Phylogenomic of extant Crinoidea (Echinodermata) reveals extensive morphological homoplasies and a Permian origin

Crinoids are echinoderms with ancient origins in the Ordovician, unique among living forms in possessing structures of attachment to the substrate. Their diversity is concentrated within Comatulida (the feather stars), which includes mobile and generally shallow-water species. The otherwise mostly sessile, stalked, and deep-water diversity—the sea lilies—encompasses Isocrinida, Hyocrinida, and Cyrtocrinida. While the relationships among Paleozoic crinoids are well established, the phylogeny of the crown group (Articulata) remains uncertain. We present the first phylogenomic analyses of crinoids reliant on novel transcriptomic and targeted-exon capture datasets spanning 119 terminals. We resolve Isocrinida as the sister group to the remainder of Articulata, which is further subdivided into Comatulida and a clade of Hyocrinida + Cyrtocrinida. We corroborate the placement of the stalked Bourgueticrinina within the otherwise stalkless comatulids, but also find the unusual feather star Atopo..., , # Data from: Phylogenomics of extant Crinoidea (Echinodermata) suggests a dual ancestry in the Permian

The data contained in this repository support the results presented in Rouse et al. (2025) *in prep*, presenting the results of the first phylogenomic analysis for Crinoidea (Echinodermata) based on both phylotranscriptomic and targeted exon-capture approaches.

## Description of the data and file structure

The repository contains six folders, which have been zipped for convenience.

The first of these, 'baits.zip', contains a single file 'aln_baits.fas', a FASTA format file containing the nucleotide sequences developed for DNA enrichment of targeted exons. The description of each sequence follows the format \"geneName-exon-organism_baitStartPosition\", so the description of the first sequence \">calret-3-Met_0\" identifies this sequence as a bait to target the third exon of the gene calret, developed from the sequence of that gene corresponding to the taxon *Metacrinus rotundus*, and st...,