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).