2.5.3 NGSadmix
The individual admixture proportions for the blue whale samples from the
Treemix analysis were estimated by NGSADMIX, a maximum-likelihood method
based on genotype likelihoods in ANGSD v0.9 (Korneliussen et al., 2014).
NGSADMIX was run with clusters (k) of 2-5, and each k value was run 10
times to look for convergence. The variant sites were filtered to
include only those covered in at least 11 individuals with a SNP p-value
of < 1e-6 and a MAF >0.01.
The genetic divergence between blue whales in the NA was also
investigated using Weir and Cockerham weighted Fst (Weir & Cockerham,
1984). The Fst was estimated with 21,81,260 SNPs filtered as in the PCA
analysis for four NWA and seven NEA present-day samples with at least
>20X coverage.