Historical demography
PSMC (Li & Durbin 2011) was used on consensus genomic sequence data to characterize historical demography by examining heterozygosity densities in 100 bp sliding windows across the genome. In the absence of near-relative fossil calibrations for martens, we compared divergence estimates from PSMC against estimates based on complete mitochondrial genomes (Schwartz et al. 2020). PSMC was run twice for each individual, once utilizing all mapped sequence data and again on data down-sampled to 20X coverage (near the lowest coverage sample) using the DownsampleSam tool (Picard v. 1.9). Results were scaled by a general mammalian mutation rate (2.2 x 10-9 per base pair per year; Kumar & Subramanian 2002) and a 5-year marten generation time, resulting in distributions of effective population size (Ne) through time. One hundredPSMC bootstrap replicates were performed and plotted for both full-coverage and down-sampled data to confirm consistent distributional shapes and enable comparison across individuals, as PSMC is sensitive to variation in coverage depth (ideal coverage >18X; Nadachowska-Brzyska et al. 2016).