Phylogenomic analyses of all major sea cucumber lineages provide a robust backbone of Holothuroidea. undefined

Sea cucumbers (Echinodermata: Holothuroidea) are a diverse and ecologically important group found in almost every benthic marine habitat across all latitudes and depths. These animals have diversified across their environments with various evolutionary innovations related to feeding, respiration, and even swimming. Recently, phylogenetic evidence from mitochondrial and nuclear markers upended the prior belief that Dendrochirotida is an ancestral branch to all Holothuroidea, instead placing Apodida as sister to all Holothuroidea. However, these results were based on a few genes with low branch support of some key nodes indicating the need for more extensive analyses. Here, we tested previously published phylogenies of sea cucumbers by applying transcriptome and genome data from 37 Holothuroidea species representing 7 orders and 13 families, including 16 transcriptomic datasets generated as part of this study. We constructed a matrix of 4,900 translated transcripts encompassing 2,689,407 amino acid sites. We used this matrix to construct phylogenetic trees and recovered fully resolved clades for each of the seven holothuroid orders, confirming the placement of a monophyletic Apodida as sister to the remaining Holothuroidea. We included 13 families representing 7 orders of Holothuroidea in our analyses. Interestingly, we found that three of these families (Stichopodidae, Synallactidae, and Cucumariidae) were polyphyletic. Additionally, we were able to bring further resolution to lineages within Neoholothuriida by recovering Persiculida as sister to Molpadida and Synallactida as sister to Dendrochirotida. Our findings support recent phylogenetic work and provide additional resolution of tree topology with full branch support. Our study highlights the need for formally revising existing taxonomic classifications of Holothuroidea and provides a foundation from which the evolution of this can be investigated.