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Phylotranscriptomic...
Phylotranscriptomic consolidation of the jawed vertebrate timetree
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- Irisarri, Iker, 1984- (författare)
- Uppsala universitet,Systematisk biologi,Univ Konstanz, Dept Biol, Lehrstuhl Zool & Evolut Biol, Univ Str 10, D-78464 Constance, Germany,Burki Lab
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- Baurain, Denis (författare)
- Univ Liege, InBioS Eukaryot Phylogen, Dept Life Sci & PhytoSYST, B-4000 Liege, Belgium
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- Brinkmann, Henner (författare)
- Leibniz Inst DSMZ German Collect Microorgan & Cell, D-38124 Braunschweig, Germany
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- Delsuc, Frédéric (författare)
- Univ Montpellier, Inst Sci Evolut, UMR 5554, CNRS,IRD,EPHE, F-34095 Montpellier, France
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- Sire, Jean-Yves (författare)
- Sorbonne Univ, Inst Biol Paris Seine, UMR7138, F-75005 Paris, France
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- Kupfer, Alexander (författare)
- Stuttgart State Museum Nat Hist, Dept Zool, D-70191 Stuttgart, Germany
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- Petersen, Jörn (författare)
- Leibniz Inst DSMZ German Collect Microorgan & Cell, D-38124 Braunschweig, Germany
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- Jarek, Michael (författare)
- Helmholtz Ctr Infect Res, Dept Genome Analyt, D-38124 Braunschweig, Germany
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- Meyer, Axel (författare)
- Univ Konstanz, Dept Biol, Lehrstuhl Zool & Evolut Biol, Univ Str 10, D-78464 Constance, Germany
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- Vences, Miguel (författare)
- Braunschweig Univ Technol, Zool Inst, D-38106 Braunschweig, Germany
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- Philippe, Hervé (författare)
- Ctr Biodivers Theory & Modelling, UMR CNRS 5321, Stn Theoret & Expt Ecol, F-09200 Moulis, France; Univ Montreal, Dept Biochim, Montreal, PQ H3C 3J7, Canada
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(creator_code:org_t)
- 2017-07-24
- 2017
- Engelska.
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Ingår i: Nature Ecology & Evolution. - : Nature Publishing Group. - 2397-334X. ; 1:9, s. 1370-1378
- Relaterad länk:
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https://europepmc.or...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on ‘standards’ for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as a model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes, and some relationships remain controversial. We tested a new bioinformatic pipeline to assemble large and accu- rate phylogenomic datasets from RNA sequencing and found this phylotranscriptomic approach to be successful and highly cost- effective. Increased sequencing effort up to about 10 Gbp allows more genes to be recovered, but shallower sequencing (1.5 Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large, curated, nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.
Ämnesord
- NATURVETENSKAP -- Biologi -- Evolutionsbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Evolutionary Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Zoologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Zoology (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
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Irisarri, Iker, ...
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Baurain, Denis
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Brinkmann, Henne ...
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Delsuc, Frédéric
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Sire, Jean-Yves
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Kupfer, Alexande ...
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Petersen, Jörn
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Jarek, Michael
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Meyer, Axel
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Vences, Miguel
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Philippe, Hervé
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