2.4 Population structure analysis
We studied the genetic structure of North Atlantic harbour porpoises by performing PCAs and admixture analyses on a set of unlinked SNPs. We used the software ngsLD (Fox et al., 2019) to prune our data of linked SNPs, considering that SNPs are in linkage disequilibrium (LD) if they are on the same chromosome/scaffold within less than 20 kb and using a minimum weight of 0.5. The PCAs were calculated withPCAngsd (Meisner & Albrechtsen, 2018), while the admixture analyses were run in NGSAdmix (Skotte et al., 2013). To assess convergence, we performed 20 independent runs, with the number of assumed populations (K) ranging from 2 to 8, a minimum tolerance for convergence of 1x10-10 and a minimum likelihood ratio value of 1x10-6.
To remove the genetic signal created by other subspecies and study the population structure of the P. p. phocoena subspecies, we excluded BLS samples and repeated the PCA and admixture analysis, with K ranging from 2 to 7. In addition, we examined the local population structure in the Baltic region by including only samples from NOS, BES, and PBS in an independent PCA and admixture analysis, with K ranging from 2 to 3.