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Dimitriou AC, Taiti S, Sfenthourakis S. Genetic evidence against monophyly of Oniscidea implies a need to revise scenarios for the origin of terrestrial isopods. Sci Rep 2019; 9:18508. [PMID: 31811226 PMCID: PMC6898597 DOI: 10.1038/s41598-019-55071-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/21/2019] [Indexed: 11/10/2022] Open
Abstract
Among the few crustacean taxa that managed to inhabit terrestrial environments, Oniscidea includes the most successful colonizers in terms of species richness and abundance. However, neither morphological traits nor molecular markers have definitively resolved phylogenetic relationships among major Oniscidea clades or established the monophyly of the taxon. Herein, we employed the highly conserved, nuclear protein-coding genes Sodium-Potassium Pump (NAK) and Phosphoenolpyruvate Carboxykinase (PEPCK), along with the traditionally used 18 s and 28 s ribosomal RNA genes, in an attempt to clarify these questions. Our dataset included sequences representing all major Oniscidea clades and closely related aquatic taxa, as suggested by previous studies. We applied Bayesian Inference and Maximum Likelihood methods and produced a robust and fully resolved phylogenetic tree that offers strong evidence against the monophyly of Oniscidea. The amphibious genus Ligia appears to be more closely related to representatives of marine suborders, while the phylogenetic pattern of the remaining Oniscidea implies a complex history of the transition from the marine environment to land. With the exception of the basal clade, all other established major clades have been recovered as monophyletic, even though relationships within these clades call for a revised interpretation of morphological characters used in terrestrial isopod taxonomy.
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Affiliation(s)
- Andreas C Dimitriou
- Department of Biological Sciences, University of Cyprus, Panepistimiou Ave. 1, 2109, Aglantzia, Nicosia, Cyprus.
| | - Stefano Taiti
- Museo di Storia Naturale, Sezione di Zoologia "La Specola", Via Romana 17, 50125, Florence, Italy
| | - Spyros Sfenthourakis
- Department of Biological Sciences, University of Cyprus, Panepistimiou Ave. 1, 2109, Aglantzia, Nicosia, Cyprus
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Dobler S, Wagschal V, Pietsch N, Dahdouli N, Meinzer F, Romey-Glüsing R, Schütte K. New ways to acquire resistance: imperfect convergence in insect adaptations to a potent plant toxin. Proc Biol Sci 2019; 286:20190883. [PMID: 31387508 PMCID: PMC6710594 DOI: 10.1098/rspb.2019.0883] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/17/2019] [Indexed: 12/22/2022] Open
Abstract
Evolution of insensitivity to the toxic effects of cardiac glycosides has become a model in the study of convergent evolution, as five taxonomic orders of insects use the same few similar amino acid substitutions in the otherwise highly conserved Na,K-ATPase α. We show here that insensitivity in pyrgomorphid grasshoppers evolved along a slightly divergent path. As in other lineages, duplication of the Na,K-ATPase α gene paved the way for subfunctionalization: one copy maintains the ancestral, sensitive state, while the other copy is resistant. Nonetheless, in contrast with all other investigated insects, the grasshoppers' resistant copy shows length variation by two amino acids in the first extracellular loop, the main part of the cardiac glycoside-binding pocket. RT-qPCR analyses confirmed that this copy is predominantly expressed in tissues exposed to the toxins, while the ancestral copy predominates in the nervous tissue. Functional tests with genetically engineered Drosophila Na,K-ATPases bearing the first extracellular loop of the pyrgomorphid genes showed the derived form to be highly resistant, while the ancestral state is sensitive. Thus, we report convergence in gene duplication and in the gene targets for toxin insensitivity; however, the means to the phenotypic end have been novel in pyrgomorphid grasshoppers.
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Affiliation(s)
- Susanne Dobler
- Molecular Evolutionary Biology, Institute of Zoology, Universität Hamburg, Hamburg, Germany
| | - Vera Wagschal
- Molecular Evolutionary Biology, Institute of Zoology, Universität Hamburg, Hamburg, Germany
| | - Niels Pietsch
- Molecular Evolutionary Biology, Institute of Zoology, Universität Hamburg, Hamburg, Germany
| | - Nadja Dahdouli
- Molecular Evolutionary Biology, Institute of Zoology, Universität Hamburg, Hamburg, Germany
| | - Fee Meinzer
- Molecular Evolutionary Biology, Institute of Zoology, Universität Hamburg, Hamburg, Germany
| | - Renja Romey-Glüsing
- Molecular Evolutionary Biology, Institute of Zoology, Universität Hamburg, Hamburg, Germany
| | - Kai Schütte
- Animal Ecology and Conservation, Institute of Zoology, Universität Hamburg, Hamburg, Germany
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Kocot KM, Struck TH, Merkel J, Waits DS, Todt C, Brannock PM, Weese DA, Cannon JT, Moroz LL, Lieb B, Halanych KM. Phylogenomics of Lophotrochozoa with Consideration of Systematic Error. Syst Biol 2018; 66:256-282. [PMID: 27664188 DOI: 10.1093/sysbio/syw079] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/24/2016] [Indexed: 01/13/2023] Open
Abstract
Phylogenomic studies have improved understanding of deep metazoan phylogeny and show promise for resolving incongruences among analyses based on limited numbers of loci. One region of the animal tree that has been especially difficult to resolve, even with phylogenomic approaches, is relationships within Lophotrochozoa (the animal clade that includes molluscs, annelids, and flatworms among others). Lack of resolution in phylogenomic analyses could be due to insufficient phylogenetic signal, limitations in taxon and/or gene sampling, or systematic error. Here, we investigated why lophotrochozoan phylogeny has been such a difficult question to answer by identifying and reducing sources of systematic error. We supplemented existing data with 32 new transcriptomes spanning the diversity of Lophotrochozoa and constructed a new set of Lophotrochozoa-specific core orthologs. Of these, 638 orthologous groups (OGs) passed strict screening for paralogy using a tree-based approach. In order to reduce possible sources of systematic error, we calculated branch-length heterogeneity, evolutionary rate, percent missing data, compositional bias, and saturation for each OG and analyzed increasingly stricter subsets of only the most stringent (best) OGs for these five variables. Principal component analysis of the values for each factor examined for each OG revealed that compositional heterogeneity and average patristic distance contributed most to the variance observed along the first principal component while branch-length heterogeneity and, to a lesser extent, saturation contributed most to the variance observed along the second. Missing data did not strongly contribute to either. Additional sensitivity analyses examined effects of removing taxa with heterogeneous branch lengths, large amounts of missing data, and compositional heterogeneity. Although our analyses do not unambiguously resolve lophotrochozoan phylogeny, we advance the field by reducing the list of viable hypotheses. Moreover, our systematic approach for dissection of phylogenomic data can be applied to explore sources of incongruence and poor support in any phylogenomic data set. [Annelida; Brachiopoda; Bryozoa; Entoprocta; Mollusca; Nemertea; Phoronida; Platyzoa; Polyzoa; Spiralia; Trochozoa.].
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Affiliation(s)
- Kevin M Kocot
- Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA.,Department of Biological Sciences and Alabama Museum of Natural History, 307 Mary Harmon Bryant Hall, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Torsten H Struck
- Natural History Museum, Department of Research and Collections, University of Oslo, PO Box 1172 Blindern, N-0318 Oslo, Norway
| | - Julia Merkel
- Johannes Gutenberg University, Institute of Zoology, 55099 Mainz, Germany
| | - Damien S Waits
- Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA
| | - Christiane Todt
- University Museum of Bergen, The Natural History Collections, University of Bergen, Allégaten 41, 5007 Bergen, Norway
| | - Pamela M Brannock
- Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA
| | - David A Weese
- Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA.,Department of Biological and Environmental Sciences, Georgia College and State University, Campus Box 81, Milledgeville, GA 31061 USA
| | - Johanna T Cannon
- Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA.,Department of Zoology, Naturhistoriska riksmuseet, Box 50007, 104 05 Stockholm, Sweden
| | - Leonid L Moroz
- The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St Augustine, FL 32080, USA
| | - Bernhard Lieb
- Johannes Gutenberg University, Institute of Zoology, 55099 Mainz, Germany
| | - Kenneth M Halanych
- Department of Biological Sciences, 101 Rouse Life Sciences, Auburn University, Auburn, AL 36849, USA
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Robertson LS, Galbraith HS, Iwanowicz D, Blakeslee CJ, Cornman RS. RNA sequencing analysis of transcriptional change in the freshwater mussel Elliptio complanata after environmentally relevant sodium chloride exposure. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2017; 36:2352-2366. [PMID: 28224655 DOI: 10.1002/etc.3774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 10/25/2016] [Accepted: 02/17/2017] [Indexed: 06/06/2023]
Abstract
To identify potential biomarkers of salt stress in a freshwater sentinel species, we examined transcriptional responses of the common mussel Elliptio complanata to controlled sodium chloride (NaCl) exposures. Ribonucleic acid sequencing (RNA-Seq) of mantle tissue identified 481 transcripts differentially expressed in adult mussels exposed to 2 ppt NaCl (1.2 ppt chloride) for 7 d, of which 290 had nonoverlapping intervals. Differentially expressed gene categories included ion and transmembrane transport, oxidoreductase activity, maintenance of protein folding, and amino acid metabolism. The rate-limiting enzyme for synthesis of taurine, an amino acid frequently linked to osmotic stress in aquatic species, was upregulated, as was the transmembrane ion pump sodium/potassium adenosine 5'-triphosphatase. These patterns confirm a primary transcriptional response to the experimental dose, albeit likely overlapping with nonspecific secondary stress responses. Substantial involvement of the heat shock protein 70 chaperone family and the water-transporting aquaporin family was not detected, however, in contrast to some studies in other bivalves. A subset of the most significantly regulated genes was confirmed by quantitative polymerase chain reaction in an independent sample. Cluster analysis showed separation of mussels exposed to 2 ppt NaCl from control mussels in multivariate space, but mussels exposed to 1 ppt NaCl were largely indistinguishable from controls. Transcriptome-scale analysis of salt exposure under laboratory conditions efficiently identified candidate biomarkers for further functional analysis and field validation. Environ Toxicol Chem 2017;36:2352-2366. © Published 2017 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
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Affiliation(s)
- Laura S Robertson
- Leetown Science Center, US Geological Survey, Kearneysville, West Virginia
| | - Heather S Galbraith
- Northern Appalachian Research Laboratory, Leetown Science Center, US Geological Survey, Wellsboro, Pennsylvania
| | - Deborah Iwanowicz
- Leetown Science Center, US Geological Survey, Kearneysville, West Virginia
| | - Carrie J Blakeslee
- Northern Appalachian Research Laboratory, Leetown Science Center, US Geological Survey, Wellsboro, Pennsylvania
| | - R Scott Cornman
- Fort Collins Science Center, US Geological Survey, Fort Collins, Colorado
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Thabet R, Rouault JD, Ayadi H, Leignel V. Structural analysis of the α subunit of Na(+)/K(+) ATPase genes in invertebrates. Comp Biochem Physiol B Biochem Mol Biol 2016; 196-197:11-18. [PMID: 26812300 DOI: 10.1016/j.cbpb.2016.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 01/18/2023]
Abstract
The Na(+)/K(+) ATPase is a ubiquitous pump coordinating the transport of Na(+) and K(+) across the membrane of cells and its role is fundamental to cellular functions. It is heteromer in eukaryotes including two or three subunits (α, β and γ which is specific to the vertebrates). The catalytic functions of the enzyme have been attributed to the α subunit. Several complete α protein sequences are available, but only few gene structures were characterized. We identified the genomic sequences coding the α-subunit of the Na(+)/K(+) ATPase, from the whole-genome shotgun contigs (WGS), NCBI Genomes (chromosome), Genomic Survey Sequences (GSS) and High Throughput Genomic Sequences (HTGS) databases across distinct phyla. One copy of the α subunit gene was found in Annelida, Arthropoda, Cnidaria, Echinodermata, Hemichordata, Mollusca, Placozoa, Porifera, Platyhelminthes, Urochordata, but the nematodes seem to possess 2 to 4 copies. The number of introns varied from 0 (Platyhelminthes) to 26 (Porifera); and their localization and length are also highly variable. Molecular phylogenies (Maximum Likelihood and Maximum Parsimony methods) showed some clusters constituted by (Chordata/(Echinodermata/Hemichordata)) or (Plathelminthes/(Annelida/Mollusca)) and a basal position for Porifera. These structural analyses increase our knowledge about the evolutionary events of the α subunit genes in the invertebrates.
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Affiliation(s)
- Rahma Thabet
- University of Sfax, Laboratory of Biodiversity and Aquatic Ecosystems UR/11ES72, Ecology and Planktonology, Department of Life Sciences, Road Soukra Km 3.5, BP1171, 3000, Sfax, Tunisia
| | - J-D Rouault
- Laboratoire Evolution, Genomes et Speciation, UPR9034, CNRS, 91198 Gif-sur-Yvette, France
| | - Habib Ayadi
- University of Sfax, Laboratory of Biodiversity and Aquatic Ecosystems UR/11ES72, Ecology and Planktonology, Department of Life Sciences, Road Soukra Km 3.5, BP1171, 3000, Sfax, Tunisia
| | - Vincent Leignel
- Université du Maine, Laboratoire Mer Molecule Sante EA 2160 FR-CNRS 3473 IUML, 72085 Le Mans, France.
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Wesener T, Sierwald P, Wägele JW. Sternites and spiracles - the unclear homology of ventral sclerites in the basal millipede order Glomeridesmida (Myriapoda, Diplopoda). ARTHROPOD STRUCTURE & DEVELOPMENT 2014; 43:87-95. [PMID: 24275250 DOI: 10.1016/j.asd.2013.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 11/07/2013] [Accepted: 11/08/2013] [Indexed: 06/02/2023]
Abstract
We report the discovery of a ventral plate in the basal and little-known chilognath millipede order Glomeridesmida. This ventral plate, interpreted here as a 'true sternite', is clearly separate from both the coxa and the more lateral stigma-carrying plates commonly referred to as 'diplopod sternites'. Therefore, the lateral, stigma-carrying plates of the Diplopoda, previously referred to as sternites, are not sternal elements, but subcoxal elements associated with the limb base. This discovery changes the nomenclature used for the ventral plates in Diplopoda, with the formerly named 'sternite' better referred to as 'stigma-carrying plate'. In helminthomorph Diplopoda, the stigma-carrying plates are apparently secondarily fused with the sternite. The main argument for the independent evolution of tracheae in insects and myriapods, the different location of their respective spiracles, no longer holds true. In all Myriapoda and Hexapoda the spiracles associated with subcoxal elements are located lateral to the limb base. This discovery shows that the arguments for an independent origin of tracheae in insects and myriapods are not uncontestable.
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Affiliation(s)
- Thomas Wesener
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for Animal Biodiversity, Adenauerallee 160, 53113 Bonn, Germany.
| | - Petra Sierwald
- Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Johann-Wolfgang Wägele
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for Animal Biodiversity, Adenauerallee 160, 53113 Bonn, Germany
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Nesnidal MP, Helmkampf M, Meyer A, Witek A, Bruchhaus I, Ebersberger I, Hankeln T, Lieb B, Struck TH, Hausdorf B. New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias. BMC Evol Biol 2013; 13:253. [PMID: 24238092 PMCID: PMC4225663 DOI: 10.1186/1471-2148-13-253] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 11/07/2013] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Within the complex metazoan phylogeny, the relationships of the three lophophorate lineages, ectoprocts, brachiopods and phoronids, are particularly elusive. To shed further light on this issue, we present phylogenomic analyses of 196 genes from 58 bilaterian taxa, paying particular attention to the influence of compositional heterogeneity. RESULTS The phylogenetic analyses strongly support the monophyly of Lophophorata and a sister-group relationship between Ectoprocta and Phoronida. Our results contrast previous findings based on rDNA sequences and phylogenomic datasets which supported monophyletic Polyzoa (= Bryozoa sensu lato) including Ectoprocta, Entoprocta and Cycliophora, Brachiozoa including Brachiopoda and Phoronida as well as Kryptrochozoa including Brachiopoda, Phoronida and Nemertea, thus rendering Lophophorata polyphyletic. Our attempts to identify the causes for the conflicting results revealed that Polyzoa, Brachiozoa and Kryptrochozoa are supported by character subsets with deviating amino acid compositions, whereas there is no indication for compositional heterogeneity in the character subsets supporting the monophyly of Lophophorata. CONCLUSION Our results indicate that the support for Polyzoa, Brachiozoa and Kryptrochozoa gathered so far is likely an artifact caused by compositional bias. The monophyly of Lophophorata implies that the horseshoe-shaped mesosomal lophophore, the tentacular feeding apparatus of ectoprocts, phoronids and brachiopods is, indeed, a synapomorphy of the lophophorate lineages. The same may apply to radial cleavage. However, among phoronids also spiral cleavage is known. This suggests that the cleavage pattern is highly plastic and has changed several times within lophophorates. The sister group relationship of ectoprocts and phoronids is in accordance with the interpretation of the eversion of a ventral invagination at the beginning of metamorphosis as a common derived feature of these taxa.
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Affiliation(s)
- Maximilian P Nesnidal
- Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
| | - Martin Helmkampf
- Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Achim Meyer
- Institute of Zoology, Johannes Gutenberg University, J-J Becher-Weg 7, D-55128 Mainz, Germany
| | - Alexander Witek
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, J-J Becherweg 32, D-55099 Mainz, Germany
| | - Iris Bruchhaus
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str 74, D-20359 Hamburg, Germany
| | - Ingo Ebersberger
- Department for Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe University, Max-von-Laue-Str 13, D-60438 Frankfurt, Germany
| | - Thomas Hankeln
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, J-J Becherweg 32, D-55099 Mainz, Germany
| | - Bernhard Lieb
- Institute of Zoology, Johannes Gutenberg University, J-J Becher-Weg 7, D-55128 Mainz, Germany
| | - Torsten H Struck
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, D-53113 Bonn, Germany
| | - Bernhard Hausdorf
- Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany
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Amelia Chemisquy M, Prevosti FJ. Evaluating the clade size effect in alternative measures of branch support. J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- María Amelia Chemisquy
- División Mastozoología; Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”; Buenos Aires Argentina - CONICET
| | - Francisco J. Prevosti
- División Mastozoología; Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”; Buenos Aires Argentina - CONICET
- Departamento de Ciencias Básicas; Universidad Nacional de Luján; Buenos Aires Argentina
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Mateos M, Hurtado LA, Santamaria CA, Leignel V, Guinot D. Molecular systematics of the deep-sea hydrothermal vent endemic Brachyuran family Bythograeidae: a comparison of three Bayesian species tree methods. PLoS One 2012; 7:e32066. [PMID: 22403623 PMCID: PMC3293879 DOI: 10.1371/journal.pone.0032066] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 01/22/2012] [Indexed: 11/19/2022] Open
Abstract
Brachyuran crabs of the family Bythograeidae are endemic to deep-sea hydrothermal vents and represent one of the most successful groups of macroinvertebrates that have colonized this extreme environment. Occurring worldwide, the family includes six genera (Allograea, Austinograea, Bythograea, Cyanagraea, Gandalfus, and Segonzacia) and fourteen formally described species. To investigate their evolutionary relationships, we conducted Maximum Likelihood and Bayesian molecular phylogenetic analyses, based on DNA sequences from fragments of three mitochondrial genes (16S rDNA, Cytochrome oxidase I, and Cytochrome b) and three nuclear genes (28S rDNA, the sodium-potassium ATPase a-subunit 'NaK', and Histone H3A). We employed traditional concatenated (i.e., supermatrix) phylogenetic methods, as well as three recently developed Bayesian multilocus methods aimed at inferring species trees from potentially discordant gene trees. We found strong support for two main clades within Bythograeidae: one comprising the members of the genus Bythograea; and the other comprising the remaining genera. Relationships within each of these two clades were partially resolved. We compare our results with an earlier hypothesis on the phylogenetic relationships among bythograeid genera based on morphology. We also discuss the biogeography of the family in the light of our results. Our species tree analyses reveal differences in how each of the three methods weighs conflicting phylogenetic signal from different gene partitions and how limits on the number of outgroup taxa may affect the results.
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Affiliation(s)
- Mariana Mateos
- Department of Wildlife and Fisheries, Texas A&M University, College Station, Texas, United States of America
| | - Luis A. Hurtado
- Department of Wildlife and Fisheries, Texas A&M University, College Station, Texas, United States of America
| | - Carlos A. Santamaria
- Department of Wildlife and Fisheries, Texas A&M University, College Station, Texas, United States of America
| | - Vincent Leignel
- Laboratoire Mer-Molécules-Santé, Université du Maine, L'Université Nantes Angers Le Mans (L'UNAM), Le Mans, France
| | - Danièle Guinot
- Département Milieux et Peuplements aquatiques, Muséum National d'Histoire Naturelle, Paris, France
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Nesnidal MP, Helmkampf M, Bruchhaus I, Hausdorf B. The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships. BMC Genomics 2011; 12:572. [PMID: 22111761 PMCID: PMC3285623 DOI: 10.1186/1471-2164-12-572] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 11/23/2011] [Indexed: 11/25/2022] Open
Abstract
Background The phylogenetic relationships of the lophophorate lineages, ectoprocts, brachiopods and phoronids, within Lophotrochozoa are still controversial. We sequenced an additional mitochondrial genome of the most species-rich lophophorate lineage, the ectoprocts. Although it is known that there are large differences in the nucleotide composition of mitochondrial sequences of different lineages as well as in the amino acid composition of the encoded proteins, this bias is often not considered in phylogenetic analyses. We applied several approaches for reducing compositional bias and saturation in the phylogenetic analyses of the mitochondrial sequences. Results The complete mitochondrial genome (16,089 bp) of Flustra foliacea (Ectoprocta, Gymnolaemata, Cheilostomata) was sequenced. All protein-encoding, rRNA and tRNA genes are transcribed from the same strand. Flustra shares long intergenic sequences with the cheilostomate ectoproct Bugula, which might be a synapomorphy of these taxa. Further synapomorphies might be the loss of the DHU arm of the tRNA L(UUR), the loss of the DHU arm of the tRNA S(UCN) and the unique anticodon sequence GAG of the tRNA L(CUN). The gene order of the mitochondrial genome of Flustra differs strongly from that of the other known ectoprocts. Phylogenetic analyses of mitochondrial nucleotide and amino acid data sets show that the lophophorate lineages are more closely related to trochozoan phyla than to deuterostomes or ecdysozoans confirming the Lophotrochozoa hypothesis. Furthermore, they support the monophyly of Cheilostomata and Ectoprocta. However, the relationships of the lophophorate lineages within Lophotrochozoa differ strongly depending on the data set and the used method. Different approaches for reducing heterogeneity in nucleotide and amino acid data sets and saturation did not result in a more robust resolution of lophotrochozoan relationships. Conclusion The contradictory and usually weakly supported phylogenetic reconstructions of the relationships among lophotrochozoan phyla based on mitochondrial sequences indicate that these alone do not contain enough information for a robust resolution of the relations of the lophotrochozoan phyla. The mitochondrial gene order is also not useful for inferring their phylogenetic relationships, because it is highly variable in ectoprocts, brachiopods and some other lophotrochozoan phyla. However, our study revealed several rare genomic changes like the evolution of long intergenic sequences and changes in the structure of tRNAs, which may be helpful for reconstructing ectoproct phylogeny.
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Affiliation(s)
- Maximilian P Nesnidal
- Zoological Museum of the University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
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Hausdorf B, Helmkampf M, Nesnidal MP, Bruchhaus I. Phylogenetic relationships within the lophophorate lineages (Ectoprocta, Brachiopoda and Phoronida). Mol Phylogenet Evol 2010; 55:1121-7. [DOI: 10.1016/j.ympev.2009.12.022] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 11/12/2009] [Accepted: 12/21/2009] [Indexed: 01/24/2023]
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Zierke S, Bakos JD. FPGA Acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods. BMC Bioinformatics 2010; 11:184. [PMID: 20385005 PMCID: PMC2868009 DOI: 10.1186/1471-2105-11-184] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Accepted: 04/12/2010] [Indexed: 01/24/2023] Open
Abstract
Background Likelihood (ML)-based phylogenetic inference has become a popular method for estimating the evolutionary relationships among species based on genomic sequence data. This method is used in applications such as RAxML, GARLI, MrBayes, PAML, and PAUP. The Phylogenetic Likelihood Function (PLF) is an important kernel computation for this method. The PLF consists of a loop with no conditional behavior or dependencies between iterations. As such it contains a high potential for exploiting parallelism using micro-architectural techniques. In this paper, we describe a technique for mapping the PLF and supporting logic onto a Field Programmable Gate Array (FPGA)-based co-processor. By leveraging the FPGA's on-chip DSP modules and the high-bandwidth local memory attached to the FPGA, the resultant co-processor can accelerate ML-based methods and outperform state-of-the-art multi-core processors. Results We use the MrBayes 3 tool as a framework for designing our co-processor. For large datasets, we estimate that our accelerated MrBayes, if run on a current-generation FPGA, achieves a 10× speedup relative to software running on a state-of-the-art server-class microprocessor. The FPGA-based implementation achieves its performance by deeply pipelining the likelihood computations, performing multiple floating-point operations in parallel, and through a natural log approximation that is chosen specifically to leverage a deeply pipelined custom architecture. Conclusions Heterogeneous computing, which combines general-purpose processors with special-purpose co-processors such as FPGAs and GPUs, is a promising approach for high-performance phylogeny inference as shown by the growing body of literature in this field. FPGAs in particular are well-suited for this task because of their low power consumption as compared to many-core processors and Graphics Processor Units (GPUs) [1].
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Affiliation(s)
- Stephanie Zierke
- Department of Computer Science and Engineering, University of South Carolina, Columbia, SC, USA
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Nesnidal MP, Helmkampf M, Bruchhaus I, Hausdorf B. Compositional Heterogeneity and Phylogenomic Inference of Metazoan Relationships. Mol Biol Evol 2010; 27:2095-104. [DOI: 10.1093/molbev/msq097] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Caron JB, Conway Morris S, Shu D. Tentaculate fossils from the Cambrian of Canada (British Columbia) and China (Yunnan) interpreted as primitive deuterostomes. PLoS One 2010; 5:e9586. [PMID: 20221405 PMCID: PMC2833208 DOI: 10.1371/journal.pone.0009586] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 01/20/2010] [Indexed: 12/04/2022] Open
Abstract
Molecular and morphological evidence unite the hemichordates and echinoderms as the Ambulacraria, but their earliest history remains almost entirely conjectural. This is on account of the morphological disparity of the ambulacrarians and a paucity of obvious stem-groups. We describe here a new taxon Herpetogaster collinsi gen. et sp. nov. from the Burgess Shale (Middle Cambrian) Lagerstätte. This soft-bodied vermiform animal has a pair of elongate dendritic oral tentacles, a flexible stolon with an attachment disc, and a re-curved trunk with at least 13 segments that is directed dextrally. A differentiated but un-looped gut is enclosed in a sac suspended by mesenteries. It consists of a short pharynx, a conspicuous lenticular stomach, followed by a narrow intestine sub-equal in length. This new taxon, together with the Lower Cambrian Phlogites and more intriguingly the hitherto enigmatic discoidal eldoniids (Cambrian-Devonian), form a distinctive clade (herein the cambroernids). Although one hypothesis of their relationships would look to the lophotrochozoans (specifically the entoprocts), we suggest that the evidence is more consistent with their being primitive deuterostomes, with specific comparisons being made to the pterobranch hemichordates and pre-radial echinoderms. On this basis some of the earliest ambulacrarians are interpreted as soft-bodied animals with a muscular stalk, and possessing prominent tentacles.
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Affiliation(s)
- Jean-Bernard Caron
- Department of Natural History-Palaeobiology, Royal Ontario Museum, Toronto, Ontario, Canada.
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Paps J, Baguñà J, Riutort M. Bilaterian phylogeny: a broad sampling of 13 nuclear genes provides a new Lophotrochozoa phylogeny and supports a paraphyletic basal acoelomorpha. Mol Biol Evol 2009; 26:2397-406. [PMID: 19602542 DOI: 10.1093/molbev/msp150] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
During the past decade, great progress has been made in clarifying the relationships among bilaterian animals. Studies based on a limited number of markers established new hypotheses such as the existence of three superclades (Deuterostomia, Ecdysozoa, and Lophotrochozoa) but left major questions unresolved. The data sets used to the present either bear few characters for many taxa (i.e., the ribosomal genes) or present many characters but lack many phyla (such as recent phylogenomic approaches) failing to provide definitive answers for all the regions of the bilaterian tree. We performed phylogenetic analyses using a molecular matrix with a high number of characters and bilaterian phyla. This data set is built from 13 genes (8,880 bp) belonging to 90 taxa from 27 bilaterian phyla. Probabilistic analyses robustly support the three superclades, the monophyly of Chordata, a spiralian clade including Brachiozoa, the basal position of a paraphyletic Acoelomorpha, and point to an ecdysozoan affiliation for Chaetognatha. This new phylogeny not only agrees with most classical molecular results but also provides new insights into the relationships between lophotrochozoans and challenges the results obtained using high-throughput strategies, highlighting the problems associated with the current trend to increase gene number rather than taxa.
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Affiliation(s)
- Jordi Paps
- Departament de Genetica, Universitat de Barcelona, Barcelona, Spain
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Affiliation(s)
- Matthew C. Brandley
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720-3160, USA
- Current address: Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Dan L. Warren
- Center for Population Biology, Section of Evolution and Ecology, University of California, Davis, CA 95616-5270, USA
| | - Adam D. Leaché
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720-3160, USA
- Current address: Genome Center and Section of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Jimmy A. McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720-3160, USA
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The complete mitochondrial genome of Watersipora subtorquata (Bryozoa, Gymnolaemata, Ctenostomata) with phylogenetic consideration of Bryozoa. Gene 2009; 439:17-24. [DOI: 10.1016/j.gene.2009.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 02/09/2009] [Accepted: 03/06/2009] [Indexed: 11/22/2022]
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21
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Jang KH, Hwang UW. Complete mitochondrial genome of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata): phylogenetic position of Bryozoa and phylogeny of lophophorates within the Lophotrochozoa. BMC Genomics 2009; 10:167. [PMID: 19379522 PMCID: PMC2678162 DOI: 10.1186/1471-2164-10-167] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Accepted: 04/21/2009] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The phylogenetic position of Bryozoa is one of the most controversial issues in metazoan phylogeny. In an attempt to address this issue, the first bryozoan mitochondrial genome from Flustrellidra hispida (Gymnolaemata, Ctenostomata) was recently sequenced and characterized. Unfortunately, it has extensive gene translocation and extremely reduced size. In addition, the phylogenies obtained from the result were conflicting, so they failed to assign a reliable phylogenetic position to Bryozoa or to clarify lophophorate phylogeny. Thus, it is necessary to characterize further mitochondrial genomes from slowly-evolving bryozoans to obtain a more credible lophophorate phylogeny. RESULTS The complete mitochondrial genome (15,433 bp) of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata), one of the most widely distributed cheliostome bryozoans, is sequenced. This second bryozoan mitochondrial genome contains the set of 37 components generally observed in other metazoans, differing from that of F. hispida (Bryozoa, Gymnolaemata, Ctenostomata), which has only 36 components with loss of tRNAser(ucn) genes. The B. neritina mitochondrial genome possesses 27 multiple noncoding regions. The gene order is more similar to those of the two remaining lophophorate phyla (Brachiopoda and Phoronida) and a chiton Katharina tunicate than to that of F. hispida. Phylogenetic analyses based on the nucleotide sequences or amino acid residues of 12 protein-coding genes showed consistently that, within the Lophotrochozoa, the monophyly of the bryozoan class Gymnolaemata (B. neritina and F. hispida) was strongly supported and the bryozoan clade was grouped with brachiopods. Echiura appeared as a subtaxon of Annelida, and Entoprocta as a sister taxon of Phoronida. The clade of Bryozoa + Brachiopoda was clustered with either the clade of Annelida-Echiura or that of Phoronida + Entoprocta. CONCLUSION This study presents the complete mitochondrial genome of a cheliostome bryozoan, B. neritina. The phylogenetic analyses suggest a close relationship between Bryozoa and Brachiopoda within the Lophotrochozoa. However, the sister group of Bryozoa + Brachiopoda is still ambiguous, although it has some attractions with Annelida-Echiura or Phoronida + Entoprocta. If the latter is a true phylogeny, lophophorate monophyly including Entoprocta is supported. Consequently, the present results imply that Brachiozoa (= Brachiopoda + Phoronida) and the recently-resurrected Bryozoa concept comprising Ectoprocta and Entoprocta may be refuted.
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Affiliation(s)
- Kuem Hee Jang
- Department of Biology, Graduate School & Department of Biology, Teachers College, Kyungpook National University, Daegu 702-701, Korea
- Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 702-701, Korea
| | - Ui Wook Hwang
- Department of Biology, Graduate School & Department of Biology, Teachers College, Kyungpook National University, Daegu 702-701, Korea
- Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 702-701, Korea
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Sáez AG, Lozano E, Zaldívar-Riverón A. Evolutionary history of Na,K-ATPases and their osmoregulatory role. Genetica 2009; 136:479-90. [PMID: 19214758 DOI: 10.1007/s10709-009-9356-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Accepted: 01/26/2009] [Indexed: 01/07/2023]
Abstract
The Na/K pump, or Na,K-ATPase, is a key enzyme to the homeostasis of osmotic pressure, cell volume, and the maintenance of electrochemical gradients. Its alpha subunit, which holds most of its functions, belongs to a large family of ATPases known as P-type, and to the subfamily IIC, which also includes H,K-ATPases. In this study, we attempt to describe the evolutionary history of IIC ATPases by doing phylogenetic analysis with most of the currently available protein sequences (over 200), and pay special attention to the relationship between their diversity and their osmoregulatory role. We include proteins derived from many completed or ongoing genome projects, many of whose IIC ATPases have not been phylogenetically analyzed previously. We show that the most likely origin of IIC proteins is prokaryotic, and that many of them are present in non-metazoans, such as algae, protozoans or fungi. We also suggest that the pre-metazoan ancestor, represented by the choanoflagellate Monosiga brevicollis, whose genome has been sequenced, presented at least two IIC-type proteins. One of these proteins would have given rise to most current animal IIC ATPases, whereas the other apparently evolved into a lineage that, so far, has only been found in nematodes. We also propose that early deuterostomes presented a single IIC gene, from which all the extant diversity of vertebrate IIC proteins originated by gene and genome duplications.
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Affiliation(s)
- Alberto G Sáez
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain.
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Helmkampf M, Bruchhaus I, Hausdorf B. Phylogenomic analyses of lophophorates (brachiopods, phoronids and bryozoans) confirm the Lophotrochozoa concept. Proc Biol Sci 2008; 275:1927-33. [PMID: 18495619 PMCID: PMC2593926 DOI: 10.1098/rspb.2008.0372] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Revised: 04/29/2008] [Accepted: 04/30/2008] [Indexed: 11/12/2022] Open
Abstract
Based on embryological and morphological evidence, Lophophorata was long considered to be the sister or paraphyletic stem group of Deuterostomia. By contrast, molecular data have consistently indicated that the three lophophorate lineages, Ectoprocta, Brachiopoda and Phoronida, are more closely related to trochozoans (annelids, molluscs and related groups) than to deuterostomes. For this reason, the lophophorate groups and Trochozoa were united to Lophotrochozoa. However, the relationships of the lophophorate lineages within Lophotrochozoa are still largely unresolved. Maximum-likelihood and Bayesian analyses were performed based on a dataset comprising 11,445 amino acid positions derived from 79 ribosomal proteins of 39 metazoan taxa including new sequences obtained from a brachiopod and a phoronid. These analyses show that the three lophophorate lineages are affiliated with trochozoan rather than deuterostome phyla. All hypotheses claiming that they are more closely related to Deuterostomia than to Protostomia can be rejected by topology testing. Monophyly of lophophorates was not recovered but that of Bryozoa including Ectoprocta and Entoprocta and monophyly of Brachiozoa including Brachiopoda and Phoronida were strongly supported. Alternative hypotheses that are refuted include (i) Brachiozoa as the sister group of Mollusca, (ii) ectoprocts as sister to all other Lophotrochozoa including Platyzoa, and (iii) ectoprocts as sister or to all other protostomes except chaetognaths.
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Affiliation(s)
- Martin Helmkampf
- Zoological Museum, University of HamburgMartin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Iris Bruchhaus
- Bernhard Nocht Institute for Tropical MedicineBernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
| | - Bernhard Hausdorf
- Zoological Museum, University of HamburgMartin-Luther-King-Platz 3, 20146 Hamburg, Germany
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Tsang L, Ma K, Ahyong S, Chan TY, Chu K. Phylogeny of Decapoda using two nuclear protein-coding genes: Origin and evolution of the Reptantia. Mol Phylogenet Evol 2008; 48:359-68. [DOI: 10.1016/j.ympev.2008.04.009] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2008] [Revised: 04/01/2008] [Accepted: 04/06/2008] [Indexed: 12/01/2022]
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Bogan AE, Roe KJ. Freshwater bivalve (Unioniformes) diversity, systematics, and evolution: status and future directions. ACTA ACUST UNITED AC 2008. [DOI: 10.1899/07-069.1] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Arthur E. Bogan
- North Carolina State Museum of Natural Sciences, Research Laboratory, 4301 Reedy Creek Road, Raleigh, North Carolina 27607 USA
| | - Kevin J. Roe
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, Iowa 50011 USA
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26
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Mateos E, Giribet G. Exploring the molecular diversity of terrestrial nemerteans (Hoplonemertea, Monostilifera, Acteonemertidae) in a continental landmass. ZOOL SCR 2008. [DOI: 10.1111/j.1463-6409.2008.00324.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Yokobori SI, Iseto T, Asakawa S, Sasaki T, Shimizu N, Yamagishi A, Oshima T, Hirose E. Complete nucleotide sequences of mitochondrial genomes of two solitary entoprocts, Loxocorone allax and Loxosomella aloxiata: implications for lophotrochozoan phylogeny. Mol Phylogenet Evol 2008; 47:612-28. [PMID: 18374604 DOI: 10.1016/j.ympev.2008.02.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Revised: 02/05/2008] [Accepted: 02/16/2008] [Indexed: 11/16/2022]
Abstract
The complete nucleotide sequences of the mitochondrial (mt) genomes of the entoprocts Loxocorone allax and Loxosomella aloxiata were determined. Both species carry the typical gene set of metazoan mt genomes and have similar organizations of their mt genes. However, they show differences in the positions of two tRNA(Leu) genes. Additionally, the tRNA(Val) gene, and half of the long non-coding region, is duplicated and inverted in the Loxos. aloxiata mt genome. The initiation codon of the Loxos. aloxiata cytochrome oxidase subunit I gene is expected to be ACG rather than AUG. The mt gene organizations in these two entoproct species most closely resemble those of mollusks such as Katharina tunicata and Octopus vulgaris, which have the most evolutionarily conserved mt gene organization reported to date in mollusks. Analyses of the mt gene organization in the lophotrochozoan phyla (Annelida, Brachiopoda, Echiura, Entoprocta, Mollusca, Nemertea, and Phoronida) suggested a close phylogenetic relationship between Brachiopoda, Annelida, and Echiura. However, Phoronida was excluded from this grouping. Molecular phylogenetic analyses based on the sequences of mt protein-coding genes suggested a possible close relationship between Entoprocta and Phoronida, and a close relationship among Brachiopoda, Annelida, and Echiura.
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Affiliation(s)
- Shin-ichi Yokobori
- Laboratory for Cellular Biochemistry, Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
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Helmkampf M, Bruchhaus I, Hausdorf B. Multigene analysis of lophophorate and chaetognath phylogenetic relationships. Mol Phylogenet Evol 2008; 46:206-14. [DOI: 10.1016/j.ympev.2007.09.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Revised: 08/20/2007] [Accepted: 09/05/2007] [Indexed: 10/22/2022]
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29
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Roeding F, Hagner-Holler S, Ruhberg H, Ebersberger I, von Haeseler A, Kube M, Reinhardt R, Burmester T. EST sequencing of Onychophora and phylogenomic analysis of Metazoa. Mol Phylogenet Evol 2007; 45:942-51. [PMID: 17933557 DOI: 10.1016/j.ympev.2007.09.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Revised: 08/29/2007] [Accepted: 09/05/2007] [Indexed: 11/16/2022]
Abstract
Onychophora (velvet worms) represent a small animal taxon considered to be related to Euarthropoda. We have obtained 1873 5' cDNA sequences (expressed sequence tags, ESTs) from the velvet worm Epiperipatus sp., which were assembled into 833 contigs. BLAST similarity searches revealed that 51.9% of the contigs had matches in the protein databases with expectation values lower than 10(-4). Most ESTs had the best hit with proteins from either Chordata or Arthropoda (approximately 40% respectively). The ESTs included sequences of 27 ribosomal proteins. The orthologous sequences from 28 other species of a broad range of phyla were obtained from the databases, including other EST projects. A concatenated amino acid alignment comprising 5021 positions was constructed, which covers 4259 positions when problematic regions were removed. Bayesian and maximum likelihood methods place Epiperipatus within the monophyletic Ecdysozoa (Onychophora, Arthropoda, Tardigrada and Nematoda), but its exact relation to the Euarthropoda remained unresolved. The "Articulata" concept was not supported. Tardigrada and Nematoda formed a well-supported monophylum, suggesting that Tardigrada are actually Cycloneuralia. In agreement with previous studies, we have demonstrated that random sequencing of cDNAs results in sequence information suitable for phylogenomic approaches to resolve metazoan relationships.
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Affiliation(s)
- Falko Roeding
- Institute of Zoology and Zoological Museum, University of Hamburg, D-20146 Hamburg, Germany
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30
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Silva VS, Nunes MA, Cordeiro JM, Calejo AI, Santos S, Neves P, Sykes A, Morgado F, Dunant Y, Gonçalves PP. Comparative effects of aluminum and ouabain on synaptosomal choline uptake, acetylcholine release and (Na+/K+)ATPase. Toxicology 2007; 236:158-77. [PMID: 17560001 DOI: 10.1016/j.tox.2007.04.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Revised: 03/16/2007] [Accepted: 04/10/2007] [Indexed: 11/25/2022]
Abstract
Closing the gap between adverse health effects of aluminum and its mechanisms of action still represents a huge challenge. Cholinergic dysfunction has been implicated in neuronal injury induced by aluminum. Previously reported data also indicate that in vivo and in vitro exposure to aluminum inhibits the mammalian (Na(+)/K(+))ATPase, an ubiquitous plasma membrane pump. This study was undertaken with the specific aim of determining whether in vitro exposure to AlCl(3) and ouabain, the foremost utilized selective inhibitor of (Na(+)/K(+))ATPase, induce similar functional modifications of cholinergic presynaptic nerve terminals, by comparing their effects on choline uptake, acetylcholine release and (Na(+)/K(+))ATPase activity, on subcellular fractions enriched in synaptic nerve endings isolated from rat brain, cuttlefish optic lobe and torpedo electric organ. Results obtained show that choline uptake by rat synaptosomes was inhibited by submillimolar AlCl(3), whereas the amount of choline taken up by synaptosomes isolated from cuttlefish and torpedo remained unchanged. Conversely, choline uptake was reduced by ouabain to a large extent in all synaptosomal preparations analyzed. In contrast to ouabain, which modified the K(+) depolarization evoked release of acetylcholine by rat, cuttlefish and torpedo synaptosomal fractions, AlCl(3) induced reduction of stimulated acetylcholine release was only observed when rat synaptosomes were challenged. Finally, it was observed that the aluminum effect on cuttlefish and torpedo synaptosomal (Na(+)/K(+))ATPase activity was slight when compared to its inhibitory action on mammalian (Na(+)/K(+))ATPase. In conclusion, inhibition of (Na(+)/K(+))ATPase by AlCl(3) and ouabain jeopardized the high-affinity (Na(+)-dependent, hemicholinium-3 sensitive) uptake of choline and the Ca(2+)-dependent, K(+) depolarization evoked release of acetylcholine by rat, cuttlefish and torpedo synaptosomal fractions. The effects of submillimolar AlCl(3) on choline uptake and acetylcholine release only resembled those of ouabain when rat synaptosomes were assayed. Therefore, important differences were found between the species regarding the cholinotoxic action of aluminum. The variability of (Na(+)/K(+))ATPase sensitivity to aluminum of cholinergic neurons might contribute to their differential susceptibility to this neurotoxic agent.
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Affiliation(s)
- Virgília S Silva
- CESAM, Departamento de Biologia, Universidade de Aveiro, 3810-193 Aveiro, Portugal
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Didier G, Laprevotte I, Pupin M, Hénaut A. Local decoding of sequences and alignment-free comparison. J Comput Biol 2007; 13:1465-76. [PMID: 17061922 DOI: 10.1089/cmb.2006.13.1465] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Subword composition plays an important role in a lot of analyses of sequences. Here we define and study the "local decoding of order N of sequences," an alternative that avoids some drawbacks of "subwords of length N" approaches while keeping informations about environments of length N in the sequences ("decoding" is taken here in the sense of hidden Markov modeling, i.e., associating some state to all positions of the sequence). We present an algorithm for computing the local decoding of order N of a given set of sequences. Its complexity is linear in the total length of the set (whatever the order N) both in time and memory space. In order to show a use of local decoding, we propose a very basic dissimilarity measure between sequences which can be computed both from local decoding of order N and composition in subwords of length N. The accuracies of these two dissimilarities are evaluated, over several datasets, by computing their linear correlations with a reference alignment-based distance. These accuracies are also compared to the one obtained from another recent alignment-free comparison.
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Affiliation(s)
- Gilles Didier
- Institut de Mathématiques de Luminy, UMR 6206, Campus de Luminay, Case 907, 13288 Marseille, France.
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Terzibasi E, Valenzano DR, Cellerino A. The short-lived fish Nothobranchius furzeri as a new model system for aging studies. Exp Gerontol 2007; 42:81-9. [PMID: 17049789 DOI: 10.1016/j.exger.2006.06.039] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Revised: 06/02/2006] [Accepted: 06/07/2006] [Indexed: 12/17/2022]
Abstract
Genetic and pharmacological research on aging is hampered by the lifespan of available vertebrate models. We recently initiated studies on Nothobranchius furzeri, a species with a maximum life expectancy in captivity of just three months which represents the shortest documented captive lifespan for a vertebrate. Further research on N. furzeri has demonstrated that 1. Short lifespan is tied with explosive growth and accelerated sexual maturation. 2. Short lifespan is correlated with expression of age-related behavioral and histological changes. 3. Lifespan and expression of age-related markers can be modulated by water temperature. 4. Resveratrol, a drug characterized for its life-extending action in Caenorhabditis elegans and Drosophila, increases lifespan and retards expression of age-related markers. 5. Aging-related genes can be easily isolated by homology cloning. Finally, different populations or species of Nothobranchius show large-scale differences in captive lifespan. In the last three years, N. furzeri has moved from biological curiosity to a promising model system for drug validation. Furthermore, this species occupies a favorable position in the Teleost's "tree of life". It is very close to the Japanese Medaka, and close to the pufferfishes and stickleback and might represent a very useful model for comparative genomics of aging.
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Turbeville JM, Smith DM. The partial mitochondrial genome of the Cephalothrix rufifrons (Nemertea, Palaeonemertea): characterization and implications for the phylogenetic position of Nemertea. Mol Phylogenet Evol 2006; 43:1056-65. [PMID: 17210260 DOI: 10.1016/j.ympev.2006.10.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 10/08/2006] [Accepted: 10/23/2006] [Indexed: 11/22/2022]
Abstract
A continuous 10.1kb fragment of the Cephalothrix rufifrons (Nemertea, Palaeonemertea) mitochondrial genome was sequenced and characterized to further assess organization of protostome mitochondrial genomes and evaluate the phylogenetic potential of gene arrangement and amino acid characters. The genome is A-T rich (72%), and this biased base composition is partly reflected in codon usage. Inferred tRNA secondary structures are typical of those reported for other metazoan mitochondrial DNAs. The arrangement of the 26 genes contained in the fragment exhibits marked similarity to those of many protostome taxa, most notably molluscs with highly conserved arrangements and a phoronid. Separate and simultaneous phylogenetic analyses of inferred amino acid sequences and gene adjacencies place the nemertean within the protostomes among coelomate lophotrochozoan taxa, but do not find a well-supported sister taxon link.
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Affiliation(s)
- J M Turbeville
- Department of Biology and Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA.
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Conway Morris S. Darwin's dilemma: the realities of the Cambrian 'explosion'. Philos Trans R Soc Lond B Biol Sci 2006; 361:1069-83. [PMID: 16754615 PMCID: PMC1578734 DOI: 10.1098/rstb.2006.1846] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Cambrian 'explosion' is widely regarded as one of the fulcrum points in the history of life, yet its origins and causes remain deeply controversial. New data from the fossil record, especially of Burgess Shale-type Lagerstätten, indicate, however, that the assembly of bodyplans is not only largely a Cambrian phenomenon, but can already be documented in fair detail. This speaks against a much more ancient origin of the metazoans, and current work is doing much to reconcile the apparent discrepancies between the fossil record, including the Ediacaran assemblages of latest Neoproterozoic age and molecular 'clocks'. Hypotheses to explain the Cambrian 'explosion' continue to be generated, but the recurrent confusion of cause and effect suggests that the wrong sort of question is being asked. Here I propose that despite its step-like function this evolutionary event is the inevitable consequence of Earth and biospheric change.
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Affiliation(s)
- Simon Conway Morris
- University of Cambridge, Department of Earth Sciences, Downing Street, Cambridge CB2 3EQ, UK.
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Passamaneck Y, Halanych KM. Lophotrochozoan phylogeny assessed with LSU and SSU data: Evidence of lophophorate polyphyly. Mol Phylogenet Evol 2006; 40:20-8. [PMID: 16556507 DOI: 10.1016/j.ympev.2006.02.001] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Revised: 12/26/2005] [Accepted: 02/01/2006] [Indexed: 11/30/2022]
Abstract
Of the three major bilaterian clades, Lophotrochozoa has the greatest diversity and disparity of body forms and is the least understood in terms of phylogenetic history. Within this clade, small nuclear ribosomal subunit (SSU or 18S) studies have failed to provide resolution and other molecular markers have insufficient taxon sampling. To examine relationships within Lophotrochozoa, we collected and complied complete SSU data and nearly complete (>90%) large nuclear ribosomal subunit (LSU or 28S) data totaling approximately 5kb per taxon, for 36 lophotrochozoans. Results of LSU and combined SSU+LSU likelihood analyses provide topologies more consistent with morphological data than analyses of SSU data alone. Namely, most phyla recognized on morphological grounds are recovered as monophyletic entities when the LSU data is considered (contra SSU data alone). These new data show with significant support that "Lophophorata" (traditionally recognized to include Brachiopoda, Phoronida, and Bryozoa) is not a monophyletic entity. Further, the data suggest that Platyzoa is real and may be derived within lophotrochozans rather than a basal or sister taxon. The recently discovered Cycliophora are allied to entoprocts, consistent with their initial placement based on morphology. Additional evidence for Syndermata (i.e., Rotifera+Acanthocephala) is also found. Although relationships among groups with trochophore-like larvae could not be resolved and nodal support values are generally low, the addition of LSU data is a considerable advance in our understanding of lophotrochozoan phylogeny from the molecular perspective.
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Affiliation(s)
- Yale Passamaneck
- Woods Hole Oceanographic Institution, Biology Department MS 33, Woods Hole, MA 02543, USA
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Waeschenbach A, Telford MJ, Porter JS, Littlewood DTJ. The complete mitochondrial genome of Flustrellidra hispida and the phylogenetic position of Bryozoa among the Metazoa. Mol Phylogenet Evol 2006; 40:195-207. [PMID: 16621614 DOI: 10.1016/j.ympev.2006.03.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2005] [Revised: 03/03/2006] [Accepted: 03/07/2006] [Indexed: 10/24/2022]
Abstract
The complete mitochondrial genome of Flustrellidra hispida (Bryozoa, Ctenostomata, Flustrellidridae) was sequenced using a transposon-mediated approach. All but one of the 36 genes were identified (trnS2). The genome is 13,026 bp long, being one of the smallest metazoan mitochondrial genomes sequenced to date with a unique gene order when compared to other Metazoa. The genome has an overall AT richness of 59.4%. We found seven regions of overlaps between tRNAs and protein-coding genes ranging from 2 to 11 nt, and seven regions of overlap between tRNAs, ranging from 1 to 8 nt, resulting in a total number of 46 overlapping nucleotides. Genes nad4, cox2, atp8, and nad3 are terminated by the abbreviated stop codon T and cytb is suggested to terminate on (ACT)AA; we postulate that mRNA editing is required to remove AC for TAA to be functional in terminating translation. Phylogenetic analysis of nucleotide and amino acid data place Flustrellidra in the Lophotrochozoa. DNA for this study originated from two populations resulting in a contig consisting of multiple haplotypes. Twenty-seven SNP sites were detected, the majority occurring in cox1 and nad5. With cox1 already established as a marker in bryozoan studies, we advocate the further testing of nad5.
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Affiliation(s)
- Andrea Waeschenbach
- Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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Lavrov DV, Lang BF. Poriferan mtDNA and animal phylogeny based on mitochondrial gene arrangements. Syst Biol 2006; 54:651-9. [PMID: 16126659 DOI: 10.1080/10635150500221044] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Phylogenetic relationships among the metazoan phyla are the subject of an ongoing controversy. Analysis of mitochondrial gene arrangements is a powerful tool to investigate these relationships; however, its previous application outside of individual animal phyla has been hampered by the lack of informative out-group data. To address this shortcoming, we determined complete mitochondrial DNA sequences for the demosponges Geodia neptuni and Tethya actinia, two representatives of the most basal animal phylum, the Porifera. With sponges as an outgroup, we investigated phylogenetic relationships of nine bilaterian phyla using both breakpoint analysis of global mitochondrial gene arrangements and maximum parsimony analysis of mitochondrial gene adjacencies. Our results provide strong support for a group that includes protostome (but not deuterostome) coelomate, pseudocoelomate, and acoelomate animals, thus clearly rejecting the Coelomata hypothesis. Two other groups of bilaterian animals, Lophotrochozoa and Ambulacraria, are also supported by our analyses. However, due to the remarkable stability of mitochondrial gene arrangements in Deuterostomia and the Ecdysozoa, conclusions on their evolutionary history cannot be drawn.
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Affiliation(s)
- Dennis V Lavrov
- Département de Biochimie, Université de Montréal, Succursale Centre-Ville, Montreal, Que, H3C 3J7, Canada.
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Kusche K, Bangel N, Mueller C, Hildebrandt JP, Weber WM. Molecular cloning and sequencing of the Na+/K+-ATPase alpha-subunit of the medical leech Hirudo medicinalis (Annelida) - implications for modelling protostomian evolution. J ZOOL SYST EVOL RES 2005. [DOI: 10.1111/j.1439-0469.2005.00330.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Dopazo H, Dopazo J. Genome-scale evidence of the nematode-arthropod clade. Genome Biol 2005; 6:R41. [PMID: 15892869 PMCID: PMC1175953 DOI: 10.1186/gb-2005-6-5-r41] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Accepted: 04/06/2005] [Indexed: 11/13/2022] Open
Abstract
The most extensive phylogenetic analysis carried out to date, including 11 complete genomes, is shown to support the Ecdysozoa hypothesis in the open-ended debate of the Coelomata-Ecdysozoa evolutionary problem. Background The issue of whether coelomates form a single clade, the Coelomata, or whether all animals that moult an exoskeleton (such as the coelomate arthropods and the pseudocoelomate nematodes) form a distinct clade, the Ecdysozoa, is the most puzzling issue in animal systematics and a major open-ended subject in evolutionary biology. Previous single-gene and genome-scale analyses designed to resolve the issue have produced contradictory results. Here we present the first genome-scale phylogenetic evidence that strongly supports the Ecdysozoa hypothesis. Results Through the most extensive phylogenetic analysis carried out to date, the complete genomes of 11 eukaryotic species have been analyzed in order to find homologous sequences derived from 18 human chromosomes. Phylogenetic analysis of datasets showing an increased adjustment to equal evolutionary rates between nematode and arthropod sequences produced a gradual change from support for Coelomata to support for Ecdysozoa. Transition between topologies occurred when fast-evolving sequences of Caenorhabditis elegans were removed. When chordate, nematode and arthropod sequences were constrained to fit equal evolutionary rates, the Ecdysozoa topology was statistically accepted whereas Coelomata was rejected. Conclusions The reliability of a monophyletic group clustering arthropods and nematodes was unequivocally accepted in datasets where traces of the long-branch attraction effect were removed. This is the first phylogenomic evidence to strongly support the 'moulting clade' hypothesis.
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Affiliation(s)
- Hernán Dopazo
- Pharmacogenomics and Comparative Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler 16, 46013 Valencia, Spain
| | - Joaquín Dopazo
- Functional Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler 16, 46013 Valencia, Spain
- Functional Genomics Node, INB, Centro de Investigación Príncipe Felipe, Autopista del Saler 16, 46013 Valencia, Spain
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Philippe H, Lartillot N, Brinkmann H. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol Biol Evol 2005; 22:1246-53. [PMID: 15703236 DOI: 10.1093/molbev/msi111] [Citation(s) in RCA: 354] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Almost a decade ago, a new phylogeny of bilaterian animals was inferred from small-subunit ribosomal RNA (rRNA) that claimed the monophyly of two major groups of protostome animals: Ecdysozoa (e.g., arthropods, nematodes, onychophorans, and tardigrades) and Lophotrochozoa (e.g., annelids, molluscs, platyhelminths, brachiopods, and rotifers). However, it received little additional support. In fact, several multigene analyses strongly argued against this new phylogeny. These latter studies were based on a large amount of sequence data and therefore showed an apparently strong statistical support. Yet, they covered only a few taxa (those for which complete genomes were available), making systematic artifacts of tree reconstruction more probable. Here we expand this sparse taxonomic sampling and analyze a large data set (146 genes, 35,371 positions) from a diverse sample of animals (35 species). Our study demonstrates that the incongruences observed between rRNA and multigene analyses were indeed due to long-branch attraction artifacts, illustrating the enormous impact of systematic biases on phylogenomic studies. A refined analysis of our data set excluding the most biased genes provides strong support in favor of the new animal phylogeny and in addition suggests that urochordates are more closely related to vertebrates than are cephalochordates. These findings have important implications for the interpretation of morphological and genomic data.
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Affiliation(s)
- Hervé Philippe
- Canadian Institute for Advanced Research and Département de Biochimie, Université de Montréal, Montréal, Québec, Canada.
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Affiliation(s)
- Kenneth M. Halanych
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849;
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