DOI: 10.5061/dryad.9w0vt4bhq
title: Data from: Phylogenomics and historical biogeography of West Indian Rock Iguanas (genus Cyclura)

description: The genus Cyclura includes nine extant species and six subspecies of West
 Indian Rock Iguanas and is one of the most imperiled genera of squamate
 reptiles globally. An understanding of species diversity, evolutionary
 relationships, diversification, and historical biogeography in this group
 is crucial for implementing sound long-term conservation strategies. We
 collected DNA samples from 1–10 individuals per taxon from all Cyclura
 taxa (n = 70 ingroup individuals), focusing where possible on
 incorporating individuals from different populations of each species. We
 also collected 1–2 individuals from each of seven outgroup species of
 iguanas (Iguana delicatissima; five Ctenosaura species) and Anolis sagrei
 (n = 12 outgroup individuals). We used targeted genomic sequence capture
 to isolate and to sequence 1,872 loci comprising of 687,308 base pairs
 (bp) from each of the 82 individuals from across the nuclear genome. We
 extracted mitochondrial reads and assembled and annotated mitogenomes for
 all Cyclura taxa plus outgroup species. We present well-supported
 phylogenomic gene tree/species tree analyses for all extant species of
 Cyclura using ASTRAL-III, SVDQuartets, and starBEAST methods, and discuss
 the taxonomic, biogeographic, and conservation implications of these data.
 We find a most recent common ancestor of the genus 9.91 million years ago.
 The earliest divergence within Cyclura separates C. pinguis from a clade
 comprising all Cyclura except C. pinguis. Within the latter group, a clade
 comprising C. carinata from the southern Lucayan Islands and C. ricordii
 from Hispaniola is the sister taxon to a clade comprising the other
 Cyclura. Among the other Cyclura, the species C. cornuta and C. stejnegeri
 (from Hispaniola and Isla Mona) form the sister taxon to a clade of
 species from Jamaica (C. collei), Cuba and Cayman Islands (C. nubila), and
 the eastern (C. rileyi) and western (C. cychlura) Lucayan Islands. Cyclura
 cychlura and C. rileyi form a clade whose sister taxon is C. nubila.
 Cyclura collei is the sister taxon to these three species combined.
description: <strong>MTDNA-</strong> The mtDNA were collected as
 bycatch from UCE sequencing and the PHYLUCE pipeline. We gathered cleaned
 contigs generated from Velvet alignments, organized by individual, and
 mapped <em>Cyclura</em> contigs to a reference mitogenome of
 <em>C. pinguis</em> (GenBank ID LN835346; Gan et al., unpubl.)
 in Geneious 10.2.5
 (Biomatters<sup>®</sup> Auckland, New Zealand) using the
 Geneious mapper
 with medium sensitivity. For outgroups, we used the reference sequence
 <em>Anolis carolinensis</em> (EU747728) for our <em>A.
 sagrei</em> sample and <em>Iguana iguana</em> (AJ278511)
 for our <em>Iguana delicatissima</em> and
 <em>Ctenosaura</em> samples (Table 1). For each taxon, we
 mapped all available contigs from all available specimens, and then
 deleted the reference genome and extracted the consensus sequence. Thus,
 each consensus mitogenome sequence is chimeric, in that it is a consensus
 of nucleotides from multiple individuals of the same taxon to improve
 overall mitogenome coverage. We retained ambiguity codes in the consensus
 sequence, then aligned all consensus sequences together to create a
 mitogenome alignment for all our <em>Cyclura</em> taxa as well
 as outgroups. We then annotated these mitogenomes using the MITOS2
 webserver (http://mitos2.bioinf.uni-leipzig.de/index.py; Bernt et al.
 2013) and verified correct annotation via alignment with the reference
 mitogenomes. We subsequently manually verified the positions of start and
 stop codons and indels in protein-coding regions of all
 alignments. UCE DATA- We then batched raw fastq reads
 into the Linux <em>phyluce</em> pipeline— a toolkit comprising
 conda-packaged Python scripts to facilitate UCE identification and
 extraction (Faircloth 2016). We used the Illumiprocessor Python script
 (Faircloth 2014), which calls Trimmomatic (Bolger et al. 2014) to trim
 adapters and low-quality sequences reads. We then assembled contigs from
 the cleaned reads using the Velvet algorithm (Zerbino and Birney 2008)
 with <em>kmer</em> = 51. We then extracted UCE loci from the
 contigs file by matching contigs to the UCE Tetrapods 5kv1 probe set
 (available at
 https://github.com/faircloth-lab/uce-probe-sets/blob/master/uce-5k-probe-set/uce-5k-probes.fasta). We aligned UCE loci using the MAFFT algorithm (Katoh and Standley 2013) with edge trimming, then removed prepended locus names from the alignments. We created a 50% complete data matrix, whereby we retained aligned UCE loci with at least 50% of the taxa represented for every retained locus. This supermatrix dataset consisted of 82 taxa, 1,872 loci, and 687,308 bp. More stringent matrices (i.e., 75%, 95%) were found in initial study to have significantly lower phylogenetic resolution and were therefore not used. We conducted all UCE bioinformatics on a Dell® (Dell Inc., Round Rock, TX) PowerEdge© Server (64c, 128gb RAM) running Ubuntu 16.04.5 as well as the CHILABOTHRUS Dell® PowerEdge© Server (16c, 128gb RAM) running Ubuntu 20.04, both at the University of North Carolina Asheville.
description: The mtDNA sequences are chimeric, each species' sequence is
 a combination of 1-8 individuals of that species sampled near each other
 that were sequenced using UCE baits.