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.