43 Validated SNPs

Dataset "Ac_43validatedSNPs.csv" presents 43 validated SNP sequences screened for use in the analyses conducted in our manuscript. RAD tags (please see NCBI SRA BioProject #PRJNA503177, BioSample #SAMN10354042) were used to identify de novo candidate SNPs with Stacks v. 1.19 (Catchen et al. 2011; Catchen et al. 2013). We allowed a maximum of two mismatches between stacks within individuals and a minimum depth of coverage of three nucleotides for ustacks, and allowed no mismatches between stacks between individuals for cstacks. We then used Stacks script export_sql.pl (snps_l=1 -F snps_u=1 -F pare_l=3) to create a whitelist of all loci containing one snp with a minor variant present in at least three samples. The whitelist was used to select a subset of 50 candidate SNPs, of which seven failed validation (LGC Genomics LLC, Beverly, MA). Dataset "Ac_43validatedSNPs.csv" presents the 43 validated SNP sequences. Further filters were applied prior to the analyses detailed in the manuscript (please see Methods: RAD Library Preparation, SNP dentification and Assessment of Function).