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Dryad

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

Cite this dataset

Mongiardino Koch, Nicolás (2023). Data from: Confusion will be my epitaph: Genome-scale discordance stifles phylogenetic resolution of Holothuroidea [Dataset]. Dryad. https://doi.org/10.5061/dryad.0p2ngf255

Abstract

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.

Funding

National Science Foundation, Award: DEB-1036368

National Science Foundation, Award: DEB-2036186

National Science Foundation, Award: OPP-1043749