DOI: 10.5061/dryad.2fj55
title: Data from: Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye

description: Background: Flatfish cranial asymmetry represents one of the most
 remarkable morphological innovations among vertebrates, and has fueled
 vigorous debate on the manner and rate at which strikingly divergent
 phenotypes evolve. A surprising result of many recent molecular
 phylogenetic studies is the lack of support for flatfish monophyly, where
 increasingly larger DNA datasets of up to 23 loci have yielded a
 polyphyletic or only weakly supported flatfish clade. Lack of resolution
 for flatfish relationships has been attributed to analytical limitations
 for dealing with processes such as nucleotide non-stationarity and
 incomplete lineage sorting (ILS). We tackle this phylogenetic problem
 using a sequence dataset comprising more than one thousand ultraconserved
 DNA element (UCE) loci covering 45 carangimorphs, the broader clade
 containing flatfishes and several other specialized lineages such as
 remoras, billfishes, and archerfishes. Results: We present a phylogeny
 based on UCE loci that unequivocally supports flatfish monophyly and a
 single origin of asymmetry. We document similar levels of discordance
 among UCE loci as in previous, smaller molecular datasets. However,
 relationships among flatfishes and carangimorphs recovered from multilocus
 concatenated and species tree analyses of our data are robust to the
 analytical framework applied and size of data matrix used. By integrating
 the UCE data with a rich fossil record, we find that the most distinctive
 carangimorph bodyplans arose rapidly during the Paleogene (66.0-23.03 Ma).
 Flatfish asymmetry, for example, likely evolved over an interval of no
 more than 2.9 million years. Conclusions: The longstanding uncertainty in
 phylogenetic hypotheses for flatfishes and their carangimorph relatives
 highlights the limitations of smaller molecular datasets when applied to
 successive, rapid divergences. Here, we recovered significant support for
 flatfish monophyly and relationships among crangimorphs through analysis
 of over 1,000 UCE loci. The resulting time-calibrated phylogeny points to
 phenotypic divergence early within carangimorph history that broadly
 matches with the predictions of adaptive models of lineage
 diversification.
description: flatfish_timetree_BMCebFossil calibrated time-tree from BEAST dating analyses.UCE alignments, 100% complete for 55 taxaUCE alignment files for 100% complete alignments (i.e. 97 UCE loci with each alignment containing all 55 taxa). Apologies for typos in some taxa names.sate-gblocks-clean-complete-matrix.tarUCE alignments containing minimum of 52 taxaUCE alignment files for 95% complete alignments (these alignments contain at least 52 of the 55 taxa from our analyses). Total of 596 UCE loci alignments. Apologies for typos in some taxa names.sate-gblocks-clean-min-52-taxa.tarUCE alignments, containing minimum of 41 taxaUCE alignments containing a minimum of 41 of our 55 sampled taxa. Total of 1014 UCE loci alignments. Apologies for typos in a few taxa names.sate-gblocks-clean-min-41-taxa.tarCarangimorpha exabayes phylogeny, 95% completeExabayes phylogeny from partitioned analysis of 596 concatenated UCE loci (corresponding to our 95% complete matrix, with 52 of 55 taxa present in each UCE locus).95p_complete_exabayes.treeCarangimorpha exabayes phylogeny, 75% complete matrixExabayes phylogeny from partitioned analysis of 1014 concatenated UCE loci (corresponding to our 75% complete matrix, with 41 of 55 taxa present in each UCE locus).75p_complete_exabayes.treeCarangimorpha exabayes phylogeny, 100% complete matrixExabayes phylogeny based on partitioned, concatenated analysis of 97 UCE loci (corresponding to our 100% complete matrix, with sequences of 55 of 55 taxa present for each locus).100p_complete_exabayes.tree