Data from: Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye

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.