DOI: 10.5061/dryad.mw6m9067p
title: Data from: Explosion of goby fish diversity at the Eocene-Oligocene transition

description: 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 hypothesis reconciles molecular clock- and fossil-based
 estimates for gobiiform diversification, dating the origin
 of Apogonidae and Gobioidei to the uppermost
 Late Cretaceous, with lower to middle Paleogene divergence of the gobioid
 backbone and an explosion of goby lineages at the EOT. Our results support
 a remarkably recent evolutionary origin of goby families and stimulate new
 questions on the seemingly exceptional diversity of the group.
description: # Data from: Explosion of goby fish diversity at the Eocene-Oligocene
 transition --- [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-calibrated tree (mcmctree-ar.nwk), and the Independent rates
 time-calibrated tree (mcmctree-ir.nwk). Gene and taxon names are
 consistent across all data files. ## Descriptions ###
 **gobiiformes-121-75p-gene** * Directory containing the FASTA-formatted,
 75%- and 95%-complete gene alignments used in phylogeny inference.
 Individual files are named by gene. ### **gobiiformes-121-75p.phylip**;
 **gobiiformes-121-95p.phylip** * Phylip-formatted 121-taxon, 75%- and
 95%-complete concatenated alignments used in phylogeny inference. ###
 **gobiiformes-121-75p.nexus**; **gobiiformes-121-95p.nexus** *
 Nexus-formatted 121-taxon, 75%- and 95%-complete partition model sets used
 in phylogeny inference. ### **iqtree-75p-genetrees.nwk**;
 **iqtree-95p-genetrees.nwk** * Newick-formatted 121-taxon, 75%- and
 95%-complete maximum likelihood genetrees. ### **iqtree-75p.nwk**;
 **iqtree-95p.nwk** * Newick-formatted 121-taxon, 75%- and 95%-complete
 maximum likelihood concatenated trees. ### **exabayes-75p.nwk**;
 **exabayes-95p.nwk** * Newick-formatted 121-taxon, 75%- and 95%-complete
 Bayesian concatenated trees. ### **astral-75p.nwk**; **astral-95p.nwk** *
 Newick-formatted 121-taxon, 75%- and 95%-complete multispecies coalescent
 genetree summary trees. ### **gobiiformes-100-9.phylip** *
 Phylip-formatted 100-taxon, 9-partition alignment used for node dating.
 ### **mcmctree-ar.nwk** * Newick-formatted, 100-taxon autocorrelated rates
 time-calibrated tree. ### **mcmctree-ir.nwk** * Newick-formatted,
 100-taxon independent rates time-calibrated tree. ## Sharing/Access
 information Data was derived from the following sources: *
 [NCBI](https://www.ncbi.nlm.nih.gov/) ## Code/Software All data files can
 be opened and interpreted with a standard text editor.