DOI: 10.5061/dryad.085dd
title: Data from: Explosive diversification of marine fishes at the Cretaceous-Paleogene boundary

description: The Cretaceous–Palaeogene (K–Pg) mass extinction is linked to the rapid
 emergence of ecologically divergent higher taxa (for example, families and
 orders) across terrestrial vertebrates, but its impact on the
 diversification of marine vertebrates is less clear. Spiny-rayed fishes
 (Acanthomorpha) provide an ideal system for exploring the effects of the
 K–Pg on fish diversification, yet despite decades of morphological and
 molecular phylogenetic efforts, resolution of both early diverging
 lineages and enormously diverse subclades remains problematic. Recent
 multilocus studies have provided the first resolved phylogenetic backbone
 for acanthomorphs and suggested novel relationships among major lineages.
 However, these new relationships and associated timescales have not been
 interrogated using phylogenomic approaches. Here, we use targeted
 enrichment of &gt;1,000 ultraconserved elements in conjunction with a
 divergence time analysis to resolve relationships among 120 major
 acanthomorph lineages and provide a new timescale for acanthomorph
 radiation. Our results include a well-supported topology that strongly
 resolves relationships along the acanthomorph backbone and the recovery of
 several new relationships within six major percomorph subclades.
 Divergence time analyses also reveal that crown ages for five of these
 subclades, and for the bulk of the species diversity in the sixth,
 coincide with the K–Pg boundary, with divergences between anatomically and
 ecologically distinctive suprafamilial clades concentrated in the first 10
 million years of the Cenozoic.
description: 1-All-Assembled-Contigs.tarAll contigs assembled from target-enriched sequence data. Also be sure to see NCBI BioProject PRJNA348720 and NCBI Targeted Locus Study database KALI00000000-KAPX00000000.2-Assembled-Contigs-That-Are-UCEs.tarOf the assembled contigs in 1-All-Assembled-Contigs.tar.gz, these are the loci, for each species, that are targeted UCE loci.3-All-Alignments-Untrimmed.tarThese are all alignments generated as part of this manuscript. Manuscripts in this archive are UNTRIMMED (we used TRIMMED alignments in the manuscript - see 4-95p-Trimmed-Alignments.tar.gz and 5-75p-Trimmed-Alignments.tar.gz for those).4-95p-Trimmed-Alignments.tarThese are the trimmed alignments used in analyses of the 95% complete (95p) data set.5-75p-Trimmed-Alignments.tarThese are the trimmed alignments used in analyses of the 75% complete (75p) data set.6-95p-Concatenated-Alignment-For-Analysis.tarContains the concatenated loci from the 95% (95p) complete data set.7-75p-Concatenated-Alignment-For-Analysis.tarContains the concatenated loci from the 75% (75p) complete data set.8-75p-Concatenated-RAxML-Analyses.tarRAxML Analysis files for the 75% (75p) complete data set. Includes unpartitioned, partitioned, and RY-coded analyses.9-95p-Concatenated-ExaBayes-Analyses.tarExaBayes analysis files for the 95% (95p) complete data set. Includes unpartitioned and partitioned analyses.10-75p-Concatenated-ExaBayes-Analyses.tarExaBayes analysis files for the 75% (75p) complete data set. Includes unpartitioned and partitioned analyses.11-75p-Astral-Analyses.tarAstral analysis files for the 75% (75p) complete data set.12-All-Phylo-Trees.tarAll phylogenetic trees from this manuscript, in a variety of formats.13-95p-Rate-Based-Partition-For-PAML.tarFiles used for rate-based partitioned of the 95% complete (95p) concatenated data, prior to analysis using PAML.14-PAML-Inputs.tarInput files (alignments, guide trees, control files) for all PAML dating analyses (baseml and mcmctree).15-Dated-Tree.tarThe dated tree resulting from mcmctree analysis.16-Dating-Figures-Inputs.tarTabular (CSV) output from mcmctree analyses that form the basis of Figures 5, S7, and S8, along with a description of steps used in R to plot the figures.README-Data-Processing-Analysis-StepsA description of the steps used to assemble the data, prepare them for phylogenetic analysis, and run analyses.README-Tree-Figure-Formatting-for-SupplementA description of the steps used to format trees for the Supplement (specifically, Figures S1-S5).fish-uce-1k-probes.MyBaits.UCE-Acanthomorphs.1Kv1.fastaDesign file for Acanthomorph baits. Also available as bait set from Arbor Biosciences (UCE-Acanthomorphs 1Kv1). Additionally same as bait set design file used in https://doi.org/10.5061/dryad.9pg8d.