Explosion of goby fish diversity at the Eocene-Oligocene transition

A rapid drop of sea level at the Eocene-Oligocene transition (EOT; 34–33 Ma) triggered a marine mass extinction event and the turnover of terrestrial fauna, but its influence on the diversification of nearshore marine fish communities is unclear. Goby fishes (Acanthomorpha: Percomorpha: Gobiiformes) provide an ideal system to investigate the hypothesis that ecological opportunity at the EOT triggered the proliferation of coastal marine fishes. However, despite more than 30 years of molecular evolutionary research, divergence time estimates for gobies are widely variable, incomplete with respect to sampling of taxonomic families and sub-familial lineages, and far older than evident by the modest fossil record. Here we use 1,314 ultraconserved element (UCE) sequences sampled from 121 species, including all gobiiform families and sub-familial goby lineages, to infer phylogeny and node ages under species tree and relaxed molecular clock models. Our time-calibrated phylogenomic hyp..., , # Data from: Explosion of goby fish diversity at the Eocene-Oligocene transition

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[Access this dataset on Dryad](10.5061/dryad.mw6m9067p)

We have submitted a single file (j.ympev.2025.108342.zip) containing our 121-taxon, 75%- and 95%-complete ultraconserved elements (UCE) multiple gene sequence alignments used for inferring gene trees (gobiiformes-121-75p-gene) and concatenated trees (gobiiformes-121-75p.phylip; gobiiformes-121-95p.phylip) with the DNA substitution models used (gobiiformes-121-75p.nexus; gobiiformes-121-95p.nexus), the maximum likelihood genetrees (iqtree-75p-genetrees.nwk; iqtree-95p-genetrees.nwk) and concatenated trees (iqtree-75p.nwk; iqtree-95p.nwk), the Bayesian concatenated trees (exabayes-75p.nwk; exabayes-95p.nwk), and the multispecies coalescent genetree summary trees (astral-75p.nwk; astral-95p.nwk), with our 100-taxon, 9-partition multiple gene sequence alignments used for node dating (gobiiformes-100-9.phylip), the Autocorrelated rates time-calibrate...,