Genetic diversity calculations
Genetic diversity was measured as two different values, the genetic diversity within a population (\({\overset{\overline{}}{H}}_{E}\)) and the genetic divergence (FST). FST was calculated for each species using the R package poolFstat (Hivertet al. , 2018). \({\overset{\overline{}}{H}}_{E}\) was estimated per population from the average expected heterozygosity of all SNPs within a 50,000bp window, including invariant sites as 0s in the calculation. This approach was relatively unbiased by depth of coverage, as \({\overset{\overline{}}{H}}_{E}\) did not correlate with average window coverage (Fig. S2). \({\overset{\overline{}}{H}}_{E}\ \)was calculated directly from the VCFs using a custom R script (GitHub: ja-Reeve/CompGenoScan/R_scripts/Heterozygosity).