2.8 Neutral and Adaptive diversity
To get further insights into how adaptive processes shaped the genetic
structure of North Atlantic Harbour porpoises, we analyzed separately
the neutral and inferred adaptive SNPs. The neutral dataset consisted of
the SNPs not found under selection in the Pcadapt genome scan and
that were in Hardy-Weinberg Equilibrium (HWE), while the adaptive
dataset comprised the outlier SNPs identified by the Pcadaptgenome scan. We performed a PCA with the R package adegenet(Jombart & Ahmed, 2011) and estimated mean pairwise-weighted Fst across
populations using vcftools (v0.1.16) (Danecek et al., 2011). In
addition, a mantel test was run with the R package vegan to test
for isolation by distance (IBD) on both the neutral and adaptive SNP
datasets.