Variant Calling and SNP Filtering.

SNP calling and genotyping were performed with the Genome Analysis Toolkit v. 3.5-0-g36282e4 HaplotypeCaller (73) run in Genome Variant Call Format (GVCF) mode followed by joint genotyping with GenotypeGVCFs. Reads were filtered from the HaplotypeCaller step to exclude those with a mapping quality <10 and to exclude those marked as secondary alignments. We excluded SNPs in repetitive regions identified during the annotation of the genome assembly (39). We also excluded multiallelic SNPs and SNPs within 6 bps of indel polymorphisms. For further filtering, thresholds were determined following Flowers et al. (30), from which most of our data come from. Statistical analyses were conducted with the R Statistical programming language (74).