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Resolution of ray-finned fish phylogeny and timing of diversification

Near, Thomas J., Eytan, Ron I., Dornburg, Alex, Kuhn, Kristen L., Moore, Jon A., Davis, Matthew P., Wainwright, Peter C., Friedman, Matt, Smith, W. Leo·2012·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.1206625109
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Abstract

Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major ray-finned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three long-standing problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the “bush at the top of the tree” that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the “Second Age of Fishes.”

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  • Some molecular phylogenetic studies failed to support Siluriphysi monophyly.

    “Nonetheless, some molecular phylogenetic studies (e.g., Figures S2, S4, and S5 in Hughes et al.’s study, and in Near et al.’s and Melo et al.’s studies)54,55,56 failed to support Siluriphysi monophyly.”

    From A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape (2026) · cites this paper as [55]

  • Although molecular phylogenetic studies have demonstrated frequent discordance between molecular data and morphological expectations, the monophyly of Siluriphysi has generally been maintained in traditional interpretations from early single-locus analyses to recent multiple genomic-scale loci, primarily to conform to morphological predictions.

    “Although numerous molecular phylogenetic studies have demonstrated frequent discordance between molecular data and morphological expectations, the monophyly of Siluriphysi has generally been maintained in traditional interpretations, from early single-locus analyses48 to recent multiple genomic-scale loci,49,50,51,52,53,54,55,56 primarily to conform to morphological predictions.”

    From A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape (2026) · cites this paper as [55]

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Metadata

Authors
Near, T. J., Eytan, R. I., Dornburg, A., Kuhn, K. L., Moore, J. A., Davis, M. P., Wainwright, P. C., Friedman, M., & Smith, W. L.
Affiliations
  • Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520;
  • Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458;
  • Department of Zoology, Fishes, The Field Museum, Chicago, IL 60605;
  • Department of Evolution and Ecology, University of California, Davis, CA 95616; and
  • Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, United Kingdom
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2012-08-06
Volume
109
Issue
34
Pages
13698-13703
ISSN
  • 0027-8424
  • 1091-6490
DOI
10.1073/pnas.1206625109
Cited by
912
References
3
Language
en

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