Fish are exploding in the kitchen of evolutionary phylogenomics.

“The Age of Fishes” – the phrase immediately brings to mind your biology textbook or natural history museum. What is it, class? “The Devonian Period.” Wrong. Fish exploded onto the scene in the Devonian (300 million years ago on the evolutionary timeline), but diversified rapidly again in the Mesozoic to Cenozoic, 120 to 60 million years ago on the timeline – a virtual “Second Age of Fishes,” according to the authors of a new paper in PNAS that tried to paper over a “lack of a single comprehensive phylogeny” that “has limited our understanding of the evolution and diversification of this radiation” of our finny friends (Near et al., “Resolution of ray-finned fish phylogeny and timing of diversification,” PNAS August 6, 2012, doi: 10.1073/pnas.1206625109).

Is it inaccurate to call these explosions? After all, the paper discussed the “radiation” or “diversification” of fish. Perhaps. But the abstract and the summary on PhysOrg used evasive words that amount to “abracadabra” incidents: we are told that the fish “appeared” and “arose.” The scientists used the more clever word “occurred” (without explaining what mutations were preserved by natural selection), while unveiling some dirty laundry in the evolutionary fish camp:

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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