Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
Open accessAbstract
Significance: Ray-finned fishes form the largest and most diverse group of vertebrates. Establishing their phylogenetic relationships is a critical step to explaining their diversity. We compiled the largest comparative genomic database of fishes that provides genome-scale support for previous phylogenetic results and used it to resolve further some contentious relationships in fish phylogeny. A vetted set of exon markers identified in this study is a promising resource for current sequencing approaches to significantly increase genetic and taxonomic coverage to resolve the tree of life for all fishes. Our time-calibrated analysis suggests that most lineages of living fishes were already established in the Mesozoic Period, more than 65 million years ago.
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Molecular dating used six undisputed Ostariophysi fossils as minimum-age constraints and a secondary constraint on the crown age of Otocephala.
“with divergence times calibrated using six undisputed Ostariophysi fossils as minimum-age constraints and a secondary constraint on the crown age of Otocephala (23).”
From Convergent genome streamlining accompanies independent miniaturization in the world’s smallest fishes (2026) · cites this paper as [23]
The Phylogenomic Analyses and Gene Genealogy Interrogation section (page unavailable) says divergence times were estimated with more than 30 fossil calibrations, not six. Our copy also does not identify a secondary constraint on the crown age of Otocephala. (LLM, conf=0.84)
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Cites
Contentious relationships in phylogenomic studies can be driven by a handful of genes
Shen, X.-X., Hittinger, C. T., & Rokas, A. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0126 · Cited by 520 · see citing works
Simion, P., Philippe, H., Baurain, D., Jager, M., Richter, D. J., Di Franco, A., Roure, B., Satoh, N., Quéinnec, É., Ereskovsky, A., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.02.031 · Cited by 518 · see citing works
Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life
Arcila, D., Ortí, G., Vari, R., Armbruster, J. W., Stiassny, M. L. J., Ko, K. D., Sabaj, M. H., Lundberg, J., Revell, L. J., & Betancur-R., R. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-016-0020 · Cited by 243 · see citing works
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Research works printed but not linked: 1
- Helfman GS, Collette BB, Facey DE, Bowen BW (2009) The Diversity of Fishes (John Wiley & Sons, Oxford), 2nd Ed.
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Davesne, D., Meunier, F. J., Schmitt, A. D., Friedman, M., Otero, O., & Benson, R. B. J. (2019) · Biological Reviews · doi:10.1111/brv.12505 · Cited by 57 · see citing works
Sudasinghe, H., Matschiner, M., Britz, R., Conway, K. W., Tan, H. H., Salzburger, W., Peichel, C. L., & Rüber, L. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2614605123
- Authors
- Hughes, L. C., Ortí, G., Huang, Y., Sun, Y., Baldwin, C. C., Thompson, A. W., Arcila, D., Betancur-R., R., Li, C., Becker, L., Bellora, N., Zhao, X., Li, X., Wang, M., Fang, C., Xie, B., Zhou, Z., Huang, H., Chen, S., Venkatesh, B., & Shi, Q.
- Affiliations
- Smithsonian Institution (US)
- Department of Biological Sciences, The George Washington University, Washington, DC 20052;
- BGI Group (China) (CN)
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560;
- Shanghai Ocean University (CN)
- Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
- University of Chinese Academy of Sciences (CN)
- Professional Committee of Native Aquatic Organisms and Water Ecosystem, China Fisheries Association, 100125 Beijing, China;
- Hainan Tropical Ocean University (CN)
- Yellow Sea Fisheries Research Institute (CN)
- Agency for Science, Technology and Research (SG)
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2018-05-14
- Volume
- 115
- Issue
- 24
- Pages
- 6249-6254
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC6004478
- OpenAlex
- W2803572653
- Cited by
- 575
- References
- 3
- Citations by year
- 2026: 54 · 2025: 57 · 2024: 82 · 2023: 63 · 2022: 89 · 2021: 88 · 2020: 78 · 2019: 42 · 2018: 20
- FWCI
- 19.91
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (publishedVersion, other-oa)
- Leiden Repository (Leiden University) (submittedVersion)
- Americanae (AECID Library) (submittedVersion, cc-by-nc-sa)
- NOAA Institutional Repository (submittedVersion, public-domain)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Funders
- National Natural Science Foundation of China (31370047)
- Shenzen Special Program for Strategic Emerging Industries (JSGG20170412153411369)
- National Science Foundation (DEB-147184, DEB-1541491, DEB-1457426, DEB-1541554)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Fish Biology and Ecology Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- Actinopterygii, fish phylogeny, teleosts, whole-genome duplication, gene genealogies, fossil calibration, fish evolution, genome-scale phylogenomics
- MeSH terms
- Animals, Exons, Fishes, Fossils, Models, Genetic, Phylogeny, Genome, Evolution, Molecular, Gene Duplication, Genomics, Transcriptome
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