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).