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Sample records for monophyletic tentacularioidea gymnorhynchoidea

  1. Molecular phylogeny and evolution of the Trypanorhyncha Diesing, 1863 (Platyhelminthes: Cestoda).

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    Palm, Harry W; Waeschenbach, Andrea; Olson, Peter D; Littlewood, D Timothy J

    2009-08-01

    Complete ssrDNA and partial lsrDNA (D1-D3) of 31 species, mainly from the Indo-Pacific region, were sequenced and added to 66 species of the marine cestode order Trypanorhyncha; thus 35% of the 277 known species were sampled. The resulting phylogenetic tree resolved two major clades that represent trypanorhynchs originally parasitizing rajiform (skate and ray) or galeoform hosts. The tree topology supports an earlier classification based on morphology that splits the order into the superfamily Eutetrarhynchoidea together with the Tentacularioidea, and the Gymnorhynchoidea together with the Lacistorhynchoidea and Otobothrioidea. Three of the five recognized superfamilies are monophyletic (Tentacularioidea, Gymnorhynchoidea, Otobothrioidea). Nodal support for the Eutetrarhynchidae and Lacistorhynchidae was poor and resulted in paraphyletic clades. Mapping of morphological characters showed the tentacular armature of the scolex to be highly variable within clades, demonstrating that armature patterns used traditionally in classification, are homoplasious. Similarly, the tetrabothriate scolex, currently utilized as a family-distinguishing character in traditional classifications, has developed independently in multiple groups. Synapomorphies for the higher taxa are detailed. Sequence data from duplicate taxa confirmed interoceanic distribution patterns and low intraspecific genetic divergence and host specificity for nine trypanorhynch species belonging to five families and four superfamilies. Four distinct lineages of trypanorhynchs can be recognized with one mainly infecting rajiform hosts whereas the others infecting both, sharks and rays. Eutetrarhynchoids and tentacularioids have secondarily invaded shark hosts whilst utilising the marine food web involving teleost fishes as intermediate hosts. Three cases of host switching from sharks to rays can be inferred within the lacistorhynchoids, in one case caused by a switch from perciform to gadiform intermediate hosts

  2. Defining a monophyletic Cardinalini: a molecular perspective.

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    Klicka, John; Burns, Kevin; Spellman, Garth M

    2007-12-01

    Within the New World nine-primaried oscine assemblage, feeding morphology and behavior have long been used as a guideline for assigning membership to subgroups. For example, birds with stout, conical bills capable of crushing heavy seeds have generally been placed within the tribe Cardinalini (cardinal-grosbeaks). Many workers have tried to characterize this group more definitively, using a variety of morphological characters; however, the characters used often conflicted with one another. Previous molecular studies addressing the monophyly of Cardinalini have had only limited sampling within the group. In this study, we analyze mtDNA sequence data from all genera and 34 of the 42 Cardinalini species (sensu [Sibley, C.G., Monroe, B.L., 1990. Distribution and Taxonomy of the Birds of the World, Yale University Press, New Haven, CT]) to address the monophyly of the group and to reconstruct the most complete phylogeny of this tribe published to date. We found strong support for a redefined Cardinalini that now includes some members previously placed within Thraupini (tanagers; the genera Piranga, Habia, Chlorothraupis, and Amaurospiza) and some members previously placed within the Parulini (wood-warblers; the genus Granatellus). In addition, some genera traditionally considered members of the Cardinalini are shown to have affinities with other groups (the genera Porphyrospiza, Parkerthraustes, and Saltator). Our redefined Cardinalini contains 48 species, six more than are listed in Sibley and Monroe's (1990) taxonomy of the group. Within the nine-primaried oscine assemblage, the Cardinalini are more closely related to the Thraupini (tanagers) than they are to the Emberizini (sparrows), Parulini (wood-warblers), or Icterini (blackbirds), consistently forming a monophyletic group with Thraupini across all analyses. The reconfigured Cardinalini is comprised of five well-supported, major clades: (1) a "masked" clade (Piranga, Cardinalis, Caryothraustes, Periporphyrus, and

  3. Phylogeny of ladybirds (Coleoptera: Coccinellidae): are the subfamilies monophyletic?

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    Magro, A; Lecompte, E; Magné, F; Hemptinne, J-L; Crouau-Roy, B

    2010-03-01

    The Coccinellidae (ladybirds) is a highly speciose family of the Coleoptera. Ladybirds are well known because of their use as biocontrol agents, and are the subject of many ecological studies. However, little is known about phylogenetic relationships of the Coccinellidae, and a precise evolutionary framework is needed for the family. This paper provides the first phylogenetic reconstruction of the relationships within the Coccinellidae based on analysis of five genes: the 18S and 28S rRNA nuclear genes and the mitochondrial 12S, 16S rRNA and cytochrome oxidase subunit I (COI) genes. The phylogenetic relationships of 67 terminal taxa, representative of all the subfamilies of the Coccinellidae (61 species, 37 genera), and relevant outgroups, were reconstructed using multiple approaches, including Bayesian inference with partitioning strategies. The recovered phylogenies are congruent and show that the Coccinellinae is monophyletic but the Coccidulinae, Epilachninae, Scymninae and Chilocorinae are paraphyletic. The tribe Chilocorini is identified as the sister-group of the Coccinellinae for the first time. Copyright 2009 Elsevier Inc. All rights reserved.

  4. Monophyletic Origin of the Metazoan Nervous System: Characterizing

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    Watkins, Russell; Beckenbach, Andrew

    In the absence of additional cases to be studied, our understanding of the likelihood of intelligent life evolving elsewhere in the universe must be framed within the context of the evolution of intelligence on this planet. Towards this end a valid model of the evolution of animal life, and in particular of the nervous system, is key. Models which describe the development of complexity within the nervous system can be positively misleading if they are not grounded in an accurate model of the true relationships of the animal phyla. If fact the evolution of animal life at its earliest stages, from protists to the sponges, Cnidaria, and Ctenophora and onward to the bilateral animal phyla is poorly characterized. Recently numerous phylogenies of the early animal radiation have been published based upon DNA sequence data, with conflicting and poorly supported results. A polyphyletic origin for the animal nervous system has been implied by the results of several studies, which would lead to the conclusion that some characteristics of the nervous systems of higher and lower animals could be convergent. We show that an equally parsimonious interpretation of the molecular sequence data published thus far is that it reflects rapid speciation events early in animal evolution among the classical ``diploblast'' phyla, as well as accelerated DNA sequence divergence among the higher animals. This could be interpreted as support for a classical phylogeny of the animal kingdom, and thus of a strictly monophyletic origin for the nervous system.

  5. Polychaeta, Annelida, and Articulata are not monophyletic: articulating the Metameria (Metazoa, Coelomata

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    Waltécio de Oliveira Almeida

    2003-03-01

    Full Text Available Polychaetes are metameric worms recognized for having parapodia, chaetae, and nuchal organs. Some authors have extended the Annelida to include Pogonophora, Echiura, and Clitellata. These suggestions are insufficient to generate a monophyletic group. They do not take into account two very large and important clades that in a cladistic analysis at a higher level are shown to be nested within the Annelida: the Ecdysozoa (arthropods and related taxa and Enterocoela (deuterostomes and related taxa. Evolutionary histories of most characters across metazoan phyla are still very poorly known. Metameres and coeloms have been considered homoplastic in the literature, and yet the homeobox genes responsible for the expression of metamerism and of paired appendages, at least, are very largely distributed among the Metazoa. A phylogenetic analysis was performed for the ingroups of Polychaeta, including Clitellata, Enterocoela, and Ecdysozoa as terminal taxa. The remaining non-metameric phyla Platyhelminthes, Nemertea, Mollusca, and Sipuncula were included to root the tree within the Bilateria. Empirical data was obtained from the literature and run with the software Hennig86 with two comparative interpretations of a priori hypotheses of primary homology: one with negative characters (coding losses and another considering only positive characters (without assumptions about losses. The most relevant conclusions are: (1 Annelida and Polychaeta are non-monophyletic, even when including Echiura, Clitellata, and Pogonophora; (2 Articulata, as traditionally circumscribed for Annelida and Arthropoda, is also not monophyletic; (3 Metameria becomes monophyletic only when Ecdysozoa and Enterocoela are included in addition to the traditional annelid taxa; (4 Ecdysozoa are the sister group of Aphrodita; (5 Clitellata are related to deposit-feeding sedentary polychaetes (scolecids, and Questidae represent their sister group; (6 Owenia plus Enterocoela form a monophyletic

  6. ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales

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    Dandekar Thomas

    2008-07-01

    Full Text Available Abstract Background Within Chlorophyceae the ITS2 secondary structure shows an unbranched helix I, except for the 'Hydrodictyon' and the 'Scenedesmus' clade having a ramified first helix. The latter two are classified within the Sphaeropleales, characterised by directly opposed basal bodies in their flagellar apparatuses (DO-group. Previous studies could not resolve the taxonomic position of the 'Sphaeroplea' clade within the Chlorophyceae without ambiguity and two pivotal questions remain open: (1 Is the DO-group monophyletic and (2 is a branched helix I an apomorphic feature of the DO-group? In the present study we analysed the secondary structure of three newly obtained ITS2 sequences classified within the 'Sphaeroplea' clade and resolved sphaeroplealean relationships by applying different phylogenetic approaches based on a combined sequence-structure alignment. Results The newly obtained ITS2 sequences of Ankyra judayi, Atractomorpha porcata and Sphaeroplea annulina of the 'Sphaeroplea' clade do not show any branching in the secondary structure of their helix I. All applied phylogenetic methods highly support the 'Sphaeroplea' clade as a sister group to the 'core Sphaeropleales'. Thus, the DO-group is monophyletic. Furthermore, based on characteristics in the sequence-structure alignment one is able to distinguish distinct lineages within the green algae. Conclusion In green algae, a branched helix I in the secondary structure of the ITS2 evolves past the 'Sphaeroplea' clade. A branched helix I is an apomorph characteristic within the monophyletic DO-group. Our results corroborate the fundamental relevance of including the secondary structure in sequence analysis and phylogenetics.

  7. A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata

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    Rota-Stabelli, Omar; Campbell, Lahcen; Brinkmann, Henner; Edgecombe, Gregory D.; Longhorn, Stuart J.; Peterson, Kevin J.; Pisani, Davide; Philippe, Hervé; Telford, Maximilian J.

    2011-01-01

    While a unique origin of the euarthropods is well established, relationships between the four euarthropod classes—chelicerates, myriapods, crustaceans and hexapods—are less clear. Unsolved questions include the position of myriapods, the monophyletic origin of chelicerates, and the validity of the close relationship of euarthropods to tardigrades and onychophorans. Morphology predicts that myriapods, insects and crustaceans form a monophyletic group, the Mandibulata, which has been contradicted by many molecular studies that support an alternative Myriochelata hypothesis (Myriapoda plus Chelicerata). Because of the conflicting insights from published molecular datasets, evidence from nuclear-coding genes needs corroboration from independent data to define the relationships among major nodes in the euarthropod tree. Here, we address this issue by analysing two independent molecular datasets: a phylogenomic dataset of 198 protein-coding genes including new sequences for myriapods, and novel microRNA complements sampled from all major arthropod lineages. Our phylogenomic analyses strongly support Mandibulata, and show that Myriochelata is a tree-reconstruction artefact caused by saturation and long-branch attraction. The analysis of the microRNA dataset corroborates the Mandibulata, showing that the microRNAs miR-965 and miR-282 are present and expressed in all mandibulate species sampled, but not in the chelicerates. Mandibulata is further supported by the phylogenetic analysis of a comprehensive morphological dataset covering living and fossil arthropods, and including recently proposed, putative apomorphies of Myriochelata. Our phylogenomic analyses also provide strong support for the inclusion of pycnogonids in a monophyletic Chelicerata, a paraphyletic Cycloneuralia, and a common origin of Arthropoda (tardigrades, onychophorans and arthropods), suggesting that previous phylogenies grouping tardigrades and nematodes may also have been subject to tree

  8. Three reciprocally monophyletic mtDNA lineages elucidate the taxonomic status of Grant's gazelles

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    Lorenzen, Eline Deidre; Arctander, Peter; Siegismund, Hans Redlef

    2008-01-01

    The intraspecific phylogeography of Grant's gazelles Nanger granti was assessed with mitochondrial DNA control region sequences. Samples of 177 individuals from 17 Kenyan and Tanzanian populations were analysed. Three highly divergent, reciprocally monophyletic lineages were found, with among group...... are discussed in reference to the four currently recognised subspecies. We suggest Grant's gazelles be raised to the superspecies Nanger (granti) comprising three taxonomic units corresponding to the three mtDNA lineages. There was no evidence of gene flow between the notata and granti lineages, despite...... (granti) petersii within the Grant's gazelles superspecies....

  9. Phylogeny and taxonomy of the Teloschistaceae (Ascomycota: Importance of monophyletic groups

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    A. Thell

    2012-03-01

    Full Text Available The molecular phylogeny of the Parmeliaceae, Physciaceae, Caliciaceae and many other families of lichen-forming fungi is now based on polyphasic approach using up to six or seven different genes of nuclear and mitochondrial DNA. As a consequence the taxonomy of the Parmeliaceae and other families can now be based on segregation of robust monophyletic groups of species. The majority of phylogenetic analyses of small species groups of the Teloschistaceae (especially of Caloplaca are based on ITS1/ITS2 sequences of nuclear DNA as the main molecular tool. There are fewer reports of polyphasic molecular data having been used in such phylogenetic analyses (Gaya 2003, 2008; Fedorenko 2009, 2012. Such investigations have indicated that the currently accepted genera Caloplaca, Fulgensia, Xanthoria and Teloschistes are polyphyletic and the delineation of Caloplaca and Xanthoria and of Caloplaca and Fulgensia is problematic. The existence of well defined monophyletic groups within species groups like those of Caloplaca cerina, C.saxicola, C. regalis, C. ferruginea, C. variabilis and Fulgensia fulgens (some of which are type species of different genera proposed in ‘premolecular time’ are found to be distributed among other monophyletic branches of the xanthorioid lichens following analysis of nuclear molecular data. As a consequence generic names proposed for the above species groups (i.e. Blastenia, Pyrenodesmia, Polycauliona etc. can be used together with Caloplaca s.str., Teloschistes, Seirophora and Fulgensia. However, it should be emphasized that following molecular analysis such groups/genera as Blastenia, Pyrenodesmia and the Caloplaca saxicola- group include far fewer species than was proposed from morphological segregation in the ‘premolecular’ period. Alternatively, molecular data confirms that the morphologically defined groups (i.e. Blastenia, Pyrenodesmia, Polycauliona etc. are just as polyphyletic as the genera Teloschistes, Seirophora

  10. Infectious hematopoietic necrosis virus: monophyletic origin of European isolates from North American genogroup M.

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    Enzmann, P J; Kurath, G; Fichtner, D; Bergmann, S M

    2005-09-23

    Infectious hematopoietic necrosis virus (IHNV) was first detected in Europe in 1987 in France and Italy, and later, in 1992, in Germany. The source of the virus and the route of introduction are unknown. The present study investigates the molecular epidemiology of IHNV outbreaks in Germany since its first introduction. The complete nucleotide sequences of the glycoprotein (G) and non-virion (NV) genes from 9 IHNV isolates from Germany have been determined, and this has allowed the identification of characteristic differences between these isolates. Phylogenetic analysis of partial G gene sequences (mid-G, 303 nucleotides) from North American IHNV isolates (Kurath et al. 2003) has revealed 3 major genogroups, designated U, M and L. Using this gene region with 2 different North American IHNV data sets, it was possible to group the European IHNV strains within the M genogroup, but not in any previously defined subgroup. Analysis of the full length G gene sequences indicated that an independent evolution of IHN viruses had occurred in Europe. IHN viruses in Europe seem to be of a monophyletic origin, again most closely related to North American isolates in the M genogroup. Analysis of the NV gene sequences also showed the European isolates to be monophyletic, but resolution of the 3 genogroups was poor with this gene region. As a result of comparative sequence analyses, several different genotypes have been identified circulating in Europe.

  11. Australian Lasioglossum + Homalictus form a monophyletic group: resolving the "Australian enigma".

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    Danforth, B N; Ji, S

    2001-04-01

    The bee genus Lasioglossum includes > 1,000 species of bees distributed on all continents except Antarctica. Lasioglossum is a major component of the bee fauna in the Holarctic, Ethiopian, and Asian regions and is an important group for investigating the evolution of social behavior in bees. Given its cosmopolitan distribution, the historical biogeography of the genus is of considerable interest. We reconstructed phylogenetic relationships among the subgenera and species within Lasioglossum s.s., using DNA sequence data from a slowly evolving nuclear gene, elongation factor-1 alpha. The entire data set includes > 1,604 aligned nucleotide sites (including three exons plus two introns) for 89 species (17 outgroups plus 72 ingroups). Parsimony and maximum likelihood analyses provide strong evidence that the primarily Indoaustralian subgenera (Homalictus, Chilalictus, Parasphecodes) form a monophyletic group. Bootstrap support for the Australian clade ranged from 73% to 77%, depending on the method of analysis. Monophyly of the Australian Lasioglossum suggests that a single colonization event (by way of Southeast Asia and New Guinea) gave rise to a lineage of > 350 native Indoaustralian bees. We discuss the implications of Australian monophyly for resolving the "Australian enigma"--the similarity in social behavior among the Australian halictine bees relative to that of Holarctic groups.

  12. Monophyletic origin of multiple clonal lineages in an asexual fish (Poecilia formosa).

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    Stöck, Matthias; Lampert, Kathrin P; Möller, Dirk; Schlupp, Ingo; Schartl, Manfred

    2010-12-01

    Despite the advantage of avoiding the costs of sexual reproduction, asexual vertebrates are very rare and often considered evolutionarily disadvantaged when compared to sexual species. Asexual species, however, may have advantages when colonizing (new) habitats or competing with sexual counterparts. They are also evolutionary older than expected, leaving the question whether asexual vertebrates are not only rare because of their 'inferior' mode of reproduction but also because of other reasons. A paradigmatic model system is the unisexual Amazon molly, Poecilia formosa, that arose by hybridization of the Atlantic molly, Poecilia mexicana, as the maternal ancestor, and the sailfin molly, Poecilia latipinna, as the paternal ancestor. Our extensive crossing experiments failed to resynthesize asexually reproducing (gynogenetic) hybrids confirming results of previous studies. However, by producing diploid eggs, female F(1) -hybrids showed apparent preadaptation to gynogenesis. In a range-wide analysis of mitochondrial sequences, we examined the origin of P. formosa. Our analyses point to very few or even a single origin(s) of its lineage, which is estimated to be approximately 120,000 years old. A monophyletic origin was supported from nuclear microsatellite data. Furthermore, a considerable degree of genetic variation, apparent by high levels of clonal microsatellite diversity, was found. Our molecular phylogenetic evidence and the failure to resynthesize the gynogenetic P. formosa together with the old age of the species indicate that some unisexual vertebrates might be rare not because they suffer the long-term consequences of clonal reproduction but because they are only very rarely formed as a result of complex genetic preconditions necessary to produce viable and fertile clonal genomes and phenotypes ('rare formation hypothesis').

  13. Clinical outcome and genetic differences within a monophyletic Dengue virus type 2 population.

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    Hapuarachchige Chanditha Hapuarachchi

    Full Text Available The exact mechanisms of interplay between host and viral factors leading to severe dengue are yet to be fully understood. Even though previous studies have implicated specific genetic differences of Dengue virus (DENV in clinical severity and virus attenuation, similar studies with large-scale, whole genome screening of monophyletic virus populations are limited. Therefore, in the present study, we compared 89 whole genomes of DENV-2 cosmopolitan clade III isolates obtained from patients diagnosed with dengue fever (DF, n = 58, dengue hemorrhagic fever (DHF, n = 30 and dengue shock syndrome (DSS, n = 1 in Singapore between July 2010 and January 2013, in order to determine the correlation of observed viral genetic differences with clinical outcomes. Our findings showed no significant difference between the number of primary and secondary infections that progressed to DHF and DSS (p>0.05 in our study cohort. Despite being highly homogenous, study isolates possessed 39 amino acid substitutions of which 10 substitutions were fixed in three main groups of virus isolates. None of those substitutions were specifically associated with DHF and DSS. Notably, two evolutionarily unique virus groups possessing C-P43T+NS1-S103T+NS2A-V83I+NS3-R337K+ NS3-I600T+ NS5-P136S and NS2A-T119N mutations were exclusively found in patients with DF, the benign form of DENV infections. Those mutants were significantly associated with mild disease outcome. These observations indicated that disease progression into DHF and DSS within our patient population was more likely to be due to host than virus factors. We hypothesize that selection for potentially less virulent groups of DENV-2 in our study cohort may be an evolutionary adaptation of viral strains to extend their survival in the human-mosquito transmission cycle.

  14. Hedysarum L. (Fabaceae: Hedysareae) Is Not Monophyletic – Evidence from Phylogenetic Analyses Based on Five Nuclear and Five Plastid Sequences

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    Liu, Pei-Liang; Wen, Jun; Duan, Lei; Arslan, Emine; Ertuğrul, Kuddisi; Chang, Zhao-Yang

    2017-01-01

    The legume family (Fabaceae) exhibits a high level of species diversity and evolutionary success worldwide. Previous phylogenetic studies of the genus Hedysarum L. (Fabaceae: Hedysareae) showed that the nuclear and the plastid topologies might be incongruent, and the systematic position of the Hedysarum sect. Stracheya clade was uncertain. In this study, phylogenetic relationships of Hedysarum were investigated based on the nuclear ITS, ETS, PGDH, SQD1, TRPT and the plastid psbA-trnH, trnC-petN, trnL-trnF, trnS-trnG, petN-psbM sequences. Both nuclear and plastid data support two major lineages in Hedysarum: the Hedysarum s.s. clade and the Sartoria clade. In the nuclear tree, Hedysarum is biphyletic with the Hedysarum s.s. clade sister to the Corethrodendron + Eversmannia + Greuteria + Onobrychis clade (the CEGO clade), whereas the Sartoria clade is sister to the genus Taverniera DC. In the plastid tree, Hedysarum is monophyletic and sister to Taverniera. The incongruent position of the Hedysarum s.s. clade between the nuclear and plastid trees may be best explained by a chloroplast capture hypothesis via introgression. The Hedysarum sect. Stracheya clade is resolved as sister to the H. sect. Hedysarum clade in both nuclear and plastid trees, and our analyses support merging Stracheya into Hedysarum. Based on our new evidence from multiple sequences, Hedysarum is not monophyletic, and its generic delimitation needs to be reconsidered. PMID:28122062

  15. Molecular phylogeny of some European heteronemertean (Nemertea) species and the monophyletic status of Riseriellus, Lineus, and Micrura.

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    Sundberg, P; Saur, M

    1998-12-01

    The 16S rRNA mitochondrial gene was used to reconstruct the relationships among 10 heteronemertean species (subclass Heteronemertea, phylum Nemertea); Lineus ruber and L. viridis are represented by more than one specimen to assess intraspecific variation in these enigmatic species, and the analysis includes in total 14 terminal taxa incorporating one palaeonemertean species (Tubulanus annulatus) for outgroup rooting. The aligned sequences were subjected to maximum parsimony, maximum-likelihood, and neighbor-joining analyses to estimate the phylogenetic relationship of the species. The results were concordant from all analyses and indicate that neither Lineus nor Micrura are monophyletic taxa, and that there is no support from a phylogenetic point of view to establish the monotypic genus Riseriellus. Copyright 1998 Academic Press.

  16. Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers.

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    Bowe, L M; Coat, G; dePamphilis, C W

    2000-04-11

    Efforts to resolve Darwin's "abominable mystery"-the origin of angiosperms-have led to the conclusion that Gnetales and various fossil groups are sister to angiosperms, forming the "anthophytes." Morphological homologies, however, are difficult to interpret, and molecular data have not provided clear resolution of relationships among major groups of seed plants. We introduce two sequence data sets from slowly evolving mitochondrial genes, cox1 and atpA, which unambiguously reject the anthophyte hypothesis, favoring instead a close relationship between Gnetales and conifers. Parsimony- and likelihood-based analyses of plastid rbcL and nuclear 18S rDNA alone and with cox1 and atpA also strongly support a gnetophyte-conifer grouping. Surprisingly, three of four genes (all but nuclear rDNA) and combined three-genome analyses also suggest or strongly support Gnetales as derived conifers, sister to Pinaceae. Analyses with outgroups screened to avoid long branches consistently identify all gymnosperms as a monophyletic sister group to angiosperms. Combined three- and four-gene rooted analyses resolve the branching order for the remaining major groups-cycads separate from other gymnosperms first, followed by Ginkgo and then (Gnetales + Pinaceae) sister to a monophyletic group with all other conifer families. The molecular phylogeny strongly conflicts with current interpretations of seed plant morphology, and implies that many similarities between gnetophytes and angiosperms, such as "flower-like" reproductive structures and double fertilization, were independently derived, whereas other characters could emerge as synapomorphies for an expanded conifer group including Gnetales. An initial angiosperm-gymnosperm split implies a long stem lineage preceding the explosive Mesozoic radiation of flowering plants and suggests that angiosperm origins and homologies should be sought among extinct seed plant groups.

  17. Multilocus microsatellite typing (MLMT of strains from Turkey and Cyprus reveals a novel monophyletic L. donovani sensu lato group.

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    Evi Gouzelou

    Full Text Available BACKGROUND: New foci of human CL caused by strains of the Leishmania donovani (L. donovani complex have been recently described in Cyprus and the Çukurova region in Turkey (L. infantum situated 150 km north of Cyprus. Cypriot strains were typed by Multilocus Enzyme Electrophoresis (MLEE using the Montpellier (MON system as L. donovani zymodeme MON-37. However, multilocus microsatellite typing (MLMT has shown that this zymodeme is paraphyletic; composed of distantly related genetic subgroups of different geographical origin. Consequently the origin of the Cypriot strains remained enigmatic. METHODOLOGY/PRINCIPAL FINDINGS: The Cypriot strains were compared with a set of Turkish isolates obtained from a CL patient and sand fly vectors in south-east Turkey (Çukurova region; CUK strains and from a VL patient in the south-west (Kuşadasi; EP59 strain. These Turkish strains were initially analyzed using the K26-PCR assay that discriminates MON-1 strains by their amplicon size. In line with previous DNA-based data, the strains were inferred to the L. donovani complex and characterized as non MON-1. For these strains MLEE typing revealed two novel zymodemes; L. donovani MON-309 (CUK strains and MON-308 (EP59. A population genetic analysis of the Turkish isolates was performed using 14 hyper-variable microsatellite loci. The genotypic profiles of 68 previously analyzed L. donovani complex strains from major endemic regions were included for comparison. Population structures were inferred by combination of bayesian model-based and distance-based approaches. MLMT placed the Turkish and Cypriot strains in a subclade of a newly discovered, genetically distinct L. infantum monophyletic group, suggesting that the Cypriot strains may originate from Turkey. CONCLUSION: The discovery of a genetically distinct L. infantum monophyletic group in the south-eastern Mediterranean stresses the importance of species genetic characterization towards better understanding

  18. Patterns of Symbiodinium spp. associations within the family Aiptasiidae, a monophyletic lineage of symbiotic of sea anemones (Cnidaria, Actiniaria)

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    Grajales, Alejandro; Rodríguez, Estefanía; Thornhill, Daniel J.

    2016-03-01

    Although the symbiotic relationships between dinoflagellates and cnidarians are well recognized, few studies have examined these associations from an evolutionary perspective. This is especially true for symbiotic sea anemones, in which many reports consist of an approximate species identification of the host, followed by the identification of the dinoflagellate symbiont using molecular genetic markers. To further explore the evolutionary history of sea anemone-dinoflagellate associations, we documented the diversity of Symbiodinium spp. in a monophyletic clade of sea anemones, the family Aiptasiidae. We combined information from several molecular genetic markers, including nuclear ITS2 and plastid cp23S-rDNA, to evaluate the patterns of evolution and diversification of Symbiodinium in the light of an existing phylogenetic framework for the sea anemone host. At the host family level, we found no evidence for coevolution or reciprocal phylogenies between host and endosymbiont. However, within some individual host species, Symbiodinium spp. exhibited patterns of host specialization and cladogenesis. This pattern suggests that coevolution between host and symbiont occurred within species and genera lineages, but that this process was regularly disrupted and symbiotic partners were recombined during the longer-term evolutionary history of the Aiptasiidae. Furthermore, we observed independent cases of phylogeographical partitioning of Symbiodinium within a single host species, suggesting that ecological speciation along an environmental gradient contributed to the diversity of associations found in nature.

  19. Multilocus phylogeny of the avian family Alaudidae (larks) reveals complex morphological evolution, non-monophyletic genera and hidden species diversity.

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    Alström, Per; Barnes, Keith N; Olsson, Urban; Barker, F Keith; Bloomer, Paulette; Khan, Aleem Ahmed; Qureshi, Masood Ahmed; Guillaumet, Alban; Crochet, Pierre-André; Ryan, Peter G

    2013-12-01

    The Alaudidae (larks) is a large family of songbirds in the superfamily Sylvioidea. Larks are cosmopolitan, although species-level diversity is by far largest in Africa, followed by Eurasia, whereas Australasia and the New World have only one species each. The present study is the first comprehensive phylogeny of the Alaudidae. It includes 83.5% of all species and representatives from all recognised genera, and was based on two mitochondrial and three nuclear loci (in total 6.4 kbp, although not all loci were available for all species). In addition, a larger sample, comprising several subspecies of some polytypic species was analysed for one of the mitochondrial loci. There was generally good agreement in trees inferred from different loci, although some strongly supported incongruences were noted. The tree based on the concatenated multilocus data was overall well resolved and well supported by the data. We stress the importance of performing single gene as well as combined data analyses, as the latter may obscure significant incongruence behind strong nodal support values. The multilocus tree revealed many unpredicted relationships, including some non-monophyletic genera (Calandrella, Mirafra, Melanocorypha, Spizocorys). The tree based on the extended mitochondrial data set revealed several unexpected deep divergences between taxa presently treated as conspecific (e.g. within Ammomanes cinctura, Ammomanes deserti, Calandrella brachydactyla, Eremophila alpestris), as well as some shallow splits between currently recognised species (e.g. Certhilauda brevirostris-C. semitorquata-C. curvirostris; Calendulauda barlowi-C. erythrochlamys; Mirafra cantillans-M. javanica). Based on our results, we propose a revised generic classification, and comment on some species limits. We also comment on the extraordinary morphological adaptability in larks, which has resulted in numerous examples of parallel evolution (e.g. in Melanocorypha mongolica and Alauda leucoptera [both

  20. Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives.

    Science.gov (United States)

    Howard-Azzeh, Mohammad; Shamseer, Larissa; Schellhorn, Herb E; Gupta, Radhey S

    2014-11-01

    Detailed phylogenetic and comparative genomic analyses are reported on 140 genome sequenced cyanobacteria with the main focus on the heterocyst-differentiating cyanobacteria. In a phylogenetic tree for cyanobacteria based upon concatenated sequences for 32 conserved proteins, the available cyanobacteria formed 8-9 strongly supported clades at the highest level, which may correspond to the higher taxonomic clades of this phylum. One of these clades contained all heterocystous cyanobacteria; within this clade, the members exhibiting either true (Nostocales) or false (Stigonematales) branching of filaments were intermixed indicating that the division of the heterocysts-forming cyanobacteria into these two groups is not supported by phylogenetic considerations. However, in both the protein tree as well as in the 16S rRNA gene tree, the akinete-forming heterocystous cyanobacteria formed a distinct clade. Within this clade, the members which differentiate into hormogonia or those which lack this ability were also separated into distinct groups. A novel molecular signature identified in this work that is uniquely shared by the akinete-forming heterocystous cyanobacteria provides further evidence that the members of this group are specifically related and they shared a common ancestor exclusive of the other cyanobacteria. Detailed comparative analyses on protein sequences from the genomes of heterocystous cyanobacteria reported here have also identified eight conserved signature indels (CSIs) in proteins involved in a broad range of functions, and three conserved signature proteins, that are either uniquely or mainly found in all heterocysts-forming cyanobacteria, but generally not found in other cyanobacteria. These molecular markers provide novel means for the identification of heterocystous cyanobacteria, and they provide evidence of their monophyletic origin. Additionally, this work has also identified seven CSIs in other proteins which in addition to the heterocystous

  1. Psammocyclopinidae fam. n., a new monophyletic group of marine Cyclopoida (Copepoda, Crustacea, with the description of Psammocyclopina georgei sp. n. from the Magellan Region

    Directory of Open Access Journals (Sweden)

    Pedro Martínez Arbizu

    2001-12-01

    Full Text Available Psammocyclopina georgei sp. n. is described from submersed sands in the Magellan Strait, South Atlantic Ocean. This is the second species of the genus, previously known only from the Indian Ocean (Mozambique. Psammocyclopina Wells, 1967 is the sistergroup of Metacyclopina Lindberg, 1953. Psammocyclopinidae fam. n. is accordingly proposed to unify these genera into one monophyletic unit. The sistergroup of the new family is a cluster of cyclopinid genera composed of Cyclopinodes Wilson, 1932, Pseudocyclopina Lang, 1946, Parapseudocyclopinodes Lindberg, 1961, Hemicyclopina Herbst, 1952, Procyclopina Herbst, 1955, Heterocydopina Plesa, 1968, Neocyclopina Herbst, 1952, and an as yet undescribed new genus (Martinez Arbizu, in prep.. Global occurrence of psammocyclopinids is briefly reviewed.

  2. Is the mega-diverse genus Ocyptamus (Diptera, Syrphidae) monophyletic? Evidence from molecular characters including the secondary structure of 28S rRNA.

    Science.gov (United States)

    Mengual, Ximo; Ståhls, Gunilla; Rojo, Santos

    2012-01-01

    Phylogenetic relationships between two New World Syrphinae taxa (Diptera, Syrphidae), i.e. the highly diverse genus Ocyptamus and the large genus Toxomerus, were analysed based on molecular characters. The monophyly of both taxa was tested and the taxonomic status of included subgenera and species groups was examined. Toxomerus constitutes the monogeneric tribe Toxomerini with more than 140 described species, while Ocyptamus (tribe Syrphini) is a very diverse genus (over 300 spp.) with multiple recognised subgenera and species groups. Sequence data from three gene regions were used: the mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) and the nuclear 28S and 18S ribosomal RNA genes. The secondary structure of two expansion segments (D2, D3) of the ribosomal 28S RNA gene is presented for the family Syrphidae and used for the first time in a multiple sequence alignment. Molecular data were analysed using parsimony, maximum likelihood and Bayesian inference. Toxomerus was always recovered as monophyletic within Ocyptamus, and relationships to other New World taxa such as Salpingogaster (Eosalpingogaster) were well-supported. Only the subgenera and species groups of Ocyptamus were consistently recovered as monophyletic lineages, thus the apparent non-monophyly of Ocyptamus demands reclassification of this clade. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. Phylogeny of nodulation and nitrogen-fixation genes in Bradyrhizobium: supporting evidence for the theory of monophyletic origin, and spread and maintenance by both horizontal and vertical transfer.

    Science.gov (United States)

    Menna, Pâmela; Hungria, Mariangela

    2011-12-01

    /housekeeping genes, in addition to shorter nodY/K sequences and the absence of nodZ, highlights a co-evolution process. Additionally, in a group of B. japonicum strains that were symbionts of soybean, vertical transfer seemed to represent the main genetic event. In conclusion, clustering of nodA and nifH gives additional support to the theory of monophyletic origin of the symbiotic genes in Bradyrhizobium and, in addition to the analysis of nodY/K and nodZ, indicates spread and maintenance of nod and nif genes through both vertical and horizontal transmission, apparently with the dominance of one or other of these events in some groups of strains.

  4. Toward monophyletic generic concepts in Magnaporthales: species with Harpophora asexual states.

    Science.gov (United States)

    Luo, Jing; Walsh, Emily; Zhang, Ning

    2015-01-01

    We investigated the phylogenetic relationships among Magnaporthales fungi with harpophora-like asexual states based on DNA sequences of ITS, MCM7, RPB1 and TEF1 genes. The results indicated that these species are polyphyletic. Based on the four-gene phylogeny, the type species of Harpophora, H. radicicola, belongs to Gaeumannomyces and thus Harpophora is treated as a synonym of Gaeumannomyces. In addition, a monotypic new genus, Falciphora, is established based on F. oryzae, previous referred as Harpophora oryzae.

  5. Aspergillus is monophyletic: Evidence from multiple gene phylogenies and extrolites profiles

    NARCIS (Netherlands)

    Kocsubé, S.; Perrone, G.; Magistà, D.; Houbraken, J.; Varga, J.; Szigeti, G.; Hubka, V.; Hong, S.-B.; Frisvad, J.C.; Samson, R.A.

    Abstract Aspergillus is one of the economically most important fungal genera. Recently, the ICN adopted the single name nomenclature which has forced mycologists to choose one name for fungi (e.g. Aspergillus, Fusarium, Penicillium, etc.). Previously two proposals for the single name nomenclature in

  6. When Naked Became Armored: An Eight-Gene Phylogeny Reveals Monophyletic Origin of Theca in Dinoflagellates

    Science.gov (United States)

    Orr, Russell J. S.; Murray, Shauna A.; Stüken, Anke; Rhodes, Lesley; Jakobsen, Kjetill S.

    2012-01-01

    The dinoflagellates are a diverse lineage of microbial eukaryotes. Dinoflagellate monophyly and their position within the group Alveolata are well established. However, phylogenetic relationships between dinoflagellate orders remain unresolved. To date, only a limited number of dinoflagellate studies have used a broad taxon sample with more than two concatenated markers. This lack of resolution makes it difficult to determine the evolution of major phenotypic characters such as morphological features or toxin production e.g. saxitoxin. Here we present an improved dinoflagellate phylogeny, based on eight genes, with the broadest taxon sampling to date. Fifty-five sequences for eight phylogenetic markers from nuclear and mitochondrial regions were amplified from 13 species, four orders, and concatenated phylogenetic inferences were conducted with orthologous sequences. Phylogenetic resolution is increased with addition of support for the deepest branches, though can be improved yet further. We show for the first time that the characteristic dinoflagellate thecal plates, cellulosic material that is present within the sub-cuticular alveoli, appears to have had a single origin. In addition, the monophyly of most dinoflagellate orders is confirmed: the Dinophysiales, the Gonyaulacales, the Prorocentrales, the Suessiales, and the Syndiniales. Our improved phylogeny, along with results of PCR to detect the sxtA gene in various lineages, allows us to suggest that this gene was probably acquired separately in Gymnodinium and the common ancestor of Alexandrium and Pyrodinium and subsequently lost in some descendent species of Alexandrium. PMID:23185516

  7. Are crocodiles really monophyletic?--Evidence for subdivisions from sequence and morphological data.

    Science.gov (United States)

    McAliley, L Rex; Willis, Ray E; Ray, David A; White, P Scott; Brochu, Christopher A; Densmore, Llewellyn D

    2006-04-01

    Recently, the phylogenetic placement of the African slender snouted crocodile, Crocodylus cataphractus, has come under scrutiny and herein we address this issue using molecular and morphological techniques. Although it is often recognized as being a "basal" form, morphological studies have traditionally placed C. cataphractus within the genus Crocodylus, while molecular studies have suggested that C. cataphractus is very distinct from other Crocodylus. To address the relationship of this species to its congeners we have sequenced portions of two nuclear genes (C-mos 302bp and ODC 294bp), and two mitochondrial genes (ND6-tRNA(glu)-cytB 347bp and control region 457bp). Analyses of these molecular datasets, both as individual gene sequences and as concatenated sequences, support the hypothesis that C. cataphractus is not a member of Crocodylus or Osteolaemus. Examination of 165 morphological characters supports and strengthens our resurrection of an historic genus, Mecistops (Gray 1844) for cataphractus.

  8. Aspergillus is monophyletic: Evidence from multiple gene phylogenies and extrolites profiles

    DEFF Research Database (Denmark)

    Kocsubé, S.; Perrone, G.; Magistà, D.;

    2016-01-01

    Circumdati and maintaining the sexual names in the other clades. The aim of our study was to test the monophyly of Aspergilli by two independent phylogenetic analyses using a multilocus phylogenetic approach. One test was run on the publicly available coding regions of six genes (RPB1, RPB2, Tsr1, Cct8, Ben...... publicly available data of the coding sequences of nine loci (18S rRNA, 5,8S rRNA, 28S rRNA (D1-D2), RPB1, RPB2, CaM, BenA, Tsr1, Cct8) of 204 different species. Both Bayesian (MrBayes) and Maximum Likelihood (RAxML) trees obtained by this second round of independent analyses strongly supported...... which were formerly part of the genera Phialosimplex and Polypaecilum. Section Cremei and the clade containing Polypaecilum and Phialosimplex are proposed as new subgenera of Aspergillus. The phylogenetic analysis also clearly shows that Aspergillus clavatoflavus and A. zonatus do not belong...

  9. When naked became armored: an eight-gene phylogeny reveals monophyletic origin of theca in dinoflagellates.

    Science.gov (United States)

    Orr, Russell J S; Murray, Shauna A; Stüken, Anke; Rhodes, Lesley; Jakobsen, Kjetill S

    2012-01-01

    The dinoflagellates are a diverse lineage of microbial eukaryotes. Dinoflagellate monophyly and their position within the group Alveolata are well established. However, phylogenetic relationships between dinoflagellate orders remain unresolved. To date, only a limited number of dinoflagellate studies have used a broad taxon sample with more than two concatenated markers. This lack of resolution makes it difficult to determine the evolution of major phenotypic characters such as morphological features or toxin production e.g. saxitoxin. Here we present an improved dinoflagellate phylogeny, based on eight genes, with the broadest taxon sampling to date. Fifty-five sequences for eight phylogenetic markers from nuclear and mitochondrial regions were amplified from 13 species, four orders, and concatenated phylogenetic inferences were conducted with orthologous sequences. Phylogenetic resolution is increased with addition of support for the deepest branches, though can be improved yet further. We show for the first time that the characteristic dinoflagellate thecal plates, cellulosic material that is present within the sub-cuticular alveoli, appears to have had a single origin. In addition, the monophyly of most dinoflagellate orders is confirmed: the Dinophysiales, the Gonyaulacales, the Prorocentrales, the Suessiales, and the Syndiniales. Our improved phylogeny, along with results of PCR to detect the sxtA gene in various lineages, allows us to suggest that this gene was probably acquired separately in Gymnodinium and the common ancestor of Alexandrium and Pyrodinium and subsequently lost in some descendent species of Alexandrium.

  10. The monophyletic origin of a remarkable sexual system in akentrogonid rhizocephalan parasites

    DEFF Research Database (Denmark)

    Glenner, Henrik; Høeg, Jens Thorvald; Stenderup, Jesper

    2010-01-01

    We use sequences from the nuclear ribosomal genes, 18S and 28S to analyze the phylogeny of the Rhizocephala Akentrogonida including two species, Clistosaccus paguri and Chthamalophilus delagei, that are critical for understanding rhizocephalan evolution but have not previously been part...

  11. Molecular phylogenetic and zoospore ultrastructural analyses of Chytridium olla establish the limits of a monophyletic Chytridiales.

    Science.gov (United States)

    Vélez, Carlos G; Letcher, Peter M; Schultz, Sabina; Powell, Martha J; Churchill, Perry F

    2011-01-01

    Chytridium olla A. Braun, the first described chytrid and an obligate algal parasite, is the type for the genus and thus the foundation of family Chytridiaceae, order Chytridiales, class Chytridiomycetes and phylum Chytridiomycota. Chytridium olla was isolated in coculture with its host, Oedogonium capilliforme. DNA was extracted from the coculture, and 18S, 28S and ITS1-5.8S-ITS2 rDNA were amplified with universal fungal primers. Free swimming zoospores and zoospores in mature sporangia were examined with electron microscopy. Molecular analyses placed C. olla in a clade in Chytridiales with isolates of Chytridium lagenaria and Phlyctochytrium planicorne. Ultrastructural analysis revealed C. olla to have a Group II-type zoospore, previously described for Chytridium lagenaria and Phlyctochytrium planicorne. On the basis of zoospore ultrastructure, family Chytridiaceae is emended to include the type of Chytridium and other species with a Group II-type zoospore, and the new family Chytriomycetaceae is delineated to include members of Chytridiales with a Group I-type zoospore.

  12. Salvia (Lamiaceae) is not monophyletic: implications for the systematics, radiation, and ecological specializations of Salvia and tribe Mentheae

    National Research Council Canada - National Science Library

    Walker, Jay B; Sytsma, Kenneth J; Treutlein, Jens; Wink, Michael

    2004-01-01

    ... • Rosmarinus • Salvia • stamen • trnL-F CiteULike     Complore     Connotea     Del.icio.us     Digg     Facebook     Reddit     Technorati     Twitter     What's this?

  13. The mitochondrial genomes of the glaucophytes Gloeochaete wittrockiana and Cyanoptyche gloeocystis: multilocus phylogenetics suggests a monophyletic archaeplastida.

    Science.gov (United States)

    Jackson, Christopher J; Reyes-Prieto, Adrian

    2014-10-03

    A significant limitation when testing the putative single origin of primary plastids and the monophyly of the Archaeplastida supergroup, comprised of the red algae, viridiplants, and glaucophytes, is the scarce nuclear and organellar genome data available from the latter lineage. The Glaucophyta are a key algal group when investigating the origin and early diversification of photosynthetic eukaryotes. However, so far only the plastid and mitochondrial genomes of the glaucophytes Cyanophora paradoxa (strain CCMP 329) and Glaucocystis nostochinearum (strain UTEX 64) have been completely sequenced. Here, we present the complete mitochondrial genomes of Gloeochaete wittrockiana SAG 46.84 (36.05 kb; 33 protein-coding genes, 6 unidentified open reading frames [ORFs], and 28 transfer RNAs [tRNAs]) and Cyanoptyche gloeocystis SAG 4.97 (33.24 kb; 33 protein-coding genes, 6 unidentified ORFs, and 26 tRNAs), which represent two genera distantly related to the "well-known" Cyanophora and Glaucocystis. The mitochondrial gene repertoire of the four glaucophyte species is highly conserved, whereas the gene order shows considerable variation. Phylogenetic analyses of 14 mitochondrial genes from representative taxa from the major eukaryotic supergroups, here including novel sequences from the glaucophytes Cyanophora tetracyanea (strain NIES-764) and Cyanophora biloba (strain UTEX LB 2766), recover a clade uniting the three Archaeplastida lineages; this recovery is dependent on our novel glaucophyte data, demonstrating the importance of greater taxon sampling within the glaucophytes.

  14. Horses naturally infected with EIAV harbor 2 distinct SU populations but are monophyletic with respect to IN.

    Science.gov (United States)

    Cervantes, Diana T; Ball, Judith M; Edwards, John; Payne, Susan

    2016-02-01

    Equine infectious anemia virus (EIAV) causes lifelong infections ranging from acutely fatal, to chronic, to asymptomatic. Within infected animals, EIAV is found as a quasispecies. Many experimental studies on EIAV, carried out in the U.S. over the past 70 years, have used either the highly virulent Wyoming (EIAVWYO) field strain or various derivatives of that strain. These infections have provided insights into the variety of genetic changes that accumulate in the env gene and LTR in experimentally infected horses. In the current study, we obtained EIAV sequences from blood samples collected from naturally infected Texas horses between 2000 and 2002. We found surface (SU) and long terminal repeat (LTR) sequences clearly related to EIAVWYO and its cell culture-adapted derivatives. Some blood samples yielded SU or LTR sequences belonging to 2 discrete clusters. In these cases, SU and LTR variation between animals was no greater than sequence variation within animals. In contrast, a portion of integrase (IN) was more homogeneous within animals than between animals. These results suggest that specific selective pressures are applied to SU and LTR sequences, potentially driving generation of two distinct sequence clusters within a horse. We speculate that viruses in one cluster may be more highly expressed and easily transmitted while those in the second cluster support long-term inapparent infection. The presence of homogeneous IN sequences within a horse supports the hypothesis that SU and LTR sequences diverged after the initial infection.

  15. Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria.

    Directory of Open Access Journals (Sweden)

    Hironobu Fukami

    Full Text Available Modern hard corals (Class Hexacorallia; Order Scleractinia are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b, with analyses of nuclear genes (ss-tubulin, ribosomal DNA of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent "robust" and "complex" clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils.

  16. Evolution of the trypanorhynch tapeworms: parasite phylogeny supports independent lineages of sharks and rays.

    Science.gov (United States)

    Olson, Peter D; Caira, Janine N; Jensen, Kirsten; Overstreet, Robin M; Palm, Harry W; Beveridge, Ian

    2010-02-01

    Trypanorhynch tapeworms (Platyhelminthes: Cestoda) are among the most diverse and abundant groups of metazoan parasites of elasmobranchs and are a ubiquitous part of the marine food webs that include these apex predators. Here we present a comprehensive analysis of their phylogeny, character evolution and host associations based on 10years of sampling effort, including representatives of 12 of 15 and 44 of 66 currently recognized trypanorhynch families and genera, respectively. Using a combination of ssrDNA and lsrDNA (Domains 1-3) for 79 and 80 taxa, respectively, we maintain one-to-one correspondence between molecules and morphology by scoring 45 characters from the same specimens used for sequencing, and provide museum vouchers for this material. Host associations are examined through likelihood-based ancestral character state reconstructions (ACSRs) and by estimating dates of divergence using strict and relaxed molecular clock models in a Bayesian context. Maximum parsimony and Bayesian inference analyses of rDNA produced well-resolved and strongly supported trees in which the trypanorhynchs formed two primary lineages and were monophyletic with respect to the diphyllidean outgroup taxa. These lineages showed marked differences in their rates of divergence which in turn resulted in differing support and stability characteristics within the lineages. Mapping of morphological characters onto the tree resulting from combined analysis of rDNA showed most traits to be highly plastic, including some previously considered of key taxonomic importance such as underlying symmetries in tentacular armature. The resulting tree was found to be congruent with the most recent morphologically based superfamily designations in the order, providing support for four proposed superfamilies, but not for the Tentacularioidea and Eutetrarhynchoidea. ACSRs based on the combined analysis of rDNA estimated the original hosts of the two primary parasite lineages to be alternatively

  17. Evidence of Two Formae Speciales in Venturia inaequalis, Responsible for Apple and Pyracantha Scab

    National Research Council Canada - National Science Library

    Le Cam, Bruno; Parisi, Luciana; Arene, Laurence

    2002-01-01

    .... Additional isolates from three related species (V. pirina, V. nashicola, and S. eriobotryae) were divided into two distinct monophyletic groups in a phylogenetic tree using ITS sequence comparison...

  18. Phylogenetics and diversification of morning glories (tribe ipomoeeae, convolvulaceae) based on whole plastome sequences

    Science.gov (United States)

    Phylogenetic studies have demonstrated the largest morning glory genus, Ipomoea, is not monophyletic, and nine other segregate genera are derived from within Ipomoea. Therefore, systematic research is focused on the monophyletic tribe Ipomoeeae (c. 650-900 species). We used whole plastid genomes to ...

  19. Numerical analysis of Thai members of the Eugenia-Syzygium group (Myrtaceae)

    NARCIS (Netherlands)

    Parnell, J.

    1999-01-01

    Four different analyses of Thai Syzygium show, with very small discrepancies, that one smaller monophyletic and one larger polyphyletic group can be recognised. The smaller monophyletic group warrants sectional rank as Syzygium section Jambosa and consists of S. anacardiifolium, S. aqueum, S. diospy

  20. A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis

    National Research Council Canada - National Science Library

    Young, JM; Kuykendall, LD; Martinez-Romero, E; Kerr, A; Sawada, H

    2001-01-01

    .... Agrobacterium radiobacter), Agrobacterium rhizogenes, Agrobacterium rubi and Agrobacterium vitis, together with Allorhizobium undicola, form a monophyletic group with all Rhizobium species, based on comparative 16S rDNA analyses...

  1. Molecular phylogeny of tribe Stachydeae (Lamiaceae subfamily Lamioideae)

    DEFF Research Database (Denmark)

    Salmaki, Yasaman; Zarre, Shahin; Ryding, Per Olof

    2013-01-01

    Although tribe Stachydeae (Lamiaceae) is considered monophyletic, relationships within the tribe are still poorly understood. The complexity of Stachydeae includes paraphyletic genera, considerable morphological plasticity, a range of ploidy levels, and presumably frequent natural hybridization. ...

  2. Enigmatic phylogeny of skuas (Aves Stercorariidae)

    NARCIS (Netherlands)

    Cohen, BL; Baker, AJ; Bleschschmidt, K; Dittmann, DL; Furness, RW; Gerwin, JA; de Korte, J.; Marshall, HD; Palma, RL; Peter, HU; Ramli, R; Siebold, [No Value; Willcox, MS; Wilson, RH; Zink, RM

    1997-01-01

    Multiple sources of evidence show that the skuas (Aves: Stercorariidae) are a monophyletic group, closely related to gulls (Laridae). On morphological and behavioural evidence the Stercorariidae are divided into two widely divergent genera, Catharacta and Stercorarius, consistent with observed level

  3. Towards a phylogenetic classification of dendrocoelid freshwater planarians (Platyhelminthes): a morphological and eclectic approach

    NARCIS (Netherlands)

    Sluys, R.; Kawakatsu, M.

    2006-01-01

    We explore and review the taxonomic distribution of morphological features that may be used as supporting apomorphies for the monophyletic status of various taxa in future, more comprehensive phylogenetic analyses of the dendrocoelid freshwater planarians and their close relatives. Characters

  4. An alternative model for the early peopling of southern South America revealed by analyses of three mitochondrial DNA haplogroups

    National Research Council Canada - National Science Library

    de Saint Pierre, Michelle; Bravi, Claudio M; Motti, Josefina M B; Fuku, Noriyuki; Tanaka, Masashi; Llop, Elena; Bonatto, Sandro L; Moraga, Mauricio

    2012-01-01

    ... seven complete mitochondrial DNA sequences. We identified two novel mtDNA monophyletic clades, preliminarily designated B2l and C1b13, which together with the recently described D1g sub-haplogroup have locally high frequencies...

  5. Mycosarcoma (Ustilaginaceae), a resurrected generic name for corn smut (Ustilago maydis) and its close relatives with hypertrophied, tubular sori

    NARCIS (Netherlands)

    McTaggart, Alistair R; Shivas, Roger G; Boekhout, Teun; Oberwinkler, Franz; Vánky, Kálmán; Pennycook, Shaun R; Begerow, Dominik

    2016-01-01

    Ustilago is a polyphyletic genus of smut fungi found mainly on Poaceae. The development of a taxonomy that reflects phylogeny requires subdivision of Ustilago into smaller monophyletic genera. Several separate systematic analyses have determined that Macalpinomyces mackinlayi, M. tubiformis, Tolypos

  6. Taxonomic revision of Elaphoglossum subsection Muscosa (Dryopteridaceae)

    NARCIS (Netherlands)

    Vasco, A.

    2011-01-01

    The present paper provides a monograph of Elaphoglossum subsect. Muscosa, a monophyletic group supported by molecular phylogenetic analyses. The monograph includes keys, full synonymy, descriptions, representative specimens examined, an index to collectors’ names and numbers, illustrations, spore

  7. Molecular phylogeny of tribe Stachydeae (Lamiaceae subfamily Lamioideae)

    DEFF Research Database (Denmark)

    Salmaki, Yasaman; Zarre, Shahin; Ryding, Per Olof

    2013-01-01

    Although tribe Stachydeae (Lamiaceae) is considered monophyletic, relationships within the tribe are still poorly understood. The complexity of Stachydeae includes paraphyletic genera, considerable morphological plasticity, a range of ploidy levels, and presumably frequent natural hybridization. ...

  8. Comparative Analyses of Reproductive Structures in Harvestmen (Opiliones) Reveal Multiple Transitions from Courtship to Precopulatory Antagonism. e66767

    National Research Council Canada - National Science Library

    Burns, Mercedes M; Hedin, Marshal; Shultz, Jeffrey W

    2013-01-01

    ... in species-rich clades. Here we examine evolution of reproductive structures in the leiobunine harvestmen or "daddy long-legs" of eastern North America, a monophyletic group that includes species in which males court...

  9. Comparative analyses of reproductive structures in harvestmen (opiliones) reveal multiple transitions from courtship to precopulatory antagonism

    National Research Council Canada - National Science Library

    Burns, Mercedes M; Hedin, Marshal; Shultz, Jeffrey W

    2013-01-01

    ... in species-rich clades. Here we examine evolution of reproductive structures in the leiobunine harvestmen or "daddy long-legs" of eastern North America, a monophyletic group that includes species in which males court...

  10. Chance and necessity in eye evolution

    National Research Council Canada - National Science Library

    Gehring, Walter J

    2011-01-01

    ...." Recent discoveries in eye evolution are in agreement with both of these theses. They confirm Darwin's assumption of a simple eye prototype and lend strong support for the notion of a monophyletic origin of the various eye types...

  11. Phylogeny of moray eels (Anguilliformes: Muraenidae), with a revised classification of true eels (Teleostei: Elopomorpha: Anguilliformes).

    Science.gov (United States)

    Tang, Kevin L; Fielitz, Christopher

    2013-02-01

    The family Muraenidae is one of the largest and most recognizable eel groups. Moray eels are key components of marine ecosystems but their relationships remain poorly understood. The phylogenetic relationships of the morays are examined herein using mitochondrial 12S and 16S sequence data, totaling 1673 bp for 139 taxa. The results of our analyses found support for a monophyletic family Muraenidae that is part of a monophyletic suborder Muraenoidei, which is revised to include the anguilliform families Heterenchelyidae and Myrocongridae, and to exclude the family Chlopsidae. The muraenids form two monophyletic subfamilies, Muraeninae and Uropterygiinae. Of the genera that had multiple species included for analysis, only the type genus of the family, Muraena, is found to be monophyletic. In the subfamily Uropterygiinae, Uropterygius is not recovered as a monophyletic genus. In the subfamily Muraeninae, the species-rich piscivorous genera, Enchelycore and Gymnothorax, and the durophagous genus, Echidna, are demonstrably not monophyletic. The monotypic Gymnomuraena is the sister group to all other muraenine species. The relationships within Muraenidae require much additional study and its genera remain in urgent need of revision. The order Anguilliformes is revised herein to include four suborders: Anguilloidei, Congroidei, Muraenoidei, and Synaphobranchoidei. All four families of the order Saccopharyngiformes are nested within Anguilliformes, recovered as part of a clade that includes Anguillidae; the saccopharyngiform families are referred to the suborder Anguilloidei sensu novum.

  12. Molecular phylogenetic relationships of Eastern Asian Cyprinidae (Pisces: Cypriniformes) inferred from cytochrome b sequences

    Institute of Scientific and Technical Information of China (English)

    HE; Shunping; LIU; Huanzhang; CHEN; Yiyu; Masayuki; Kuwah

    2004-01-01

    Complete mitochondrial cytochrome b sequences of 54 species, including 18 newly sequenced, were analyzed to infer the phylogenetic relationships within the family Cyprinidae in East Asia. Phylogenetic trees were generated using various tree-building methods, including Neighbor-joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods, with Myxocyprinus asiaticus (family Catostomidae) as the designated outgroup. The results from NJ and ML methods were mostly similar, supporting some existing subfamilies within Cyprinidae as monophyletic, such as Cultrinae, Xenocyprinae and Gobioninae (including Gobiobotinae). However, genera within the subfamily "Danioninae" did not form a monophyletic group. The subfamily Leuciscinae was divided into two unrelated groups: the "Leuciscinae" in East Asia forming as a monophyletic group together with Cultrinae and Xenocyprinae, while the Leuciscinae in Europe, Siberia, and North America as another monophyletic group. The monophyly of subfamily Cyprininae sensu Howes was supported by NJ and ML trees and is basal in the tree. The position of Acheilognathinae, a widely accepted monophyletic group represented by Rhodeus sericeus, was not resolved.

  13. Genus Tetrastemma Ehrenberg, 1831 (Phylum Nemertea)--a natural group? Phylogenetic relationships inferred from partial 18S rRNA sequences.

    Science.gov (United States)

    Strand, Malin; Sundberg, Per

    2005-10-01

    We investigated the monophyletic status of the hoplonemertean taxon Tetrastemma by reconstructing the phylogeny for 22 specimens assigned to this genus, together with another 25 specimens from closely related hoplonemertean genera. The phylogeny was based on partial 18S rRNA sequences using Bayesian and maximum likelihood analyses. The included Tetrastemma-species formed a well-supported clade, although the within-taxon relationships were unsettled. We conclude that the name Tetrastemma refers to a monophyletic taxon, but that it cannot be defined by morphological synapomorphies, and our results do not imply that all the over 100 species assigned to this genus belong to it. The results furthermore indicate that the genera Amphiporus and Emplectonema are non-monophyletic.

  14. Phylogenetic relationships among higher Nemertean (Nemertea) Taxa inferred from 18S rDNA sequences.

    Science.gov (United States)

    Sundberg, P; Turbeville, J M; Lindh, S

    2001-09-01

    We estimated the phylogenetic relationships of 15 nemertean (phylum Nemertea) species from the four subclasses Hoplo-, Hetero-, Palaeo-, and Bdellonemertea with 18S rDNA sequence data. Three outgroup taxa were used for rooting: Annelida, Platyhelminthes, and Mollusca. Parsimony and maximum-likelihood analyses supported the monophyletic status of the Heteronemertea and a taxon consisting of hoplonemerteans and Bdellonemertea, while indicating that Palaeonemertea is paraphyletic. The monophyletic status of the two nemertean classes Anopla and Enopla is not supported by the data. The unambiguous clades are well supported, as assessed by a randomization test (bootstrapping) and branch support values. Copyright 2001 Academic Press.

  15. Candidatus "Scalindua brodaea", spec. nov., Candidatus "Scalindua wagneri", spec. nov., two new species of anaerobic ammonium oxidizing bacteria

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Schmid, M.; Walsh, K.; Webb, R.; Rijpstra, W.I.C.; Pas-Schoonen, K. van de; Verbruggen, M.J.; Hill, T.; Moffett, B.; Fuerst, J.; Schouten, S.; Harris, James; Shaw, P.; Jetten, M.S.M.; Strous, M.

    2003-01-01

    Anaerobic ammonium oxidation (anammox) is both a promising process in wastewater treatment and a long overlooked microbial physiology that can contribute significantly to biological nitrogen cycling in the world's oceans. Anammox is mediated by a monophyletic group of bacteria that branches deeply i

  16. Limited variation during circulation of a polyomavirus in the human population involves the COCO-VA toggling site of Middle and Alternative T-antigen(s)

    NARCIS (Netherlands)

    S. Kazem (Siamaque); C. Lauber (Chris); E. van der Meijden (Els); S. Kooijman (Sander); A.A. Kravchenko (Alexander A.); M.C.W. Feltkamp (Mariet C.W.); A.E. Gorbalenya (Alexander); J.C. Browning (John C.); K. Busam (Klaus); S. Bialasiewicz (Seweryn); T. Benoit (Taylor); P. Fleckman (Philip); L.C. Hughey (Lauren C.); R.W.A. Janssens (René W.A.); F. Mechinaud (Francoise); E. Pope (Elena); A.S. Rosenberg (Arlene S.); E. Rácz (Emoke); G. Sadler (Genevieve); S.N. Tabrizi (Sepehr N.); E. de Vries (E.); R.C. Wang (Richard C.)

    2016-01-01

    textabstractWe have recently shown that the trichodysplasia spinulosa-associated polyomavirus (TSPyV) belongs to a large monophyletic group of mammalian polyomaviruses that experienced accelerated codon-constrained Val-Ala (COCO-VA) toggling at a protein site common to both Middle and Alternative T-

  17. Identifying the Transition between Single and Multiple Mating of Queens in Fungus-Growing Ants

    DEFF Research Database (Denmark)

    Villesen, Palle; Murakami, Takahiro; Schultz, Ted R.

    2002-01-01

    Obligate mating of females (queens) with multiple males has evolved only rarely in social Hymenoptera (ants, social bees, social wasps) and for reasons that are fundamentally different from those underlying multiple mating in other animals. The monophyletic tribe of ('attine') fungus-growing ants...

  18. The taxonomy and biogeography of the exhausta group of the genus Baeturia Stål, 1866 (Homoptera, Tibicinidae)

    NARCIS (Netherlands)

    Boer, de A.J.

    1994-01-01

    The exhausta group is proposed for a supposedly monophyletic group of eight species of the cicada genus Baeturia Stal, 1866. Three species (B. bicolorata Distant, B. exhausta Guérin Méneville, and B. vanderhammeni Blöte) are redescribed and five species B. colossea, B. maai, B. rossi, B. versicolor,

  19. A new genus for the Lesser Moorhen Gallinula angulata Sundevall, 1850 (Aves, Rallidae

    Directory of Open Access Journals (Sweden)

    George Sangster

    2015-11-01

    Full Text Available Molecular phylogenetic analysis has demonstrated that the genus Gallinula is not monophyletic and comprises four major lineages. A review of the nomenclature of Gallinula shows that generic names are available for three lineages but that a fourth is as yet unnamed. A new monotypic genus, Paragallinula gen. nov., is described for Lesser Moorhen (Gallinula angulata Sundevall, 1850.

  20. Resolving taxonomic confusion in the sea chubs (F. Kyphosidae)

    DEFF Research Database (Denmark)

    Knudsen, Steen Wilhelm; Clements, Kendall

    2013-01-01

    complete taxon sampling from these fishes, and species delimitation was determined on the basis of congruence between monophyletic groupings in the molecular phylogeny combined with comparison of morphological variation in type material. The results overall indicate that our understanding of species...

  1. Diversity and ancestry of flatworms infecting blood of nontetrapod craniates "fishes".

    Science.gov (United States)

    Orélis-Ribeiro, Raphael; Arias, Cova R; Halanych, Kenneth M; Cribb, Thomas H; Bullard, Stephen A

    2014-01-01

    We herein review all published molecular studies (life history, taxonomy, and phylogeny) and summarize all GenBank sequences and primer sets for the "fish blood flukes". Further, by analysing new and all available sequence data for the partial D1-D2 domains of 28S from 83 blood fluke taxa, we explore the evolutionary expansion of flatworm parasitism in the blood of craniates. Based on this analysis, the blood flukes infecting marine bony fishes (Euteleostei) are monophyletic. The clade comprising the chondrichthyan blood fluke plus the marine euteleost blood flukes is the sister group to tetrapod blood flukes (spirorchiids and schistosomes). The innominate blood fluke cercariae from freshwater gastropods were monophyletic and sister to the clade comprising spirorchiids and schistosomes, but low nodal support indicated that they may represent a distinct blood fluke lineage with phylogenetic affinities also to fish blood flukes. Blood flukes that utilize gastropod intermediate hosts were monophyletic (unidentified gastropod cercariae+tetrapod blood flukes) and those utilizing bivalves and polychaetes were monophyletic (marine fish blood flukes). Low or no taxon sampling among blood flukes of basal fish lineages and primary division freshwater fish lineages are significant data gaps needing closure. We also note that no record of an infection exists in a hagfish (Myxiniformes), lamprey (Petromyzontiformes), or nontetrapod sarcopterygiian, i.e., coelacanth (Coelacanthimorpha) or lungfish (Dipnoi). The present phylogenetic analysis reiterated support for monophyly of Schistosomatidae and paraphyly of spirorchiids, with the blood flukes of freshwater turtles basal to those of marine turtles and schistosomes.

  2. The Yellow-green Bush-tanager is neither a bush-tanager nor a sparrow: Molecular phylogenetics reveals that Chlorospingus flavovirens is a tanager (Aves: Passeriformes; Thraupidae).

    Science.gov (United States)

    Avendaño, Jorge Enrique; Barker, F Keith; Cadena, Carlos Daniel

    2016-07-06

    Molecular phylogenetic analyses of the genus Chlorospingus (Aves: Emberizidae) indicate that the genus is not monophyletic because Chlorospingus flavovirens is actually a member of the tanager family (Thraupidae), in which its closest relatives are members of the genus Bangsia. We thus propose that C. flavovirens be transferred to Thraupidae and to the genus Bangsia.

  3. 2. The Amsterdam Declaration on fungal nomenclature

    DEFF Research Database (Denmark)

    Hawksworth, David L.; Crous, Pedro W.; Redhead, Scott A.;

    2011-01-01

    where there is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated...

  4. The taxonomy and biogeography of the bloetei group of the genus Baetura Stål, 1866 (Homoptera, Tibicinidae)

    NARCIS (Netherlands)

    Boer, de A.J.

    1989-01-01

    The bloetei group is proposed for a monophyletic group of 18 species of the genus Baeturia Stål, 1866. Fifteen species are described as new ( B. bilebanarai, B. bismarckensis, B. bloetei, B. boulardi, B. brandti, B. cristovalensis, B. gressitti, B. macgillavryi, B. manusensis, B. marginata, B. menda

  5. Candidatus "Scalindua brodaea", spec. nov., Candidatus "Scalindua wagneri", spec. nov., two new species of anaerobic ammonium oxidizing bacteria

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Schmid, M.; Walsh, K.; Webb, R.; Rijpstra, W.I.C.; Pas-Schoonen, K. van de; Verbruggen, M.J.; Hill, T.; Moffett, B.; Fuerst, J.; Schouten, S.; Harris, James; Shaw, P.; Jetten, M.S.M.; Strous, M.

    2003-01-01

    Anaerobic ammonium oxidation (anammox) is both a promising process in wastewater treatment and a long overlooked microbial physiology that can contribute significantly to biological nitrogen cycling in the world's oceans. Anammox is mediated by a monophyletic group of bacteria that branches deeply

  6. Segregation of Leptatherum from Microstegium (Andropogoneae, Poaceae) confirmed by Internal Transcribed Spacer DNA sequences

    NARCIS (Netherlands)

    Chen, C.-H.; Veldkamp, J.F.; Kuoh, C.-S.; Tsai, C.-C.; Chiang, Y.-C.

    2009-01-01

    Phylogenetic analyses of Microstegium (Andropogoneae, Poaceae) and some other Andropogoneae species were conducted inferred from the ITS/5.8S sequences. As a result of this study, Microstegium is polyphyletic. There are two rather distant monophyletic clades, one with Microstegium nudum (type of

  7. Two new species in the Ectoedemia (Fomoria) weaveri-group from Asia (Lepidoptera: Nepticulidae)

    NARCIS (Netherlands)

    Nieukerken, van E.J.

    2008-01-01

    Two new species are described in the monophyletic Ectoedemia (Fomoria) weaveri group: E. (F.) festivitatis spec. nov. from mountains in Nepal, China (Yunnan) and northern Vietnam, feeding on shrubby Hypericum species, and E. (F.) degeeri spec. nov. from Turkey, food plant unknown. The species group

  8. Molecular phylogenetics of emydine turtles: taxonomic revision and the evolution of shell kinesis.

    Science.gov (United States)

    Feldman, Chris R; Parham, James Ford

    2002-03-01

    The 10 extant species of emydine turtles represent an array of morphological and ecological forms recognizable and popular among scientists and hobbyists. Nevertheless, the phylogenetic affinities of most emydines remain contentious. Here, we examine the evolutionary relationships of emydine turtles using 2092 bp of DNA encoding the mitochondrial genes cyt b, ND4, and adjacent tRNAs. These data contain 339 parsimony informative characters that we use to erect hypotheses of relationships for the Emydinae. Both maximum parsimony and maximum likelihood methods yield a monophyletic Emydinae in which all but three nodes are well resolved. Emys orbicularis, Emydoidea blandingii, and Clemmys marmorata form a monophyletic clade, as do the species of Terrapene. Clemmys muhlenbergii and Clemmys insculpta form a third monophyletic group that may be sister to all other emydines. Clemmys guttata is problematic and probably related to Terrapene. Based on this phylogeny, and previous molecular work on the group, we suggest the following taxonomic revisions: (1) Clemmys should be restricted to a single species, C. guttata. (2) Calemys should be resurrected for C. muhlenbergii and C. insculpta. (3) Emys should be expanded to include three species: E. orbicularis, E. blandingii, and E. marmorata. Furthermore, our analyses show that neither kinetic-shelled nor akinetic-shelled emydines form monophyletic groups. Therefore, shell kinesis was either independently gained in Emys and Terrapene or secondarily lost in E. marmorata and C. guttata. Parsimony, paleontological evidence, and the multiple origins of shell kinesis in related turtle lineages (especially geoemydines) support the independent origin of plastral kinesis.

  9. Is morphology in Cercospora a reliable reflection of generic affinity?

    NARCIS (Netherlands)

    Bakhshi, Mounes; Arzanlou, Mahdi; Babai-Ahari, Asadollah; Groenewald, Johannes Z.; Crous, Pedro W.

    2015-01-01

    Cercospora (Mycosphaerellaceae) is a large genus of fungi comprising many important plant pathogens. In recent years DNA-based studies have revealed multiple genera of cercosporoid fungi being poly- and paraphyletic. Among these genera, the genus Cercospora has always been perceived as monophyletic.

  10. Molecular data from the chloroplast rpoC1 gene suggest a deep and distinct dichotomy of contemporary spermatophytes into two monophyla: gymnosperms (including Gnetales) and angiosperms.

    Science.gov (United States)

    Samigullin, T K; Martin, W F; Troitsky, A V; Antonov, A S

    1999-09-01

    Partial sequences of the rpoC1 gene from two species of angiosperms and three species of gymnosperms (8330 base pairs) were determined and compared. The data obtained support the hypothesis that angiosperms and gymnosperms are monophyletic and none of the recent groups of the latter is sister to angiosperms.

  11. Resurrection of the genus Aphyllon for New World broomrapes (Orobanche s.l., Orobanchaceae).

    Science.gov (United States)

    Schneider, Adam C

    2016-01-01

    Recent phylogenetic studies support a monophyletic clade of New World broomrapes (Orobanche sects. Gymnocaulis and Nothaphyllon) sister to the Old World genus Phelipanche. I place the New World taxa in the genus Aphyllon, propose 21 new combinations, and provide a list of currently accepted taxa.

  12. Convergent coevolution in the domestication of coral mushrooms by fungus-growing ants

    DEFF Research Database (Denmark)

    Munkacsi, A B; Pan, J J; Villesen, Palle

    2004-01-01

    of parallel coevolution, where the symbionts of each functional group are members of monophyletic groups. However, there is one outstanding exception in the fungus-growing ant system, the unidentified cultivar grown only by ants in the Apterostigma pilosum group. We classify this cultivar in the coral...

  13. A taxonomic revision of the Asian keelback snakes, genus Amphiesma (Serpentes: Colubridae: Natricinae), with description of a new species.

    Science.gov (United States)

    Guo, Peng; Zhu, Fei; Liu, Qin; Zhang, Liang; Li, Jian X; Huang, Yu Y; Pyron, R Alexander

    2014-01-01

    The Asian keelback snakes (genus Amphiesma) are a widely distributed group of Old World natricines, inhabiting a variety of niches and exhibiting significant morphological variation. Recent molecular phylogenies suggest that this genus is not monophyletic, and that additional cryptic diversity is also likely present. We conducted a phylogenetic analysis of the group based on 3162 bp of one mitochondrial gene (Cyt. b) and three nuclear genes (C-mos, Rag1, NT3), sampling 18 species in addition to those sequenced in previous works. All analyses consistently show that Amphiesma consists of three distinct, monophyletic lineages with strong support. We divide Amphiesma into three genera, Amphiesma, Hebius, and Herpetoreas. The genus Amphiesma is monotypic, Herpetoreas contains three species, and Hebius comprises the remaining 39 species. On the basis of a combination of molecular analyses and external morphological comparisons, we describe a new species in the Herpetoreas group from China as H. burbrinki sp. nov. Several other species are shown to be non-monophyletic or contain significant levels of intraspecific genetic diversity. Another Old World natricine genera, Xenochrophis is also found to be non-monophyletic. Our results indicate that further taxonomic revisions are needed in Natricinae, at multiple levels. 

  14. Towards a phylogenetic classification of dendrocoelid freshwater planarians (Platyhelminthes): a morphological and eclectic approach

    NARCIS (Netherlands)

    Sluys, R.; Kawakatsu, M.

    2006-01-01

    We explore and review the taxonomic distribution of morphological features that may be used as supporting apomorphies for the monophyletic status of various taxa in future, more comprehensive phylogenetic analyses of the dendrocoelid freshwater planarians and their close relatives. Characters examin

  15. The phyletic status of the genus Planaria (Platyhelminthes, Turbellaria, Tricladida)

    NARCIS (Netherlands)

    Ball, Ian R.; Gourbault, Nicole

    1978-01-01

    The amphiatlantic distribution of the genus Planaria is incompatible with our current hypothesis of the historical biogeography of freshwater planarians. New anatomical studies suggest the possibility that the genus is not strictly monophyletic; new karyological data are strongly corroborative of th

  16. Catalogue of the remains of marine carnivora in the collection of the Institute of Taxonomic Zoology, University of Amsterdam (Zoological Museum Amsterdam)

    NARCIS (Netherlands)

    NN,

    1988-01-01

    As is usual in university museums, the Zoological Museum of the University of Amsterdam (now Institute of Taxonomic Zoology) had in its collection some representative material of marine Carnivora (Pinnipedia, at the time it was believed that the animals belonged to a monophyletic taxon). Some

  17. Molecular phylogeny of the Thyropygus allevatus group of giant millipedes and some closely related groups

    DEFF Research Database (Denmark)

    Pimvichai, P.; Enghoff, Henrik; Panha, S.

    2013-01-01

    from six genera in the subfamilies Harpagophorinae and Rhynchoproctinae, as well as nine new morphotypes (regarded as new species), were performed with the DNA sequences from two mitochondrial gene fragments (16S rRNA and COI). The genus Thyropygus (Harpagophorinae) was recovered as monophyletic under...

  18. Ribbon worm relationships: a phylogeny of the phylum Nemertea.

    Science.gov (United States)

    Thollesson, Mikael; Norenburg, Jon L

    2003-02-22

    We present the most extensive phylogenetic analysis to date, to our knowledge, of higher-level nemertean relationships, based on sequence data from four different genes (the nuclear genes for nuclear large subunit rRNA (28S rRNA) and histone H3 (H3), and the mitochondrial genes for mitochondrial large subunit rRNA (16S rRNA) and cytochrome c oxidase subunit I (COI)). Well-supported clades are, in general, compatible with earlier, more limited, analyses, and current classification is largely in agreement with our results, although there are some notable exceptions. Bdellonemertea (represented by Malacobdella) is found to be a part of Monostilifera, and Polystilifera is the monophyletic sister group to Monostilifera. Cratenemertidae is the sister group to the remaining monostiliferans (including Malacobdella), a group to which we apply the new name Distromatonemertea. Heteronemertea is monophyletic and forms a clade with Hubrechtella; for this clade we introduce the name Pilidiophora. Finally, Pilidiophora and Hoplonemertea (with Malacobdella) form a monophyletic group, and we introduce the name Neonemertea to refer to this group. Palaeonemertea is found to be non-monophyletic and basal among nemerteans.

  19. Molecular phylogeny of the subfamily Stevardiinae Gill, 1858 (Characiformes: Characidae): classification and the evolution of reproductive traits.

    Science.gov (United States)

    Thomaz, Andréa T; Arcila, Dahiana; Ortí, Guillermo; Malabarba, Luiz R

    2015-07-21

    The subfamily Stevardiinae is a diverse and widely distributed clade of freshwater fishes from South and Central America, commonly known as "tetras" (Characidae). The group was named "clade A" when first proposed as a monophyletic unit of Characidae and later designated as a subfamily. Stevardiinae includes 48 genera and around 310 valid species with many species presenting inseminating reproductive strategy. No global hypothesis of relationships is available for this group and currently many genera are listed as incertae sedis or are suspected to be non-monophyletic. We present a molecular phylogeny with the largest number of stevardiine species analyzed so far, including 355 samples representing 153 putative species distributed in 32 genera, to test the group's monophyly and internal relationships. The phylogeny was inferred using DNA sequence data from seven gene fragments (mtDNA: 12S, 16S and COI; nuclear: RAG1, RAG2, MYH6 and PTR). The results support the Stevardiinae as a monophyletic group and a detailed hypothesis of the internal relationships for this subfamily. A revised classification based on the molecular phylogeny is proposed that includes seven tribes and also defines monophyletic genera, including a resurrected genus Eretmobrycon, and new definitions for Diapoma, Hemibrycon, Bryconamericus sensu stricto, and Knodus sensu stricto, placing some small genera as junior synonyms. Inseminating species are distributed in several clades suggesting that reproductive strategy is evolutionarily labile in this group of fishes.

  20. A new classification of Chelicerata

    NARCIS (Netherlands)

    Hammen, van der L.

    1977-01-01

    Progress in classification of Chelicerata has been thwarted especially by two factors, viz., the concept of mites as one monophyletic group, and the opinion that this group consists of species with a highly modified plan of construction and without any trace of true segmentation. The only characters

  1. Revision der Gattung Orophea Blume (Annonaceae)

    NARCIS (Netherlands)

    Keßler, P.J.A.

    1988-01-01

    The genus Orophea Blume (Annonaceae: Saccopetaleae) has been revised with the following main results: — The genus in the circumscription of most authors is not monophyletic, but biphyletic. The genus Mezzettiopsis Ridley has to be reinstated. — Pseuduvaria, Mitrephora, Petalolophus, Oreomitra, Schef

  2. Re-examining the phylogeny of clinically relevant Candida species and allied genera based on multigene analyses

    NARCIS (Netherlands)

    Tsui, Clement K M; Daniel, Heide-Marie; Robert, Vincent; Meyer, Wieland

    Yeasts of the artificial genus Candida include plant endophytes, insect symbionts, and opportunistic human pathogens. Phylogenies based on rRNA gene and actin sequences confirmed that the genus is not monophyletic, and the relationships among Candida species and allied teleomorph genera are not

  3. Phylogeny of minute carabid beetles and their relatives based upon DNA sequence data (Coleoptera, Carabidae, Trechitae)

    Science.gov (United States)

    Maddison, David R.; Ober, Karen A.

    2011-01-01

    Abstract The phylogeny of ground beetles of supertribe Trechitae is inferred using DNA sequences of genes that code for 28S ribosomal RNA, 18S ribosomal RNA, and wingless. Within the outgroups, austral psydrines are inferred to be monophyletic, and separate from the three genera of true Psydrina (Psydrus, Nomius, Laccocenus); the austral psydrines are formally removed from Psydrini and are treated herein as their own tribe, Moriomorphini Sloane. All three genes place Gehringia with Psydrina. Trechitae is inferred to be monophyletic, and sister to Patrobini. Within trechites, evidence is presented that Tasmanitachoides is not a tachyine, but is instead a member of Trechini. Perileptus is a member of subtribe Trechodina. Against Erwin’s hypothesis of anillines as a polyphyletic lineage derived from the tachyine genus Paratachys, the anillines sampled are monophyletic, and not related to Paratachys. Zolini, Pogonini, Tachyina, and Xystosomina are all monophyletic, with the latter two being sister groups. The relationships of the subtribe Bembidiina were studied in greater detail. Phrypeus is only distantly related to Bembidion, and there is no evidence from sequence data that it belongs within Bembidiina. Three groups that have been recently considered to be outside of the large genus Bembidion are shown to be derived members of Bembidion, related to subgroups: Cillenus is related to the Ocydromus complex of Bembidion, Zecillenus is related to the New Zealand subgenus Zeplataphus, and Hydrium is close to subgenus Metallina. The relationships among major lineages of Trechitae are not, however, resolved with these data. PMID:22379388

  4. A Plastid Gene Phylogeny of the Yam Genus, Dioscorea: Roots, Fruits and Madagascar

    NARCIS (Netherlands)

    Wilkin, P.; Schols, P.; Chase, M.; Chayamarit, K.; Furness, C.; Huysmans, S.; Rakotonasolo, F.; Smets, E.; Thapyai, C.

    2005-01-01

    Following recent phylogenetic studies of the families and genera of Dioscoreales, the identification of monophyletic infrageneric taxa in the pantropical genus Dioscorea is a priority. A phylogenetic analysis based on sequence data from the plastid genes rbcL and matK is presented, using 67 species

  5. Introduction and synthesis: plant phylogeny and the origin of major biomes

    NARCIS (Netherlands)

    Pennington, R.T.; Cronk, Q.C.B.; Richardson, J.E.

    2004-01-01

    Phylogenetic trees based upon DNA sequence data, when calibrated with a dimension of time, allow inference of: (i) the pattern of accumulation of lineages through time; (ii) the time of origin of monophyletic groups; (iii) when lineages arrived in different geographical areas; (iv) the time of origi

  6. Systematics and Population Genetics of a Phylogenetic Species Within the Fusarium solani Species Complex Associated with Human Infections

    Science.gov (United States)

    The Fusarium solani species complex (FSSC) is a monophyletic group comprising dozens of phylogenetic and biological species, and represents the most common species complex associated with fusarial infections of mammals, particularly mycotic keratitis. Previous work found that approximately 75% of k...

  7. Phylogenetic relationships of the triclads (Platyhelminthes, Seriata, Tricladida)

    NARCIS (Netherlands)

    Sluys, Ronald

    1989-01-01

    1. A phylogenetic hypothesis for the triclads is presented and the characters on which it is based are discussed. 2. The sister group of the Tricladida is formed by the Bothrioplanida, and together the two taxa share a sistergroup relationship with the Proseriata. 3. The monophyletic status of the

  8. Book Chapter Title: Entomophthoromycota: a new overview of some of the oldest terrestrial fungi

    Science.gov (United States)

    The Entomophthoromycota is a newly described fungal phylum comprising what seem to be the oldest of all extant terrestrial (nonflagellate) fungi. These fungi, formerly treated in the now rejected Zygomycota, form a monophyletic group that is genetically, morphologically, developmentally, and biologi...

  9. A website for all angiosperm families – http://www.mobot.org/mobot/research/apweb/

    NARCIS (Netherlands)

    Stevens, P.F.

    2002-01-01

    Currently both those teaching and those learning about phylogenies face a variety of problems. There are several systems to chose from, yet there is no explicitly phylogenetic system (in the sense of recognizing only strictly monophyletic groups) where all those groups are described. Conventional fa

  10. Re-Evaluation of Morphological Characters Questions Current Views of Pinniped Origins

    Directory of Open Access Journals (Sweden)

    Koretsky I. A.

    2016-08-01

    Full Text Available The origin of pinnipeds has been a contentious issue, with opposite sides debating monophyly or diphyly. This review uses evidence from the fossil record, combined with comparative morphology, molecular and cytogenetic investigations to evaluate the evolutionary history and phylogenetic relationships of living and fossil otarioid and phocoid pinnipeds. Molecular investigations support a monophyletic origin of pinnipeds, but disregard vital morphological data. Likewise, morphological studies support diphyly, but overlook molecular analyses. This review will demonstrate that a monophyletic origin of pinnipeds should not be completely accepted, as is the current ideology, and a diphyletic origin remains viable due to morphological and paleobiological analyses. Critical examination of certain characters, used by supporters of pinniped monophyly, reveals different polarities, variability, or simply convergence. The paleontological record and our morphological analysis of important characters supports a diphyletic origin of pinnipeds, with otarioids likely arising in the North Pacific from large, bear-like animals and phocids arising in the North Atlantic from smaller, otter-like ancestors. Although members of both groups are known by Late Oligocene time, each developed and invaded the aquatic environment separately from their much earlier, common arctoid ancestor. Therefore, we treat the superfamily Otarioidea as being monophyletic, including the families Enaliarctidae, Otariidae (fur seals/sea lions, Desmatophocidae, and Odobenidae (walruses and extinct relatives, and the superfamily Phocoidea as monophyletic, including only the family Phocidae, with four subfamilies (Devinophocinae, Phocinae, Monachinae, and Cystophorinae.

  11. Phylogeography and conservation genetics of the Caribbean Zamia clade: an integrated systematic approach with SSRs and single copy nuclear genes

    Science.gov (United States)

    The Zamia pumila L. complex (Cycadales: Zamiaceae) is a monophyletic, diploid (2n = 16) and distinctive assemblage of cycad populations restricted to the West Indies and southeastern U. S. that has been treated as comprising one to nine species. Our research project seeks to simultaneously investi...

  12. Description of the mature larva of Ampulicomorpha schajovskoyi De Santis & Vidal Sarmiento (Hymenoptera: Embolemidae).

    Science.gov (United States)

    Guglielmino, Adalgisa; Bückle, Christoph

    2013-01-01

    The mature larva of Ampulicomorpha schajovskoyi De Santis & Vidal Sarmiento, 1977, is described and figured for the first time. Larval characters of Dryinidae and Embolemidae are discussed in regard to possible synapomorphies of each family and of both families together (Dryinidae + Embolemidae) as monophyletic groups. Some larval characters are compared with the corresponding conditions in other Chrysidoidea families.

  13. A large phylogeny of turtles (Testudines) using molecular data

    NARCIS (Netherlands)

    Guillon, J.-M.; Guéry, L.; Hulin, V.; Girondot, M.

    2012-01-01

    Turtles (Testudines) form a monophyletic group with a highly distinctive body plan. The taxonomy and phylogeny of turtles are still under discussion, at least for some clades. Whereas in most previous studies, only a few species or genera were considered, we here use an extensive compilation of DNA

  14. Introduction and synthesis: plant phylogeny and the origin of major biomes

    NARCIS (Netherlands)

    Pennington, R.T.; Cronk, Q.C.B.; Richardson, J.E.

    2004-01-01

    Phylogenetic trees based upon DNA sequence data, when calibrated with a dimension of time, allow inference of: (i) the pattern of accumulation of lineages through time; (ii) the time of origin of monophyletic groups; (iii) when lineages arrived in different geographical areas; (iv) the time of origi

  15. Bacterial-induced calcium oscillations are common to nitrogen-fixing associations of nodulating legumes and non-legumes

    NARCIS (Netherlands)

    Granqvist, E.; Sun, J.; Camp, Op den R.; Pujic, P.; Hill, L.; Normand, P.; Morris, R.J.; Downie, J.A.; Geurts, R.; Oldroyd, G.E.D.

    2015-01-01

    •Plants that form root-nodule symbioses are within a monophyletic ‘nitrogen-fixing’ clade and associated signalling processes are shared with the arbuscular mycorrhizal symbiosis. Central to symbiotic signalling are nuclear-associated oscillations in calcium ions (Ca2+), occurring in the root hairs

  16. Phylogeny of minute carabid beetles and their relatives based upon DNA sequence data (Coleoptera, Carabidae, Trechitae

    Directory of Open Access Journals (Sweden)

    David Maddison

    2011-11-01

    Full Text Available The phylogeny of ground beetles of supertribe Trechitae is inferred using DNA sequences of genes that code for 28S ribosomal RNA, 18S ribosomal RNA, and wingless. Within the outgroups, austral psydrines are inferred to be monophyletic, and separate from the three genera of true Psydrina (Psydrus, Nomius, Laccocenus; the austral psydrines are formally removed from Psydrini and are treated herein as their own tribe, Moriomorphini Sloane. All three genes place Gehringia with Psydrina. Trechitae is inferred to be monophyletic, and sister to Patrobini.Within trechites, evidence is presented that Tasmanitachoides is not a tachyine, but is instead a member of Trechini. Perileptus is a member of subtribe Trechodina. Against Erwin’s hypothesis of anillines as a polyphyletic lineage derived from the tachyine genus Paratachys, the anillines sampled are monophyletic, and not related to Paratachys. Zolini, Pogonini, Tachyina, and Xystosomina are all monophyletic, with the latter two being sister groups. The relationships of the subtribe Bembidiina were studied in greater detail. Phrypeus is only distantly related to Bembidion, and there is no evidence from sequence data that it belongs within Bembidiina. Three groups that have been recently considered to be outside of the large genus Bembidion are shown to be derived members of Bembidion, related to subgroups: Cillenus is related to the Ocydromus complex of Bembidion, Zecillenus is related to the New Zealand subgenus Zeplataphus, and Hydrium is close to subgenus Metallina. The relationships among major lineages of Trechitae are not, however, resolved with these data.

  17. The deep phylogeny of jumping spiders (Araneae, Salticidae

    Directory of Open Access Journals (Sweden)

    Wayne Maddison

    2014-09-01

    Full Text Available In order to resolve better the deep relationships among salticid spiders, we compiled and analyzed a molecular dataset of 169 salticid taxa (and 7 outgroups and 8 gene regions. This dataset adds many new taxa to previous analyses, especially among the non-salticoid salticids, as well as two new genes – wingless and myosin heavy chain. Both of these genes, and especially the better sampled wingless, confirm many of the relationships indicated by other genes. The cocalodines are placed as sister to lapsiines, in a broader clade with the spartaeines. Cocalodines, lapsiines, and spartaeines are each supported as monophyletic, though the first two have no known morphological synapomorphies. The lyssomanines appear to be non-monophyletic, of three separate groups: (1 Lyssomanes plus Chinoscopus, (2 Onomastus, and (3 the remainder of Old World species. Several previously-inferred relationships continue to be supported: hisponines as sister to the Salticoida, Amycoida as sister to the remaining Salticoida, and Saltafresia as monophyletic. The relationship of Salticus with Philaeus and relatives is now considered well enough corroborated to move the latter into the subfamily Salticinae. A new clade consisting of the Plexippoida + Aelurilloida + Leptorchesteae + Salticinae is recognized. Nungia is found to be an astioid, and Echeclus, Gedea and Diplocanthopoda to be hasariines. The euophryines are corroborated as monophyletic. The agoriines Agorius and Synagelides are salticoids, within the sister group to amycoids, but their further placement is problematical, perhaps because of their nuclear ribosomal genes’ high GC bias, as also seen in the similarly problematic Eupoa.

  18. Introduction and synthesis: plant phylogeny and the origin of major biomes

    NARCIS (Netherlands)

    Pennington, R.T.; Cronk, Q.C.B.; Richardson, J.E.

    2004-01-01

    Phylogenetic trees based upon DNA sequence data, when calibrated with a dimension of time, allow inference of: (i) the pattern of accumulation of lineages through time; (ii) the time of origin of monophyletic groups; (iii) when lineages arrived in different geographical areas; (iv) the time of

  19. Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci

    DEFF Research Database (Denmark)

    Rasmusen, L. H.; Dargis, R.; Iversen, Katrine Højholt

    2016-01-01

    with infective endocarditis were whole genome sequenced. We compared the phylogenetic analyses based on single genes (recA, sodA, gdh), multigene (MLSA), SNPs, and core-genome sequences. The six phylogenetic analyses generally showed a similar pattern of six monophyletic clusters, though a few differences were...

  20. Identifying the transition between single and multiple mating of queens in fungus-growing ants

    DEFF Research Database (Denmark)

    Villesen, Palle; Murakami, Takahiro; Schultz, Ted R

    2002-01-01

    Obligate mating of females (queens) with multiple males has evolved only rarely in social Hymenoptera (ants, social bees, social wasps) and for reasons that are fundamentally different from those underlying multiple mating in other animals. The monophyletic tribe of ('attine') fungus-growing ants...

  1. Comments on Greguss’s phylogenetical tree of plants

    NARCIS (Netherlands)

    Lam, H.J.

    1957-01-01

    Recently (1955) I have published a new version of a phylogenetical tree of the Cormophyta, based on morphology, mainly ramification, leaf types, and sporangia. The concept is monophyletic but its basis is strewn with so many queries that the way is open to a number of different opinions. I add a

  2. Molecular phylogenetic study at the generic boundary between the lichen-forming fungi Caloplaca and Xanthoria (Ascomycota, Teloschistaceae)

    DEFF Research Database (Denmark)

    Søchting, Ulrik; Lutzoni, François

    2003-01-01

    A molecular phylogenetic analysis of rDNA was performed for seven Caloplaca, seven Xanthoria, one Fulgensia and five outgroup species. Phylogenetic hypotheses are constructed based on nuclear small and large subunit rDNA, separately and in combination. Three strongly supported major monophyletic...

  3. Taxonomy and phylogeny of the Caloplaca cerina group in Europe

    DEFF Research Database (Denmark)

    Soun, J.; Vondrak, J.; Sochting, U.

    2011-01-01

    Using ITS nrDNA sequence data, the Caloplaca cerina group (Teloschistaceae) is defined here as a monophyletic, but internally richly branched lineage. The group is also characterized by a combination of morphological and anatomical characters. Its internal lineages are supported by phenotypic...

  4. Molecular phylogeny of the Bothriocephalidea (Cestoda): molecular data challenge morphological classification.

    Science.gov (United States)

    Brabec, Jan; Waeschenbach, Andrea; Scholz, Tomáš; Littlewood, D Timothy J; Kuchta, Roman

    2015-10-01

    In this study, the relationships of the cestode order Bothriocephalidea, parasites of marine and freshwater bony fish, were assessed using multi-gene molecular phylogenetic analyses. The dataset included 59 species, covering approximately 70% of currently recognised genera, a sample of bothriocephalidean biodiversity gathered through an intense 15year effort. The order as currently circumscribed, while monophyletic, includes three non-monophyletic and one monophyletic families. Bothriocephalidae is monophyletic and forms the most derived lineage of the order, comprised of a single freshwater and several marine clades. Biogeographic patterns within the freshwater clade are indicative of past radiations having occurred in Africa and North America. The earliest diverging lineages of the order comprise a paraphyletic Triaenophoridae. The Echinophallidae, consisting nearly exclusively of parasites of pelagic fish, was also resolved as paraphyletic with respect to the Bothriocephalidae. Philobythoides sp., the only representative included from the Philobythiidae, a unique family of parasites of bathypelagic fish, was sister to the genus Eubothrium, the latter constituting one of the lineages of the paraphyletic Triaenophoridae. Due to the weak statistical support for most of the basal nodes of the Triaenophoridae and Echinophallidae, as well as the lack of obvious morphological synapomorphies shared by taxa belonging to the statistically well-supported lineages, the current family-level classification, although mostly non-monophyletic, is provisionally retained, with the exception of the family Philobythiidae, which is recognised as a synonym of the Triaenophoridae. In addition, Schyzocotyle is resurrected to accommodate the invasive Asian fish tapeworm, Schyzocotyle acheilognathi (Yamaguti, 1934) n. comb. (syn. Bothriocephalus acheilognathi Yamaguti, 1934), which is of veterinary importance, and Schyzocotyle nayarensis (Malhotra, 1983) n. comb. (syn. Ptychobothrium

  5. Phylogeny and evolution of Perezia (Asteraceae: Mutisieae: Nassauviinae)

    Institute of Scientific and Technical Information of China (English)

    Beryl B. SIMPSON; Mary T. K. ARROYO; Sandra SIPE; Marta DIAS de MORAES; Joshua McDILL

    2009-01-01

    A molecular phylogenetic analysis of most of the species of Perezia reveals that, as traditionally defined, the genus is not monophyletic with two species more closely related to Nassauvia than to Perezia. In addition, our results show that Burkartia (Perezia) lanigera is related to Acourtia and is the only member of that clade in South America. The remaining species are monophyletic and show a pattern of an early split between a western temperate and an eastern subtropical clade of species. Within the western clade, the phylogeny indicates a pattern of diversification that proceeded from southern, comparatively low-elevation habitats to southern high-elevation habitats, and ultimately into more northern high-elevation habitats. The most derived clades are found in the high central Andes, where significant radiation has occurred.

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

    Science.gov (United States)

    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.

  7. Phylogenetic relationships of the Culicomorpha inferred from 18S and 5.8S ribosomal DNA sequences. (Diptera:Nematocera).

    Science.gov (United States)

    Miller, B R; Crabtree, M B; Savage, H M

    1997-05-01

    We investigated the evolutionary origins of the mosquito family Culicidae by examination of 18S and 5.8S ribosomal gene sequence divergence. Phylogenetic analyses demonstrated that within the infraorder Culicomorpha, taxa in the families Corethrellidae, Chaoboridae and Culicidae formed a monophyletic group; there was support for a sister relationship between this lineage and a representative of the Chironomidae. A chaoborid midge was the closest relative of the mosquitoes. Taxa from four genera of mosquitoes formed a monophyletic group; lack of a spacer in the 5.8S gene was unique to members of the Culicidae. A member of the genus Anopheles formed the most basal lineage among the mosquitoes analysed. Phylogenetic relationships were unresolved for representatives in the families Dixidae, Simuliidae and Ceratopogonidae.

  8. The microsoroid ferns: Inferring the relationships of a highly diverse lineage of Paleotropical epiphytic ferns (Polypodiaceae, Polypodiopsida).

    Science.gov (United States)

    Kreier, Hans-Peter; Zhang, Xian-Chun; Muth, Heiko; Schneider, Harald

    2008-09-01

    The relationships of the microsoroid ferns were studied using a DNA sequence-based phylogenetic approach. Nucleotide sequences for up to four chloroplast genome regions were assembled for 107 samples from 87 species. Microsoroids s.l. include six lineages of which two are species rich. The results indicate that several genera are not monophyletic (e.g. Microsorum), several controversial genera are confirmed to be monophyletic (e.g. Leptochilus), and some genera new to science should be recognized (M. membranaceum clade). Unique insights were gained into the biogeographic history of this highly diverse epiphytic vascular plant lineage that is widespread in continental Asia to Australasia. Evidence was found for splits into lineages diversifying in parallel in continental Asia and Malesia. No evidence was recovered for an African radiation because all African microsoroid species either also are found in Asia or have sister species in continental Asia. In contrast, evidence for independent radiations were discovered for the Australasian region.

  9. Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.

    Science.gov (United States)

    Breider, Sven; Scheuner, Carmen; Schumann, Peter; Fiebig, Anne; Petersen, Jörn; Pradella, Silke; Klenk, Hans-Peter; Brinkhoff, Thorsten; Göker, Markus

    2014-01-01

    Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.

  10. Phylogenetic relationships within the lophophorate lineages (Ectoprocta, Brachiopoda and Phoronida).

    Science.gov (United States)

    Hausdorf, Bernhard; Helmkampf, Martin; Nesnidal, Maximilian P; Bruchhaus, Iris

    2010-06-01

    We produced two new EST datasets of so far uncovered clades of ectoprocts to investigate the phylogenetic relationships within the lophophorate lineages, Ectoprocta, Brachiopoda and Phoronida. Maximum-likelihood analyses based on 78 ribosomal proteins of 62 metazoan taxa support the monophyly of Ectoprocta and a sister group relationship of Phylactolaemata living in freshwater and the mainly marine Gymnolaemata. Hypotheses suggesting that Ectoprocta is diphyletic with phylactolaemates forming a clade with phoronids or paraphyletic with respect to Entoprocta could be rejected by topology tests. The hypotheses that Stenolaemata are the sister group of all other ectoprocts, that Stenolaemata constitutes a monophyletic group with Cheilostomata, and that Phylactolaemata have been derived from Ctenostomata could also be excluded. However, the hypothesis that Phylactolaemata and Stenolaemata form a monophyletic group could not be rejected. Brachiopoda and Phoronida constitute a monophylum, Brachiozoa. The hypotheses that phoronids are the sister group of articulate or inarticulate brachiopods could be rejected by topology tests, thus confirming the monophyly of Brachiopoda.

  11. Phylogeny and biogeography of Triportheidae (Teleostei: Characiformes) based on molecular data.

    Science.gov (United States)

    Mariguela, T C; Roxo, F F; Foresti, F; Oliveira, C

    2016-03-01

    Triportheidae represents a relatively small family of characiform fishes with highly modified morphology. The relationship among characiform families is still unclear, and a phylogenetic analysis for the family including a representative number of Triportheus species has never been performed. Here, we inferred a phylogeny for 19 of the 22 species recognized for this family and two possible new Triportheus species using two mitochondrial and three nuclear genes. Our results show that (1) Triportheidae is monophyletic and a sister group of the clade consisting of the families Bryconidae and Gasteropelecidae; (2) Triportheus is monophyletic, but some species need to be reviewed and described; (3) all genera in Triportheidae, except for Agoniates originated in the period between Early Oligocene and Early Miocene; and (4) speciation in Triportheidae coincides with important geological events in South America, reinforcing the importance of time-calibrated trees to study fish evolution. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Phylogeny of higher taxa of hexapoda according to 12sRNA sequences

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The phylogenetic relationship of Hexapoda has been debated for a long time, which will be resolved mainly depending on the settlement of monophyly, affinities and interrelationships among Protura, Collembola and Diplura. Mitochondrial 12sRNA gene about 355 bp fragments from one proturan species, two collembolan species, two dipluran species and one oribatid species were sequenced. The Kimura 2-parameter distances were calculated and a series of molecular phylogenetic trees were reconstructed by using the N-J method, from which the following points were drawn: (ⅰ) Protura and Collembola compose a monophyletic group representing absent-cerci; (ⅱ) Diplura is not a monophyletic group, in which Campodeoid with filiform cerci belongs to a clade and Japygoid with pincer cerci and Ectognatha com-pose another clade, that is, Insecta s. str. stemmed from Japygoid. So it would be suggested that the phylogenetic relationship of Hexapoda is [Parainsecta (Collembola + Pro-tura) +Campodeoid +Insecta (Japygoid + Ectognatha)].

  13. Phylogenetic position of Dysteria derouxi (Ciliophora:Phyllopharyngea: Dysteriida) inferred from the small subunit ribosomal RNA gene sequence

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The complete small subunit rRNA (SSrRNA) gene sequence of a marine ciliate, Dysteria derouxi Gong and Song, 2004, was determined to be of 1 708 nucleotides. The phylogenetic position of this species within the class Phyllopharyngea was deduced using distance matrix, maximum parsimony and maximum likelihood methods. Dysteria derouxi, together with other available ciliates of the class Phyllopharyngea, forms a monophyletic clade with strong bootstrap support in the distance matrix, maximum parsimony and likelihood tree construction methods, while the dysterids are, as a monophyletic group, phylogenetically close to the clade of chlamydodontids [values of 100% LS(least-squares), 100% NJ(neighbor-joining)]. In addition, the trees indicate that dysteriids may be a higher or specialized group within the class, which corresponds well to the morphology and infraciliature.

  14. Phylogenetic relationship of Podocopida (Ostracoda: Podocopa) based on 18S ribosomal DNA sequences

    Institute of Scientific and Technical Information of China (English)

    YU Na; ZHAO Meiying; CHEN Liqiao; YANG Pin

    2006-01-01

    Nucleotide sequences from 18S rDNA of 11 ostracodes, which represent four suborders and six superfamilies ofpodocopidan, were determined. The phylogenetic relationships were analyzed based on three kinds of methods (maximum-likelihood, maximum-parsimony,and neighbor-joining), and the three topologies gained were basically similar. The results have showed that (1) a monophyletic Podocopida was supported strongly; (2) the phylogenetic relationships of four suborders were (Darwinulocopina plus (Bairdiocopina plus (Cytherocopina plus Cypridocopina))), which indicated that a close relationship between Cytherocopina and Cypridocopina, and Darwinulocopina had separated early from the main podocopinan; (3) Cypridocopinan formed a monophyletic group, among which the phylogenetic relationship of three superfamilies was (Cypridoidea plus (Macrocypridoidea plus Pontocypridoidea)).

  15. Phylogenetic relationships of Loxosceles and Sicarius spiders are consistent with Western Gondwanan vicariance.

    Science.gov (United States)

    Binford, Greta J; Callahan, Melissa S; Bodner, Melissa R; Rynerson, Melody R; Núñez, Pablo Berea; Ellison, Christopher E; Duncan, Rebecca P

    2008-11-01

    The modern geographic distribution of the spider family Sicariidae is consistent with an evolutionary origin on Western Gondwana. Both sicariid genera, Loxosceles and Sicarius are diverse in Africa and South/Central America. Loxosceles are also diverse in North America and the West Indies, and have species described from Mediterranean Europe and China. We tested vicariance hypotheses using molecular phylogenetics and molecular dating analyses of 28S, COI, 16S, and NADHI sequences. We recover reciprocal monophyly of African and South American Sicarius, paraphyletic Southern African Loxosceles and monophyletic New World Loxosceles within which an Old World species group that includes L. rufescens is derived. These patterns are consistent with a sicariid common ancestor on Western Gondwana. North American Loxosceles are monophyletic, sister to Caribbean taxa, and resolved in a larger clade with South American Loxosceles. With fossil data this pattern is consistent with colonization of North America via a land bridge predating the modern Isthmus of Panama.

  16. DNA barcoding Satyrine butterflies (Lepidoptera: Nymphalidae) in China.

    Science.gov (United States)

    Yang, Mingsheng; Zhai, Qing; Yang, Zhaofu; Zhang, Yalin

    2016-07-01

    We investigated the effectiveness of the standard 648 bp mitochondrial COI barcode region in discriminating among Satyrine species from China. A total of 214 COI sequences were obtained from 90 species, including 34 species that have never been barcoded. Analyses of genetic divergence show that the mean interspecific genetic divergence is about 16-fold higher than within species, and little overlap occurs between them. Neighbour-joining (NJ) analyses showed that 48 of the 50 species with two or more individuals, including two cases with deep intraspecific divergence (>3%), are monophyletic. Furthermore, when our sequences are combined with the conspecific sequences sampled from distantly geographic regions, the "barcoding gap" still exists, and all related species are recovered to be monophyletic in NJ analysis. Our study demonstrates that COI barcoding is effective in discriminating among the satyrine species of China, and provides a reference library for their future molecular identification.

  17. First data on the molecular phylogeography of scincid lizards of the genus Mabuya.

    Science.gov (United States)

    Mausfeld, P; Vences, M; Schmitz, A; Veith, M

    2000-10-01

    A 487-bp fragment of the mitochondrial 16S rRNA gene was sequenced in 26 species of the circumtropical lizard genus Mabuya and used to analyze phylogenetic relationships within the genus. The species from Africa and Madagascar formed a monophyletic group relative to the included Asian and South American taxa. The Malagasy species included (M. elegans, M. cf. dumasi, and M. comorensis) did not appear as a monophylum. Combined and separate analysis of the 16S data and additional sequences of the mitochondrial 12S rRNA, ND4, and cytochrome b genes (a total of 2255 bp) in one Asian, two Malagasy, and two African species also did not result consistently in a monophyletic grouping of the Malagasy taxa. However, a monophylum containing African and Malagasy taxa was strongly supported by the combined analysis. These preliminary results indicate that Mabuya probably colonized Madagascar from Africa through the Mozambique Channel.

  18. Relationships of scincid lizards (Mabuya spp; Reptilia: Scincidae) from the Cape Verde islands based on mitochondrial and nuclear DNA sequences.

    Science.gov (United States)

    Brehm, A; Jesus, J; Pinheiro, M; Harris, D J

    2001-05-01

    Partial DNA sequences from two mitochondrial (mt) and one nuclear gene (cytochrome b, 12S rRNA, and C-mos) were used to estimate the phylogenetic relationships among the six extant species of skinks endemic to the Cape Verde Archipelago. The species form a monophyletic unit, indicating a single colonization of the islands, probably from West Africa. Mabuya vaillanti and M. delalandii are sister taxa, as indicated by morphological characters. Mabuya fogoensis and M. stangeri are closely related, but the former is probably paraphyletic. Mabuya spinalis and M. salensis are also probably paraphyletic. Within species, samples from separate islands always form monophyletic groups. Some colonization events can be hypothesized, which are in line with the age of the islands. C-mos variation is concordant with the topology derived from mtDNA.

  19. Cladistic analysis of the genus Ebenus (Fabaceae-Hedysareae based on morphological data

    Directory of Open Access Journals (Sweden)

    Akram Kaveh

    2012-09-01

    Full Text Available In this study, cladistic analysis of characteristics morphological dataset using 21 characters for 26 taxa, including 19 taxa of Ebenus, 2 taxa of Taverniera, 2 taxa of Onobrychis and 2 taxa of Hedysarum as ingroups plus Alhagi persarum as an outgroup were chosen in phylogenetic analyses. Maximum parsimony approach as implemented in PAUP* with a heuristic search was employed. Fifty shortest trees with L=17.88 steps and a CI=0.709 and an RI=0.901 were generated. The analysis revealed that Ebenus was monophyletic. None of its multi-specific sections, Ebenidium and Euebenus, were monophyletic. E. cretica and E. stellata were basalmost branches that followed by a clade consisting of the remaining species. Onobrychis and Hedysarum were strongly allied with Ebenus.

  20. Taxonomic review and phylogenetic analysis of Enchodontoidei.

    Science.gov (United States)

    Silva, Hilda M A; Gallo, Valéria

    2011-06-01

    Enchodontoidei are extinct marine teleost fishes with a long temporal range and a wide geographic distribution. As there has been no comprehensive phylogenetic study of this taxon, we performed a parsimony analysis using a data matrix with 87 characters, 31 terminal taxa for ingroup, and three taxa for outgroup. The analysis produced 93 equally parsimonious trees (L = 437 steps; CI = 0. 24; RI = 0. 49). The topology of the majority rule consensus tree was: (Sardinioides + Hemisaurida + (Nardorex + (Atolvorator + (Protostomias + Yabrudichthys ) + (Apateopholis + (Serrilepis + (Halec + Phylactocephalus ) + (Cimolichthys + (Prionolepis + ( (Eurypholis + Saurorhamphus ) + (Enchodus + (Paleolycus + Parenchodus ))))))) + ( (Ichthyotringa + Apateodus ) + (Rharbichthys + (Trachinocephalus + ( (Apuliadercetis + Brazilodercetis ) + (Benthesikyme + (Cyranichthys + Robertichthys ) + (Dercetis + Ophidercetis )) + (Caudadercetis + (Pelargorhynchus + (Nardodercetis + (Rhynchodercetis + (Dercetoides + Hastichthys )))))). The group Enchodontoidei is not monophyletic. Dercetidae form a clade supported by the presence of very reduced neural spines and possess a new composition. Enchodontidae are monophyletic by the presence of middorsal scutes, and Rharbichthys was excluded. Halecidae possess a new composition, with the exclusion of Hemisaurida. This taxon and Nardorex are Aulopiformes incertae sedis.

  1. A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis.

    Science.gov (United States)

    Young, J M; Kuykendall, L D; Martínez-Romero, E; Kerr, A; Sawada, H

    2001-01-01

    Rhizobium, Agrobacterium and Allorhizobium are genera within the bacterial family Rhizobiaceae, together with Sinorhizobium. The species of Agrobacterium, Agrobacterium tumefaciens (syn. Agrobacterium radiobacter), Agrobacterium rhizogenes, Agrobacterium rubi and Agrobacterium vitis, together with Allorhizobium undicola, form a monophyletic group with all Rhizobium species, based on comparative 16S rDNA analyses. Agrobacterium is an artificial genus comprising plant-pathogenic species. The monophyletic nature of Agrobacterium, Allorhizobium and Rhizobium and their common phenotypic generic circumscription support their amalgamation into a single genus, Rhizobium. Agrobacterium tumefaciens was conserved as the type species of Agrobacterium, but the epithet radiobacter would take precedence as Rhizobium radiobacter in the revised genus. The proposed new combinations are Rhizobium radiobacter, Rhizobium rhizogenes, Rhizobium rubi, Rhizobium undicola and Rhizobium vitis.

  2. Two herpesviruses associated with disease in wild Atlantic loggerhead sea turtles (Caretta caretta).

    Science.gov (United States)

    Stacy, Brian A; Wellehan, James F X; Foley, Allen M; Coberley, Sadie S; Herbst, Lawrence H; Manire, Charles A; Garner, Michael M; Brookins, Milagros D; Childress, April L; Jacobson, Elliott R

    2008-01-01

    Herpesviruses are associated with lung-eye-trachea disease and gray patch disease in maricultured green turtles (Chelonia mydas) and with fibropapillomatosis in wild sea turtles of several species. With the exception fibropapillomatosis, no other diseases of wild sea turtles of any species have been associated with herpesviral infection. In the present study, six necropsied Atlantic loggerhead sea turtles (Caretta caretta) had gross and histological evidence of viral infection, including oral, respiratory, cutaneous, and genital lesions characterized by necrosis, ulceration, syncytial cell formation, and intranuclear inclusion bodies. Nested polymerase chain reaction targeting a conserved region of the herpesvirus DNA-dependent-DNA polymerase gene yielded two unique herpesviral sequences referred to as loggerhead genital-respiratory herpesvirus and loggerhead orocutaneous herpesvirus. Phylogenetic analyses indicate that these viruses are related to and are monophyletic with other chelonian herpesviruses within the subfamily alpha-herpesvirinae. We propose the genus Chelonivirus for this monophyletic group of chelonian herpesviruses.

  3. Rounding up the usual suspects: a standard target-gene approach for resolving the interfamilial phylogenetic relationships of ecribellate orb-weaving spiders with a new family-rank classification (Araneae, Araneoidea)

    DEFF Research Database (Denmark)

    Dimitrov, Dimitar; Benevidas, Ligia R.; Arnedo, Miquel A.;

    2017-01-01

    We test the limits of the spider superfamily Araneoidea and reconstruct its interfamilial relationships using standard molecular markers. The taxon sample (363 terminals) comprises for the first time representatives of all araneoid families, including the first molecular data of the family...... Synaphridae. We use the resulting phylogenetic framework to study web evolution in araneoids. Araneoidea is monophyletic and sister to Nicodamoidea rank. n. Orbiculariae are not monophyletic and also include the RTA clade, Oecobiidae and Hersiliidae. Deinopoidea is paraphyletic with respect to a lineage...... holarchaeids but the family remains diphyletic even if Holarchaea is considered an anapid. The orb-web is ancient, having evolved by the early Jurassic; a single origin of the orb with multiple “losses” is implied by our analyses. By the late Jurassic, the orb-web had already been transformed into different...

  4. Phylogenetic diversity of the Rickettsiae.

    Science.gov (United States)

    Weisburg, W G; Dobson, M E; Samuel, J E; Dasch, G A; Mallavia, L P; Baca, O; Mandelco, L; Sechrest, J E; Weiss, E; Woese, C R

    1989-08-01

    Small subunit rRNA sequences have been determined for representative strains of six species of the family Rickettsiaceae: Rickettsia rickettsii, Rickettsia prowazekii, Rickettsia typhi, Coxiella burnetii, Ehrlichia risticii, and Wolbachia persica. The relationships among these sequences and those of other eubacteria show that all members of the family Rickettsiaceae belong to the so-called purple bacterial phylum. The three representatives of the genus Rickettsia form a tight monophyletic cluster within the alpha subdivision of the purple bacteria. E. risticii also belongs to the alpha subdivision and shows a distant yet specific relationship to the genus Rickettsia. However, the family as a whole is not monophyletic, in that C. burnetii and W. persica are members of the gamma subdivision. The former appears to show a specific, but rather distant, relationship to the genus Legionella.

  5. Phylogenetic relationships in the Niviventer-Chiromyscus complex (Rodentia, Muridae inferred from molecular data, with description of a new species

    Directory of Open Access Journals (Sweden)

    Alexander Balakirev

    2014-11-01

    Full Text Available Based on molecular data for mitochondrial (Cyt b, COI and nuclear (IRBP, GHR genes, and morphological examinations of museum specimens, we examined diversity, species boundaries, and relationships within and between the murine genera Chiromyscus and Niviventer. Phylogenetic patterns recovered demonstrate that Niviventer sensu lato is not monophyletic but instead includes Chiromyscus chiropus, the only previously recognized species of Chiropus. To maintain the genera Niviventer and Chiropus as monophyletic lineages, the scope and definition of the genus Chiromyscus is revised to include at least three distinct species: Chiromyscus chiropus (the type species of Chiromyscus, C. langbianis (previously regarded as a species of Niviventer, and a new species, described in this paper under the name C. thomasi sp. n.

  6. Cladochytriales--a new order in Chytridiomycota.

    Science.gov (United States)

    Mozley-Standridge, Sharon E; Letcher, Peter M; Longcore, Joyce E; Porter, David; Simmons, D Rabern

    2009-04-01

    Recently, molecular and ultrastructural analyses have resulted in revised phylogenetic hypotheses in the phylum Chytridiomycota. The order Chytridiales, once considered monophyletic, has been subdivided into several new orders. However, the most recent analyses indicate that the emended Chytridiales is also polyphyletic. One monophyletic lineage in Chytridiales includes Cladochytrium, Nowakowskiella, and five other genera. Many of the chytrids in this clade have often been observed growing on decaying plant tissue and other cellulosic substrates from aquatic habitats and moist soils. In this study we analysed combined nu-rRNA gene sequences (partial SSU and LSU) of 30 isolates from North American aquatic and soil samples. Based on molecular monophyly and zoospore ultrastructure, we designate this clade as a new order, Cladochytriales, which includes four families: Cladochytriaceae, Nowakowskiellaceae, Septochytriaceae fam. nov., and Endochytriaceae.

  7. Establishing a community-wide DNA barcode library as a new tool for arctic research

    DEFF Research Database (Denmark)

    Wirta, Helena; Várkonyi, Gergely; Rasmussen, Claus

    2016-01-01

    DNA sequences offer powerful tools for describing the members and interactions of natural communities. In this study, we establish the to-date most comprehensive library of DNA barcodes for a terrestrial site, including all known macroscopic animals and vascular plants of an intensively studied......-based species inventories, derive a snapshot of faunal turnover in space and time and describe the abundance and phenology of species in the rapidly changing arctic environment. Overall, 403 terrestrial animal and 160 vascular plant species were recorded by morphology-based techniques. DNA barcodes (CO1......) offered high resolution in discriminating among the local animal taxa, with 92% of morphologically distinguishable taxa assigned to unique Barcode Index Numbers (BINs) and 93% to monophyletic clusters. For vascular plants, resolution was lower, with 54% of species forming monophyletic clusters based...

  8. Rapid Emergence of Highly Pathogenic Avian Influenza Subtypes from a Subtype H5N1 Hemagglutinin Variant.

    Science.gov (United States)

    de Vries, Erik; Guo, Hongbo; Dai, Meiling; Rottier, Peter J M; van Kuppeveld, Frank J M; de Haan, Cornelis A M

    2015-05-01

    In 2014, novel highly pathogenic avian influenza A H5N2, H5N5, H5N6, and H5N8 viruses caused outbreaks in Asia, Europe, and North America. The H5 genes of these viruses form a monophyletic group that evolved from a clade 2.3.4 H5N1 variant. This rapid emergence of new H5Nx combinations is unprecedented in the H5N1 evolutionary history.

  9. What do we know about the phylogeny of the Semi-Aquatic Bugs (Hemiptera: Heteroptera: Gerromorpha)?

    DEFF Research Database (Denmark)

    Damgaard, Jakob

    2012-01-01

    The present study summarizes knowledge about phylogenetic relationships of the heteropteran infraorder Gerromorpha. A phylogeny for all families and subfamilies, and for all genera but those assigned to the two most diverse families, Veliidae and Gerridae, is compiled from the many studies by the...... by the late Dr. Nils Moller Andersen. Comparisons with recently published studies, including DNA sequence data show that the superfamilies Hydrometroidea and Gerroidea, the family Veliidae, the subfamily Mesoveliinae, and the genera Mesovelia and Microvelia are probably not monophyletic...

  10. Degenerate mitochondria

    OpenAIRE

    van der Giezen, Mark; Tovar, Jorge

    2005-01-01

    Mitochondria are the main sites of biological energy generation in eukaryotes. These organelles are remnants of a bacterial endosymbiont that took up residence inside a host cell over 1,500 million years ago. Comparative genomics studies suggest that the mitochondrion is monophyletic in origin. Thus, the original mitochondrial endosymbiont has evolved independently in anaerobic and aerobic environments that are inhabited by diverse eukaryotic lineages. This process has resulted in a collectio...

  11. Taxonomy of the genus Passerina (Thymelaeaceae)

    OpenAIRE

    C. L. Bredenkamp; A. E. van Wyk

    2003-01-01

    Passerina L. is mainly a southern African genus, comprising 20 species and four subspecies. A few species occur along the Great Escarpment, two extend into Zimbabwe and Mozambique, but most are concentrated in the Cape Floristic Region. Palynological. macromorphological and anatomical evidence was used in the delimitation of the genus and its infrageneric taxa. A cladistic study supports Passerina as a monophyletic genus. A genus treatment, key to species and a full species treatment are give...

  12. The tropical African legume Scorodophloeus clade includes two undescribed Hymenostegia segregate genera and Micklethwaitia, a rare, monospecific genus from Mozambique

    DEFF Research Database (Denmark)

    Mackinder, B. A.; Saslis-Lagoudakis, H.; Wieringa, J. J.

    2013-01-01

    Legume subfamily Caesalpinioideae accommodates approximately 2250 species in 171 genera which traditionally are placed in four tribes: Caesalpinieae, Cassieae, Cercideae and Detarieae. The monophyletic tribe Detarieae includes the Amherstieae subclade which contains about 55 genera. Our knowledge......, and the previously unsampled rare monospecific genus Micklethwaitia from Mozambique. Zenkerella is suggested as a possible sister genus to the Scorodophloeus clade. © 2013 South African Association of Botanists....

  13. Phylogeny and nomenclature of the genus Talaromyces and taxa accommodated in Penicillium subgenus Biverticillium

    OpenAIRE

    Samson, R.A.; Yilmaz, N.; Houbraken, J.; Spierenburg, H.; Seifert, K.A.; Peterson, S.W.; Varga, J.; Frisvad, Jens Christian

    2011-01-01

    The taxonomic history of anamorphic species attributed to Penicillium subgenus Biverticillium is reviewed, along with evidence supporting their relationship with teleomorphic species classified in Talaromyces. To supplement previous conclusions based on ITS, SSU and/or LSU sequencing that Talaromyces and subgenus Biverticillium comprise a monophyletic group that is distinct from Penicillium at the generic level, the phylogenetic relationships of these two groups with other genera of Trichocom...

  14. Reinforcing and expanding the predictions of the disturbance vicariance hypothesis in Amazonian harlequin frogs: A molecular phylogenetic and climate envelope modelling approach

    OpenAIRE

    Lötters, Stefan; van der Meijden, Arie; Rödder, Dennis; Köster, Timo E.; Kraus, Tanja; La Marca, Enrique; Haddad, Célio F B; Veith, Michael

    2010-01-01

    The disturbance vicariance hypothesis (DV) has been proposed to explain speciation in Amazonia, especially its edge regions, e. g. in eastern Guiana Shield harlequin frogs (Atelopus) which are suggested to have derived from a cool-adapted Andean ancestor. In concordance with DV predictions we studied that (i) these amphibians display a natural distribution gap in central Amazonia; (ii) east of this gap they constitute a monophyletic lineage which is nested within a pre-Andean/western clade; (...

  15. Molecular paleobiological insights into the origin of the Brachiopoda.

    Science.gov (United States)

    Sperling, Erik A; Pisani, Davide; Peterson, Kevin J

    2011-01-01

    Most studies of brachiopod evolution have been based on their extensive fossil record, but molecular techniques, due to their independence from the rock record, can offer new insights into the evolution of a clade. Previous molecular phylogenetic hypotheses of brachiopod interrelationships place phoronids within the brachiopods as the sister group to the inarticulates, whereas morphological considerations suggest that Brachiopoda is a monophyletic group. Here, these hypotheses were tested with a molecular phylogenetic analysis of seven nuclear housekeeping genes combined with three ribosomal genes. The combined analysis finds brachiopods to be monophyletic, but with relatively weak support, and the craniid as the sister taxon of all other brachiopods. Phylogenetic-signal dissection suggests that the weak support is caused by the instability of the craniid, which is attracted to the phoronids. Analysis of slowly evolving sites results in a robustly supported monophyletic Brachiopoda and Inarticulata (Linguliformea+Craniiformea), which is regarded as the most likely topology for brachiopod interrelationships. The monophyly of Brachiopoda was further tested with microRNA-based phylogenetics, which are small, noncoding RNA genes whose presence and absence can be used to infer phylogenetic relationships. Two novel microRNAs were characterized supporting the monophyly of brachiopods. Congruence of the traditional molecular phylogenetic analysis, microRNAs, and morphological cladograms suggest that Brachiopoda is monophyletic with Phoronida as its likely sister group. Molecular clock analysis suggests that extant phoronids have a Paleozoic divergence despite their conservative morphology, and that the early brachiopod fossil record is robust, and is not affected by taphonomic factors relating to the late-Precambrian/early-Cambrian phosphogenic event.

  16. Complete nucleotide sequence of Sida golden mosaic Florida virus and phylogenetic relationships with other begomoviruses infecting malvaceous weeds in the Caribbean.

    Science.gov (United States)

    Fiallo-Olivé, Elvira; Martínez-Zubiaur, Yamila; Moriones, Enrique; Navas-Castillo, Jesús

    2010-09-01

    The complete genome sequence of two isolates of the bipartite begomovirus (genus Begomovirus, family Geminiviridae) Sida golden mosaic Florida virus (SiGMFV) is presented. We propose that both isolates, found infecting Malvastrum coromandelianum (family Malvaceae) in Cuba, belong to a new strain of SiGMFV. Phylogenetic analysis showed that SiGMFV DNA-A is located in a monophyletic cluster that includes begomoviruses infecting malvaceous weeds from the Caribbean.

  17. Characteristics and distribution of Listeria spp., including Listeria species newly described since 2009

    OpenAIRE

    Orsi, Renato H; Wiedmann, Martin

    2016-01-01

    The genus Listeria is currently comprised of 17 species, including 9 Listeria species newly described since 2009. Genomic and phenotypic data clearly define a distinct group of six species (Listeria sensu strictu) that share common phenotypic characteristics (e.g., ability to grow at low temperature, flagellar motility); this group includes the pathogen Listeria monocytogenes. The other 11 species (Listeria sensu lato) represent three distinct monophyletic groups, which may warrant recognitio...

  18. Multigene-based analyses on evolutionary phylogeny of two controversial ciliate orders: Pleuronematida and Loxocephalida (Protista, Ciliophora, Oligohymenophorea).

    Science.gov (United States)

    Gao, Feng; Katz, Laura A; Song, Weibo

    2013-07-01

    Relationships among members of the ciliate subclass Scuticociliatia (Ciliophora, Oligohymenophorea) are largely unresolved. Phylogenetic studies of its orders Pleuronematida and Loxocephalida were initially based on small subunit ribosomal RNA gene (SSU-rDNA) analyses of a limited number of taxa. Here we characterized 37 sequences (SSU-rDNA, ITS-5.8S and LSU-rDNA) from 21 taxonomically controversial members of these orders. Phylogenetic trees constructed to assess the inter- and intra-generic relationships of pleuronematids and loxocephalids reveal the following: (1) the order Loxocephalida and its two families Loxocephalidae and Cinetochilidae are not monophyletic when more taxa are added; (2) the core pleuronematids are divided into two fully supported clades, however, the order Pleuronematida is not monophyletic because Cyclidium glaucoma is closer to Thigmotrichida; (3) the family Pleuronematidae and the genus Schizocalyptra are monophyletic, though rDNA sequences of Pleuronema species are highly variable; (4) Pseudoplatynematum and Sathrophilus are closely related to the subclass Astomatia, while Cinetochilum forms a monophyletic group with the subclass Apostomatia; and (5) Hippocomos falls in the order Pleuronematida and is closely related to Eurystomatellidae and Cyclidium plouneouri. Further, in an effort to provide a better resolution of evolutionary relationships, the secondary structures of ITS2 transcripts and the variable region 4 (V4) of the small subunit ribosomal RNA (SSU-rRNA) are predicted, revealing that ITS2 structures are conserved at the order level while V4 region structures are more variable than ITS2 structures. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Almeidea A. St.-Hil. belongs to Conchocarpus J.C. Mikan (Galipeinae, Rutaceae): evidence from morphological and molecular data, with a first analysis of subtribe Galipeinae.

    Science.gov (United States)

    Bruniera, Carla Poleselli; Kallunki, Jacquelyn A; Groppo, Milton

    2015-01-01

    Subtribe Galipeinae (tribe Galipeeae, subfamily Rutoideae) is the most diverse group of Neotropical Rutaceae, with 28 genera and approximately 130 species. One of its genera is Almeidea, whose species are morphologically similar to those of the genus Conchocarpus. Species of Almeidea occur in the Atlantic Rain Forest of Eastern Brazil, with one species (Almeidea rubra) also present in Bolivia. The objective of this study was to perform a phylogenetic analysis of Almeidea, using a broader sampling of Galipeinae and other Neotropical Rutaceae, the first such study focused on this subtribe. To achieve this objective, morphological data and molecular data from the nuclear markers ITS-1 and ITS-2 and the plastid markers trnL-trnF and rps16 were obtained. Representatives of eight genera of Galipeinae and three genera of Pilocarpinae (included also in Galipeeae) and Hortia (closely related to Galipeeae) were used. Five species of Almeidea and seven of Conchocarpus were included, given the morphological proximity between these two genera. Individual (for each molecular marker) and combined phylogenetic analyses were made, using parsimony and Bayesian inference as optimization criteria. Results showed Galipeinae as monophyletic, with the species of Almeidea also monophyletic (supported by the presence of pantocolporate pollen) and nested in a clade with a group of species of Conchocarpus, a non-monophyletic group. Additionally, C. concinnus appeared in a group with Andreadoxa, Erythrochiton, and Neoraputia, other members of Galipeinae. As a result, Conchocarpus would be monophyletic only with the exclusion of a group of species related to C. concinnus and with the inclusion of all species of Almeidea with the group of species of Conchocarpus that includes its type species, C. macrophyllus. Thus, species of Almeidea are transferred to Conchocarpus, and the new combinations are made here.

  20. Mother-to-infant transmission of intestinal bifidobacterial strains has an impact on the early development of vaginally delivered infant's microbiota.

    Directory of Open Access Journals (Sweden)

    Hiroshi Makino

    Full Text Available OBJECTIVES: Bifidobacterium species are one of the major components of the infant's intestine microbiota. Colonization with bifidobacteria in early infancy is suggested to be important for health in later life. However, information remains limited regarding the source of these microbes. Here, we investigated whether specific strains of bifidobacteria in the maternal intestinal flora are transmitted to their infant's intestine. MATERIALS AND METHODS: Fecal samples were collected from healthy 17 mother and infant pairs (Vaginal delivery: 12; Cesarean section delivery: 5. Mother's feces were collected twice before delivery. Infant's feces were collected at 0 (meconium, 3, 7, 30, 90 days after birth. Bifidobacteria isolated from feces were genotyped by multilocus sequencing typing, and the transitions of bifidobacteria counts in infant's feces were analyzed by quantitative real-time PCR. RESULTS: Stains belonging to Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium catenulatum, Bifidobacterium longum subsp. longum, and Bifidobacterium pseudocatenulatum, were identified to be monophyletic between mother's and infant's intestine. Eleven out of 12 vaginal delivered infants carried at least one monophyletic strain. The bifidobacterial counts of the species to which the monophyletic strains belong, increased predominantly in the infant's intestine within 3 days after birth. Among infants delivered by C-section, monophyletic strains were not observed. Moreover, the bifidobacterial counts were significantly lower than the vaginal delivered infants until 7 days of age. CONCLUSIONS: Among infants born vaginally, several Bifidobacterium strains transmit from the mother and colonize the infant's intestine shortly after birth. Our data suggest that the mother's intestine is an important source for the vaginal delivered infant's intestinal microbiota.

  1. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence.

    Science.gov (United States)

    Alfaro, Michael E; Zoller, Stefan; Lutzoni, François

    2003-02-01

    Bayesian Markov chain Monte Carlo sampling has become increasingly popular in phylogenetics as a method for both estimating the maximum likelihood topology and for assessing nodal confidence. Despite the growing use of posterior probabilities, the relationship between the Bayesian measure of confidence and the most commonly used confidence measure in phylogenetics, the nonparametric bootstrap proportion, is poorly understood. We used computer simulation to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony bootstrap proportion (MP-BP). We simulated the evolution of DNA sequence on 17-taxon topologies under 18 evolutionary scenarios and examined the performance of these methods in assigning confidence to correct monophyletic and incorrect monophyletic groups, and we examined the effects of increasing character number on support value. BMCMC-PP and ML-BP were often strongly correlated with one another but could provide substantially different estimates of support on short internodes. In contrast, BMCMC-PP correlated poorly with MP-BP across most of the simulation conditions that we examined. For a given threshold value, more correct monophyletic groups were supported by BMCMC-PP than by either ML-BP or MP-BP. When threshold values were chosen that fixed the rate of accepting incorrect monophyletic relationship as true at 5%, all three methods recovered most of the correct relationships on the simulated topologies, although BMCMC-PP and ML-BP performed better than MP-BP. BMCMC-PP was usually a less biased predictor of phylogenetic accuracy than either bootstrapping method. BMCMC-PP provided high support values for correct topological bipartitions with fewer characters than was needed for nonparametric bootstrap.

  2. Phylogenetic analysis of symbionts in feather-feeding lice of the genus Columbicola: evidence for repeated symbiont replacements

    OpenAIRE

    Smith, Wendy A.; Oakeson, Kelly F.; Johnson, Kevin P.; Reed, David L.; Carter, Tamar; Smith, Kari L; Koga, Ryuichi; Fukatsu, Takema; Dale H Clayton; Dale, Colin

    2013-01-01

    Background Many groups of insects have obligate bacterial symbionts that are vertically transmitted. Such associations are typically characterized by the presence of a monophyletic group of bacteria living in a well-defined host clade. In addition the phylogeny of the symbiotic bacteria is typically congruent with that of the host, signifying co-speciation. Here we show that bacteria living in a single genus of feather lice, Columbicola (Insecta: Phthiraptera), present an exception to this ty...

  3. Genomic organization and molecular phylogenies of the beta (β keratin multigene family in the chicken (Gallus gallus and zebra finch (Taeniopygia guttata: implications for feather evolution

    Directory of Open Access Journals (Sweden)

    Sawyer Roger H

    2010-05-01

    Full Text Available Abstract Background The epidermal appendages of reptiles and birds are constructed of beta (β keratins. The molecular phylogeny of these keratins is important to understanding the evolutionary origin of these appendages, especially feathers. Knowing that the crocodilian β-keratin genes are closely related to those of birds, the published genomes of the chicken and zebra finch provide an opportunity not only to compare the genomic organization of their β-keratins, but to study their molecular evolution in archosaurians. Results The subfamilies (claw, feather, feather-like, and scale of β-keratin genes are clustered in the same 5' to 3' order on microchromosome 25 in chicken and zebra finch, although the number of claw and feather genes differs between the species. Molecular phylogenies show that the monophyletic scale genes are the basal group within birds and that the monophyletic avian claw genes form the basal group to all feather and feather-like genes. Both species have a number of feather clades on microchromosome 27 that form monophyletic groups. An additional monophyletic cluster of feather genes exist on macrochromosome 2 for each species. Expression sequence tag analysis for the chicken demonstrates that all feather β-keratin clades are expressed. Conclusions Similarity in the overall genomic organization of β-keratins in Galliformes and Passeriformes suggests similar organization in all Neognathae birds, and perhaps in the ancestral lineages leading to modern birds, such as the paravian Anchiornis huxleyi. Phylogenetic analyses demonstrate that evolution of archosaurian epidermal appendages in the lineage leading to birds was accompanied by duplication and divergence of an ancestral β-keratin gene cluster. As morphological diversification of epidermal appendages occurred and the β-keratin multigene family expanded, novel β-keratin genes were selected for novel functions within appendages such as feathers.

  4. Structure-Function Similarities between a Plant Receptor-like Kinase and the Human Interleukin-1 Receptor-associated Kinase-4*

    OpenAIRE

    2011-01-01

    Phylogenetic analysis has previously shown that plant receptor-like kinases (RLKs) are monophyletic with respect to the kinase domain and share an evolutionary origin with the animal interleukin-1 receptor-associated kinase/Pelle-soluble kinases. The lysin motif domain-containing receptor-like kinase-3 (LYK3) of the legume Medicago truncatula shows 33% amino acid sequence identity with human IRAK-4 over the kinase domain. Using the structure of this animal kinase as a template, homology model...

  5. Origen y evolución de los Platyrrhini (Primates, Anthropoidea), con especial referencia a los registros de Argentina

    OpenAIRE

    Tejedor, M F

    1998-01-01

    The are new light about the Platyrrhini origin provided by the fossil record of the Old World, which demonstrates that catarrhines and platyrrhines are certainly a monophyletic group. Although the exact provenance of the Platyrrhini is uncertain at this time, some characters of the latter are shared with primitive anthropoid primates from the Fayum Depression, in the Egyptian late Eocene-early Oligocene, and then we can accept an African origin for platyrrhines. Symplesiomorphies exhibited by...

  6. Relationships among characiform fishes inferred from analysis of nuclear and mitochondrial gene sequences.

    Science.gov (United States)

    Calcagnotto, Daniela; Schaefer, Scott A; DeSalle, Rob

    2005-07-01

    Suprafamilial relationships among characiform fishes and implications for the taxonomy and biogeographic history of the Characiformes were investigated by parsimony analysis of four nuclear and two mitochondrial genes across 124 ingroup and 11 outgroup taxa. Simultaneous analysis of 3660 aligned base pairs from the mitochondrial 16S and cytochrome b genes and the nuclear recombination activating gene (RAG2), seven in absentia (sia), forkhead (fkh), and alpha-tropomyosin (trop) gene loci confirmed the non-monophyly of the African and Neotropical assemblages and corroborated many suprafamilial groups proposed previously on the basis of morphological features. The African distichodontids plus citharinids were strongly supported as a monophyletic Citharinoidei that is the sistergroup to all other characiforms, which form a monophyletic Characoidei composed of two large clades. The first represents an assemblage of both African and Neotropical taxa, wherein a monophyletic African Alestidae is sister to a smaller clade comprised of the Neotropical families Ctenolucidae, Lebiasinidae, and the African Hepsetidae, with that assemblage sister to a strictly Neotropical clade comprised of the Crenuchidae and Erythrinidae. The second clade within the Characoidei is strictly Neotropical and includes all other Characiformes grouped into two well supported major clades. The first, corresponding to a traditional definition of the Characidae, is congruent with some groupings previously supported by morphological evidence. The second clade comprises a monophyletic Anostomoidea that is sister to a clade formed by the families Hemiodontidae, Parodontidae, and Serrasalmidae, with that assemblage, in turn, the sistergroup of the Cynodontidae. Serrasalmidae, traditionally regarded as a subfamily of Characidae, was recovered as the sistergroup of (Anostomoidea (Parodontidae+Hemiodontidae)) and the family Cynodontidae was recovered with strong support as the sistergroup to this assemblage

  7. Species Diversity and Polymorphism in the Exophiala spinifera Clade Containing Opportunistic Black Yeast-Like Fungi

    OpenAIRE

    2003-01-01

    A monophyletic group of black yeast-like fungi containing opportunistic pathogens around Exophiala spinifera is analyzed using sequences of the small-subunit (SSU) and internal transcribed spacer (ITS) domains of ribosomal DNA. The group contains yeast-like and annellidic species (anamorph genus Exophiala) in addition to sympodial taxa (anamorph genera Ramichloridium and Rhinocladiella). The new species Exophiala oligosperma, Ramichloridium basitonum, and Rhinocladiella similis are introduced...

  8. Systematics and Ethnobotany of Salvia Subgenus Calosphace and Origins of the Hallucinogenic Sage, Salvia divinorum

    OpenAIRE

    Jenks, Aaron Allon

    2008-01-01

    Salvia subgenus Calosphace (Lamiaceae), the largest of 5 subgenera with some 500 species and strongly supported as monophyletic, has received no comprehensive systematic research since the initial establishment of 91 taxonomic sections. Representative taxa of 73 sections of Calosphace were sampled to investigate the phylogenetic relationships and identify major lineages using chloroplast (intergenic spacer, psbA-trnH) and nuclear DNA (ribosomal spacer region, ITS). Phylogenetic analysis of t...

  9. Halwaxiids and the early evolution of the lophotrochozoans.

    Science.gov (United States)

    Morris, Simon Conway; Caron, Jean-Bernard

    2007-03-02

    Halkieriids and wiwaxiids are cosmopolitan sclerite-bearing metazoans from the Lower and Middle Cambrian. Although they have similar scleritomes, their phylogenetic position is contested. A new scleritomous fossil from the Burgess Shale has the prominent anterior shell of the halkieriids but also bears wiwaxiid-like sclerites. This new fossil defines the monophyletic halwaxiids and indicates that they have a key place in early lophotrochozoan history.

  10. EST based phylogenomics of Syndermata questions monophyly of Eurotatoria

    Science.gov (United States)

    2008-01-01

    Background The metazoan taxon Syndermata comprising Rotifera (in the classical sense of Monogononta+Bdelloidea+Seisonidea) and Acanthocephala has raised several hypotheses connected to the phylogeny of these animal groups and the included subtaxa. While the monophyletic origin of Syndermata and Acanthocephala is well established based on morphological and molecular data, the phylogenetic position of Syndermata within Spiralia, the monophyletic origin of Monogononta, Bdelloidea, and Seisonidea and the acanthocephalan sister group are still a matter of debate. The comparison of the alternative hypotheses suggests that testing the phylogenetic validity of Eurotatoria (Monogononta+Bdelloidea) is the key to unravel the phylogenetic relations within Syndermata. The syndermatan phylogeny in turn is a prerequisite for reconstructing the evolution of the acanthocephalan endoparasitism. Results Here we present our results from a phylogenomic approach studying i) the phylogenetic position of Syndermata within Spiralia, ii) the monophyletic origin of monogononts and bdelloids and iii) the phylogenetic relations of the latter two taxa to acanthocephalans. For this analysis we have generated EST libraries of Pomphorhynchus laevis, Echinorhynchus truttae (Acanthocephala) and Brachionus plicatilis (Monogononta). By extending these data with database entries of B. plicatilis, Philodina roseola (Bdelloidea) and 25 additional metazoan species, we conducted phylogenetic reconstructions based on 79 ribosomal proteins using maximum likelihood and bayesian approaches. Our findings suggest that the phylogenetic position of Syndermata within Spiralia is close to Platyhelminthes, that Eurotatoria are not monophyletic and that bdelloids are more closely related to acanthocephalans than monogononts. Conclusion Mapping morphological character evolution onto molecular phylogeny suggests the (partial or complete) reduction of the corona and the emergence of a retractable anterior end (rostrum

  11. EST based phylogenomics of Syndermata questions monophyly of Eurotatoria

    Directory of Open Access Journals (Sweden)

    Bucher Gregor

    2008-12-01

    Full Text Available Abstract Background The metazoan taxon Syndermata comprising Rotifera (in the classical sense of Monogononta+Bdelloidea+Seisonidea and Acanthocephala has raised several hypotheses connected to the phylogeny of these animal groups and the included subtaxa. While the monophyletic origin of Syndermata and Acanthocephala is well established based on morphological and molecular data, the phylogenetic position of Syndermata within Spiralia, the monophyletic origin of Monogononta, Bdelloidea, and Seisonidea and the acanthocephalan sister group are still a matter of debate. The comparison of the alternative hypotheses suggests that testing the phylogenetic validity of Eurotatoria (Monogononta+Bdelloidea is the key to unravel the phylogenetic relations within Syndermata. The syndermatan phylogeny in turn is a prerequisite for reconstructing the evolution of the acanthocephalan endoparasitism. Results Here we present our results from a phylogenomic approach studying i the phylogenetic position of Syndermata within Spiralia, ii the monophyletic origin of monogononts and bdelloids and iii the phylogenetic relations of the latter two taxa to acanthocephalans. For this analysis we have generated EST libraries of Pomphorhynchus laevis, Echinorhynchus truttae (Acanthocephala and Brachionus plicatilis (Monogononta. By extending these data with database entries of B. plicatilis, Philodina roseola (Bdelloidea and 25 additional metazoan species, we conducted phylogenetic reconstructions based on 79 ribosomal proteins using maximum likelihood and bayesian approaches. Our findings suggest that the phylogenetic position of Syndermata within Spiralia is close to Platyhelminthes, that Eurotatoria are not monophyletic and that bdelloids are more closely related to acanthocephalans than monogononts. Conclusion Mapping morphological character evolution onto molecular phylogeny suggests the (partial or complete reduction of the corona and the emergence of a retractable

  12. Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction

    OpenAIRE

    Fernández, Rosa; Edgecombe, Gregory D.; Giribet, Gonzalo

    2016-01-01

    Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousan...

  13. Phylogenetic analysis of Attalea (Arecaceae) : insights into the historical biogeography of a recently diversified Neotropical plant group

    OpenAIRE

    Freitas,C.; Meerow, A. W.; Pintaud, Jean-Christophe; Henderson, A.; Noblick, L.; COSTA, F. R. C.; Barbosa, C. E.; Barrington, D.

    2016-01-01

    We present a dated phylogenetic tree for the Neotropical genus Attalea (Arecaceae). We used six orthologues from the nuclear WRKY gene family across 98 accessions to address relationships among species and biogeographical hypotheses. We found that the formerly recognized groups within Attalea are not monophyletic and therefore there is no support for multiple genera as previously thought. Species of Attalea-like palms from the Atlantic forest form a well-supported clade sister to the Attalea ...

  14. MADS-box gene evolution-structure and transcription patterns

    DEFF Research Database (Denmark)

    Johansen, Bo; Pedersen, Louise B; Skipper, Martin;

    2002-01-01

    This study presents a phylogenetic analysis of 198 MADS-box genes based on 420 parsimony-informative characters. The analysis includes only MIKC genes; therefore several genes from gymnosperms and pteridophytes are excluded. The strict consensus tree identifies all major monophyletic groups known...... three classes of MADS-box genes to be transcribed in the stamens and carpels. Thus the analysis does not support the ABC model as formulated at present....

  15. A Comparison of Three Molecular Markers for the Identification of Populations of Globodera pallida

    OpenAIRE

    Hoolahan, Angelique H.; Blok, Vivian C.; Gibson, Tracey; Dowton, Mark

    2012-01-01

    Potato cyst nematodes cost the potato industry substantial financial losses annually. Through the use of molecular markers, the distribution and infestation routes of these nematodes can be better elucidated, permitting the development of more effective preventative methods. Here we assess the ability of three molecular markers to resolve multiple representatives of five Globodera pallida populations as monophyletic groups. Molecular markers included a region of the rbp-1 gene (an effector), ...

  16. Topological incongruence between nuclear and chloroplast DNA trees suggesting hybridization in the urophyllum group of the genus Fagopyrum (Polygonaceae).

    Science.gov (United States)

    Nishimoto, Yuriko; Ohnishi, Ohmi; Hasegawa, Masami

    2003-04-01

    We performed phylogenetic analyses of Fagopyrum species in the urophyllum group based on nucleotide sequences of two nuclear genes, FLORICAULA/LEAFY (FLO/LFY) and AGAMOUS (AG), and three segments of chloroplast DNA (cpDNA), rbcL-accD, trnK intron, and trnC-rpoB spacer. The FLO/LFY and AG sequences turned out to be phylogenetically more informative at the intrageneric level than the cpDNA sequences. Congruence among these gene trees, inferred by a maximum-likelihood (ML) method, demonstrated that topologies were partially incongruent between the nuclear and chloroplast DNA phylogenies. The nuclear DNA sequence data supported a monophyletic relation of F. statice, F. gilesii, and F. jinshaense, whereas the former two species formed another monophyletic relation with the F. capillatum-F. gracilipes-F. gracilipedoides-F. rubifolium clade excluding F. jinshaense in the synthetic cpDNA phylogeny. In addition, two divergent sequences of FLO/LFY were found in F. rubifolium (tetraploid). One of these was sister to F. gracilipedoides and another was sister to F. statice, and a monophyletic relation of these two genes was rejected by a bootstrap analysis. These results suggest that hybridization may have occurred during diversification of Fagopyrum species in the urophyllum group, and that F. rubifolium is possibly allotetraploid species.

  17. Taxon-rich multigene phylogeny of photosynthetic euglenoids (Euglenophyceae

    Directory of Open Access Journals (Sweden)

    Jong Im eKim

    2015-08-01

    Full Text Available To establish taxonomy and understand phylogenetic relationships among strains and species of the photosynthetic euglenoids, we performed phylogenetic analyses based on a four gene sequence dataset (nr SSU and LSU rDNA, and pt SSU and LSU rDNA from 343 taxa (including three outgroup. The phylogenetic tree based on the combined dataset was split into two major clades: Euglenaceae and Phacaceae. The family Euglenaceae was a well-supported monophyletic group containing eight genera (Colacium, Cryptoglena, Euglena, Euglenaformis, Euglenaria, Monomorphina, Strombomonas, and Trachelomonas, each representing a monophyletic lineage, except for the genus Euglena. The genus Euglena was divided into three subclades (A1, A2, and A3 and was paraphyletic due to Euglena archeoplastidiata being grouped with the genus Euglenaria and E. cf. velata with the genus Colacium. The family Phacaceae was supported as a monophyletic group and contained three genera (Discoplastis, Lepocinclis, and Phacus. The genus Phacus contained traditionally defined members as well as the non-traditional P. warszewiczii and P. limnophila, which support the generic concept of Linton et al. (2010.

  18. Molecular phylogeny of black flies (Diptera: Simuliidae) from Thailand, using ITS2 rDNA.

    Science.gov (United States)

    Thanwisai, Aunchalee; Kuvangkadilok, Chaliow; Baimai, Visut

    2006-01-01

    The sequences of the second internal transcribed spacer (ITS2) of ribosomal DNA (rDNA) were determined for 40 black fly species from Thailand, belonging to 4 subgenera of the genus Simulium, namely Gomphostilbia (12 species), Nevermannia (5 species), Montisimulium (1 species), Simulium sensu stricto (21 species), and an unknown subgenus with one species (Simulium baimaii). The length of the ITS2 ranged from 247 to 308 bp. All black fly species had high AT content, ranging from 71 to 83.8%. Intraindividual variation (clonal variation) occurred in 13 species, ranging from 0.3 to 1.1%. Large intrapopulation and interpopulation heterogeneities exist in S. feuerboni from the same and different locations in Doi Inthanon National Park, northern Thailand. Phylogenetic relationships among 40 black fly species were examined using PAUP (version 4.0b10) and MrBAYS (version 3.0B4). The topology of the trees revealed two major monophyletic clades. The subgenus Simulium and Simulium baimaii were placed in the first monophyletic clade, whereas the subgenera Nevermannia + Montisimulium were placed as the sister group to the subgenus Gomphostilbia in the second monophyletic clade. Our results suggest that S. baimaii belongs to the malyschevi-group or variegatum-group in the subgenus Simulium. The molecular phylogeny generally agrees with existing morphology-based phylogenies.

  19. Ascospore morphology is a poor predictor of the phylogenetic relationships of Neurospora and Gelasinospora.

    Science.gov (United States)

    Dettman, J R; Harbinski, F M; Taylor, J W

    2001-10-01

    The genera Neurospora and Gelasinospora are conventionally distinguished by differences in ascospore ornamentation, with elevated longitudinal ridges (ribs) separated by depressed grooves (veins) in Neurospora and spherical or oval indentations (pits) in Gelasinospora. The phylogenetic relationships of representatives of 12 Neurospora and 4 Gelasinospora species were assessed with the DNA sequences of four nuclear genes. Within the genus Neurospora, the 5 outbreeding conidiating species form a monophyletic group with N. discreta as the most divergent, and 4 of the homothallic species form a monophyletic group. In combined analysis, each of the conventionally defined Gelasinospora species was more closely related to a Neurospora species than to another Gelasinospora species. Evidently, the Neurospora and Gelasinospora species included in this study do not represent two clearly resolved monophyletic sister genera, but instead represent a polyphyletic group of taxa with close phylogenetic relationships and significant morphological similarities. Ascospore morphology, the character that the distinction between the genera Neurospora and Gelasinospora is based upon,was not an accurate predictor of phylogenetic relationships.

  20. Polyphyly of the fern family Tectariaceae sensu Ching: Insights from cpDNA sequence data

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Tectariaceae are a pantropical fern family of about 20 genera, among which 8 are distributed in China. The morphological distinctiveness of the family is widely recognized, yet relatively little systematic research has been conducted on members of Tectariaceae. Phylogenetic analyses of chloroplast DNA sequence data (rbcL and atpB) from 15 species representing all 8 genera in China were carried out under parsimony criteria and Bayesian inference. The phylogenetic reconstructions indicated that the fern family Tectariaceae as traditionally circumscribed are polyphyletic. Ctenitis, Dryopsis, Lastreopsis clustered with and should be included within the newly-defined Dryopteridaceae, and Pleocnemia is also tentatively assigned to it. A narrowly monophyletic Tectariaceae is identified, which includes Ctenitopsis, Hemigramma, Pteridrys, Quercifilix, and Tectaria. In the single rbcL analysis, Arthropteris clustered with the above-mentioned monophyletic Tectariaceae. Although further investigations are still needed to identify infrafamilial relationships within the monophyletic Tectariaceae and to redefine several problematic genera, we propose a working concept here that better reflects the inferred evolutionary history of this group.

  1. Polyphyly of the fern family Tectariaceae sensu Ching: insights from cpDNA sequence data.

    Science.gov (United States)

    Liu, HongMei; Zhang, XianChun; Chen, ZhiDuan; Dong, ShiYong; Qiu, YinLong

    2007-12-01

    Tectariaceae are a pantropical fern family of about 20 genera, among which 8 are distributed in China. The morphological distinctiveness of the family is widely recognized, yet relatively little systematic research has been conducted on members of Tectariaceae. Phylogenetic analyses of chloroplast DNA sequence data (rbcL and atpB) from 15 species representing all 8 genera in China were carried out under parsimony criteria and Bayesian inference. The phylogenetic reconstructions indicated that the fern family Tectariaceae as traditionally circumscribed are polyphyletic. Ctenitis, Dryopsis, Lastreopsis clustered with and should be included within the newly-defined Dryopteridaceae, and Pleocnemia is also tentatively assigned to it. A narrowly monophyletic Tectariaceae is identified, which includes Ctenitopsis, Hemigramma, Pteridrys, Quercifilix, and Tectaria. In the single rbcL analysis, Arthropteris clustered with the above-mentioned monophyletic Tectariaceae. Although further investigations are still needed to identify infrafamilial relationships within the monophyletic Tectariaceae and to redefine several problematic genera, we propose a working concept here that better reflects the inferred evolutionary history of this group.

  2. A cladistic analysis of Aristotle's animal groups in the Historia animalium.

    Science.gov (United States)

    von Lieven, Alexander Fürst; Humar, Marcel

    2008-01-01

    The Historia animalium (HA) of Aristotle contains an extraordinarily rich compilation of descriptions of animal anatomy, development, and behaviour. It is believed that Aristotle's aim in HA was to describe the correlations of characters rather than to classify or define animal groups. In order to assess if Aristotle, while organising his character correlations, referred to a pre-existing classification that underlies the descriptions in HA, we carried out a cladistic analysis according to the following procedure: by disentangeling 147 species and 40 higher taxa-designations from 157 predicates in the texts, we transcribed Aristotle's descriptions on anatomy and development of animals in books I-V of HA into a character matrix for a cladistic analysis. By analysing the distribution of characters as described in his books, we obtained a non-phylogenetic dendrogram displaying 58 monophyletic groups, 29 of which have equivalents among Aristotle's group designations. Eleven Aristotelian groupings turned out to be non-monophyletic, and six of them are inconsistent with the monophyletic groups. Twelve of 29 taxa without equivalents in Aristotle's works have equivalents in modern classifications. With this analysis we demonstate there exists a fairly consistent underlying classification in the zoological works of Aristotle. The peculiarities of Aristotle's character basis are discussed and the dendrogram is compared with a current phylogenetic tree.

  3. Phylogenetic relationships and limb loss in sub-Saharan African scincine lizards (Squamata: Scincidae).

    Science.gov (United States)

    Whiting, Alison S; Bauer, Aaron M; Sites, Jack W

    2003-12-01

    Skinks are the largest family of lizards and are found worldwide in a diversity of habitats. One of the larger and more poorly studied groups of skinks includes members of the subfamily Scincinae distributed in sub-Saharan Africa. Sub-Saharan African scincines are one of the many groups of lizards that show limb reduction and loss, and the genus Scelotes offers an excellent opportunity to look at limb loss in a phylogenetic context. Phylogenetic relationships were reconstructed for a total of 52 taxa representing all subfamilies of skinks as well as other Autarchoglossan families using sequence from six gene regions including; 12S, 16S, and cytochrome b (mitochondrial), as well as alpha-Enolase, 18S, and C-mos (nuclear). The family Scincidae is recovered as monophyletic and is the sister taxon to a (Cordylidae+Xantusiidae) clade. Within skinks the subfamily Acontinae is monophyletic and sister group to all remaining skinks. There is no support for the monophyly of the subfamilies Lygosominae and Scincinae, but sub-Saharan African scincines+Feylinia form a well supported monophyletic group. The monophyly of Scelotes is confirmed, and support is found for two geographic groups within the genus. Reconstructions of ancestral states for limb and digital characters show limited support for the reversal or gain of both digits and limbs, but conservative interpretation of the results suggest that limb loss is common, occurring multiple times throughout evolutionary history, and is most likely not reversible.

  4. First molecular evidence for the existence of a Tardigrada + Arthropoda clade.

    Science.gov (United States)

    Giribet, G; Carranza, S; Baguñà, J; Riutort, M; Ribera, C

    1996-01-01

    The complete 18S rDNA gene sequence of Macrobiotus group hufelandi (Tardigrada) was obtained and aligned with 18S rDNA and rRNA gene sequences of 24 metazoans (mainly protostomes). Discrete character (maximum-parsimony) and distance (neighbor-joining) methods were used to infer their phylogeny. The evolution of bootstrap proportions with sequence length (pattern of resolved nodes, PRN) was studied to test the resolution of the nodes in neighbor-joining trees. The results show that arthropods are monophyletic. Tardigrades represent the sister group of arthropods (in parsimony analyses) or they are related with crustaceans (distance analysis and PRN). Arthropoda are divided into two main evolutionary lines, the Hexapoda + Crustacea line (weakly supported), and the Myriapoda + Chelicerata line. The Hexapoda + Crustacea line includes Pentastomida, but the internal resolution is far from clear. The Insecta (Ectognatha) are monophyletic, but no evidence for the monophyly of Hexapoda is found. The Chelicerata are a monophyletic group and the Myriapoda cluster close to Arachnida. Overall, the results obtained represent the first molecular evidence for a Tardigrada + Arthropoda clade. In addition, the congruence between molecular phylogenies of the Arthropoda from other authors and this obtained here indicates the need to review those obtained solely on morphological characters.

  5. Molecular phylogenetics of North American phoxinins (Actinopterygii: Cypriniformes: Leuciscidae) based on RAG1 and S7 nuclear DNA sequence data.

    Science.gov (United States)

    Bufalino, Angelo P; Mayden, Richard L

    2010-04-01

    Most molecular phylogenetic hypotheses for North American (NA) phoxinins are based on mitochondrial DNA sequences (mtDNA) and the resulting hypotheses are rather variable, though there is general support for three major lineages of NA phoxinins: western, creek chub-plagopterin (CC-P), and open posterior myodome (OPM) clades. Support for a monophyletic NA phoxinin group has varied among studies. This study utilizes nuclear DNA (nDNA) sequences from the RAG1 (exon 3) and S7 (intron 1) gene regions to evaluate the phylogenetic relationships and monophyly of NA phoxinins. Results from the nDNA analyses provide overall support for the western, CC-P, and OPM clades. The CC-P clade had the best overall resolution and support in the individual and combined analyses of the nDNA data. Resolution of the western clade was fairly good, with most analyses recovering a monophyletic Gila clade. The OPM clade demonstrated the highest degree of topological variability among the analyses. The RAG1 analyses failed to recover a monophyletic NA phoxinin group by resolving the European leuciscins, inclusive Notemigonus crysoleucas, within the NA phoxinin topology. Most analyses recovered a strongly supported shiner clade though, similar to several mtDNA studies; there was a high degree of topological variability among the results.

  6. When molecules support morphology: Phylogenetic reconstruction of the family Onuphidae (Eunicida, Annelida) based on 16S rDNA and 18S rDNA.

    Science.gov (United States)

    Budaeva, Nataliya; Schepetov, Dmitry; Zanol, Joana; Neretina, Tatiana; Willassen, Endre

    2016-01-01

    Onuphid polychaetes are tubicolous marine worms commonly reported worldwide from intertidal areas to hadal depths. They often dominate in benthic communities and have economic importance in aquaculture and recreational fishing. Here we report the phylogeny of the family Onuphidae based on the combined analyses of nuclear (18S rDNA) and mitochondrial (16S rDNA) genes. Results of Bayesian and Maximum Likelihood analyses supported the monophyly of Onuphidae and its traditional subdivision into two monophyletic subfamilies: Onuphinae and Hyalinoeciinae. Ten of 22 recognized genera were monophyletic with strong node support; four more genera included in this study were either monotypic or represented by a single species. None of the genera appeared para- or polyphyletic and this indicates a strong congruence between the traditional morphology-based systematics of the family and the newly obtained molecular-based phylogenetic reconstructions. Intergeneric relationships within Hyalinoeciinae were not resolved. Two strongly supported monophyletic groups of genera were recovered within Onuphinae: ((Onuphis, Aponuphis), Diopatra, Paradiopatra) and (Hirsutonuphis, (Paxtonia, (Kinbergonuphis, Mooreonuphis))). A previously accepted hypothesis on the subdivision of Onuphinae into the Onuphis group of genera and the Diopatra group of genera was largely rejected.

  7. Combined mitochondrial and nuclear sequences support the monophyly of forcipulatacean sea stars.

    Science.gov (United States)

    Foltz, D W; Bolton, M T; Kelley, S P; Kelley, B D; Nguyen, A T

    2007-05-01

    Previous molecular phylogenetic analyses of forcipulatacean sea stars (Echinodermata: Asteroidea) have reconstructed a non-monophyletic order Forcipulatida, provided that two or more forcipulate families are included. This result could mean that one or more assumptions of the reconstruction method was violated, or else the traditional classification could be erroneous. The present molecular phylogenetic analysis included 12 non-forcipulatacean and 39 forcipulatacean sea stars, with multiple representatives of all but one of the forcipulate families and/or subfamilies. Bayesian analysis of approximately 4.2kb of sequence data representing seven partitions (nuclear 18S rRNA and 28S rRNA, mitochondrial 12S rRNA, 16S rRNA, 5 tRNAs and cytochrome oxidase I with first and second codon positions analyzed separately from third codon positions) recovered a consensus tree with three well-supported clades (78%-100% bootstrap support) that corresponded at least approximately to traditional taxonomic ranks: the superorder Forcipulatacea (Forcipulatida + Brisingida) + Pteraster, the Brisingida/Brisingidae and Asteriidae + Rathbunaster + Pycnopodia. When a molecular clock was enforced, the partitioned Bayesian analysis recovered the traditional Forcipulatacea. Five of six genera represented by two or more species were monophyletic with 100% bootstrap support. Most of the traditional subfamilial and familial groupings within the Forcipulatida were either unresolved or non-monophyletic. The separate partitions differed considerably in estimates of model parameters, mainly between nuclear sequences (with high GC content, low rates of sequence substitution and high transition/transversion rate ratios) and mitochondrial sequences.

  8. Global phylogeny and biogeography of grammitid ferns (Polypodiaceae).

    Science.gov (United States)

    Sundue, Michael A; Parris, Barbara S; Ranker, Tom A; Smith, Alan R; Fujimoto, Erin L; Zamora-Crosby, Delia; Morden, Clifford W; Chiou, Wen-Liang; Chen, Cheng-Wei; Rouhan, Germinal; Hirai, Regina Y; Prado, Jefferson

    2014-12-01

    We examined the global historical biogeography of grammitid ferns (Polypodiaceae) within a phylogenetic context. We inferred phylogenetic relationships of 190 species representing 31 of the 33 currently recognized genera of grammitid ferns by analyzing DNA sequence variation of five plastid DNA regions. We estimated the ages of cladogenetic events on an inferred phylogeny using secondary fossil calibration points. Historical biogeographical patterns were inferred via ancestral area reconstruction. Our results supported four large-scale phylogenetic and biogeographic patterns: (1) a monophyletic grammitid clade that arose among Neotropical polypod ancestors about 31.4 Ma; (2) a paraphyletic assemblage of clades distributed in the Neotropics and the Afro-Malagasy region; (3) a large clade distributed throughout the Asia-Malesia-Pacific region that originated about 23.4 Ma; and, (4) an Australian or New Zealand origin of the circumaustral genus Notogrammitis. Most genera were supported as monophyletic except for Grammitis, Oreogrammitis, Radiogrammitis, and Zygophlebia. Grammitid ferns are a well-supported monophyletic group with two biogeographically distinct lineages: a primarily Neotropical grade exhibiting several independent successful colonizations to the Afro-Malagasy region and a primarily Paleotropical clade exhibiting multiple independent dispersals to remote Pacific islands and temperate, austral regions.

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

    Directory of Open Access Journals (Sweden)

    Paola Pedraza-Penalosa

    2015-04-01

    Full Text Available 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.

  10. Disentangling the Collema-Leptogium complex through a molecular phylogenetic study of the Collemataceae (Peltigerales, lichen-forming Ascomycota).

    Science.gov (United States)

    Otálora, Mónica A G; Aragón, Gregorio; Molina, M Carmen; Martínez, Isabel; Lutzoni, François

    2010-01-01

    Family Collemataceae (Peltigerales, Ascomycota) includes species of cyanolichens with foliose to fruticose or crustose thalli, with simple or septate ascospores. The current classification divides this family into two groups on the basis of ascospore types. The objective of this study was to evaluate the phylogenetic relationships within this family. Combined DNA sequence data from the nuclear large subunit and mitochondrial small subunit ribosomal RNA genes were used to evaluate monophyly of the family and the relationships between the largest genera of this family. The results revealed that this family is not monophyletic. Genera Staurolemma and Physma, currently classified within the Collemataceae, were found nested within the Pannariaceae. The second result of this study confirms that the genera Collema and Leptogium, both part of the Collemataceae s. str., are not monophyletic and that the presence of a thallus cortex is not a synapomorphy for Leptogium. The main taxonomic conclusion is that families Collemataceae and Pannariaceae were recircumscribed in light of molecular findings with the latter family now including Staurolemma and Physma. Genera Collema and Leptogium form a single mixed monophyletic group. Inferred ancestral character states within the Collema-Leptogium complex revealed that the ancestor of this family had a thallus without cortex and that a cortex evolved at least twice relatively early in the evolution of the Collemataceae s. str. These independent gains of a thallus cortex seems to be associated with a transition from colonizing bare rocks and soils in semi-arid and exposed habitats to epiphytism in shady humid forests.

  11. Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires.

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    Lin, Yu-Hsin; Waddell, Peter J; Penny, David

    2002-07-10

    Complete mitochondrial genomes are reported for a pika (Ochotona collaris) and a vole (Volemys kikuchii) then analysed together with 35 other mitochondrial genomes from mammals. With standard phylogenetic methods the pika joins with the other lagomorph (rabbit) and the vole with the other murid rodents (rat and mouse). In addition, with hedgehog excluded, the seven rodent genomes consistently form a homogeneous group in the unrooted placental tree. Except for uncertainty of the position of tree shrew, the clade Glires (monophyletic rodents plus lagomorphs) is consistently found. The unrooted tree obtained by ProtML (Protein Maximum Likelihood, a program in MOLPHY) is compatible with a reclassification of mammals [Syst. Biol. 48, 1-5 (1999)] which is also supported by other recent studies. However, when this tree is rooted with marsupials plus platypus, the outgroup often joins the lineage leading to the three murid rodents, so the rodents are no longer monophyletic. Apart from misplacing the root, the presence of the outgroups also distorts other parts of the unrooted tree. Either constraining the tree to maintain rodents monophyletic, or omitting murids, maintains the ingroup tree and sees the outgroup join on the edge to Xenarthra, to Afrotheria, or to these two groups together. This emphasises the importance of carrying out both an unrooted and a rooted analysis. It is known from cancer research that murid rodents have reduced activity in some DNA repair mechanisms and this alters their substitution pattern - this may be the case for mitochnodrial DNA as well. Comparing nucleotide compositions may identify taxa that differ in aspects of their DNA repair mechanisms.

  12. Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes).

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    Vélez-Zuazo, Ximena; Agnarsson, Ingi

    2011-02-01

    Sharks are a diverse and ecologically important group, including some of the ocean's largest predatory animals. Sharks are also commercially important, with many species suffering overexploitation and facing extinction. However, despite a long evolutionary history, commercial, and conservation importance, phylogenetic relationships within the sharks are poorly understood. To date, most studies have either focused on smaller clades within sharks, or sampled taxa sparsely across the group. A more detailed species-level phylogeny will offer further insights into shark taxonomy, provide a tool for comparative analyses, as well as facilitating phylogenetic estimates of conservation priorities. We used four mitochondrial and one nuclear gene to investigate the phylogenetic relationships of 229 species (all eight Orders and 31 families) of sharks, more than quadrupling the number of taxon sampled in any prior study. The resulting Bayesian phylogenetic hypothesis agrees with prior studies on the major relationships of the sharks phylogeny; however, on those relationships that have proven more controversial, it differs in several aspects from the most recent molecular studies. The phylogeny supports the division of sharks into two major groups, the Galeomorphii and Squalimorphii, rejecting the hypnosqualean hypothesis that places batoids within sharks. Within the squalimorphs the orders Hexanchiformes, Squatiniformes, Squaliformes, and Pristiophoriformes are broadly monophyletic, with minor exceptions apparently due to missing data. Similarly, within Galeomorphs, the orders Heterodontiformes, Lamniformes, Carcharhiniformes, and Orectolobiformes are broadly monophyletic, with a couple of species 'misplaced'. In contrast, many of the currently recognized shark families are not monophyletic according to our results. Our phylogeny offers some of the first clarification of the relationships among families of the order Squaliformes, a group that has thus far received relatively

  13. Phylogeny and divergence times of some racerunner lizards (Lacertidae: Eremias) inferred from mitochondrial 16S rRNA gene segments.

    Science.gov (United States)

    Guo, Xianguang; Dai, Xin; Chen, Dali; Papenfuss, Theodore J; Ananjeva, Natalia B; Melnikov, Daniel A; Wang, Yuezhao

    2011-11-01

    Eremias, or racerunners, is a widespread lacertid genus occurring in China, Mongolia, Korea, Central Asia, Southwest Asia and Southeast Europe. It has been through a series of taxonomic revisions, but the phylogenetic relationships among the species and subgenera remain unclear. In this study, a frequently studied region of the mitochondrial 16S rRNA was used to (i) reassess the phylogenetic relationships of some Eremias species, (ii) test if the viviparous species form a monophyletic group, and (iii) estimate divergence time among lineages using a Bayesian relaxed molecular-clock approach. The resulting phylogeny supports monophyly of Eremias sensu Szczerbak and a clade comprising Eremias, Acanthodactylus and Latastia. An earlier finding demonstrating monophyly of the subgenus Pareremias is corroborated, with Eremias argus being the sister taxon to Eremias brenchleyi. We present the first evidence that viviparous species form a monophyletic group. In addition, Eremias przewalskii is nested within Eremias multiocellata, suggesting that the latter is likely a paraphyletic species or a species complex. Eremias acutirostris and Eremias persica form a clade that is closely related to the subgenus Pareremias. However, the subgenera Aspidorhinus, Scapteira, and Rhabderemias seem not to be monophyletic, respectively. The Bayesian divergence-time estimation suggests that Eremias originated at about 9.9 million years ago (with the 95% confidence interval ranging from 7.6 to 12 Ma), and diversified from Late Miocene to Pleistocene. Specifically, the divergence time of the subgenus Pareremias was dated to about 6.3 million years ago (with the 95% confidence interval ranging from 5.3 to 8.5 Ma), which suggests that the diversification of this subgenus might be correlated with the evolution of an East Asian monsoon climate triggered by the rapid uplift of the Tibetan Plateau approximately 8 Ma.

  14. Do we need many genes for phylogenetic inference?

    Science.gov (United States)

    Aleshin, V V; Konstantinova, A V; Mikhailov, K V; Nikitin, M A; Petrov, N B

    2007-12-01

    Fifty-six nuclear protein coding genes from Taxonomically Broad EST Database and other databases were selected for phylogenomic-based examination of alternative phylogenetic hypotheses concerning intergroup relationship between multicellular animals (Metazoa) and other representatives of Opisthokonta. The results of this work support sister group relationship between Metazoa and Choanoflagellata. Both of these groups form the taxon Holozoa along with the monophyletic Ichthyosporea or Mesomycetozoea (a group that includes Amoebidium parasiticum, Sphaeroforma arctica, and Capsaspora owczarzaki). These phylogenetic hypotheses receive high statistical support both when utilizing whole alignment and when only 5000 randomly selected alignment positions are used. The presented results suggest subdivision of Fungi into Eumycota and lower fungi, Chytridiomycota. The latter form a monophyletic group that comprises Chytridiales+Spizellomycetales+Blastocladiales (Batrachochytrium, Spizellomyces, Allomyces, Blastocladiella), contrary to the earlier reports based on the analysis of 18S rRNA and a limited set of protein coding genes. The phylogenetic distribution of genes coding for a ubiquitin-fused ribosomal protein S30 implies at least three independent cases of gene fusion: in the ancestors of Holozoa, in heterotrophic Heterokonta (Oomycetes and Blastocystis) and in the ancestors of Cryptophyta and Glaucophyta. Ubiquitin-like sequences fused with ribosomal protein S30 outside of Holozoa are not FUBI orthologs. Two independent events of FUBI replacement by the ubiquitin sequence were detected in the lineage of C. owczarzaki and in the monophyletic group of nematode worms Tylenchomorpha+Cephalobidae. Bursaphelenchus xylophilus (Aphelenchoidoidea) retains a state typical of the rest of the Metazoa. The data emphasize the fact that the reliability of phylogenetic reconstructions depends on the number of analyzed genes to a lesser extent than on our ability to recognize

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

    Science.gov (United States)

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

    2014-01-01

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

  16. From surnames to linguistic and genetic diversity: five centuries of internal migrations in Spain.

    Science.gov (United States)

    Rodríguez-Díaz, Roberto; Blanco-Villegas, María José; Manni, Franz

    2017-09-01

    In a previous study concerning 33,753 single Spanish surnames (considered as tokens) occurring 51,419,788 times we have shown that the present-day geography of contemporary surname variability in Spain still corresponds to the political geography of the country at the end of the Middle Ages. Here we reprocess the same database, by clustering surnames with Self-Organizing Maps (SOMs) according to their geographic distribution, to identify the monophyletic surnames showing a geo-historical origin in one of the 47 provinces of continental Spain. They are 25,714, and they occur 12,348,109 times, meaning that about 75% of the Spanish population bears a surname that had a polyphyletic origin. From monophyletic surnames we compute migration matrices accounting for the internal migrations that took place since five centuries ago, when Spanish surnames started to be patrilineally inherited. The mono/ polyphyletic classification we obtain fits ancient census data and is compatible with published molecular diversity of the Y-chromosomes associated to selected Spanish surnames. Monophyletic surnames indicate that i) the provinces exhibiting a higher percentage of autochthonous surnames are also ii) those from which emigration corresponds to a local isolation-by-distance model of diffusion and iii) those that attracted a lower number of immigrants. These are also the provinces where languages other than Castilian are spoken. We suggest that demographic stability explains linguistic resilience, as people prefer to move to areas in which the linguistic variety is more similar to their own. So far the reciprocal influence of migration and language has been investigated at local scales, here we outline how to investigate it at national scales and for time-depths of centuries.

  17. The Mitochondrial Genomes of the Nudibranch Mollusks, Melibe leonina and Tritonia diomedea, and Their Impact on Gastropod Phylogeny.

    Directory of Open Access Journals (Sweden)

    Joseph L Sevigny

    Full Text Available The phylogenetic relationships among certain groups of gastropods have remained unresolved in recent studies, especially in the diverse subclass Opisthobranchia, where nudibranchs have been poorly represented. Here we present the complete mitochondrial genomes of Melibe leonina and Tritonia diomedea (more recently named T. tetraquetra, two nudibranchs from the unrepresented Cladobranchia group, and report on the resulting phylogenetic analyses. Both genomes coded for the typical thirteen protein-coding genes, twenty-two transfer RNAs, and two ribosomal RNAs seen in other species. The twelve-nucleotide deletion previously reported for the cytochrome oxidase 1 gene in several other Melibe species was further clarified as three separate deletion events. These deletions were not present in any opisthobranchs examined in our study, including the newly sequenced M. leonina or T. diomedea, suggesting that these previously reported deletions may represent more recently divergent taxa. Analysis of the secondary structures for all twenty-two tRNAs of both M. leonina and T. diomedea indicated truncated d arms for the two serine tRNAs, as seen in some other heterobranchs. In addition, the serine 1 tRNA in T. diomedea contained an anticodon not yet reported in any other gastropod. For phylogenetic analysis, we used the thirteen protein-coding genes from the mitochondrial genomes of M. leonina, T. diomedea, and seventy-one other gastropods. Phylogenetic analyses were performed for both the class Gastropoda and the subclass Opisthobranchia. Both Bayesian and maximum likelihood analyses resulted in similar tree topologies. In the Opisthobranchia, the five orders represented in our study were monophyletic (Anaspidea, Cephalaspidea, Notaspidea, Nudibranchia, Sacoglossa. In Gastropoda, two of the three traditional subclasses, Opisthobranchia and Pulmonata, were not monophyletic. In contrast, four of the more recently named gastropod clades (Vetigastropoda

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

    Science.gov (United States)

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

    2012-06-01

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

  19. [Fauna of monogeneans (Monogenea, Platyhelminthes) of gudgeons (Gobioninae, Cyprinidae). 1. Composition, structure, and characteristics of distribution].

    Science.gov (United States)

    Gerasev, P I

    2008-01-01

    Monogeneans parasitize 31 gudgeon species of 130, and 13 gudgeon genera of 30 known. Monogenea from gudgeon comprise 48 species of the genus Dactylogyrus, 1 Bivaginogyrus (Dactylogyridae), 18 Ancyrocephalus s. l. (Ancyrocephalidae), 6 Gyrodactylus (Gyrodactylidae), 3 Paradiplozoon, and 1 species of the genus Sindiplozoon (Diplozoidae). The following characters were used in the morphological analysis: (1) structure of the copulatory organ, (2) morphology of the anchors, marginal hooks and bars, (3) characteristic of attachment on gills. Among the Dactylogyrus species parasitizing gudgeon, 30 monophyletic species groups and 13 levels of morphological organization were established. The first level comprises dactylogyrids without the additional ventral bar of haptor. It includes species with the copulatory organ of pro-cryptomeres type. This type is ancestral for dactylogyrids of the Amur/China fauna. Levels II-IV; VI, etc. are derivates of level I. Levels VII-VIII can be characterized by the jamming type of attachment characteristic for Dactylogyrus sphyrna or D. anchoratus, when marginal hooks penetrate gill filaments towards the anchors. Levels IX-XII include species with the attachment by clasping, when the anchors directed towards each other. Some species groups of Dactylogyrus (V, XIII) switched onto gudgeons from other fishes (Cultrinae, Xenocyprininae, Hypophthalmichthinae). Species of the genus Ancyrocephalus s. l. form two levels of morphological organization and 8 monophyletic groups. Repeated switches of ancyrocephalids from freshwater gobies to gudgeons and their switches from gudgeons to other fishes were shown. Species of the genus Hemibarbus serve as hosts for morphologically peculiar species groups of Dactylogyrus and Ancyrocephalus s. l. We can conclude that gyrodactylids from gudgeons do not form a natural monophyletic group. This parasite fauna originated as a result of multiple switches from phylogenetically distant but ecologically similar hosts

  20. Basal jawed vertebrate phylogenomics using transcriptomic data from Solexa sequencing.

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    Ming Chen

    Full Text Available The traditionally accepted relationships among basal jawed vertebrates have been challenged by some molecular phylogenetic analyses based on mitochondrial sequences. Those studies split extant gnathostomes into two monophyletic groups: tetrapods and piscine branch, including Chondrichthyes, Actinopterygii and sarcopterygian fishes. Lungfish and bichir are found in a basal position on the piscine branch. Based on transcriptomes of an armored bichir (Polypterus delhezi and an African lungfish (Protopterus sp. we generated, expressed sequences and whole genome sequences available from public databases, we obtained 111 genes to reconstruct the phylogenetic tree of basal jawed vertebrates and estimated their times of divergence. Our phylogenomic study supports the traditional relationship. We found that gnathostomes are divided into Chondrichthyes and the Osteichthyes, both with 100% support values (posterior probabilities and bootstrap values. Chimaeras were found to have a basal position among cartilaginous fishes with a 100% support value. Osteichthyes were divided into Actinopterygii and Sarcopterygii with 100% support value. Lungfish and tetrapods form a monophyletic group with 100% posterior probability. Bichir and two teleost species form a monophyletic group with 100% support value. The previous tree, based on mitochondrial data, was significantly rejected by an approximately unbiased test (AU test, p = 0. The time of divergence between lungfish and tetrapods was estimated to be 391.8 Ma and the divergence of bichir from pufferfish and medaka was estimated to be 330.6 Ma. These estimates closely match the fossil record. In conclusion, our phylogenomic study successfully resolved the relationship of basal jawed vertebrates based on transtriptomes, EST and whole genome sequences.

  1. Phylogenetic relationships of Proboscoida Broch, 1910 (Cnidaria, Hydrozoa): Are traditional morphological diagnostic characters relevant for the delimitation of lineages at the species, genus, and family levels?

    Science.gov (United States)

    Cunha, Amanda F; Collins, Allen G; Marques, Antonio C

    2017-01-01

    Overlapping variation of morphological characters can lead to misinterpretation in taxonomic diagnoses and the delimitation of different lineages. This is the case for hydrozoans that have traditionally been united in the family Campanulariidae, a group known for its wide morphological variation and complicated taxonomic history. In a recently proposed phylogenetic classification of leptothecate hydrozoans, this family was restricted to a more narrow sense while a larger clade containing most species traditionally classified in Campanulariidae, along with members of Bonneviellidae, was established as the suborder Proboscoida. We used molecular data to infer the phylogenetic relationships among campanulariids and assess the traditional classification of the family, as well as the new classification scheme for the group. The congruity and relevance of diagnostic characters were also evaluated. While mostly consistent with the new phylogenetic classification of Proboscoida, our increased taxon sampling resulted in some conflicts at the family level, specially regarding the monophyly of Clytiidae and Obeliidae. Considering the traditional classification, only Obeliidae is close to its original scope (as subfamily Obeliinae). At the genus level, Campanularia and Clytia are not monophyletic. Species with Obelia-like medusae do not form a monophyletic group, nor do species with fixed gonophores, indicating that these characters do not readily diagnose different genera. Finally, the species Orthopyxis integra, Clytia gracilis, and Obelia dichotoma are not monophyletic, suggesting that most of their current diagnostic characters are not informative for their delimitation. Several diagnostic characters in this group need to be reassessed, with emphasis on their variation, in order to have a consistent taxonomic and phylogenetic framework for the classification of campanulariid hydrozoans. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Phylogeny of the bee genus Halictus (Hymenoptera: halictidae) based on parsimony and likelihood analyses of nuclear EF-1alpha sequence data.

    Science.gov (United States)

    Danforth, B N; Sauquet, H; Packer, L

    1999-12-01

    We investigated higher-level phylogenetic relationships within the genus Halictus based on parsimony and maximum likelihood (ML) analysis of elongation factor-1alpha DNA sequence data. Our data set includes 41 OTUs representing 35 species of halictine bees from a diverse sample of outgroup genera and from the three widely recognized subgenera of Halictus (Halictus s.s., Seladonia, and Vestitohalictus). We analyzed 1513 total aligned nucleotide sites spanning three exons and two introns. Equal-weights parsimony analysis of the overall data set yielded 144 equally parsimonious trees. Major conclusions supported in this analysis (and in all subsequent analyses) included the following: (1) Thrincohalictus is the sister group to Halictus s.l., (2) Halictus s.l. is monophyletic, (3) Vestitohalictus renders Seladonia paraphyletic but together Seladonia + Vestitohalictus is monophyletic, (4) Michener's Groups 1 and 3 are monophyletic, and (5) Michener's Group 1 renders Group 2 paraphyletic. In order to resolve basal relationships within Halictus we applied various weighting schemes under parsimony (successive approximations character weighting and implied weights) and employed ML under 17 models of sequence evolution. Weighted parsimony yielded conflicting results but, in general, supported the hypothesis that Seladonia + Vestitohalictus is sister to Michener's Group 3 and renders Halictus s.s. paraphyletic. ML analyses using the GTR model with site-specific rates supported an alternative hypothesis: Seladonia + Vestitohalictus is sister to Halictus s.s. We mapped social behavior onto trees obtained under ML and parsimony in order to reconstruct the likely historical pattern of social evolution. Our results are unambiguous: the ancestral state for the genus Halictus is eusociality. Reversal to solitary behavior has occurred at least four times among the species included in our analysis. Copyright 1999 Academic Press.

  3. Searching for natural lineages within the Cerylonid Series (Coleoptera: Cucujoidea).

    Science.gov (United States)

    Robertson, James A; Whiting, Michael F; McHugh, Joseph V

    2008-01-01

    Phylogenetic relationships within the diverse beetle superfamily Cucujoidea are poorly known. The Cerylonid Series (C.S.) is the largest of all proposed superfamilial cucujoid groups, comprising eight families and representing most of the known cucujoid species diversity. The monophyly of the C.S., however, has never been formally tested and the higher-level relationships among and within the constituent families remain equivocal. Here we present a phylogenetic study based on 18S and 28S rDNA for 16 outgroup taxa and 61 C.S. ingroup taxa, representing seven of the eight C.S. families and 20 of 39 subfamilies. We test the monophyly of the C.S., investigate the relationships among the C.S. families, and test the monophyly of the constituent families and subfamilies. Phylogenetic reconstruction of the combined data was achieved via standard static alignment parsimony analyses, Direct Optimization using parsimony, and partitioned Bayesian analysis. All three analyses support the paraphyly of Cucujoidea with respect to Tenebrionoidea and confirm the monophyly of the C.S. The C.S. families Bothrideridae, Cerylonidae, Discolomatidae, Coccinellidae and Corylophidae are supported as monophyletic in all analyses. Only the Bayesian analysis recovers a monophyletic Latridiidae. Endomychidae is recovered as polyphyletic in all analyses. Of the 14 subfamilies with multiple terminals in this study, 11 were supported as monophyletic. The corylophid subfamily Corylophinae and the coccinellid subfamilies Chilocorinae and Scymninae are recovered as paraphyletic. A sister grouping of Anamorphinae+Corylophidae is supported in all analyses. Other taxonomic implications are discussed in light of our results.

  4. The complete mitochondrial genome of the geophilomorph centipede Strigamia maritima.

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    Helen E Robertson

    Full Text Available Strigamia maritima (Myriapoda; Chilopoda is a species from the soil-living order of geophilomorph centipedes. The Geophilomorpha is the most speciose order of centipedes with over a 1000 species described. They are notable for their large number of appendage bearing segments and are being used as a laboratory model to study the embryological process of segmentation within the myriapods. Using a scaffold derived from the recently published genome of Strigamia maritima that contained multiple mitochondrial protein-coding genes, here we report the complete mitochondrial genome of Strigamia, the first from any geophilomorph centipede. The mitochondrial genome of S. maritima is a circular molecule of 14,938 base pairs, within which we could identify the typical mitochondrial genome complement of 13 protein-coding genes and 2 ribosomal RNA genes. Sequences resembling 16 of the 22 transfer RNA genes typical of metazoan mitochondrial genomes could be identified, many of which have clear deviations from the standard 'cloverleaf' secondary structures of tRNA. Phylogenetic trees derived from the concatenated alignment of protein-coding genes of S. maritima and >50 other metazoans were unable to resolve the Myriapoda as monophyletic, but did support a monophyletic group of chilopods: Strigamia was resolved as the sister group of the scolopendromorph Scolopocryptos sp. and these two (Geophilomorpha and Scolopendromorpha, along with the Lithobiomorpha, formed a monophyletic group the Pleurostigmomorpha. Gene order within the S. maritima mitochondrial genome is unique compared to any other arthropod or metazoan mitochondrial genome to which it has been compared. The highly unusual organisation of the mitochondrial genome of Strigamia maritima is in striking contrast with the conservatively evolving nuclear genome: sampling of more members of this order of centipedes will be required to see whether this unusual organization is typical of the Geophilomorpha or

  5. Phylogenetic relationships of the South American Doradoidea (Ostariophysi: Siluriformes

    Directory of Open Access Journals (Sweden)

    José L. O. Birindelli

    Full Text Available A phylogenetic analysis based on 311 morphological characters is presented for most species of the Doradidae, all genera of the Auchenipteridae, and representatives of 16 other catfish families. The hypothesis that was derived from the six most parsimonious trees support the monophyly of the South American Doradoidea (Doradidae plus Auchenipteridae, as well as the monophyly of the clade Doradoidea plus the African Mochokidae. In addition, the clade with Sisoroidea plus Aspredinidae was considered sister to Doradoidea plus Mochokidae. Within the Auchenipteridae, the results support the monophyly of the Centromochlinae and Auchenipterinae. The latter is composed of Tocantinsia, and four monophyletic units, two small with Asterophysusand Liosomadoras, and Pseudotatiaand Pseudauchenipterus, respectively, and two large ones with the remaining genera. Within the Doradidae, parsimony analysis recovered Wertheimeriaas sister to Kalyptodoras, composing a clade sister to all remaining doradids, which include Franciscodorasand two monophyletic groups: Astrodoradinae (plus Acanthodorasand Agamyxis and Doradinae (new arrangement. Wertheimerinae, new subfamily, is described for Kalyptodoras and Wertheimeria. Doradinae is corroborated as monophyletic and composed of four groups, one including Centrochirand Platydoras, the other with the large-size species of doradids (except Oxydoras, another with Orinocodoras, Rhinodoras, and Rhynchodoras, and another with Oxydorasplus all the fimbriate-barbel doradids. Based on the results, the species of Opsodoras are included in Hemidoras; and Tenellus, new genus, is described to include Nemadoras trimaculatus, N. leporhinusand Nemadoras ternetzi. Due to conflicting hypotheses of the phylogenetic position of Acanthodoras, Agamyxis, and Franciscodoras, these are considered as incertae sedisin Doradidae. All suprageneric taxa of the Doradoidea are diagnosed based on synapomorphic morphological characteristics.

  6. Mitogenomics of 'Old World Acraea' butterflies reveals a highly divergent 'Bematistes'.

    Science.gov (United States)

    Timmermans, M J T N; Lees, D C; Thompson, M J; Sáfián, Sz; Brattström, O

    2016-04-01

    Afrotropical Acraeini butterflies provide a fascinating potential model system to contrast with the Neotropical Heliconiini, yet their phylogeny remains largely unexplored by molecular methods and their generic level nomenclature is still contentious. To test the potential of mitogenomes in a simultaneous analysis of the radiation, we sequenced the full mitochondrial genomes of 19 African species. Analyses show the potential of mitogenomic phylogeny reconstruction in this group. Inferred relationships are largely congruent with a previous multilocus study. We confirm a monophyletic Telchinia to include the Asiatic Pareba with a complicated paraphylum, traditional (sub)genus Acraea, toward the base. The results suggest that several proposed subgenera and some species groups within Telchinia are not monophyletic, while two other (sub)genera could possibly be combined. Telchinia was recovered without strong support as sister to the potentially interesting system of distasteful model butterflies known as Bematistes, a name that is suppressed in some treatments. Surprisingly, we find that this taxon has remarkably divergent mitogenomes and unexpected synapomorphic tRNA rearrangements. These gene order changes, combined with evidence for deviating dN/dS ratios and evidence for episodal diversifying selection, suggest that the ancestral Bematistes mitogenome has had a turbulent past. Our study adds genetic support for treating this clade as a distinct genus, while the alternative option, adopted by some authors, of Acraea being equivalent to Acraeini merely promotes redundancy. We pave the way for more detailed mitogenomic and multi-locus molecular analyses which can determine how many genera are needed (possibly at least six) to divide Acraeini into monophyletic groups that also facilitate communication about their biology. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Identification of a new clade of hepatitis B virus genotype F.

    Science.gov (United States)

    Mojsiejczuk, Laura Noelia; Torres, Carolina; Fainboin, Hugo Alberto; Galdame, Omar Andres; Campos, Rodolfo Hector; Flichman, Diego Martin

    2015-08-01

    Hepatitis B virus (HBV) is classified into eight main genotypes (A-H) and several subgenotypes. Here, three new genotype F complete genome sequences isolated from patients from Buenos Aires city are reported. The new sequences form a separate monophyletic group from the previously known subgenotype F4 strains. Based on results of phylogenetic, genetic distance and evolutionary analyses, the name F4b is proposed for these isolates and F4a for the formerly known as F4. The identification of new clusters allows deepening the knowledge about the diversification process and evolutionary history of HBV.

  8. Convergent coevolution in the domestication of coral mushrooms by fungus-growing ants

    DEFF Research Database (Denmark)

    Munkacsi, A.B.; Pan, J.J.; Villesen, P.

    2004-01-01

    of parallel coevolution, where the symbionts of each functional group are members of monophyletic groups. However, there is one outstanding exception in the fungus-growing ant system, the unidentified cultivar grown only by ants in the Apterostigma pilosum group. We classify this cultivar in the coral-mushroom...... family Pterulaceae using phylogenetic reconstructions based on broad taxon sampling, including the first mushroom collected from the garden of an ant species in the A. pilosum group. The domestication of the pterulaceous cultivar is independent from the domestication of the gilled mushrooms cultivated...

  9. The aberrant millipede genus Pteridoiulus and its position in a revised molecular phylogeny of the family Julidae (Diplopoda : Julida)

    DEFF Research Database (Denmark)

    Enghoff, Henrik; Petersen, Gitte; Seberg, Ole

    2013-01-01

    A phylogenetic analysis of 62 species (32 genera) of the Palaearctic millipede family Julidae, including the aberrant alpine genus Pteridoiulus Verhoeff, 1913, was made based on partial sequences of the mitochondrial 16S rRNA (16S) gene and the nuclear 28SrRNA(28S) gene, respectively. The two......MAFTTand run inTNT both with gaps treated as a fifth state, and as missing, and finally the alignments were used as input in a maximum likelihood (ML) analysis. The order Julida and the family Julidae were recovered as monophyletic under all weight sets in POY, as well as in the TNT andMLanalyses. Likewise...

  10. From the phylogeny of the Satyrinae butterflies to the systematics of Euptychiina (lepidoptera: nymphalidae): history, progress and prospects.

    Science.gov (United States)

    Marín, M A; Peña, C; Freitas, A V L; Wahlberg, N; Uribe, S I

    2011-01-01

    We review the various proposals of evolutionary and classification schemes for Satyrinae and particularly Euptychiina butterflies, assessing progress and prospects of research for the group. Among the highlights is the proposal to include Morphini, Brassolini and Amathusiini as part of Satyrinae. Although it is clear that this hypothesis requires further investigation, phylogenetic studies recently conducted recover this clade as part of Satyrinae with high support. The phylogenetic analyses for Euptychiina carried out to date recover the monophyly of the group and have identified a variety of genera as non-monophyletic. Further work is necessary to resolve the position of the subtribe and the evolutionary relationships of several genera.

  11. Sharp phylogeographic breaks and patterns of genealogical concordance in the brine shrimp Artemia franciscana.

    Science.gov (United States)

    Maniatsi, Stefania; Kappas, Ilias; Baxevanis, Athanasios D; Farmaki, Theodora; Abatzopoulos, Theodore J

    2009-12-18

    Genealogical concordance is a critical overlay of all phylogenetic analyses, irrespective of taxonomic level. To assess such patterns of congruence we have compiled and derived sequence data for two mitochondrial (16S rRNA, COI) and two nuclear (ITS1, p26) markers in 14 American populations of the hypersaline branchiopod Artemia franciscana. Cladistic analysis revealed three reciprocally monophyletic mitochondrial clades. For nuclear DNA, incomplete lineage sorting was evident presumably as a result of slower coalescence or male-mediated dispersal. Our findings capture the genealogical interval between gene splitting and population divergence. In this sense, strong indications are provided in favour of a superspecies status and ongoing speciation in A. franciscana.

  12. Species-level para- and polyphyly in DNA barcode gene trees

    DEFF Research Database (Denmark)

    Mutanen, Marko; Kivelä, Sami M.; Vos, Rutger A.

    2016-01-01

    between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service "Monophylizer...... to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling...

  13. Diversity of microorganisms isolated from the soil sample surround Chroogomphus rutilus in the Beijing region

    DEFF Research Database (Denmark)

    Wang, P; Liu, Y; Yin, Y

    2011-01-01

    to isolate and classify beneficial microorganisms that could affect its growth, which could be used in future research on artificial cultivation. In total, 342 isolates were isolated from soil samples collected around a C. rutilus colony in the Beijing region. Of these, 22 bacterial and 14 fungal isolates....... Using internal transcribed spacer (ITS) sequence analysis, fungal isolates were divided into four monophyletic clusters: Penicillium, Trichoderma, Mortierella, and Bionectria. Moreover, the phylogenetic diversity of these isolates was analysed. The results indicated that numerous microorganisms were...

  14. The Madagascan endemic myrmicine ants related to Eutetramorium (Hymenoptera: Formicidae): taxonomy of the genera Eutetramorium Emery, Malagidris nom. n., Myrmisaraka gen. n., Royidris gen. n., and Vitsika gen. n.

    Science.gov (United States)

    Bolton, Barry; Fisher, Brian L

    2014-04-24

    The monophyletic group of myrmicine ant genera related to Eutetramorium is described and its taxonomy is documented. The group is endemic in Madagascar and contains five genera: Eutetramorium Emery, 1899 (3 species, 1 of which is new); Malagidris nom. n., a replacement name for Brunella Forel, 1917, junior homonym of Brunella Smith, G.W. 1909 (Crustacea) (6 species, 5 of which are new); Myrmisaraka gen. n. (2 species, both new); Royidris gen. n. (15 species, 11 of which are new); Vitsika gen. n. (14 species, all of which are new). Keys to the worker caste are provided for all genera, and provisional keys to known males are given for Malagidris and Vitsika.

  15. Isleria, a new genus of antwren (Aves: Passeriformes: Thamnophilidae)

    Science.gov (United States)

    Bravo, Gustavo A.; Chesser, R. Terry; Brumfield, Robb T.

    2012-01-01

    A comprehensive molecular phylogenetic analysis of the family Thamnophilidae indicated that the genus Myrmotherula is not monophyletic. The clade composed of M. guttata and M. hauxwelli is only distantly related to other members of the genus and should be removed from Myrmotherula. The phenotypic distinctiveness of the clade argues against merging it with its sister group Thamnomanes and no generic name is available for the guttata-hauxwelli clade. Consequently, we describe the genus Isleria for these two species, and designate Myrmothera guttata as its type species.

  16. From the phylogeny of the Satyrinae butterflies to the systematics of Euptychiina (Lepidoptera: Nymphalidae): history, progress and prospects

    Energy Technology Data Exchange (ETDEWEB)

    Marin, M.A.; Uribe, S.I., E-mail: mamarin0@bt.unal.edu.c [Universidad Nacional de Colombia, Medellin (Colombia). Grupo de Investigacion en Sistematica Molecular; Pena, C. [Universidad Nacional Mayor de San Marcos, Lima (Peru). Museo de Historia Natural; Freitas, A.V.L. [Universidade Estadual de Campinas (IB/UNICAMP), SP (Brazil). Inst. de Biologia. Dept. de Biologia Animal e Museu de Zoologia; Wahlberg, N. [University of Turku (Finland). Dept. of Biology. Lab. of Genetics

    2011-01-15

    We review the various proposals of evolutionary and classification schemes for Satyrinae and particularly Euptychiina butterflies, assessing progress and prospects of research for the group. Among the highlights is the proposal to include Morphini, Brassolini and Amathusiini as part of Satyrinae. Although it is clear that this hypothesis requires further investigation, phylogenetic studies recently conducted recover this clade as part of Satyrinae with high support. The phylogenetic analyses for Euptychiina carried out to date recover the monophyly of the group and have identified a variety of genera as non-monophyletic. Further work is necessary to resolve the position of the subtribe and the evolutionary relationships of several genera. (author)

  17. A phylogenetic analysis of the myxobacteria: basis for their classification

    Science.gov (United States)

    Shimkets, L.; Woese, C. R.

    1992-01-01

    The primary sequence and secondary structural features of the 16S rRNA were compared for 12 different myxobacteria representing all the known cultivated genera. Analysis of these data show the myxobacteria to form a monophyletic grouping consisting of three distinct families, which lies within the delta subdivision of the purple bacterial phylum. The composition of the families is consistent with differences in cell and spore morphology, cell behavior, and pigment and secondary metabolite production but is not correlated with the morphological complexity of the fruiting bodies. The Nannocystis exedens lineage has evolved at an unusually rapid pace and its rRNA shows numerous primary and secondary structural idiosyncrasies.

  18. Earthworms and their Nephridial Symbionts: Co-diversification and Maintenance of the Symbiosis

    DEFF Research Database (Denmark)

    Lund, Marie Braad; Holmstrup, Martin; Davidson, Seana K.

    Earthworms harbor in their nephridia (excretory organs) symbiotic bacteria which densely colonize a specific part of the nephridia, called the ampulla [1]. The symbiosis is species-specific and the symbionts form their own monophyletic genus Verminephrobacter (β-proteobacteria) [2...... showed no significant differences in growth rate and fecundity between symbiotic and aposymbiotic worms. Thus the symbionts do not appear to have an effect on worm fitness, under growth conditions tested. The underlying functional and maintaining mechanisms of this symbiosis remain a conundrum. [1] Knop...

  19. Molecular and morphological phylogenetics of chelonine parasitoid wasps (Hymenoptera: Braconidae), with a critical assessment of divergence time estimations.

    Science.gov (United States)

    Kittel, Rebecca N; Austin, Andrew D; Klopfstein, Seraina

    2016-08-01

    Parasitoid wasps of the subfamily Cheloninae are both species rich and poorly known. Although the taxonomy of Cheloninae appears to be relatively stable, there is no clear understanding of relationships among higher-level taxa. We here applied molecular phylogenetic analyses using three markers (COI, EF1α, 28S) and 37 morphological characters to elucidate the evolution and systematics of these wasps. Analyses were based on 83 specimens representing 13 genera. All genera except Ascogaster, Phanerotoma, and Pseudophanerotoma formed monophyletic groups; Furcidentia (stat. rev.) is raised to generic rank. Neither Chelonus (Chelonus) nor Chelonus (Microchelonus) were recovered as monophyletic, but together formed a monophyletic lineage. The tribes Chelonini and Odontosphaeropygini formed monophyletic groups, but the Phanerotomini sensu Zettel and Pseudophanerotomini were retrieved as either para- or polyphyletic. The genera comprising the former subfamily Adeliinae were confirmed as being nested within the Cheloninae. To estimate the age of the subfamily, we used 16 fossil taxa. Three approaches were compared: fixed-rate dating, node dating, and total-evidence dating, with age estimates differing greatly between the three methods. Shortcomings of each approach in relation to our dataset are discussed, and none of the age estimates is deemed sufficiently reliable. Given that most dating studies use a single method only, in most cases without presenting analyses on the sensitivity to priors, it is likely that numerous age estimates in the literature suffer from a similar lack of robustness. We argue for a more rigorous approach to dating analyses and for a faithful presentation of uncertainties in divergence time estimates. Given the results of the phylogenetic analysis the following taxonomic changes are proposed: Furcidentia Zettel (stat. rev.), previously treated as a subgenus of Pseudophanerotoma Zettel is raised to generic rank; Microchelonus Szépligeti (syn. nov

  20. Mitochondrial d-loop sequence variation and phylogeny of gobiobotine fishes

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The mitochondrial DNA control region is amplified and sequenced from 8 genera and 10 species of gobiobotine fishes. The phylogenetic tree of Gobiobotinae and some representative species of other Cyprinid subfamilies obtained by the method of neighborhood joining, maximum likelihood and maximum parsimony with Danio rerio as an outgroup indicates that Gobiobotinae fishes are a monophyletic group which is close to Gobioninae subfamily. Gobiobotinae should be included into subfamily Gobioninae in terms of phylogenetic analysis. The research result supports that Gobiobotinae can be divided into genus Xenophysogobio and Gobiobotia. Xenophysogobio is the most primitive genera in the subfamily.

  1. Phylogenetic Study of Mangifera laurina and its Related Species Using cpDNA trnL-F Spacer Markers

    Directory of Open Access Journals (Sweden)

    FITMAWATI

    2010-03-01

    Full Text Available Phylogenetic study of cpDNA intergenic spacer trnL-F of Mangifera laurina and their related species within the genus Mangifera in Indonesia was conducted using Rutaceae as the outgroup. This study was to reconstruct phylogenetic relationships and to understand infraspecific relationships within Mangifera based on cpDNA trnL-F intergenic spacer sequences. The results showed that Mangifera sp. Hiku (mangga hiku as the basic cultivar in the clade, and it supported the monophyletic group in Mangifera. And phylogenetic construction indicated that Mangifera sp. Hiku was the progenitor of M. laurina and their related species.

  2. Convergent coevolution in the domestication of coral mushrooms by fungus-growing ants

    DEFF Research Database (Denmark)

    Munkacsi, A.B.; Pan, J.J.; Villesen, P.;

    2004-01-01

    of parallel coevolution, where the symbionts of each functional group are members of monophyletic groups. However, there is one outstanding exception in the fungus-growing ant system, the unidentified cultivar grown only by ants in the Apterostigma pilosum group. We classify this cultivar in the coral-mushroom...... family Pterulaceae using phylogenetic reconstructions based on broad taxon sampling, including the first mushroom collected from the garden of an ant species in the A. pilosum group. The domestication of the pterulaceous cultivar is independent from the domestication of the gilled mushrooms cultivated...

  3. Biogeography and Phylogeny of Wood-feeding Cockroaches in the Genus Cryptocercus

    Directory of Open Access Journals (Sweden)

    Kiyoto Maekawa

    2011-07-01

    Full Text Available Subsocial, xylophagous cockroaches of the genus Cryptocercus exhibit a disjunct distribution, with representatives in mature montane forests of North America, China, Korea and the Russian Far East. All described species are wingless and dependent on rotting wood for food and shelter at all stages of their life cycle; consequently, their distribution is tied to that of forests and strongly influenced by palaeogeographical events. Asian and American lineages form distinct monophyletic groups, comprised of populations with complex geographic substructuring. We review the phylogeny and distribution of Cryptocercus, and discuss splitting events inferred from molecular data.

  4. Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: further evidence from a nuclear gene of the systematic chaos in the family.

    Science.gov (United States)

    He, Shunping; Mayden, Richard L; Wang, Xuzheng; Wang, Wei; Tang, Kevin L; Chen, Wei-Jen; Chen, Yiyu

    2008-03-01

    The family Cyprinidae is the largest freshwater fish group in the world, including over 200 genera and 2100 species. The phylogenetic relationships of major clades within this family are simply poorly understood, largely because of the overwhelming diversity of the group; however, several investigators have advanced different hypotheses of relationships that pre- and post-date the use of shared-derived characters as advocated through phylogenetic systematics. As expected, most previous investigations used morphological characters. Recently, mitochondrial DNA (mtDNA) sequences and combined morphological and mtDNA investigations have been used to explore and advance our understanding of species relationships and test monophyletic groupings. Limitations of these studies include limited taxon sampling and a strict reliance upon maternally inherited mtDNA variation. The present study is the first endeavor to recover the phylogenetic relationships of the 12 previously recognized monophyletic subfamilies within the Cyprinidae using newly sequenced nuclear DNA (nDNA) for over 50 species representing members of the different previously hypothesized subfamily and family groupings within the Cyprinidae and from other cypriniform families as outgroup taxa. Hypothesized phylogenetic relationships are constructed using maximum parsimony and Basyesian analyses of 1042 sites, of which 971 sites were variable and 790 were phylogenetically informative. Using other appropriate cypriniform taxa of the families Catostomidae (Myxocyprinus asiaticus), Gyrinocheilidae (Gyrinocheilus aymonieri), and Balitoridae (Nemacheilus sp. and Beaufortia kweichowensis) as outgroups, the Cyprinidae is resolved as a monophyletic group. Within the family the genera Raiamas, Barilius, Danio, and Rasbora, representing many of the tropical cyprinids, represent basal members of the family. All other species can be classified into variably supported and resolved monophyletic lineages, depending upon analysis

  5. Triatominae as a model of morphological plasticity under ecological pressure

    Directory of Open Access Journals (Sweden)

    Dujardin JP

    1999-01-01

    Full Text Available The use of biochemical and genetic characters to explore species or population relationships has been applied to taxonomic questions since the 60s. In responding to the central question of the evolutionary history of Triatominae, i.e. their monophyletic or polyphyletic origin, two important questions arise (i to what extent is the morphologically-based classification valid for assessing phylogenetic relationships? and (ii what are the main mechanisms underlying speciation in Triatominae? Phenetic and genetic studies so far developed suggest that speciation in Triatominae may be a rapid process mainly driven by ecological factors.

  6. Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities

    DEFF Research Database (Denmark)

    Aylward, Frank O.; McDonald, Bradon R.; Adams, Sandra M.

    2013-01-01

    versatility, and environmental adaptations. Our multilocus phylogenetic and average amino acid identity (AAI) analyses confirm that Sphingomonas, Sphingobium, Sphingopyxis, and Novosphingobium are well-resolved monophyletic groups with the exception of Sphingomonas sp. strain SKA58, which we propose belongs...... compounds in many of the genomes, suggesting that plant-based compounds or chemical contaminants may be sources of nitrogen and sulfur. Many of these sphingomonads appear to be adapted to oligotrophic environments, but several contain genomic features indicative of host associations. Our work provides...

  7. The hybrid nature of the Eukaryota and a consilient view of life on Earth.

    Science.gov (United States)

    McInerney, James O; O'Connell, Mary J; Pisani, Davide

    2014-06-01

    The origin of the eukaryotic cell, which is known as eukaryogenesis, has puzzled scientists for more than 100 years, and many hypotheses have been proposed. Recent analyses of new data enable the safe elimination of some of these hypotheses, whereas support for other hypotheses has increased. In this Opinion article, we evaluate the available theories for their compatibility with empirical observations and conclude that cellular life consists of two primary, paraphyletic prokaryotic groups and one secondary, monophyletic group that has symbiogenic origins - the eukaryotes.

  8. Phylogenetic relationships of the genera of Ptiloneuridae (Psocodea, 'Psocoptera', Epipsocetae) and a test on the monophyly of Brasineura Silva-Neto & García Aldrete and Loneuroides García Aldrete.

    Science.gov (United States)

    Silva-Neto, Alberto Moreira Da; Aldrete, Alfonso N García; Rafael, José Albertino

    2016-08-10

    The phylogenetic relationships of the genera of Ptiloneuridae were inferred on the basis of morphological characters of adult specimens. Two distinct clades are recognized: one, including Belicania, Euplocania, Omilneura, Perucania, Timnewia and Triplocania, and the other, including Brasineura, Loneura, Loneuroides, Ptiloneura, Ptiloneuropsis and Willreevesia. Brasineura and Loneuroides are recognized as monophyletic. A correction of nomenclature for the parts of the phallosome in Brasineura was made; we also modified the identification key to the genera of Ptiloneuridae, in the couplets that separate Loneura from Brasineura.

  9. The advertisement call of Bokermannohyla flavopicta Leite, Pezzuti & Garcia, 2012 (Anura: Hylidae) from the mountains of Chapada Diamantina, Bahia, Brazil.

    Science.gov (United States)

    Rocha, Pedro Carvalho; Thompson, Julia Resende; Leite, Felipe Sá Fortes; Garcia, Paulo Christiano De Anchietta

    2016-01-07

    Bokermannohyla Faivovich, Haddad, Garcia, Frost, Campbell & Wheeler (2005) is a Brazilian treefrog genus currently composed of 32 species (Brandão et al. 2012; Leite et al. 2012; Frost 2015). The genus comprehends four, putatively monophyletic, species groups: B. circumdata, B. claresignata, B. martinsi, and B. pseudopseudis (sensu Faivovich et al. 2005). The B. pseudopseudis group includes nine species: B. alvarengai (Bokermann 1956), B. flavopicta Leite et al. 2012, B. ibitiguara (Cardoso 1983), B. itapoty Lugli & Haddad 2006a, B. oxente Lugli & Haddad 2006b, B. pseudopseudis (Miranda-Ribeiro 1937), B. sagarana Leite et al. 2011, B. sapiranga Brandão et al. 2012, and B. saxicola (Bokermann 1964).

  10. A new Hyphessobrycon (Ostariophysi: Characiformes: Characidae) from the middle Amazon basin, Brazil.

    Science.gov (United States)

    Lima, Flávio C T; Coutinho, Daniel P; Wosiacki, Wolmar B

    2014-10-08

    Hyphessobrycon montagi, new species, is described from tributaries of the Rio Arapiuns, a left margin affluent of the lower Rio Tapajós, Amazon basin, Pará, Brazil. The new species can be diagnosed from all its congeners by the possession of a combination of two well-defined humeral blotches, connected by a narrow stripe, and a caudal peduncle blotch. A putatively monophyletic Hyphessobrycon heterorhabdus species-group, restricted to H. heterorhabdus, H. amapaensis, and H. eschwartzae, is herein proposed based on shared derived features of color pattern. Alternative proposals of a "Hyphessobrycon heterorhabdus group" presented in the recent literature are evaluated and criticized.

  11. Wolbachia detection: an assessment of standard PCR protocols.

    Science.gov (United States)

    Simões, P M; Mialdea, G; Reiss, D; Sagot, M-F; Charlat, S

    2011-05-01

    Wolbachia is a large monophyletic genus of intracellular bacteria, traditionally detected using PCR assays. Its considerable phylogenetic diversity and impact on arthropods and nematodes make it urgent to assess the efficiency of these screening protocols. The sensitivity and range of commonly used PCR primers and of a new set of 16S primers were evaluated on a wide range of hosts and Wolbachia strains. We show that certain primer sets are significantly more efficient than others but that no single protocol can ensure the specific detection of all known Wolbachia infections.

  12. Three New Monotypic Genera of the Caloplacoid Lichens (Teloschistaceae, Lichen-Forming Ascomycetes).

    Science.gov (United States)

    Kondratyuk, Sergii Y; Lőkös, Lászlo; Kim, Jung A; Kondratiuk, Anna S; Jeong, Min Hye; Jang, Seol Hwa; Oh, Soon-Ok; Hur, Jae-Seoun

    2015-09-01

    Three monophyletic branches are strongly supported in a phylogenetic analysis of the Teloschistaceae based on combined data sets of internal transcribed spacer and large subunit nrDNA and 12S small subunit mtDNA sequences. These are described as new monotypic genera: Jasonhuria S. Y. Kondr., L. Lőkös et S. -O. Oh, Loekoesia S. Y. Kondr., S. -O. Oh et J. -S. Hur and Olegblumia S. Y. Kondr., L. Lőkös et J. -S. Hur. Three new combinations for the type species of these genera are proposed.

  13. Equine arteritis virus: a new isolate from the presumable first carrier stallion in Argentina and its genetic relationships among the four reported unique Argentinean strains.

    Science.gov (United States)

    Metz, Germán E; Serena, María S; Ocampos, Giselle Martín; Panei, Carlos J; Fernandez, Verónica L; Echeverría, María G

    2008-01-01

    Equine arteritis virus (EAV) was isolated from a testicle of the presumable first stallion infected with EAV in Argentina. This virus isolate (named LT-LP-ARG) was confirmed by GP5-specific PCR and indirect immunofluorescence assays. The PCR product was sequenced, and the phylogenetic analysis revealed that the LT-LP-ARG strain of EAV forms a monophyletic group, together with other strains previously isolated in our laboratory (LP02 group). However, all Argentinean EAV strains belong to a polyphyletic group. We believe that the virus isolate presented in this report could be the origin of EAV infection in our country.

  14. Molecular phylogeny of Enchytraeidae (Oligochaeta) indicates separate invasions of the terrestrial environment

    DEFF Research Database (Denmark)

    Christensen, Bent; Glenner, Henrik

    2010-01-01

    Enchytraeus have also invaded other habitats. Historically the littoral zone of the sea is undoubtedly the first terrestrial or semi-terrestrial habitat where dead plant material accumulates to any greater extent and Enchytraeus and Lumbricillus may represent early successful attempts to exploit this resource...... segregations of the two genera Enchytraeus and Lumbricillus leaving the remaining genera included in this study as a later segregated major monophyletic branch. Extant members of the two former genera dominate in decaying seaweed in the littoral zone along the sea although members of in particular the genus...

  15. Description of a new genus for Euptychia hilara (C. Felder & R. Felder, 1867) (Lepidoptera: Nymphalidae: Satyrinae).

    Science.gov (United States)

    Nakahara, Shinichi; Janzen, Daniel H; Hallwachs, Winnie; Espeland, Marianne

    2015-09-04

    Based on external morphology, food plant records for caterpillars, and molecular analysis, Euptychia hilara (C. Felder & R. Felder, 1867) is removed from Euptychia Hübner 1818. A new genus, Inbio Nakahara & Espeland gen. nov., is proposed for this taxon. Inbio hilara comb. nov. is a member of a monophyletic clade containing Cyllopsis Felder, 1869, Paramacera Butler, 1868, and Atlanteuptychia Freitas, Barbosa & Mielke, 2013, although it can be morphologically distinguished from these genera. Lectotypes for Neonympha hilara C. Felder & R. Felder, 1867 and Euptychia anacleta Butler, 1877 (a synonym of E. hilara) are designated herein.

  16. A mountain of millipedes I

    DEFF Research Database (Denmark)

    Enghoff, Henrik

    2014-01-01

    Twenty new species of the millipede genus Chaleponcus Attems, 1914, are described from the Udzungwa Mountains: C. netus sp. nov., C. quasimodo sp. nov., C. malleolus sp. nov., C. scopus sp. nov., C. nikolajscharffi sp. nov., C. mwanihanensis sp. nov., C. basiliscus sp. nov., C. krai sp. nov., C. ...... and unusual tarsal setation of a few species tentatively suggest adaptive radiation......., they constitute the Chaleponcus dabagaensis-group, well characterized by apparently apomorphic gonopodal characters, presumably monophyletic, and the first example of a major radiation within the Udzungwas. All species are restricted to altitudes >1390 m, all but one were found in only one, rarely two forest...

  17. Echinothurioid phylogeny and the phylogenetic significance of Kamptosoma (Echinoidea: Echinodermata)

    Science.gov (United States)

    Mooi, Rich; Constable, Heather; Lockhart, Susanne; Pearse, John

    2004-07-01

    The Echinothurioida is an unusual group of regular sea urchins that are characterized by soft, flexible tests and in some cases, hoof-shaped spines used for locomotion across soft, deep-sea sediments. As far as is known, all species are armed with venom-bearing spines that have been known to cause serious injury in humans. There are 50 species of echinothurioids arranged in 11 extant genera. Their fossil record is very poor, being limited to two additional fossil taxa (one of which is only tentatively considered an echinothurioid), two assigned to extant taxa, and three of more dubious affinity. With very few exceptions, only disjointed plates are preserved—and those very rarely. Today, echinothurioids are found around the globe from as far north as the Arctic Circle and as far south as Antarctica, with a bathymetric distribution ranging from inshore on coral reefs to depths of almost 5000 m. The majority of species are characteristic of the deep sea, and consequently little is known about these urchins. Many are known only from type and associated material. Their fragile tests, deep benthic habitat, and rarity make it difficult to develop a complete picture of their morphology, and as we demonstrate, breakage of the test can lead to misinterpretations of plate architecture in some taxa. The sole Antarctic species, Kamptosoma asterias, is usually considered an echinothurioid, but its unusual morphology has made its position difficult to ascertain. In addition, previous genus-level phylogenies do not test the monophyly of the genera, and some studies even suggest that the echinothurioids themselves do not constitute a monophyletic group. This study focuses on finding a species level phylogeny of the echinothurioids in order to perform these tests, and to place the enigmatic Kamptosoma in a phylogenetic context that determines whether it is indeed an echinothurioid, and if so, to which clade it is most closely related. The present analysis surveys ambulacral

  18. Molecular characterization of Hepatozoon species in reptiles from the Seychelles.

    Science.gov (United States)

    Harris, D James; Maia, João P M C; Perera, Ana

    2011-02-01

    Hepatozoon parasites were examined for the first time in reptiles from the Seychelles Islands. Although both prevalence and intensity were low, Hepatozoon species were detected in individuals from 2 endemic species, the lizard Mabuya wrightii and the snake Lycognathophis seychellensis. This was confirmed using visual identification and through sequencing part of the 18s rRNA gene. Phylogenetic analysis indicates that the Hepatozoon on the Seychelles form a monophyletic lineage, although more data are clearly needed to stabilize estimates of relationships based on this marker.

  19. [Analysis phylogenetic relationship of Gynostemma (Cucurbitaceae)].

    Science.gov (United States)

    Qin, Shuang-shuang; Li, Hai-tao; Wang, Zhou-yong; Cui, Zhan-hu; Yu, Li-ying

    2015-05-01

    The sequences of ITS, matK, rbcL and psbA-trnH of 9 Gynostemma species or variety including 38 samples were compared and analyzed by molecular phylogeny method. Hemsleya macrosperma was designated as outgroup. The MP and NJ phylogenetic tree of Gynostemma was built based on ITS sequence, the results of PAUP phylogenetic analysis showed the following results: (1) The eight individuals of G. pentaphyllum var. pentaphyllum were not supported as monophyletic in the strict consensus trees and NJ trees. (2) It is suspected whether G. longipes and G. laxum should be classified as the independent species. (3)The classification of subgenus units of Gynostemma plants is supported.

  20. Phylogeny of protostome worms derived from 18S rRNA sequences.

    Science.gov (United States)

    Winnepenninckx, B; Backeljau, T; De Wachter, R

    1995-07-01

    The phylogenetic relationships of protostome worms were studied by comparing new complete 18S rRNA sequences of Vestimentifera, Pogonophora, Sipuncula, Echiura, Nemertea, and Annelida with existing 18S rRNA sequences of Mollusca, Arthropoda, Chordata, and Platyhelminthes. Phylogenetic trees were inferred via neighbor-joining and maximum parsimony analyses. These suggest that (1) Sipuncula and Echiura are not sister groups; (2) Nemertea are protostomes; (3) Vestimentifera and Pogonophora are protostomes that have a common ancestor with Echiura; and (4) Vestimentifera and Pogonophora are a monophyletic clade.

  1. Codonoboea (Gesneriaceae Sections in Peninsular Malaysia

    Directory of Open Access Journals (Sweden)

    Chung Lu Lim

    2014-12-01

    Full Text Available Codonoboea is the largest genus of Gesneriaceae in Peninsular Malaysia with 92 species. Nine sections,   Boeopsis, Codonoboea, Didymanthus, Glossadenia, Heteroboea, Pectinati, Reptantes, Salicini and Venusti, have been erected based on morphological characters, such as habit, leaf arrangement and shape, type of inflorescence, number of flowers, corolla type and nectary type. Recent molecular phylogenetic study using ITS and trnL-F sequences show that only section Heteroboea is monophyletic. While the sections of Codonoboea can no longer be maintained as   formal taxonomic taxa, as informal groupings they are useful in identification and in constructing keys.

  2. Comparative analysis of LTR and structural genes in an equine infectious anemia virus strain isolated from a feral horse in Japan.

    Science.gov (United States)

    Dong, Jianbao; Cook, Frank R; Haga, Takeshi; Horii, Yoichiro; Norimine, Junzo; Misawa, Naoaki; Goto, Yoshitaka; Zhu, Wei

    2014-12-01

    Although equine infectious anemia virus (EIAV) poses a major threat to the equine industry worldwide, the molecular epidemiology of this virus is poorly understood. Recently, an EIAV strain (EIAVMiyazaki2011-A) representing a new monophyletic group was discovered in feral horses in southern Japan. In the present study, the EIAVMiyazaki2011-A proviral genome is compared with evolutionarily divergent EIAV isolates to investigate conservation of functional elements or motifs within the long terminal repeats (LTRs) and structural genes. This analysis represents a significant step forward in increasing understanding of the molecular conservation and variation between geographically distinct strains of this equine lentivirus.

  3. The first species of Aplastodiscus endemic to the Brazilian Cerrado (Anura, Hylidae)

    Science.gov (United States)

    Berneck, Bianca V. M.; Giaretta, Ariovaldo A.; Brandão, Reuber A.; Cruz, Carlos A. G.; Haddad, Célio F. B.

    2017-01-01

    Abstract The genus Aplastodiscus includes 14 nominal species in four monophyletic groups with occurrence in the Atlantic Forest and Brazilian Cerrado (Brazilian Savanna) of South America. A recent study reviewed the taxonomy and phylogenetic relationships of the genus and suggested a third species for the Aplastodiscus perviridis Group. Herein, on the basis of morphology and advertisement call, we describe this species and test its monophyly. The new species is the only Aplastodiscus with endemic occurrence in the Cerrado Biome. In addition, its geographical distribution and conservation status are discussed. PMID:28138301

  4. Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa.

    Science.gov (United States)

    Sperling, Erik A; Peterson, Kevin J; Pisani, Davide

    2009-10-01

    The relationships at the base of the metazoan tree have been difficult to robustly resolve, and there are several different hypotheses regarding the interrelationships among sponges, cnidarians, ctenophores, placozoans, and bilaterians, with each hypothesis having different implications for the body plan of the last common ancestor of animals and the paleoecology of the late Precambrian. We have sequenced seven nuclear housekeeping genes from 17 new sponges, bringing the total to 29 species analyzed, including multiple representatives of the Demospongiae, Calcarea, Hexactinellida, and Homoscleromorpha, and analyzed a data set also including six nonmetazoan outgroups and 36 eumetazoans using a variety of phylogenetic methods and evolutionary models. We used leaf stability to identify rogue taxa and investigate their effect on the support of the nodes in our trees, and we identified clades most likely to represent phylogenetic artifacts through the comparison of trees derived using different methods (and models) and through site-stripping analyses. Further, we investigated compositional heterogeneity and tested whether amino acid composition bias affected our results. Finally, we used Bayes factors to compare our results against previously published phylogenies. All our maximum likelihood (ML) and Bayesian analyses find sponges to be paraphyletic, with all analyses finding three extant paraphyletic sponge lineages, Demospongiae plus Hexactinellida, Calcarea, and Homoscleromorpha. All but one of our ML and Bayesian analyses support the monophyly of Eumetazoa (here Cnidaria + Bilateria) and a sister group relationship between Placozoa (here Trichoplax adhaerens) and Eumetazoa. Bayes factors invariably provide decisive support in favor of poriferan paraphyly when compared against either a sister group relationship between Porifera and Cnidaria or with a monophyletic Porifera with respect to a monophyletic Eumetazoa. Although we were able to recover sponge monophyly

  5. Multiple origins of life

    Science.gov (United States)

    Raup, D. M.; Valentine, J. W.

    1983-01-01

    There is some indication that life may have originated readily under primitive earth conditions. If there were multiple origins of life, the result could have been a polyphyletic biota today. Using simple stochastic models for diversification and extinction, we conclude: (1) the probability of survival of life is low unless there are multiple origins, and (2) given survival of life and given as many as 10 independent origins of life, the odds are that all but one would have gone extinct, yielding the monophyletic biota we have now. The fact of the survival of our particular form of life does not imply that it was unique or superior.

  6. Lake Baikal: a unique place to study evolution of sponges and their stress response in an environment nearly unimpaired by anthropogenic perturbation.

    Science.gov (United States)

    Efremova, Sofia M; Itskovich, Valeria B; Parfenova, Valentina; Drucker, Valentin V; Müller, Werner E G; Schröder, Heinz C

    2002-06-01

    Lake Baikal is considered as a unique place to study evolution. In this review, we report on recent data on the evolution of endemic freshwater sponges of this ancient lake. Nucleotide sequence data support the idea that these sponges are of monophyletic origin and evolved from Spongillidae. Baikalian sponges form the dominating biomass in the benthos of the lake. Data on the expression of the biomarker heat shock protein 70, revealed that the endemic sponge species of Lake Baikal are useful as bioindicators to assess the anthropogenic impact on the lake.

  7. Evidence for a "Founder Effect" among HIV-infected injection drug users (IDUs in Pakistan

    Directory of Open Access Journals (Sweden)

    Yanagihara Richard

    2010-01-01

    Full Text Available Abstract Background We have previously reported a HIV-1 subtype A infection in a community of injection drug users (IDUs in Karachi, Pakistan. We now show that this infection among the IDUs may have originated from a single source. Methods Phylogenetic analysis was performed of partial gag sequences, generated using PCR, from 26 HIV-positive IDU samples. Results Our results showed formation of a tight monophyletic group with an intra-sequence identity of Conclusion Specific measures need to implemented to control transmission of HIV infection in Pakistan through infected migrant workers.

  8. A phylogenetic analysis of the myxobacteria: basis for their classification

    Science.gov (United States)

    Shimkets, L.; Woese, C. R.

    1992-01-01

    The primary sequence and secondary structural features of the 16S rRNA were compared for 12 different myxobacteria representing all the known cultivated genera. Analysis of these data show the myxobacteria to form a monophyletic grouping consisting of three distinct families, which lies within the delta subdivision of the purple bacterial phylum. The composition of the families is consistent with differences in cell and spore morphology, cell behavior, and pigment and secondary metabolite production but is not correlated with the morphological complexity of the fruiting bodies. The Nannocystis exedens lineage has evolved at an unusually rapid pace and its rRNA shows numerous primary and secondary structural idiosyncrasies.

  9. Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera

    Science.gov (United States)

    Mutanen, Marko; Kivelä, Sami M.; Vos, Rutger A.; Doorenweerd, Camiel; Ratnasingham, Sujeevan; Hausmann, Axel; Huemer, Peter; Dincă, Vlad; van Nieukerken, Erik J.; Lopez-Vaamonde, Carlos; Vila, Roger; Aarvik, Leif; Decaëns, Thibaud; Efetov, Konstantin A.; Hebert, Paul D. N.; Johnsen, Arild; Karsholt, Ole; Pentinsaari, Mikko; Rougerie, Rodolphe; Segerer, Andreas; Tarmann, Gerhard; Zahiri, Reza; Godfray, H. Charles J.

    2016-01-01

    The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service “Monophylizer” to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the

  10. Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of Kingdom Fungi inferred from RNA polymerase II subunit genes

    Directory of Open Access Journals (Sweden)

    Hodson Matthew C

    2006-09-01

    Full Text Available Abstract Background At present, there is not a widely accepted consensus view regarding the phylogenetic structure of kingdom Fungi although two major phyla, Ascomycota and Basidiomycota, are clearly delineated. Regarding the lower fungi, Zygomycota and Chytridiomycota, a variety of proposals have been advanced. Microsporidia may or may not be fungi; the Glomales (vesicular-arbuscular mycorrhizal fungi may or may not constitute a fifth fungal phylum, and the loss of the flagellum may have occurred either once or multiple times during fungal evolution. All of these issues are capable of being resolved by a molecular phylogenetic analysis which achieves strong statistical support for major branches. To date, no fungal phylogeny based upon molecular characters has satisfied this criterion. Results Using the translated amino acid sequences of the RPB1 and RPB2 genes, we have inferred a fungal phylogeny that consists largely of well-supported monophyletic phyla. Our major results, each with significant statistical support, are: (1 Microsporidia are sister to kingdom Fungi and are not members of Zygomycota; that is, Microsporidia and fungi originated from a common ancestor. (2 Chytridiomycota, the only fungal phylum having a developmental stage with a flagellum, is paraphyletic and is the basal lineage. (3 Zygomycota is monophyletic based upon sampling of Trichomycetes, Zygomycetes, and Glomales. (4 Zygomycota, Basidiomycota, and Ascomycota form a monophyletic group separate from Chytridiomycota. (5 Basidiomycota and Ascomycota are monophyletic sister groups. Conclusion In general, this paper highlights the evolutionary position and significance of the lower fungi (Zygomycota and Chytridiomycota. Our results suggest that loss of the flagellum happened only once during early stages of fungal evolution; consequently, the majority of fungi, unlike plants and animals, are nonflagellated. The phylogeny we infer from gene sequences is the first one that is

  11. Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of kingdom Fungi inferred from RNA polymerase II subunit genes.

    Science.gov (United States)

    Liu, Yajuan J; Hodson, Matthew C; Hall, Benjamin D

    2006-09-29

    At present, there is not a widely accepted consensus view regarding the phylogenetic structure of kingdom Fungi although two major phyla, Ascomycota and Basidiomycota, are clearly delineated. Regarding the lower fungi, Zygomycota and Chytridiomycota, a variety of proposals have been advanced. Microsporidia may or may not be fungi; the Glomales (vesicular-arbuscular mycorrhizal fungi) may or may not constitute a fifth fungal phylum, and the loss of the flagellum may have occurred either once or multiple times during fungal evolution. All of these issues are capable of being resolved by a molecular phylogenetic analysis which achieves strong statistical support for major branches. To date, no fungal phylogeny based upon molecular characters has satisfied this criterion. Using the translated amino acid sequences of the RPB1 and RPB2 genes, we have inferred a fungal phylogeny that consists largely of well-supported monophyletic phyla. Our major results, each with significant statistical support, are: (1) Microsporidia are sister to kingdom Fungi and are not members of Zygomycota; that is, Microsporidia and fungi originated from a common ancestor. (2) Chytridiomycota, the only fungal phylum having a developmental stage with a flagellum, is paraphyletic and is the basal lineage. (3) Zygomycota is monophyletic based upon sampling of Trichomycetes, Zygomycetes, and Glomales. (4) Zygomycota, Basidiomycota, and Ascomycota form a monophyletic group separate from Chytridiomycota. (5) Basidiomycota and Ascomycota are monophyletic sister groups. In general, this paper highlights the evolutionary position and significance of the lower fungi (Zygomycota and Chytridiomycota). Our results suggest that loss of the flagellum happened only once during early stages of fungal evolution; consequently, the majority of fungi, unlike plants and animals, are nonflagellated. The phylogeny we infer from gene sequences is the first one that is congruent with the widely accepted morphology

  12. The Immature Stages of Protodasyapha (Protodasyapha hirtuosa (Philippi and their Comparison with the Immature Stages of other Pangoniini (Diptera: Tabanidae: Pangoniinae

    Directory of Open Access Journals (Sweden)

    González Christian R

    1998-01-01

    Full Text Available The terrestrial immature stages of the Chilean horse fly, Protodasyapha (Protodasyapha hirtuosa (Philippi, are described. P.(P. hirtuosa resembles Ectenopsis vulpecula Macquart and Caenoprosopon trichocera (Bigot from Australia, and Esenbeckia delta Hine from North America, in both the larval and pupal stages. Some characters that are shared between these species are unique and provide evidence of their monophyletic origin. Larvae of P. hirtuosa were found 3-5 below of the soil surface and associated with larvae of Coleoptera, Lepidoptera and Diptera.

  13. Fomitiporia cupressicola sp. nov., a parasite on Cupressus arizonica, and additional unnamed clades in the southern USA and northern Mexico, determined by multilocus phylogenetic analyses.

    Science.gov (United States)

    Amalfi, Mario; Raymundo, Tania; Valenzuela, Ricardo; Decock, Cony

    2012-01-01

    Fomitiporia cupressicola sp. nov., found in living Cupressus arizonica, is described on the basis of several collections originating from a high altitude forest in the northern Sierra Madre Occidental, Mexico. The species forms a monophyletic clade, basal to a larger lineage comprising species originating mainly from temperate to Mediterranean areas of the northern hemisphere. The phylogenetic approach in Fomitiporia also revealed multiple unnamed clades within the F. robusta complex in the southern USA and northern Mexico, representing potential species. The status of the F. robusta complex in North America is discussed briefly.

  14. Ancient proteins resolve the evolutionary history of Darwin's South American ungulates

    DEFF Research Database (Denmark)

    Welker, Frido; Collins, Matthew J.; Thomas, Jessica A.

    2015-01-01

    like 180 years ago, it is no clearer whether they had one origin or several, arose before or after the Cretaceous/Palaeogene transition 66.2 million years ago, or are more likely to belong with the elephants and sirenians of superorder Afrotheria than with the euungulates (cattle, horses, and allies....... The resulting consensus tree agrees well with recent higher-level mammalian phylogenies. Toxodon and Macrauchenia form a monophyletic group whose sister taxon is not Afrotheria or any of its constituent clades as recently claimed, but instead crown Perissodactyla (horses, tapirs, and rhinoceroses...

  15. Further studies on Boreonectes Angus, 2010, with a molecular phylogeny of the Palaearctic species of the genus

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    Robert B. Angus

    2017-03-01

    Full Text Available Karyotypes are given for Boreonectes emmerichi (Falkenström, 1936 from its type locality at Kangding, China, and for B. alpestris (Dutton & Angus, 2007 from the St Gotthard and San Bernardino passes in the Swiss Alps. A phylogeny based on sequence data from a combination of mitochondrial and nuclear genes recovered western Palaearctic species of Boreonectes as monophyletic with strong support. Boreonectes emmerichi was placed as sister to the north American forms of B. griseostriatus (De Geer, 1774, although with low support. The diversity of Palaearctic species of the B. griseostriatus species group is discussed.

  16. Evolution and diversity of green plant cell walls.

    Science.gov (United States)

    Popper, Zoë A

    2008-06-01

    Plant cells are surrounded by a dynamic cell wall that performs many essential biological roles, including regulation of cell expansion, the control of tissue cohesion, ion-exchange and defence against microbes. Recent evidence shows that the suite of polysaccharides and wall proteins from which the plant cell wall is composed shows variation between monophyletic plant taxa. This is likely to have been generated during the evolution of plant groups in response to environmental stress. Understanding the natural variation and diversity that exists between cell walls from different taxa is key to facilitating their future exploitation and manipulation, for example by increasing lignocellulosic content or reducing its recalcitrance for use in biofuel generation.

  17. Evolutionary analysis of pollinaria morphology of subtribe Aeridinae (Orchidaceae

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    Topik Hidayat

    2006-12-01

    Full Text Available HIDAYAT,  TOPIK; YUKAWA,  TOMOHISA; ITO, MOTOMI.  2006. Evolutionary analysis of  pollinaria morphology of subtribe Aeridinae (Orchidaceae. Reinwardtia 12(3: 223–235. –– Pollinarium is one of the distinct synapomorphies of Orchidaceae. With using characters  derived from the  pollinarium,  phylogenetic relationships among  genera of subtribe  Aeridinae was examined. Cladistic analysis showed that (1 Subtribe  Aeridinae is monophyletic group. (2 Five of six groups constructed in the analysis are consistent with the groups recognized in previous molecular  phylogenetic analyses.  (3 The  genera Cleisostoma and  Phalaenopsis are  non-monophyletic group. (4 Pollinarium morphology endorses monophyly  Trichoglottis  and Phalaenopsis alliances.  (5 Although transformation of the stipe and viscidium shapes in the subtribe is subjected to parallelism, the results showed that these characters are much useful in determining relationships in the subtribe than those of pollinium.

  18. MOLECULAR SYSTEMATICS OF IRIDACEAE: A COMBINED ANALYSIS OF FOUR PLASTID DNA SEQUENCE MATRICES

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    M.W. CHASE

    2000-01-01

    Full Text Available Iridaceae are one of the largest families of Lilianae and probably also among the best studied families of monocotyledons. To further evaluate generic, tribal and subfamilial relationships, we have produced four plastid DNA data sets for 57 genera of Iridaceae plus outgroups: rps4, rbcL (both protein coding genes, and the trnL intron snd the trnL-F inter-gene spacer. All four matrices produce highly congruent, although not identical trees, and we thus analysed them in a combined analysis, which produced a highly resolved and well supported topology. In each of the individual trees, some genera or groups of genera are misplaced relative to Goldblatt’s and Rudall’s morphological cladistic studies, but the combined analysis produced a pattern much more similar to these previous ideas of relationships. In the combined tree, all subfamilies were resolved as monophyletic clades, except Nivenioideae, which formed a grade in which Ixioideae were embedded. The achlorophyllous Geosiris (sometimes referred to Geosiridaceae or Burmanniaceae fell within the nivenioid grade. Most of the tribes are monophyletic, except for Ixieae, Watsonieae and Sisyrinchieae, but the topology within Ixioideae is not strongly supported due to extremely low levels of sequence divergence. Isophysis is sister to the rest of the family, and Diplarrhena falls in a well supported position as sister to Irideae/Sisyrinchieae/Tigridieae/Mariceae; Bobartia of Sisyrinchieae is supported as a member of Irideae.

  19. Deep molecular divergence and exceptional morphological stasis in dwarf cannibal snails Nata sensu lato Watson, 1934 (Rhytididae) of southern Africa.

    Science.gov (United States)

    Moussalli, Adnan; Herbert, David G

    2016-02-01

    The genus Nata Watson, 1934 is a southern African endemic belonging to the Gondwanan family of carnivorous snails, Rhytididae. We present a molecular phylogeny of the genus based on two mitochondrial (16S and COI) and two nuclear genes (ITS2 and 28S RNA), and complement this with an appraisal of morphological characters relating to both the shell and soft parts. We identify four reciprocally monophyletic lineages for which valid names are already available, plus two undescribed species restricted to the Albany Thicket Biome. We show that Nata sensu lato may not be monophyletic. Rather there exist two deep lineages within Nata s.l., one lineage potentially sister to a clade dominated by the Australian and New Zealand radiation, and the other occupying a basal position within Rhytididae. Accordingly we recommend a revision recognising two genera, namely Nata s.s. and Natella respectively. Despite deep molecular divergences within Nata s.s., phenotypic evolution has been remarkably conserved, and contrasts greatly with that exhibited across other major lineages within the Rhytididae.

  20. Phylogenetic relationships of Acheilognathidae (Cypriniformes: Cyprinoidea) as revealed from evidence of both nuclear and mitochondrial gene sequence variation: evidence for necessary taxonomic revision in the family and the identification of cryptic species.

    Science.gov (United States)

    Chang, Chia-Hao; Li, Fan; Shao, Kwang-Tsao; Lin, Yeong-Shin; Morosawa, Takahiro; Kim, Sungmin; Koo, Hyeyoung; Kim, Won; Lee, Jae-Seong; He, Shunping; Smith, Carl; Reichard, Martin; Miya, Masaki; Sado, Tetsuya; Uehara, Kazuhiko; Lavoué, Sébastien; Chen, Wei-Jen; Mayden, Richard L

    2014-12-01

    Bitterlings are relatively small cypriniform species and extremely interesting evolutionarily due to their unusual reproductive behaviors and their coevolutionary relationships with freshwater mussels. As a group, they have attracted a great deal of attention in biological studies. Understanding the origin and evolution of their mating system demands a well-corroborated hypothesis of their evolutionary relationships. In this study, we provide the most comprehensive phylogenetic reconstruction of species relationships of the group based on partitioned maximum likelihood and Bayesian methods using DNA sequence variation of nuclear and mitochondrial genes on 41 species, several subspecies and three undescribed species. Our findings support the monophyly of the Acheilognathidae. Two of the three currently recognized genera are not monophyletic and the family can be subdivided into six clades. These clades are further regarded as genera based on both their phylogenetic relationships and a reappraisal of morphological characters. We present a revised classification for the Acheilognathidae with five genera/lineages: Rhodeus, Acheilognathus (new constitution), Tanakia (new constitution), Paratanakia gen. nov., and Pseudorhodeus gen. nov. and an unnamed clade containing five species currently referred to as "Acheilognathus". Gene trees of several bitterling species indicate that the taxa are not monophyletic. This result highlights a potentially dramatic underestimation of species diversity in this family. Using our new phylogenetic framework, we discuss the evolution of the Acheilognathidae relative to classification, taxonomy and biogeography. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. Diversity of Microorganisms Isolated from the Soil Sample surround Chroogomphus rutilus in the Beijing Region

    Directory of Open Access Journals (Sweden)

    Peng Wang, Yu Liu, Yonggang Yin, Haojie Jin, Shouxian Wang, Feng Xu, Shuang Zhao, Xiaoli Geng

    2011-01-01

    Full Text Available Artificially cultivating Chroogomphus rutilus is too inefficient to be commercially feasible. Furthermore, isolating C. rutilus mycelia in the wild is difficult. Thus, it is important to determine the natural habitat of its fruiting body. This study focused on the ecology of the C. rutilus habitat to isolate and classify beneficial microorganisms that could affect its growth, which could be used in future research on artificial cultivation. In total, 342 isolates were isolated from soil samples collected around a C. rutilus colony in the Beijing region. Of these, 22 bacterial and 14 fungal isolates were selected for sequencing and phylogenetic analysis, based on their growth characteristics and colony morphology. Using 16S rRNA gene sequence analysis, the bacterial isolates were divided into two monophyletic clusters which had significant hits to the genera Bacillus and Pseudomonas, respectively. Using internal transcribed spacer (ITS sequence analysis, fungal isolates were divided into four monophyletic clusters: Penicillium, Trichoderma, Mortierella, and Bionectria. Moreover, the phylogenetic diversity of these isolates was analysed. The results indicated that numerous microorganisms were present in C. rutilus habitat. This was the first reported examination of the microbiological ecology of C. rutilus.

  2. Phylogenetic revision of Camarosporium (Pleosporineae, Dothideomycetes) and allied genera.

    Science.gov (United States)

    Wanasinghe, D N; Hyde, K D; Jeewon, R; Crous, P W; Wijayawardene, N N; Jones, E B G; Bhat, D J; Phillips, A J L; Groenewald, J Z; Dayarathne, M C; Phukhamsakda, C; Thambugala, K M; Bulgakov, T S; Camporesi, E; Gafforov, Y S; Mortimer, P E; Karunarathna, S C

    2017-06-01

    A concatenated dataset of LSU, SSU, ITS and tef1 DNA sequence data was analysed to investigate the taxonomic position and phylogenetic relationships of the genus Camarosporium in Pleosporineae (Dothideomycetes). Newly generated sequences from camarosporium-like taxa collected from Europe (Italy) and Russia form a well-supported monophyletic clade within Pleosporineae. A new genus Camarosporidiella and a new family Camarosporidiellaceae are established to accommodate these taxa. Four new species, Neocamarosporium korfii, N. lamiacearum, N. salicorniicola and N. salsolae, constitute a strongly supported clade with several known taxa for which the new family, Neocamarosporiaceae, is introduced. The genus Staurosphaeria based on S. lycii is resurrected and epitypified, and shown to accommodate the recently introduced genus Hazslinszkyomyces in Coniothyriaceae with significant statistical support. Camarosporium quaternatum, the type species of Camarosporium and Camarosporomyces flavigena cluster together in a monophyletic clade with significant statistical support and sister to the Leptosphaeriaceae. To better resolve interfamilial/intergeneric level relationships and improve taxonomic understanding within Pleosporineae, we validate Camarosporiaceae to accommodate Camarosporium and Camarosporomyces. The latter taxa along with other species are described in this study.

  3. Phylogenetic relationships of butterflies of the tribe Acraeini (Lepidoptera, Nymphalidae, Heliconiinae) and the evolution of host plant use.

    Science.gov (United States)

    Silva-Brandão, Karina Lucas; Wahlberg, Niklas; Francini, Ronaldo Bastos; Azeredo-Espin, Ana Maria L; Brown, Keith S; Paluch, Márlon; Lees, David C; Freitas, André V L

    2008-02-01

    The tribe Acraeini (Nymphalidae, Heliconiinae) is believed to comprise between one and seven genera, with the greatest diversity in Africa. The genera Abananote, Altinote, and Actinote (s. str.) are distributed in the Neotropics, while the genera Acraea, Bematistes, Miyana, and Pardopsis have a Palaeotropical distribution. The monotypic Pardopsis use herbaceous plants of the family Violaceae, Acraea and Bematistes feed selectively on plants with cyanoglycosides belonging to many plant families, but preferentially to Passifloraceae, and all Neotropical species with a known life cycle feed on Asteraceae only. Here, a molecular phylogeny is proposed for the butterflies of the tribe Acraeini based on sequences of COI, EF-1alpha and wgl. Both Maximum Parsimony and Bayesian analyses showed that the tribe is monophyletic, once the genus Pardopsis is excluded, since it appears to be related to Argynnini. The existing genus Acraea is a paraphyletic group with regard to the South American genera, and the species of Acraea belonging to the group of "Old World Actinote" is the sister group of the Neotropical genera. The monophyly of South American clade is strongly supported, suggesting a single colonization event of South America. The New World Actinote (s. str.) is monophyletic, and sister to Abananote+Altinote (polyphyletic). Based on the present results it was possible to propose a scenario for the evolution in host plant use within Acraeini, mainly concerning the use of Asteraceae by the South American genera.

  4. Phylogenetic relationships of true butterflies (Lepidoptera: Papilionoidea) inferred from COI, 16S rRNA and EF-1α sequences.

    Science.gov (United States)

    Kim, Man Il; Wan, Xinlong; Kim, Min Jee; Jeong, Heon Cheon; Ahn, Neung-Ho; Kim, Ki-Gyoung; Han, Yeon Soo; Kim, Iksoo

    2010-11-01

    The molecular phylogenetic relationships among true butterfly families (superfamily Papilionoidea) have been a matter of substantial controversy; this debate has led to several competing hypotheses. Two of the most compelling of those hypotheses involve the relationships of (Nymphalidae + Lycaenidae) + (Pieridae + Papilionidae) and (((Nymphalidae + Lycaenidae) + Pieridae) + Papilionidae). In this study, approximately 3,500 nucleotide sequences from cytochrome oxidase subunit I (COI), 16S ribosomal RNA (16S rRNA), and elongation factor-1 alpha (EF-1α) were sequenced from 83 species belonging to four true butterfly families, along with those of three outgroup species belonging to three lepidopteran superfamilies. These sequences were subjected to phylogenetic reconstruction via Bayesian Inference (BI), Maximum Likelihood (ML), and Maximum Parsimony (MP) algorithms. The monophyletic Pieridae and monophyletic Papilionidae evidenced good recovery in all analyses, but in some analyses, the monophylies of the Lycaenidae and Nymphalidae were hampered by the inclusion of single species of the lycaenid subfamily Miletinae and the nymphalid subfamily Danainae. Excluding those singletons, all phylogenetic analyses among the four true butterfly families clearly identified the Nymphalidae as the sister to the Lycaenidae and identified this group as a sister to the Pieridae, with the Papilionidae identified as the most basal linage to the true butterfly, thus supporting the hypothesis: (Papilionidae + (Pieridae + (Nymphalidae + Lycaenidae))).

  5. MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda.

    Science.gov (United States)

    Campbell, Lahcen I; Rota-Stabelli, Omar; Edgecombe, Gregory D; Marchioro, Trevor; Longhorn, Stuart J; Telford, Maximilian J; Philippe, Hervé; Rebecchi, Lorena; Peterson, Kevin J; Pisani, Davide

    2011-09-20

    Morphological data traditionally group Tardigrada (water bears), Onychophora (velvet worms), and Arthropoda (e.g., spiders, insects, and their allies) into a monophyletic group of invertebrates with walking appendages known as the Panarthropoda. However, molecular data generally do not support the inclusion of tardigrades within the Panarthropoda, but instead place them closer to Nematoda (roundworms). Here we present results from the analyses of two independent genomic datasets, expressed sequence tags (ESTs) and microRNAs (miRNAs), which congruently resolve the phylogenetic relationships of Tardigrada. Our EST analyses, based on 49,023 amino acid sites from 255 proteins, significantly support a monophyletic Panarthropoda including Tardigrada and suggest a sister group relationship between Arthropoda and Onychophora. Using careful experimental manipulations--comparisons of model fit, signal dissection, and taxonomic pruning--we show that support for a Tardigrada + Nematoda group derives from the phylogenetic artifact of long-branch attraction. Our small RNA libraries fully support our EST results; no miRNAs were found to link Tardigrada and Nematoda, whereas all panarthropods were found to share one unique miRNA (miR-276). In addition, Onychophora and Arthropoda were found to share a second miRNA (miR-305). Our study confirms the monophyly of the legged ecdysozoans, shows that past support for a Tardigrada + Nematoda group was due to long-branch attraction, and suggests that the velvet worms are the sister group to the arthropods.

  6. Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae).

    Science.gov (United States)

    Daïnou, K; Mahy, G; Duminil, J; Dick, C W; Doucet, J-L; Donkpégan, A S L; Pluijgers, M; Sinsin, B; Lejeune, P; Hardy, O J

    2014-07-01

    The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological systematics to identify significant evolutionary units and infer their evolutionary and biogeographical history. We detected five geographically coherent genetic clusters using nSSRs and three levels of genetic differentiation. First, one West African cluster matched perfectly with the morphospecies M. regia that formed a monophyletic clade at both DNA sequences. Second, a West African M. excelsa cluster formed a monophyletic group at plastid DNA and was more related to M. regia than to Central African M. excelsa, but shared many haplotypes with the latter at nuclear DNA. Third, three Central African clusters appeared little differentiated and shared most of their haplotypes. Although gene tree paraphyly could suggest a single species in Milicia following the phylogenetic species concept, the existence of mutual haplotypic exclusivity and nonadmixed genetic clusters in the contact area of the two taxa indicate strong reproductive isolation and, thus, two species following the biological species concept. Molecular dating of the first divergence events showed that speciation in Milicia is ancient (Tertiary), indicating that long-living tree taxa exhibiting genetic speciation may remain similar morphologically.

  7. Phylogeny of Elatinaceae and the Tropical Gondwanan Origin of the Centroplacaceae(Malpighiaceae, Elatinaceae) Clade

    Science.gov (United States)

    Xi, Zhenxiang; Peterson, Kylee; Rushworth, Catherine; Beaulieu, Jeremy; Davis, Charles C.

    2016-01-01

    The flowering plant family Elatinaceae is a widespread aquatic lineage inhabiting temperate and tropical latitudes, including ∼35(-50) species. Its phylogeny remains largely unknown, compromising our understanding of its systematics. Moreover, this group is particularly in need of attention because the biogeography of most aquatic plant clades has yet to be investigated, resulting in uncertainty about whether aquatic plants show histories that deviate from terrestrial plants. We inferred the phylogeny of Elatinaceae from four DNA regions spanning 59 accessions across the family. An expanded sampling was used for molecular divergence time estimation and ancestral area reconstruction to infer the biogeography of Elatinaceae and their closest terrestrial relatives, Malpighiaceae and Centroplacaceae. The two genera of Elatinaceae, Bergia and Elatine, are monophyletic, but several traditionally recognized groups within the family are non-monophyletic. Our results suggest two ancient biogeographic events in the Centroplacaceae(Malpighiaceae, Elatinaceae) clade involving western Gondwana, while Elatinaceae shows a more complicated biogeographic history with a high degree of continental endemicity. Our results indicate the need for further taxonomic investigation of Elatinaceae. Further, our study is one of few to implicate ancient Gondwanan biogeography in extant angiosperms, especially significant given the Centroplacaceae(Malpighiaceae, Elatinaceae) clade's largely tropical distribution. Finally, Elatinaceae demonstrates long-term continental in situ diversification, which argues against recent dispersal as a universal explanation commonly invoked for aquatic plant distributions. PMID:27684711

  8. A comprehensive molecular phylogeny for the hornbills (Aves: Bucerotidae).

    Science.gov (United States)

    Gonzalez, Juan-Carlos T; Sheldon, Ben C; Collar, Nigel J; Tobias, Joseph A

    2013-05-01

    The hornbills comprise a group of morphologically and behaviorally distinct Palaeotropical bird species that feature prominently in studies of ecology and conservation biology. Although the monophyly of hornbills is well established, previous phylogenetic hypotheses were based solely on mtDNA and limited sampling of species diversity. We used parsimony, maximum likelihood and Bayesian methods to reconstruct relationships among all 61 extant hornbill species, based on nuclear and mtDNA gene sequences extracted largely from historical samples. The resulting phylogenetic trees closely match vocal variation across the family but conflict with current taxonomic treatments. In particular, they highlight a new arrangement for the six major clades of hornbills and reveal that three groups traditionally treated as genera (Tockus, Aceros, Penelopides) are non-monophyletic. In addition, two other genera (Anthracoceros, Ocyceros) were non-monophyletic in the mtDNA gene tree. Our findings resolve some longstanding problems in hornbill systematics, including the placement of 'Penelopides exharatus' (embedded in Aceros) and 'Tockus hartlaubi' (sister to Tropicranus albocristatus). We also confirm that an Asiatic lineage (Berenicornis) is sister to a trio of Afrotropical genera (Tropicranus [including 'Tockus hartlaubi'], Ceratogymna, Bycanistes). We present a summary phylogeny as a robust basis for further studies of hornbill ecology, evolution and historical biogeography.

  9. Retroposon analysis of major cetacean lineages: the monophyly of toothed whales and the paraphyly of river dolphins.

    Science.gov (United States)

    Nikaido, M; Matsuno, F; Hamilton, H; Brownell, R L; Cao, Y; Ding, W; Zuoyan, Z; Shedlock, A M; Fordyce, R E; Hasegawa, M; Okada, N

    2001-06-19

    SINE (short interspersed element) insertion analysis elucidates contentious aspects in the phylogeny of toothed whales and dolphins (Odontoceti), especially river dolphins. Here, we characterize 25 informative SINEs inserted into unique genomic loci during evolution of odontocetes to construct a cladogram, and determine a total of 2.8 kb per taxon of the flanking sequences of these SINE loci to estimate divergence times among lineages. We demonstrate that: (i) Odontocetes are monophyletic; (ii) Ganges River dolphins, beaked whales, and ocean dolphins diverged (in this order) after sperm whales; (iii) three other river dolphin taxa, namely the Amazon, La Plata, and Yangtze river dolphins, form a monophyletic group with Yangtze River dolphins being the most basal; and (iv) the rapid radiation of extant cetacean lineages occurred some 28-33 million years B.P., in strong accord with the fossil record. The combination of SINE and flanking sequence analysis suggests a topology and set of divergence times for odontocete relationships, offering alternative explanations for several long-standing problems in cetacean evolution.

  10. A phylogenetic analysis of the emberizid sparrows based on three mitochondrial genes.

    Science.gov (United States)

    Carson, Rebecca J; Spicer, Greg S

    2003-10-01

    Previous molecular phylogenetic studies have examined the taxonomic relationships among a number of typical emberizid sparrow genera. To help clarify these relationships, we sequenced a 1673 base pair fragment for the complete sequence of three mitochondrial genes: adenosine triphosphatase (Atp8 and Atp6) and cytochrome oxidase subunit III (COIII) for 38 sparrow species, along with Passerina amoena (Cardinalidae) and Piranga ludoviciana (Thraupidae) which were selected as the outgroups. Our analysis confirms the monophyly of traditional genera such as Junco, Melospiza, and Zonotrichia. Although Calcarius and Plectrophenax are often thought to be putative emberizids, all our analyses placed these genera basal to all other sparrows examined. As observed with Calcarius, Spizella did not form a monophyletic group, with S. arborea being the sister-taxon to Passerella iliaca. Our analyses also suggest that Aimophila ruficeps is probably more closely related to the "brown towhees" (Pipilo aberti, P. crissalis, and P. fuscus) than its putative congeners. The genus Ammodramus was also not monophyletic, since it appears that Passerculus sandwichensis is more closely related to A. henslowii and A. leconteii then either one is related to its congener A. savannarum. Finally, our analyses exhibited other unsuspected associations, such as the sister-taxon relationships between Amphispiza bilineata and the Chondestes grammacus/Calamospiza melanocorys clade, and Amphispiza belli and Pooecetes gramineus.

  11. Mitochondrial genome structure and evolution in the living fossil vampire squid, Vampyroteuthis infernalis, and extant cephalopods.

    Science.gov (United States)

    Yokobori, Shin-ichi; Lindsay, Dhugal J; Yoshida, Mari; Tsuchiya, Kotaro; Yamagishi, Akihiko; Maruyama, Tadashi; Oshima, Tairo

    2007-08-01

    Complete nucleotide sequences of mitochondrial (mt) genomes of the "living fossil" cephalopod Vampyroteuthis infernalis (Vampyromorpha) and the cuttlefish Sepia esculenta (Sepiida) were determined. The V. infernalis mt genome structure is identical to the incirrate octopod Octopus vulgaris mt genome structure, and is therefore more similar to that of the polyplacophoran Katharina tunicata, than to that of the other "living fossil" cephalopod Nautilus macromphalus. The mt genome structure of S. esculenta is identical to that of Sepia officinalis. Molecular phylogenetic analyses based on the mt protein genes from the completely sequenced cephalopod mt genomes suggested the monophyletic relationship of two myopsid squids Loligo bleekeri and Sepiotheuthis lessoniana, and the monophyletic relationship of two oegopsid squids Watasenia scintillans, and Todarodes pacificus. Sepiida appeared as the sister group of Teuthida (Myopsida + Oegopsida). The phylogenetic position of Vampyromorpha appeared as the sister group of Octopoda, although the monophyly of Vampyromorpha and Decapodiformes cannot be rejected outright by our phylogenetic analyses. The hypothesis that Vampyromorpha is basal among the coleoid cephalopods can be rejected because of low statistical support. Therefore, it is reasonable to recognize three major groups in Coleoidea--Vampyromorpha, Octopoda, and Decapodiformes.

  12. Biogeographic history of the species complex Basileuterus culicivorus (Aves, Parulidae) in the Neotropics.

    Science.gov (United States)

    Vilaça, Sibelle Torres; Santos, Fabrício Rodrigues

    2010-11-01

    The taxonomic status of Basileuterus culicivorus complex has been under debate for a long time. There are uncertainties about the relationships among recognized species (B. culicivorus and B. hypoleucus), and whether B. culicivorus can be considered as a single species. In order to elucidate the phylogenetic relationships among these species and their biogeographic history we used a broad geographic sampling from Mexico to Argentina of B. culicivorus and B. hypoleucus. Using a mitochondrial gene, a nuclear intron and microsatellites we identified highly structured groups according to their spatial distribution. The known subspecies of B. culicivorus formed monophyletic groups, except two ones from Brazil and Paraguay. Basileuterus hypoleucus sequences did not form a monophyletic clade, being more related to B. culicivorus from Brazil and Paraguay. The divergence time analysis indicated that the deep separation of the basal lineages of B. culicivorus occurred in Late Pliocene. Contrasting with the other geographically structured populations from Central and South America, the clade of birds from Brazil, Paraguay and Argentina showed a remarkably high population growth starting in the mid-Pleistocene, according to the most plausible evolutionary scenario expected for parulid birds of a range expansion directed southwards.

  13. Molecular phylogeny of Threskiornithidae (Aves: Pelecaniformes) based on nuclear and mitochondrial DNA.

    Science.gov (United States)

    Ramirez, J L; Miyaki, C Y; Del Lama, S N

    2013-07-30

    The family Threskiornithidae includes 13 genera and 32 species, and it is traditionally divided into 2 subfamilies: Plataleinae and Threskiornithinae. We present a phylogenetic reconstruction to test the monophyly of currently accepted subfamilies, including 15 species from both subfamilies and 10 genera of family Threskiornithidae. Phylogenetic trees were inferred on the basis of the mitochondrial 16S rRNA gene and the nuclear intron 7 of β-fibrinogen. Threskiornithidae was recovered as a monophyletic group. Plataleinae formed a monophyletic group, but nested within Threskiornithinae, which was thus paraphyletic. Two major phylogenetic groups were identified: the 'endemic New World clade', including genera endemic to the American continent, and the 'widespread clade', comprising the remaining species. These phylogenetic groups diverged about 39-42 million years ago, i.e., before the separation of South America and Antarctica. Our results agree with an initial vicariance due to Gondwana break-up and subsequent colonization of species from the Old World to the New World.

  14. Revision of the Nearctic species of Callomyia Meigen (Diptera: Platypezidae) and phylogeny of the genus.

    Science.gov (United States)

    Cumming, Heather J; Wheeler, Terry A

    2016-05-18

    The Nearctic fauna of the genus Callomyia Meigen is revised and a phylogeny of the world species, based on morphological characters, is presented. Although morphological data are used primarily to delimit species, molecular sequence data (DNA barcodes) are used where possible, to help determine species boundaries and associate sexes. Species descriptions, diagnoses, and distribution maps are presented, along with illustrations of habitus, male terminalia, and additional important diagnostic characters. A key to the Nearctic species is provided. Ten species are recorded from the Nearctic Region including three new species: C. argentea Cumming sp. nov., C. arnaudi Cumming sp. nov., C. bertae Kessel, C. browni Cumming sp. nov., C. calla Kessel, C. corvina Kessel, C. gilloglyorum Kessel, C. proxima Johnson, C. velutina Johnson, and C. venusta Snow. The female of C. velutina is described, and three new synonyms are proposed: C. cleta Kessel is a junior synonym of C. calla syn. nov.; C. clara Kessel is a junior synonym of C. corvina syn. nov.; and C. liardia Kessel & Buegler is a junior synonym of C. proxima syn. nov. Phylogenetic relationships within the genus are reconstructed. The genus is monophyletic based primarily on the setulose R1 wing vein, female antennal size and three larval characters. The Nearctic species do not form a monophyletic group with respect to the Old World species.

  15. Multilocus phylogeny of the New-World mud turtles (Kinosternidae) supports the traditional classification of the group.

    Science.gov (United States)

    Spinks, Phillip Q; Thomson, Robert C; Gidiş, Müge; Bradley Shaffer, H

    2014-07-01

    A goal of modern taxonomy is to develop classifications that reflect current phylogenetic relationships and are as stable as possible given the inherent uncertainties in much of the tree of life. Here, we provide an in-depth phylogenetic analysis, based on 14 nuclear loci comprising 10,305 base pairs of aligned sequence data from all but two species of the turtle family Kinosternidae, to determine whether recent proposed changes to the group's classification are justified and necessary. We conclude that those proposed changes were based on (1) mtDNA gene tree anomalies, (2) preliminary analyses that do not fully capture the breadth of geographic variation necessary to motivate taxonomic changes, and (3) changes in rank that are not motivated by non-monophyletic groups. Our recommendation, for this and other similar cases, is that taxonomic changes be made only when phylogenetic results that are statistically well-supported and corroborated by multiple independent lines of genetic evidence indicate that non-monophyletic groups are currently recognized and need to be corrected. We hope that other members of the phylogenetics community will join us in proposing taxonomic changes only when the strongest phylogenetic data demand such changes, and in so doing that we can move toward stable, phylogenetically informed classifications of lasting value.

  16. Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.: Implication for Conservation and Agricultural Practices.

    Directory of Open Access Journals (Sweden)

    Marie Florence Sandrine Ngo Ngwe

    Full Text Available Yams (Dioscorea spp. consist of approximately 600 species. Presently, these species are threatened by genetic erosion due to many factors such as pest attacks and farming practices. In parallel, complex taxonomic boundaries in this genus makes it more challenging to properly address the genetic diversity of yam and manage its germplasm. As a first step toward evaluating and preserving the genetic diversity yam species, we use a phylogenetic diversity (PD approach that has the advantage to investigate phylogenetic relationships and test hypotheses of species monophyly while alleviating to the problem of ploidy variation within and among species. The Bayesian phylogenetic analysis of 62 accessions from 7 species from three regions of Cameroon showed that most Dioscorea sections were monophyletic, but species within sections were generally non-monophyletic. The wild species D. praehensilis and cultivated D. cayenensis were the species with the highest PD. At the opposite, D. esculenta has a low PD and future studies should focus on this species to properly address its conservation status. We also show that wild species show a stronger genetic structure than cultivated species, which potentially reflects the management of the yam germplasm by farmers. These findings show that phylogenetic diversity is a promising approach for an initial investigation of genetic diversity in a crop consisting of closely related species.

  17. Phylogeny of hard- and soft-tick taxa (Acari: Ixodida) based on mitochondrial 16S rDNA sequences.

    Science.gov (United States)

    Black, W C; Piesman, J

    1994-01-01

    Ticks are parasitiform mites that are obligate hematophagous ectoparasites of amphibians, reptiles, birds, and mammals. A phylogeny for tick families, subfamilies, and genera has been described based on morphological characters, life histories, and host associations. To test the existing phylogeny, we sequenced approximately 460 bp from the 3' end of the mitochondrial 16S rRNA gene (rDNA) in 36 hard- and soft-tick species; a mesostigmatid mite, Dermanyssus gallinae, was used as an outgroup. Phylogenies derived using distance, maximum-parsimony, or maximum-likelihood methods were congruent. The existing phylogeny was largely supported with four exceptions. In hard ticks (Ixodidae), members of Haemaphysalinae were monophyletic with the primitive Amblyomminae and members of Hyalomminae grouped within the Rhipicephalinae. In soft ticks (Argasidae), the derived phylogeny failed to support a monophyletic relationship among members of Ornithodorinae and supported placement of Argasinae as basal to the Ixodidae, suggesting that hard ticks may have originated from an Argas-like ancestor. Because most Argas species are obligate bird octoparasites, this result supports earlier suggestions that hard ticks did not evolve until the late Cretaceous. PMID:7937832

  18. Mitochondrial phylogenomics of modern and ancient equids.

    Directory of Open Access Journals (Sweden)

    Julia T Vilstrup

    Full Text Available The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy's zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga. Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya.

  19. Phylogenetic analysis of heterothallic Neurospora species.

    Science.gov (United States)

    Skupski, M P; Jackson, D A; Natvig, D O

    1997-02-01

    We examined the phylogenetic relationships among five heterothallic species of Neurospora using restriction fragment polymorphisms derived from cosmid probes and sequence data from the upstream regions of two genes, al-1 and frq. Distance, maximum likelihood, and parsimony trees derived from the data support the hypothesis that strains assigned to N. sitophila, N. discreta, and N. tetrasperma form respective monophyletic groups. Strains assigned to N. intermedia and N. crassa, however, did not form two respective monophyletic groups, consistent with a previous suggestion based on analysis of mitochondrial DNAs that N. crassa and N. intermedia may be incompletely resolved sister taxa. Trees derived from restriction fragments and the al-1 sequence position N. tetrasperma as the sister species of N. sitophila. None of the trees produced by our data supported a previous analysis of sequences in the region of the mating type idiomorph that grouped N. crassa and N. sitophila as sister taxa, as well as N. intermedia and N. tetrasperma as sister taxa. Moreover, sequences from al-1, frq, and the mating-type region produced different trees when analyzed separately. The lack of consensus obtained with different sequences could result from the sorting of ancestral polymorphism during speciation or gene flow across species boundaries, or both.

  20. Phylogeny of the Paracalanidae Giesbrecht, 1888 (Crustacea: Copepoda: Calanoida).

    Science.gov (United States)

    Cornils, Astrid; Blanco-Bercial, Leocadio

    2013-12-01

    The Paracalanidae are ecologically-important marine planktonic copepods that occur in the epipelagic zone in temperate and tropical waters. They are often the dominant taxon - in terms of biomass and abundance - in continental shelf regions. As primary consumers, they form a vital link in the pelagic food web between primary producers and higher trophic levels. Despite the ecological importance of the taxon, evolutionary and systematic relationships within the family remain largely unknown. A multigene phylogeny including 24 species, including representatives for all seven genera, was determined based on two nuclear genes, small-subunit (18S) ribosomal RNA and Histone 3 (H3) and one mitochondrial gene, cytochrome c oxidase subunit I (COI). The molecular phylogeny was well supported by Maximum likelihood and Bayesian inference analysis; all genera were found to be monophyletic, except for Paracalanus, which was separated into two distinct clades: the Paracalanus aculeatus group and Paracalanus parvus group. The molecular phylogeny also confirmed previous findings that Mecynocera and Calocalanus are genera of the family Paracalanidae. For comparison, a morphological phylogeny was created for 35 paracalanid species based on 54 morphological characters derived from published descriptions. The morphological phylogeny did not resolve all genera as monophyletic and bootstrap support was not strong. Molecular and morphological phylogenies were not congruent in the positioning of Bestiolina and the Paracalanus species groups, possibly due to the lack of sufficient phylogenetically-informative morphological characters. Copyright © 2013 Elsevier Inc. All rights reserved.

  1. A multilocus phylogeny of a major New World avian radiation: the Vireonidae.

    Science.gov (United States)

    Slager, David L; Battey, C J; Bryson, Robert W; Voelker, Gary; Klicka, John

    2014-11-01

    The family Vireonidae represents one of the most widespread and well-known New World avian radiations, but a robust species-level phylogeny of the group is lacking. Here, we infer a phylogeny of Vireonidae using multilocus data obtained from 221 individuals from 46 of 52 vireonid species (representing all four genera) and five "core Corvoidea" outgroups. Our results show Vireonidae to be monophyletic, consistent with a single colonization of the New World by an Asian ancestor. Cyclarhis and Vireolanius are monophyletic genera that diverged early from the rest of Vireonidae. Hylophilus is polyphyletic, represented by three distinct clades concordant with differences in morphology, habitat, and voice. The poorly known South American species Hylophilus sclateri is embedded within the genus Vireo. Vireo, in turn, consists of several well-supported intrageneric clades. Overall, tropical vireonid species show much higher levels of intraspecific genetic structure than temperate species and several currently recognized species are probably comprised of multiple cryptic species. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. Phylogenetics and diversification of morning glories (tribe Ipomoeeae, Convolvulaceae) based on whole plastome sequences.

    Science.gov (United States)

    Eserman, Lauren A; Tiley, George P; Jarret, Robert L; Leebens-Mack, Jim H; Miller, Richard E

    2014-01-01

    Morning glories are an emerging model system, and resolving phylogenetic relationships is critical for understanding their evolution. Phylogenetic studies demonstrated that the largest morning glory genus, Ipomoea, is not monophyletic, and nine other genera are derived from within Ipomoea. Therefore, systematic research is focused on the monophyletic tribe Ipomoeeae (ca. 650-900 species). We used whole plastomes to infer relationships across Ipomoeeae. Whole plastomes were sequenced for 29 morning glory species, representing major lineages. Phylogenies were estimated using alignments of 82 plastid genes and whole plastomes. Divergence times were estimated using three fossil calibration points. Finally, evolution of root architecture, flower color, and ergot alkaloid presence was examined. Phylogenies estimated from both data sets had nearly identical topologies. Phylogenetic results are generally consistent with prior phylogenetic hypotheses. Higher-level relationships with weak support in previous studies were recovered here with strong support. Molecular dating analysis suggests a late Eocene divergence time for the Ipomoeeae. The two clades within the tribe, Argyreiinae and Astripomoeinae, diversified at similar times. Reconstructed most recent common ancestor of the Ipomoeeae had blue flowers, an association with ergot-producing fungi, and either tuberous or fibrous roots. Phylogenetic results provide confidence in relationships among Ipomoeeae lineages. Divergence time estimation results provide a temporal context for diversification of morning glories. Ancestral character reconstructions support previous findings that morning glory morphology is evolutionarily labile. Taken together, our study provides strong resolution of the morning glory phylogeny, which is broadly applicable to the evolution and ecology of these fascinating species.

  3. Phylogeny of fireflies (Coleoptera: Lampyridae) inferred from mitochondrial 16S ribosomal DNA, with references to morphological and ethological traits

    Institute of Scientific and Technical Information of China (English)

    LI Xueyan; YANG Shuang; XIE Meng; LIANG Xingcai

    2006-01-01

    We sequenced partial mitochondrial 16S ribosomal DNA (16S rDNA) of 18 firefly species from Southwest of China.Combined with homologous sequences previously reported, phylogenetic trees including Japanese, Korean and Chinese species were reconstructed by neighbor-joining, maximum parsimony and Bayesian methods. All reconstructions agree on most nodes of the trees. Monophyly of Lampyridae is not supported because Rhagophthalmus ohbai in Rhagophthalmidae is included within it. Lamprigera, a genus placed unreliably in Lampyrinae, shows a close relationship to Amydetinae. Monophyly of Luciolinae is not supported because Pristolycus sagulatus (Lampyrinae) is included within it. In the Luciolinae, monophyly of Curtos and Hotaria is well established, respectively, but both morphological and molecular data continue to indicate that Luciola is not monophyletic and its subdivision is indeed necessary. Within the Lampyrinae, both Pyrocoelia and Diaphanes are not monophyletic, but monophyly of Pyrocoelia + Diaphanes is well supported. Phylogeny of Diaphanes is discussed for the first time. Generic placement of a newly discovered species (Diaphanes pectinealis Li et Liang)sharing some characters of Pyrocoelia and Diaphanes challenges the delimitation of these two similar genera. With references to the firefly mating systems, we suggest that more emphases should be placed on those sexually selected characters such as antennal structure in taxonomy of Lampyridae.

  4. A RAD-based phylogenetics for Orestias fishes from Lake Titicaca.

    Science.gov (United States)

    Takahashi, Tetsumi; Moreno, Edmundo

    2015-12-01

    The fish genus Orestias is endemic to the Andes highlands, and Lake Titicaca is the centre of the species diversity of the genus. Previous phylogenetic studies based on a single locus of mitochondrial and nuclear DNA strongly support the monophyly of a group composed of many of species endemic to the Lake Titicaca basin (the Lake Titicaca radiation), but the relationships among the species in the radiation remain unclear. Recently, restriction site-associated DNA (RAD) sequencing, which can produce a vast number of short sequences from various loci of nuclear DNA, has emerged as a useful way to resolve complex phylogenetic problems. To propose a new phylogenetic hypothesis of Orestias fishes of the Lake Titicaca radiation, we conducted a cluster analysis based on morphological similarities among fish samples and a molecular phylogenetic analysis based on RAD sequencing. From a morphological cluster analysis, we recognised four species groups in the radiation, and three of the four groups were resolved as monophyletic groups in maximum-likelihood trees based on RAD sequencing data. The other morphology-based group was not resolved as a monophyletic group in molecular phylogenies, and some members of the group were diverged from its sister group close to the root of the Lake Titicaca radiation. The evolution of these fishes is discussed from the phylogenetic relationships.

  5. Phylogenetic and cophylogenetic relationships of entomopathogenic nematodes (Heterorhabditis: Rhabditida) and their symbiotic bacteria (Photorhabdus: Enterobacteriaceae).

    Science.gov (United States)

    Maneesakorn, Patchareewan; An, Ruisheng; Daneshvar, Hannah; Taylor, Kara; Bai, Xiaodong; Adams, Byron J; Grewal, Parwinder S; Chandrapatya, Angsumarn

    2011-05-01

    Mutualistic association between entomopathogenic Photorhabdus bacteria and Heterorhabditis nematodes represents one of the emerging model systems in symbiosis studies, yet little is known about this partnership from a coevolutionary perspective. Herein, we investigated phylogenetic and cophylogenetic relationships of Heterorhabditis and Photorhabdus strains using molecular markers Internal Transcribed Spacer and gyrase B gene sequences, respectively. The phylogenies presented consistent, well supported, monophyletic groups in the parsimonious and likelihood analyses for both the nematode and bacterial strains and supported the placement of currently recognized taxa, from which a potentially new Heterorhabditis species represented by a Thailand strain MP68 was identified. While the nematode strains with distant geographic distributions showed no detectable phylogenetic divergence within H. bacteriophora or H. georgiana monophyletic groups, their respective symbiotic bacteria speciated into two Photorhabdus species: P. luminescens and P. temperata, indicating the occurrence of duplication. Although such evolutionary process reduces the phylogenetic congruence between Heterorhabditis nematodes and Photorhabdus bacteria, global cophylogenetic tests using ParaFit detected a highly significant correlation between the two phylogenies (ParaFitGlobal = 0.001). Further, the associations between H. zealandica, H. indica and H. megidis strains and their symbiotic bacteria exhibited significant contribution to the overall cophylogenetic structure. Overall, this study reveals evidence of coevolution between Photorhabdus bacteria and Heterorhabditis nematodes and provides a framework for further examination of the evolution of these associations. Copyright © 2011 Elsevier Inc. All rights reserved.

  6. Phylogenetic analyses of cyclidiids (Protista, Ciliophora, Scuticociliatia) based on multiple genes suggest their close relationship with thigmotrichids.

    Science.gov (United States)

    Gao, Feng; Gao, Shan; Wang, Pu; Katz, Laura A; Song, Weibo

    2014-06-01

    Cyclidiids and thigmotrichids are two diverse groups of scuticociliates, a diverse clade of ciliates that is often difficult to investigate due to the small size and conserved morphology among its members. Compared to other groups (e.g. hypotrichs and oligotrichs), the scuticociliates have received relatively little attention and their phylogenetic relationships are largely unresolved. To contribute to our understanding of their evolutionary history, we characterized 26 sequences for three linked genes (SSU-rDNA, 5.8S and LSU-rDNA) from 14 isolates of cyclidiids and thigmotrichids. Phylogenetic analyses reveal the following: (1) traditional cyclidiids are associated with thigmotrichs rather than pleuronematids as expected; (2) the validity of the newly-reported genus Falcicyclidium is confirmed by the molecular data and we suggest to transfer this genus to the family Ctedoctematidae; (3) both the genera Cyclidium and Protocyclidium are not monophyletic and the separation of Protocyclidium from Cyclidium is not supported; (4) the genus Cristigera is a well supported monophyletic group and may stand for a new family; (5) according to both morphological and molecular information, Cyclidium plouneouriDragesco, 1963 should be assigned in the genus Falcicyclidium and thus a new combination is suggested: Falcicyclidium plouneouri (Dragesco, 1963) n. comb.; and (6) based on the data available, a new genus is suggested: Acucyclidium gen. nov. with the type species, Acucyclidium atractodes (Fan et al., 2011a) n. comb. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Evolution and Phylogenetic Diversity of Yam Species (Dioscorea spp.): Implication for Conservation and Agricultural Practices.

    Science.gov (United States)

    Ngo Ngwe, Marie Florence Sandrine; Omokolo, Denis Ndoumou; Joly, Simon

    2015-01-01

    Yams (Dioscorea spp.) consist of approximately 600 species. Presently, these species are threatened by genetic erosion due to many factors such as pest attacks and farming practices. In parallel, complex taxonomic boundaries in this genus makes it more challenging to properly address the genetic diversity of yam and manage its germplasm. As a first step toward evaluating and preserving the genetic diversity yam species, we use a phylogenetic diversity (PD) approach that has the advantage to investigate phylogenetic relationships and test hypotheses of species monophyly while alleviating to the problem of ploidy variation within and among species. The Bayesian phylogenetic analysis of 62 accessions from 7 species from three regions of Cameroon showed that most Dioscorea sections were monophyletic, but species within sections were generally non-monophyletic. The wild species D. praehensilis and cultivated D. cayenensis were the species with the highest PD. At the opposite, D. esculenta has a low PD and future studies should focus on this species to properly address its conservation status. We also show that wild species show a stronger genetic structure than cultivated species, which potentially reflects the management of the yam germplasm by farmers. These findings show that phylogenetic diversity is a promising approach for an initial investigation of genetic diversity in a crop consisting of closely related species.

  8. Phylogenetic relationships of Cyprinidae (Teleostei: Cypriniformes) inferred from the partial S6K1 gene sequences and implication of indel sites in intron 1

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The family Cyprinidae is widely distributed in East Asia, and has the important phylogenetic signifi- cance in the fish evolution. In this study, the 5′ end partial sequences (containing exon 1, exon 2 and indel 1) of S6K1 gene were obtained from 30 representative species in Cyprinidae and outgroup using PCR amplification and sequencing. The phylogenetic relationships of Cyprinidae were reconstructed with neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML), and Bayesian meth- ods. Myxocyprinus asiaticus (Catostomidae) was assigned to the outgroup taxon. Similar phylogenetic relationships within the family Cyprinidae were achieved with the four analyses. Leuciscini and Barbini were monophyletic lineages respectively with the high nodal supports. Leuciscini comprises Hypophthalmichthyinae, Xenocyprinae, Cultrinae, Gobioninae, Acheilognathinae and East Asian species of Leuciscinae and Danioninae. Monophyly of East Asian clade was supported with high nodal support. Barbini comprises Schizothoracinae, Barbinae, Cyprininae and Labeoninae. The monophyletic lineage consisting of Danio rerio, D. myersi, and Rasbora trilineata was basal in the tree. In addition, the large fragment indels in intron 1 were analyzed to improve the understanding of Cyprinidae relationships. The results showed that the large fragment indels were correlated with the relations among species. Some conserved regions in intron 1 were thought to be involved in the functional regulation. However, no correlation was found between sequence variations and species characteristic size.

  9. Molecular phylogenetics of New World searobins (Triglidae; Prionotinae).

    Science.gov (United States)

    Portnoy, David S; Willis, Stuart C; Hunt, Elizabeth; Swift, Dominic G; Gold, John R; Conway, Kevin W

    2017-02-01

    Phylogenetic relationships among members of the New World searobin genera Bellator and Prionotus (Family Triglidae, Subfamily Prionotinae) and among other searobins in the families Triglidae and Peristediidae were investigated using both mitochondrial and nuclear DNA sequences. Phylogenetic hypotheses derived from maximum likelihood and Bayesian methodologies supported a monophyletic Prionotinae that included four well resolved clades of uncertain relationship; three contained species in the genus Prionotus and one contained species in the genus Bellator. Bellator was always recovered within the genus Prionotus, a result supported by post hoc model testing. Two nominal species of Prionotus (P. alatus and P. paralatus) were not recovered as exclusive lineages, suggesting the two may comprise a single species. Phylogenetic hypotheses also supported a monophyletic Triglidae but only if armored searobins (Family Peristediidae) were included. A robust morphological assessment is needed to further characterize relationships and suggest classification of clades within Prionotinae; for the time being we recommend that Bellator be considered a synonym of Prionotus. Relationships between armored searobins (Family Peristediidae) and searobins (Family Triglidae) and relationships within Triglidae also warrant further study.

  10. Phylogeny and evolution of charophytic algae and land plants%轮藻和陆地植物系统发育及其进化

    Institute of Scientific and Technical Information of China (English)

    仇寅龙

    2008-01-01

    Charophytic algae and land plants together make up a monophyletic group, streptophytes, which represents one of the main lineages of multicellular eukaryotes and has contributed greatly to the change of the environment on earth in the Phanerozoic Eon. Significant progress has been made to understand phylogenetic relationships among members of this group by phylogenetic studies of morphological and molecular data over the last twenty-five years. Mesostigma viride is now regarded as among the earliest diverging unicellular organisms in streptophytes. Characeae are the sister group to land plants. Liverworts represent the first diverging lineage of land plants. Hornworts and lycophytes are extant representatives of bryophytes and vascular plants, respectively, when early land plants changed from gametophyte to sporophyte as the dominant generation in the life cycle. Equisetum, Psilotaceae, and ferns constitute the monophyletic group of monilophytes, which are sister to seed plants. Gnetales are related to conifers, not to angiosperms as previously thought. Amborella, Nymphaeales, Hydatellaceae, Illiciales, Trimeniaceae, and Austrobaileya represent the earliest diverging lineages of extant angiosperms. These phylogenetic results, together with recent progress on elucidating genetic and developmental aspects of the plant life cycle, multicellularity, and gravitropism, will facilitate evolutionary developmental studies of these key traits, which will help us to gain mechanistic understanding on how plants adapted to environmental challenges when they colonized the land during one of the major transitions in evolution of life.

  11. Phylogeny and classification of bacteria in the genera Clavibacter and Rathayibacter on the basis of 16s rRNA gene sequence analyses.

    Science.gov (United States)

    Lee, I M; Bartoszyk, I M; Gundersen-Rindal, D E; Davis, R E

    1997-01-01

    A phylogenetic analysis by parsimony of 16S rRNA gene sequences (16S rDNA) revealed that species and subspecies of Clavibacter and Rathayibacter form a discrete monophyletic clade, paraphyletic to Corynebacterium species. Within the Clavibacter-Rathayibacter clade, four major phylogenetic groups (subclades) with a total of 10 distinct taxa were recognized: (I) species C. michiganensis; (II) species C. xyli; (III) species R. iranicus and R. tritici; and (IV) species R. rathayi. The first three groups form a monophyletic cluster, paraphyletic to R. rathayi. On the basis of the phylogeny inferred, reclassification of members of Clavibacter-Rathayibacter group is proposed. A system for classification of taxa in Clavibacter and Rathayibacter was developed based on restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified 16S rDNA sequences. The groups delineated on the basis of RFLP patterns of 16S rDNA coincided well with the subclades delineated on the basis of phylogeny. In contrast to previous classification systems, which are based primarily on phenotypic properties and are laborious, the RFLP analyses allow for rapid differentiation among species and subspecies in the two genera. PMID:9212413

  12. Molecular phylogeny of Pamphagidae (Acridoidea, Orthoptera) from China based on mitochondrial cytochrome oxidase Ⅱ sequences

    Institute of Scientific and Technical Information of China (English)

    Dao-Chuan Zhang; Hong-Yan Han; Hong Yin; Xin-Jiang Li; Zhan Yin; Xiang-Chu Yin

    2011-01-01

    Phylogenetic relationships of Pamphagidae were examined using cytochrome oxidase subunit Ⅱ (COII) mtDNA sequences (684 bp). Twenty-seven species of Acridoidea from 20 genera were sequenced to obtain mtDNA data, along with four species from the GenBank nucleotide database. The purpose of this study was analyzing the phylogenetic relationships among subfamilies within Pamphagidae and interpreting the phylogenetic position of this family within the Acridoidea superfamily. Phylogenetic trees were reconstructed using neighbor-joining (NJ), maximum parsimony (MP) and Bayesian inference (BI) methods. The 684 bp analyzed fragment included 126 parsimony informative sites. Sequences diverged 1.0%-l1.1% between genera within subfamilies, and 8.8%-12.3% between subfamilies. Amino acid sequence diverged 0-6.1% between genera within subfamilies, and 0.4%-7.5% between subfamilies. Our phylogenetic trees revealed the monophyly of Pamphagidae and three distinct major groups within this family. Moreover, several well supported and stable clades were found in Pamphagidae. The global clustering results were similar to that obtained through classical morphological classification: Prionotropisinae, Thrinchinae and Pamphaginae were monophyletic groups. However, the current genus Filchnerella (Prionotropisinae) was not a monophyletic group and the genus Asiotmethis (Prionotropisinae) was a sister group of the genus Thrinchus (Thrinchinae). Further molecular and morphological studies are required to clarify the phylogenetic relationships of the genera Filchnerella and Asiotmethis.

  13. Molecular phylogeny of the Ellobiidae (Gastropoda: Panpulmonata) supports independent terrestrial invasions.

    Science.gov (United States)

    Romero, Pedro E; Pfenninger, Markus; Kano, Yasunori; Klussmann-Kolb, Annette

    2016-04-01

    Gastropods of the family Ellobiidae are an interesting group in which to study transitions from intertidal to terrestrial realms. However, the phylogenetic relationships within this family still lack resolution. We present a phylogenetic hypothesis of the Ellobiidae based on Bayesian and maximum likelihood phylograms. We used nuclear (18S, 28S, H3) and mitochondrial (16S, 12S, COI) data, increasing the numbers of markers and data, and making this the most comprehensive phylogenetic study of the family to date. Our results support phylogenetic hypotheses derived from morphological data, and provide a supported framework to evaluate the internal relationships within Ellobiidae. The resulting phylogenetic trees support the previous hypothesis that the Ellobiidae are monophyletic only if the Trimusculinae (Otina, Smeagol and Trimusculus) are considered part of this family. In addition, we found that the Carychiinae, Ellobiinae and Pythiinae are reciprocally monophyletic and closely related, with the Carychiinae as sister group to Ellobiinae. Relationships within Melampodinae and Pedipedinae and their phylogenetic positions remain unresolved. Land invasion by the Ellobiidae occurred independently in Carychiinae and Pythia during different geological times (Mesozoic and Cenozoic, respectively). Diversification in the family does not appear to be related to past climate and biotic changes, neither the Cretaceous-Paleogene boundary nor the lowering of the sea level in the Oligocene.

  14. Molecular phylogeny of Arthrotardigrada (Tardigrada).

    Science.gov (United States)

    Jørgensen, Aslak; Faurby, Søren; Hansen, Jesper G; Møbjerg, Nadja; Kristensen, Reinhardt M

    2010-03-01

    Tardigrades are microscopic ecdysozoans with a worldwide distribution covering marine, limnic and terrestrial habitats. They are regarded as a neglected phylum with regard to studies of their phylogeny. During the last decade molecular data have been included in the investigation of tardigrades. However, the marine arthrotardigrades are still poorly sampled due to their relative rarity, difficult identification and minute size even for tardigrades. In the present study, we have sampled various arthrotardigrades and sequenced the 18S and partial 28S ribosomal subunits. The phylogenetic analyses based on Bayesian inference and maximum parsimony inferred Heterotardigrada (Arthrotardigrada+Echiniscoidea) and Eutardigrada to be monophyletic. Arthrotardigrada was inferred to be paraphyletic as the monophyletic Echiniscoidea is included within the arthrotardigrades. The phylogenetic positions of Stygarctidae and Batillipedidae are poorly resolved with low branch support. The Halechiniscidae is inferred to be polyphyletic as the currently recognized Styraconyxinae is not part of the family. Archechiniscus is the sister-group to the Halechiniscidae and Orzeliscus is placed as one of the basal halechiniscids. The phylogeny of the included eutardigrade taxa resembles the current molecular phylogenies. The genetic diversity within Arthrotardigrada is much larger (18S 15.1-26.5%, 28S 7.2-20.7%) than within Eutardigrada (18S 1.0-12.6%, 28S 1.3-8.2%). This can be explained by higher substitution rates in the arthrotardigrades or by a much younger evolutionary age of the sampled eutardigrades.

  15. Total evidence phylogeny and the evolution of adult bioluminescence in fireflies (Coleoptera: Lampyridae).

    Science.gov (United States)

    Martin, Gavin J; Branham, Marc A; Whiting, Michael F; Bybee, Seth M

    2017-02-01

    Fireflies are some of the most captivating organisms on the planet. They have a rich history as subjects of scientific study, especially in relation to their bioluminescent behavior. Yet, the phylogenetic relationships of fireflies are still poorly understood. Here, we present the first total evidence approach to reconstruct lampyrid phylogeny using both a molecular matrix from six loci and an extensive morphological matrix. Using this phylogeny we test the hypothesis that adult bioluminescence evolved after the origin of the firefly clade. The ancestral state of adult bioluminescence is recovered as non-bioluminescent with one to six gains and five to ten subsequent losses. The monophyly of the family, as well as the subfamilies is also tested. Ototretinae, Cyphonocerinae, Luciolinae (incl. Pristolycus), Amydetinae, "cheguevarinae" sensu Jeng 2008, and Photurinae are highly supported as monophyletic. With the exception of four taxa, Lampyrinae is also recovered as monophyletic with high support. Based on phylogenetic and morphological data Lamprohiza, Phausis, and Lamprigera are transferred to Lampyridae incertae sedis.

  16. Molecular phylogeny and systematics of the highly polymorphic Rumex bucephalophorus complex (Polygonaceae).

    Science.gov (United States)

    Talavera, M; Balao, F; Casimiro-Soriguer, R; Ortiz, M Á; Terrab, A; Arista, M; Ortiz, P L; Stuessy, T F; Talavera, S

    2011-12-01

    Rumex bucephalophorus is a very polymorphic species that has been subjected to various taxonomic studies in which diverse infraspecific taxa have been recognised on the basis of diaspore traits. In this study we used molecular markers (ITS and AFLP) to explore this remarkable diversity, to test previous hypotheses of classification, and attempt to explain biogeographic patterns. Results show that R. bucephalophorus forms a monophyletic group in which diversification began around 4.2 Mya, at the end of Messinian Salinity Crisis. The two molecular markers clearly show a deep divergence separating subsp. bucephalophorus from all other subspecific taxa, among which subsp. canariensis also constitutes a separate and well distinguishable unit. In contrast, subspecies hispanicus and subsp. gallicus constitute a monophyletic group in which three subgroups can be recognised: subsp. hispanicus, subsp. gallicus var. gallicus and subsp. gallicus var. subaegeus. However, these three subgroups are not clearly distinguished genetically or morphologically, so that in formal classification it would be preferable to treat them at the varietal level.

  17. Mitochondrial genes reveal cryptic diversity in plant-breeding frogs from Madagascar (Anura, Mantellidae, Guibemantis).

    Science.gov (United States)

    Lehtinen, Richard M; Nussbaum, Ronald A; Richards, Christina M; Cannatella, David C; Vences, Miguel

    2007-09-01

    One group of mantellid frogs from Madagascar (subgenus Pandanusicola of Guibemantis) includes species that complete larval development in the water-filled leaf axils of rainforest plants. This group consists of six described species: G. albolineatus, G. bicalcaratus, G. flavobrunneus, G. liber, G. pulcher, and G. punctatus. We sequenced the 12S and 16S mitochondrial rRNA genes ( approximately 1.8 kb) from multiple specimens (35 total) of all six species to assess phylogenetic relationships within this group. All reconstructions strongly supported G. liber as part of the Pandanusicola clade, even though this species does not breed in plant leaf axils. This result confirms a striking reversal of reproductive specialization. However, all analyses also indicated that specimens assigned to G. liber include genetically distinct allopatric forms that do not form a monophyletic group. Most other taxa that were adequately sampled (G. bicalcaratus, G. flavobrunneus, and G. pulcher) likewise consist of several genetically distinct lineages that do not form monophyletic groups. These results suggest that many of the recognized species in this group are complexes of cryptic species.

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

    Science.gov (United States)

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

    2014-09-01

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

  19. Phylogenetic relationships of Aristida and relatives (Poaceae, Aristidoideae) based on noncoding chloroplast (trnL-F, rpl16) and nuclear (ITS) DNA sequences.

    Science.gov (United States)

    Cerros-Tlatilpa, Rosa; Columbus, J Travis; Barker, Nigel P

    2011-11-01

    The cosmopolitan and ecologically important grass subfamily Aristidoideae comprises the widely distributed genus Aristida (250-290 species), Stipagrostis (50 species, with an African-Asian distribution), and Sartidia (five species, Africa and Madagascar). The subfamily includes species with C(3) (Sartidia and a single species of Aristida) and C(4) photosynthetic pathways. Rigorous phylogenetic reconstructions of species relationships are required to explain the biogeographic, physiological, and ecological diversity within this subfamily. Chloroplast (trnL-F, rpl16) and nuclear (ITS) DNA sequences were obtained from 198 accessions, and the combined data set was subjected to parsimony, maximum likelihood, and Bayesian inference analyses. Dating analyses calibrated using previously published node ages were conducted to determine the ages of major radiations. The C(3) Sartidia is sister to a monophyletic Stipagrostis, and the (Sartidia, Stipagrostis) clade is sister to Aristida. Within Aristida, the only known C(3) species, A. longifolia, is sister to the remainder of the genus. Infrageneric sections of Aristida were not supported, and there are no synapomorphic morphological characters for the clades retrieved. Within Aristida, monophyletic Australian, African, North American, and South American clades are retrieved. The subfamily dates back to the late Miocene, with the major lineages present by the Pliocene. With one exception, regional clades of Aristida evolved in the Pliocene. The C(3) photosynthetic pathway is hypothesized to be the pleisomorphic condition for the subfamily, wherein two independent C(4) pathways (each with unique anatomical and genetic features) evolved, one within Aristida and one in Stipagrostis.

  20. Molecular phylogenetics of Meliaceae (Sapindales) based on nuclear and plastid DNA sequences.

    Science.gov (United States)

    Muellner, Alexandra N; Samuel, Rosabelle; Johnson, Sheila A; Cheek, Martin; Pennington, Terence D; Chase, Mark W

    2003-03-01

    Phylogenetic analyses of Meliaceae, including representatives of all four currently recognized subfamilies and all but two tribes (32 genera and 35 species, respectively), were carried out using DNA sequence data from three regions: plastid genes rbcL, matK (partial), and nuclear 26S rDNA (partial). Individual and combined phylogenetic analyses were performed for the rbcL, matK, and 26S rDNA data sets. Although the percentage of informative characters is highest in the segment of matK sequenced, rbcL provides the greatest number of informative characters of the three regions, resulting in the best resolved trees. Results of parsimony analyses support the recognition of only two subfamilies (Melioideae and Swietenioideae), which are sister groups. Melieae are the only tribe recognized previously that are strongly supported as monophyletic. The members of the two small monogeneric subfamilies, Quivisianthe and Capuronianthus, fall within Melioideae and Swietenioideae, respectively, supporting their taxonomic inclusion in these groups. Furthermore, the data indicate a close relationship between Aglaieae and Guareeae and a possible monophyletic origin of Cedreleae of Swietenioideae. For Trichilieae (Melioideae) and Swietenieae (Swietenioideae) lack of monophyly is indicated.

  1. A comprehensive molecular phylogeny of dalytyphloplanida (platyhelminthes: rhabdocoela) reveals multiple escapes from the marine environment and origins of symbiotic relationships.

    Science.gov (United States)

    Van Steenkiste, Niels; Tessens, Bart; Willems, Wim; Backeljau, Thierry; Jondelius, Ulf; Artois, Tom

    2013-01-01

    In this study we elaborate the phylogeny of Dalytyphloplanida based on complete 18S rDNA (156 sequences) and partial 28S rDNA (125 sequences), using a Maximum Likelihood and a Bayesian Inference approach, in order to investigate the origin of a limnic or limnoterrestrial and of a symbiotic lifestyle in this large group of rhabditophoran flatworms. The results of our phylogenetic analyses and ancestral state reconstructions indicate that dalytyphloplanids have their origin in the marine environment and that there was one highly successful invasion of the freshwater environment, leading to a large radiation of limnic and limnoterrestrial dalytyphloplanids. This monophyletic freshwater clade, Limnotyphloplanida, comprises the taxa Dalyelliidae, Temnocephalida, and most Typhloplanidae. Temnocephalida can be considered ectosymbiotic Dalyelliidae as they are embedded within this group. Secondary returns to brackish water and marine environments occurred relatively frequently in several dalyeliid and typhloplanid taxa. Our phylogenies also show that, apart from the Limnotyphloplanida, there have been only few independent invasions of the limnic environment, and apparently these were not followed by spectacular speciation events. The distinct phylogenetic positions of the symbiotic taxa also suggest multiple origins of commensal and parasitic life strategies within Dalytyphloplanida. The previously established higher-level dalytyphloplanid clades are confirmed in our topologies, but many of the traditional families are not monophyletic. Alternative hypothesis testing constraining the monophyly of these families in the topologies and using the approximately unbiased test, also statistically rejects their monophyly.

  2. [Molecular characterization of Sigmodon hirsutus (Rodentia: Cricetidae) populations in Venezuela].

    Science.gov (United States)

    Lessmann, Janeth; Arrivillaga, Jazzmín; Aguilera, Marisol

    2011-06-01

    Recent phylogenetic studies based on cytochrome b gene sequence, have determined that the species historically known as Sigmodon hispidus (Rodentia) from South America comprises a species S. hirsutus of paraphyletic origin. The aim of this study was to test the hypothesis that populations from Venezuela, represent the sensu strict form, ancestral haplotypes, and monophyletic subspecieS. For this, 12 individual sequences from three localities of different biogeographic regions in Venezuela were evaluated and sequenced based on cyto b. Additionally, the sequences were used to develop a cladistic analysis and genetic distance calculations, and to compare this information with two individual sequences of Sigmodon specimens available in Genbank. Phylogenetic analyses show that the three populations of S. hirsutus of Venezuela form an ancestral and monophyletic subclade supported by high bootstrap values and significant genetic distance between subclade within the S. hirsutus. Besides, the existence of two lineages suggests two subspecies, S. hirsutus hirsutus from Venezuela, and S. hirsutus mexicanus from Mexico-Central America, but, both species need formal description.

  3. Globally intertwined evolutionary history of giant barrel sponges

    Science.gov (United States)

    Swierts, Thomas; Peijnenburg, Katja T. C. A.; de Leeuw, Christiaan A.; Breeuwer, Johannes A. J.; Cleary, Daniel F. R.; de Voogd, Nicole J.

    2017-09-01

    Three species of giant barrel sponge are currently recognized in two distinct geographic regions, the tropical Atlantic and the Indo-Pacific. In this study, we used molecular techniques to study populations of giant barrel sponges across the globe and assessed whether the genetic structure of these populations agreed with current taxonomic consensus or, in contrast, whether there was evidence of cryptic species. Using molecular data, we assessed whether giant barrel sponges in each oceanic realm represented separate monophyletic lineages. Giant barrel sponges from 17 coral reef systems across the globe were sequenced for mitochondrial (partial CO1 and ATP6 genes) and nuclear (ATPsβ intron) DNA markers. In total, we obtained 395 combined sequences of the mitochondrial CO1 and ATP6 markers, which resulted in 17 different haplotypes. We compared a phylogenetic tree constructed from 285 alleles of the nuclear intron ATPsβ to the 17 mitochondrial haplotypes. Congruent patterns between mitochondrial and nuclear gene trees of giant barrel sponges provided evidence for the existence of multiple reproductively isolated species, particularly where they occurred in sympatry. The species complexes in the tropical Atlantic and the Indo-Pacific, however, do not form separate monophyletic lineages. This rules out the scenario that one species of giant barrel sponge developed into separate species complexes following geographic separation and instead suggests that multiple species of giant barrel sponges already existed prior to the physical separation of the Indo-Pacific and tropical Atlantic.

  4. Streptacidiphilus gen. nov., acidophilic actinomycetes with wall chemotype I and emendation of the family Streptomycetaceae (Waksman and Henrici (1943)AL) emend. Rainey et al. 1997.

    Science.gov (United States)

    Kim, Seung Bum; Lonsdale, John; Seong, Chi-Nam; Goodfellow, Michael

    2003-01-01

    The taxonomic position of acidophilic actinomycetes selectively isolated from acidic soils and litter was examined using a polyphasic approach. The distinct 16S rDNA phyletic branch formed by representative strains was equated with related monophyletic clades that corresponded to the genera Kitasatospora and Streptomyces. The acidophilic isolates also exhibited a distinctive pH profile, a unique 16S rDNA signature, and contained major amounts of LL-diaminopimelic acid, galactose and rhamnose in whole-organism hydrolysates. It is proposed that these acidophilic actinomycetes be assigned to a new genus, Streptacidiphilus gen. nov., on the basis of genotypic and phenotypic differences. Three species were defined on the basis of DNA:DNA pairing and phenotypic data, namely, Streptacidiphilus albus sp. nov., the type species, Streptacidiphilus neutrinimicus sp. nov. and Streptacidiphilus carbonis sp. nov. Members of the genera Kitasatospora, Streptacidiphilus and Streptomyces share a number of key characteristics and form a stable monophyletic branch in the 16S rDNA tree. It is, therefore, proposed that the description of the family Streptomycetaceae be emended to account for properties shown by Kitasatospora and Streptacidiphilus species.

  5. Phylogenetic relationships of elapid snakes based on cytochrome b mtDNA sequences.

    Science.gov (United States)

    Slowinski, J B; Keogh, J S

    2000-04-01

    Published molecular phylogenetic studies of elapid snakes agree that the marine and Australo-Melanesian forms are collectively monophyletic. Recent studies, however, disagree on the relationships of the African, American, and Asian forms. To resolve the relationships of the African, American, and Asian species to each other and to the marine/Australo-Melanesian clade, we sequenced the entire cytochrome b gene for 28 elapids; 2 additional elapid sequences from GenBank were also included. This sample includes all African, American, and Asian genera (except for the rare African Pseudohaje), as well as a representative sample of marine/Australo-Melanesian genera. The data were analyzed by the methods of maximum-parsimony and maximum-likelihood. Both types of analyses yielded similar trees, from which the following conclusions can be drawn: (1) Homoroselaps falls outside a clade formed by the remaining elapids; (2) the remaining elapids are divisible into two broad sister clades, the marine/Australo-Melanesian species vs the African, American, and Asian species; (3) American coral snakes cluster with Asian coral snakes; and (4) the "true" cobra genus Naja is probably not monophyletic as the result of excluding such genera as Boulengerina and Paranaja.

  6. Guanchochroma wildpretii gen. et spec. nov. (Ochrophyta Provides New Insights into the Diversification and Evolution of the Algal Class Synchromophyceae.

    Directory of Open Access Journals (Sweden)

    Maria Schmidt

    Full Text Available A new relative of the chrysophyte genus Chrysopodocystis was found in Tenerife and termed Guanchochroma wildpretii. This unicellular alga was most noticeably discernible from Chrysopodocystis socialis (the only species of this genus by the presence of a cyst-like stage with a multilayered lorica, which also functions as a dispersal unit and shows secondary wall growth. Secondary expansion of loricae (cell casings not involved in cell division, usually with a more or less pronounced opening has never been observed previously and marks a unique feature of the new taxon. Plastids are non-randomly distributed within cells of G. wildpretii. 18S rRNA gene analyses identified the two species as sister lineages and placed them in a monophyletic group with the Synchromophyceae, a heterokont algal (Ochrophyta class characterized by the presence of chloroplast complexes. Yet, neither Chrysopodocystis nor Guanchochroma showed this feature in ultrastructure analyses. Additionally, their 18S rRNA genes possessed distinct inserts, the highest GC-content known for Ochrophyta and exceptionally long branches on the Ochrophyta 18S rDNA phylogenetic tree, suggesting substantially increased substitution rates along their branch compared to Synchromophyceae. Plastid marker data (rbcL recovered a monophyletic clade of Chrysopodocystis, Guanchochroma and Synchromophyceae as well, yet with lower supports for internal split order due to limited resolution of the marker. Evidence for the sequence of events leading to the formation of the plastid complex of Synchromophyceae still remains ambiguous because of the apparently short timeframe in which they occurred.

  7. Towards a Supertree of Arthropoda: A Species-Level Supertree of the Spiny, Slipper and Coral Lobsters (Decapoda: Achelata.

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    Katie E Davis

    Full Text Available While supertrees have been built for many vertebrate groups (notably birds, mammals and dinosaurs, invertebrates have attracted relatively little attention. The paucity of supertrees of arthropods is particularly surprising given their economic and ecological importance, as well as their overwhelming contribution to biodiversity. The absence of comprehensive archives of machine-readable source trees, coupled with the need for software implementing repeatable protocols for managing them, has undoubtedly impeded progress. Here we present a supertree of Achelata (spiny, slipper and coral lobsters as a proof of concept, constructed using new supertree specific software (the Supertree Toolkit; STK and following a published protocol. We also introduce a new resource for archiving and managing published source trees. Our supertree of Achelata is synthesised from morphological and molecular source trees, and represents the most complete species-level tree of the group to date. Our findings are consistent with recent taxonomic treatments, confirming the validity of just two families: Palinuridae and Scyllaridae; Synaxidae were resolved within Palinuridae. Monophyletic Silentes and Stridentes lineages are recovered within Palinuridae, and all sub-families within Scyllaridae are found to be monophyletic with the exception of Ibacinae. We demonstrate the feasibility of building larger supertrees of arthropods, with the ultimate objective of building a complete species-level phylogeny for the entire phylum using a divide and conquer strategy.

  8. Phylogeny and biogeography of exindusiate Andean Polystichum (Dryopteridaceae).

    Science.gov (United States)

    McHenry, Monique A; Barrington, David S

    2014-02-01

    Uplift of the tropical Andes had a significant impact on the diversification of South American flora and fauna. Recent biogeographic inquiries have established patterns of Andean divergence, but investigations on ferns are scant. The fern genus Polystichum Roth (Dryopteridaceae) combines widespread geographic and elevational distribution with a large number of species to form an ideal system for investigation of the origin and diversification patterns of a fern lineage in the tropical Andes. The relationships among 42 Polystichum species, including taxa from all major biogeographic regions, were analyzed with 2591 aligned nucleotides from four plastid markers using maximum parsimony and Bayesian inference. The resulting phylogeny was then used to estimate divergence times and reconstruct both ancestral areas and ancestral elevations. Tropical Andean South American polystichums that lack an indusium (sori exindusiate) were confirmed to form a monophyletic group. This exindusiate Andean Polystichum clade diverged from a middle-elevation forest lineage now rich in species endemic to Mexico during the middle Miocene (13.12 million years ago). The majority of diversification that followed took place in the montane regions of the central Andes with radiations to the northern Andes, southeastern Brazil, and alpine regions. The monophyletic exindusiate Andean Polystichum lineage diverged from a Mexican lineage in the middle Miocene and diversified in the central Andes before dispersing northward. This south-to-north dispersal pattern, documented for many other Andean lineages, corresponds with episodes of uplift in the tropical Andes.

  9. A molecular phylogenetic investigation of Opisthonecta and related genera (Ciliophora, Peritrichia, Sessilida).

    Science.gov (United States)

    Williams, Daniel; Clamp, John C

    2007-01-01

    The gene encoding 18S small subunit ribosomal RNA (ssu rRNA) was sequenced in the sessiline peritrichs Opisthonecta minima and Opisthonecta matiensis, whose free-swimming, paedomorphic trophonts resemble telotrochs. Using these new sequences, phylogenetic trees were constructed with four different methods to test a previously published association between Opisthonecta henneguyi and members of the families Vorticellidae and Astylozoidae. All trees had similar topologies, with O. minima, O. henneguyi, Vorticella microstoma, and Astylozoon enriquesi forming a well-supported, certainly monophyletic clade. On the basis of genetic evidence, genera of the families Opisthonectidae and Astylozoidae are assigned to the family Vorticellidae, which already includes some species with free-swimming morphotypes. The ssu rRNA sequence of O. matiensis places it in the family Epistylididae; its taxonomic revision will be left to another group of authors. A close association of Ophrydium versatile with members of the family Vorticellidae was confirmed, casting doubt on the validity of the family Ophrydiidae. Epistylis galea, Campanella umbellaria, and Opercularia microdiscum are confirmed as comprising an extremely distinct, monophyletic, but morphologically heterogeneous clade that is basal to other clades of sessiline peritrichs.

  10. Paenungulata: a comparison of the hemoglobin sequences from elephant, hyrax, and manatee.

    Science.gov (United States)

    Kleinschmidt, T; Czelusniak, J; Goodman, M; Braunitzer, G

    1986-09-01

    Inspection of the amino acid differences among hemoglobin sequences of a wide range of mammalian species suggested that at alpha 19, alpha 110, alpha 111, beta 23, beta 44, and beta 56, synapomorphies group manatee (Trichechus inungius, Sirenia), Indian and African elephant (Elephas maximus and Loxodonta africana, Proboscidea), and rock hyrax (Procavia habessinica, Hyracoidea) into a monophyletic clade. Results obtained by parsimony analysis provide evidence for this grouping--and thus support for the genealogical validity of Simpson's superorder Paenungulata, which contains as the extant orders Proboscidea, Sirenia, and Hyracoidea. All of the 39 most, or nearly most, parsimonious of 10,395 trees constructed from a tandemly combined alpha- and beta-hemoglobin sequence for 103 vertebrate species (of which 79 were mammals from 16 extant orders), depicted Paenungulata as one of the most anciently separated branches of Eutheria. It was found on examining thousands of alternative trees that to not group Proboscidea, Hyracoidea, and Sirenia in a monophyletic clade required at least four additional substitutions.

  11. Deep phylogeny and evolution of slime moulds (mycetozoa).

    Science.gov (United States)

    Fiore-Donno, Anna Maria; Nikolaev, Sergey I; Nelson, Michaela; Pawlowski, Jan; Cavalier-Smith, Thomas; Baldauf, Sandra L

    2010-01-01

    Mycetozoa, characterized by spore-bearing fruiting bodies, are the most diverse Amoebozoa. They traditionally comprise three taxa: Myxogastria, Dictyostelia and Protostelia. Myxogastria and Dictyostelia typically have multispored fruiting bodies, but controversy exists whether they are related or arose independently from different unicellular ancestors. Protostelid slime moulds, with single-spored fruiting bodies, are possible evolutionary intermediates between them and typical amoebae, but have received almost no molecular study. Protostelid morphology is so varied that they might not be monophyletic. We therefore provide 38 new 18S rRNA and/or EF-1alpha gene sequences from Mycetozoa and related species, including four protostelids and the enigmatic Ceratiomyxa fruticulosa. Phylogenetic analyses support the monophyly of Dictyostelia, Myxogastria, and Ceratiomyxa (here collectively called "macromycetozoa") and show that protostelids are Amoebozoa, mostly related to non-fruiting amoebae of the class Variosea, but may not be monophyletic; some phylogenetic relationships remain poorly resolved. Ceratiomyxa fruticulosa, originally regarded as a myxogastrid, but in recent decades included in Protostelia, is a deeply diverging sister to Myxogastria. The protostelids studied here plus varipodid amoebae and the flagellates Phalansterium and Multicilia together probably form the outgroup to macromycetozoa plus Archamoebae. Thus protostelids and Variosea are especially significant for understanding the evolutionary transition from solitary amoebae to macromycetozoa.

  12. Molecular Phylogeny of Giant Clams Based on Mitochondrial DNA Cytochrome C Oxidase I Gene

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    AGUS NURYANTO

    2007-12-01

    Full Text Available There is an uncertainty for the relationships among giant clam species of Tridacninae, in particular among species belongs to subgenus Chametrachea i.e. Tridacna crocea, T. maxima, and T. squamosa based on different genetic markers. This study examined the relationships among three species within subgenus Chametrachea compared to the previous studies. Neighbour Joining, Maximum Parsimony and Maximum Likelihood tree were constructed based on 455 bp of the mitochondrial DNA cytochrome c oxidase I gene from T. crocea, T. squamosa, T. maxima, T. gigas, and several sequences derived from Genbank for the outgroups. The results showed that giant clams formed a monophyletic group. Within Tridacna group, T. crocea was more closely related to T. squamosa than to T. maxima and they formed a monophyletic group. T. crocea and T. squamosa were sister taxa and sister group to T. maxima and T. gigas. Close affinity between T. crocea and T. squamosa was also supported by high similarity on nucleotide level (94.30% and concordant with the results of the previous studies using mitochondrial 16S rRNA and nuclear 18S rRNA.

  13. Convergent evolution of a complex fruit structure in the tribe Brassiceae (Brassicaceae).

    Science.gov (United States)

    Hall, Jocelyn C; Tisdale, Tracy E; Donohue, Kathleen; Wheeler, Andrew; Al-Yahya, Mohammed A; Kramer, Elena M

    2011-12-01

    Many angiosperms have fruit morphologies that result in seeds from the same plant having different dispersal capabilities. A prime example is found in the Brassiceae (Brassicaceae), which has many members with segmented or heteroarthrocarpic fruits. Since only 40% of the genera are heteroarthrocarpic, this tribe provides an opportunity to study the evolution of an ecologically significant novelty and its variants. We analyzed nuclear (PHYA) and plastid (matK) sequences from 66 accessions using maximum parsimony, maximum likelihood, and Bayesian inference approaches. The evolution of heteroarthrocarpy and its variants was evaluated using maximum parsimony and maximum likelihood ancestral state reconstructions. Although nuclear and plastid phylogenies are incongruent with each other, the following findings are consistent: (1) Cakile, Crambe, Vella, and Zilla lineages are monophyletic; (2) the Nigra lineage is not monophyletic; and (3) within the Cakile clade, Cakile, Didesmus, and Erucaria are paraphyletic. Despite differences in the matK and PHYA topologies at both deep and shallow nodes, similar patterns of morphological evolution emerge. Heteroarthrocarpy, a complex morphological trait, has evolved multiple times across the tribe. Moreover, there are convergent transitions in dehiscence capabilities and fruit disarticulation across the tribe. We present the first explicit analysis of fruit evolution within the Brassiceae, which exemplifies evolutionary lability. The repeated loss and gain of segment dehiscence and disarticulation suggests conservation in the genetic pathway controlling abscission with differential expression across taxa. This study provides a strong foundation for future studies of mechanisms underlying variation in dispersal capabilities of Brassiceae.

  14. Phylogeny of Trachylepis sp. (Reptilia) from Turkey inferred from mtDNA sequences.

    Science.gov (United States)

    Güçlü, Ozgür; Candan, Kamil; Kankiliç, Tolga; Kumlutaş, Yusuf; Durmuş, Salih Hakan; Poulakakis, Nikos; Ilgaz, Cetin

    2014-12-01

    The taxonomic status of the species included into the genus Trachylepis in Turkey are doubtful. So far, three morphological species have been attributed to this genus in Turkey; Trachylepis aurata. T. vittata, and T. septemtaeniata. Here, we investigated the taxonomy of the Turkish Trachylepis species by employing phylogenetic and phylogeographic approaches and using mitochondrial DNA (cytochrome b and 12 S rRNA). In total, 45 Trachylepis and 6 Mabuya specimens were used analyzed. Phylogenetic analyses were carried out using Maximum Likelihood (ML) and Bayesian Inference (BI) methods. The phylogenetic relationships and the genetic distances retrieved, revealed that the Turkish species, which currently recognized as Trachylepis, are highly diversified, forming a distinct clade that shows closer phylogenetic affinity with the species of the genus Mabuya rather than the other Trachylepis species. In this clade, the three Turkish species are monophyletic with T. vittata to branch off first in late Miocene (10.54 Mya). The other two species (T. septemtaeniata and T. aurata) seem to have sister group relationship that diverged at the end of Messinian Salinity Crisis (5.27 Mya). As a whole, the examination of mtDNA lineages in the Turkish lizards of the genus Trachylepis may contribute substantially to the refining of their taxonomic status, since the three species of Turkey, although monophyletic, represent a distinct radiation that would could probably recognized as a different genus in Mabuya sensu lato.

  15. Mitochondrial 16S rRNA sequence variations and phylogeny of the Chinese sisorid catfishes

    Institute of Scientific and Technical Information of China (English)

    GUO Xianguang; ZHANG Yaoguang; HE Shunping; CHEN Yiyu

    2004-01-01

    Partial sequences of mitochondrial 16S rRNA gene were obtained by PCR amplification for comparisons among nine species of glyptosternoid fishes and six species of non-glyptosternoids representing 10 sisorid genera. There are compositional biases in the A-rich unpaired regions and G-rich paired regions. A-G transitions are primarily responsible for the Ts/Tv bias in unpaired regions. The overall substitution rate in unpaired regions is almost two times higher than that in the paired regions. Saturation plots at comparable levels of sequence divergence demonstrate no saturation effects. Phylogenetic analyses using both maximum likelihood and Bayesian methods support the monophyly of Sisoridae. Chinese sisorid catfishes are composed of two major lineages, one represented by (Gagata (Bagarius, Glyptothorax)) and the other by "glyptosternoids + Pseudecheneis".The glyptosternoids may not be a monophyletic group. A previous hypothesis referring to Pseudecheneis as the sister group of monophyletic glyptosternoids, based on morphological evidence, is not supported by the molecular data.Pseudecheneis is shown to be a sister taxon of Glaridoglanis.Pareuchiloglanis might be paraphyletic with Pseudexostoma and Euchiloglanis. Our results also support the hypothesis that Pareuchiloglanis anteanalis might be considered as the synonyms of Pareuchiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi.

  16. Mitochondrial cytochrome b sequence variations and phylogeny of the East Asian bagrid catfishes

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The mitochondrial DNA cytochrome b gene was sequenced from 8 bagrid catfishes in China. Aligned with cytochrome b sequences from 9 bagrid catfishes in Japan, Korea and Russia retrieved from GenBank, and selected Silurus meridionalis, Liobagrus anguillicauda, Liobagrus reini and Phenacogrammus interruptus as outgroups, we constructed a matrix of 21 DNA sequences. The Kimura's two-parameter distances were calculated and molecular phylogenetic trees were constructed by using the maximum parsimony (MP) and neighbor-joining (NJ) methods. The results show that (i) there exist 3-bp deletions of mitochondrial cytochrome b gene compared with cypriniforms and characiforms; (ii) the molecular phylogenetic tree suggests that bagrid catfishes form a monophyletic group, and the genus Mystus is the earliest divergent in the East Asian bagrid catfishes, as well as the genus Pseudobagrus is a monophyletic group but the genus Pelteobagrus and Leiocassis are complicated; and (iii) the evolution rate of the East Asian bagrids mitochondrial cytochrome b gene is about 0.18%~0.30% sequence divergence per million years.

  17. Phylogeny of benthic Phyllodocidae (Polychaeta) based on morphological and molecular data.

    Science.gov (United States)

    Eklöf, Jenny; Pleijel, Fredrik; Sundberg, Per

    2007-10-01

    A combined molecular (18S rDNA, 28S rDNA, 16S rDNA and COI) and morphological analysis of the benthic phyllodocids is presented for the first time. Nineteen phyllodocids and two outgroup taxa are assessed using parsimony, maximum likelihood and Bayesian analyses. We demonstrate high degrees in homoplasy in the traditionally used morphological phyllodocid characters, and show that all the three current subfamilies Phyllodocinae, Eteoninae and Notophyllinae are non-monophyletic. The genera Eulalia, Eumida, Protomystides, Pseudomystides, Pterocirrus and Sige form a well-supported group, as does Mystides and Nereiphylla. Another clade with strong support includes Eteone and Paranaitis, although with Eteone nested within a paraphyletic Paranaitis. The relationship between these two taxa indicate that the unusual arrangement of modified cirri on the first segments in Eteone is due to a fusion of segment 1 and 2 where the cirri of segment 1 have been reduced. Eulalia is non-monophyletic and should be split, minimally into two groups. Our results are ambiguous regarding the ancestral phyllodocid condition of absence-presence of median antenna or nuchal papilla and uniramous or biramous parapodia, but shows that the absence of cirri on segment 3 (previously an apomorphy, for e.g., Mystides, Pseudomystides and Hesionura) is maximally homoplastic.

  18. Comparative sperm ultrastructure in Nemertea.

    Science.gov (United States)

    von Döhren, J; Beckers, P; Vogeler, R; Bartolomaeus, T

    2010-07-01

    Although the monophyly of Nemertea is strongly supported by unique morphological characters and results of molecular phylogenetic studies, their ingroup relationships are largely unresolved. To contribute solving this problem we studied sperm ultrastructure of 12 nemertean species that belong to different subtaxa representing the commonly recognized major monophyletic groups. The study yielded a set of 26 characters with an unexpected variation among species of the same genus (Tubulanus and Procephalothrix species), whereas other species varied in metric values or only one character state (Ramphogordius). In some species, the sperm nucleus has grooves (Zygonemertes virescens, Amphiporus imparispinosus) that may be twisted and give a spiral shape to the sperm head (Paranemertes peregrina, Emplectonema gracile). To make the characters from sperm ultrastructure accessible for further phylogenetic analyses, they were coded in a character matrix. Published data for eight species turned out to be sufficiently detailed to be included. Comparative evaluation of available information on the sperm ultrastructure suggests that subtaxa of Heteronemertea and Hoplonemertea are supported as monophyletic by sperm morphology. However, the data do not provide information on the existing contradictions regarding the internal relationships of "Palaeonemertea." Nevertheless, our study provides evidence that sperm ultrastructure yields numerous potentially informative characters that will be included in upcoming phylogenetic analyses.

  19. Heterochromatin patterns and karyotype relationships within and between the genera Brycon and Salminus (Pisces, Characidae

    Directory of Open Access Journals (Sweden)

    Vladimir Pavan Margarido

    1999-09-01

    Full Text Available Chromosomes of two Brycon species (B. lundii and B. microlepis and Salminus hilarii were analyzed. Based on constitutive heterochromatin distribution patterns, karyotypic relationships within and between Bryconinae and Salmininae were examined. A monophyletic origin for the genus Brycon, comprising at least two chromosome synapomorphies (presence of two large submetacentric bearing paracentromeric and telomeric heterochromatin, is suggested. Moreover, Bryconinae and Salmininae may represent a monophyletic unit among Characidae, as they share several chromosome features.Foram analisados os cromossomos de duas espécies de peixes do gênero Brycon (B. lundii e B. microlepis e de Salminus hilarii. Principalmente baseado no padrão de distribuição da heterocromatina constitutiva, foram discutidas as relações cariotípicas dentro e entre os grupos Bryconinae e Salmininae. É sugerida uma origem monofilética para o gênero Brycon, com pelo menos duas sinapomorfias cromossômicas (presença de dois grandes submetacêntricos apresentando blocos pericentromérico e telomérico de heterocromatina constitutiva. Ainda, Bryconinae e Salmininae, compartilhando vários caracteres cromossômicos, podem formar uma unidade monofilética entre os Characidae, na qual outros caracídeos não estão incluídos.

  20. A survey of the Cape Floristic Region of South Africa for the presence of cyst nematodes (Nematoda: Heteroderidae).

    Science.gov (United States)

    Knoetze, Rinus; Swart, Antoinette

    2014-12-09

    A survey was performed to detect the presence of cyst nematodes in the Cape Floristic Region of South Africa. Soil was collected in the rhizosphere of the dominant plant species within blocks of indigenous vegetation and cysts were extracted from them. A total of 81 blocks of indigenous vegetation were sampled as described. Cysts were detected in 7 of these samples, representing 6 different vegetation types. One set of primers was used to amplify the ITS regions from these cysts, including the 5.8S ribosomal gene, as well as short parts of the 18S and 28S ribosomal genes. ITS-rDNA sequences from the indigenous isolates were aligned with selected sequences of other species from the Heteroderidae. Phylogenetic analyses to resolve the relationships between indigenous isolates and selected representatives of the Heteroderidae were conducted using the Maximum Parsimony method. The consensus tree resulting from alignment of the circumfenestrate cysts revealed that isolates SK18, WK1 and WK26 are included in a clade of Globodera species that parasitise non-solanaceous plants, forming a monophyletic group with G. millefolii, G. artemisiae, and an unidentified Globodera sp. from Portugal. In a tree resulting from the alignment of the Heterodera spp., isolates OK14 and WK2 are included in the Afenestrata group, forming a monophyletic group with H. orientalis.This survey unearthed at least four potentially new species of cyst nematodes, which may prove invaluable for the study of the evolution and biogeography of the group.

  1. Phylogenetic position and generic differentiation of Epithemateae (Gesneriaceae) inferred from plastid DNA sequence data.

    Science.gov (United States)

    Mayer, Veronika; Möller, Michael; Perret, Mathieu; Weber, Anton

    2003-02-01

    The systematic position and generic differentiation of the morphologically and geographically outstanding tribe Epithemateae (Gesneriaceae) was analyzed using the rbcL/atpB-spacer and trnL-F intron-spacer regions of chloroplast DNA. In our analysis Epithemateae forms a strongly supported monophyletic clade (bootstrap [BS] = 100%; jackknife [JK] = 100%; decay index [DI] = 12) and appears as sister to the rest of the paleotropical Gesneriaceae (= subfamily Cyrtandroideae). The paleotropical Gesneriaceae form a monophyletic group (BS = 88%; JK = 85%; DI = 3) that is sister to the neotropical Gesneriaceae (subfamily Gesnerioideae) plus Austral Gesneriaceae (subfamily Coronantheroideae) (BS = 99%; JK = 98%; DI = 10). Within Epithemateae Rhynchoglossum is sister to the remaining Epithemateae (BS = 97%; JK = 96%; DI = 12), in which Epithema is sister to a clade of two genera: Loxonia/Stauranthera (BS = 68%; JK = 64%; DI = 1), which form, together with Epithema, a sister clade (BS = 85%; JK = 83%; DI = 2) to Whytockia and Monophyllaea. While the support for Loxonia and Stauranthera is moderate, the relationship of Whytockia and Monophyllaea is very strongly supported (BS = 100%; JK = 100%; DI = 13). Apart from the somewhat surprising (but well-substantiated) isolated position of Rhynchoglossum, the results are in perfect accordance with the relationships worked out earlier on grounds of architectural and floral characters. Especially remarkable is the predicted coherence between the morphologically and geographically different genera Whytockia and Monophyllaea.

  2. Origin and relationships of Saintpaulia (Gesneriaceae) based on ribosomal DNA internal transcribed spacer (ITS) sequences.

    Science.gov (United States)

    Moller, M; Cronk, Q

    1997-07-01

    Phylogenetic relationships of eight species of Saintpaulia H. Wendl., 19 species of Streptocarpus Lindl. (representing all major growth forms within the genus), and two outgroups (Haberlea rhodopensis Friv., Chirita spadiciformis W. T. Wang) were examined using comparative nucleotide sequences from the two internal transcribed spacers (ITS) of nuclear ribosomal DNA. The length of the ITS 1 region ranged from 228 to 249 base pairs (bp) and the ITS 2 region from 196 to 245 bp. Pairwise sequence divergence across both spacers for ingroup and outgroup species ranged from 0 to 29%. Streptocarpus is not monophyletic, and Saintpaulia is nested within Streptocarpus subgenus Streptocarpella. Streptocarpus subgenus Streptocarpus is monophyletic. The ITS sequence data demonstrate that the unifoliate Streptocarpus species form a clade, and are also characterized by a unique 47-bp deletion in ITS 2. The results strongly support the monophyly of (1) Saintpaulia, and (2) Saintpaulia plus the African members of the subgenus Streptocarpella of Streptocarpus. The data suggest the evolution of Saintpaulia from Streptocarpus subgenus Streptocarpella. The differences in flower and vegetative characters are probably due to ecological adaptation leading to a relatively rapid radiation of Saintpaulia.

  3. Phylogenetic relationships in Myrceugenia (Myrtaceae) based on plastid and nuclear DNA sequences.

    Science.gov (United States)

    Murillo-A, José; Ruiz-P, Eduardo; Landrum, Leslie R; Stuessy, Tod F; Barfuss, Michael H J

    2012-02-01

    Myrceugenia is a genus endemic to South America with a disjunct distribution: 12 species occurring mainly in central Chile and approximately 25 in southeastern Brazil. Relationships are reconstructed within Myrceugenia from four plastid markers (partial trnK-matK, rpl32-trnL, trnQ-5'rps16 and rpl16) and two ribosomal nuclear regions (ETS and ITS) using maximum parsimony and Bayesian analyses. Relationships inferred previously from morphological data are not completely consistent with those from molecular data. All molecular analyses support the hypothesis that Myrceugenia is monophyletic, except for M. fernadeziana that falls outside the genus. Chilean species and Brazilian species form two separate lineages. Chilean species form three early diverging clades, whereas Brazilian species are a strongly supported monophyletic group in a terminal position. Least average evolutionary divergence, low resolution, short branches, and high species diversity found in the Brazilian clade suggest rapid radiation. Geographical distributions and phylogenetic reconstructions suggest that extant Myrceugenia species arose in northern Chile followed by colonization southward and finally to the Juan Fernández Islands and southeastern Brazil.

  4. Mandibular and hyoid muscles of Galeomorph sharks (Chondrichthyes: Elasmobranchii), with remarks on their phylogenetic intrarelationships.

    Science.gov (United States)

    Soares, Mateus C; de Carvalho, Marcelo R

    2013-10-01

    The superorder Galeomorph comprises the orders Heterodontiformes, Orectolobiformes, Lamniformes, and Carcharhiniformes. Recent morphological and molecular support that it is a monophyletic taxon. The phyletic relationship within the Galeomorphi are also well resolved. However, only few morphological characters of the mandibular and hyoid muscles have been employed, and a detailed description of these muscles and their variations may contribute new interpretations of homology and to the discussion of different hypothesis of intrarelationships. This paper provides a detailed description of mandibular and hyoid arch muscles in galeomorph sharks, within a comparative elasmobranch framework, with the objective to discuss putative homologies that may elucidate our understanding of galeomorph evolution. Twenty-eight galeomorph species were dissected, described, illustrated and compared with other elasmobranchs and with data from the literature. The Galeomorphi are supported as monophyletic by presenting the m. levator labii superioris attached directly to the neurocranium, different from the attachment through a tendon in basal squalomorphs. Heterodontiformes and Orectolobiformes share particular variations in the position and insertion of the m. levator labii superioris and the presence of a well-defined m. levator hyomandibulae. Lamniformes and Carcharhiniformes show similar patterns in the position and attachment of the m. levator labii superioris, subdivision of the m. adductor mandibulae, and the presence of an almost indivisible m. levator hyomandibulae and m. constrictor hyoideus dorsalis, similar to the condition, albeit independently, in basal squalomorphs. No specific mandibular or hyoid arch muscle character was found to support the clade composed of Orectolobiformes, Lamniformes, and Carcharhiniformes, as advocated by recent phylogenetic analyses.

  5. Phylogenetic relationships and morphological diversity in Darwin's finches and their relatives.

    Science.gov (United States)

    Burns, Kevin J; Hackett, Shannon J; Klein, Nedra K

    2002-06-01

    Despite the importance of Darwin's finches to the development of evolutionary theory, the origin of the group has only recently been examined using a rigorous, phylogenetic methodology that includes many potential outgroups. Knowing the evolutionary relationships of Darwin's finches to other birds is important for understanding the context from which this adaptive radiation arose. Here we show that analysis of mitochondrial DNA sequence data from the cytochrome b gene confirm that Darwin's finches are monophyletic. In addition, many taxa previously proposed as the sister taxon to Darwin's finches can be excluded as their closest living relative. Darwin's finches are part of a well-supported monophyletic group of species, all of which build a domed nest. All but two of the non-Darwin's finches included in this clade occur on Caribbean islands and most are Caribbean endemics. These close relatives of Darwin's finches show a diversity of bill types and feeding behaviors similar to that observed among Darwin's finches themselves. Recent studies have shown that adaptive evolution in Darwin's finches occurred relatively quickly. Our data show that among the relatives of Darwin's finches, the evolution of bill diversity was also rapid and extensive.

  6. Towards a Supertree of Arthropoda: A Species-Level Supertree of the Spiny, Slipper and Coral Lobsters (Decapoda: Achelata).

    Science.gov (United States)

    Davis, Katie E; Hesketh, Thomas W; Delmer, Cyrille; Wills, Matthew A

    2015-01-01

    While supertrees have been built for many vertebrate groups (notably birds, mammals and dinosaurs), invertebrates have attracted relatively little attention. The paucity of supertrees of arthropods is particularly surprising given their economic and ecological importance, as well as their overwhelming contribution to biodiversity. The absence of comprehensive archives of machine-readable source trees, coupled with the need for software implementing repeatable protocols for managing them, has undoubtedly impeded progress. Here we present a supertree of Achelata (spiny, slipper and coral lobsters) as a proof of concept, constructed using new supertree specific software (the Supertree Toolkit; STK) and following a published protocol. We also introduce a new resource for archiving and managing published source trees. Our supertree of Achelata is synthesised from morphological and molecular source trees, and represents the most complete species-level tree of the group to date. Our findings are consistent with recent taxonomic treatments, confirming the validity of just two families: Palinuridae and Scyllaridae; Synaxidae were resolved within Palinuridae. Monophyletic Silentes and Stridentes lineages are recovered within Palinuridae, and all sub-families within Scyllaridae are found to be monophyletic with the exception of Ibacinae. We demonstrate the feasibility of building larger supertrees of arthropods, with the ultimate objective of building a complete species-level phylogeny for the entire phylum using a divide and conquer strategy.

  7. Phylogeny of Gracilariaceae (Rhodophyta): evidence from plastid and mitochondrial nucleotide sequences.

    Science.gov (United States)

    Lyra, Goia de M; Costa, Emmanuelle da S; de Jesus, Priscila B; de Matos, João Carlos G; Caires, Taiara A; Oliveira, Mariana C; Oliveira, Eurico C; Xi, Zhenxiang; Nunes, José Marcos de C; Davis, Charles C

    2015-04-01

    Gracilariaceae are mostly pantropical red algae and include ~230 species in seven genera. Infrafamilial classification of the group has long been based on reproductive characters, but previous phylogenies have shown that traditionally circumscribed groups are not monophyletic. We performed phylogenetic analyses using two plastid (universal plastid amplicon and rbcL) and one mitochondrial (cox1) loci from a greatly expanded number of taxa to better assess generic relationships and understand patterns of character distributions. Our analyses produce the most well-supported phylogeny of the family to date, and indicate that key characteristics of spermatangia and cystocarp type do not delineate genera as commonly suggested. Our results further indicate that Hydropuntia is not monophyletic. Given their morphological overlap with closely related members of Gracilaria, we propose that Hydropuntia be synonymized with the former. Our results additionally expand the known ranges of several Gracilariaceae species to include Brazil. Lastly, we demonstrate that the recently described Gracilaria yoneshigueana should be synonymized as G. domingensis based on morphological and molecular characters. These results demonstrate the utility of DNA barcoding for understanding poorly known and fragmentary materials of cryptic red algae.

  8. The Analysis of Near Full-Length Genome Sequences of HIV Type 1 Subtype A Viruses from Russia Supports the Monophyly of Major Intrasubtype Clusters

    Science.gov (United States)

    Fernández-García, Aurora; Revilla, Ana; Vázquez-de Parga, Elena; Vinogradova, Anna; Rakhmanova, Aza; Karamov, Eduard; Carrera, Cristina; Delgado, Elena; Pérez-Álvarez, Lucía; Nájera, Rafael; Osmanov, Saladin

    2012-01-01

    Abstract The HIV-1 epidemic in Russia has been insufficiently studied, with only 11 complete genome sequences from this country currently available, only three of which are of the locally predominant genetic form, the former Soviet Union (FSU) subtype A variant (AFSU). Here we analyze 10 newly derived AFSU near full-length genome sequences from Russia. Samples were selected based on phylogenetic clustering in protease-reverse transcriptase in two of the major AFSU clusters, V77IPR (n=6), widely circulating in Russia and other FSU countries, and ASP1 (n=4), predominant in St. Petersburg. The phylogenetic analysis shows that the V77IPR genomes group in a monophyletic cluster together with 10 previously obtained AFSU genome sequences from Uzbekistan, Kazakhstan, Russia, and Cyprus, all bearing the V77I substitution in protease. Similarly, the four ASP1 genomes group in a monophyletic cluster. These results therefore show that the monophyly of V77IPR and ASP1 AFSU clusters is supported in near complete genomes. PMID:22251084

  9. [Genetic characteristics of viral quasispecies of HIV-1 CRF07_BC among intravenous drug users].

    Science.gov (United States)

    Xin, Ruo-Lei; Ma, Ze-Qin; Cheng, Chun-Lin; Xing, Hui; Hong, Kun-Xue; Ruan, Yu-Hua; Li, Jia; Lu, Hong-Yan; Shao, Yi-Ming; He, Xiang

    2013-05-01

    To explore the genetic characteristics of viral quasispecies in HIV-1 CRF07_BC infections among intravenous drug users (IDU), the gp120 fragments of HIV-1 env gene were amplified from plasma samples collected from 6 CRF07_BC infected persons using single genome amplification and sequencing (SGA/ SGS) method, and 11 to 28 sequences were obtained from these samples, respectively, A neighbor-joining phylogenetic tree was reconstructed to describe the genetic characteristics of viral quasispecies. The Simplot, segments' phylogenetic trees and diversity plots based on average pairwise distance (APD) were used to identify the recombination events between quasispecies. The SGA sequences derived from single specimen formed a large monophyletic cluster in the neighbor-joining phylogenetic tree and showed the complex topologic structures of viral quasispecies. Of the 6 CRF07_BC infected patients, only one possessed the high genetic homogeneity, whereas the other five individuals showed high heterogeneity, with two to four subclusters inside the monophyletic cluster for each specimen. In addition, the recombinant events were identified among viral quasispecies from 3 cases. The results show SGA technique and phylogenetic analyses are useful tool to investigate the intrahost CRF07_BC gp120 complex quasispecies variation and high genetic diversity.

  10. Higher phylogeny of frugivorous flies (Diptera, Tephritidae, Dacini): localised partition conflicts and a novel generic classification.

    Science.gov (United States)

    Virgilio, Massimiliano; Jordaens, Kurt; Verwimp, Christophe; White, Ian M; De Meyer, Marc

    2015-04-01

    The phylogenetic relationships within and among subtribes of the fruit fly tribe Dacini (Ceratitidina, Dacina, Gastrozonina) were investigated by sequencing four mitochondrial and one nuclear gene fragment. Bayesian, maximum likelihood and maximum parsimony analyses were implemented on two datasets. The first, aiming at obtaining the strongest phylogenetic signal (yet, having lower taxon coverage), consisted of 98 vouchers and 2338 concatenated base pairs (bp). The second, aiming at obtaining the largest taxonomic coverage (yet, providing lower resolution), included 159 vouchers and 1200 concatenated bp. Phylogenetic relationships inferred by different tree reconstruction methods were largely congruent and showed a general agreement between concatenated tree topologies. Yet, local conflicts in phylogenetic signals evidenced a number of critical sectors in the phylogeny of Dacini fruit flies. All three Dacini subtribes were recovered as monophyletic. Yet, within the subtribe Ceratitidina only Perilampsis and Capparimyia formed well-resolved monophyletic groups while Ceratitis and Trirhithrum did not. Carpophthoromyia was paraphyletic because it included Trirhithrum demeyeri and Ceratitis connexa. Complex phylogenetic relationships and localised conflict in phylogenetic signals were observed within subtribe Dacina with (a) Dacus, (b) Bactrocera (Zeugodacus) and (c) all other Bactrocera species forming separate clades. The subgenus Bactrocera (Zeugodacus) is therefore raised to generic rank (Zeugodacus Hendel stat. nov.). Additionally, Bactrocera subgenera grouped under the Zeugodacus group should be considered under new generic combinations. Although there are indications that Zeugodacus and Dacus are sister groups, the exact relationship between Zeugodacus stat. nov., Dacus and Bactrocera still needs to be properly resolved.

  11. CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy.

    Science.gov (United States)

    Zuo, Guanghong; Hao, Bailin

    2015-10-01

    A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements.

  12. Molecular phylogeny of land and freshwater planarians (Tricladida, Platyhelminthes): from freshwater to land and back.

    Science.gov (United States)

    Alvarez-Presas, Marta; Baguñà, Jaume; Riutort, Marta

    2008-05-01

    The suborder Tricladida (phylum Platyhelminthes) comprises the well-known free-living flatworms, taxonomically grouped into three infraorders according to their ecology: Maricola (marine planarians), Paludicola (freshwater planarians), and Terricola (land planarians). Molecular analyses have demonstrated that the Paludicola are paraphyletic, the Terricola being the sister group of one of the three paludicolan families, the Dugesiidae. However, neither 18S rDNA nor COI based trees have been able to resolve the relationships among species of Terricola and Dugesiidae, particularly the monophyly of Terricola. Here, we present new molecular data including sequences of nuclear genes (18S rDNA, 28S rDNA) and a mitochondrial gene (COI) of a wider sample of dugesiid and terricolan species. The new sequences have been analyzed, together with those previously obtained, in independent and concatenated analyses using maximum likelihood and bayesian methods. The results show that, although some parts of the trees remain poorly resolved, they support a monophyletic origin for Terricola followed by a likely return of some species to freshwater habitats. Relationships within the monophyletic group of Dugesiidae are clearly resolved, and relationships among some terricolan subfamilies are also clearly established and point to the need for a thorough revision of Terricola taxonomy.

  13. Phylogeny of the monopisthocotylea and Polyopisthocotylea (Platyhelminthes) inferred from 28S rDNA sequences.

    Science.gov (United States)

    Mollaret, I; Jamieson, B G; Justine, J L

    2000-02-01

    This study focuses on the phylogenetic relationships within the Polyopisthocotylea and Monopisthocotylea, two groups that are often grouped within the monogeneans, a group of disputed paraphyly. Phylogenetic analyses were conducted with multiple outgroups chosen according to two hypotheses, a paraphyletic Monogenea or a monophyletic Monogenea, and with three methods, namely maximum parsimony, neighbour joining and maximum likelihood. Sequences used were from the partial domain C1, full domain D1, and partial domain C2 (550 nucleotides, 209 unambiguously aligned sites) from the 28S ribosomal RNA gene for 16 species of monopisthocotyleans, 26 polyopisthocotyleans including six polystomatids, and other Platyhelminthes (61 species in total, 27 new sequences). Results were similar with outgroups corresponding to the two hypotheses. Within the Monopisthocotylea, relationships were: ¿[(Udonella, capsalids), monocotylids], (diplectanids, ancyrocephalids)¿; each of these families was found to be monophyletic and their monophyly was supported by high bootstrap values in neighbour joining and maximum parsimony. Within the Polyopisthocotylea, the polystomatids were the sister-group of all others. Among the latter, Hexabothrium, parasite of chondrichthyans, was the most basal, and the mazocraeids, mainly parasites of clupeomorph teleosts, were the sister-groups of all other studied polyopisthocotyleans, these, mainly parasites of euteleosts, being polytomous.

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

    Science.gov (United States)

    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.

  15. Farming termites determine the genetic population structure of Termitomyces fungal symbionts.

    Science.gov (United States)

    Nobre, Tânia; Fernandes, Cecília; Boomsma, Jacobus J; Korb, Judith; Aanen, Duur K

    2011-05-01

    Symbiotic interactions between macrotermitine termites and their fungal symbionts have a moderate degree of specificity. Consistent with horizontal symbiont transmission, host switching has been frequent over evolutionary time so that single termite species can often be associated with several fungal symbionts. However, even in the few termite lineages that secondarily adopted vertical symbiont transmission, the fungal symbionts are not monophyletic. We addressed this paradox by studying differential transmission of fungal symbionts by alate male and female reproductives, and the genetic population structure of Termitomyces fungus gardens across 74 colonies of Macrotermes bellicosus in four west and central African countries. We confirm earlier, more limited, studies showing that the Termitomyces symbionts of M. bellicosus are normally transmitted vertically and clonally by dispersing males. We also document that the symbionts associated with this termite species belong to three main lineages that do not constitute a monophyletic group. The most common lineage occurs over the entire geographical region that we studied, including west, central and southern Africa, where it is also associated with the alternative termite hosts Macrotermes subhyalinus and Macrotermes natalensis. While Termitomyces associated with these alternative hosts are horizontally transmitted and recombine freely, the genetic population structure of the same Termitomyces associated with M. bellicosus is consistent with predominantly clonal reproduction and only occasional recombination. This implies that the genetic population structure of Termitomyces is controlled by the termite host and not by the Termitomyces symbiont.

  16. Delineating species with DNA barcodes: a case of taxon dependent method performance in moths.

    Directory of Open Access Journals (Sweden)

    Mari Kekkonen

    Full Text Available The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs, few studies have compared their performance. This study compares the performance of one morphology-based and four DNA-based (BIN, parsimony networks, ABGD, GMYC methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65% OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90% in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work.

  17. Multilocus and multiregional phylogeny reconstruction of the genus Sarcophaga (Diptera, Sarcophagidae).

    Science.gov (United States)

    Buenaventura, Eliana; Pape, Thomas

    2017-02-01

    The flesh-fly genus Sarcophaga is extremely diverse and contains ca. 30% of the species in the family Sarcophagidae (∼3000 species). The phylogenetic position of the genus-group taxa Helicobia, Lipoptilocnema, and Peckia remains uncertain with respect to the hyperdiverse Sarcophaga, due to conflicting phylogenetic trees and insufficient sampling in recent studies. We present maximum-likelihood and Bayesian phylogenetic analyses of 145 species of 48 subgenera of the genus Sarcophaga from all biogeographic regions based on the molecular markers COI, 28 D1-D3 expansion regions, EF1α, and white. Our analyses find (Lipoptilocnema+Peckia) as the sister group of the monophyletic Sarcophaga. The genus Helicobia is placed outside Sarcophaga. Our hypotheses suggest that the ancestor shared by Sarcophaga and its sister clade originated in the Neotropical region, and the subsequent range expansion might be related to the formation of the Isthmus of Panama. This study supports the monophyly of most of the subgenera of Sarcophaga included here, and it shows the evolution of this genus to be a rapid radiation occurring in the Nearctic region with a subsequent dispersal into the Old World. The subgeneric clusters within Sarcophaga are in agreement with the current classification, with only Mauritiella, Rosellea, Helicophagella, Liosarcophaga, and Sarcorohdendorfia being non-monophyletic. We also validate the monotypic condition of 10 subgenera. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. The complete mitogenome sequence of the Japanese oak silkmoth, Antheraea yamamai (Lepidoptera: Saturniidae).

    Science.gov (United States)

    Kim, Seong Ryeol; Kim, Man Il; Hong, Mee Yeon; Kim, Kee Young; Kang, Pil Don; Hwang, Jae Sam; Han, Yeon Soo; Jin, Byung Rae; Kim, Iksoo

    2009-09-01

    The 15,338-bp long complete mitochondrial genome (mitogenome) of the Japanese oak silkmoth, Antheraea yamamai (Lepidoptera: Saturniidae) was determined. This genome has a gene arrangement identical to those of all other sequenced lepidopteran insects, but differs from the most common type, as the result of the movement of tRNA(Met) to a position 5'-upstream of tRNA(Ile). No typical start codon of the A. yamamai COI gene is available. Instead, a tetranucleotide, TTAG, which is found at the beginning context of all sequenced lepidopteran insects was tentatively designated as the start codon for A. yamamai COI gene. Three of the 13 protein-coding genes (PCGs) harbor the incomplete termination codon, T or TA. All tRNAs formed stable stem-and-loop structures, with the exception of tRNA(Ser)(AGN), the DHU arm of which formed a simple loop as has been observed in many other metazoan mt tRNA(Ser)(AGN). The 334-bp long A + T-rich region is noteworthy in that it harbors tRNA-like structures, as has also been seen in the A + T-rich regions of other insect mitogenomes. Phylogenetic analyses of the available species of Bombycoidea, Pyraloidea, and Tortricidea bolstered the current morphology-based hypothesis that Bombycoidea and Pyraloidea are monophyletic (Obtectomera). As has been previously suggested, Bombycidae (Bombyx mori and B. mandarina) and Saturniidae (A. yamamai and Caligula boisduvalii) formed a reciprocal monophyletic group.

  19. Complete nucleotide sequence and organization of the mitogenome of the silk moth Caligula boisduvalii (Lepidoptera: Saturniidae) and comparison with other lepidopteran insects.

    Science.gov (United States)

    Hong, Mee Yeon; Lee, Eun Mee; Jo, Yong Hun; Park, Hae Chul; Kim, Seong Ryul; Hwang, Jae Sam; Jin, Byung Rae; Kang, Pil Don; Kim, Ki-Gyoung; Han, Yeon Soo; Kim, Iksoo

    2008-04-30

    The 15,360-bp long complete mitogenome of Caligula boisduvalii possesses a gene arrangement and content identical to other completely sequenced lepidopteran mitogenomes, but different from the common arrangement found in most insect order, as the result of the movement of tRNA(Met) to a position 5'-upstream of tRNA Ile. The 330-bp A+T-rich region is apparently capable of forming a stem-and-loop structure, which harbors the conserved flanking sequences at both ends. Dissimilar to what has been seen in other sequenced lepidopteran insects, the initiation codon for C. boisduvalii COI appears to be TTG, which is a rare, but apparently possible initiation codon. The ATP8, ATP6, ND4L, and ND6 genes, which neighbor another PCG at their 3' end, all harbored potential sequences for the formation of a hairpin structure. This is suggestive of the importance of such structures for the precise cleavage of the mRNA of mature PCGs. Phylogenetic analyses of available sequenced species of Bombycoidea, Pyraloidea, and Tortricidea supported the morphology-based current hypothesis that Bombycoidea and Pyraloidea are monophyletic (Obtectomera). As previously suggested, Bombycidae (Bombyx mori and B. mandarina) and Saturniidae (Antheraea pernyi and C. boisduvalii) formed a reciprocal monophyletic group.

  20. The evolutionary origins of the southern ocean Philobryid bivalves: hidden biodiversity, ancient persistence.

    Directory of Open Access Journals (Sweden)

    Jennifer A Jackson

    Full Text Available Philobryids (Bivalvia: Arcoida are one of the most speciose marine bivalve families in the Southern Ocean and are common throughout the Southern Hemisphere. Considering this diversity and their brooding reproductive mode (limiting long-distance dispersal, this family may have been present in the Southern Ocean since its inception. However Philobrya and Adacnarca appear only in the Quaternary fossil record of the Antarctic, suggesting a much more recent incursion. Molecular dating provides an independent means of measuring the time of origin and radiation of this poorly known group. Here we present the first combined molecular and morphological investigation of the Philobryidae in the Southern Ocean. Two nuclear loci (18S and 28S were amplified from 35 Southern Ocean Adacnarca and Philobrya specimens, with a combined sequence length of 2,282 base pairs (bp. Adacnarca specimens (A. nitens and A. limopsoides were resolved as a strongly supported monophyletic group. Genus Philobrya fell into two strongly supported groups ('sublaevis' and 'magellanica/wandelensis', paraphyletic with Adacnarca. The A. nitens species complex is identified as at least seven morpho-species through morphological and genetic analysis of taxon clustering. Phylogenetic analyses resolve Philobryidae as a strongly supported monophyletic clade and sister taxon to the Limopsidae, as anticipated by their classification into the superfamily Limopsoidea. Bayesian relaxed clock analyses of divergence times suggest that genus Adacnarca radiated in the Southern Ocean from the Early Paleogene, while P. sublaevis and P. wandelensis clades radiated in the late Miocene, following the formation of the Antarctic Circumpolar Current.

  1. Sinophysis and Pseudophalacroma are distantly related to typical Dinophysoid dinoflagellates (Dinophysales, Dinophyceae).

    Science.gov (United States)

    Gómez, Fernando; Moreira, David; López-García, Purificación

    2012-01-01

    Dinophysoid dinoflagellates are usually considered a large monophyletic group. Large subunit and small subunit (SSU) rDNA phylogenies suggest a basal position for Amphisoleniaceae (Amphisolenia,Triposolenia) with respect to two sister groups, one containing most Phalacroma species plus Oxyphysis and the other Dinophysis,Ornithocercus, Dinophysoid dinoflagellates are usually considered a large monophyletic group. Large subunit and small subunit (SSU) rDNA phylogenies suggest a basal position for Amphisoleniaceae (Amphisolenia,Triposolenia) with respect to two sister groups, one containing most Phalacroma species plus Oxyphysis and the other Dinophysis,Ornithocercus, Histioneis,Citharistes and some Phalacroma species. We provide here new SSU rDNA sequences of Pseudophalacroma (pelagic) and Sinophysis (the only benthic dinophysoid genus). Molecular phylogenies support that they are very divergent with respect to the main clade of Dinophysales. Additional molecular markers of these two key genera are needed to elucidate the evolutionary relations among the dinophysoid dinoflagellates. Histioneis,Citharistes and some Phalacroma species. We provide here new SSU rDNA sequences of Pseudophalacroma (pelagic) and Sinophysis (the only benthic dinophysoid genus). Molecular phylogenies support that they are very divergent with respect to the main clade of Dinophysales. Additional molecular markers of these two key genera are needed to elucidate the evolutionary relations among the dinophysoid dinoflagellates.

  2. Phylogeny of five species of Nusuttodinium gen. nov. (Dinophyceae), a genus of unarmoured kleptoplastidic dinoflagellates.

    Science.gov (United States)

    Takano, Yoshihito; Yamaguchi, Haruyo; Inouye, Isao; Moestrup, Øjvind; Horiguchi, Takeo

    2014-12-01

    Cells of five unarmoured kleptoplastidic dinoflagellates, Amphidinium latum, Amphidinium poecilochroum, Gymnodinium amphidinioides, Gymnodinium acidotum and Gymnodinium aeruginosum were observed under light and/or scanning electron microscopy and subjected to single-cell PCR. The SSU rDNA and the partial LSU rDNA of all the examined species were sequenced, and the SSU rDNA of G. myriopyrenoides was sequenced. Phylogenetic analyses revealed that the unarmoured kleptoplastidic species formed a monophyletic clade within the Gymnodinium-clade sensu Daugbjerg et al. (2000). The sister taxa for this clade were Gymnodinium palustre and Spiniferodinium galeiforme, both of which possess brown-coloured chloroplasts. The results indicated that acquisition of kleptoplastidy in these unarmoured dinoflagellates was a single event and that these unarmoured kleptoplastidic dinoflagellates may have evolved from a form with permanent chloroplasts. Molecular trees suggested that the acquisition of kleptoplastidy took place in a marine habitat and later some species colonized the freshwater habitat. Because these unarmoured kleptoplastidic dinoflagellates are monophyletic and characterized by distinct morphological and cytological features (including the presence of the same type of apical groove, absence of nuclear chambers in the nuclear envelope, absence of genuine chloroplasts, and the possession of kleptochloroplasts), we propose the establishment of a new genus, Nusuttodinium, to accommodate all these dinoflagellates.

  3. A divergent Cardinium found in daddy long-legs (Arachnida: Opiliones).

    Science.gov (United States)

    Chang, Jin; Masters, Amber; Avery, Amanda; Werren, John H

    2010-11-01

    Recent studies indicate that a newly described bacterial endosymbiont, Cardinium, is widespread in arthropods and induces different reproductive manipulations in hosts. In this study, we used a portion of the 16S rRNA gene of the Cardinium to screen 16 Opilionid species from the suborder Palptores. We found the incidence of Cardinium in these Opiliones was significantly higher than in other pooled arthropods (31.2% versus 7.2%, P=0.007). Phylogenetic analyses using maximum parsimony (MP) and Bayesian analysis revealed two distinct clades in Opiliones. One is a divergent monophyletic clade with strong support that has so far not been found in other arthropods, and a second one contains Cardinium both from Opiliones and other arthropods. There is not complete concordance of the Cardinium strains with host phylogeny, suggesting some horizontal movement of the bacteria among Opiliones. Although the divergence in the sequenced 16S rRNA region between the Cardinium infecting Opiliones and Cardinium from other arthropods is greater than among Cardinium found in other arthropods, all are monophyletic with respect to the outgroup bacteria (endosymbionts of Acanthamoeba). Based on high pairwise genetic distances, deep branch, and a distinct phylogenetic grouping, we conclude that some Opiliones harbor a newly discovered Cardinium clade. Copyright © 2010 Elsevier Inc. All rights reserved.

  4. Diversification of the silverspot butterflies (Nymphalidae) in the Neotropics inferred from multi-locus DNA sequences.

    Science.gov (United States)

    Massardo, Darli; Fornel, Rodrigo; Kronforst, Marcus; Gonçalves, Gislene Lopes; Moreira, Gilson Rudinei Pires

    2015-01-01

    The tribe Heliconiini (Lepidoptera: Nymphalidae) is a diverse group of butterflies distributed throughout the Neotropics, which has been studied extensively, in particular the genus Heliconius. However, most of the other lineages, such as Dione, which are less diverse and considered basal within the group, have received little attention. Basic information, such as species limits and geographical distributions remain uncertain for this genus. Here we used multilocus DNA sequence data and the geographical distribution analysis across the entire range of Dione in the Neotropical region in order to make inferences on the evolutionary history of this poorly explored lineage. Bayesian time-tree reconstruction allows inferring two major diversification events in this tribe around 25mya. Lineages thought to be ancient, such as Dione and Agraulis, are as recent as Heliconius. Dione formed a monophyletic clade, sister to the genus Agraulis. Dione juno, D. glycera and D. moneta were reciprocally monophyletic and formed genetic clusters, with the first two more close related than each other in relation to the third. Divergence time estimates support the hypothesis that speciation in Dione coincided with both the rise of Passifloraceae (the host plants) and the uplift of the Andes. Since the sister species D. glycera and D. moneta are specialized feeders on passion-vine lineages that are endemic to areas located either within or adjacent to the Andes, we inferred that they co-speciated with their host plants during this vicariant event. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. Evolutionary relationships among basal fungi (Chytridiomycota and Zygomycota): Insights from molecular phylogenetics.

    Science.gov (United States)

    Tanabe, Yuuhiko; Watanabe, Makoto M; Sugiyama, Junta

    2005-10-01

    Evolutionary relationships of the two basal fungal phyla Chytridiomycota and Zygomycota are reviewed in light of recent molecular phylogenetic investigation based on rDNA (nSSU, nLSU rDNA), entire mitochondrial genomes, and nuclear protein coding gene sequences (e.g., EF-1alpha, RPB1). Accumulated molecular evidence strongly suggests that the two basal fungal phyla are not monophyletic. For example, the chytridiomycete order Blastocladiales appears to be closely related to the zygomycete order Entomophthorales. Within the Zygomycota, a monophyletic clade, consisting of the Dimargaritales, Harpellales, and Kickxellales, which is characterized by a shared unique septal ultrastructure, was identified. Moreover, evidence for the exclusion of zygomycete orders Amoebidiales and Eccrinales from the Fungi, and their placement at the Animal-Fungi boundary has been clearly documented. Microsporidia, a group of amitochondriate organisms currently under intensive study, is not supported as derived within the Fungi, but a fungal affinity cannot be ruled out. Taking these molecular phylogenetic studies into account, we proposed a hypothetical evolutionary framework of basal fungi.

  6. A new mammal skull from the Lower Cretaceous of China with implications for the evolution of obtuse-angled molars and 'amphilestid' eutriconodonts.

    Science.gov (United States)

    Gao, Chun-Ling; Wilson, Gregory P; Luo, Zhe-Xi; Maga, A Murat; Meng, Qingjin; Wang, Xuri

    2010-01-22

    We report the discovery of Juchilestes liaoningensis, a new genus and species of eutriconodont mammal from the Lujiatun Site of the Lower Cretaceous Yixian Formation (123.2 +/- 1.0 Ma; Lower Aptian). The holotype preserves a partial skull and full dentition. Among eutriconodonts, its lower dentition is similar to taxa formerly assigned to the paraphyletic group of 'amphilestids'. Some have considered 'amphilestid' molars to represent the structural intermediate between the lower molars of the 'triconodont' pattern of cusps in alignment and the fully triangulate and more derived therian molars. However, 'amphilestid' taxa were previously represented only by the lower dentition. Our study reveals, for the first time, the upper dentition and skull structure of an 'amphilestid', and shows that at least some eutriconodonts have an obtuse-angled cusp pattern on molars in middle positions of the long molar series. Its petrosal is similar to those of other eutriconodonts and spalacotheroid 'symmetrodonts'. Our phylogenetic analyses suggest that (i) Juchilestes is most closely related to the Early Cretaceous Hakusanodon from Japan, in the same Eastern Asiatic geographic region; (ii) 'amphilestids' are not monophyletic; and (iii) eutriconodonts might not be a monophyletic group, although this hypothesis must be further tested.

  7. CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy

    Directory of Open Access Journals (Sweden)

    Guanghong Zuo

    2015-10-01

    Full Text Available A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements.

  8. Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): a proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses.

    Science.gov (United States)

    Tao, Wenjing; Mayden, Richard L; He, Shunping

    2013-03-01

    Despite many efforts to resolve evolutionary relationships among major clades of Cyprinidae, some nodes have been especially problematic and remain unresolved. In this study, we employ four nuclear gene fragments (3.3kb) to infer interrelationships of the Cyprinidae. A reconstruction of the phylogenetic relationships within the family using maximum parsimony, maximum likelihood, and Bayesian analyses is presented. Among the taxa within the monophyletic Cyprinidae, Rasborinae is the basal-most lineage; Cyprinine is sister to Leuciscine. The monophyly for the subfamilies Gobioninae, Leuciscinae and Acheilognathinae were resolved with high nodal support. Although our results do not completely resolve relationships within Cyprinidae, this study presents novel and significant findings having major implications for a highly diverse and enigmatic clade of East-Asian cyprinids. Within this monophyletic group five closely-related subgroups are identified. Tinca tinca, one of the most phylogenetically enigmatic genera in the family, is strongly supported as having evolutionary affinities with this East-Asian clade; an established yet remarkable association because of the natural variation in phenotypes and generalized ecological niches occupied by these taxa. Our results clearly argue that the choice of partitioning strategies has significant impacts on the phylogenetic reconstructions, especially when multiple genes are being considered. The most highly partitioned model (partitioned by codon positions within genes) extracts the strongest phylogenetic signals and performs better than any other partitioning schemes supported by the strongest 2Δln Bayes factor. Future studies should include higher levels of taxon sampling and partitioned, model-based analyses.

  9. Multilocus perspectives on the monophyly and phylogeny of the order Charadriiformes (Aves

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    Houde Peter

    2007-03-01

    Full Text Available Abstract Background The phylogeny of shorebirds (Aves: Charadriiformes and their putative sister groups was reconstructed using approximately 5 kilobases of data from three nuclear loci and two mitochondrial genes, and compared to that based on two other nuclear loci. Results Charadriiformes represent a monophyletic group that consists of three monophyletic suborders Lari (i.e., Laridae [including Sternidae and Rynchopidae], Stercorariidae, Alcidae, Glareolidae, Dromadidae, and Turnicidae, Scolopaci (i.e., Scolopacidae [including Phalaropidae], Jacanidae, Rostratulidae, Thinocoridae, Pedionomidae, and Charadrii (i.e., Burhinidae, Chionididae, Charadriidae, Haematopodidae, Recurvirostridae, and presumably Ibidorhynchidae. The position of purported "gruiform" buttonquails within Charadriiformes is confirmed. Skimmers are most likely sister to terns alone, and plovers may be paraphyletic with respect to oystercatchers and stilts. The Egyptian Plover is not a member of the Glareolidae, but is instead relatively basal among Charadrii. None of the putative sisters of Charadriiformes were recovered as such. Conclusion Hypotheses of non-monophyly and sister relationships of shorebirds are tested by multilocus analysis. The monophyly of and interfamilial relationships among shorebirds are confirmed and refined. Lineage-specific differences in evolutionary rates are more consistent across loci in shorebirds than other birds and may contribute to the congruence of locus-specific phylogenetic estimates in shorebirds.

  10. Evolution of the interhaemal barrier in the placenta of rodents

    DEFF Research Database (Denmark)

    Mess, A M; Carter, A M

    2009-01-01

    A recent phylogenetic analysis achieved good resolution between the 5 suborders of rodent. As a novel finding it suggested a basal split that gave rise to a monophyletic group comprising Hystricomorpha and Sciuromorpha. We asked whether the new tree could cast light on the evolution of the interh......A recent phylogenetic analysis achieved good resolution between the 5 suborders of rodent. As a novel finding it suggested a basal split that gave rise to a monophyletic group comprising Hystricomorpha and Sciuromorpha. We asked whether the new tree could cast light on the evolution...... of the interhaemal barrier in rodents where at least seven variants have been described. To supplement existing data we first examined the placenta of the common gundi, Ctenodactylus gundi. It was shown to be haemochorial with a single layer of syncytiotrophoblast in the interhaemal membrane but with nests...... of cytotrophoblast elsewhere. Next we used character mapping on the recent tree to determine the pattern of evolution of the placenta with respect to principal type (e.g. haemochorial) and the trophoblast found within the interhaemal barrier. This indicated that the common ancestor of living rodents had...

  11. Phylogeny and nomenclature of the genus Talaromyces and taxa accommodated in Penicillium subgenus Biverticillium

    DEFF Research Database (Denmark)

    Samson, R.A.; Yilmaz, N.; Houbraken, J.;

    2011-01-01

    The taxonomic history of anamorphic species attributed to Penicillium subgenus Biverticillium is reviewed, along with evidence supporting their relationship with teleomorphic species classified in Talaromyces. To supplement previous conclusions based on ITS, SSU and/or LSU sequencing that Talarom......The taxonomic history of anamorphic species attributed to Penicillium subgenus Biverticillium is reviewed, along with evidence supporting their relationship with teleomorphic species classified in Talaromyces. To supplement previous conclusions based on ITS, SSU and/or LSU sequencing...... that Talaromyces and subgenus Biverticillium comprise a monophyletic group that is distinct from Penicillium at the generic level, the phylogenetic relationships of these two groups with other genera of Trichocomaceae was further studied by sequencing a part of the RPB1 (RNA polymerase II largest subunit) gene....... Talaromyces species and most species of Penicillium subgenus Biverticillium sensu Pitt reside in a monophyletic clade distant from species of other subgenera of Penicillium. For detailed phylogenetic analysis of species relationships, the ITS region (incl. 5.8S nrDNA) was sequenced for the available type...

  12. Higher-level phylogeny of the Hymenoptera inferred from mitochondrial genomes.

    Science.gov (United States)

    Mao, Meng; Gibson, Tracey; Dowton, Mark

    2015-03-01

    Higher-level hymenopteran relationships remain unresolved in both morphological and molecular analyses. In this study, we present the most comprehensive analyses of hymenopteran relationships based on 48 mitochondrial (mt) genomes. One complete and two nearly complete mt genomes representing three hymenopteran superfamilies were newly sequenced. We assessed the influence of inclusion/exclusion of 3rd codon positions, alignment approaches, partition schemes and phylogenetic approaches on topology and nodal support within the Hymenoptera. The results showed that the topologies were sensitive to the variation of dataset and analytical approach. However, some robust and highly supported relationships were recovered: the Ichneumonomorpha was monophyletic; the Trigonalyoidea+Megalyroidea and the Diaprioidea+Chalcidoidea were consistently recovered; the Cynipoidea was generally recovered as the sister group to the Diaprioidea+Chalcidoidea. In addition, the monophyletic Aculeata and Proctotrupomorpha were recovered in some analyses. Several gene rearrangements were detected in each of the three newly sequenced mt genomes. Specifically, the Ibalia leucospoides mt genome harbors a large inversion of a gene block from trnE to trnS2. Inverted, duplicated A+T rich regions were detected in the Ibalia leucospoides mt genome, which probably played an important role during the formation of the large gene block inversion via recombination.

  13. Utility of COI, CAD and morphological data for resolving relationships within the genus Sarcophaga (sensu lato) (Diptera: Sarcophagidae): a preliminary study.

    Science.gov (United States)

    Meiklejohn, Kelly A; Wallman, James F; Pape, Thomas; Cameron, Stephen L; Dowton, Mark

    2013-10-01

    Currently there are ≈ 3000 known species of Sarcophagidae (Diptera), which are classified into 173 genera in three subfamilies. Almost 25% of sarcophagids belong to the genus Sarcophaga (sensu lato) however little is known about the validity of, and relationships between the ≈ 150 (or more) subgenera of Sarcophaga s.l. In this preliminary study, we evaluated the usefulness of three sources of data for resolving relationships between 35 species from 14 Sarcophaga s.l. subgenera: the mitochondrial COI barcode region, ≈ 800 bp of the nuclear gene CAD, and 110 morphological characters. Bayesian, maximum likelihood (ML) and maximum parsimony (MP) analyses were performed on the combined dataset. Much of the tree was only supported by the Bayesian and ML analyses, with the MP tree poorly resolved. The genus Sarcophaga s.l. was resolved as monophyletic in both the Bayesian and ML analyses and strong support was obtained at the species-level. Notably, the only subgenus consistently resolved as monophyletic was Liopygia. The monophyly of and relationships between the remaining Sarcophaga s.l. subgenera sampled remain questionable. We suggest that future phylogenetic studies on the genus Sarcophaga s.l. use combined datasets for analyses. We also advocate the use of additional data and a range of inference strategies to assist with resolving relationships within Sarcophaga s.l.

  14. Molecular phylogeny of the insect order Hymenoptera: apocritan relationships.

    Science.gov (United States)

    Dowton, M; Austin, A D

    1994-10-11

    Phylogenetic relationships among the major groups of hymenopteran insects were investigated by using comparative sequence information from the mitochondrial 16S rRNA gene. The placement of the ectoparasitic Stephanidae as the sister group to the remaining Apocrita confirmed ectoparasitism as the ground plan biology for the Apocrita. Endoparasitism evolved at least eight times within the Apocrita, and the consequent association with polydnaviruses and virus-like particles evolved at least three times. The Evaniomorpha were consistently placed as basal to the remaining Apocrita but were not resolved as monophyletic. The Gasteruptiidae were resolved as the sister group to the Evaniidae, but the relationship between the Trigonalyoidea and the Evanioidea was unclear. The Proctotrupomorpha (sensu Rasnitsyn) was resolved by topology-dependent permutation tail probability (T-PTP) testing as monophyletic, with strong evidence for a sister group relationship between the Platygastroidea and the Chalcidoidea. Strong evidence was found for the monophyly of the Ichneumonomorpha (Ichneumonidae + Braconidae) and the sister-group relationship between the Aculeata (Vespomorpha) and the Ichneumonomorpha.

  15. A Comparison of Three Molecular Markers for the Identification of Populations of Globodera pallida.

    Science.gov (United States)

    Hoolahan, Angelique H; Blok, Vivian C; Gibson, Tracey; Dowton, Mark

    2012-03-01

    Potato cyst nematodes cost the potato industry substantial financial losses annually. Through the use of molecular markers, the distribution and infestation routes of these nematodes can be better elucidated, permitting the development of more effective preventative methods. Here we assess the ability of three molecular markers to resolve multiple representatives of five Globodera pallida populations as monophyletic groups. Molecular markers included a region of the rbp-1 gene (an effector), a non-coding nuclear DNA region (the ITS region), and a novel marker for G. pallida, a ∼3.4 kb non-coding mitochondrial DNA (mtDNA) region. Multiple phylogenetic analysis methods were performed on the three DNA regions separately, and on a data set of these three regions combined. The analyses of the combined data set were similar to that of the sole mtDNA marker; resolving more populations as monophyletic groups, relative to that of the ITS region and rbp-1 gene region. This suggests that individual markers may be inadequate for distinguishing populations of G. pallida. The use of this new non-coding mtDNA marker may provide further insights into the historical distribution of G. pallida, as well as enable the development of more sensitive diagnostic methods.

  16. A comprehensive molecular phylogeny of dalytyphloplanida (platyhelminthes: rhabdocoela reveals multiple escapes from the marine environment and origins of symbiotic relationships.

    Directory of Open Access Journals (Sweden)

    Niels Van Steenkiste

    Full Text Available In this study we elaborate the phylogeny of Dalytyphloplanida based on complete 18S rDNA (156 sequences and partial 28S rDNA (125 sequences, using a Maximum Likelihood and a Bayesian Inference approach, in order to investigate the origin of a limnic or limnoterrestrial and of a symbiotic lifestyle in this large group of rhabditophoran flatworms. The results of our phylogenetic analyses and ancestral state reconstructions indicate that dalytyphloplanids have their origin in the marine environment and that there was one highly successful invasion of the freshwater environment, leading to a large radiation of limnic and limnoterrestrial dalytyphloplanids. This monophyletic freshwater clade, Limnotyphloplanida, comprises the taxa Dalyelliidae, Temnocephalida, and most Typhloplanidae. Temnocephalida can be considered ectosymbiotic Dalyelliidae as they are embedded within this group. Secondary returns to brackish water and marine environments occurred relatively frequently in several dalyeliid and typhloplanid taxa. Our phylogenies also show that, apart from the Limnotyphloplanida, there have been only few independent invasions of the limnic environment, and apparently these were not followed by spectacular speciation events. The distinct phylogenetic positions of the symbiotic taxa also suggest multiple origins of commensal and parasitic life strategies within Dalytyphloplanida. The previously established higher-level dalytyphloplanid clades are confirmed in our topologies, but many of the traditional families are not monophyletic. Alternative hypothesis testing constraining the monophyly of these families in the topologies and using the approximately unbiased test, also statistically rejects their monophyly.

  17. Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.

    Directory of Open Access Journals (Sweden)

    Sven eBreider

    2014-08-01

    Full Text Available Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov. and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.

  18. Complete mitochondrial genomes elucidate phylogenetic relationships of the deep-sea octocoral families Coralliidae and Paragorgiidae

    Science.gov (United States)

    Figueroa, Diego F.; Baco, Amy R.

    2014-01-01

    In the past decade, molecular phylogenetic analyses of octocorals have shown that the current morphological taxonomic classification of these organisms needs to be revised. The latest phylogenetic analyses show that most octocorals can be divided into three main clades. One of these clades contains the families Coralliidae and Paragorgiidae. These families share several taxonomically important characters and it has been suggested that they may not be monophyletic; with the possibility of the Coralliidae being a derived branch of the Paragorgiidae. Uncertainty exists not only in the relationship of these two families, but also in the classification of the two genera that make up the Coralliidae, Corallium and Paracorallium. Molecular analyses suggest that the genus Corallium is paraphyletic, and it can be divided into two main clades, with the Paracorallium as members of one of these clades. In this study we sequenced the whole mitochondrial genome of five species of Paragorgia and of five species of Corallium to use in a phylogenetic analysis to achieve two main objectives; the first to elucidate the phylogenetic relationship between the Paragorgiidae and Coralliidae and the second to determine whether the genera Corallium and Paracorallium are monophyletic. Our results show that other members of the Coralliidae share the two novel mitochondrial gene arrangements found in a previous study in Corallium konojoi and Paracorallium japonicum; and that the Corallium konojoi arrangement is also found in the Paragorgiidae. Our phylogenetic reconstruction based on all the protein coding genes and ribosomal RNAs of the mitochondrial genome suggest that the Coralliidae are not a derived branch of the Paragorgiidae, but rather a monophyletic sister branch to the Paragorgiidae. While our manuscript was in review a study was published using morphological data and several fragments from mitochondrial genes to redefine the taxonomy of the Coralliidae. Paracorallium was subsumed

  19. Hepatitis C virus diversification in Argentina: comparative analysis between the large city of Buenos Aires and the small rural town of O'Brien.

    Directory of Open Access Journals (Sweden)

    Marcelo D Golemba

    Full Text Available BACKGROUND: The estimated prevalence of HCV infection in Argentina is around 2%. However, higher rates of infection have been described in population studies of small urban and rural communities. The aim of this work was to compare the origin and diversification of HCV-1b in samples from two different epidemiological scenarios: Buenos Aires, a large cosmopolitan city, and O'Brien, a small rural town with a high prevalence of HCV infection. PATIENTS AND METHODS: The E1/E2 and NS5B regions of the viral genome from 83 patients infected with HCV-1b were sequenced. Phylogenetic analysis and Bayesian Coalescent methods were used to study the origin and diversification of HCV-1b in both patient populations. RESULTS: Samples from Buenos Aires showed a polyphyletic behavior with a tMRCA around 1887-1900 and a time of spread of infection approximately 60 years ago. In contrast, samples from ÓBrien showed a monophyletic behavior with a tMRCA around 1950-1960 and a time of spread of infection more recent than in Buenos Aires, around 20-30 years ago. CONCLUSION: Phylogenetic and coalescence analysis revealed a different behavior in the epidemiological histories of Buenos Aires and ÓBrien. HCV infection in Buenos Aires shows a polyphyletic behavior and an exponential growth in two phases, whereas that in O'Brien shows a monophyletic cluster and an exponential growth in one single step with a more recent tMRCA. The polyphyletic origin and the probability of encountering susceptible individuals in a large cosmopolitan city like Buenos Aires are in agreement with a longer period of expansion. In contrast, in less populated areas such as O'Brien, the chances of HCV transmission are strongly restricted. Furthermore, the monophyletic character and the most recent time of emergence suggest that different HCV-1b ancestors (variants that were in expansion in Buenos Aires had the opportunity to colonize and expand in O'Brien.

  20. Phylogenetic systematics of the Eucarida (Crustacea malacostraca

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    Martin L. Christoffersen

    1988-01-01

    Full Text Available Ninety-four morphological characters belonging to particular ontogenetic sequences within the Eucarida were used to produce a hierarchy of 128 evolutionary novelties (73 synapomorphies and 55 homoplasies and to delimit 15 monophyletic taxa. The following combined Recent-fossil sequenced phylogenetic classification is proposed: Superorder Eucarida; Order Euphausiacea; Family Bentheuphausiidae; Family Euphausiidae; Order Amphionidacea; Order Decapoda; Suborder Penaeidea; Suborder Pleocyemata; Infraorder Stenopodidea; Infraorder Reptantia; Infraorder Procarididea, Infraorder Caridea. The position of the Amphionidacea as the sister-group of the Decapoda is corroborated, while the Reptantia are proposed to be the sister-group of the Procarididea + Caridea for the first time. The fossil groups Uncina Quenstedt, 1850, and Palaeopalaemon Whitfield, 1880, are included as incertae sedis taxa within the Reptantia, which establishes the minimum ages of all the higher taxa of Eucarida except the Procarididea and Caridea in the Upper Devonian. The fossil group "Pygocephalomorpha" Beurlen, 1930, of uncertain status as a monophyletic taxon, is provisionally considered to belong to the "stem-group" of the Reptantia. Among the more important characters hypothesized to have evolved in the stem-lineage of each eucaridan monophyletic taxon are: (1 in Eucarida, attachement of post-zoeal carapace to all thoracic somites; (2 in Euphausiacea, reduction of endopod of eighth thoracopod; (3 in Bentheuphausiidae, compound eyes vestigial, associated with abyssal life; (4 in Euphausiidae, loss of endopod of eighth thoracopod and development of specialized luminescent organs; (5 in Amphionidacea + Decapoda, ambulatory ability of thoracic exopods reduced, scaphognathite, one pair of maxillipedes, pleurobranch gill series and carapace covering gills, associated with loss of pelagic life; (6 in Amphionidacea, unique thoracic brood pouch in females formed by inflated carapace and

  1. Phylogeny of the higher Libelluloidea (Anisoptera: Odonata): an exploration of the most speciose superfamily of dragonflies.

    Science.gov (United States)

    Ware, Jessica; May, Michael; Kjer, Karl

    2007-10-01

    Although libelluloid dragonflies are diverse, numerous, and commonly observed and studied, their phylogenetic history is uncertain. Over 150 years of taxonomic study of Libelluloidea Rambur, 1842, beginning with Hagen (1840), [Rambur, M.P., 1842. Neuropteres. Histoire naturelle des Insectes, Paris, pp. 534; Hagen, H., 1840. Synonymia Libellularum Europaearum. Dissertation inaugularis quam consensu et auctoritate gratiosi medicorum ordinis in academia albertina ad summos in medicina et chirurgia honores.] and Selys (1850), [de Selys Longchamps, E., 1850. Revue des Odonates ou Libellules d'Europe [avec la collaboration de H.A. Hagen]. Muquardt, Bruxelles; Leipzig, 1-408.], has failed to produce a consensus about family and subfamily relationships. The present study provides a well-substantiated phylogeny of the Libelluloidea generated from gene fragments of two independent genes, the 16S and 28S ribosomal RNA (rRNA), and using models that take into account non-independence of correlated rRNA sites. Ninety-three ingroup taxa and six outgroup taxa were amplified for the 28S fragment; 78 ingroup taxa and five outgroup taxa were amplified for the 16S fragment. Bayesian, likelihood and parsimony analyses of the combined data produce well-resolved phylogenetic hypotheses and several previously suggested monophyletic groups were supported by each analysis. Macromiinae, Corduliidae s. s., and Libellulidae are each monophyletic. The corduliid (s.l.) subfamilies Synthemistinae, Gomphomacromiinae, and Idionychinae form a monophyletic group, separate from the Corduliinae. Libellulidae comprises three previously accepted subfamilies (Urothemistinae, a very restricted Tetrathemistinae, and a modified Libellulinae) and five additional consistently recovered groups. None of the other previously proposed subfamilies are supported. Bayesian analyses run with an additional 71 sequences obtained from GenBank did not alter our conclusions. The evolution of adult and larval morphological

  2. Two new species of Romulea (Iridaceae: Crocoideae from the west­ ern Karoo, Northern Cape and notes on infrageneric classification and range extensions

    Directory of Open Access Journals (Sweden)

    J. C. Manning

    2004-12-01

    Full Text Available Two new species of Romulea are described from Northern Cape, raising the number of species in southern Africa to 76. R. collina J.C.Manning & Goldblatl is endemic to the Hantamsberg near Calvinia. It is distinguished in subgenus Spatalanthus by its clumped habit, yellow flowers with dark markings in the throat, and short papery bracts. A re-examination of rela­tionships within the subgenus suggests that section Cruciatae is not monophyletic and it is accordingly no longer recog­nized as separate from section  Spatalanthus. R. eburnea J.C.Manning & Goldblatt is a distinctive species of subgenus Spatalanthus from the Komsberg near Sutherland. It is distinguished by its golden yellow flowers with the apical third of the tepals coloured pale creamy apricot, bracts with broad, translucent margins and tips, and an unusually long perianth tube, 10-13 mm long.

  3. Complete mitochondrial genome of Ptychobarbus kaznakovi (Teleostei: Cypriniformes: Cyprinidae), and repetitive sequences in the D-loop.

    Science.gov (United States)

    Ma, Qingzhan; Wu, Bo; Li, Jiuxuan; Song, Zhaobin

    2016-05-01

    The complete mitochondrial DNA genome of Ptychobarbus kaznakovi was sequenced and characterized. The genome is 16,842 bp in length. Similar with most teleosts, it has two ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and one displacement loop (D-loop) region. Conserved sequence blocks, including ETAS, CSB-B, D, E, F, and CSB1-3, were identified in the D-loop, which is similar to other species in Cypriniformes. Nevertheless, a 55 bp tandem repeat array was also identified at 3' end of the D-loop, which is the first finding in Schizothoracinae. Phylogenetic analysis showed that the species of Ptychobarbus (P. dipogon and P. kaznakovi) formed a monophyletic group and represented close relationship to the species without scales in Schizothoracinae.

  4. Sorodiplophrys stercorea: Another Novel Lineage of Sorocarpic Multicellularity.

    Science.gov (United States)

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

    2016-09-01

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

  5. The evolution of the Ecdysozoa.

    Science.gov (United States)

    Telford, Maximilian J; Bourlat, Sarah J; Economou, Andrew; Papillon, Daniel; Rota-Stabelli, Omar

    2008-04-27

    Ecdysozoa is a clade composed of eight phyla: the arthropods, tardigrades and onychophorans that share segmentation and appendages and the nematodes, nematomorphs, priapulids, kinorhynchs and loriciferans, which are worms with an anterior proboscis or introvert. Ecdysozoa contains the vast majority of animal species and there is a great diversity of body plans among both living and fossil members. The monophyly of the clade has been called into question by some workers based on analyses of whole genome datasets. We review the evidence that now conclusively supports the unique origin of these phyla. Relationships within Ecdysozoa are also controversial and we discuss the molecular and morphological evidence for a number of monophyletic groups within this superphylum.

  6. Salmonella enterica serovar Typhi and the pathogenesis of typhoid fever.

    Science.gov (United States)

    Dougan, Gordon; Baker, Stephen

    2014-01-01

    Salmonella enterica serovar Typhi, the cause of typhoid, is host restricted to humans. S. Typhi has a monophyletic population structure, indicating that typhoid in humans is a relatively new disease. Antimicrobial usage is reshaping the current S. Typhi global population and may be driving the emergence of a specific haplotype, H58, that is well adapted to transmission in modern settings and is able to resist antimicrobial killing more efficiently than other S. Typhi. Evidence gathered through genomics and functional studies using the mouse and in vitro cell systems, together with clinical investigations, has provided insight into the mechanisms that underpin the pathogenesis of human typhoid and host restriction. Here we review the latest scientific advances in typhoid research and discuss how these novel approaches are changing our understanding of the disease.

  7. Coding-complete sequencing classifies parrot bornavirus 5 into a novel virus species.

    Science.gov (United States)

    Marton, Szilvia; Bányai, Krisztián; Gál, János; Ihász, Katalin; Kugler, Renáta; Lengyel, György; Jakab, Ferenc; Bakonyi, Tamás; Farkas, Szilvia L

    2015-11-01

    In this study, we determined the sequence of the coding region of an avian bornavirus detected in a blue-and-yellow macaw (Ara ararauna) with pathological/histopathological changes characteristic of proventricular dilatation disease. The genomic organization of the macaw bornavirus is similar to that of other bornaviruses, and its nucleotide sequence is nearly identical to the available partial parrot bornavirus 5 (PaBV-5) sequences. Phylogenetic analysis showed that these strains formed a monophyletic group distinct from other mammalian and avian bornaviruses and in calculations performed with matrix protein coding sequences, the PaBV-5 and PaBV-6 genotypes formed a common cluster, suggesting that according to the recently accepted classification system for bornaviruses, these two genotypes may belong to a new species, provisionally named Psittaciform 2 bornavirus.

  8. Molecular epidemiology of Fonsecaea species.

    Science.gov (United States)

    Najafzadeh, Mohammad Javad; Sun, Jiufeng; Vicente, Vania A; Klaassen, Corne H W; Bonifaz, Alexandro; Gerrits van den Ende, A H G; Menken, Steph B J; de Hoog, G Sybren

    2011-03-01

    To assess population diversities among 81 strains of fungi in the genus Fonsecaea that had been identified down to species level, we applied amplified fragment-length polymorphism (AFLP) technology and sequenced the internal transcribed spacer regions and the partial cell division cycle, beta-tubulin, and actin genes. Many species of the genus Fonsecaea cause human chromoblastomycosis. Strains originated from a global sampling of clinical and environmental sources in the Western Hemisphere, Asia, Africa, and Europe. According to AFLP fingerprinting, Fonsecaea isolates clustered in 5 groups corresponding with F. pedrosoi, F. monophora, and F. nubica: the latter 2 species each comprised 2 groups, and F. pedrosoi appeared to be of monophyletic origin. F. pedrosoi was found nearly exclusively in Central and South America. F. monophora and F. nubica were distributed worldwide, but both showed substantial geographic structuring. Clinical cases outside areas where Fonsecaea is endemic were probably distributed by human migration.

  9. Histological observation of some primitive euconodonts of Late Cambrian from Liaoning

    Institute of Scientific and Technical Information of China (English)

    GUO Wei; DONG Xiping; ZENG Xiaochun; ZHAO Le

    2005-01-01

    The histology of some euconodonts of Late Cambrian from Benxi and Fuxian County, Liaoning Province is studied by the oil-immersion technique. The histological characteristics of six primitive species of euconodonts - Proconodontus muelleri, Proconodontus tenuiserratus, Granatodontus ani, Rotundoconus tricarinatus, Teridontus nakamurai and Cordylodus proavus are describedin detail. Tubular dentine and atubular (parallel- and wavy-lamellar) dentine are found in the basal bodies of the primitive euconodonts Proconodontus tenuiserratus and Proconodontus muelleri, respectively. The tubular dentine and spherulitic dentine are also recognized from the basal bodies of Granatodontus ani and Rotundoconus tricarinatus. Since the histological characteristics of the studied six species of euconodonts belonging to Proconodontus lineage and Teridontus lineage Sensu Miller (Univ Kansas Paleontol Contr, 1980, 99: 1-39)seems to be almost the same, euconodonts are proposed as possibly monophyletic herein.

  10. Crinoids from Svalbard in the aftermath of the end−Permian mass extinction

    Directory of Open Access Journals (Sweden)

    Salamon Mariusz A.

    2015-09-01

    Full Text Available The end-Permian mass extinction constituted a major event in the history of crinoids. It led to the demise of the major Paleozoic crinoid groups including cladids, disparids, flexibles and camerates. It is widely accepted that a single lineage, derived from a late Paleozoic cladid ancestor (Ampelocrinidae, survived this mass extinction. Holocrinid crinoids (Holocrinus, Holocrinida along with recently described genus Baudicrinus (Encrinida, the only crinoid groups known from the Early Triassic, are considered the stem groups for the post-Paleozoic monophyletic subclass Articulata. Here, we report preliminary data on unexpectedly diverse crinoid faunas comprising at least four orders from the Lower Triassic (Induan and Olenekian of Svalbard, extending their stratigraphic ranges deeper into the early Mesozoic. These findings strongly imply that the recovery of crinoids in the aftermath of the end-Permian extinction began much earlier at higher palaeolatitudes than in the central Tethys.

  11. Revision of the fossil batomorphs from the Cretaceous of Lebanon, and their impact on our understanding of the early step of the evolution of the clade

    DEFF Research Database (Denmark)

    Kachacha, Georges

    group to the remaining batomorphs. The remaining guitarfish from Lebanon present a crown paraphyletic assemblage sister to Rajidae, which, together, are included in the order Rajiformes. Eight Lebanese guitarfishes are distributed into four different clades which allowed me to reconsider the generic......'s detailed studies were performed enabling to give new insights on the complexity and diversity of their enameloid microstructure. A bundled crystallite enameloid is widespread among Rhinobatoidei teeth tested so far, whereas, the parallel bundled enameloid component is considered an apomorphy for this group...... Raja. Finally, Platyrhinidae is recognized as a monophyletic group of true guitarfish, successively rooted by Britobatos primarmatus and Rhombopterygia rajoides. Keywords: batomorphs; Upper Cretaceous; enameloid microstructure; cladistics...

  12. Sharp Phylogeographic Breaks and Patterns of Genealogical Concordance in the Brine Shrimp Artemia franciscana

    Directory of Open Access Journals (Sweden)

    Theodora Farmaki

    2009-12-01

    Full Text Available Genealogical concordance is a critical overlay of all phylogenetic analyses, irrespective of taxonomic level. To assess such patterns of congruence we have compiled and derived sequence data for two mitochondrial (16S rRNA, COI and two nuclear (ITS1, p26 markers in 14 American populations of the hypersaline branchiopod Artemia franciscana. Cladistic analysis revealed three reciprocally monophyletic mitochondrial clades. For nuclear DNA, incomplete lineage sorting was evident presumably as a result of slower coalescence or male-mediated dispersal. Our findings capture the genealogical interval between gene splitting and population divergence. In this sense, strong indications are provided in favour of a superspecies status and ongoing speciation in A. franciscana.

  13. Genetic identification of cryptic genospecies of Haemophilus causing urogenital and neonatal infections by PCR using specific primers targeting genes coding for 16S rRNA.

    Science.gov (United States)

    Quentin, R; Ruimy, R; Rosenau, A; Musser, J M; Christen, R

    1996-06-01

    Previous genetic analysis of Haemophilus influenzae strains isolated from genital and neonatal infections identified a group of biotype IV that constitutes a cryptic genospecies only distantly related to H. influenzae and H. Haemolyticus. Small-subunit rRNA genes of two representative strains of this genital Haemophilus genospecies (strains 16N and 2406) were sequenced. The analysis indicated that these strains form a monophyletic unit with H. haemolyticus and H. influenzae biogroups Influenzae and Aegyptius and are more closely related to H. haemolyticus than to H. influenzae biogroups Influenzae and Aegyptius. 16S rRNA gene sequences were used to formulate primers for PCR-based identification of cryptic genital Haemophilus organisms. A 242-bp fragment was amplified from strains belonging to the genital Haemophilus genospecies but not from strains of 12 other Haemophilus species, including strains of H. influenzae biotype IV sensu stricto.

  14. Comparative sequence analysis of 16S rRNA gene of Pasteurella multocida serogroup B isolates from different animal species.

    Science.gov (United States)

    Dey, S; Singh, V P; Kumar, A A; Sharma, B; Srivastava, S K; Singh, Nem

    2007-08-01

    The phylogenetic relationships of five isolates of Pasteurella multocida serotype B:2 belonging to buffalo, cattle, pig, sheep and goat were investigated by comparative sequence analysis of 16S rRNA gene. The 1468bp fragment of 16S rRNA gene sequence comparison showed that the isolates of cattle (PM75), pig (PM49) and sheep (PM82) shared 99.9% homology with the buffalo isolate (vaccine strain P52) whereas, the goat isolate (PM86) shared 99.8% homology with the vaccine strain. The 16S rRNA gene sequences of these isolates were also found monophyletic with type B reference strain NCTC 10323 of P. multocida subsp. multocida. The present study indicated the close relationships of haemorrhagic septicaemia causing P. multocida serotype B:2 isolates of buffalo and cattle with other uncommon hosts (pig, sheep and goat).

  15. Diversity of microorganisms isolated from the soil sample surround Chroogomphus rutilus in the Beijing region

    DEFF Research Database (Denmark)

    Wang, P; Liu, Y; Yin, Y;

    2011-01-01

    to isolate and classify beneficial microorganisms that could affect its growth, which could be used in future research on artificial cultivation. In total, 342 isolates were isolated from soil samples collected around a C. rutilus colony in the Beijing region. Of these, 22 bacterial and 14 fungal isolates....... Using internal transcribed spacer (ITS) sequence analysis, fungal isolates were divided into four monophyletic clusters: Penicillium, Trichoderma, Mortierella, and Bionectria. Moreover, the phylogenetic diversity of these isolates was analysed. The results indicated that numerous microorganisms were......Artificially cultivating Chroogomphus rutilus is too inefficient to be commercially feasible. Furthermore, isolating C. rutilus mycelia in the wild is difficult. Thus, it is important to de-termine the natural habitat of its fruiting body. This study focused on the ecology of the C. rutilus habitat...

  16. A Comprehensive Bioinformatics Analysis of the Nudix Superfamily in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    D. Gunawardana

    2009-01-01

    Full Text Available Nudix enzymes are a superfamily with a conserved common reaction mechanism that provides the capacity for the hydrolysis of a broad spectrum of metabolites. We used hidden Markov models based on Nudix sequences from the PFAM and PROSITE databases to identify Nudix hydrolases encoded by the Arabidopsis genome. 25 Nudix hydrolases were identified and classified into 11 individual families by pairwise sequence alignments. Intron phases were strikingly conserved in each family. Phylogenetic analysis showed that all multimember families formed monophyletic clusters. Conserved familial sequence motifs were identified with the MEME motif analysis algorithm. One motif (motif 4 was found in three diverse families. All proteins containing motif 4 demonstrated a degree of preference for substrates containing an ADP moiety. We conclude that HMM model-based genome scanning and MEME motif analysis, respectively, can significantly improve the identification and assignment of function of new members of this mechanistically-diverse protein superfamily.

  17. Elucidating the origin of the ExbBD components of the TonB system through Bayesian inference and maximum-likelihood phylogenies.

    Science.gov (United States)

    Marmon, Livingstone

    2013-12-01

    Uptake of ferric siderophores, vitamin B12, and other molecules in gram-negative bacteria is mediated by a multi-protein complex known as the TonB system. The ExbB and ExbD protein components of the TonB system play key energizing roles and are homologous with the flagellar motor proteins MotA and MotB. Here, the phylogenetic relationships of ExbBD and MotAB were investigated using Bayesian inference and the maximum-likelihood method. Phylogenetic trees of these proteins suggest that they are separated into distinct monophyletic groups and have originated from a common ancestral system. Several horizontal gene transfer events for ExbB-ExbD are also inferred, and a model for the evolution of the TonB system is proposed. Copyright © 2013 Elsevier Inc. All rights reserved.

  18. Taxonomy of the genus Passerina (Thymelaeaceae

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    C. L. Bredenkamp

    2003-12-01

    Full Text Available Passerina L. is mainly a southern African genus, comprising 20 species and four subspecies. A few species occur along the Great Escarpment, two extend into Zimbabwe and Mozambique, but most are concentrated in the Cape Floristic Region. Palynological. macromorphological and anatomical evidence was used in the delimitation of the genus and its infrageneric taxa. A cladistic study supports Passerina as a monophyletic genus. A genus treatment, key to species and a full species treatment are given. Each species treatment includes a taxonomic diagnosis, description and notes on taxonomy, etymology, economic value and distribution. Illustrations of representative species are provided and distribution maps are included for each species.  P. esterhuyseniae Bredenk. & A.E.van Wyk is newly described. A list of excluded species names highlights the previous cosmopolitan taxonomic interpretation of Passerina. as many names are now in synony my under other genera of the Thymelaeaceae.

  19. Phylogenetic analysis of the gut bacterial microflora of the fungus-growing termite Odontotermes formosanus.

    Science.gov (United States)

    Shinzato, Naoya; Muramatsu, Mizuho; Matsui, Toru; Watanabe, Yoshio

    2007-04-01

    We constructed a bacterial 16S rRNA gene clone library from the gut microbial community of O. formosanus and phylogenetically analyzed it in order to contribute to the evolutional study of digestive symbiosis and method development for termite control. After screening by restriction fragment length polymorphism (RFLP) analysis, 56 out of 280 clones with unique RFLP patterns were sequenced and phylogenetically analyzed. The representative phylotypes were affiliated to four phylogenetic groups, Firmicutes, the Bacteroidetes/Chlorobi group, Proteobacteria, and Actinobacteria of the domain Bacteira. No one clone affiliated with the phylum Spirochaetes was identified, in contrast to the case of wood-feeding termites. The phylogenetic analysis revealed that nearly half of the representative clones (25 phylotypes) formed monophyletic clusters with clones obtained from other termite species, especially with the sequences retrieved from fungus-growing termites. These results indicate that the presence of termite-specific bacterial lineages implies a coevolutional relationship of gut microbes and host termites.

  20. Cladistic analysis and revised classification of fossil and recent mysticetes

    DEFF Research Database (Denmark)

    Steeman, Mette Elstrup

    2007-01-01

    A cladistic analysis that includes representatives of all recent genera of mysticetes and several fossil species that were previously referred to the family Cetotheriidae, with tooth-bearing mysticetes and an archaeocete as an outgroup, is presented here. The result of this analysis forms the base...... of a revised classification of Mysticeti. Cetotheriidae is redefined as a monophyletic family, which includes the genera Cetotherium, Piscobalaena, and a new subfamily Herpetocetinae, including Herpetocetus, Nannocetus, Metopocetus, and Cephalotropis. Eschrichtiidae is the closest sister taxon to Cetotheriidae....... A few species are referred to Eomysticetoidea, whereas the remaining species that were previously referred to Cetotheriidae appear in four clades that branch off from the lineage leading to Balaenopteridae. These are a Mauicetus clade and three clades that are named as new families Aglaocetidae...

  1. Analysis of the variable sites and phylogenetic studies of complete mitochondrial DNA based on the Siniperca scherzeri (Perciformes: Sinipercidae) from four different areas.

    Science.gov (United States)

    Chu, Wuying; Chen, Dunxue; Wang, Kaizhuo; Li, Yulong; Du, Shaojun; Zhang, Jianshe

    2013-06-01

    In this study, we cloned and sequenced the complete mitochondrial DNAs of Chinese mandarin fish, Siniperca scherzeri populations from four different areas of the Yangtze River and the Pearl River systems in China. In the Yangtze River system, fish samples were taken from three regions, Dongting Lake (DT), Poyang Lake (PL) and Xiangjiang River (XR). In the Pearl River system, fish samples were collected from the Lijiang River (LR). The sizes of their complete mitochondrial genome were 16,502 bp (LR), 16,508 bp (PL), 16,502 bp (XR) and 16,508 bp (DT), respectively. The organization of the S. scherzeri mitochondrial genomes was similar to those reported from other fish mitochondrial genomes. Phylogenetic analyses using N-J computational algorithms showed that the Sinipercidaes are monophyletic and can be divided into two genera, Siniperca and Coreoperca. The S. scherzeri could be divided into two groups along the Yangtze River system and the Pearl River.

  2. Molecular phylogeny of Acer monspessulanum L. subspecies from Iran inferred using the ITS region of nuclear ribosomal DNA

    Directory of Open Access Journals (Sweden)

    HANIF KHADEMI

    2016-04-01

    Full Text Available Abstract. Khademi H, Mehregan I, Assadi M, Nejadsatari T, Zarre S. 2015. Molecular phylogeny of Acer monspessulanum L. subspecies from Iran inferred using the ITS region of nuclear ribosomal DNA. Biodiversitas 17: 16-23. This study was carried out on the Acer monspessulanum complex growing wild in Iran. Internal transcribed spacer (ITS sequences for 75 samples representing five different subspecies of Acer monspessulanum were analyzed. Beside this, 86 previously published ITS sequences from GenBank were used to test the monophyly of the complex worldwide. Phylogenetic analyses were conducted using Bayesian inference and maximum parsimony. The results indicate that most samples of A. monspessulanum species from Iran were part of a monophyletic clade with 8 samples of A. ibericum from Georgia, A. hyrcanum from Iran and one of A. sempervirens from Greece (PP= 1; BS= 79%. Our results indicate that use of morphological characteristics coupled with molecular data will be most effective.

  3. Molecular phylogeny of Ascotricha, including two new marine algae-associated species.

    Science.gov (United States)

    Cheng, Xiaoli; Li, Wei; Cai, Lei

    2015-01-01

    Phylogenetic analyses based on a broad taxonomic sampling of Ascotricha were conducted using the sequences of nuc rDNA region encompassing the internal transcribed spacers 1 and 2, along with the 5.8S rDNA (ITS), partial nuc 18S rDNA (18S) and partial β-tubulin gene (TUB2). Hypoxyloid Xylariaceae and xylarioid Xylariaceae were inferred as two distinct lineages in the Xylariaceae in the combined ITS-TUB2 phylogeny. Within xylarioid Xylariaceae species of Ascotricha form a monophyletic group. Two new marine algae-associated fungi, Ascotricha longipila and A. parvispora, are described on the basis of morphological and molecular characters and the combination, A. sinuosa, is proposed. A synopsis of the morphological characters and a dichotomous key to Ascotricha species are provided. © 2015 by The Mycological Society of America.

  4. A new species of Chaetostoma Tschudi (Siluriformes: Loricariidae from Colombia with a definition of the C. anale species group

    Directory of Open Access Journals (Sweden)

    Gustavo A. Ballen

    2011-01-01

    Full Text Available Chaetostoma formosae sp. nov. is described from piedmont tributaries of the upper río Meta on the Cordillera Oriental in Colombia. The new species is distinguished from its congeners by the presence of an elongate unbranched anal-fin ray with two posterior dermal ridges in mature males, the presence of strongly recurved cheek odontodes, the presence of a parieto-supraoccipital dermal keel, the posterior margin of the pelvic-fin strongly projected and angulate in shape in mature males, and by details of coloration. The new species belongs to an informal monophyletic group herein called the Chaetostoma anale species group, along with two additional species, C. anale and C. jegui, from Colombia and Brazil respectively, based on an apomorphic modification of the anal fin in mature males.

  5. Evolution of the placenta and associated reproductive characters in bats

    DEFF Research Database (Denmark)

    Carter, Anthony M; Mess, Andrea

    2008-01-01

    Recent advances in molecular phylogenetics indicate that the order Chiroptera is monophyletic and that one of four lineages of microbats (Rhinolophoidea) shares a common origin with megabats. Against this background we undertook a comprehensive analysis of placental evolution in bats. We defined...... a range of characters and character states associated with female reproduction, early development, placentation and the neonate. These were then mapped on a pre-existing hypothesis of bat relationships that represents the current view from molecular studies. Our purpose was threefold. First......, on the assumption of bat monophyly, we wished to establish the stem species pattern of extant chiropterans. Secondly, we asked whether there are derived character conditions in support of a common origin for Rhinolophoidea and the megabats. Thirdly, we looked for evolutionary character transformations...

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

    Science.gov (United States)

    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.

  7. Molecular and morphological evidence supports the species status of the Mahachai fighter Betta sp. Mahachai and reveals new species of Betta from Thailand.

    Science.gov (United States)

    Sriwattanarothai, N; Steinke, D; Ruenwongsa, P; Hanner, R; Panijpan, B

    2010-08-01

    Two regions of mitochondrial (mt) DNA, cytochrome c oxidase subunit 1 (COI) and 16S rRNA, were sequenced in nine species of Betta from Thailand and Indonesia. Most species showed little intraspecific COI variation (adjusted mean = 0.48%) including the putative species Betta sp. Mahachai, but one species (Betta smaragdina) included three lineages showing much greater divergence (7.03-13.48%) that probably represent overlooked species. These findings were confirmed by maximum likelihood analysis and Bayesian inference, which revealed well-supported corresponding monophyletic clades. Based on these results and morphological differences, the putative species Betta sp. Mahachai from central Thailand is a species distinct from other members of the B. splendens group and represents a new and hitherto undescribed species. Furthermore, this study also demonstrated the probable existence of two overlooked Betta species found in the Khorat plateau basin, illustrating the utility of mitochondrial genetic markers in the revelation of overlooked diversity.

  8. A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade

    DEFF Research Database (Denmark)

    Ugelvig, L. V.; Vila, R.; Pierce, N. E.

    2011-01-01

    . The evolutionary history of this butterfly section is particularly important to understand the evolution of life history diversity connected to food-plant and host-ant associations in the larval stage. In the present study, we use a combination of four nuclear and two mitochondrial genes to reconstruct...... the phylogeny of the Glaucopsyche section, and in particular, to study the relationships among and within the Phengaris-Maculinea species. We find a clear pattern between the clades recovered in the Glaucopsyche section phylogeny and their food-plant associations, with only the Phengaris-Maculinea clade...... utilising more than one plant family. Maculinea is, for the first time, recovered with strong support as a monophyletic group nested within Phengaris, with the closest relative being the rare genus Caerulea. The genus Glaucopsyche is polyphyletic, including the genera Sinia and Iolana. Interestingly, we...

  9. srRNA evolution and phylogenetic relationships of the genus Naegleria (Protista: Rhizopoda).

    Science.gov (United States)

    Baverstock, P R; Illana, S; Christy, P E; Robinson, B S; Johnson, A M

    1989-05-01

    A rapid RNA sequencing technique was used to partially sequence the small-subunit ribosomal RNA (srRNA) of four species of the amoeboid genus Naegleria. The extent of nucleotide sequence divergence between the two most divergent species was roughly similar to that found between mammals and frogs. However, the pattern of variation among the Naegleria species was quite different from that found for those species of tetrapods characterized to date. A phylogenetic analysis of the consensus Naegleria sequence showed that Naegleria was not monophyletic with either Acanthamoeba castellanii or Dictyostelium discoideum, two other amoebas for which sequences were available. It was shown that the semiconserved regions of the srRNA molecule evolve in a clocklike fashion and that the clock is time dependent rather than generation dependent.

  10. Phylogenetic relationships of five species of Dorippinae (Crustacea, Decapoda) revealed by 16S rDNA sequence analysis

    Institute of Scientific and Technical Information of China (English)

    FANYu; LIXinzheng; SONGLinsheng; CAIZhonghua

    2004-01-01

    A molecular phylogeny is presented for the subfamily Dorippinae (including 9 individuals, representing 5 species and 4 genera), based on the sequence data from 16S rRNA gene. Two-cluster test between lineages in these phylogenetic trees has been performed. On the basis of rate constancy, the rate of nucleotide substitutions of 16S rDNA sequence data is estimated as 0.27% per million years. The analysis strongly supports the recognition of the Dorippinae as a monophyletic subfamily. Phylogenetic tree indicates that the subfamily Dorippinae is divided into two main clades, and genus Dorippe appears basal in the subfamily, diverging from other species 36.6 Ma ago. It is also clear that the Heikea is closely related to the genus Neodorippe. The divergence time between them is 15.8 Ma.

  11. The phylogenetic relationships of introduced Aphelinus (Hymenoptera: Aphelinidae), biological control agents of the Russian wheat aphid (Homoptera: Aphididae)

    Institute of Scientific and Technical Information of China (English)

    Yu Cheng Zhu; Quentin Q.Fang

    2009-01-01

    Several species of Aphelinus have been introduced to the US from the Old World for biological control of the Russian wheat aphid, Diuraphis noxia (Modvilko). Reproductive incompatibility has been observed among populations collected from different geographic areas. We examined whether or not the reproductive incompatibility between strains of A. asychis was caused by distant phylogenetic relationships. Ribosomal DNA sequences of internal transcribed spacers 2 (ITS2) were analyzed in several species of Aphelinus collected from multiple sites of Europe and Asia. The phylogenetic analysis showed that strains within the species A. albipodus and A. asychis are not monophyletic, and two clearly divergent clades were revealed among sequenced samples. Our results suggest that the reproductive incompatibility between three exotic strains ofA. asychis was more likely caused by divergence of phylogeny than by symbiotic bacteria.

  12. Phylogenetic studies of Chinese labeonine fishes (Teleostei:Cyprinidae) based on the mitochondrial 16S rRNA gene

    Institute of Scientific and Technical Information of China (English)

    LI Junbing; WANG Xuzhen; HE Shunping; CHEN Yiyu

    2005-01-01

    The mitochondrial 16S ribosomal RNA gene is sequenced from 24 ingroups taxa, including 18 species from Labeoninae grouped in 13 genera. Phylogenetic analyses are subjected to neighbor joining, maximum parsimony, maximum likelihood and Bayesian analyses. Phylogenetic analysis indicates that Labeoninae is basically a monophyletic assemblage and can be divided into 2 major clades: one comprising the genera Cirrhinus, Crossocheilus and Garra; and the other consisting of the genera Labeo, Sinilabeo, Osteochilus, Pseudoorossocheilus, Parasinilabeo, Ptychidio, Semilabeo, Pseudogyricheilus, Rectori and Discogobio. According to our present analysis,the features such as the presence of the adhesive disc on the chin and the pharyngeal teeth in 2 rows used in the traditional taxonomy of Labeoninae provide scarce information for phylogeny of labeonine fishes.

  13. Two new species of Romulea (Iridaceae: Crocoideae from the west­ ern Karoo, Northern Cape and notes on infrageneric classification and range extensions

    Directory of Open Access Journals (Sweden)

    J. C. Manning

    2004-12-01

    Full Text Available Two new species of Romulea are described from Northern Cape, raising the number of species in southern Africa to 76. R. collina J.C.Manning & Goldblatl is endemic to the Hantamsberg near Calvinia. It is distinguished in subgenus Spatalanthus by its clumped habit, yellow flowers with dark markings in the throat, and short papery bracts. A re-examination of rela­tionships within the subgenus suggests that section Cruciatae is not monophyletic and it is accordingly no longer recog­nized as separate from section  Spatalanthus. R. eburnea J.C.Manning & Goldblatt is a distinctive species of subgenus Spatalanthus from the Komsberg near Sutherland. It is distinguished by its golden yellow flowers with the apical third of the tepals coloured pale creamy apricot, bracts with broad, translucent margins and tips, and an unusually long perianth tube, 10-13 mm long.

  14. A potentially novel overlapping gene in the genomes of Israeli acute paralysis virus and its relatives

    Directory of Open Access Journals (Sweden)

    Price Nicholas

    2009-09-01

    Full Text Available Abstract The Israeli acute paralysis virus (IAPV is a honeybee-infecting virus that was found to be associated with colony collapse disorder. The IAPV genome contains two genes encoding a structural and a nonstructural polyprotein. We applied a recently developed method for the estimation of selection in overlapping genes to detect purifying selection and, hence, functionality. We provide evolutionary evidence for the existence of a functional overlapping gene, which is translated in the +1 reading frame of the structural polyprotein gene. Conserved orthologs of this putative gene, which we provisionally call pog (predicted overlapping gene, were also found in the genomes of a monophyletic clade of dicistroviruses that includes IAPV, acute bee paralysis virus, Kashmir bee virus, and Solenopsis invicta (red imported fire ant virus 1.

  15. Taxonomy and phylogeny of a new Central American beetle genus: (Coleoptera: Scarabaeidae

    Directory of Open Access Journals (Sweden)

    María Milagro Coca-Abia

    2006-06-01

    Full Text Available A new genus and two species of Melolonthinae from Honduras and Nicaragua are described. A phylogenetic analysis, carried out using morphological characters, suggests that Catrachia is a strongly supported monophyletic group. Catrachia is therefore established as a new genus, constituted by two new species, Catrachia mariana and Catrachia nica. Rev. Biol. Trop. 54(1: 000-000. Epub 2006 Mar 31.En este trabajo se describe el género Catrachia y dos especies nuevas, Catrachia mariana y Catrachia nica de Honduras y Nicaragua respectivamente. En análisis filogenético basado en caracteres morfológicos demostró que Catrachia es un grupo monofilético fuertemente soportado lo cual permite su consideración como género nuevo.

  16. Calcareous tubeworms of the Phanerozoic

    Directory of Open Access Journals (Sweden)

    Vinn, Olev

    2009-12-01

    Full Text Available Morphological similarities indicate that Palaeozoic problematic tubeworms, e.g. tentaculitids, cornulitids, microconchids, trypanoporids, Anticalyptraea, and Tymbochoos, form a monophyletic group. This group may also include hederelloids. Members of this group share affinities with lophophorates and their evolution could have partly been driven by predation. The extinction of Palaeozoic tubeworms in the Middle Jurassic was possibly at least partly caused by the ecological pressure by serpulid and sabellid polychaetes. The input of Palaeozoic tubeworms to the general ocean biocalcification system may have been smaller in the Ordovician to Jurassic than that of calcareous polychaetes in the Late Triassic to Recent. There seems to have been some correlation between the aragonite–calcite seas and the skeletal mineralogy of Triassic–Recent polychaete tubeworms.

  17. Psychrophilic yeasts from Antarctica and European glaciers: description of Glaciozyma gen. nov., Glaciozyma martinii sp. nov. and Glaciozyma watsonii sp. nov.

    Science.gov (United States)

    Turchetti, Benedetta; Thomas Hall, Skye R; Connell, Laurie B; Branda, Eva; Buzzini, Pietro; Theelen, Bart; Müller, Wally H; Boekhout, Teun

    2011-09-01

    Field campaigns in Antarctica, Greenland and the Italian glaciers aiming to explore the biodiversity of these disappearing environments identified several undescribed yeast strains unable to grow at temperature above 20°C and belonging to unknown species. Fourteen of these strains were selected and grouped based on their morphological and physiological characteristics. Sequences of the D1/D2 and ITS regions of the ribosomal RNA demonstrated that the strains belong to unknown species related to Leucosporidium antarcticum. The new genus Glaciozyma is proposed and two new species are described, namely Glaciozyma martinii sp. nov. and Glaciozyma watsonii sp. nov. Additionally, re-classification of Leucosporidium antarcticum as Glaciozyma antarctica is proposed. Strains of Glaciozyma form a monophyletic clade and a well separated lineage within class Microbotryomycetes (Pucciniomycotina, Basidiomycota). The description of Glaciozyma genus and the re-classification of L. antarcticum reduce the polyphyletic nature of the genus Leucosporidium.

  18. Molecular evidence of two cryptic species of Stramonita (Mollusca, Muricidae in the southeastern Atlantic coast of Brazil

    Directory of Open Access Journals (Sweden)

    Juliana Beltramin De Biasi

    Full Text Available Abstract Snails of the genus Stramonita are commonly found in the rocky intertidal habitat of the western Atlantic Ocean coast. They belong to a monophyletic taxon that occurs along the tropical and warm-temperate Atlantic and eastern Pacific rocky shores. This genus comprises different valid species and members of the S. haemastoma complex. In the present study, samples of Stramonita were collected from three different regions of southeastern Brazil. Partial sequences of two mitochondrial genes, COI and 16S rRNA, were used to compare nucleotides sequences between Stramonita specimens. Levels of nucleotide divergence greater than 2% across the three sampled regions were used for differentiation at the species level. One of the identified species was S. brasiliensis, which has recently been described by molecular analysis; the other species may represent S. haemastoma, not yet described in the southeastern Brazilian coast.

  19. Pachyseris inattesa sp. n. (Cnidaria, Anthozoa, Scleractinia: a new reef coral species from the Red Sea and its phylogenetic relationships

    Directory of Open Access Journals (Sweden)

    Tullia Isotta Terraneo

    2014-08-01

    Full Text Available A new scleractinian coral species, Pachyseris inattesa sp. n., is described from the Red Sea. Despite a superficial resemblance with some species in the agariciid genus Leptoseris with which it has been previously confused, P. inattesa sp. n. has micro-morphological characters typical of the genus Pachyseris. This genus, once part of the Agariciidae, is comprised of five extant species and is widely distributed throughout the tropical Indo-Pacific. It is currently incertae sedis as a result of recent molecular analysis and appears to be closely related to the Euphylliidae. A molecular phylogenetic reconstruction including P. inattesa sp.n., the genus type species P. rugosa, and P. speciosa, all present in the Red Sea, was performed using the mitochondrial intergenic spacer between COI and 16S-rRNA. The results confirm that P. inattesa sp. n. is a monophyletic lineage closely related to the other Pachyseris species examined.

  20. Pachyseris inattesa sp. n. (Cnidaria, Anthozoa, Scleractinia): a new reef coral species from the Red Sea and its phylogenetic relationships.

    Science.gov (United States)

    Terraneo, Tullia I; Berumen, Michael L; Arrigoni, Roberto; Waheed, Zarinah; Bouwmeester, Jessica; Caragnano, Annalisa; Stefani, Fabrizio; Benzoni, Francesca

    2014-01-01

    A new scleractinian coral species, Pachyseris inattesa sp. n., is described from the Red Sea. Despite a superficial resemblance with some species in the agariciid genus Leptoseris with which it has been previously confused, P. inattesa sp. n. has micro-morphological characters typical of the genus Pachyseris. This genus, once part of the Agariciidae, is comprised of five extant species and is widely distributed throughout the tropical Indo-Pacific. It is currently incertae sedis as a result of recent molecular analysis and appears to be closely related to the Euphylliidae. A molecular phylogenetic reconstruction including P. inattesa sp. n., the genus type species P. rugosa, and P. speciosa, all present in the Red Sea, was performed using the mitochondrial intergenic spacer between COI and 16S-rRNA. The results confirm that P. inattesa sp. n. is a monophyletic lineage closely related to the other Pachyseris species examined.

  1. Molecular phylogeny of the arthrostylidioid bamboos (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae) and new genus Didymogonyx.

    Science.gov (United States)

    Tyrrell, Christopher D; Santos-Gonçalves, Ana Paula; Londoño, Ximena; Clark, Lynn G

    2012-10-01

    We present the first multi-locus chloroplast phylogeny of Arthrostylidiinae, a subtribe of neotropical woody bamboos. The morphological diversity of Arthrostylidiinae makes its taxonomy difficult and prior molecular analyses of bamboos have lacked breadth of sampling within the subtribe, leaving internal relationships uncertain. We sampled 51 taxa, chosen to span the range of taxonomic diversity and morphology, and analyzed a combined chloroplast DNA dataset with six chloroplast regions: ndhF, trnD-trnT, trnC-rpoB, rps16-trnQ, trnT-trnL, and rpl16. A consensus of maximum parsimony and Bayesian inference analyses reveals monophyly of the Arthrostylidiinae and four moderately supported lineages within it. Six previously recognized genera were monophyletic, three polyphyletic, and two monotypic; Rhipidocladum sect. Didymogonyx is here raised to generic status. When mapped onto our topology, many of the morphological characters show homoplasy. Copyright © 2012 Elsevier Inc. All rights reserved.

  2. A study on the geophylogeny of clinical and environmental Vibrio cholerae in Kenya.

    Directory of Open Access Journals (Sweden)

    John Kiiru

    Full Text Available Cholera remains a significant public health challenge in many sub-Saharan countries including Kenya. We have performed a combination of phylogenetic and phenotypic analysis based on whole genome DNA sequences derived from 40 environmental and 57 clinical V. cholerae from different regions of Kenya isolated between 2005 and 2010. Some environmental and all clinical isolates mapped back onto wave three of the monophyletic seventh pandemic V. cholerae El Tor phylogeny but other environmental isolates were phylogenetically very distinct. Thus, the genomes of the Kenyan V. cholerae O1 El Tor isolates are clonally related to other El Tor V. cholerae isolated elsewhere in the world and similarly harbour antibiotic resistance-associated STX elements. Further, the Kenyan O1 El Tor isolates fall into two distinct clades that may have entered Kenya independently.

  3. Brown algal morphogenesis: Atomic Force Microscopy as a tool to study the role of mechanical forces

    Directory of Open Access Journals (Sweden)

    Benoit eTesson

    2014-09-01

    Full Text Available Over the last few years, a growing interest has been directed toward the use of macroalgae as a source of energy, food and molecules for the cosmetic and pharmaceutical industries. Besides this, macroalgal development remains poorly understood compared to other multicellular organisms. Brown algae (Phaeophyceae form a monophyletic lineage of usually large multicellular algae which evolved independently from land plants. In their environment, they are subjected to strong mechanical forces (current, waves and tide, in response to which they modify rapidly and reversibly their morphology. Because of their specific cellular features (cell wall composition, cytoskeleton organization, deciphering how they cope with these forces might help discover new control mechanisms of cell wall softening and cellulose synthesis. Despite the current scarcity in knowledge on brown algal cell wall dynamics and protein composition, we will illustrate, in the light of methods adapted to Ectocarpus siliculosus, to what extent atomic force microscopy can contribute to advance this field of investigation.

  4. Molecular phylogeny and biogeography of the highly specialized grade schizothoracine fishes (Teleostei:Cyprinidae) inferred from cytochrome b sequences

    Institute of Scientific and Technical Information of China (English)

    HE DeKui; CHEN YiFeng

    2007-01-01

    We recovered the phylogenetic relationships among 23 species and subspecies of the highly specialized grade schizothoracine fishes distributing at 36 geographical sites in the Tibetan Plateau and its surrounding regions by analyzing sequences of cytochrome b genes. Furthermore, we estimated the possible divergent times among lineages based on a historical geological isolation event in the Tibetan Plateau. The molecular data revealed that the highly specialized grade schizothoracine fishes were not a monophyletic group, but were the same as genera Gymnocypris and Schizogypsis. Our results indicated that the molecular phylogenetic relationships apparently reflected their geographical and historical associations with drainages, namely species from the same and adjacent drainages clustered together and had close relationships. The divergence times of different lineages were well consistent with the rapid uplift phases of the Tibetan Plateau in the late Cenozoic, suggesting that the origin and evolution of schizothoracine fishes were strongly influenced by environment changes resulting from the upheaval of the Tibetan Plateau.

  5. Mitochondrial COI and morphological specificity of the mealy aphids (Hyalopterus ssp. collected from different hosts in Europe (Hemiptera, Aphididae

    Directory of Open Access Journals (Sweden)

    Rimantas Rakauskas

    2013-07-01

    Full Text Available Forty three European population samples of mealy aphids from various winter and summer host plants were attributed to respective species of Hyalopterus by means of their partial sequences of mitochondrial COI gene. Used Hyalopterus samples emerged as monophyletic relative to outgroup and formed three major clades representing three host specific mealy aphid species in the Neighbor joining, Maximum parsimony, Maximum likelihood and Bayesian inference trees. H. pruni and H. persikonus emerged as a sister species, whilst H. amygdali was located basally. Samples representing different clades in the molecular trees were used for canonical discrimination analysis based on twenty two morphological characters. Length of the median dorsal head hair enabled a 97.3 % separation of H. amygdali from the remaining two species. No single character enabled satisfactory discrimination between apterous viviparous females of H. pruni and H. persikonus. A modified key for the morphological identification of Hyalopterus species is suggested and their taxonomic status discussed.

  6. Phylogeny of New World Salvia subgenus Calosphace (Lamiaceae) based on cpDNA (psbA-trnH) and nrDNA (ITS) sequence data.

    Science.gov (United States)

    Jenks, Aaron A; Walker, Jay B; Kim, Seung-Chul

    2013-07-01

    Salvia subgenus Calosphace (Lamiaceae) is economically and ethnomedicinally significant and comprised of more than 500 species. Although strongly supported as monophyletic, it has received no comprehensive systematic research since the initial establishment of 91 taxonomic sections in 1939. Representative taxa of 73 sections of Calosphace were sampled to investigate the phylogenetic relationships and identify major lineages using chloroplast (intergenic spacer psbA-trnH) and nuclear ribosomal DNA (internal transcribed spacer). Phylogenetic analysis of the combined data sets established monophyly of seven sections (Blakea, Corrugatae, Erythrostachys, Hastatae, Incarnatae, Microsphace, and Sigmoideae) and four major lineages (S. axillaris, "Hastatae clade", "Uliginosae clade", and "core Calosphace"). Sections spanning two or more centers of diversity are not supported by our results; rather, supported relationships exhibit significant geographic structure. Mexico is supported as the geographic origin of Calosphace, and no more than seven dispersal events to South America are required to account for current disjunct distributions.

  7. Study of evolution and developmental mechanism of stamen in Salvia hypoleuca Benth. (Lamiaceae and related taxa using Electron Microscopy and molecular phylogenetic tools

    Directory of Open Access Journals (Sweden)

    Maryam-Sadat Asadollahi

    2014-11-01

    Full Text Available The genus Salvia L. includes a group of plants having two stamens with a special morphology. Natural groups within this genus consist of species with special type of stamen morphology. In this paper, phylogenetic placement and developmental stages of stamen of S. hypoleuca Benth. were studied. Examination of this and related species showed that each flower had two stamens with posterior thecae not expressed and the distal posterior ends of the adjacent connectives were fused into a complex structure blocking access to nectar. All species with such type of stamens grouped into a monophyletic clade with robust support. Study of stamen development in S. hypoleuca showed that normal, anterior thecae were evolved before the other organs and that the stamen found its final matured form before flower opened. In an opened flower, stamen and reproductive organs could be found in their final maturestage. In addition, it seemed that stamen development in related species should be similar.

  8. Stenostomum cf. leucops (Platyhelminthes in Thailand: a surface observation using scanning electron microscopy and phylogenetic analysis based on 18S ribosomal DNA sequences

    Directory of Open Access Journals (Sweden)

    Arin Ngamniyom

    2016-02-01

    Full Text Available The genus Stenostomum contains small turbellaria that are widely distributed in freshwater environments worldwide. However, there are only rare reports or studies of this genus from Thailand. Therefore, the objective of this study was to report S. cf. leucops in Thailand collected from Pathum Thani Province. The worm morphology and surface topography using scanning electron microscopy were determined. Moreover, the phylogenetic tree of S. cf. leucops was analysed with 17 flatworms based on the 18S ribosomal DNA sequences. The phylogenetic relationship shared a common ancestry of Catenulida species, and S. cf. leucops displayed a monophyletic pattern within Stenostomum spp. The results of the morphological and molecular data are discussed. These results may increase the knowledge of freshwater microturbellarians in Thailand.

  9. Two new species of Euptychia Hübner, 1818 from the upper Amazon basin (Lepidoptera, Nymphalidae, Satyrinae).

    Science.gov (United States)

    Neild, Andrew F E; Nakahara, Shinichi; Zacca, Thamara; Fratello, Steven; Lamas, Gerardo; Le Crom, Jean-François; Dolibaina, Diego R; Dias, Fernando M S; Casagrande, Mirna M; Mielke, Olaf H H; Espeland, Marianne

    2015-01-01

    Two new species of Euptychia Hübner, 1818 are described from the upper Amazon basin: Euptychia attenboroughi Neild, Nakahara, Fratello & Le Crom, sp. n. (type locality: Amazonas, Venezuela), and Euptychia sophiae Zacca, Nakahara, Dolibaina & Dias, sp. n. (type locality: Acre, Brazil). Their unusual facies prompted molecular and phylogenetic analyses of one of the species resulting in support for their classification in monophyletic Euptychia. Diagnostic characters for the two species are presented based on wing morphology, wing pattern, presence of androconial patches on the hindwing, and genitalia. Our results indicate that the projection of the tegumen above the uncus, previously considered a synapomorphy for Euptychia, is not shared by all species in the genus. The adults and their genitalia are documented, and distribution data and a map are provided.

  10. Phylogenetic Status and Morphological Characters of Rhabditolaimus anoplophorae (Rhabditida: Diplogastridae).

    Science.gov (United States)

    Kanzaki, Natsumi; Giblin-Davis, Robin M

    2014-03-01

    Rhabditolaimus anoplophorae Kanzaki and Futai was re-isolated from its type host (carrier), the cerambycid beetle Anoplophora malasiaca, collected in an experimental field of the Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan. The nematode was cultured on nematode growth medium plates seeded with Escherichia coli OP50, and its morphological characters and molecular profile were examined to modernize the description. Scanning electron microscopic and light microscopy revealed the presence of four stomatal flaps, a very long gymnostom, a single ventral papilla in males, and a horizontal slit-like vulval opening in females. The positions of the deirids, hemizonids, phasmids, and rectal glands are additionally described, and the absence of a male bursa was confirmed. Phylogenetically, the genus forms a well-supported clade in the family Diplogastridae. Rhabditolaimus anoplophorae is a member of the monophyletic Rhabditolaimus clade and is closely related to R. leuckarti and several undescribed species.

  11. DNA barcoding and phylogeny of Calidris and Tringa (Aves: Scolopacidae).

    Science.gov (United States)

    Huang, Zuhao; Tu, Feiyun

    2017-07-01

    The avian genera Calidris and Tringa are the largest of the widespread family of Scolopacidae. The phylogeny of members of the two genera is still a matter of controversial. Mitochondrial cytochrome c oxidase subunit I (COI) can serve as a fast and accurate marker for the identification and phylogeny of animal species. In this study, we analyzed the COI barcodes of thirty-one species of the two genera. All the species had distinct COI sequences. Two hundred and twenty-one variable sites were identified. Kimura two-parameter distances were calculated between barcodes. Neighbor-joining and maximum likelihood methods were used to construct phylogenetic trees. All the species could be discriminated by their distinct clades in the phylogenetic trees. The phylogenetic trees grouped all the species of Calidris and Tringa into different monophyletic clade, respectively. COI data showed a well-supported phylogeny for Calidris and Tringa species.

  12. Phylogeny of the owlet-nightjars (Aves: Aegothelidae) based on mitochondrial DNA sequence

    Science.gov (United States)

    Dumbacher, J.P.; Pratt, T.K.; Fleischer, R.C.

    2003-01-01

    The avian family Aegothelidae (Owlet-nightjars) comprises nine extant species and one extinct species, all of which are currently classified in a single genus, Aegotheles. Owlet-nightjars are secretive nocturnal birds of the South Pacific. They are relatively poorly studied and some species are known from only a few specimens. Furthermore, their confusing morphological variation has made it difficult to cluster existing specimens unambiguously into hierarchical taxonomic units. Here we sample all extant owlet-nightjar species and all but three currently recognized subspecies. We use DNA extracted primarily from museum specimens to obtain mitochondrial gene sequences and construct a molecular phylogeny. Our phylogeny suggests that most species are reciprocally monophyletic, however A. albertisi appears paraphyletic. Our data also suggest splitting A. bennettii into two species and splitting A. insignis and A. tatei as suggested in another recent paper. ?? 2003 Elsevier Science (USA). All rights reserved.

  13. Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium.

    Science.gov (United States)

    Wong, Vanessa K; Pickard, Derek J; Barquist, Lars; Sivaraman, Karthikeyan; Page, Andrew J; Hart, Peter J; Arends, Mark J; Holt, Kathryn E; Kane, Leanne; Mottram, Lynda F; Ellison, Louise; Bautista, Ruben; McGee, Chris J; Kay, Sally J; Wileman, Thomas M; Kenney, Linda J; MacLennan, Calman A; Kingsley, Robert A; Dougan, Gordon

    2013-01-01

    Proteins exhibiting hyper-variable sequences within a bacterial pathogen may be associated with host adaptation. Several lineages of the monophyletic pathogen Salmonella enterica serovar Typhi (S. Typhi) have accumulated non-synonymous mutations in the putative two-component regulatory system yehUT. Consequently we evaluated the function of yehUT in S. Typhi BRD948 and S. Typhimurium ST4/74. Transcriptome analysis identified the cstA gene, encoding a carbon starvation protein as the predominantly yehUT regulated gene in both these serovars. Deletion of yehUT had no detectable effect on the ability of these mutant Salmonella to invade cultured epithelial cells (S. Typhi and S. Typhimurium) or induce colitis in a murine model (S. Typhimurium only). Growth, metabolic and antimicrobial susceptibility tests identified no obvious influences of yehUT on these phenotypes.

  14. Characterisation of the chemical profiles of Brazilian and Andean morphotypes belonging to the Anastrepha fraterculus complex (Diptera, Tephritidae)

    Science.gov (United States)

    Vaníčková, Lucie; Břízová, Radka; Pompeiano, Antonio; Ferreira, Luana Lima; de Aquino, Nathaly Costa; Tavares, Raphael de Farias; Rodriguez, Laura D.; Mendonça, Adriana de Lima; Canal, Nelson Augusto; do Nascimento, Ruth Rufino

    2015-01-01

    Abstract Fruit fly sexual behaviour is directly influenced by chemical and non-chemical cues that play important roles in reproductive isolation. The chemical profiles of pheromones and cuticular hydrocarbons (CHs) of eight fruit fly populations of the Andean, Brazilian-1 and Brazilian-3 morphotypes of the Anastrepha fraterculus cryptic species complex originating from Colombia (four populations) and Brazil (four populations) were analysed using two-dimensional gas chromatography with mass spectrometric detection. The resulting chemical diversity data were studied using principal component analyses. Andean morphotypes could be discriminated from the Brazilian-1 and Brazilian-3 morphotypes by means of male-borne pheromones and/or male and female CH profiles. The Brazilian-1 and Brazilian-3 morphotypes were found to be monophyletic. The use of chemical profiles as species- and sex-specific signatures for cryptic species separations is discussed. PMID:26798260

  15. Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci.

    Science.gov (United States)

    Rasmussen, L H; Dargis, R; Højholt, K; Christensen, J J; Skovgaard, O; Justesen, U S; Rosenvinge, F S; Moser, C; Lukjancenko, O; Rasmussen, S; Nielsen, X C

    2016-10-01

    Identification of Mitis group streptococci (MGS) to the species level is challenging for routine microbiology laboratories. Correct identification is crucial for the diagnosis of infective endocarditis, identification of treatment failure, and/or infection relapse. Eighty MGS from Danish patients with infective endocarditis were whole genome sequenced. We compared the phylogenetic analyses based on single genes (recA, sodA, gdh), multigene (MLSA), SNPs, and core-genome sequences. The six phylogenetic analyses generally showed a similar pattern of six monophyletic clusters, though a few differences were observed in single gene analyses. Species identification based on single gene analysis showed their limitations when more strains were included. In contrast, analyses incorporating more sequence data, like MLSA, SNPs and core-genome analyses, provided more distinct clustering. The core-genome tree showed the most distinct clustering.

  16. Phylogeny, identification and nomenclature of the genus Aspergillus

    DEFF Research Database (Denmark)

    Samson, R.A.; Visagie, C.M.; Houbraken, J.;

    2014-01-01

    Aspergillus comprises a diverse group of species based on morphological, physiological and phylogenetic characters, which significantly impact biotechnology, food production, indoor environments and human health. Aspergillus was traditionally associated with nine teleomorph genera, but phylogenetic...... data suggest that together with genera such as Polypaecilum, Phialosimplex, Dichotomomyces and Cristaspora, Aspergillus forms a monophyletic clade closely related to Penicillium. Changes in the International Code of Nomenclature for algae, fungi and plants resulted in the move to one name per species......, meaning that a decision had to be made whether to keep Aspergillus as one big genus or to split it into several smaller genera. The International Commission of Penicillium and Aspergillus decided to keep Aspergillus instead of using smaller genera. In this paper, we present the arguments for this decision...

  17. Discovering the Hidden Secondary Metabolome of Myxococcus xanthus: a Study of Intraspecific Diversity▿

    Science.gov (United States)

    Krug, Daniel; Zurek, Gabriela; Revermann, Ole; Vos, Michiel; Velicer, Gregory J.; Müller, Rolf

    2008-01-01

    As a monophyletic group, the myxobacteria are known to produce a broad spectrum of secondary metabolites. However, the degree of metabolic diversity that can be found within a single species remains unexplored. The model species Myxococcus xanthus produces several metabolites also present in other myxobacterial species, but only one compound unique to M. xanthus has been found to date. Here, we compare the metabolite profiles of 98 M. xanthus strains that originate from 78 locations worldwide and include 20 centimeter-scale isolates from one location. This screen reveals a strikingly high level of intraspecific diversity in the M. xanthus secondary metabolome. The identification of 37 nonubiquitous candidate compounds greatly exceeds the small number of secondary metabolites previously known to derive from this species. These results suggest that M. xanthus may be a promising source of future natural products and that thorough intraspecific screens of other species could reveal many new compounds of interest. PMID:18378661

  18. [Estimation of the relationship of the gymnosperms and angiosperms on the basis of the data obtained by biochemical methods].

    Science.gov (United States)

    Semikhov, V F; Aref'eva, L P; Zolkin, S Iu; Timoshenko, A S; Novozhilova, O A; Kostrikin, D S

    2004-01-01

    The phylogenetic relationships of gymnospermous and angiospermous plants were studied. To this end, 13 antisera to seed proteins of plant taxa representing all the four classes of the gymnosperms were obtained. The antigens used in immunochemical reactions with these antisera included the proteins of 134 seed samples representing 91 families from all the 11 subclasses of dicotyledons and 64 seed samples representing 33 families from five out of six classes of monocotyledons (according to Takhtajan, 1996). Immunochemical analysis was performed by the methods of double immunodiffusion in agar gel (two variants) and immunoelectroblotting. In addition, some samples of seed proteins were analyzed for amino acid composition. The results corroborate the concept that the seed plants are a monophyletic taxon. The angiosperms have apparently originated from a progymnospermous ancestor or have branched from the main stem of gymnosperms prior to its division into the recent phyla. No common ancestor of all subclasses of the angiosperms has been identified.

  19. Pachyseris inattesa sp. n. (Cnidaria, Anthozoa, Scleractinia): A new reef coral species from the red sea and its phylogenetic relationships

    KAUST Repository

    Terraneo, Tullia I.

    2014-08-13

    A new scleractinian coral species, Pachyseris inattesa sp. n., is described from the Red Sea. Despite a superficial resemblance with some species in the agariciid genus Leptoseris with which it has been previously confused, P. inattesa sp. n. has micro-morphological characters typical of the genus Pachyseris. This genus, once part of the Agariciidae, is comprised of five extant species and is widely distributed throughout the tropical Indo-Pacific. It is currently incertae sedis as a result of recent molecular analysis and appears to be closely related to the Euphylliidae. A molecular phylogenetic reconstruction including P. inattesa sp. n., the genus type species P. rugosa, and P. speciosa, all present in the Red Sea, was performed using the mitochondrial intergenic spacer between COI and 16S-rRNA. The results confirm that P. inattesa sp. n. is a monophyletic lineage closely related to the other Pachyseris species examined. © Tullia I. Terraneo et al.

  20. The myxomycete genus Schenella: morphological and DNA sequence evidence for synonymy with the gasteromycete genus Pyrenogaster.

    Science.gov (United States)

    Estrada-Torres, Arturo; Gaither, Thomas W; Miller, Dennis L; Lado, Carlos; Keller, Harold W

    2005-01-01

    The genus Schenella has proven difficult to classify since its description as a new genus in 1911. Macbride placed it with the Myxomycetes but it was unclear with which myxomycete, if any, it should be grouped. Recent identification of abundant samples of Schenella has aided a re-evaluation of its classification as a myxomycete. Morphological evidence based on light and scanning electron microscopy of recently collected specimens and on the type specimen of Macbride suggested that it might be synonymous with the gasteromycete Pyrenogaster Analysis of DNA sequences from freshly isolated samples indicates that the genus Schenella is related closely to an anciently diverged, monophyletic group of fungi that includes several gasteromycete genera, among them Geastrum, Sphaerobolus and Pseudocolus. Comparisons of the morphology and DNA sequences of authentically identified specimens of Pyrenogaster atrogleba indicate that it is synonymous with Schenella simplex. The nomenclatural implications of this discovery are discussed.

  1. Systematic position of Myrtama Ovcz. & Kinz. based on morphological and nrDNA ITS sequence evidence

    Institute of Scientific and Technical Information of China (English)

    ZHANG Daoyuan; ZHANG Yuan; GASKIN J. F.; CHEN Zhiduan

    2006-01-01

    Myrtama is a genus named from Myricaria elegans Royle in the 1970's in terms of its morphological peculiarities. The establishment of this genus and its systematic position have been disputed since its inception. ITS sequences from 10 species of Tamaricaceae are reported, and analyzed by PAUP 4.0b8 and Bayesian Inference to reconstruct the phylogenies. A single ITS tree is generated from maximum parsimony and MrBayes analyses, respectively. The molecular data set shows strong support for Tamarix and Myricaria as monophyletic genera,and Myrtama as a sister group to the genus Myricaria.Based on morphological differences, a single morphological tree is also generated, in which two major lineages existed but Myrtama is a sister group to Tamarix, rather than Myricaria. The evidence from DNA sequences and morphological characters supports that Myicaria elegans should be put into neither Myricaria nor Tamarix, but kept in its own monotypic genus.

  2. Two newly recognized species of Hemidactylus (Squamata, Gekkonidae) from the Arabian Peninsula and Sinai, Egypt.

    Science.gov (United States)

    Smíd, Jiří; Moravec, Jiří; Kratochvíl, Lukáš; Gvoždík, Václav; Nasher, Abdul Karim; Busais, Salem M; Wilms, Thomas; Shobrak, Mohammed Y; Carranza, Salvador

    2013-01-01

    A recent molecular phylogeny of the Arid clade of the genus Hemidactylus revealed that the recently described H. saba and two unnamed Hemidactylus species from Sinai, Saudi Arabia and Yemen form a well-supported monophyletic group within the Arabian radiation of the genus. The name 'Hemidactylus saba species group' is suggested for this clade. According to the results of morphological comparisons and the molecular analyses using two mitochondrial (12S and cytb) and four nuclear (cmos, mc1r, rag1, rag2) genes, the name Hemidactylus granosus Heyden, 1827 is resurrected from the synonymy of H. turcicus for the Sinai and Saudi Arabian species. The third species of this group from Yemen is described formally as a new species H. ulii sp. n. The phylogenetic relationships of the members of 'Hemidactylus saba species group' are evaluated and the distribution and ecology of individual species are discussed.

  3. A reappraisal of Aspergillus section Nidulantes with descriptions of two new sterigmatocystin-producing species

    DEFF Research Database (Denmark)

    Hubka, Vit; Nováková, Alena; Peterson, Stephen W.;

    2016-01-01

    that codon usage analysis can easily distinguish between these paralogues, and we provide primer pair options to allow benA amplifications. Two new sect. Nidulantes species are described from European caves, A. croceus (Spain) and A. askiburgiensis (Czech Republic). The analysis of exometabolites showed......Aspergillus section Nidulantes is a speciose group of microscopic fungi whose species are important in indoor air quality, food spoilage, mycotoxin production and human pathogenicity. We assembled as many species from the section as possible with either type specimens or protologues for analysis....... DNA sequences were obtained from up to four loci to conduct phylogenetic analysis of sect. Nidulantes and other species in subgenus Nidulantes. Comparisons of phenetic characters were made. Our goal was to recognize monophyletic taxa for section Nidulantes as well as the other taxa in the subgenus...

  4. Mammalian mitogenomic relationships and the root of the eutherian tree.

    Science.gov (United States)

    Arnason, Ulfur; Adegoke, Joseph A; Bodin, Kristina; Born, Erik W; Esa, Yuzine B; Gullberg, Anette; Nilsson, Maria; Short, Roger V; Xu, Xiufeng; Janke, Axel

    2002-06-11

    The strict orthology of mitochondrial (mt) coding sequences has promoted their use in phylogenetic analyses at different levels. Here we present the results of a mitogenomic study (i.e., analysis based on the set of protein-coding genes from complete mt genomes) of 60 mammalian species. This number includes 11 new mt genomes. The sampling comprises all but one of the traditional eutherian orders. The previously unrepresented order Dermoptera (flying lemurs) fell within Primates as the sister group of Anthropoidea, making Primates paraphyletic. This relationship was strongly supported. Lipotyphla ("insectivores") split into three distinct lineages: Erinaceomorpha, Tenrecomorpha, and Soricomorpha. Erinaceomorpha was the basal eutherian lineage. Sirenia (dugong) and Macroscelidea (elephant shrew) fell within the African clade. Pholidota (pangolin) joined the Cetferungulata as the sister group of Carnivora. The analyses identified monophyletic Pinnipedia with Otariidae (sea lions, fur seals) and Odobenidae (walruses) as sister groups to the exclusion of Phocidae (true seals).

  5. Reassessment of the systematic position of Orthocomotis DOGNIN (Lepidoptera: Tortricidae) based on molecular data with description of new species of Euliini.

    Science.gov (United States)

    Razowski, Józef; Tarcz, Sebastian; Wojtusiak, Janusz; Pelz, Volker

    2013-01-01

    The application of molecular analyses for resolving taxonomic problems in the family Torticidae (Lepidoptera) is still uncommon. The majority of papers concern the assessment of population variability of economically important species; reports on the systematic positions ofNeotropical Tortricidae taxa are rare. The Neotropical genus Orthocomotis was classified initially as a member of the tribe Euliini. Then, based on genital morphology, it was moved to the tribe Polyorthini. A comparison of homologous 606 bp fragments of the COI mitochondrial gene revealed that Orthocomotis should be transfered back into the tribe Euliini. Based on an analysis ofphylogenetic relationships the studied genera of Euliini form a monophyletic cluster, clearly separated from tribe Polyorthini in which they were temporarily included. Moreover, in the current paper we describe two new species of the tribe Euliini: Galomecalpa lesta RAZOWSKI & PELZ, sp. n., Gauruncus ischyros RAZOWSKI & PELZ, sp. n.

  6. On the systematic position of Baltimartyria Skalski, 1995 and description of a new species from Baltic amber (Lepidoptera, Micropterigidae

    Directory of Open Access Journals (Sweden)

    Wolfram Mey

    2011-09-01

    Full Text Available This paper describes a rare case of a male moth in Baltic amber in an excellent position for establishing a species. The moth represents the second species of the genus Baltimartyria Skalski, 1995, described herein as B. rasnitsyni sp. n. The detection of this new species prompts research on the systematic position of the genus within the family Micropterigidae. The genus was found to provide none of the apomorphic characters that would allow placement in one of the monophyletic lineages within the family. The genus is provisionally assigned to the “southern sabatincoid group”, a weakly supported assemblage of Southern Hemisphere genera. The sister genus has still to be determined. Baltimartyria is the first North Hemisphere representative in this group. Some general aspects of historical biogeography relevant for the group are briefly discussed.

  7. Phylogenetic relationships of subfamilies in the family Hesperiidae (Lepidoptera: Hesperioidea) from China.

    Science.gov (United States)

    Yuan, Xiangqun; Gao, Ke; Yuan, Feng; Wang, Ping; Zhang, Yalin

    2015-06-10

    Hesperiidae is one of the largest families of butterflies. Our knowledge of the higher systematics on hesperiids from China is still very limited. We infer the phylogenetic relationships of the subfamilies of Chinese skippers based on three mitochondrial genes (cytochrome b (Cytb), the NADH dehydrogenase subunit 1 (ND1) and cytochrome oxidase I (COI)). In this study, 30 species in 23 genera were included in the Bayesian and maximum likelihood analyses. The subfamily Coeliadinae, Eudaminae, Pyrginae and Heteropterinae were recovered as a monophyletic clade with strong support. The subfamily Hesperiinae formed a clade, but support for monophyly was weak. Our results imply that the five subfamilies of Chinese Hesperiidae should be divided into: Coeliadinae, Eudaminae, Pyrginae, Heteropterinae and Hesperiinae. The relationships of the five subfamilies should be as follows: Coeliadinae + (Eudaminae + (Pyrginae + (Heteropterinae + Hesperiinae))).

  8. Ancient photosynthetic eukaryote biofilms in an Atacama Desert coastal cave

    Science.gov (United States)

    Azua-Bustos, A.; Gonzalez-Silva, C.; Mancilla, R.A.; Salas, L.; Palma, R.E.; Wynne, J.J.; McKay, C.P.; Vicuna, R.

    2009-01-01

    Caves offer a stable and protected environment from harsh and changing outside prevailing conditions. Hence, they represent an interesting habitat for studying life in extreme environments. Here, we report the presence of a member of the ancient eukaryote red algae Cyanidium group in a coastal cave of the hyperarid Atacama Desert. This microorganism was found to form a seemingly monospecific biofilm growing under extremely low photon flux levels. Our work suggests that this species, Cyanidium sp. Atacama, is a new member of a recently proposed novel monophyletic lineage of mesophilic "cave" Cyanidium sp., distinct from the remaining three other lineages which are all thermo-acidophilic. The cave described in this work may represent an evolutionary island for life in the midst of the Atacama Desert. ?? Springer Science + Business Media, LLC 2009.

  9. Selaginella P. Beauv. from Minas Gerais, Brazil

    Directory of Open Access Journals (Sweden)

    Gustavo Heringer

    2016-03-01

    Full Text Available Selaginella P. Beauv. is the only genus in the family Selaginellaceae Willk. The genus is monophyletic, has a cosmopolitan distribution, contains about 750 species and can be characterized by the presence of rhizophores, leaves, a ligule, heterospory and adaxial, reniform sporangia. Twenty species were found in the study area: Selaginella alstonii, S. contigua, S. convoluta, S. decomposita, S. erectifolia, S. erythropus, S. flexuosa, S. jungermannioides, S. macrostachya, S. marginata, S. microphylla, S. muscosa, S. producta, S. sellowii, S. sematophylla, S. suavis, S. sulcata, S. tenella, S. tenuissima and S. vestiens. Two new species records for the state are presented (S. jungermannioides and S. tenella. We present descriptions of the genus and species, an identification key, the synonyms pertaining to Brazil, illustrations, and comments about the taxonomy and distribution of species in Brazil.

  10. Review of Baeolidia, the largest genus of Aeolidiidae (Mollusca: Nudibranchia), with the description of five new species.

    Science.gov (United States)

    Carmona, Leila; Pola, Marta; Gosliner, Terrence M; Cervera, Juan Lucas

    2014-05-28

    This paper discusses the systematics of the aeolid genus Baeolidia Bergh, 1888. To date, this monophyletic genus is the most diverse within Aeolidiidae with sixteen valid species. Excluding Baeolidia cryoporos Bouchet, 1977, the genus is restricted to the Indo-Pacific and Eastern Pacific. Species of Baeolidia show a huge intrageneric variability in several morphological characters. Only oral glands, if present, may distinguish Baeolidia from other aeolidiids genera. Aeolidiella occidentalis Bergh, 1875, Aeolidiella faustina Bergh, 1900 and Spurilla orientalis Bergh, 1905 are transferred to Baeolidia but they are considered nomina dubia. Five new species, Baeolidia rieae sp. nov., Baeolidia variabilis sp. nov., Baeolidia lunaris sp. nov., Baeolidia gracilis sp. nov. and Baeolidia scottjohnsoni sp. nov. are described.

  11. Semiochemistry of the Scarabaeoidea.

    Science.gov (United States)

    Vuts, József; Imrei, Zoltán; Birkett, Michael A; Pickett, John A; Woodcock, Christine M; Tóth, Miklós

    2014-02-01

    The superfamily Scarabaeoidea comprises a large and diverse monophyletic group. Members share ancestral characteristics, but often exhibit considerable differences in their ecology, physiology, or mating strategies. A large number of species are regarded as pests of crop or amenity plants, while others are beneficial to humans and even may be extremely rare as a result of anthropogenic activities. A significant number of chemical ecology-based studies have been conducted with the Scarabaeoidea in order to characterize semiochemicals influencing their behavior, such as pheromones and plant-derived allelochemicals. These may be used either to control or preserve populations of the beetles, depending upon pest or beneficial status. This paper is a review of the role and identity of the semiochemicals of the Scarabaeoidea, with comments on possible future research and applied opportunities in the field of chemical ecology.

  12. The indefinable term ‘prokaryote’ and the polyphyletic origin of genes

    Indian Academy of Sciences (India)

    MASSIMO DI GIULIO

    2017-06-01

    An analysis has been performed on implications existing between the presence/absence of the evolutionary stage of the prokaryote, that is to say, the presence/absence of common characteristics between archaea and bacteria, and the monophyletic/polyphyletic origin of genes of proteins. Thereafter, a theorem stating that: ‘the polyphyletic origin of proteins would imply the absence of common characteristics between bacteria and archaea and therefore the lack of the evolutionary stage of the prokaryote, and vice versa that the indefinable prokaryote stage implies a polyphyletic origin of proteins’, has been made and validated. The conclusion is that given the absence of truth in common characteristics between archaea and bacteria, the origin of genes of proteins should have been polyphyletic.

  13. phylogenetic analyses reveal a unique species of elaphe (serpentes, colubridae) new to science

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    the snakes comprising the monophyletic group referred to as ratsnakes are found throughout asia,europe and the new world.recently,three snake samples likely belonging to the ratsnakes were collected in zoige county,sichuan province,china.species identity was difficult to delimit morphologically because the specimens were juveniles and partially damaged.subsequently,a molecular phylogenetic approach was used.portions of three mitochondrial genes (cyt b,nd4 and 12s rrna) were sequenced and analyzed.the results showed that they were sister to the genus elaphe.very little genetic variation was found among the three samples.the minimum genetic distances between these samples and those within elaphe were greater than any currently recognized species within the genus.we conclude that this likely represents a new species within the genus elaphe.adult specimens and a morphologic description are needed for further study.

  14. The Use of DNA Barcoding in Identification and Conservation of Rosewood (Dalbergia spp.)

    DEFF Research Database (Denmark)

    Hartvig, Ida; Czako, Mihaly; Kjaer, Erik Dahl

    2015-01-01

    efforts of Dalbergia species in Indochina. We used the recommended rbcL, matK and ITS barcoding markers on 95 samples covering 31 species of Dalbergia, and tested their discrimination ability with both traditional distance-based as well as different model-based machine learning methods. We specifically...... discriminated among Dalbergia species with high accuracy. We found that ITS yielded the single highest discrimination rate (100%), but due to difficulties in obtaining high-quality sequences from degraded material, the better overall choice for Dalbergia seems to be the standard rbcL+matK barcode......, as this yielded discrimination rates close to 90% and amplified well. The distance-based method TaxonDNA showed the highest identification rates overall, although a more complete specimen sampling is needed to conclude on the best analytic method. We found strong support for a monophyletic Dalbergia oliveri...

  15. Evolution of Scale Worms

    DEFF Research Database (Denmark)

    Gonzalez, Brett Christopher

    of adaptability and convergent evolution between relatively closely related scale worms. While some morphological and behavioral modifications in cave polynoids reflected troglomorphism, other modifications like eye loss were found to stem from a common ancestor inhabiting the deep sea, further corroborating...... the deep sea ancestry of scale worm cave fauna. In conclusion, while morphological characterization across Aphroditiformia appears deceptively easy due to the presence of elytra, convergent evolution during multiple early radiations across wide ranging habitats have confounded our ability to reconstruct......) caves, and the interstitium, recovering six monophyletic clades within Aphroditiformia: Acoetidae, Aphroditidae, Eulepethidae, Iphionidae, Polynoidae, and Sigalionidae (inclusive of the former ‘Pisionidae’ and ‘Pholoidae’), respectively. Tracing of morphological character evolution showed a high degree...

  16. Evolutionary History of Ascomyceteous Yeasts

    Energy Technology Data Exchange (ETDEWEB)

    Haridas, Sajeet; Riley, Robert; Salamov, Asaf; Goker, Markus; Klenk, Hans-Peter; Kurtzman, Cletus P.; Blackwell, Meredith; Grigoriev, Igor; Jeffries, Thomas W.

    2014-06-06

    Yeasts are important for many industrial and biotechnological processes and show remarkable diversity despite morphological similarities. We have sequenced the genomes of 16 ascomycete yeasts of taxonomic and industrial importance including members of Saccharomycotina and Taphrinomycotina. A comparison of these with several other previously published yeast genomes have added increased confidence to the phylogenetic positions of previously poorly placed species including Saitoella complicata, Babjeviella inositovora and Metschnikowia bicuspidata. Phylogenetic analysis also showed that yeasts with alternative nuclear codon usage where CUG encodes serine instead of leucine are monophyletic within the Saccharomycotina. Most of the yeasts have compact genomes with a large fraction of single exon genes with Lipomyces starkeyi and the previously published Pneumocystis jirovecii being notable exceptions. Intron analysis suggests that early diverging species have more introns. We also observed a large number of unclassified lineage specific non-simple repeats in these genomes.

  17. The tempo and mode of barnacle evolution

    DEFF Research Database (Denmark)

    Pérez-Losada, Marcos; Harp, Margaret; Høeg, Jens T

    2008-01-01

    (outgroup) species representing almost all the Thoracica families to assess the tempo and mode of barnacle evolution. Using phylogenetic methods of maximum parsimony, maximum likelihood, and Bayesian inference and 14 fossil calibrations, we found that: (1) Iblomorpha form a monophyletic group; (2......) pedunculated barnacles without shell plates (Heteralepadomorpha) are not ancestral, but have evolved, at least twice, from plated forms; (3) the ontogenetic pattern with 5-->6-->8-->12+ plates does not reflect Thoracica shell evolution; (4) the traditional asymmetric barnacles (Verrucidae) and the Balanomorpha......) the Thoracica suborders evolved since the Early Carboniferous (340mya) with the final radiation of the Sessilia in the Upper Jurassic (147mya). These results, therefore, reject many of the underlying hypotheses about character evolution in the Cirripedia Thoracica, stimulate a variety of new thoughts...

  18. Phylogenetic analysis of Porphyromonas species isolated from the oral cavity of Australian marsupials.

    Science.gov (United States)

    Mikkelsen, Deirdre; Milinovich, Gabriel J; Burrell, Paul C; Huynh, Sharnan C; Pettett, Lyndall M; Blackall, Linda L; Trott, Darren J; Bird, Philip S

    2008-09-01

    Porphyromonas species are frequently isolated from the oral cavity and are associated with periodontal disease in both animals and humans. Black, pigmented Porphyromonas spp. isolated from the gingival margins of selected wild and captive Australian marsupials with varying degrees of periodontal disease (brushtail possums, koalas and macropods) were compared phylogenetically to Porphyromonas strains from non-marsupials (bear, wolf, coyote, cats and dogs) and Porphyromonas gingivalis strains from humans using 16S rRNA gene sequence analysis. The results of the phylogenetic analysis identified three distinct groups of strains. A monophyletic P. gingivalis group (Group 1) contained only strains isolated from humans and a Porphyromonas gulae group (Group 2) was divided into three distinct subclades, each containing both marsupial and non-marsupial strains. Group 3, which contained only marsupial strains, including all six strains isolated from captive koalas, was genetically distinct from P. gulae and may constitute a new Porphyromonas species.

  19. A preliminary phylogenetic analysis of the Capsalidae (Platyhelminthes: Monogenea: Monopisthocotylea) inferred from large subunit rDNA sequences.

    Science.gov (United States)

    Whittington, I D; Deveney, M R; Morgan, J A T; Chisholm, L A; Adlard, R D

    2004-05-01

    Phylogenetic relationships within the Capsalidae (Monogenea) were examined using large subunit ribosomal DNA sequences from 17 capsalid species (representing 7 genera, 5 subfamilies), 2 outgroup taxa (Monocotylidae) plus Udonella caligorum (Udonellidae). Trees were constructed using maximum likelihood, minimum evolution and maximum parsimony algorithms. An initial tree, generated from sequences 315 bases long, suggests that Capsalinae, Encotyllabinae, Entobdellinae and Trochopodinae are monophyletic, but that Benedeniinae is paraphyletic. Analyses indicate that Neobenedenia, currently in the Benedeniinae, should perhaps be placed in a separate subfamily. An additional analysis was made which omitted 3 capsalid taxa (for which only short sequences were available) and all outgroup taxa because of alignment difficulties. Sequence length increased to 693 bases and good branch support was achieved. The Benedeniinae was again paraphyletic. Higher-level classification of the Capsalidae, evolution of the Entobdellinae and issues of species identity in Neobenedenia are discussed.

  20. Mitochondrial COI and morphological specificity of the mealy aphids (Hyalopterus ssp.) collected from different hosts in Europe (Hemiptera, Aphididae).

    Science.gov (United States)

    Rakauskas, Rimantas; Havelka, Jekaterina; Zaremba, Audrius

    2013-01-01

    Forty three European population samples of mealy aphids from various winter and summer host plants were attributed to respective species of Hyalopterus by means of their partial sequences of mitochondrial COI gene. Used Hyalopterus samples emerged as monophyletic relative to outgroup and formed three major clades representing three host specific mealy aphid species in the Neighbor joining, Maximum parsimony, Maximum likelihood and Bayesian inference trees. Hyalopterus pruni and Hyalopterus persikonus emerged as a sister species, whilst Hyalopterus amygdali was located basally. Samples representing different clades in the molecular trees were used for canonical discrimination analysis based on twenty two morphological characters. Length of the median dorsal head hair enabled a 97.3 % separation of Hyalopterus amygdali from the remaining two species. No single character enabled satisfactory discrimination between apterous viviparous females of Hyalopterus pruni and Hyalopterus persikonus. A modified key for the morphological identification of Hyalopterus species is suggested and their taxonomic status discussed.

  1. Molecular phylogeny of the Neoplecostominae and Hypoptopomatinae (Siluriformes: Loricariidae) using multiple genes.

    Science.gov (United States)

    Cramer, Christian Andreas; Bonatto, Sandro L; Reis, Roberto E

    2011-04-01

    A phylogenetic analysis is provided for representatives of more than one hundred species of the catfish family Loricariidae, including nearly all genera of the subfamilies Neoplecostominae and Hypoptopomatinae. This analysis is based on fragments of the subunit 1 of the cytochrome c oxidase gene (COI), the recombination activating genes 1 (RAG1) and 2 (RAG2), and the F-Reticulon 4 gene. We obtained an alignment of 4678 contiguous nucleotides for 136 species of 50 loricariid genera from five loricariid subfamilies, and ten outgroup species from five loricarioid families. Our results from Maximum Parsimony, Maximum Likelihood, and Bayesian analyses show the following set of interrelationships ((((Hypoptopomatinae, Neoplecostominae) Hypostominae), Loricariinae) Delturinae). However, neither Hypoptopomatinae nor Neoplecostominae were recovered as monophyletic groups. A previously hypothesized monophyly of Hypoptopomatini and Otothyrini was refuted. Furthermore, the genera Pareiorhaphis, Pareiorhina, Hisonotus and Parotocinclus were recovered as polyphyletic. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. Reassessment of the taxonomic position of Iranocypris typhlops Bruun & Kaiser, 1944 (Actinopterygii, Cyprinidae).

    Science.gov (United States)

    Farashi, Azita; Kaboli, Mohammad; Rezaei, Hamid Reza; Naghavi, Mohammad Reza; Rahimian, Hassan; Coad, Brian W

    2014-01-01

    The Iranian cave barb (Iranocypris typhlops Bruun & Kaiser, 1944) is a rare and endemic species of the family Cyprinidae known from a single locality in the Zagros Mountains, western Iran. This species is "Vulnerable" according to the IUCN Red List and is one of the top four threatened freshwater fish species in Iran. Yet, the taxonomic position of I. typhlops is uncertain. We examined phylogenetic relationships of this species with other species of the family Cyprinidae based on the mitochondrial cytochrome b gene. Our results show that I. typhlops is monophyletic and is sister taxon of a cluster formed by Garra rufa (Heckel, 1843) and Garra barreimiae (Fowler & Steinitz, 1956) within a clade that includes other species of the genus Garra. Based on previous molecular and morphological studies, as well as our new results, we recommend that I. typhlops should be transferred to the genus Garra Hamilton, 1822.

  3. Reassessment of the taxonomic position of Iranocypris typhlops Bruun & Kaiser, 1944 (Actinopterygii, Cyprinidae

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    Azita Farashi

    2014-01-01

    Full Text Available The Iranian cave barb (Iranocypris typhlops Bruun & Kaiser, 1944 is a rare and endemic species of the family Cyprinidae known from a single locality in the Zagros Mountains, western Iran. This species is “Vulnerable” according to the IUCN Red List and is one of the top four threatened freshwater fish species in Iran. Yet, the taxonomic position of I. typhlops is uncertain. We examined phylogenetic relationships of this species with other species of the family Cyprinidae based on the mitochondrial cytochrome b gene. Our results show that I. typhlops is monophyletic and is sister taxon of a cluster formed by Garra rufa (Heckel, 1843 and Garra barreimiae (Fowler & Steinitz, 1956 within a clade that includes other species of the genus Garra. Based on previous molecular and morphological studies, as well as our new results, we recommend that I. typhlops should be transferred to the genus Garra Hamilton, 1822.

  4. Chloroplast Genome Sequence Annotation of Dendrobium nobile (Asparagales: Orchidaceae), an Endangered Medicinal Orchid from Northeast India.

    Science.gov (United States)

    Biswal, Devendra; Konhar, Ruchishree; Debnath, Manish; Parameswaran, Sriram; Sundar, Durai; Tandon, Pramod

    2017-05-19

    Orchidaceae constitutes one of the largest families of angiosperms. Owing to the significance of orchids in plant biology, market needs and current sustainable technology levels, basic research on the biology of orchids and their applications in the orchid industry is increasing. Although chloroplast (cp) genomes continue to be evolutionarily informative, there is very limited information available on orchid chloroplast genomes in public repositories. Here, we report the complete cp genome sequence of Dendrobium nobile from Northeast India (Orchidaceae, Asparagales), bearing the GenBank accession number KX377961, which will provide valuable information for future research on orchid genomics and evolution, as well as the medicinal value of orchids. Phylogenetic analyses using Bayesian methods recovered a monophyletic grouping of all Dendrobium species (D. nobile, D. huoshanense, D. officinale, D. pendulum, D. strongylanthum and D. chrysotoxum). The relationships recovered among the representative orchid species from the four subfamilies, i.e., Cypripedioideae, Epidendroideae, Orchidoideae and Vanilloideae, were consistent within the family Orchidaceae.

  5. The genetic control of eye development and its implications for the evolution of the various eye-types.

    Science.gov (United States)

    Gehring, Walter J

    2002-01-01

    Mutations in the Pax 6 homologs of mammals and insects prevent eye development and targeted expression of both mammal and insect Pax 6 homologs is capable of inducing functional ectopic eyes. Supported by RNA interference experiments in planarians and nemerteans, these findings indicate that Pax 6 is a universal master control gene for eye morphogenesis. Since all metazoan eyes use rhodopsin as a photoreceptor molecule and the same master control gene for eye development, we postulate a monophyletic origin of the various eye types. The finding of well developed eyes in jellyfish which essentially lack a brain, leads us to propose that the eye as a sensory organ evolved before the brain which is an information processing organ. The finding of highly developed eyes with a lens, vitreous body, stacked membranes like a retina and shielding pigment in unicellular dinoflagellates, raises the possibility that the prototypic eyes might have been acquired from symbionts.

  6. Larsenianthus, a new Asian genus of Gingers (Zingiberaceae with four species

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    W. John Kress

    2010-11-01

    Full Text Available Larsenianthus W.J.Kress & Mood, gen. nov. is described with one new combination and three new species. Larsenianthus careyanus (Benth. W.J.Kress & Mood, comb. nov., is widespread in India and present-day Bangladesh; L. wardianus W.J.Kress, Thet Htun & Bordelon, sp. nov., is from upper Myanmar in Kachin State; L. assamensis S.Dey, Mood, & S.Choudhury, sp. nov., is restricted to Assam, India; and L. arunachalensis M.Sabu, Sanoj & T.Rajesh Kumar, sp. nov., has only been found in Arunachal Pradesh, India. A phylogenetic analysis using the plastid trnK intron and nuclear ITS DNA sequence data indicates that the four species of Larsenianthus form a monophyletic lineage that is sister to Hedychium, a geographically widespread genus of about 50 species in tribe Zingibereae of subfamily Zingiberoideae. A dichotomous key and three-locus DNA barcodes are provided as aids for the identification of the four species of Larsenianthus.

  7. Hydrophylax bahuvistara, a new species of fungoid frog (Amphibia: Ranidae from peninsular India

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    Anand D. Padhye

    2015-09-01

    Full Text Available Hydrophylax bahuvistara, a new species of fungoid frog, is described from peninsular India. It can be separated from its congeners based on a combination of characters including wider head, outline of snout in dorsal view truncated, finger and toe tips without lateroventral groove, foot moderately webbed, metatarsals of 4th and 5th toes closely set, outer metatarsal tubercle small, foot length less than or equal to half of snout vent length, dorsal parts of shank without glandular folds and sparse horny spinules, and heels touch each other when the legs are folded at right angles to the body.  Genetically, H. bahuvistara forms a monophyletic group with H. malabaricus as a sister clade separated by a raw distance of 4.0 to 4.5% in the 16s rRNA gene.  Morphometrically, H. bahuvistara forms a significantly different cluster from H. malabaricus and H. gracilis in Discriminant Analysis.  

  8. A new species of Rhinopetitia Géry 1964 (Ostariophysi: Characiformes: Characidae) from the Rio Teles Pires, Rio Tapajós basin, Brazil.

    Science.gov (United States)

    Netto-Ferreira, A L; Birindelli, J L O; Sousa, L M; Menezes, N A

    2014-05-01

    A new species of Rhinopetitia is described from the Rio Teles Pires, a major tributary of the Rio Tapajós. The new taxon is distinguished from its only congener, Rhinopetitia myersi, by having all premaxillary teeth in both rows with seven to nine cusps, maxillary teeth with seven or eight cusps, a distinct dark midlateral stripe on the body and a round humeral blotch (v. outer series of premaxillary teeth with three cusps and inner series of premaxillary teeth with three to five cusps, maxillary teeth with three to five cusps, the absence of a dark midlateral stripe and humeral blotch). Putative characters suggesting a close relationship between Rhinopetitia, Bryconacidnus, Ceratobranchia, Monotocheirodon, Odontostoechus, Othonocheirodus and Rhinobrycon are presented. This putative clade is included in the Stevardiinae, a monophyletic group within the Characidae. © 2014 The Fisheries Society of the British Isles.

  9. New species of Moenkhausia Eigenmann, 1903 (Characiformes: Characidae with comments on the Moenkhausia oligolepis species complex

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    Ricardo C. Benine

    Full Text Available A new species of Moenkhausia is described from tributaries of the rio Paraguay, Brazil. The new species is diagnosed from congeners by characters related to body coloration, the number of lateral line scales, the degree of poring of the lateral line, and number of scales rows above and below the lateral line. Molecular analyses using partial sequences of the mitochondrial gene Cytochrome Oxidase I from specimens of the new species and specimens belonging to morphologically similar species demonstrated that the new species is easily differentiated by their high genetic distance and by their position in the phylogenetic hypothesis obtained through the Maximum Parsimony methodology. The analyses of three samples of M. oligolepis also revealed that they have high genetic distances and belong to different monophyletic groups suggesting that this species corresponds to a species complex rather than a single species.

  10. A new species of Moenkhausia Eigenmann (Characiformes: Characidae) from the upper rio Juruena basin, Central Brazil.

    Science.gov (United States)

    Dagosta, Fernando C P; Marinho, Manoela M F; Benine, Ricardo C

    2015-10-19

    Moenkhausia lineomaculata, new species, is described herein from the upper rio Juruena, upper rio Tapajós basin. The new species seems to be part of a monophyletic group formed by M. cosmops, M. cotinho, M. diktyota, M. forestii, M. oligolepis, M. sanctaefilomenae, and M. pyrophthalma, the Moenkhausia oligolepis/M. sanctaefilomenae complex, by sharing a reticulated color pattern on body and the presence of a light area preceding a wide, dark caudal-peduncle blotch. The new species is distinguished from these species, except M. cotinho, by the presence of longitudinal series of dark dots on body, and from M. cotinho by the humeral blotch evenly pigmented along its length and by having the dark line along horizontal septum starting approximately at the vertical through dorsal-fin origin. The new species presents intraspecific variation in lateral-line scales perforation, a feature often present in species of the aforementioned group.

  11. Cyptotrama (Physalacriaceae, Agaricales) from Asia.

    Science.gov (United States)

    Qin, Jiao; Yang, Zhu-Liang

    2016-04-01

    Cyptotrama was divided into several sections, of which sect. Xerulina was often treated as a separate genus by some mycologists. In this study, collections of Cyptotrama from East Asia, Southeast Asia, and South Asia were studied. For comparison, materials from North America and New Zealand were analysed. Our multi-gene phylogenetic analyses indicated that Cyptotrama is monophyletic and Xerulina should be treated as a section within the genus Cyptotrama. Different scenarios of morphological character evolution in Cyptotrama are discovered. A total of seven species of Cyptotrama can be recognized from Asia, three of which, Cyptotrama angustispora, C. glabra, and C. shennongjia, are new to science. Meanwhile, three taxa previously placed in Xerulina or Marasmius were proved to be members of Cyptotrama, and the new combinations, namely Cyptotrama trogioides, C. megaspora, and C. myochroa, are accordingly proposed. A key for the diagnosis of worldwide Cyptotrama species is provided.

  12. alpha-Crystallin A sequences of Alligator mississippiensis and the lizard Tupinambis teguixin: molecular evolution and reptilian phylogeny.

    Science.gov (United States)

    de Jong, W W; Zweers, A; Versteeg, M; Dessauer, H C; Goodman, M

    1985-11-01

    The amino acid sequences of the eye lens protein alpha-crystallin A from many mammalian and avian species, two frog species, and a dogfish have provided detailed information about the molecular evolution of this protein and allowed some useful inferences about phylogenetic relationships among these species. We now have isolated and sequenced the alpha-crystallins of the American alligator and the common tegu lizard. The reptilian alpha A chains appear to have evolved as slowly as those of other vertebrates, i.e., at two to three amino acid replacements per 100 residues in 100 Myr. The lack of charged replacements and the general types and distribution of replacements also are similar to those in other vertebrate alpha A chains. Maximum-parsimony analyses of the total data set of 67 vertebrate alpha A sequences support the monophyletic origin of alligator, tegu, and birds and favor the grouping of crocodilians and birds as surviving sister groups in the subclass Archosauria.

  13. Not all spotted cats are leopards: evidence for a Hemilienardia ocellata species complex (Gastropoda: Conoidea: Raphitomidae

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    Alexander E. Fedosov

    2017-02-01

    Full Text Available The small conoidean Hemilienardia ocellata is one of the easily recognizable Indo-Pacific “turrids”, primarily because of its remarkable eyespot colour pattern. Morphological and molecular phylogenetic analyses revealed four species that share this “characteristic” colour pattern but demonstrate consistent differences in size and shell proportions. Three new species – Hemilienardia acinonyx sp. nov. from the Philippines, H. lynx sp. nov. from Papua New Guinea and H. pardus sp. nov. from the Society and Loyalty Islands – are described based on the results of phylogenetic analyses. Although the H. ocellata species complex clade falls in a monophyletic Hemilienardia, H. ocellata and H. acinonyx sp. nov. possess a radula with semi-enrolled or notably flattened triangular marginal teeth, a condition that diverges substantially from the standard radular morphology of Hemilienardia and other raphitomids.

  14. Molecular phylogeny of grey mullets (Teleostei: Mugilidae) in Greece: evidence from sequence analysis of mtDNA segments.

    Science.gov (United States)

    Papasotiropoulos, Vasilis; Klossa-Kilia, Elena; Alahiotis, Stamatis N; Kilias, George

    2007-08-01

    Mitochondrial DNA sequence analysis has been used to explore genetic differentiation and phylogenetic relationships among five species of the Mugilidae family, Mugil cephalus, Chelon labrosus, Liza aurata, Liza ramada, and Liza saliens. DNA was isolated from samples originating from the Messolongi Lagoon in Greece. Three mtDNA segments (12s rRNA, 16s rRNA, and CO I) were PCR amplified and sequenced. Sequencing analysis revealed that the greatest genetic differentiation was observed between M. cephalus and all the other species studied, while C. labrosus and L. aurata were the closest taxa. Dendrograms obtained by the neighbor-joining method and Bayesian inference analysis exhibited the same topology. According to this topology, M. cephalus is the most distinct species and the remaining taxa are clustered together, with C. labrosus and L. aurata forming a single group. The latter result brings into question the monophyletic origin of the genus Liza.

  15. Mosquitoes of Anopheles hyrcanus (Diptera, Culicidae) Group: Species Diagnostic and Phylogenetic Relationships.

    Science.gov (United States)

    Khrabrova, Natalia V; Andreeva, Yulia V; Sibataev, Anuarbek K; Alekseeva, Svetlana S; Esenbekova, Perizat A

    2015-09-01

    Herein, we report the results of study of Anopheles species in Primorsk and Khabarovsk regions of Russia. Three species of the Anopheles hyrcanus group: An. kleini, An. pullus, and An. lesteri were identified by molecular taxonomic diagnostics for the first time in Russia. Surprisingly, An. sinensis, which earlier was considered the only species of Anopheles in Russian Far East, was not observed. We analyzed nucleotide variation in the 610-bp fragment of the 5' end of the cytochrome c oxidase subunit I (COI) region. All species possessed a distinctive set of COI sequences. A maximum likelihood phylogenetic tree was constructed for members of the hyrcanus group. The examined Anopheles hyrcanus group members could be divided into two major subgroups: subgroup 1 (An. hyrcanus and An. pullus) and subgroup 2 (An. sinensis, An. kleini, and An. lesteri), which were found to be monophyletic.

  16. The mitochondrial 16 s rRNA reveals high anthropogenic influence on land snail diversity in a preliminary island survey.

    Science.gov (United States)

    Abu-Bakar, Siti-Balkhis; Razali, Norhanis M; Naggs, Fred; Wade, Christopher; Mohd-Nor, Siti-Azizah; Aileen-Tan, Shau-Hwai

    2014-03-01

    A total of 30 specimens belonging to five species, namely; Cryptozona siamensis, Sarika resplendens and Sarika sp. from the family Ariophantidae as well as Quantula striata and Quantula sp. from the family Dyakiidae were collected from the Langkawi Island in Northern Peninsular Malaysia. All specimens were identified through comparisons of shell morphology and amplification of a 500 bp segment of the 16S rRNA mtDNA gene. To assess phylogenetic insights, the sequences were aligned using ClustalW and phylogenetic trees were constructed. The analyses showed two major lineages in both Maximum Parsimony and Neighbour Joining phylogenetic trees. Each putative taxonomic group formed a monophyletic cluster. Our study revealed low species and intraspecies genetic diversities based on the 16S rRNA gene sequences. Thus, this study has provided an insight of land snail diversity in populations of an island highly influenced by anthropogenic activities through complementary use of shell morphological and molecular data.

  17. Introgression of mitochondrial DNA among lineages in a hybridogenetic ant.

    Science.gov (United States)

    Darras, Hugo; Aron, Serge

    2015-02-01

    We report a remarkable pattern of incongruence between nuclear and mitochondrial variations in a social insect, the desert ant Cataglyphis hispanica. This species reproduces by social hybridogenesis. In all populations, two distinct genetic lineages coexist; non-reproductive workers develop from hybrid crosses between the lineages, whereas reproductive offspring (males and new queens) are typically produced asexually by parthenogenesis. Genetic analyses based on nuclear markers revealed that the two lineages remain highly differentiated despite constant hybridization for worker production. Here, we show that, in contrast with nuclear DNA, mitochondrial DNA (mtDNA) does not recover the two lineages as monophyletic. Rather, mitochondrial haplotypes cluster according to their geographical origin. We argue that this cytonuclear incongruence stems from introgression of mtDNA among lineages, and review the mechanisms likely to explain this pattern under social hybridogenesis.

  18. Emerging trends in molecular systematics and molecular phylogeny of mayflies (Insecta: Ephemeroptera

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    K.G. Sivaramakrishnan

    2011-08-01

    Full Text Available Current trends are reviewed in the molecular systematics and phylogeny of the Ephemeroptera (mayflies, an ancient monophyletic lineage of pterygote insects. Theories of mayfly origins are analyzed, followed by a discussion of higher classification schemes in light of recent developments in molecular systematics. Ephemeroptera evolution is a classic example of ancient rapid radiation, presenting challenges for phylogenetic analysis. The utility of combined studies of morphological and molecular data is substantiated with examples and the role of molecular systematics in unraveling the taxonomy of cryptic species complexes is highlighted. The importance of DNA barcoding in mayfly taxonomy is discussed in the light of recent progress, and future contributions of genetics to the study of taxonomy, ecology and evolution in mayflies are discussed.

  19. Opsins in onychophora (velvet worms) suggest a single origin and subsequent diversification of visual pigments in arthropods.

    Science.gov (United States)

    Hering, Lars; Henze, Miriam J; Kohler, Martin; Kelber, Almut; Bleidorn, Christoph; Leschke, Maren; Nickel, Birgit; Meyer, Matthias; Kircher, Martin; Sunnucks, Paul; Mayer, Georg

    2012-11-01

    Multiple visual pigments, prerequisites for color vision, are found in arthropods, but the evolutionary origin of their diversity remains obscure. In this study, we explore the opsin genes in five distantly related species of Onychophora, using deep transcriptome sequencing and screening approaches. Surprisingly, our data reveal the presence of only one opsin gene (onychopsin) in each onychophoran species, and our behavioral experiments indicate a maximum sensitivity of onychopsin to blue-green light. In our phylogenetic analyses, the onychopsins represent the sister group to the monophyletic clade of visual r-opsins of arthropods. These results concur with phylogenomic support for the sister-group status of the Onychophora and Arthropoda and provide evidence for monochromatic vision in velvet worms and in the last common ancestor of Onychophora and Arthropoda. We conclude that the diversification of visual pigments and color vision evolved in arthropods, along with the evolution of compound eyes-one of the most sophisticated visual systems known.

  20. [What gene and chromosomes say about the origin and evolution of insects and other arthropods].

    Science.gov (United States)

    Lukhtanov, V A; Kuznetsova, V G

    2010-09-01

    At the turn of the 21st century, the use of molecular and molecular cytogenetic methods led to revolutionary advances in systematics of insects and other arthropods. Analysis of nuclear and mitochondrial genes, as well as investigation of structural rearrangements in the mitochondrial chromosome convincingly supported the Pancrustacea hypothesis, according to which insects originated directly from crustaceans, whereas myriapods are not closely related to them. The presence of the specific telomeric motif TTAGG confirmed the monophyletic origin of arthropods (Arthropoda) and the assignment of tongue worms (Pentastomida) to this type. Several different types of telomeric sequences have been found within the class of insects. Investigation of the molecular organization of these sequences may shed light on the relationships between the orders Diptera, Siphonaptera, and Mecoptera and on the origin of such enigmatic groups as the orders Strepsiptera, Zoraptera and suborder Coleorrhyncha.

  1. Two new species of Vestrogothia (Phosphatocopina, Crustacea) of Orsten-type preservation from the Upper Cambrian in western Hunan, South China

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Although fossils of Orsten-type preservation represented by Skaracarida and Phosphatocopina were first reported from the Middle and Upper Cambrian in western Hunan, South China in 2005, diversified phosphatocopine species have never been appropriately described and elucidated in terms of their evolutionary relationships. Here, we described two new species of Phosphatocopina, Vestrogothia anterispinata sp. nov. and V. bispinata sp. nov. The evolutionary relationship among all the valid species of Phosphatocopina is discussed and the phylogeny of Phosphatocopina is reestablished using cladistic analysis. Accordingly, phosphatocopines primitively evolved along two lineages: one evolved towards the emergence of lobes; the other evolved towards the emergence of dorsal spines. Respectively, lobes originated independently three times, and dorsal spines originated only once. With regard to the dorsal rims, interdorsum originated first, whereas dorsal furrow originated independently twice on the basis of interdorsum. Probably Hesslandona may represent a polyphyletic group, whereas Vestrogothia a monophyletic group.

  2. Phylogeny of genus Glossina (Diptera: Glossinidae) according to ITS2 sequences

    Institute of Scientific and Technical Information of China (English)

    陈小爱; 李嵩; 李昌本; 赵寿元; Aksoy; Serap

    1999-01-01

    The flies of genus Glossina (Diptera: Glossinidae) are an important vector of African trypanosomiases which cause diseases in humans and animals. The ribosomal DNA Internal Transcribed Spacer-2 (ITS-2) region sequences from different Glossina species were PCR-amplified and analyzed in order to construct a molecular phylogeny for genus Glossina. Trees generated by parsimony confirmed the monophyletic taxonomic placement of genus Glossina where fusca group species formed the deepest branch followed by morsitans and palpalis groups, respectively. The placement of Glossina austeni by both the traditional morphological and biochemical criteria has been controversial. Results presented here, based on ITS-2 locus sequence analysis, suggest that Glossina austeni can be placed into a separate subgenerus which forms a sister-group relationship with the morsitans group species.

  3. Phylogeny of Ptychostomum (Bryaceae, Musci) inferred from sequences of nuclear ribosomal DNA internal transcribed spacer (ITS) and chloroplast rps4

    Institute of Scientific and Technical Information of China (English)

    Chen-Ying WANG; Jian-Cheng ZHAO

    2009-01-01

    The phylogeny of Ptychostomum was first undertaken based on analysis of the internal transcribed spacer (ITS) region of the nuclear ribosomal (nr) DNA and by combining data from nrDNA ITS and chloroplast DNA rps4 sequences. Maximum parsimony, maximum likelihood, and Bayesian analyses all support the conclu-sion that the reinstated genus Ptychostomum is not monophyletic. Ptychostomum funkii (Schwagr.) J. R. Spence (= Bryum funkii Schwagr.) is placed within a clade containing the type species of Bryum, B. argenteum Hedw. The remaining members of Ptychostomum investigated in the present study constitute another well-supported clade. The results are congruent with previous molecular analyses. On the basis of phylogenetic evidence, we agree with Bryum lonchocaulon Mull. Hal., Bryum pallescens Schleich. ex Schwagr., and Bryum pallens Sw. to Ptychostomum.

  4. Phylogeny of Chinese Allium (Liliaceae) using PCR-RFLP analysis

    Institute of Scientific and Technical Information of China (English)

    何兴金; 葛颂; 许介眉; 洪德元

    2000-01-01

    Eighteen representative species were selected from all the nine sections of Chinese Allium on the basis of the classification of morphology and cytotaxonomy. The trnK and rpL16 gene fragments of chloroplast DNA were amplified from 18 species by PCR method. The two cpDNA fragments were digested by 26 restriction enzymes, and 303 polymorphic restriction sites were found, of which 163 were informative. The restriction site data were analyzed with PAUP (version 3.1.1) and MEGA (version 1.01) as well as PHYLIP. As a result, the genus Allium could be classified into six subgenera. The recognition of Sect. Anguinum in the Flora of China is reasonable, Sect. Rhizirideum, Sect. Haplostemon and Sect. Cepa are not monophyletic. The infrageneric system of this genus was also discussed.

  5. A nuclear DNA based phylogeny of endemic sand dune ants of the genus Mycetophylax (Emery, 1913): how morphology is reflected in molecular data.

    Science.gov (United States)

    Cardoso, Danon Clemes; Cristiano, Maykon Passos; Heinze, Jürgen; Tavares, Mara Garcia

    2014-01-01

    Molecular methods have substantially advanced our knowledge about ant systematics in the past few years. Here, we infer the molecular phylogeny of sand dune ants of the genus Mycetophylax, Emery 1913 (Formicidae: Myrmicinae: Attini) using 730 base pairs of DNA sequences of the two nuclear genes longwave rhodopsin and wingless. Our analyses indicate that Mycetophylax is monophyletic, as suggested by its morphological characters. M. morschi, previously considered a species of Cyphomyrmex due to a scrobe-like impressed area on the head, forms a well-supported cluster with the two other species of Mycetophylax, M. conformis and M. simplex. Our analysis yields the first comprehensive phylogeny of Mycetophylax based on molecular data and includes specimens from localities within a wide distributional range as well as all species belonging to the genus following the recent taxonomic revision.

  6. Molecular Epidemiology of Fonsecaea Species

    Science.gov (United States)

    Najafzadeh, Mohammad Javad; Sun, Jiufeng; Vicente, Vania A.; Klaassen, Corne H.W.; Bonifaz, Alexandro; van den Ende, A.H.G. Gerrits; Menken, Steph B.J.

    2011-01-01

    To assess population diversities among 81 strains of fungi in the genus Fonsecaea that had been identified down to species level, we applied amplified fragment-length polymorphism (AFLP) technology and sequenced the internal transcribed spacer regions and the partial cell division cycle, β-tubulin, and actin genes. Many species of the genus Fonsecaea cause human chromoblastomycosis. Strains originated from a global sampling of clinical and environmental sources in the Western Hemisphere, Asia, Africa, and Europe. According to AFLP fingerprinting, Fonsecaea isolates clustered in 5 groups corresponding with F. pedrosoi, F. monophora, and F. nubica: the latter 2 species each comprised 2 groups, and F. pedrosoi appeared to be of monophyletic origin. F. pedrosoi was found nearly exclusively in Central and South America. F. monophora and F. nubica were distributed worldwide, but both showed substantial geographic structuring. Clinical cases outside areas where Fonsecaea is endemic were probably distributed by human migration. PMID:21392438

  7. A revision of Evaniscus (Hymenoptera, Evaniidae using ontology-based semantic phenotype annotation

    Directory of Open Access Journals (Sweden)

    Patricia Mullins

    2012-09-01

    Full Text Available The Neotropical evaniid genus Evaniscus Szépligeti currently includes six species. Two new species are described, Evaniscus lansdownei Mullins, sp. n. from Colombia and Brazil and E. rafaeli Kawada, sp. n. from Brazil. Evaniscus sulcigenis Roman, syn. n., is synonymized under E. rufithorax Enderlein. An identification key to species of Evaniscus is provided. Thirty-five parsimony informative morphological characters are analyzed for six ingroup and four outgroup taxa. A topology resulting in a monophyletic Evaniscus is presented with E. tibialis and E. rafaeli as sister to the remaining Evaniscus species. The Hymenoptera Anatomy Ontology and other relevant biomedical ontologies are employed to create semantic phenotype statements in Entity-Quality (EQ format for species descriptions. This approach is an early effort to formalize species descriptions and to make descriptive data available to other domains.

  8. Transfer of Tsukamurella wratislaviensis Goodfellow et a. 1995 to the genus Rhodococcus as Rhodococcus wratislaviensis comb. nov..

    Science.gov (United States)

    Goodfellow, Michael; Chun, Jongsik; Stackebrandt, Erko; Kroppenstedt, Reiner M

    2002-05-01

    A polyphasic study was undertaken to clarify the taxonomic position of the type strain (N805T) of Tsukamurella wratislaviensis. This organism showed a combination of phenotypic properties, notably chemotaxonomic markers, consistent with its classification in the genus Rhodococcus. Comparative 16S rDNA sequencing studies indicated that strain 805T falls into the Rhodococcus erythropolis subclade, where it forms a monophyletic group with the type strains of Rhodococcus opacus and Rhodococcus percolatus. The close relationship between these strains was underpinned by the results of mycolic acid analyses. However, strain N805T was distinguished from the R. opacus and R. percolatus strains in DNA-DNA pairing experiments and by using a range of phenotypic properties. In light of these studies, it is clear that strain N805T is misclassified in the genus Tsukamurella. It is, therefore, proposed that Tsukamurella wratislaviensis Goodfellow et al. 1995 be transferred to the genus Rhodococcus as Rhodococcus wratislaviensis comb. nov..

  9. Evolutionary dynamics and genetic diversity from three genes of Anguillid rhabdovirus

    DEFF Research Database (Denmark)

    Bellec, Laure; Cabon, Joelle; Bergmann, Sven

    2014-01-01

    Wild freshwater eel populations have dramatically declined in recent past decades in Europe and America, partially through the impact of several factors including the wide spread of infectious diseases. The anguillid rhabdoviruses eel virus European X (EVEX) and eel virus American (EVA) potentially...... play a role in this decline, even if their real contribution is still unclear. In this study, we investigate the evolutionary dynamics and genetic diversity of anguiillid rhabdoviruses by analysing sequences from the glycoprotein, nucleoprotein and phosphoprotein (P) genes of 57 viral strains collected...... from seven countries over 40 years using maximum-likelihood and Bayesian approaches. Phylogenetic trees from the three genes are congruent and allow two monophyletic groups, European and American, to be clearly distinguished. Results of nucleotide substitution rates per site per year indicate...

  10. Skull anatomy of the miniaturized gecko Sphaerodactylus roosevelti (Squamata: Gekkota).

    Science.gov (United States)

    Daza, Juan D; Abdala, Virginia; Thomas, Richard; Bauer, Aaron M

    2008-11-01

    A detailed description of the skull and jaw of the gecko Sphaerodactylus roosevelti is presented. The bones are described articulated and isolated with special consideration given to the type of suture among joining elements. S. roosevelti was compared with 109 gekkotan species to evaluate the osteological variation and to find characters for cladistic analysis. Changes in the skull associated with the miniaturization process are discussed within the sphaerodactylid geckos. A noticeable increase of overlapping sutures was observed in the snout of the smallest sphaerodactylids compared to other gekkotans. This pattern is convergent with that in miniaturized pygopodids and may be attributed to adaptations for decreasing mechanical resistance of the cranium during feeding or burrowing. New cranial characters support Sphaerodactylinae as a monophyletic group and should be useful for resolving questions such as their relationship with other gekkotans.

  11. [Identification of common medicinal snakes in medicated liquor of Guangdong by COI barcode sequence].

    Science.gov (United States)

    Liao, Jing; Chao, Zhi; Zhang, Liang

    2013-11-01

    To identify the common snakes in medicated liquor of Guangdong using COI barcode sequence,and to test the feasibility. The COI barcode sequences of collected medicinal snakes were amplified and sequenced. The sequences combined with the data from GenBank were analyzed for divergence and building a neighbor-joining(NJ) tree with MEGA 5.0. The genetic distance and NJ tree demonstrated that there were 241 variable sites in these species, and the average (A + T) content of 56.2% was higher than the average (G + C) content of 43.7%. The maximum interspecific genetic distance was 0.2568, and the minimum was 0. 1519. In the NJ tree,each species formed a monophyletic clade with bootstrap supports of 100%. DNA barcoding identification method based on the COI sequence is accurate and can be applied to identify the common medicinal snakes.

  12. Phylogenetic resolution within the Elephantidae using fossil DNA sequence from the American mastodon (Mammut americanum) as an outgroup.

    Science.gov (United States)

    Yang, H; Golenberg, E M; Shoshani, J

    1996-02-06

    DNA was extracted from the extinct American mastodon, the extinct woolly mammoth, and the modern Asian and African elephants to test the traditional morphologically based phylogeny within Elephantidae. Phylogenetic analyses of the aligned sequences of the mitochondrial gene cytochrome b support a monophyletic Asian elephant-woolly mammoth clade when the American mastodon is used as an outgroup. Previous molecular studies were unable to resolve the relationships of the woolly mammoth, Asian elephant, and African elephant because the sequences appear to have evolved at heterogeneous rates and inappropriate outgroups were used for analysis. The results demonstrate the usefulness of fossil molecular data from appropriate sister taxa for resolving phylogenies of highly derived or early radiating lineages.

  13. Phylogenetic analysis of European species of Proteocephalus (Cestoda: Proteocephalidea): compatibility of molecular and morphological data, and parasite-host coevolution.

    Science.gov (United States)

    Skeríková, A; Hypsa, V; Scholz, T V

    2001-08-01

    The phylogeny of European species of the tapeworm genus Proteocephalus was studied, based on partial 18S rDNA and morphological data. The group was found to be monophyletic. The analysis showed a low informative value of available morphological characters in comparison with molecular data. The morphological matrix resulted in a poorly resolved tree which is, however, compatible with the topology (Proteocephalus osculatus (Proteocephalus torulosus (Proteocephalus macrocephalus, Proteocephalus filicollis) (Proteocephalus tetrastomus, Proteocephalus percae, Proteocephalus longicollis))) based on the 18S rDNA data. A comparison performed by the program TreeMap showed a lack of significant congruency between parasite and host phylogenies. Therefore, the distribution of species in their hosts appears to be independent of the phylogeny and it is likely to be a result of host-switching, rather than co-speciation events.

  14. Population structure of Salmonella investigated by amplified fragment length polymorphism

    DEFF Research Database (Denmark)

    Torpdahl, M.; Ahrens, Peter

    2004-01-01

    Aims: This study was undertaken to investigate the usefulness of amplified fragment length polymorphism (AFLP) in determining the population structure of Salmonella. Methods and Results: A total of 89 strains were subjected to AFLP analysis using the enzymes BglII and BspDI, a combination......-based cluster analysis. The tree resulting from the subgroup analysis clearly separated all subgroups with high bootstrap values with the species S. bongori being the most distantly related of the subgroups. The tree resulting from the analysis of the SARB collection showed that some serotypes are very clonal...... whereas others are highly divergent. Conclusions: AFLP clearly clustered strains representing the subgroups of Salmonella together with high bootstrap values and the serotypes of subspecies enterica were divided into polyphyletic or monophyletic types corresponding well with multilocus enzyme...

  15. Identification of genes for sulfolipid synthesis in primitive red alga Cyanidioschyzon merolae.

    Science.gov (United States)

    Sato, Norihiro; Kobayashi, Satomi; Aoki, Motohide; Umemura, Tomonari; Kobayashi, Isao; Tsuzuki, Mikio

    2016-01-29

    Sulfoquinovosyl diacylglycerol is one of the lipids that construct thylakoid membranes, and is distributed from cyanobacteria to plastids in plants including a red lineage. One of the most primitive red algae, Cyanidioschyzon melorae, similar to cyanobacteria and green plants, possesses homologs of the SQD1 and SQD2 genes that code for UDP-sulfoquinovose and sulfoquinovosyl diacylglycerol synthases, respectively, for the synthesis of sulfoquinovosyl diacylglycerol. We here revealed the structural properties of SQD1 and SQD2 homologs in C. melorae intrinsic to those of the authentic proteins, and verified their enzymatic functions through heterologous expression in cyanobacterial disruptants as to the corresponding genes. The results demonstrated that the system of sulfoquinovosyl diacylglycerol synthesis could have been conserved through evolution of cyanobacteria to plastids in a red lineage, which is compatible with the monophyletic origin of plastids. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Taxonomy of the genus Passerina (Thymelaeaceae

    Directory of Open Access Journals (Sweden)

    C. L. Bredenkamp

    2003-12-01

    Full Text Available Passerina L. is mainly a southern African genus, comprising 20 species and four subspecies. A few species occur along the Great Escarpment, two extend into Zimbabwe and Mozambique, but most are concentrated in the Cape Floristic Region. Palynological. macromorphological and anatomical evidence was used in the delimitation of the genus and its infrageneric taxa. A cladistic study supports Passerina as a monophyletic genus. A genus treatment, key to species and a full species treatment are given. Each species treatment includes a taxonomic diagnosis, description and notes on taxonomy, etymology, economic value and distribution. Illustrations of representative species are provided and distribution maps are included for each species.  P. esterhuyseniae Bredenk. & A.E.van Wyk is newly described. A list of excluded species names highlights the previous cosmopolitan taxonomic interpretation of Passerina. as many names are now in synony my under other genera of the Thymelaeaceae.

  17. Complex archaea that bridge the gap between prokaryotes and eukaryotes.

    Science.gov (United States)

    Spang, Anja; Saw, Jimmy H; Jørgensen, Steffen L; Zaremba-Niedzwiedzka, Katarzyna; Martijn, Joran; Lind, Anders E; van Eijk, Roel; Schleper, Christa; Guy, Lionel; Ettema, Thijs J G

    2015-05-14

    The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.

  18. Evolutionary and structural diversity of fungal laccases.

    Science.gov (United States)

    Valderrama, Brenda; Oliver, Patricia; Medrano-Soto, Arturo; Vazquez-Duhalt, Rafael

    2003-01-01

    Fungal laccases have been extensively exploited for industrial purposes and there is a wealth of information available regarding their reaction mechanism, biological role and several molecular aspects, including cloning, heterologous expression and transcriptional analyses. Here we present the reconstruction of the fungal laccase loci evolution inferred from the comparative analysis of 48 different sequences. The topology of the phylogenetic trees indicate that a single monophyletic branch exists for fungal laccases and that laccase isozyme genes may have evolved independently, possibly through duplication-divergence events. Laccases are copper-containing enzymes generally identified by the utilization of substituted p-diphenol substrates. Interestingly, our approach permitted the assignment of two copper-containing oxidases, preliminarily catalogued as laccases, to a different evolutionary group, distantly related to the main branch of bona fide laccases.

  19. A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation.

    Science.gov (United States)

    Mullins, Patricia L; Kawada, Ricardo; Balhoff, James P; Deans, Andrew R

    2012-01-01

    The Neotropical evaniid genus Evaniscus Szépligeti currently includes six species. Two new species are described, Evaniscus lansdownei Mullins, sp. n. from Colombia and Brazil and Evaniscus rafaeli Kawada, sp. n. from Brazil. Evaniscus sulcigenis Roman, syn. n., is synonymized under Evaniscus rufithorax Enderlein. An identification key to species of Evaniscus is provided. Thirty-five parsimony informative morphological characters are analyzed for six ingroup and four outgroup taxa. A topology resulting in a monophyletic Evaniscus is presented with Evaniscus tibialis and Evaniscus rafaeli as sister to the remaining Evaniscus species. The Hymenoptera Anatomy Ontology and other relevant biomedical ontologies are employed to create semantic phenotype statements in Entity-Quality (EQ) format for species descriptions. This approach is an early effort to formalize species descriptions and to make descriptive data available to other domains.

  20. Description of the mitochondrial genome of the tree coral Dendrophyllia arbuscula (Anthozoa, Scleractinia).

    Science.gov (United States)

    Luz, Bruna Louise Pereira; Capel, Kátia Cristina Cruz; Stampar, Sérgio Nascimento; Kitahara, Marcelo Visentini

    2016-07-01

    Dendrophylliidae is one of the few monophyletic families within the Scleractinia that embraces zooxanthellate and azooxanthellate species represented by both solitary and colonial forms. Among the exclusively azooxanthellate genera, Dendrophyllia is reported worldwide from 1 to 1200 m deep. To date, although three complete mitochondrial (mt) genomes from representatives of the family are available, only that from Turbinaria peltata has been formally published. Here we describe the complete nucleotide sequence of the mt genome from Dendrophyllia arbuscula that is 19 069 bp in length and comprises two rDNAs, two tRNAs, and 13 protein-coding genes arranged in the canonical scleractinian mt gene order. No genes overlap, resulting in the presence of 18 intergenic spacers and one of the longest scleractinian mt genome sequenced to date.

  1. Isolation and characterization of a new fungal genus and species, Aphanoascella galapagosensis, from carapace keratitis of a Galapagos tortoise (Chelonoidis nigra microphyes).

    Science.gov (United States)

    Sutton, D A; Marín, Y; Thompson, E H; Wickes, B L; Fu, J; García, D; Swinford, A; de Maar, T; Guarro, J

    2013-02-01

    A new fungal genus and species, Aphanoascella galapagosensis, recovered from carapace keratitis in a Galapagos tortoise residing in a south Texas zoological collection, is characterized and described. The presence of a pale peridium composed of textura epidermoidea surrounded by scarce Hülle cell-like chlamydospores, and the characteristic reticulate ascospores with an equatorial rim separates it from other genera within the Onygenales. The phylogenetic tree inferred from the analysis of D1/D2 sequences demonstrates that this fungus represents a new lineage within that order. As D1/D2 and ITS sequence data also shows a further separation of Aphanoascus spp. into two monophyletic groups, we propose to retain the generic name Keratinophyton for species whose ascospores are pitted and display a conspicuous equatorial rim, and thereby propose new combinations in this genus for four Aphanoascus species.

  2. A Jurassic stem pleurodire sheds light on the functional origin of neck retraction in turtles

    Science.gov (United States)

    Anquetin, Jérémy; Tong, Haiyan; Claude, Julien

    2017-01-01

    Modern turtles are composed of two monophyletic groups, notably diagnosed by divergent neck retraction mechanisms. Pleurodires (side-necked turtles) bend their neck sideways and protect their head under the anterior margin of the carapace. Cryptodires (hidden-necked turtles) withdraw their neck and head in the vertical plane between the shoulder girdles. These two mechanisms of neck retraction appeared independently in the two lineages and are usually assumed to have evolved for protective reasons. Here we describe the neck of Platychelys oberndorferi, a Late Jurassic early stem pleurodire, and find remarkable convergent morphological and functional similarities with modern cryptodires. Partial vertical neck retraction in this taxon is interpreted to have enabled fast forward projection of the head during underwater prey capture and offers a likely explanation to the functional origin of neck retraction in modern cryptodires. Complete head withdrawal for protection may therefore have resulted from an exaptation in that group. PMID:28206991

  3. Phylogeny and species differentiation of Mollitrichosiphum spp.(Aphididae, Greenideinae) based on mitochondrial COI and Cyt b genes

    Institute of Scientific and Technical Information of China (English)

    Ruiling ZHANG; Xiaolei HUANG; Liyun JIANG; Gexia QIAO

    2011-01-01

    Phylogenetic analyses based on mitochondrial genes were conducted to reconstruct species relationships within the aphid genus Mollitrichosiphum (Aphididae,Greenideinae).MP and Bayesian analysis results using COI and Cyt b datasets,and combined MP,ML and Bayesian analysis of both were consistent with a morphologically supported monophyly.Subdivision of the genus into two subgenera was strongly supported.Samples of each included species form monophyletic clade,respectively;and the result implied the valid status of related species in this genus.These results suggest some surprising hypotheses regarding the phylogeography of the genus:the uplift of the Tibetan Plateau,reorganization of major river catchments and the isolation of Hainan Island were probably important factors contributing to the diversification of species in this genus [Current Zoology 57 (6):806-815,2011].

  4. Phylogenetics of the Phlebotomine Sand Fly Group Verrucarum (Diptera: Psychodidae: Lutzomyia)

    Science.gov (United States)

    Cohnstaedt, Lee W.; Beati, Lorenza; Caceres, Abraham G.; Ferro, Cristina; Munstermann, Leonard E.

    2011-01-01

    Within the sand fly genus Lutzomyia, the Verrucarum species group contains several of the principal vectors of American cutaneous leishmaniasis and human bartonellosis in the Andean region of South America. The group encompasses 40 species for which the taxonomic status, phylogenetic relationships, and role of each species in disease transmission remain unresolved. Mitochondrial cytochrome c oxidase I (COI) phylogenetic analysis of a 667-bp fragment supported the morphological classification of the Verrucarum group into series. Genetic sequences from seven species were grouped in well-supported monophyletic lineages. Four species, however, clustered in two paraphyletic lineages that indicate conspecificity—the Lutzomyia longiflocosa–Lutzomyia sauroida pair and the Lutzomyia quasitownsendi–Lutzomyia torvida pair. COI sequences were also evaluated as a taxonomic tool based on interspecific genetic variability within the Verrucarum group and the intraspecific variability of one of its members, Lutzomyia verrucarum, across its known distribution. PMID:21633028

  5. Phylogenetic analysis of the sharpshooter genus Subrasaca Young, 1977 (Hemiptera, Cicadellidae, Cicadellini

    Directory of Open Access Journals (Sweden)

    Roberta dos Santos da Silva

    2015-02-01

    Full Text Available The South American sharpshooter genus Subrasaca comprises 14 species. Some species of this genus are quite common in the Brazilian Atlantic Rainforest. In this paper, a phylogenetic analysis of Subrasaca, based on a matrix of 20 terminal taxa and 72 morphological characters of the head, thorax, and male and female genitalia, is presented. The analysis yielded six equally most parsimonious trees (197 steps, CI = 0.6091, RI = 0.5722, and RC = 0.3486. The results suggest that Subrasaca is a monophyletic taxon, although the genus branch is not robust. The clade showing the highest bootstrap and Bremer scores is formed by species with longitudinal dark brown to black stripes on the forewings (S. bimaculata, S. constricta, S. curvovittata, and S. flavolineata, followed by S. atronasa + S. austera.

  6. Complete mitochondrial genome of Drabescoides nuchalis (Hemiptera: Cicadellidae).

    Science.gov (United States)

    Wu, Yunfei; Dai, Renhuai; Zhan, Hongping; Qu, Ling

    2016-09-01

    The complete mitochondrial genome (mitogenome) of Drabescoides nuchalis (Hemiptera: Cicadellidae) was sequenced. It is 15 309 bp in length with 75.62% (A + T) content and comprises 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNA genes, and a non-coding region (GenBank accession no. KR349344). Gene order is identical to that of the inferred ancestral insect genome. All PCGs start with an ATN codon and terminate with TAA except ND4, which has an incomplete stop codon (T). The anticodons are identical to those of Drosophila yakuba. The phylogenetic tree confirms D. nuchalis and two Cicadellidae species are clustered into a clade, and Cicadellidae is a monophyletic group and provides support for the sister relationship of leafhopper and treehopper.

  7. Carnivorans at the Great American Biotic Interchange: new discoveries from the northern neotropics.

    Science.gov (United States)

    Forasiepi, Analia M; Soibelzon, Leopoldo H; Gomez, Catalina Suarez; Sánchez, Rodolfo; Quiroz, Luis I; Jaramillo, Carlos; Sánchez-Villagra, Marcelo R

    2014-11-01

    We report two fossil procyonids, Cyonasua sp. and Chapalmalania sp., from the late Pliocene of Venezuela (Vergel Member, San Gregorio Formation) and Colombia (Ware Formation), respectively. The occurrence of these pre-Holocene procyonids outside Argentina and in the north of South America provides further information about the Great American Biotic Interchange (GABI). The new specimens are recognized in the same monophyletic group as procyonids found in the southern part of the continent, the "Cyonasua group," formed by species of Cyonasua and Chapalmalania. The phylogenetic analysis that includes the two new findings support the view that procyonids dispersed from North America in two separate events (initially, previous to the first major migration wave-GABI 1-and then within the last major migration wave-GABI 4-). This involved reciprocal lineage migrations from North to South America, and included the evolution of South American endemic forms.

  8. PhySortR: a fast, flexible tool for sorting phylogenetic trees in R

    Directory of Open Access Journals (Sweden)

    Timothy G. Stephens

    2016-05-01

    Full Text Available A frequent bottleneck in interpreting phylogenomic output is the need to screen often thousands of trees for features of interest, particularly robust clades of specific taxa, as evidence of monophyletic relationship and/or reticulated evolution. Here we present PhySortR, a fast, flexible R package for classifying phylogenetic trees. Unlike existing utilities, PhySortR allows for identification of both exclusive and non-exclusive clades uniting the target taxa based on tip labels (i.e., leaves on a tree, with customisable options to assess clades within the context of the whole tree. Using simulated and empirical datasets, we demonstrate the potential and scalability of PhySortR in analysis of thousands of phylogenetic trees without a priori assumption of tree-rooting, and in yielding readily interpretable trees that unambiguously satisfy the query. PhySortR is a command-line tool that is freely available and easily automatable.

  9. Mitochondrial genome organization and vertebrate phylogenetics

    Directory of Open Access Journals (Sweden)

    Pereira Sérgio Luiz

    2000-01-01

    Full Text Available With the advent of DNA sequencing techniques the organization of the vertebrate mitochondrial genome shows variation between higher taxonomic levels. The most conserved gene order is found in placental mammals, turtles, fishes, some lizards and Xenopus. Birds, other species of lizards, crocodilians, marsupial mammals, snakes, tuatara, lamprey, and some other amphibians and one species of fish have gene orders that are less conserved. The most probable mechanism for new gene rearrangements seems to be tandem duplication and multiple deletion events, always associated with tRNA sequences. Some new rearrangements seem to be typical of monophyletic groups and the use of data from these groups may be useful for answering phylogenetic questions involving vertebrate higher taxonomic levels. Other features such as the secondary structure of tRNA, and the start and stop codons of protein-coding genes may also be useful in comparisons of vertebrate mitochondrial genomes.

  10. New Calisto species from Cuba, with insights on the relationships of Cuban and Bahamian taxa (Lepidoptera, Nymphalidae, Satyrinae).

    Science.gov (United States)

    Núnez Aguila, Rayner; Matos-Maraví, Pável F; Wahlberg, Niklas

    2013-01-01

    Three new species and a new subspecies of Calisto Hübner are described from Cuba, Calisto torrei sp. n. Núñez, Calisto dissimulatum sp. n. Núñez, Calisto aquilum sp. n. Núñez, and Calisto aquilum occidentalis ssp. n. Núñez. The immature stages of C. torrei and C. dissimulatum are also described. Notes on the distribution and biology of the species are given. All Cuban and Bahamian taxa form a monophyletic group which seems to have originated in northeastern Cuba spreading later to the west. DNA sequence data also allowed to recognize both Bahamian taxa, Calisto sibylla and Calisto apollinis stat. n., as distinct species, and to synonymize Calisto herophile parsonsi syn. n. under Calisto herophile.

  11. Osteological evidence for sister group relationship between pseudo-toothed birds (Aves: Odontopterygiformes) and waterfowls (Anseriformes)

    Science.gov (United States)

    Bourdon, Estelle

    2005-12-01

    The phylogenetic affinities of the extinct pseudo-toothed birds have remained controversial. Some authors noted that they resemble both pelicans and allies (Pelecaniformes) and tube-nosed birds (Procellariiformes), but assigned them to a distinct taxon, the Odontopterygiformes. In most recent studies, the pseudo-toothed birds are referred to the family Pelagornithidae inside the Pelecaniformes. Here, I perform a cladistic analysis with five taxa of the pseudo-toothed birds including two undescribed new species from the Early Tertiary of Morocco. The present hypothesis strongly supports a sister group relationship of pseudo-toothed birds (Odontopterygiformes) and waterfowls (Anseriformes). The Odontoanserae (Odontopterygiformes plus Anseriformes) are the sister group of Neoaves. The placement of the landfowls (Galliformes) as the sister taxon of all other neognathous birds does not support the consensus view that the Galloanserae (Galliformes plus Anseriformes) are monophyletic.

  12. The domestication of the probiotic bacterium Lactobacillus acidophilus.

    Science.gov (United States)

    Bull, Matthew J; Jolley, Keith A; Bray, James E; Aerts, Maarten; Vandamme, Peter; Maiden, Martin C J; Marchesi, Julian R; Mahenthiralingam, Eshwar

    2014-11-26

    Lactobacillus acidophilus is a Gram-positive lactic acid bacterium that has had widespread historical use in the dairy industry and more recently as a probiotic. Although L. acidophilus has been designated as safe for human consumption, increasing commercial regulation and clinical demands for probiotic validation has resulted in a need to understand its genetic diversity. By drawing on large, well-characterised collections of lactic acid bacteria, we examined L. acidophilus isolates spanning 92 years and including multiple strains in current commercial use. Analysis of the whole genome sequence data set (34 isolate genomes) demonstrated L. acidophilus was a low diversity, monophyletic species with commercial isolates essentially identical at the sequence level. Our results indicate that commercial use has domesticated L. acidophilus with genetically stable, invariant strains being consumed globally by the human population.

  13. Molecular systematics of higher primates: genealogical relations and classification.

    Science.gov (United States)

    Miyamoto, M M; Koop, B F; Slightom, J L; Goodman, M; Tennant, M R

    1988-01-01

    We obtained 5' and 3' flanking sequences (5.4 kilobase pairs) from the psi eta-globin gene region of the rhesus macaque (Macaca mulatta) and combined them with available nucleotide data. The completed sequence, representing 10.8 kilobase pairs of contiguous noncoding DNA, was compared to the same orthologous regions available for human (Homo sapiens, as represented by five different alleles), common chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), and orangutan (Pongo pygmaeus). The nucleotide sequence for Macaca mulatta provided the outgroup perspective needed to evaluate better the relationships of humans and great apes. Pairwise comparisons and parsimony analysis of these orthologues clearly demonstrated (i) that humans and great apes share a high degree of genetic similarity and (ii) that humans, chimpanzees, and gorillas form a natural monophyletic group. These conclusions strongly favor a genealogical classification for higher primates consisting of a single family (Hominidae) with two subfamilies (Homininae for Homo, Pan, and Gorilla and Ponginae for Pongo). PMID:3174657

  14. Phylogenetic relations between microbats, megabats and primates (Mammalia: Chiroptera and Primates).

    Science.gov (United States)

    Pettigrew, J D; Jamieson, B G; Robson, S K; Hall, L S; McAnally, K I; Cooper, H M

    1989-11-30

    We examine the paraphylectic hypothesis of bat origins, both in the light of previous discussions, and in the light of new evidence from our analyses of neurological traits and wing morphology. Megabats share with primates a variety of complex details in the organization of neural pathways that have not been found in any other mammalian group, particularly not in microbats. The features previously used to link microbats and megabats have been examined and found to be questionable bases for support of a monophyletic origin. In particular, morphological analyses of the musculoskeletal adaptations associated with the flight apparatus are consistent with two separate origins of the mammalian wing. Taken together, these analyses suggest that megabats evolved from an early branch of the primate lineage. This branch was comprised of moderate-sized, phytophagous gliders, of which the other living descendants are the dermopterans. Microbats, in contrast, probably evolved much earlier from small, agile insectivores whose forelimbs had long metacarpals in relation to their phalanges.

  15. Encephalization, adaptation and evolution of chiroptera: A statistical analysis with further evidence for bat monophyly.

    Science.gov (United States)

    Lapointe, F; Baron, G; Legendre, P

    1999-08-01

    As part of a large-scale study on brain morphometrics and adaptations in mammals, we addressed the problem of chiropteran evolution. A specific statistical framework was designed to test which of two competing hypotheses (bat monophyly vs. diphyly) is more strongly supported by quantitative brain data. Our analyses, based on 120 species, revealed that megabats and microbats were more closely related to each other than to primates, and illustrated the convergent adaptations of the brain of bats to similar trophic (i.e. feeding related) niches. Ecologically-corrected characters were then used to derive a new phylogeny which also supports the chiropteran clade. The monophyletic origin of bats is the preferred hypothesis to explain brain quantitative evolution in chiropterans and primates.

  16. Two new species of Euptychia Hübner, 1818 from the upper Amazon basin (Lepidoptera, Nymphalidae, Satyrinae)

    Science.gov (United States)

    Neild, Andrew F. E.; Nakahara, Shinichi; Zacca, Thamara; Fratello, Steven; Lamas, Gerardo; Le Crom, Jean-François; Dolibaina, Diego R.; Dias, Fernando M. S.; Casagrande, Mirna M.; Mielke, Olaf H. H.; Espeland, Marianne

    2015-01-01

    Abstract Two new species of Euptychia Hübner, 1818 are described from the upper Amazon basin: Euptychia attenboroughi Neild, Nakahara, Fratello & Le Crom, sp. n. (type locality: Amazonas, Venezuela), and Euptychia sophiae Zacca, Nakahara, Dolibaina & Dias, sp. n. (type locality: Acre, Brazil). Their unusual facies prompted molecular and phylogenetic analyses of one of the species resulting in support for their classification in monophyletic Euptychia. Diagnostic characters for the two species are presented based on wing morphology, wing pattern, presence of androconial patches on the hindwing, and genitalia. Our results indicate that the projection of the tegumen above the uncus, previously considered a synapomorphy for Euptychia, is not shared by all species in the genus. The adults and their genitalia are documented, and distribution data and a map are provided. PMID:26798283

  17. Morphological, physiological and molecular genetic characterization ofArabidopsis himalaica, with reference toA. thaliana.

    Science.gov (United States)

    Tsukaya, H; Yokoyama, J; Ikeda, H; Kuroiwa, H; Kuroiwa, T; Iwatsuki, K

    1997-03-01

    Arabidopsis himalaica (Edgeworth) O.E. Schulz, a poorly characterized species typical of HimalayanArabidopsis, was analyzed in terms of its morphology, physiology, chromosome number and molecular genetics, in comparison withA. thaliana which is the standard species in the genusArabidopsis. From view point of developmental genetics, several features which are specific toA. himalaica seem not to be derived by single-gene mutations inA. thaliana. Phylogenetic analyses based onrbcL sequences suggested that genusArabidopsis is not monophyletic. The detailed characterization ofA. himalaica should provide clues to understand the trait of evolution of particular features of Himalayan species ofArabidopsis and their genetic basis.

  18. Evolutionary position of Peruvian land snails (Orthalicidae among Stylommatophora (Mollusca: Gastropoda

    Directory of Open Access Journals (Sweden)

    Jorge Ramirez

    2011-07-01

    Full Text Available The genera Bostryx and Scutalus (Orthalicidae: Bulimulinae are endemics from South America. They are mainly distributed on the western slopes of the Peruvian Andes. The goal of the present work was to assess their evolutionary position among the stylommatophoran gastropods based on the 16S rRNA mitochondrial marker. Four sequences were obtained, and along with 28 sequences of other Stylommatophora retrieved from the GenBank, were aligned with ClustalX. The phylogenetic reconstruction was carried out using the methods of Neighbor-Joining, Maximum Parsimony, Maximum Likelihood and Bayesian inference. The multiple sequence alignment had 371 sites, with indels. The two genera of the family Orthalicidae for the first time included in a molecular phylogeny (Bostryx and Scutalus, formed a monophyletic group along with another member of the superfamily Orthalicoidea (Placostylus, result that is comparable with that obtained with nuclear markers. Their evolutionary relationship with other land snails is also discussed.

  19. Isolated and synergistic effects of chemical and structural defenses of two species of Tethya (Porifera: Demospongiae)

    Science.gov (United States)

    Ribeiro, Suzi Meneses; Cassiano, Keila Mara; Cavalcanti, Diana Negrão; Teixeira, Valéria Laneuville; Pereira, Renato Crespo

    2012-02-01

    Sponges are an important source of many interesting secondary metabolites with multiple ecological roles. Sponges can also use their spicules as a means of deterring consumers. The present study investigated the importance of chemicals and spicules as defensive strategies against predation for two congeneric sponge species from the Brazilian coast, Tethya rubra and Tethya maza. Crude extract and spicules differed somewhat in their effectiveness between these sponge species, with T. maza better defended than T. rubra against predation by the hermit crab Calcinus tibicen and synergistic effects stronger in T. rubra. These results show that defensive strategies may be similar between sponge species possessing monophyletic origin, and reveal the importance of research on congeneric species to understand the ecology and evolution of defensive strategies.

  20. Non-monophyly of most supraspecific taxa of calcareous sponges (Porifera, Calcarea) revealed by increased taxon sampling and partitioned Bayesian analysis of ribosomal DNA.

    Science.gov (United States)

    Dohrmann, Martin; Voigt, Oliver; Erpenbeck, Dirk; Wörheide, Gert

    2006-09-01

    Calcareous sponges (Porifera, Calcarea) play an important role for our understanding of early metazoan evolution, since several molecular studies suggested their closer relationship to Eumetazoa than to the other two sponge 'classes,' Demospongiae and Hexactinellida. The division of Calcarea into the subtaxa Calcinea and Calcaronea is well established by now, but their internal relationships remain largely unresolved. Here, we estimate phylogenetic relationships within Calcarea in a Bayesian framework, using full-length 18S and partial 28S ribosomal DNA sequences. Both genes were analyzed separately and in combination and were further partitioned by stem and loop regions, the former being modelled to take non-independence of paired sites into account. By substantially increasing taxon sampling, we show that most of the traditionally recognized supraspecific taxa within Calcinea and Calcaronea are not monophyletic, challenging the existing classification system, while monophyly of Calcinea and Calcaronea is again highly supported.

  1. Erwinia mallotivora sp., a new pathogen of papaya (Carica papaya) in Peninsular Malaysia.

    Science.gov (United States)

    Amin, Noriha Mat; Bunawan, Hamidun; Redzuan, Rohaiza Ahmad; Jaganath, Indu Bala S

    2010-12-24

    Erwinia mallotivora was isolated from papaya infected with dieback disease showing the typical symptoms of greasy, water-soaked lesions and spots on leaves. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain belonged to the genus Erwinia and was united in a monophyletic group with E. mallotivora DSM 4565 (AJ233414). Earlier studies had indicated that the causal agent for this disease was E. papayae. However, our current studies, through Koch's postulate, have confirmed that papaya dieback disease is caused by E. mallotivora. To our knowledge, this is the first new discovery of E. mallotivora as a causal agent of papaya dieback disease in Peninsular Malaysia. Previous reports have suggested that E. mallotivora causes leaf spot in Mallotus japonicus. However, this research confirms it also to be pathogenic to Carica papaya.

  2. Erwinia mallotivora sp., a New Pathogen of Papaya (Carica papaya in Peninsular Malaysia

    Directory of Open Access Journals (Sweden)

    Noriha Mat Amin

    2010-12-01

    Full Text Available Erwinia mallotivora was isolated from papaya infected with dieback disease showing the typical symptoms of greasy, water-soaked lesions and spots on leaves. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain belonged to the genus Erwinia and was united in a monophyletic group with E. mallotivora DSM 4565 (AJ233414. Earlier studies had indicated that the causal agent for this disease was E. papayae. However, our current studies, through Koch’s postulate, have confirmed that papaya dieback disease is caused by E. mallotivora. To our knowledge, this is the first new discovery of E. mallotivora as a causal agent of papaya dieback disease in Peninsular Malaysia. Previous reports have suggested that E. mallotivora causes leaf spot in Mallotus japonicus. However, this research confirms it also to be pathogenic to Carica papaya.

  3. Pachyseris inattesa sp. n. (Cnidaria, Anthozoa, Scleractinia): a new reef coral species from the Red Sea and its phylogenetic relationships

    Science.gov (United States)

    Terraneo, Tullia I.; Berumen, Michael L.; Arrigoni, Roberto; Waheed, Zarinah; Bouwmeester, Jessica; Caragnano, Annalisa; Stefani, Fabrizio; Benzoni, Francesca

    2014-01-01

    Abstract A new scleractinian coral species, Pachyseris inattesa sp. n., is described from the Red Sea. Despite a superficial resemblance with some species in the agariciid genus Leptoseris with which it has been previously confused, P. inattesa sp. n. has micro-morphological characters typical of the genus Pachyseris. This genus, once part of the Agariciidae, is comprised of five extant species and is widely distributed throughout the tropical Indo-Pacific. It is currently incertae sedis as a result of recent molecular analysis and appears to be closely related to the Euphylliidae. A molecular phylogenetic reconstruction including P. inattesa sp. n., the genus type species P. rugosa, and P. speciosa, all present in the Red Sea, was performed using the mitochondrial intergenic spacer between COI and 16S-rRNA. The results confirm that P. inattesa sp. n. is a monophyletic lineage closely related to the other Pachyseris species examined. PMID:25152672

  4. Phylogenetic affinity of tree shrews to Glires is attributed to fast evolution rate.

    Science.gov (United States)

    Lin, Jiannan; Chen, Guangfeng; Gu, Liang; Shen, Yuefeng; Zheng, Meizhu; Zheng, Weisheng; Hu, Xinjie; Zhang, Xiaobai; Qiu, Yu; Liu, Xiaoqing; Jiang, Cizhong

    2014-02-01

    Previous phylogenetic analyses have led to incongruent evolutionary relationships between tree shrews and other suborders of Euarchontoglires. What caused the incongruence remains elusive. In this study, we identified 6845 orthologous genes between seventeen placental mammals. Tree shrews and Primates were monophyletic in the phylogenetic trees derived from the first or/and second codon positions whereas tree shrews and Glires formed a monophyly in the trees derived from the third or all codon positions. The same topology was obtained in the phylogeny inference using the slowly and fast evolving genes, respectively. This incongruence was likely attributed to the fast substitution rate in tree shrews and Glires. Notably, sequence GC content only was not informative to resolve the controversial phylogenetic relationships between tree shrews, Glires, and Primates. Finally, estimation in the confidence of the tree selection strongly supported the phylogenetic affiliation of tree shrews to Primates as a monophyly.

  5. Adaptation to thermotolerance in Rhizopus coincides with virulence as revealed by avian and invertebrate infection models, phylogeny, physiological and metabolic flexibility.

    Science.gov (United States)

    Kaerger, Kerstin; Schwartze, Volker U; Dolatabadi, Somayeh; Nyilasi, Ildikó; Kovács, Stella A; Binder, Ulrike; Papp, Tamás; Hoog, Sybren de; Jacobsen, Ilse D; Voigt, Kerstin

    2015-01-01

    Mucormycoses are fungal infections caused by the ancient Mucorales. They are rare, but increasingly reported. Predisposing conditions supporting and favoring mucormycoses in humans and animals include diabetic ketoacidosis, immunosuppression and haematological malignancies. However, comprehensive surveys to elucidate fungal virulence in ancient fungi are limited and so far focused on Lichtheimia and Mucor. The presented study focused on one of the most important causative agent of mucormycoses, the genus Rhizopus (Rhizopodaceae). All known clinically-relevant species are thermotolerant and are monophyletic. They are more virulent compared to non-clinically, mesophilic species. Although adaptation to elevated temperatures correlated with the virulence of the species, mesophilic strains showed also lower virulence in Galleria mellonella incubated at permissive temperatures indicating the existence of additional factors involved in the pathogenesis of clinical Rhizopus species. However, neither specific adaptation to nutritional requirements nor stress resistance correlated with virulence, supporting the idea that Mucorales are predominantly saprotrophs without a specific adaptation to warm blooded hosts.

  6. Toxoplasma gondii aspartic protease 1 is not essential in tachyzoites.

    Science.gov (United States)

    Polonais, Valerie; Shea, Michael; Soldati-Favre, Dominique

    2011-08-01

    Aspartic proteases are important virulence factors for pathogens and are recognized as attractive drug targets. Seven aspartic proteases (ASPs) have been identified in Toxoplasma gondii genome. Bioinformatics and phylogenetic analyses regroup them into five monophyletic groups. Among them, TgASP1, a coccidian specific aspartic protease related to the food vacuole plasmepsins, is associated with the secretory pathway in non-dividing cells and relocalizes in close proximity to the nascent inner membrane complex (IMC) of daughter cells during replication. Despite a potential role for TgASP1 in IMC formation, the generation of a conventional knockout of the TgASP1 gene revealed that this protease is not required for T. gondii tachyzoite survival or for proper IMC biogenesis.

  7. Genomic Evolution of the Ascomycete Yeasts

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Robert; Haridas, Sajeet; Salamov, Asaf; Boundy-Mills, Kyria; Goker, Markus; Hittinger, Chris; Klenk, Hans-Peter; Lopes, Mariana; Meir-Kolthoff, Jan P.; Rokas, Antonis; Rosa, Carlos; Scheuner, Carmen; Soares, Marco; Stielow, Benjamin; Wisecaver, Jennifer H.; Wolfe, Ken; Blackwell, Meredith; Kurtzman, Cletus; Grigoriev, Igor; Jeffries, Thomas

    2015-03-16

    Yeasts are important for industrial and biotechnological processes and show remarkable metabolic and phylogenetic diversity despite morphological similarities. We have sequenced the genomes of 16 ascomycete yeasts of taxonomic and industrial importance including members of Saccharomycotina and Taphrinomycotina. Phylogenetic analysis of these and previously published yeast genomes helped resolve the placement of species including Saitoella complicata, Babjeviella inositovora, Hyphopichia burtonii, and Metschnikowia bicuspidata. Moreover, we find that alternative nuclear codon usage, where CUG encodes serine instead of leucine, are monophyletic within the Saccharomycotina. Most of the yeasts have compact genomes with a large fraction of single exon genes, and a tendency towards more introns in early-diverging species. Analysis of enzyme phylogeny gives insights into the evolution of metabolic capabilities such as methanol utilization and assimilation of alternative carbon sources.

  8. Farming termites determine the genetic population structure of Termitomyces fungal symbionts

    DEFF Research Database (Denmark)

    Nobre, Tânia; Fernandes, Cecília; Boomsma, Jacobus J

    2011-01-01

    fungal symbionts. However, even in the few termite lineages that secondarily adopted vertical symbiont transmission, the fungal symbionts are not monophyletic. We addressed this paradox by studying differential transmission of fungal symbionts by alate male and female reproductives, and the genetic......Symbiotic interactions between macrotermitine termites and their fungal symbionts have a moderate degree of specificity. Consistent with horizontal symbiont transmission, host switching has been frequent over evolutionary time so that single termite species can often be associated with several...... associated with the alternative termite hosts Macrotermes subhyalinus and Macrotermes natalensis. While Termitomyces associated with these alternative hosts are horizontally transmitted and recombine freely, the genetic population structure of the same Termitomyces associated with M. bellicosus is consistent...

  9. A taxonomic framework for cable bacteria and proposal of the candidate genera Electrothrix and Electronema

    DEFF Research Database (Denmark)

    Trojan, Daniela; Schreiber, Lars; Bjerg, Jesper Tataru;

    2016-01-01

    Cable bacteria are long, multicellular filaments that can conduct electric currents over centimeter-scale distances. All cable bacteria identified to date belong to the deltaproteobacterial family Desulfobulbaceae and have not been isolated in pure culture yet. Their taxonomic delineation and exact......RNA gene sequences of 16 individual cable bacteria filaments from freshwater, salt marsh, and marine sites of four geographic locations are presented. These sequences formed a distinct, monophyletic sister clade to the genus Desulfobulbus and could be divided into six coherent, species-level clusters......, arranged as two genus-level groups. The same grouping was retrieved by phylogenetic analysis of full or partial dsrAB genes encoding the dissimilatory sulfite reductase. Based on these results, it is proposed to accommodate cable bacteria within two novel candidate genera: the mostly marine “Candidatus...

  10. Frequent mitochondrial gene rearrangements at the hymenopteran nad3-nad5 junction.

    Science.gov (United States)

    Dowton, Mark; Castro, Lyda R; Campbell, Sarah L; Bargon, Sharmilla D; Austin, Andrew D

    2003-05-01

    We characterized the organization of mitochondrial genes from a diverse range of hymenopterans. Of the 21 taxa characterized, 12 had distinct, derived organizations. Some rearrangements were consistent with the duplication-random loss mechanism, while others were not. Local inversions were relatively common, i.e., rearrangements characterized by the movement of genes from one mitochondrial strand to the other, opposite or close to their ancestral position. This type of rearrangement is inconsistent with the duplication/random loss model of mitochondrial gene rearrangement. Instead, they are best explained by the operation of recombination. Taxa with derived organizations were restricted to a single, monophyletic group of wasps, the Apocrita, which comprise about 90% of all hymenopterans.

  11. Systematics, evolution, and biology of scelionid and platygastrid wasps.

    Science.gov (United States)

    Austin, A D; Johnson, N F; Dowton, M

    2005-01-01

    The Platygastroidea comprises two families of parasitoids, Scelionidae and Platygastridae, and nearly 4500 described species. They parasitize a diverse array of insects as well as spiders. Idiobiont endoparasitism of eggs is the putative ground plan biology, as reflected by all scelionids, but most Platygastridae are koinobiont endoparasitoids of immature Auchenorrhyncha, Sternorrhyncha, and Cecidomyiidae. The superfamily is demonstrably monophyletic but its phylogenetic position remains uncertain. Relationships within the Platygastroidea are also poorly known and the group is in need of comprehensive phylogenetic study. Significant information is available on host relationships and biology, although much of this is biased to a few genera of Telenominae that are employed as biocontrol agents. Hosts for many genera are unknown, in particular those that inhabit leaf litter or parasitize solitary host eggs. The Trissolcus basalis-Nezara viridula parasitoid-host association has become a favored model system in ecological, behavioral, and physiological research on insects.

  12. First cytogenetic analysis of Ichthyoelephas humeralis (Günther, 1860) by conventional and molecular methods with comments on the karyotypic evolution in Prochilodontidae

    Science.gov (United States)

    Tursellino, Mauro Nirchio; Silva, Duílio Mazzoni Zerbinato de Andrade; Abad, César Quezada; Blacio, Wilmer Arnoldo Moreira; Romero, Omar Rogerio Sánchez; Oliveira, Claudio

    2016-01-01

    Abstract We used conventional cytogenetic techniques (Giemsa, C-banding, Ag-NOR), and fluorescent in situ hybridization (FISH) with 5S and 18S rDNA probes to investigate the karyotype and cytogenetic characteristics of Ichthyoelephas humeralis (Günther, 1860) from Ecuador. The specimens studied have a karyotype with 2n=54 biarmed chromosomes (32 M + 22 SM) and C-positive heterochromatin located on the centromeric, pericentromeric, interstitial, and terminal regions of some chromosomes. The nucleolus organizer regions occurred terminally on the long arm of chromosome pair 2. FISH confirmed the presence of only one 18S rDNA cluster with nonsyntenic localization with the 5S rDNA. Cytogenetic data allow us to refute the earlier morphological hypothesis of a sister relationship between Semaprochilodus Fowler, 1941 and Ichthyoelephas Posada Arango, 1909 and support the molecular proposal that Ichthyoelephas is a sister group to the monophyletic clade containing Prochilodus Agassiz, 1829 and Semaprochilodus. PMID:28123682

  13. Ecological genetics and evolution of the Large Blue butterfly – consequences of an extraordinary lifecycle

    DEFF Research Database (Denmark)

    Ugelvig, Line Vej

    The large blue butterflies (genus Maculinea) have received much attention from both scientists and the general public. The reason for this is their highly specialized life cycle that depends on the dual presence of a species specific larval food-plant and host-ant. The genus consists of at least...... six species, which are all confined to grasslands. This habitat type has declined rapidly in the last century, and all Maculinea species are locally threatened in large parts of their distribution ranges. Appropriate future conservation of these species requires detailed knowledge on their complex...... molecular and morphological datasets. By including additional taxa and genetic markers to the existing molecular dataset, I improved the molecular phylogeny of the Glaucopsyche section where the two genera are placed, and find high support for Maculinea being a monophyletic clade. The relationships within...

  14. A new Andean species of Philodryas (Dipsadidae, Xenodontinae) from Ecuador.

    Science.gov (United States)

    Zaher, Hussam; Arredondo, Juan C; Valencia, Jorge H; Arbeláez, Ernesto; Rodrigues, Miguel T; Altamirano-Benavides, Marco

    2014-04-04

    We describe a new species of Philodryas from the highlands of southern Ecuador. The new species is distinguished from all known species of Philodryas by a unique combination of coloration, scalation, and hemipenial characters. The new species resembles Philodryas simonsii in color pattern. However, they differ notoriously by their hemipenial morphology. The three other trans-Andean members of the genus (Philodryas simonsii, Philodryas chamissonis, and Philodryas tachymenoides), along with the new species, compose a probably monophyletic group that may be characterized by the presence of ungrooved postdiastemal teeth in the maxilla. Unlike most species of the genus Philodryas, the new species shows a restricted distribution, being apparently endemic to a small region of high-altitude (3150-4450m) grasslands in the southern Andes of Ecuador.

  15. First cytogenetic analysis of Ichthyoelephas humeralis (Günther, 1860 by conventional and molecular methods with comments on the karyotypic evolution in Prochilodontidae

    Directory of Open Access Journals (Sweden)

    Mauro Nirchio Tursellino

    2016-11-01

    Full Text Available We used conventional cytogenetic techniques (Giemsa, C-banding, Ag-NOR, and fluorescent in situ hybridization (FISH with 5S and 18S rDNA probes to investigate the karyotype and cytogenetic characteristics of Ichthyoelephas humeralis (Günther, 1860 from Ecuador. The specimens studied have a karyotype with 2n=54 biarmed chromosomes (32 M + 22 SM and C-positive heterochromatin located on the centromeric, pericentromeric, interstitial, and terminal regions of some chromosomes. The nucleolus organizer regions occurred terminally on the long arm of chromosome pair 2. FISH confirmed the presence of only one 18S rDNA cluster with nonsyntenic localization with the 5S rDNA. Cytogenetic data allow us to refute the earlier morphological hypothesis of a sister relationship between Semaprochilodus Fowler, 1941 and Ichthyoelephas Posada Arango, 1909 and support the molecular proposal that Ichthyoelephas is a sister group to the monophyletic clade containing Prochilodus Agassiz, 1829 and Semaprochilodus.

  16. 九种鲱科鱼类线粒体DNA细胞色素b基因相对速率测试及分歧时间估计%Phylogenetic analysis and relative-rate test of nine Clupeidae fishes ( Osteichthyes: Clupeiformes) inferred from cytochrome b gene sequence of mitochondrial DNA

    Institute of Scientific and Technical Information of China (English)

    程起群; 卢大儒

    2006-01-01

    对鲱科9种鱼类的线粒体细胞色素b(cytb)基因序列进行综合分析.结果表明:(1)用NeighbourJoining(NJ)法构建的分子系统树显示盖纹沙丁鱼属的3种鱼类形成一个单系类群,鲱属2种鱼类形成一个单系类群,它们的bootstrap支持率均为100%.金色小沙丁鱼和短体小沙丁鱼形成一个单系类群,在NJ树中的支持率达到或超过50%.欧洲黍鲱与太平洋鲱和大西洋鲱是单系起源,其bootstrap支持率高达100%.系统发育结果还支持沙丁鱼属鱼类与盖纹沙丁鱼属鱼类是单系类群,支持率分别为87%和95%.但单系类群Ⅰ(包括大西洋鲱、太平洋鲱、欧洲黍鲱)和单系类群Ⅱ(包括欧洲沙丁鱼、加州沙丁鱼、南美拟沙丁鱼、斑点盖纹沙丁鱼)之间的系统发育关系尚不明确,因为它们之间的支持率很低.(2)dN/dS的比值显著的小于1(Ztest),提示由于功能限制,cytb基因受到强烈的负选择作用.(3)基于Tajima的1D和2D相对速率测试表明,分子钟假说在鲱科鱼类中是成立的;鲱科鱼类的分歧时间是0.12至13.45百万年间.%Phylogenetic analysis and relative- rate test of 9 Clupeidae fishes were performed using the cytochrome b(cytb) gene sequence data. Based on Kimura-2-Parameter(K2P) distance, bootstrapped NJ tree ( 1000 replicates) was generated from these 9 cytb gene sequences of Clupeidae fishes. Three species of genus Sardinops are monophyletic group, 2 species of genus Clupea are monophyletic group, and their bootstrap values are both 100%. Sardinella aurita and Sardinella maderensis are monophyletic group, their bootstrap value reached or exceed 50%. Sprattus sprattus which is a species of genus Sprattus, has a monophyletic origin with genus Clupea, their bootstrap value was 100%. The number of synonymous nucleotide substitution per synonymous site (dS) and the number of nonsynonymous nucleotide substitution per nonsynonymous site (dN) of cytb gene among Clupeidae fishes were calculated

  17. Molecular phylogeny of Vipera Laurenti, 1768 and the related genera Macrovipera (Reuss, 1927) and Daboia (Gray, 1842), with comments about neurotoxic Vipera aspis aspis populations.

    Science.gov (United States)

    Garrigues, Thomas; Dauga, Catherine; Ferquel, Elisabeth; Choumet, Valérie; Failloux, Anna-Bella

    2005-04-01

    We used mtDNA sequences (cytochrome b and NADH dehydrogenase subunit 2) to reconstruct molecular phylogenies of Vipera sensu lato, Vipera sensu stricto, and Vipera aspis. Three major clades were identified within the Vipera s.l. group: (1) the European vipers, (2) the oriental vipers, consisting of Montivipera (Vipera 2) plus Macrovipera lebetina, and (3) a group of Asian and North African vipers consisting of Daboia russelii, V. palaestinae, and Macrovipera mauritanica. We also distinguished three clades within the monophyletic European Vipera group: V. ammodytes, V. aspis, and V. latastei, and Pelias with monophyly of Vipera 1 uncertain. Within V. aspis, the specimens collected in France formed the sister group of an Italian clade. The "neurotoxic" French population of V. aspis, which has a specific venom profile, separated from other French V. aspis early in the history of this group.

  18. Multilocus DNA sequencing of the whiskey fungus reveals a continental-scale speciation pattern.

    Science.gov (United States)

    Scott, J A; Ewaze, J O; Summerbell, R C; Arocha-Rosete, Y; Maharaj, A; Guardiola, Y; Saleh, M; Wong, B; Bogale, M; O'Hara, M J; Untereiner, W A

    2017-01-01

    Baudoinia was described to accommodate a single species, B. compniacensis. Known as the 'whiskey fungus', this species is the predominant member of a ubiquitous microbial community known colloquially as 'warehouse staining' that develops on outdoor surfaces subject to periodic exposure to ethanolic vapours near distilleries and bakeries. Here we examine 19 strains recovered from environmental samples near industrial settings in North America, South America, the Caribbean, Europe and the Far East. Molecular phylogenetic analysis of a portion of the nucLSU rRNA gene confirms that Baudoinia is a monophyletic lineage within the Teratosphaeriaceae (Capnodiales). Multilocus phylogenetic analysis of nucITS rRNA (ITS1-5.8S-ITS2) and partial nucLSU rRNA, beta-tubulin (TUB) and elongation factor 1-alpha (TEF1) gene sequences further indicates that Baudoinia consists of five strongly supported, geographically patterned lineages representing four new species (viz. Baudoinia antilliensis, B. caledoniensis, B. orientalis and B. panamericana).

  19. Exocelina baliem sp. n., the only known pond species of New Guinea Exocelina Broun, 1886 (Coleoptera, Dytiscidae, Copelatinae

    Directory of Open Access Journals (Sweden)

    Helena Shaverdo

    2013-05-01

    Full Text Available Exocelina baliem sp. n. is described from the Baliem Valley in the Central Mountain Range of New Guinea (Papua Province, Indonesia.striolate elytra, different structure and setation of the male and female genitalia and tarsomeres, and inhabiting swampy ponds, the new species differs from all known New Guinea species, which have smooth elytra and are stream associated. It forms a monophyletic group with the Australian E. ferruginea (Sharp, 1882 and New Caledonian E. inexspectata Wewalka, Balke & Hendrich, 2010, based on shape of the paramere and structure of the male tarsi. Habitus, protarsomeres, and male and female genitalia are illustrated, comparing some structures with E. ferruginea and two New Guinea stream species. We briefly discuss the biogeographic relevance of this discovery.

  20. More Cercospora Species Infect Soybeans across the Americas than Meets the Eye.

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    Ana Paula Gomes Soares

    Full Text Available Diseases of soybean caused by Cercospora spp. are endemic throughout the world's soybean production regions. Species diversity in the genus Cercospora has been underestimated due to overdependence on morphological characteristics, symptoms, and host associations. Currently, only two species (Cercospora kikuchii and C. sojina are recognized to infect soybean; C. kikuchii causes Cercospora leaf blight (CLB and purple seed stain (PSS, whereas C. sojina causes frogeye leaf spot. To assess cryptic speciation among pathogens causing CLB and PSS, phylogenetic and phylogeographic analyses were performed with isolates from the top three soybean producing countries (USA, Brazil, and Argentina; collectively accounting for ~80% of global production. Eight nuclear genes and one mitochondrial gene were partially sequenced and analyzed. Additionally, amino acid substitutions conferring fungicide resistance were surveyed, and the production of cercosporin (a polyketide toxin produced by many Cercospora spp. was assessed. From these analyses, the long-held assumption of C. kikuchii as the single causal agent of CLB and PSS was rejected experimentally. Four cercosporin-producing lineages were uncovered with origins (about 1 Mya predicted to predate agriculture. Some of the Cercospora spp. newly associated with CLB and PSS appear to represent undescribed species; others were not previously reported to infect soybeans. Lineage 1, which contained the ex-type strain of C. kikuchii, was monophyletic and occurred in Argentina and Brazil. In contrast, lineages 2 and 3 were polyphyletic and contained wide-host range species complexes. Lineage 4 was monophyletic, thrived in Argentina and the USA, and included the generalist Cercospora cf. flagellaris. Interlineage recombination was detected, along with a high frequency of mutations linked to fungicide resistance in lineages 2 and 3. These findings point to cryptic Cercospora species as underappreciated global