DOI: 10.5061/dryad.xksn02vvq
title: Data from: Phylogenomic of extant Crinoidea (Echinodermata) reveals extensive morphological homoplasies and a Permian origin

description: 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 Atopocrinus closest to the stalked hyocrinids, showing the
 extreme lability of these body plans. Taxonomic revisions within
 Comatulida are much needed, with major problems particularly within
 Antedonidae. Divergence time estimates place the origin of Articulata
 within the Permian, contradicting the prevailing views that consider the
 clade a post-Paleozoic radiation. A revision of the Permian fossil record
 is needed to understand the emergence of living crinoids.
description: # 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 "&gt;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 starting in position 0. Taxon codes are
 as follows - Met: *Metacrinus rotundus*; Crino: *Lamberticrinus messingi*;
 Cya: *Cyathidium pourtalesi*; Oligo: *Oligometra carpenteri*. The second
 folder, named 'dating.zip', contains the files used for running
 approximate likelihood divergence time estimation using the program
 MCMCtree. These include: 1. Two phylogenetic trees in newick format (.tre
 file extension) with calibration priors specified as node labels. These
 correspond to either uniform of 10% truncated Cauchy distributions, which
 are specified in the name of the file. The trees can be visualized using
 software such as FigTree. 2. Two concatenated alignments in sequential
 phylip format (.phy file extension) containing a small number of either
 randomly-sampled or clock-like loci drawn from the full datasets, coded as
 amino acids and spanning 119 taxa (same number as the tree files). These
 were generated in R using code from the *genesortR* script. The files can
 be opened with a text editor or and alignment visualizer such as SeaView.
 3. Eight control files (.ctl file extension) used to set up the divergence
 time estimation runs in MCMCtree using either one of the matrices
 described above, either one of the trees described above, as well as two
 different molecular clock models (autocorrelated vs uncorrelated). The
 combination of these options produces eight different analyses, each run
 using one of these files in duplicate to assess convergence. The files can
 be opened with any text editor. The third folder, named
 'phylotranscriptomic.zip', contain five files that include the
 main results of the assembly and analysis of crinoid phylotranscriptomic
 data. These include: 1. Two concatenated supermatrices of amino
 acid-encoded aligned loci in FASTA format (.fa file extension). These were
 generated using the phylogenoic workflow Agalma v.2.0. The first of these
 contains the sequences for all 12,011 one-to-one orthologs recovered
 ('transcriptome_supermatrix_full.fa'), while the second contains
 only the highest-occupancy loci, representing an 80% occupancy matrix that
 was used for all subsequent downstream analyses
 ('transcriptome_supermatrix_80p_occ.fa'). 2. Two RAxML-style
 partition files (.txt file extension) containing information of the start
 and end position of all loci contained in the aforementioned matrices
 ('transcriptome_partitions_full.txt' and
 'transcriptome_partitions_80p_occ.txt'). 3. A phylogenetic tree
 in newick format (.tre file extension) containing the phylogenetic tree
 resulting from the analysis of the 80% phylotranscriptomic occupancy
 matrix with IQ-TREE2, with bootstrap support values specified as node
 labels. This tree corresponds to that shown in Fig. 2 of the manuscript.
 The remaining three folders each contain the same set of files, and all
 correspond to the analysis of the crinoid targeted exon-capture data. Each
 of the folders contains files corresponding to the data (and results drawn
 from them) encoded as either amino acids
 ('targeted_exon_capture_AA.zip'), nucleotides
 ('targeted_exon_capture_DNA.zip'), or nucleotides with third
 positions removed to limit the extent of saturation
 ('targeted_exon_capture_DNA_trimmed.zip'). The files contained
 within each are: 1. A phylogenetic tree in newick format (.tre file
 extension) beginning with the name 'alltrees' which include all
 the phylogenetic trees inferred individually from each locus. These were
 obtained using the phylogenomic inference pipeline ParGenes v.1.2.0.
 Support values were estimated using 100 replicates of non-parametric
 bootstrap and are placed as node labels. 2. A phylogenetic tree in newick
 format (.tre file extension) beginning with the name 'ASTRAL'
 which includes the species tree reconstructed using ASTRAL-IV based on the
 aforementioned gene trees. Support values (local posterior probabilities)
 are placed as node labels. Nodes in the gene trees with support values
 &lt; 10% were first imported into R and collapsed using functions from
 packages *phangorn* and *ips*. 3. A phylogenetic tree in newick format
 (.tre file extension) beginning with the name 'IQTREE' which
 includes the species tree reconstructed using IQ-TREE2 using a best-fit
 merged partitioned model and 1,000 replicates of ultrafast bootstrap
 (placed as node values). 4. The corresponding concatentated supermatrix in
 FASTA format (.fa file extension). 5. The corresponding RAxML-style
 partition file (.txt file extension). ## Sharing/Access information
 Software used to generate these files include: * Dos Reis M. & Yang Z.
 2011. Approximate likelihood calculation on a phylogeny for Bayesian
 estimation of divergence times. *Molecular biology and evolution*, **28**:
 2161-2172. * Dunn C.W., Howison M. & Zapata F. 2013. Agalma: an
 automated phylogenomics workflow. *BMC bioinformatics*, **14**: 330. *
 Heibl C. 2008. IPS: R language interfaces to diverse phylogenetic software
 packages.
 [http://www.christophheibl.de/Rpackages.html](http://www.christophheibl.de/Rpackages.html). * Minh B.Q., Schmidt H.A., Chernomor O., Schrempf D., Woodhams M.D., von Haeseler A. & Lanfear R. 2020. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. *Molecular Biology and Evolution*, **37**: 1530–1534. * Mongiardino Koch N. 2021. Phylogenomic subsampling and the search for phylogenetically reliable loci. *Molecular Biology and Evolution*, **38**: 4025-4038. * Morel B., Kozlov A.M. & Stamatakis A. 2018. ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes. *Bioinformatics*, **35**: 1771-1773. * R Core Team. 2024. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. [https://www.R-project.org/](https://www.R-project.org/) * Schliep K.P. 2011. phangorn: phylogenetic analysis in R. *Bioinformatics*, **27**: 592-593. * Zhang C., Nielsen R. & Mirarab S. 2025. ASTER: A Package for Large-Scale Phylogenomic Reconstructions. *Molecular Biology and Evolution*, **42**: msaf172.