Data from: Phylogenomics and historical biogeography of West Indian Rock Iguanas (genus Cyclura)

<p>The genus <em>Cyclura</em> 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 <em>Cyclura</em> 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 (<em>Iguana delicatissima</em>; five <em>Ctenosaura</em> species) and <em>Anolis sagrei</em> (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 <em>Cyclura</em> taxa plus outgroup species. We present well-supported phylogenomic gene tree/species tree analyses for all extant species of <em>Cyclura</em> 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 <em>Cyclura</em> separates <em>C. pinguis</em> from a clade comprising all <em>Cyclura</em> except <em>C. pinguis</em>. Within the latter group, a clade comprising <em>C. carinata</em> from the southern Lucayan Islands and <em>C. ricordii</em> from Hispaniola is the sister taxon to a clade comprising the other <em>Cyclura</em>. Among the other <em>Cyclura</em>, the species <em>C. cornuta</em> and <em>C. stejneger</em>i (from Hispaniola and Isla Mona) form the sister taxon to a clade of species from Jamaica (<em>C. collei</em>), Cuba and Cayman Islands (<em>C. nubila</em>), and the eastern (<em>C. rileyi</em>) and western (<em>C. cychlura</em>) Lucayan Islands. <em>Cyclura</em> <em>cychlura</em> and <em>C. rileyi</em> form a clade whose sister taxon is <em>C. nubila</em>. <em>Cyclura</em> collei is the sister taxon to these three species combined.</p>