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, 109 (34), 13698-703

Resolution of Ray-Finned Fish Phylogeny and Timing of Diversification

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Resolution of Ray-Finned Fish Phylogeny and Timing of Diversification

Thomas J Near et al. Proc Natl Acad Sci U S A.

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."

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Actinopterygian time-calibrated phylogeny based on nine nuclear genes and 36 fossil age constraints. Bars represent the posterior distribution of divergence-time estimates. Gray bars identify nodes supported with BPP ≥ 0.95, and white bars mark nodes with BPP < 0.95. Nodes with age priors taken from the fossil record are marked with a “c.” For full details on calibration see Materials and Methods and Fig. S2. The time-calibrated tree is scaled to the geological time scale with absolute time given in millions of years.
Fig. 2.
Fig. 2.
Posterior distribution of molecular age estimates and patterns of calibration sharing across studies of ray-finned fish phylogeny. (A) Posterior distribution of molecular age estimates, in millions of years, for 14 actinopterygian lineages, resulting from analyses of whole mtDNA genomes (blue), the rag1 nuclear gene (orange), the rag1 nuclear gene using the calibrations from this study (yellow), and the nine nuclear gene dataset presented in this study (green). The circle represents the mean of the posterior estimate and the whiskers mark the upper and lower 95% highest posterior density of the age estimates. Gray boxes mark the oldest fossils for a given lineage, those with dashed lines were used as calibration age priors (see Materials and Methods) and those with solid black lines were not used as age calibrations. Line drawings of ray-finned fish species are based on photographs of specimens housed at the Peabody Museum of Natural History, Yale University, New Haven, CT. (B) Frequency of calibrations shared between this study and those using whole mtDNA genomes (blue) and the rag1 nuclear gene (orange) binned by the age of the fossil calibration in millions of years (Ma).

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