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 >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.
All contigs assembled from target-enriched sequence data. Also be sure to see NCBI BioProject PRJNA348720 and NCBI Targeted Locus Study database KALI00000000-KAPX00000000.
Of the assembled contigs in 1-All-Assembled-Contigs.tar.gz, these are the loci, for each species, that are targeted UCE loci.
These 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).
These are the trimmed alignments used in analyses of the 95% complete (95p) data set.
These are the trimmed alignments used in analyses of the 75% complete (75p) data set.
Contains the concatenated loci from the 95% (95p) complete data set.
Contains the concatenated loci from the 75% (75p) complete data set.
RAxML Analysis files for the 75% (75p) complete data set. Includes unpartitioned, partitioned, and RY-coded analyses.
ExaBayes analysis files for the 95% (95p) complete data set. Includes unpartitioned and partitioned analyses.
ExaBayes analysis files for the 75% (75p) complete data set. Includes unpartitioned and partitioned analyses.
Astral analysis files for the 75% (75p) complete data set.
All phylogenetic trees from this manuscript, in a variety of formats.
Files used for rate-based partitioned of the 95% complete (95p) concatenated data, prior to analysis using PAML.
Input files (alignments, guide trees, control files) for all PAML dating analyses (baseml and mcmctree).
The dated tree resulting from mcmctree analysis.
Tabular (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.
A description of the steps used to assemble the data, prepare them for phylogenetic analysis, and run analyses.
A description of the steps used to format trees for the Supplement (specifically, Figures S1-S5).
Design 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.