DOI: 10.5061/dryad.573n5tb51
title: Data from: Conserved ZZ/ZW sex chromosomes in Caribbean croaking geckos (Aristelliger : Sphaerodactylidae)

description: Current understanding of sex chromosome evolution is largely dependent on
 species with highly degenerated, heteromorphic sex chromosomes, but by
 studying species with recently evolved or morphologically indistinct sex
 chromosomes we can greatly increase our understanding of sex chromosome
 origins, degeneration, and turnover. Here, we examine sex chromosome
 evolution and stability in the gecko genus Aristelliger. We used RADseq to
 identify sex-specific markers and show that four Aristelliger species,
 spanning the phylogenetic breadth of the genus, share a conserved ZZ/ZW
 system syntenic with avian chromosome two. These conserved sex chromosomes
 contrast with many other gecko sex chromosome systems by showing a degree
 of stability among a group known for its dynamic sex determining
 mechanisms. Cytogenetic data from A. expectatus revealed homomorphic sex
 chromosomes with an accumulation of repetitive elements on the W
 chromosome. Taken together, the large number of female-specific A.
 praesignis RAD markers and the accumulation of repetitive DNA on the A.
 expectatus W karyotype suggests that the Z and W chromosomes are highly
 differentiated despite their overall morphological similarity. We discuss
 this paradoxical situation and suggest that it may, in fact, be common in
 many animal species.
description: We generated single-digest RADseq libraries for 10 males and 10
 females of <em>Aristelliger praesignis</em> using a modified
 protocol from Etter et al. (2012) as described in Gamble et al.
 (2015). Libraries were sequenced using paired-end 125 bp reads on an
 Illumina HiSeq2500 at the Medical College of Wisconsin. We analyzed the
 RADseq data using a previously described bioinformatic pipeline (Gamble et
 al., 2015). Raw Illumina reads were demultiplexed, trimmed, and filtered
 using the process_radtags function in STACKS (1.41, Catchen, Amores,
 Hohenlohe, Cresko, & Postlethwait, 2011). We used RADtools (1.2.4,
 Baxter et al., 2011) to generate RADtags for each individual and
 identified candidate loci and alleles from the forward reads. We then used
 a custom python script (Gamble et al., 2015) to identify putative
 sex-specific markers from the RADtools output, i.e. markers found in one
 sex but not the other. The script also generated a list of “confirmed”
 sex-specific RAD marker that excluded any sex-specific markers found in
 the original read files of the opposite sex. Finally, we used Geneious
 (R11, Kearse et al., 2012) to assemble the forward and reverse reads of
 “confirmed” sex-specific RAD markers.  We PCR amplified
 and Sanger sequenced the mitochondrial gene NADH dehydrogenase subunit 2
 (ND2) and adjacent tRNAs with the primers L4437b (Macey, Larson, Ananjeva,
 & Papenfuss, 1997), L5005 (Jennings, Pianka, & Donnellan,
 2003), and H5934a (Arevalo, Davis, & Sites Jr, 1994). We aligned
 these new sequences with previously published sequences (Gamble,
 Greenbaum, Jackman, Russell, & Bauer, 2012) in Geneious (R9.1.6,
 Kearse et al. 2012) using MUSCLE (Edgar, 2004) and inspected the resulting
 alignment by eye for errors. We constructed a maximum likelihood tree
 using RAxML (V8.2, Stamatakis, 2014) with a GTR+GAMMA model. Branch
 support was generated using 1000 bootstrap replicates. We included
 <i>Quedenfeldtia trachyblepharus</i> and
 <i>Quedenfeldtia moerens </i>as outgroups. Finally, we
 calculated between group genetic p-distance for putative species using
 MEGA X (V10.1, Kumar, Stecher, Li, Knyaz, & Tamura,
 2018).