DNA extraction and sequencing
From the tissue samples, we purified DNA for library preparation using
the Biotools Speedtools Tissue DNA Extraction kit. Next, we used
the restriction enzyme Pst1 to prepare the libraries for
genome-wide genotyping with GBS (Genotyping by Sequencing ). The
sequencing was done in an Illumina HiSeq2500 sequencer, and once the
sequences were obtained we characterized single nucleotide polymorphisms
(SNPs). For this purpose, we used the UNEAK pipeline, implemented in
TASSEL v.3.0 (Bradbury et al. 2007), and specifically designed for
samples of species without a reference genome. The sequences were pruned
to eliminate sequencing errors using the error rate threshold parameter.
The resulting database consisted of 83,648 SNPs with a coverage of 5.68
± 6.56 (mean ± sd) and missing site rate of 0.49 ± 0.33. We then
discarded loci with minor allele frequencies < 0.01, and those
that were sequenced in less than 10% of individuals. The final database
consisted of 73,291 loci, with a single SNP per locus and a coverage of
6.6 ± 6.75 and a missingness of 0.42 ± 0.31. This dataset was the one
used to analyze the neutral variation of our samples.