3.2 SNP variation
RAD-sequencing of 139 P. auritus samples generated a total of 838,425,400 reads after filtering out low-quality samples and reads. The number of raw sequence reads per sample ranged from 133,185 to 16 million. The mean coverage depth ranged from 5x to 26x across individual samples (mean = 8x, median = 7x, Appendix 2). From these reads, we assembled 2,979 high-quality RAD loci and a total of 32,966 SNPs that were present in 80% or more samples. Using a minor allele frequency cutoff of 5%, we retained 1631 RAD loci encompassing 3,092 SNPs. Across sampling sites, the number of segregating sites ranged from 1,834 to 13,335 (mean = 8,473) and nucleotide diversity (π) ranged from 0.0041 to 0.0062/bp (mean = 0.0055/bp).