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.