Data from: Confusion will be my epitaph: Genome-scale discordance stifles phylogenetic resolution of Holothuroidea

Sea cucumbers (Holothuroidea) are a diverse clade of echinoderms found
from intertidal waters to the bottom of the deepest oceanic trenches.
Their reduced skeletons and limited number of phylogenetically-informative
traits have long obfuscated morphological classifications.
Sanger-sequenced molecular datasets have also failed to constrain the
position of major lineages. Noteworthy, topological uncertainty has
hindered a resolution for Neoholothuriida, a highly diverse clade of
Permo-Triassic age. We perform the first phylogenomic analysis of
Holothuroidea, combining existing datasets with 12 novel transcriptomes.
Using a highly-curated dataset of 1,100 orthologs, our efforts
recapitulate previous results, struggling to resolve interrelationships
among neoholothuriid clades. Three approaches to phylogenetic
reconstruction (concatenation under both site-homogeneous and
site-heterogeneous models, and coalescent-aware inference) result in
alternative resolutions, all of which are recovered with strong support
and across a range of datasets filtered for phylogenetic usefulness. We
explore this intriguing result using gene-wise log-likelihood scores and
attempt to correlate these with a large set of gene properties. While
presenting novel ways of exploring and visualizing support for alternative
trees, we are unable to discover significant predictors of topological
preference, and our efforts fail to favor one topology. Neoholothuriid
genomes seem to retain an amalgam of signals derived from multiple
phylogenetic histories.