Genomic DNA was extracted using the Qiagen DNeasy animal blood and tissue kit (Qiagen, Valencia, USA). The library was prepared using the double-digest RADseq protocol [35 (link)], with modifications (see electronic supplementary material, methods) and sequenced on a single Illumina HiSeq 2000 lane, at the UCLA Neuroscience Genomics Core facility. Raw data were de-multiplexed, quality filtered and trimmed to 95 bp, using the ‘process_rad_tags' script available in stacks v. 1.09 [36 (link)]. Loci were assembled using the stacks ‘de novo_map.pl' pipeline, while the ‘populations' script was used to filter loci and create output files (for raw data filtering and loci assembly see electronic supplementary material, methods). Loci were shared between the seven populations (p = 7), in at least 65% of individuals within a group (r = 0.65) and with a coverage of 8× (m = 8). We used only the first SNP of each sequence and removed loci with minor allele frequencies lower than 1.5% (i.e. at least two individuals must have the unique allele). Our quality control and filtering resulted in a total of 1174 loci and a data matrix that was 84% complete. We used pgdspider 2.0 [37 (link)] to convert the resulting structure files into other formats.
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