations on unrooted phylogenetic networks, one of which is a generalization of the well-known nearest-neighbor interchange (NNI) operation on phylogenetic trees. We show that any unrooted phylogenetic network can be transformed into any other such network using only these operations. This generalizes the well-known fact that any phylogenetic tree can be transformed into any other such tree using only NNI operations. It also allows us to define a generalization of tree space and to define some new metrics on unrooted phylogenetic networks. To prove our main results, we employ some fascinating new connections between phylogenetic networks and cubic graphs that we have recently discovered. Our results should be useful in developing new strategies to search for optimal phylogenetic networks, a topic that has recently generated some interest in the literature, as well as for providing new ways to compare networks.

  6. Flight speeds among bird species: allometric and phylogenetic effects.

    PubMed

    Alerstam, Thomas; Rosén, Mikael; Bäckman, Johan; Ericson, Per G P; Hellgren, Olof

    2007-08-01

    Flight speed is expected to increase with mass and wing loading among flying animals and aircraft for fundamental aerodynamic reasons. Assuming geometrical and dynamical similarity, cruising flight speed is predicted to vary as (body mass)(1/6) and (wing loading)(1/2) among bird species. To test these scaling rules and the general importance of mass and wing loading for bird flight speeds, we used tracking radar to measure flapping flight speeds of individuals or flocks of migrating birds visually identified to species as well as their altitude and winds at the altitudes where the birds were flying. Equivalent airspeeds (airspeeds corrected to sea level air density, Ue) of 138 species, ranging 0.01-10 kg in mass, were analysed in relation to biometry and phylogeny. Scaling exponents in relation to mass and wing loading were significantly smaller than predicted (about 0.12 and 0.32, respectively, with similar results for analyses based on species and independent phylogenetic contrasts). These low scaling exponents may be the result of evolutionary restrictions on bird flight-speed range, counteracting too slow flight speeds among species with low wing loading and too fast speeds among species with high wing loading. This compression of speed range is partly attained through geometric differences, with aspect ratio showing a positive relationship with body mass and wing loading, but additional factors are required to fully explain the small scaling exponent of Ue in relation to wing loading. Furthermore, mass and wing loading accounted for only a limited proportion of the variation in Ue. Phylogeny was a powerful factor, in combination with wing loading, to account for the variation in Ue. These results demonstrate that functional flight adaptations and constraints associated with different evolutionary lineages have an important influence on cruising flapping flight speed that goes beyond the general aerodynamic scaling effects of mass and wing loading.

  7. A taxonomic and phylogenetic revision of the Penicillium sclerotiorum complex

    PubMed Central

    Rivera, K.G.; Seifert, K.A.

    2011-01-01

    The morphological concept of Penicillium sclerotiorum (subgenus Aspergilloides) includes strains with monoverticillate, vesiculate conidiophores, and vivid orange to red colony colours, with colourful sclerotia sometimes produced. Multigene phylogenetic analyses with the nuclear ribosomal internal transcribed spacer (ITS) region, cytochrome c oxidase subunit 1 (cox1), β-tubulin (benA), translation elongation factor 1-α (tef1-α), and calmodulin (cmd), reveal that the P. sclerotiorum morphospecies is a complex of seven phylogenetically distinct species, three of which were recently described, namely P. guanacastense, P. mallochii, and P. viticola. Three previously unidentified species are described here as P. cainii, P. jacksonii, and P. johnkrugii. The phylogenetic species are morphologically similar, but differ in combinations of colony characters, sclerotium production, conidiophore stipe roughening and branching, and conidial shape. Ecological characters and differences in geographical distribution further characterise some of the species, but increased sampling is necessary to confirm these differences. The fungal DNA barcode, the ITS, and the animal DNA barcode, cox1, have lower species resolving ability in our phylogenetic analyses, but still allow identification of all the species. Tef1-α and cmd were superior in providing fully resolved, statistically well-supported phylogenetic trees for this species complex, whereas benA resolved all species but had some issues with paraphyly. Penicillium adametzioides and P. multicolor, considered synonyms of P. sclerotiorum by some previous authors, do not belong to the P. sclerotiorum complex. Taxonomic novelties: New species: Penicillium cainii K.G. Rivera, Malloch & Seifert, P. jacksonii K.G. Rivera, Houbraken & Seifert, P. johnkrugii K.G. Rivera, Houbraken & Seifert. PMID:22308047

  8. 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

  9. 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

  10. Phylogenetic Interrelationships of Ginglymodian Fishes (Actinopterygii: Neopterygii)

    PubMed Central

    López-Arbarello, Adriana

    2012-01-01

    The Ginglymodi is one of the most common, though poorly understood groups of neopterygians, which includes gars, macrosemiiforms, and “semionotiforms.” In particular, the phylogenetic relationships between the widely distributed “semionotiforms,” and between them and other ginglymodians have been enigmatic. Here, the phylogenetic relationships between eight of the 11 “semionotiform” genera, five genera of living and fossil gars and three macrosemiid genera, are analysed through cladistic analysis, based on 90 morphological characters and 37 taxa, including 7 out-group taxa. The results of the analysis show that the Ginglymodi includes two main lineages: Lepisosteiformes and †Semionotiformes. The genera †Pliodetes, †Araripelepidotes, †Lepidotes, †Scheenstia, and †Isanichthys are lepisosteiforms, and not semionotiforms, as previously thought, and these taxa extend the stratigraphic range of the lineage leading to gars back up to the Early Jurassic. A monophyletic †Lepidotes is restricted to the Early Jurassic species, whereas the strongly tritoral species previously referred to †Lepidotes are referred to †Scheenstia. Other species previously referred to †Lepidotes represent other genera or new taxa. The macrosemiids are well nested within semionotiforms, together with †Semionotidae, here restricted to †Semionotus, and a new family including †Callipurbeckia n. gen. minor (previously referred to †Lepidotes), †Macrosemimimus, †Tlayuamichin, †Paralepidotus, and †Semiolepis. Due to the numerous taxonomic changes needed according to the phylogenetic analysis, this article also includes formal taxonomic definitions and diagnoses for all generic and higher taxa, which are new or modified. The study of Mesozoic ginglymodians led to confirm Patterson’s observation that these fishes show morphological affinities with both halecomorphs and teleosts. Therefore, the compilation of large data sets including the Mesozoic

  11. Phylogenetic Analysis of Poliovirus Sequences.

    PubMed

    Jorba, Jaume

    2016-01-01

    Comparative genomic sequencing is a major surveillance tool in the Polio Laboratory Network. Due to the rapid evolution of polioviruses (~1 % per year), pathways of virus transmission can be reconstructed from the pathways of genomic evolution. Here, we describe three main phylogenetic methods; estimation of genetic distances, reconstruction of a maximum-likelihood (ML) tree, and estimation of substitution rates using Bayesian Markov chain Monte Carlo (MCMC). The data set used consists of complete capsid sequences from a survey of poliovirus sequences available in GenBank. PMID:26983737

  12. Phylogenetic placement of the Spirosomaceae

    NASA Technical Reports Server (NTRS)

    Woese, C. R.; Maloy, S.; Mandelco, L.; Raj, H. D.

    1990-01-01

    Comparative analysis of 16S rRNA sequences shows that the family Spirosomaceae belongs within the eubacterial phylum defined by the flavobacteria and bacteriodes. Its constituent genera, Spirosoma, Flectobacillus, and Runella form a monophyletic grouping therein. The phylogenetic assignment is based not only upon evolutionary distance analysis, but also upon sequence signatures and higher order structural synapomorphies in 16S rRNA. Another genus peripherally associated with the Spirosomaceae, Ancylobacter ("Microcyclus"), does not cluster with the flavobacteria and their relatives, but rather belongs to the alpha subdivision of the purple bacteria.

  13. Assessment of phylogenetic structure in genome size--gene content correlations.

    PubMed

    Prasad, Vibhu Ranjan; Isler, Karin

    2012-05-01

    Gene content and gene-coding percentage can be predicted from genome size in newly sequenced organisms. Here, we investigate whether these predictions are influenced by phylogenetic relationships between the involved species. Combining a highly resolved phylogenetic tree with a large compilation of gene content data, our results reveal the presence of significant phylogenetic structure in the correlations between genome size and gene content in both bacteria and eukaryotes. The variation in log(gene content) explained by log(genome size) in combination with phylogeny was found to be 97% in bacteria and 55% in eukaryotes. Further, in bacteria, gene-coding percentages are only significantly correlated to genome size if phylogenetic information is taken into account in the analyses. These findings support the usage of phylogenetic correlation models for gene content predictions.

  14. 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.

  15. 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

  16. Phylogenetic approaches for studying diversification.

    PubMed

    Morlon, Hélène

    2014-04-01

    Estimating rates of speciation and extinction, and understanding how and why they vary over evolutionary time, geographical space and species groups, is a key to understanding how ecological and evolutionary processes generate biological diversity. Such inferences will increasingly benefit from phylogenetic approaches given the ever-accelerating rates of genetic sequencing. In the last few years, models designed to understand diversification from phylogenetic data have advanced significantly. Here, I review these approaches and what they have revealed about diversification in the natural world. I focus on key distinctions between different models, and I clarify the conclusions that can be drawn from each model. I identify promising areas for future research. A major challenge ahead is to develop models that more explicitly take into account ecology, in particular the interaction of species with each other and with their environment. This will not only improve our understanding of diversification; it will also present a new perspective to the use of phylogenies in community ecology, the science of interaction networks and conservation biology, and might shift the current focus in ecology on equilibrium biodiversity theories to non-equilibrium theories recognising the crucial role of history.

  17. 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.

  18. Phylogenetic Analysis of the Bifidobacterium Genus Using Glycolysis Enzyme Sequences

    PubMed Central

    Brandt, Katelyn; Barrangou, Rodolphe

    2016-01-01

    Bifidobacteria are important members of the human gastrointestinal tract that promote the establishment of a healthy microbial consortium in the gut of infants. Recent studies have established that the Bifidobacterium genus is a polymorphic phylogenetic clade, which encompasses a diversity of species and subspecies that encode a broad range of proteins implicated in complex and non-digestible carbohydrate uptake and catabolism, ranging from human breast milk oligosaccharides, to plant fibers. Recent genomic studies have created a need to properly place Bifidobacterium species in a phylogenetic tree. Current approaches, based on core-genome analyses come at the cost of intensive sequencing and demanding analytical processes. Here, we propose a typing method based on sequences of glycolysis genes and the proteins they encode, to provide insights into diversity, typing, and phylogeny in this complex and broad genus. We show that glycolysis genes occur broadly in these genomes, to encode the machinery necessary for the biochemical spine of the cell, and provide a robust phylogenetic marker. Furthermore, glycolytic sequences-based trees are congruent with both the classical 16S rRNA phylogeny, and core genome-based strain clustering. Furthermore, these glycolysis markers can also be used to provide insights into the adaptive evolution of this genus, especially with regards to trends toward a high GC content. This streamlined method may open new avenues for phylogenetic studies on a broad scale, given the widespread occurrence of the glycolysis pathway in bacteria, and the diversity of the sequences they encode. PMID:27242688

  19. 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

  20. Phylogenetic Analysis of the Bifidobacterium Genus Using Glycolysis Enzyme Sequences.

    PubMed

    Brandt, Katelyn; Barrangou, Rodolphe

    2016-01-01

    Bifidobacteria are important members of the human gastrointestinal tract that promote the establishment of a healthy microbial consortium in the gut of infants. Recent studies have established that the Bifidobacterium genus is a polymorphic phylogenetic clade, which encompasses a diversity of species and subspecies that encode a broad range of proteins implicated in complex and non-digestible carbohydrate uptake and catabolism, ranging from human breast milk oligosaccharides, to plant fibers. Recent genomic studies have created a need to properly place Bifidobacterium species in a phylogenetic tree. Current approaches, based on core-genome analyses come at the cost of intensive sequencing and demanding analytical processes. Here, we propose a typing method based on sequences of glycolysis genes and the proteins they encode, to provide insights into diversity, typing, and phylogeny in this complex and broad genus. We show that glycolysis genes occur broadly in these genomes, to encode the machinery necessary for the biochemical spine of the cell, and provide a robust phylogenetic marker. Furthermore, glycolytic sequences-based trees are congruent with both the classical 16S rRNA phylogeny, and core genome-based strain clustering. Furthermore, these glycolysis markers can also be used to provide insights into the adaptive evolution of this genus, especially with regards to trends toward a high GC content. This streamlined method may open new avenues for phylogenetic studies on a broad scale, given the widespread occurrence of the glycolysis pathway in bacteria, and the diversity of the sequences they encode. PMID:27242688

  1. 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.

  2. 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

  3. 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

  4. Community Phylogenetics: Assessing Tree Reconstruction Methods and the Utility of DNA Barcodes

    PubMed Central

    Boyle, Elizabeth E.; Adamowicz, Sarah J.

    2015-01-01

    Studies examining phylogenetic community structure have become increasingly prevalent, yet little attention has been given to the influence of the input phylogeny on metrics that describe phylogenetic patterns of co-occurrence. Here, we examine the influence of branch length, tree reconstruction method, and amount of sequence data on measures of phylogenetic community structure, as well as the phylogenetic signal (Pagel’s λ) in morphological traits, using Trichoptera larval communities from Churchill, Manitoba, Canada. We find that model-based tree reconstruction methods and the use of a backbone family-level phylogeny improve estimations of phylogenetic community structure. In addition, trees built using the barcode region of cytochrome c oxidase subunit I (COI) alone accurately predict metrics of phylogenetic community structure obtained from a multi-gene phylogeny. Input tree did not alter overall conclusions drawn for phylogenetic signal, as significant phylogenetic structure was detected in two body size traits across input trees. As the discipline of community phylogenetics continues to expand, it is important to investigate the best approaches to accurately estimate patterns. Our results suggest that emerging large datasets of DNA barcode sequences provide a vast resource for studying the structure of biological communities. PMID:26110886

  5. Phylogenomic Analyses Support Traditional Relationships within Cnidaria

    PubMed Central

    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. PMID:26465609

  6. Phylogenetic classification of Cordyceps and the clavicipitaceous fungi

    PubMed Central

    Sung, Gi-Ho; Hywel-Jones, Nigel L.; Sung, Jae-Mo; Luangsa-ard, J. Jennifer; Shrestha, Bhushan; Spatafora, Joseph W.

    2007-01-01

    Cordyceps, comprising over 400 species, was historically classified in the Clavicipitaceae, based on cylindrical asci, thickened ascus apices and filiform ascospores, which often disarticulate into part-spores. Cordyceps was characterized by the production of well-developed often stipitate stromata and an ecology as a pathogen of arthropods and Elaphomyces with infrageneric classifications emphasizing arrangement of perithecia, ascospore morphology and host affiliation. To refine the classification of Cordyceps and the Clavicipitaceae, the phylogenetic relationships of 162 taxa were estimated based on analyses consisting of five to seven loci, including the nuclear ribosomal small and large subunits (nrSSU and nrLSU), the elongation factor 1α (tef1), the largest and the second largest subunits of RNA polymerase II (rpb1 and rpb2), β-tubulin (tub), and mitochondrial ATP6 (atp6). Our results strongly support the existence of three clavicipitaceous clades and reject the monophyly of both Cordyceps and Clavicipitaceae. Most diagnostic characters used in current classifications of Cordyceps (e.g., arrangement of perithecia, ascospore fragmentation, etc.) were not supported as being phylogenetically informative; the characters that were most consistent with the phylogeny were texture, pigmentation and morphology of stromata. Therefore, we revise the taxonomy of Cordyceps and the Clavicipitaceae to be consistent with the multi-gene phylogeny. The family Cordycipitaceae is validated based on the type of Cordyceps, C. militaris, and includes most Cordyceps species that possess brightly coloured, fleshy stromata. The new family Ophiocordycipitaceae is proposed based on Ophiocordyceps Petch, which we emend. The majority of species in this family produce darkly pigmented, tough to pliant stromata that often possess aperithecial apices. The new genus Elaphocordyceps is proposed for a subclade of the Ophiocordycipitaceae, which includes all species of Cordyceps that parasitize

  7. Phylogenetic relationships of Nembrothinae (Mollusca: Doridacea: Polyceridae) inferred from morphology and mitochondrial DNA.

    PubMed

    Pola, Marta; Cervera, J Lucas; Gosliner, Terrence M

    2007-06-01

    Within the Polyceridae, Nembrothinae includes some of the most striking and conspicuous sea slugs known, although several features of their biology and phylogenetic relationships remain unknown. This paper reports a phylogenetic analysis based on partial sequences of two mitochondrial genes (cytochrome c oxidase subunit I and 16S rRNA) and morphology for most species included in Nembrothinae. Our phylogenetic reconstructions using both molecular and combined morphological and molecular data support the taxonomic splitting of Nembrothinae into several taxa. Excluding one species (Tambja tentaculata), the monophyly of Roboastra was supported by all the phylogenetic analyses of the combined molecular data. Nembrotha was monophyletic both in the morphological and molecular analyses, always with high support. However, Tambja was recovered as para- or polyphyletic, depending on the analysis performed. Our study also rejects the monophyly of "phanerobranch" dorids based on molecular data.

  8. Food additives

    PubMed Central

    Spencer, Michael

    1974-01-01

    Food additives are discussed from the food technology point of view. The reasons for their use are summarized: (1) to protect food from chemical and microbiological attack; (2) to even out seasonal supplies; (3) to improve their eating quality; (4) to improve their nutritional value. The various types of food additives are considered, e.g. colours, flavours, emulsifiers, bread and flour additives, preservatives, and nutritional additives. The paper concludes with consideration of those circumstances in which the use of additives is (a) justified and (b) unjustified. PMID:4467857

  9. Phylogenetic selection of target species in Amaryllidaceae tribe Haemantheae for acetylcholinesterase inhibition and affinity to the serotonin reuptake transport protein

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We present phylogenetic analyses of 37 taxa of Amaryllidaceae, tribe Haemantheae and Amaryllis belladonna L. as an outgroup, in order to provide a phylogenetic framework for the selection of candidate plants for lead discoveries in relation to Alzheimer´s disease and depression. DNA sequences from t...

  10. Phylogenetic evaluation of taxonomic definition of didelphid mouse opossum of the genus Thylamys from valleys of Coquimbo region, Chile.

    PubMed

    Boric-Bargetto, Dusan; Zúñiga-Reinoso, Álvaro; Cancino, Ricardo A; González-Acuña, Daniel; Rodríguez-Serrano, Enrique; Palma, R Eduardo; Hernández, Cristián E

    2016-01-01

    Only two species of Didelphidae are currently recognized in Chile, the sister species Thylamys elegans, endemic of Mediterranean ecorregion and Thylamys pallidior, the inhabitant of the Puna and desert canyons. Three subspecies have been described for T. elegans: T. e. elegans, T. e. coquimbensis and T. e. soricinus. However, a recent study based on morphological analyses, synonymized T. elegans coquimbensis from the Coquimbo valleys (30-31° S) with T. pallidior and proposed that T. elegans and T. pallidior could be in sympatry at Coquimbo valleys between Fray Jorge (30°40'S) and Paiguano (30°02' S). We assess the current definition of T. e. coquimbensis and T. e. elegans, as well as this taxonomical conflict among the mouse opossums from the Coquimbo valleys through phylogenetic analyses of cytochrome b mitochondrial gene sequences. In this study, for the first time, we used specimens from the type localities of T. e. coquimbensis and T. e. elegans. In addition, we analyzed diagnostic cranial structures for this taxonomic revision. The results supported two allopatric clades, allowing us to keep the taxonomic definition of T. e. elegans and T. e. coquimbensis as phylogenetic reciprocal monophyletic clades and polyphyletic with T. pallidior. This result corroborates previous morphological analyses, which support that mouse opossums from the Coquimbo valleys are T. e. coquimbensis, thus extending its geographic distribution to the coast of Coquimbo and Atacama regions. We don´t have evidence for sympatric distribution between T. elegans and T. pallidior in the Coquimbo region. PMID:27394783

  11. ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling.

    PubMed

    Cheng, Yiming; Perocchi, Fabiana

    2015-07-01

    ProtPhylo is a web-based tool to identify proteins that are functionally linked to either a phenotype or a protein of interest based on co-evolution. ProtPhylo infers functional associations by comparing protein phylogenetic profiles (co-occurrence patterns of orthology relationships) for more than 9.7 million non-redundant protein sequences from all three domains of life. Users can query any of 2048 fully sequenced organisms, including 1678 bacteria, 255 eukaryotes and 115 archaea. In addition, they can tailor ProtPhylo to a particular kind of biological question by choosing among four main orthology inference methods based either on pair-wise sequence comparisons (One-way Best Hits and Best Reciprocal Hits) or clustering of orthologous proteins across multiple species (OrthoMCL and eggNOG). Next, ProtPhylo ranks phylogenetic neighbors of query proteins or phenotypic properties using the Hamming distance as a measure of similarity between pairs of phylogenetic profiles. Candidate hits can be easily and flexibly prioritized by complementary clues on subcellular localization, known protein-protein interactions, membrane spanning regions and protein domains. The resulting protein list can be quickly exported into a csv text file for further analyses. ProtPhylo is freely available at http://www.protphylo.org.

  12. Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field.

    PubMed

    Nakagawa, Satoshi; Takai, Ken; Inagaki, Fumio; Hirayama, Hisako; Nunoura, Takuro; Horikoshi, Koki; Sako, Yoshihiko

    2005-10-01

    Epsilon-Proteobacteria is increasingly recognized as an ecologically significant group of bacteria, particularly in deep-sea hydrothermal environments. In this study, we studied the spatial distribution, diversity and physiological characteristics of the epsilon-Proteobacteria in various microbial habitats in the vicinity of a deep-sea hydrothermal vent occurring in the Iheya North field in the Mid-Okinawa Trough, by using culture-dependent and -independent approaches. The habitats studied were inside and outside hydrothermal plume, and annelid polychaete tubes. In addition, we deployed colonization devices near the vent emission. The polychaete tubes harboured physiologically and phylogenetically diverse microbial community. The in situ samplers were predominantly colonized by epsilon-Proteobacteria. Energy metabolism of epsilon-Proteobacteria isolates was highly versatile. Tree topology generated from the metabolic traits was significantly different (P = 0.000) from that of 16S rRNA tree, indicating current 16S rRNA gene-based analyses do not provide sufficient information to infer the physiological characteristics of epsilon-Proteobacteria. Nevertheless, culturability of epsilon-Proteobacteria in various microbial habitats differed among the phylogenetic subgroups. Members of Sulfurimonas were characterized by the robust culturability, and the other phylogenetic subgroups appeared to lose culturability in seawater, probably because of the sensitivity to oxygen. These results provide new insight into the ecophysiological characteristics of the deep-sea hydrothermal vent epsilon-Proteobacteria, which has never been assessed by comparative analysis of the 16S rRNA genes.

  13. Phylogenetic studies of transmission dynamics in generalized HIV epidemics: An essential tool where the burden is greatest?

    PubMed Central

    Dennis, Ann M.; Herbeck, Joshua T.; Brown, Andrew Leigh; Kellam, Paul; de Oliveira, Tulio; Pillay, Deenan; Fraser, Christophe; Cohen, Myron S.

    2014-01-01

    Efficient and effective HIV prevention measures for generalized epidemics in sub-Saharan Africa have not yet been validated at the population-level. Design and impact evaluation of such measures requires fine-scale understanding of local HIV transmission dynamics. The novel tools of HIV phylogenetics and molecular epidemiology may elucidate these transmission dynamics. Such methods have been incorporated into studies of concentrated HIV epidemics to identify proximate and determinant traits associated with ongoing transmission. However, applying similar phylogenetic analyses to generalized epidemics, including the design and evaluation of prevention trials, presents additional challenges. Here we review the scope of these methods and present examples of their use in concentrated epidemics in the context of prevention. Next, we describe the current uses for phylogenetics in generalized epidemics, and discuss their promise for elucidating transmission patterns and informing prevention trials. Finally, we review logistic and technical challenges inherent to large-scale molecular epidemiological studies of generalized epidemics, and suggest potential solutions. PMID:24977473

  14. Complete mitochondrial DNA sequence of the endangered fish (Bahaba taipingensis): Mitogenome characterization and phylogenetic implications

    PubMed Central

    Zhao, Linlin; Gao, Tianxiang; Lu, Weihua

    2015-01-01

    Abstract To understand the systematic status of Bahaba taipingensis within Sciaenidae, the complete mitochondrial genome (mitogenome) sequence of Chinese bahaba has recently been determined by long PCR and primer walking methods. The complete mitochondrial genome is 16500 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) as well as a control region (CR) as other bony fishes. Within the control region, we identified the extended termination associated sequence domain (ETAS), the central conserved sequence block domain (CSB-D, SCB-E and CSB-F) and the conserved sequence block domain (CSB-1, CSB-2 and CSB-3). Phylogenetic analyses revealed that Bahaba taipingensis is more closely related to Pseudosciaeniae than Argyrosominae and Sciaeninae. Additionally, Bahaba taipingensis is the sister taxon of Miichthys miiuy, and those two are sister to Collichthys plus Larimichthys. PMID:26798311

  15. A new species of Allodaposuchus (Eusuchia, Crocodylia) from the Maastrichtian (Late Cretaceous) of Spain: phylogenetic and paleobiological implications.

    PubMed

    Blanco, Alejandro; Fortuny, Josep; Vicente, Alba; Luján, Àngel H; García-Marçà, Jordi Alexis; Sellés, Albert G

    2015-01-01

    Background. The Late Cretaceous is a keystone period to understand the origin and early radiation of Crocodylia, the group containing all extant lineages of crocodilians. Among the taxa described from the latest Cretaceous of Europe, the genus Allodaposuchus is one of the most common but also one of the most controversial. However, because of its fragmentary record, several issues regarding its phylogenetic emplacement and its ecology remain unsolved or unknown. The discovery of a single specimen attributed to Allodaposuchus, represented by both cranial and postcranial remains, from the Casa Fabà site (Tremp Basin, NE Spain) in the lower red unit of the Tremp Fm. (early Maastrichtian, Late Cretaceous) offers a unique opportunity to deepen in the phylogenetic relationships of the group and its ecological features. Methods. The specimen is described in detail, and CT scan of the skull is performed in order to study the endocranial morphology as well as paratympanic sinuses configuration. In addition, myological and phylogenetic analyses are also carried out on the specimen for to shed light in ecological and phylogenetic issues, respectively. Results. The specimen described herein represents a new species, Allodaposuchus hulki sp. nov., closely related to the Romanian A. precedens. The CT scan of the skull revealed an unexpected paratympanic sinuses configuration. Allosaposuchus hulki exhibits an "anterodorsal tympanic sinus" not observed in any other extant or extinct crocodilian. The caudal tympanic recesses are extremely enlarged, and the expanded quadratic sinus seems to be connected to the middle-ear channel. Phylogenetic analyses confirm the emplacement of the informal taxonomic group 'Allodaposuchia' at the base of Crocodylia, being considered the sister group of Borealosuchus and Planocraniidae. Discussion. Although this is a preliminary hypothesis, the unique paratympanic configuration displayed by A. hulki suggests that it could possess a high

  16. A new species of Allodaposuchus (Eusuchia, Crocodylia) from the Maastrichtian (Late Cretaceous) of Spain: phylogenetic and paleobiological implications

    PubMed Central

    Blanco, Alejandro; Fortuny, Josep; Vicente, Alba; Luján, Àngel H.; García-Marçà, Jordi Alexis

    2015-01-01

    Background. The Late Cretaceous is a keystone period to understand the origin and early radiation of Crocodylia, the group containing all extant lineages of crocodilians. Among the taxa described from the latest Cretaceous of Europe, the genus Allodaposuchus is one of the most common but also one of the most controversial. However, because of its fragmentary record, several issues regarding its phylogenetic emplacement and its ecology remain unsolved or unknown. The discovery of a single specimen attributed to Allodaposuchus, represented by both cranial and postcranial remains, from the Casa Fabà site (Tremp Basin, NE Spain) in the lower red unit of the Tremp Fm. (early Maastrichtian, Late Cretaceous) offers a unique opportunity to deepen in the phylogenetic relationships of the group and its ecological features. Methods. The specimen is described in detail, and CT scan of the skull is performed in order to study the endocranial morphology as well as paratympanic sinuses configuration. In addition, myological and phylogenetic analyses are also carried out on the specimen for to shed light in ecological and phylogenetic issues, respectively. Results. The specimen described herein represents a new species, Allodaposuchus hulki sp. nov., closely related to the Romanian A. precedens. The CT scan of the skull revealed an unexpected paratympanic sinuses configuration. Allosaposuchus hulki exhibits an “anterodorsal tympanic sinus” not observed in any other extant or extinct crocodilian. The caudal tympanic recesses are extremely enlarged, and the expanded quadratic sinus seems to be connected to the middle-ear channel. Phylogenetic analyses confirm the emplacement of the informal taxonomic group ‘Allodaposuchia’ at the base of Crocodylia, being considered the sister group of Borealosuchus and Planocraniidae. Discussion. Although this is a preliminary hypothesis, the unique paratympanic configuration displayed by A. hulki suggests that it could possess a high

  17. A new species of Allodaposuchus (Eusuchia, Crocodylia) from the Maastrichtian (Late Cretaceous) of Spain: phylogenetic and paleobiological implications.

    PubMed

    Blanco, Alejandro; Fortuny, Josep; Vicente, Alba; Luján, Àngel H; García-Marçà, Jordi Alexis; Sellés, Albert G

    2015-01-01

    Background. The Late Cretaceous is a keystone period to understand the origin and early radiation of Crocodylia, the group containing all extant lineages of crocodilians. Among the taxa described from the latest Cretaceous of Europe, the genus Allodaposuchus is one of the most common but also one of the most controversial. However, because of its fragmentary record, several issues regarding its phylogenetic emplacement and its ecology remain unsolved or unknown. The discovery of a single specimen attributed to Allodaposuchus, represented by both cranial and postcranial remains, from the Casa Fabà site (Tremp Basin, NE Spain) in the lower red unit of the Tremp Fm. (early Maastrichtian, Late Cretaceous) offers a unique opportunity to deepen in the phylogenetic relationships of the group and its ecological features. Methods. The specimen is described in detail, and CT scan of the skull is performed in order to study the endocranial morphology as well as paratympanic sinuses configuration. In addition, myological and phylogenetic analyses are also carried out on the specimen for to shed light in ecological and phylogenetic issues, respectively. Results. The specimen described herein represents a new species, Allodaposuchus hulki sp. nov., closely related to the Romanian A. precedens. The CT scan of the skull revealed an unexpected paratympanic sinuses configuration. Allosaposuchus hulki exhibits an "anterodorsal tympanic sinus" not observed in any other extant or extinct crocodilian. The caudal tympanic recesses are extremely enlarged, and the expanded quadratic sinus seems to be connected to the middle-ear channel. Phylogenetic analyses confirm the emplacement of the informal taxonomic group 'Allodaposuchia' at the base of Crocodylia, being considered the sister group of Borealosuchus and Planocraniidae. Discussion. Although this is a preliminary hypothesis, the unique paratympanic configuration displayed by A. hulki suggests that it could possess a high

  18. Experimental design in phylogenetics: testing predictions from expected information.

    PubMed

    San Mauro, Diego; Gower, David J; Cotton, James A; Zardoya, Rafael; Wilkinson, Mark; Massingham, Tim

    2012-07-01

    Taxon and character sampling are central to phylogenetic experimental design; yet, we lack general rules. Goldman introduced a method to construct efficient sampling designs in phylogenetics, based on the calculation of expected Fisher information given a probabilistic model of sequence evolution. The considerable potential of this approach remains largely unexplored. In an earlier study, we applied Goldman's method to a problem in the phylogenetics of caecilian amphibians and made an a priori evaluation and testable predictions of which taxon additions would increase information about a particular weakly supported branch of the caecilian phylogeny by the greatest amount. We have now gathered mitogenomic and rag1 sequences (some newly determined for this study) from additional caecilian species and studied how information (both expected and observed) and bootstrap support vary as each new taxon is individually added to our previous data set. This provides the first empirical test of specific predictions made using Goldman's method for phylogenetic experimental design. Our results empirically validate the top 3 (more intuitive) taxon addition predictions made in our previous study, but only information results validate unambiguously the 4th (less intuitive) prediction. This highlights a complex relationship between information and support, reflecting that each measures different things: Information is related to the ability to estimate branch length accurately and support to the ability to estimate the tree topology accurately. Thus, an increase in information may be correlated with but does not necessitate an increase in support. Our results also provide the first empirical validation of the widely held intuition that additional taxa that join the tree proximal to poorly supported internal branches are more informative and enhance support more than additional taxa that join the tree more distally. Our work supports the view that adding more data for a single (well

  19. Climate and species richness predict the phylogenetic structure of African mammal communities.

    PubMed

    Kamilar, Jason M; Beaudrot, Lydia; Reed, Kaye E

    2015-01-01

    We have little knowledge of how climatic variation (and by proxy, habitat variation) influences the phylogenetic structure of tropical communities. Here, we quantified the phylogenetic structure of mammal communities in Africa to investigate how community structure varies with respect to climate and species richness variation across the continent. In addition, we investigated how phylogenetic patterns vary across carnivores, primates, and ungulates. We predicted that climate would differentially affect the structure of communities from different clades due to between-clade biological variation. We examined 203 communities using two metrics, the net relatedness (NRI) and nearest taxon (NTI) indices. We used simultaneous autoregressive models to predict community phylogenetic structure from climate variables and species richness. We found that most individual communities exhibited a phylogenetic structure consistent with a null model, but both climate and species richness significantly predicted variation in community phylogenetic metrics. Using NTI, species rich communities were composed of more distantly related taxa for all mammal communities, as well as for communities of carnivorans or ungulates. Temperature seasonality predicted the phylogenetic structure of mammal, carnivoran, and ungulate communities, and annual rainfall predicted primate community structure. Additional climate variables related to temperature and rainfall also predicted the phylogenetic structure of ungulate communities. We suggest that both past interspecific competition and habitat filtering have shaped variation in tropical mammal communities. The significant effect of climatic factors on community structure has important implications for the diversity of mammal communities given current models of future climate change.

  20. Climate and Species Richness Predict the Phylogenetic Structure of African Mammal Communities

    PubMed Central

    Kamilar, Jason M.; Beaudrot, Lydia; Reed, Kaye E.

    2015-01-01

    We have little knowledge of how climatic variation (and by proxy, habitat variation) influences the phylogenetic structure of tropical communities. Here, we quantified the phylogenetic structure of mammal communities in Africa to investigate how community structure varies with respect to climate and species richness variation across the continent. In addition, we investigated how phylogenetic patterns vary across carnivores, primates, and ungulates. We predicted that climate would differentially affect the structure of communities from different clades due to between-clade biological variation. We examined 203 communities using two metrics, the net relatedness (NRI) and nearest taxon (NTI) indices. We used simultaneous autoregressive models to predict community phylogenetic structure from climate variables and species richness. We found that most individual communities exhibited a phylogenetic structure consistent with a null model, but both climate and species richness significantly predicted variation in community phylogenetic metrics. Using NTI, species rich communities were composed of more distantly related taxa for all mammal communities, as well as for communities of carnivorans or ungulates. Temperature seasonality predicted the phylogenetic structure of mammal, carnivoran, and ungulate communities, and annual rainfall predicted primate community structure. Additional climate variables related to temperature and rainfall also predicted the phylogenetic structure of ungulate communities. We suggest that both past interspecific competition and habitat filtering have shaped variation in tropical mammal communities. The significant effect of climatic factors on community structure has important implications for the diversity of mammal communities given current models of future climate change. PMID:25875361

  1. Direct phylogenetic evidence for lateral transfer of elongation factor-like gene

    PubMed Central

    Kamikawa, Ryoma; Inagaki, Yuji; Sako, Yoshihiko

    2008-01-01

    Genes encoding elongation factor-like (EFL) proteins, which show high similarity to elongation factor-1α (EF-1α), have been found in phylogenetically distantly related eukaryotes. The sporadic distribution of “EFL-containing” lineages within “EF-1α-containing” lineages indirectly, but strongly, suggests lateral gene transfer as the principal driving force in EFL evolution. However, one of the most critical aspects in the above hypothesis, the donor lineages in any putative cases of lateral EFL gene transfer, remained unclear. In this study, we provide direct evidence for lateral transfer of an EFL gene through the analyses of 10 diatom EFL genes. All diatom EFL homologues tightly clustered in phylogenetic analyses, suggesting acquisition of the exogenous EFL gene early in diatom evolution. Our survey additionally identified Thalassiosira pseudonana as a eukaryote bearing EF-1α and EFL genes and secondary EFL gene loss in Phaeodactylum tricornutum, the complete genome of which encodes only the EF-1α gene. Most importantly, the EFL phylogeny recovered a robust grouping of homologues from diatoms, the cercozoan Bigelowiella natans, and the foraminifer Planoglabratella opecularis, with the diatoms nested within the Bigelowiella plus Planoglabratella (Rhizaria) grouping. The particular relationships recovered are further consistent with two characteristic sequence motifs. The best explanation of our data analyses is an EFL gene transfer from a foraminifer to a diatom, the first case in which the donor–recipient relationship was clarified. Finally, based on a reverse transcriptase quantitative PCR assay and the genome information of Thalassiosira and Phaeodactylum, we propose the loss of elongation factor function in Thalassiosira EF-1α. PMID:18458344

  2. Comparative study of notoungulate (Placentalia, Mammalia) bony labyrinths and new phylogenetically informative inner ear characters

    PubMed Central

    Macrini, Thomas E; Flynn, John J; Ni, Xijun; Croft, Darin A; Wyss, André R

    2013-01-01

    The phylogenetic relationships of notoungulates, an extinct group of predominantly South American herbivores, remain poorly resolved with respect to both other placental mammals and among one another. Most previous phylogenetic analyses of notoungulates have not included characters of the internal cranium, not least because few such features, including the bony labyrinth, have been described for members of the group. Here we describe the inner ears of the notoungulates Altitypotherium chucalensis (Mesotheriidae), Pachyrukhos moyani (Hegetotheriidae) and Cochilius sp. (Interatheriidae) based on reconstructions of bony labyrinths obtained from computed tomography imagery. Comparisons of the bony labyrinths of these taxa with the basally diverging notoungulate Notostylops murinus (Notostylopidae), an isolated petrosal from Itaboraí, Brazil, referred to Notoungulata, and six therian outgroups, yielded an inner ear character matrix of 25 potentially phylogenetically informative characters, 14 of them novel to this study. Two equivocally optimized character states potentially support a pairing of Mesotheriidae and Hegetotheriidae, whereas four others may be diagnostic of Notoungulata. Three additional characters are potentially informative for diagnosing more inclusive clades: one for crown Placentalia; another for a clade containing Kulbeckia, Zalambdalestes, and Placentalia; and a third for Eutheria (crown Placentalia plus stem taxa). Several other characters are apomorphic for at least one notoungulate in our study and are of potential interest for broader taxonomic sampling within Notoungulata to clarify currently enigmatic interrelationships. Measures of the semicircular canals were used to infer agility (e.g. capable of quick movements vs. lethargic movements) of these taxa. Agility scores calculated from these data generally corroborate interpretations based on postcranial remains of these or closely related species. We provide estimates of the low

  3. Eye-Size Variability in Deep-Sea Lanternfishes (Myctophidae): An Ecological and Phylogenetic Study

    PubMed Central

    de Busserolles, Fanny; Fitzpatrick, John L.; Paxton, John R.; Marshall, N. Justin; Collin, Shaun P.

    2013-01-01

    One of the most common visual adaptations seen in the mesopelagic zone (200–1000 m), where the amount of light diminishes exponentially with depth and where bioluminescent organisms predominate, is the enlargement of the eye and pupil area. However, it remains unclear how eye size is influenced by depth, other environmental conditions and phylogeny. In this study, we determine the factors influencing variability in eye size and assess whether this variability is explained by ecological differences in habitat and lifestyle within a family of mesopelagic fishes characterized by broad intra- and interspecific variance in depth range and luminous patterns. We focus our study on the lanternfish family (Myctophidae) and hypothesise that lanternfishes with a deeper distribution and/or a reduction of bioluminescent emissions have smaller eyes and that ecological factors rather than phylogenetic relationships will drive the evolution of the visual system. Eye diameter and standard length were measured in 237 individuals from 61 species of lanternfishes representing all the recognised tribes within the family in addition to compiling an ecological dataset including depth distribution during night and day and the location and sexual dimorphism of luminous organs. Hypotheses were tested by investigating the relationship between the relative size of the eye (corrected for body size) and variations in depth and/or patterns of luminous-organs using phylogenetic comparative analyses. Results show a great variability in relative eye size within the Myctophidae at all taxonomic levels (from subfamily to genus), suggesting that this character may have evolved several times. However, variability in eye size within the family could not be explained by any of our ecological variables (bioluminescence and depth patterns), and appears to be driven solely by phylogenetic relationships. PMID:23472203

  4. The Complete Mitochondrial Genome of Corizus tetraspilus (Hemiptera: Rhopalidae) and Phylogenetic Analysis of Pentatomomorpha

    PubMed Central

    Guo, Zhong-Long; Wang, Juan; Shen, Yu-Ying

    2015-01-01

    Insect mitochondrial genome (mitogenome) are the most extensively used genetic information for molecular evolution, phylogenetics and population genetics. Pentatomomorpha (>14,000 species) is the second largest infraorder of Heteroptera and of great economic importance. To better understand the diversity and phylogeny within Pentatomomorpha, we sequenced and annotated the complete mitogenome of Corizus tetraspilus (Hemiptera: Rhopalidae), an important pest of alfalfa in China. We analyzed the main features of the C. tetraspilus mitogenome, and provided a comparative analysis with four other Coreoidea species. Our results reveal that gene content, gene arrangement, nucleotide composition, codon usage, rRNA structures and sequences of mitochondrial transcription termination factor are conserved in Coreoidea. Comparative analysis shows that different protein-coding genes have been subject to different evolutionary rates correlated with the G+C content. All the transfer RNA genes found in Coreoidea have the typical clover leaf secondary structure, except for trnS1 (AGN) which lacks the dihydrouridine (DHU) arm and possesses a unusual anticodon stem (9 bp vs. the normal 5 bp). The control regions (CRs) among Coreoidea are highly variable in size, of which the CR of C. tetraspilus is the smallest (440 bp), making the C. tetraspilus mitogenome the smallest (14,989 bp) within all completely sequenced Coreoidea mitogenomes. No conserved motifs are found in the CRs of Coreoidea. In addition, the A+T content (60.68%) of the CR of C. tetraspilus is much lower than that of the entire mitogenome (74.88%), and is lowest among Coreoidea. Phylogenetic analyses based on mitogenomic data support the monophyly of each superfamily within Pentatomomorpha, and recognize a phylogenetic relationship of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Pyrrhocoroidea + Coreoidea)))). PMID:26042898

  5. Phylogenetic analysis in Myrcia section Aulomyrcia and inferences on plant diversity in the Atlantic rainforest

    PubMed Central

    Staggemeier, Vanessa Graziele; Diniz-Filho, José Alexandre Felizola; Forest, Félix; Lucas, Eve

    2015-01-01

    Background and Aims Myrcia section Aulomyrcia includes ∼120 species that are endemic to the Neotropics and disjunctly distributed in the moist Amazon and Atlantic coastal forests of Brazil. This paper presents the first comprehensive phylogenetic study of this group and this phylogeny is used as a basis to evaluate recent classification systems and to test alternative hypotheses associated with the history of this clade. Methods Fifty-three taxa were sampled out of the 120 species currently recognized, plus 40 outgroup taxa, for one nuclear marker (ribosomal internal transcribed spacer) and four plastid markers (psbA-trnH, trnL-trnF, trnQ-rpS16 and ndhF). The relationships were reconstructed based on Bayesian and maximum likelihood analyses. Additionally, a likelihood approach, ‘geographic state speciation and extinction’, was used to estimate region- dependent rates of speciation, extinction and dispersal, comparing historically climatic stable areas (refugia) and unstable areas. Key Results Maximum likelihood and Bayesian inferences indicate that Myrcia and Marlierea are polyphyletic, and the internal groupings recovered are characterized by combinations of morphological characters. Phylogenetic relationships support a link between Amazonian and north-eastern species and between north-eastern and south-eastern species. Lower extinction rates within glacial refugia suggest that these areas were important in maintaining diversity in the Atlantic forest biodiversity hotspot. Conclusions This study provides a robust phylogenetic framework to address important ecological questions for Myrcia s.l. within an evolutionary context, and supports the need to unite taxonomically the two traditional genera Myrcia and Marlierea in an expanded Myrcia s.l. Furthermore, this study offers valuable insights into the diversification of plant species in the highly impacted Atlantic forest of South America; evidence is presented that the lowest extinction rates are found inside

  6. Evidence of novel phylogenetic lineages of methanogenic archaea from hypersaline microbial mats.

    PubMed

    García-Maldonado, José Q; Bebout, Brad M; Everroad, R Craig; López-Cortés, Alejandro

    2015-01-01

    Methanogenesis in hypersaline and high-sulfate environments is typically dominated by methylotrophic methanogens because sulfate reduction is thermodynamically favored over hydrogenotrophic methanogenesis in these environments. We characterized the community composition of methanogenic archaea in both unmanipulated and incubated microbial mats from different hypersaline environments in Baja California Sur, Mexico. Clone libraries of methyl coenzyme-M reductase (mcrA) sequences and DGGE band patterns of 16S rRNA and mcrA sequences showed that the methanogen community in these microbial mats is dominated by methylotrophic methanogens of the genus Methanohalophilus. However, phylogenetic analyses of mcrA sequences from these mats also revealed two new lineages corresponding to putative hydrogenotrophic methanogens related with the strictly hydrogenotrophic order Methanomicrobiales. Stimulated methane production under decreased salinity and sulfate concentrations also suggested the presence of hydrogenotrophic methanogens in these samples. The relative abundance of mcrA gene and transcripts, estimated by SYBR green I qPCR assays, suggested the activity of different phylogenetic groups of methanogens, including the two novel clusters, in unmanipulated samples of hypersaline microbial mats. Using geochemical and molecular approaches, we show that substrate limitation and values of salinity and sulfate higher than 3 % and 25 mM (respectively) are potential environmental constraints for methanogenesis in these environments. Microcosm experiments with modifications of salinity and sulfate concentrations and TMA addition showed that upper salt and sulfate concentrations for occurrence of methylotrophic methanogenesis were 28 % and 263 mM, respectively. This study provides phylogenetic information about uncultivated and undescribed methanogenic archaea from hypersaline environments.

  7. The Complete Mitochondrial Genome of Corizus tetraspilus (Hemiptera: Rhopalidae) and Phylogenetic Analysis of Pentatomomorpha.

    PubMed

    Yuan, Ming-Long; Zhang, Qi-Lin; Guo, Zhong-Long; Wang, Juan; Shen, Yu-Ying

    2015-01-01

    Insect mitochondrial genome (mitogenome) are the most extensively used genetic information for molecular evolution, phylogenetics and population genetics. Pentatomomorpha (>14,000 species) is the second largest infraorder of Heteroptera and of great economic importance. To better understand the diversity and phylogeny within Pentatomomorpha, we sequenced and annotated the complete mitogenome of Corizus tetraspilus (Hemiptera: Rhopalidae), an important pest of alfalfa in China. We analyzed the main features of the C. tetraspilus mitogenome, and provided a comparative analysis with four other Coreoidea species. Our results reveal that gene content, gene arrangement, nucleotide composition, codon usage, rRNA structures and sequences of mitochondrial transcription termination factor are conserved in Coreoidea. Comparative analysis shows that different protein-coding genes have been subject to different evolutionary rates correlated with the G+C content. All the transfer RNA genes found in Coreoidea have the typical clover leaf secondary structure, except for trnS1 (AGN) which lacks the dihydrouridine (DHU) arm and possesses a unusual anticodon stem (9 bp vs. the normal 5 bp). The control regions (CRs) among Coreoidea are highly variable in size, of which the CR of C. tetraspilus is the smallest (440 bp), making the C. tetraspilus mitogenome the smallest (14,989 bp) within all completely sequenced Coreoidea mitogenomes. No conserved motifs are found in the CRs of Coreoidea. In addition, the A+T content (60.68%) of the CR of C. tetraspilus is much lower than that of the entire mitogenome (74.88%), and is lowest among Coreoidea. Phylogenetic analyses based on mitogenomic data support the monophyly of each superfamily within Pentatomomorpha, and recognize a phylogenetic relationship of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Pyrrhocoroidea + Coreoidea)))). PMID:26042898

  8. Comparative study of notoungulate (Placentalia, Mammalia) bony labyrinths and new phylogenetically informative inner ear characters.

    PubMed

    Macrini, Thomas E; Flynn, John J; Ni, Xijun; Croft, Darin A; Wyss, André R

    2013-11-01

    The phylogenetic relationships of notoungulates, an extinct group of predominantly South American herbivores, remain poorly resolved with respect to both other placental mammals and among one another. Most previous phylogenetic analyses of notoungulates have not included characters of the internal cranium, not least because few such features, including the bony labyrinth, have been described for members of the group. Here we describe the inner ears of the notoungulates Altitypotherium chucalensis (Mesotheriidae), Pachyrukhos moyani (Hegetotheriidae) and Cochilius sp. (Interatheriidae) based on reconstructions of bony labyrinths obtained from computed tomography imagery. Comparisons of the bony labyrinths of these taxa with the basally diverging notoungulate Notostylops murinus (Notostylopidae), an isolated petrosal from Itaboraí, Brazil, referred to Notoungulata, and six therian outgroups, yielded an inner ear character matrix of 25 potentially phylogenetically informative characters, 14 of them novel to this study. Two equivocally optimized character states potentially support a pairing of Mesotheriidae and Hegetotheriidae, whereas four others may be diagnostic of Notoungulata. Three additional characters are potentially informative for diagnosing more inclusive clades: one for crown Placentalia; another for a clade containing Kulbeckia, Zalambdalestes, and Placentalia; and a third for Eutheria (crown Placentalia plus stem taxa). Several other characters are apomorphic for at least one notoungulate in our study and are of potential interest for broader taxonomic sampling within Notoungulata to clarify currently enigmatic interrelationships. Measures of the semicircular canals were used to infer agility (e.g. capable of quick movements vs. lethargic movements) of these taxa. Agility scores calculated from these data generally corroborate interpretations based on postcranial remains of these or closely related species. We provide estimates of the low

  9. Eye-size variability in deep-sea lanternfishes (Myctophidae): an ecological and phylogenetic study.

    PubMed

    de Busserolles, Fanny; Fitzpatrick, John L; Paxton, John R; Marshall, N Justin; Collin, Shaun P

    2013-01-01

    One of the most common visual adaptations seen in the mesopelagic zone (200-1000 m), where the amount of light diminishes exponentially with depth and where bioluminescent organisms predominate, is the enlargement of the eye and pupil area. However, it remains unclear how eye size is influenced by depth, other environmental conditions and phylogeny. In this study, we determine the factors influencing variability in eye size and assess whether this variability is explained by ecological differences in habitat and lifestyle within a family of mesopelagic fishes characterized by broad intra- and interspecific variance in depth range and luminous patterns. We focus our study on the lanternfish family (Myctophidae) and hypothesise that lanternfishes with a deeper distribution and/or a reduction of bioluminescent emissions have smaller eyes and that ecological factors rather than phylogenetic relationships will drive the evolution of the visual system. Eye diameter and standard length were measured in 237 individuals from 61 species of lanternfishes representing all the recognised tribes within the family in addition to compiling an ecological dataset including depth distribution during night and day and the location and sexual dimorphism of luminous organs. Hypotheses were tested by investigating the relationship between the relative size of the eye (corrected for body size) and variations in depth and/or patterns of luminous-organs using phylogenetic comparative analyses. Results show a great variability in relative eye size within the Myctophidae at all taxonomic levels (from subfamily to genus), suggesting that this character may have evolved several times. However, variability in eye size within the family could not be explained by any of our ecological variables (bioluminescence and depth patterns), and appears to be driven solely by phylogenetic relationships.

  10. Molecular phylogenetics, species diversity, and biogeography of the Andean lizards of the genus Proctoporus (Squamata: Gymnophthalmidae).

    PubMed

    Goicoechea, Noemí; Padial, José M; Chaparro, Juan C; Castroviejo-Fisher, Santiago; De la Riva, Ignacio

    2012-12-01

    The family Gymnophthalmidae comprises ca. 220 described species of Neotropical lizards distributed from southern Mexico to Argentina. It includes 36 genera, among them Proctoporus, which contains six currently recognized species occurring across the yungas forests and wet montane grasslands of the Amazonian versant of the Andes from central Peru to central Bolivia. Here, we investigate the phylogenetic relationships and species limits of Proctoporus and closely related taxa by analyzing 2121 base pairs of mitochondrial (12S, 16S, and ND4) and nuclear (c-mos) genes. Our taxon sampling of 92 terminals includes all currently recognized species of Proctoporus and 15 additional species representing the most closely related groups to the genus. Maximum parsimony, maximum likelihood and Bayesian phylogenetic analyses recovered a congruent, fully resolved, and strongly supported hypothesis of relationships that challenges previous phylogenetic hypotheses and classifications, and biogeographic scenarios. Our main results are: (i) discovery of a strongly supported clade that includes all species of Proctoporus and within which are nested the monotypic Opipeuter xestus (a genus that we consider a junior synonym of Proctoporus), and two species of Euspondylus, that are therefore transferred to Proctoporus; (ii) the paraphyly of Proctoporus bolivianus with respect to P. subsolanus, which is proposed as a junior synonym of P. bolivianus; (iii) the detection of seven divergent and reciprocally monophyletic lineages (five of them previously assigned to P. bolivianus) that are considered confirmed candidate species, which implies that more candidate species are awaiting formal description and naming than currently recognized species in the genus; (iv) rejection of the hypothesis that Proctoporus diversified following a south to north pattern parallel to the elevation of the Andes; (v) species diversity in Proctoporus is the result of in situ diversification through vicariance in

  11. Phylogenetic Analysis of Rhinosporidium seeberi’s 18S Small-Subunit Ribosomal DNA Groups This Pathogen among Members of the Protoctistan Mesomycetozoa Clade

    PubMed Central

    Herr, Roger A.; Ajello, Libero; Taylor, John W.; Arseculeratne, Sarath N.; Mendoza, Leonel

    1999-01-01

    For the past 100 years the phylogenetic affinities of Rhinosporidium seeberi have been controversial. Based on its morphological features, it has been classified as a protozoan or as a member of the kingdom Fungi. We have amplified and sequenced nearly a full-length 18S small-subunit (SSU) ribosomal DNA (rDNA) sequence from R. seeberi. Using phylogenetic analysis, by parsimony and distance methods, of R. seeberi’s 18S SSU rDNA and that of other eukaryotes, we found that this enigmatic pathogen of humans and animals clusters with a novel group of fish parasites referred to as the DRIP clade (Dermocystidium, rossete agent, Ichthyophonus, and Psorospermium), near the animal-fungal divergence. Our phylogenetic analyses also indicate that R. seeberi is the sister taxon of the two Dermocystidium species used in this study. This molecular affinity is remarkable since members of the genus Dermocystidium form spherical structures in infected hosts, produce endospores, have not been cultured, and possess mitochondria with flat cristae. With the addition of R. seeberi to this clade, the acronym DRIP is no longer appropriate. We propose to name this monophyletic clade Mesomycetozoa to reflect the group’s phylogenetic association within the Eucarya. PMID:10449446

  12. Phylogenetic organization of bacterial activity.

    PubMed

    Morrissey, Ember M; Mau, Rebecca L; Schwartz, Egbert; Caporaso, J Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J; Liu, Cindy M; Hayer, Michaela; McHugh, Theresa A; Marks, Jane C; Price, Lance B; Hungate, Bruce A

    2016-09-01

    Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism's ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with (13)C and (18)O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions.

  13. Phylogenetic organization of bacterial activity

    PubMed Central

    Morrissey, Ember M; Mau, Rebecca L; Schwartz, Egbert; Caporaso, J Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J; Liu, Cindy M; Hayer, Michaela; McHugh, Theresa A; Marks, Jane C; Price, Lance B; Hungate, Bruce A

    2016-01-01

    Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism's ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with 13C and 18O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions. PMID:26943624

  14. Advances in the phylogenesis of Agaricales and its higher ranks and strategies for establishing phylogenetic hypotheses§

    PubMed Central

    Zhao, Rui-lin; Desjardin, Dennis E.; Soytong, Kasem; Hyde, Kevin D.

    2008-01-01

    We present an overview of previous research results on the molecular phylogenetic analyses in Agaricales and its higher ranks (Agaricomycetes/Agaricomycotina/Basidiomycota) along with the most recent treatments of taxonomic systems in these taxa. Establishing phylogenetic hypotheses using DNA sequences, from which an understanding of the natural evolutionary relationships amongst clades may be derived, requires a robust dataset. It has been recognized that single-gene phylogenies may not truly represent organismal phylogenies, but the concordant phylogenetic genealogies from multiple-gene datasets can resolve this problem. The genes commonly used in mushroom phylogenetic research are summarized. PMID:18837104

  15. Mitochondrial genomes of Japanese Babina frogs (Ranidae, Anura): unique gene arrangements and the phylogenetic position of genus Babina.

    PubMed

    Kakehashi, Ryosuke; Kurabayashi, Atsushi; Oumi, Shohei; Katsuren, Seiki; Hoso, Masaki; Sumida, Masayuki

    2013-01-01

    Genus Babina is a member of Ranidae, a large family of frogs, currently comprising 10 species. Three of them are listed as endangered species. To identify mitochondrial (mt) genes suitable for future population genetic analyses for endangered species, we determined the complete nucleotide sequences of the mt genomes of 3 endangered Japanese Babina frogs, B. holsti, B. okinavana, and B. subaspera and 1 ranid frog Lithobates catesbeianus. The genes of NADH dehydrogenase subunit 5 (nad5) and the control region (CR) were found to have high sequence divergences and to be usable for population genetics studies. At present, no consensus on the phylogenetic position of genus Babina has been reached. To resolve this problem, we performed molecular phylogenetic analyses with the largest dataset used to date (11,345 bp from 2 ribosomal RNA- and 13 protein-encoding genes) in studies dealing with Babina phylogeny. These analyses revealed monophyly of Babina and Odorrana. It is well known that mt gene rearrangements of animals can provide usable phylogenetic information. Thus, we also compared the mt gene arrangements among Babina species and other related genera. Of the surveyed species, only L. catesbeianus manifested typical neobatrachian-type mt gene organization. In the B. okinavana, an additional pseudogene of tRNA-His (trnH) was observed in the CR downstream region. Furthermore, in the B. holsti and B. subaspera, the trnH/nad5 block was translocated from its typical position to the CR downstream region, and the translocated trnH became a pseudogene. The position of the trnH pseudogene is consistent with the translocated trnH position reported in Odorrana. Consequently, the trnH rearrangement seems to be a common ancestry characteristic (synapomorphy) of Babina and Odorrana. Based on the "duplication and deletion" gene rearrangement model, a single genomic duplication event can explain the order of derived mt genes found in Babina and Odorrana.

  16. Molecular phylogenetic characterization of common murine rodents from Manipur, Northeast India.

    PubMed

    Chingangbam, Dhananjoy S; Laishram, Joykumar M; Suzuki, Hitoshi

    2015-01-01

    The Indian subcontinent and Southeast Asia are hotspots of murine biodiversity, but no species from the Arakan Mountain system that demarcates the border between the two areas has been subjected to molecular phylogenetic analyses. We examined the mitochondrial cytochrome b gene sequences in six murine species (the Rattus rattus species complex, R. norvegicus, R. nitidus, Berylmys manipulus, Niviventer sp. and Mus musculus) from Manipur, which is located at the western foot of the mountain range. The sequences of B. manipulus and Niviventer sp. examined here were distinct from available congeneric sequences in the databases, with sequence divergences of 10-15%. Substantial degrees of intrapopulation divergence were detected in R. nitidus and the R. rattus species complex from Manipur, implying ancient habitation of the species in this region, while the recent introduction by modern and prehistoric human activities was suggested for R. norvegicus and M. musculus, respectively. In the nuclear gene Mc1r, also analyzed here, the R. rattus species complex from Manipur was shown to possess allelic sequences related to those from the Indian subcontinent in addition to those from East Asia. These results not only fill gaps in the phylogenetic knowledge of each taxon examined but also provide valuable insight to better understand the biogeographic importance of the Arakan Mountain system in generating the species and genetic diversity of murine rodents. PMID:26119663

  17. Complete mitochondrial DNA sequences of six snakes: phylogenetic relationships and molecular evolution of genomic features.

    PubMed

    Dong, Songyu; Kumazawa, Yoshinori

    2005-07-01

    Complete mitochondrial DNA (mtDNA) sequences were determined for representative species from six snake families: the acrochordid little file snake, the bold boa constrictor, the cylindrophiid red pipe snake, the viperid himehabu, the pythonid ball python, and the xenopeltid sunbeam snake. Thirteen protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions were identified in these mtDNAs. Duplication of the control region and translocation of the tRNALeu gene were two notable features of the snake mtDNAs. The duplicate control regions had nearly identical nucleotide sequences within species but they were divergent among species, suggesting concerted sequence evolution of the two control regions. In addition, the duplicate control regions appear to have facilitated an interchange of some flanking tRNA genes in the viperid lineage. Phylogenetic analyses were conducted using a large number of sites (9570 sites in total) derived from the complete mtDNA sequences. Our data strongly suggested a new phylogenetic relationship among the major families of snakes: ((((Viperidae, Colubridae), Acrochordidae), (((Pythonidae, Xenopeltidae), Cylindrophiidae), Boidae)), Leptotyphlopidae). This conclusion was distinct from a widely accepted view based on morphological characters in denying the sister-group relationship of boids and pythonids, as well as the basal divergence of nonmacrostomatan cylindrophiids. These results imply the significance to reconstruct the snake phylogeny with ample molecular data, such as those from complete mtDNA sequences.

  18. Preliminary phylogenetic analysis of the Andean clade and the placement of new Colombian blueberries (Ericaceae, Vaccinieae)

    PubMed Central

    Pedraza-Peñalosa, Paola; Salinas, Nelson R.; Virnig, Anne Lucy S.; Wheeler, Ward C.

    2015-01-01

    Abstract The blueberry tribe Vaccinieae (Ericaceae) is particularly diverse in South America and underwent extensive radiation in Colombia where many endemics occur. Recent fieldwork in Colombia has resulted in valuable additions to the phylogeny and as well in the discovery of morphologically noteworthy new species that need to be phylogenetically placed before being named. This is particularly important, as the monophyly of many of the studied genera have not been confirmed. In order to advance our understanding of the relationships within neotropical Vaccinieae and advice the taxonomy of the new blueberry relatives, here we present the most comprehensive phylogenetic analysis for the Andean clade. Anthopterus, Demosthenesia, and Pellegrinia are among the putative Andean genera recovered as monophyletic, while other eight Andean genera were not. The analyses also showed that genera that have been traditionally widely defined are non-monophyletic and could be further split into more discrete groups. Four newly discovered Colombian Vaccinieae are placed in the monophyletic Satyria s.s. and the Psammisia I clade. Although these new species are endemic to the Colombian Western Cordillera and Chocó biogeographic region and three are not known outside of Las Orquídeas National Park, they do not form sister pairs. PMID:25987883

  19. Phylogenetic and chemical diversity of fungal endophytes isolated from Silybum marianum (L) Gaertn. (milk thistle)

    PubMed Central

    Raja, Huzefa A.; Kaur, Amninder; El-Elimat, Tamam; Figueroa, Mario; Kumar, Rahul; Deep, Gagan; Agarwal, Rajesh; Faeth, Stanley H.; Cech, Nadja B.; Oberlies, Nicholas H.

    2015-01-01

    Use of the herb milk thistle (Silybum marianum) is widespread, and its chemistry has been studied for over 50 years. However, milk thistle endophytes have not been studied previously for their fungal and chemical diversity. We examined the fungal endophytes inhabiting this medicinal herb to determine: (1) species composition and phylogenetic diversity of fungal endophytes; (2) chemical diversity of secondary metabolites produced by these organisms; and (3) cytotoxicity of the pure compounds against the human prostate carcinoma (PC-3) cell line. Forty-one fungal isolates were identified from milk thistle comprising 25 operational taxonomic units based on BLAST search via GenBank using published authentic sequences from nuclear ribosomal internal transcribed spacer sequence data. Maximum likelihood analyses of partial 28S rRNA gene showed that these endophytes had phylogenetic affinities to four major classes of Ascomycota, the Dothideomycetes, Sordariomycetes, Eurotiomycetes, and Leotiomycetes. Chemical studies of solid–substrate fermentation cultures led to the isolation of four new natural products. In addition, 58 known secondary metabolites, representing diverse biosynthetic classes, were isolated and characterized using a suite of nuclear magnetic resonance and mass spectrometry techniques. Selected pure compounds were tested against the PC-3 cell line, where six compounds displayed cytotoxicity. PMID:26000195

  20. Genetic and phylogenetic analysis of glycoprotein of rabies virus isolated from several species in Brazil.

    PubMed

    Sato, Go; Itou, Takuya; Shoji, Youko; Miura, Yasuo; Mikami, Takeshi; Ito, Mikako; Kurane, Ichiro; Samara, Samir I; Carvalho, Adolorata A B; Nociti, Darci P; Ito, Fumio H; Sakai, Takeo

    2004-07-01

    Genetic and phylogenetic analyses of the region containing the glycoprotein (G) gene, which is related to pathogenicity and antigenicity, and the G-L intergenic region were carried out in 14 Brazilian rabies virus isolates. The isolates were classified as dog-related rabies virus (DRRV) or vampire bat-related rabies virus (VRRV), by nucleoprotein (N) analysis. The nucleotide and amino acid (AA) homologies of the area containing the G protein gene and G-L intergenic region were generally lower than those of the ectodomain. In both regions, nucleotide and deduced AA homologies were lower among VRRVs than among DRRVs. There were AA differences between DRRV and VRRV at 3 antigenic sites and epitopes (IIa, WB+ and III), suggesting that DRRV and VRRV can be distinguished by differences of antigenicity. In a comparison of phylogenetic trees between the ectodomain and the area containing the G protein gene and G-L intergenic region, the branching patterns of the chiropteran and carnivoran rabies virus groups differed, whereas there were clear similarities in patterns within the DRRV and VRRV groups. Additionally, the VRRV isolates were more closely related to chiropteran strains isolated from Latin America than to Brazilian DRRV. These results indicate that Brazilian rabies virus isolates can be classified as DRRV or VRRV by analysis of the G gene and the G-L intergenic region, as well as by N gene analysis. PMID:15297743

  1. Molecular cytogenetic insights to the phylogenetic affinities of the giraffe (Giraffa camelopardalis) and pronghorn (Antilocapra americana).

    PubMed

    Cernohorska, Halina; Kubickova, Svatava; Kopecna, Olga; Kulemzina, Anastasia I; Perelman, Polina L; Elder, Frederick F B; Robinson, Terence J; Graphodatsky, Alexander S; Rubes, Jiri

    2013-08-01

    Five families are traditionally recognized within higher ruminants (Pecora): Bovidae, Moschidae, Cervidae, Giraffidae and Antilocapridae. The phylogenetic relationships of Antilocapridae and Giraffidae within Pecora are, however, uncertain. While numerous fusions (mostly Robertsonian) have accumulated in the giraffe's karyotype (Giraffa camelopardalis, Giraffidae, 2n = 30), that of the pronghorn (Antilocapra americana, Antilocapridae, 2n = 58) is very similar to the hypothesised pecoran ancestral state (2n = 58). We examined the chromosomal rearrangements of two species, the giraffe and pronghorn, using a combination of fluorescence in situ hybridization painting probes and BAC clones derived from cattle (Bos taurus, Bovidae). Our data place Moschus (Moschidae) closer to Bovidae than Cervidae. Although the alternative (i.e., Moschidae + Cervidae as sister groups) could not be discounted in recent sequence-based analyses, cytogenetics bolsters conclusions that the former is more likely. Additionally, DNA sequences were isolated from the centromeric regions of both species and compared. Analysis of cenDNA show that unlike the pronghorn, the centromeres of the giraffe are probably organized in a more complex fashion comprising different repetitive sequences specific to single chromosomal pairs or groups of chromosomes. The distribution of nucleolar organiser region (NOR) sites, often an effective phylogenetic marker, were also examined in the two species. In the giraffe, the position of NORs seems to be autapomorphic since similar localizations have not been found in other species within Pecora. PMID:23896647

  2. Phylogenetic distribution of compatible solute synthesis genes support a freshwater origin for cyanobacteria.

    PubMed

    Blank, Carrine E

    2013-10-01

    Previous work using ancestral state reconstruction of habitat salinity preference proposed that the early cyanobacteria likely lived in a freshwater environment. The aim of this study was to test that hypothesis by performing phylogenetic analyses of the genes underlying salinity preferences in the cyanobacteria. Phylogenetic analysis of compatible solute genes shows that sucrose synthesis genes were likely ancestral in the cyanobacteria, and were also likely inherited during the cyanobacterial endosymbiosis and into the photosynthetic algae and land plants. In addition, the genes for the synthesis of compatible solutes that are necessary for survival in marine and hypersaline environments (such as glucosylglycerol, glucosylglycerate, and glycine betaine) were likely acquired independently high up (i.e., more recently) in the cyanobacterial tree. Because sucrose synthesis is strongly associated with growth in a low salinity environment, this independently supports a freshwater origin for the cyanobacteria. It is also consistent with geologic evidence showing that the early oceans were much warmer and saltier than modern oceans-sucrose synthesis alone would have been insufficient for early cyanobacteria to have colonized early Precambrian oceans that had a higher ionic strength. Indeed, the acquisition of an expanded set of new compatible solute genes may have enabled the historical colonization of marine and hypersaline environments by cyanobacteria, midway through their evolutionary history. PMID:27007313

  3. Phylogenetic analysis of Maverick/Polinton giant transposons across organisms.

    PubMed

    Haapa-Paananen, Saija; Wahlberg, Niklas; Savilahti, Harri

    2014-09-01

    Polintons are a recently discovered group of large transposable elements (<40Kb in size) encoding up to 10 different proteins. The increasing number of genome sequencing projects has led to the discovery of these elements in genomes of protists, fungi, and animals, but not in plants. The RepBase database of eukaryotic repetitive elements currently contains consensus sequences and information of 70 Polinton elements from 28 organisms. Previous phylogenetic analyses have shown the relationship of Polintons to linear plasmids, bacteriophages, and retroviruses. However, a comprehensive phylogenetic analysis of all known Polintons has been lacking. We retrieved the Polinton consensus sequences from the most recent version of RepBase, and compiled amino acid sequences for the two most common Polinton-specific genes, the DNA polymerase-B and retroviral-like integrase. O