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Phylotranscriptomic consolidation of the jawed vertebrate timetree
Open accessAbstract
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 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 novel bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and find this phylotranscriptomic approach successful and highly cost-effective. Increased sequencing effort up to ca. 10Gbp allows recovering more genes, but shallower sequencing (1.5Gbp) 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.
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“The remaining 662 were screened for contaminations with Forty-Two [12, 13] using 78 ribosomal protein markers, and 89 samples were further discarded because they were too contaminated (Data file 1, Data set 1), leaving 573 samples.”
From Decontamination, pooling and dereplication of the 678 samples of the Marine Microbial Eukaryote Transcriptome Sequencing Project (2021) · cites this paper as [13]
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Metadata
- Authors
- Irisarri, I., Baurain, D., Brinkmann, H., Delsuc, F., Sire, J.-Y., Kupfer, A., Petersen, J., Jarek, M., Meyer, A., Vences, M., & Philippe, H.
- Affiliations
- Uppsala University (SE)
- University of Liège (BE)
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures (DE)
- Centre National de la Recherche Scientifique (FR)
- Sorbonne Université (FR)
- Staatliches Museum für Naturkunde Stuttgart (DE)
- Helmholtz Centre for Infection Research (DE)
- University of Konstanz (DE)
- Corresponding author
- Irisarri, Iker
- Philippe, Hervé
- ORCID
- Venue
- Nature Ecology & Evolution
- Published
- 2017-07-24
- Volume
- 1
- Issue
- 9
- Pages
- 1370-1378
- ISSN
- 2397-334X (ISSN-L)
- PMC
- PMC5584656
- OpenAlex
- W2739198517
- Cited by
- 299
- References
- 55
- Citations by year
- 2026: 22 · 2025: 26 · 2024: 23 · 2023: 35 · 2022: 31 · 2021: 52 · 2020: 32 · 2019: 48 · 2018: 27 · 2017: 3
- FWCI
- 12.29
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Ecology & Evolution (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- KOPS (University of Konstanz) (submittedVersion)
- HZI (Helmholtz Centre for Infection Research) (submittedVersion, cc-by-nc-sa)
- HAL (submittedVersion, other-oa)
- ORBi (University of Liège) (submittedVersion)
- Funders
- Alexander von Humboldt-Stiftung (1150725)
- European Commission (273900)
- Deutsche Forschungsgemeinschaft (1117545)
- Agence Nationale de la Recherche (ANR-10-LABX-0041, 2017-, ANR-12-BSV7-0020, ANR-10-LABX- 41, 12-BSV7-020, ANR-12, ANR-10, 10-LABX-41)
- Fonds De La Recherche Scientifique - FNRS (# 2.5020.11, 1117545, 2.5020)
- Fédération Wallonie-Bruxelles (1117545, 2.5020.11)
- Universität Konstanz
- Instituto de Física de Cantabria
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Keywords
- jawed vertebrates, Gnathostomata, timetree, phylotranscriptomics, phylogenomics, divergence time estimation, mitochondrial genome, transcriptome assembly, phylogenetic diversity, macroevolution
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