3.3.1 Principal component analysis
Our initial PCA performed on blue, fin and sei whales which grouped into distinct clusters when Principal Component 1 (PC1) and PC2 were plotted (Fig. 2B). One of the historical samples (NWa-CM1) was intermediate between the blue and fin whale cluster indicating it was a blue-fin hybrid which was also confirmed with D-statistics test. Two other historical samples (NWa5 and NWa6) also showed significant fin whale introgression from D-statistics analysis and were removed from further population studies.
The second PCA using LASER was performed for blue whale samples that did not show high fin whale introgression (Fig. 2C). Most NA samples clustered together, with the Antarctica sample being distinct on PC1. PC2 indicated that two blue whale samples from NEA (NE-Ar and NE3) and NWA (NW-M6 and NW9) were outliers to the main cluster of NA samples, which can be attributed to genomic variability within the NA samples and the low total variability accounted by PC2. PC2 accounted for ~9% of total variability of reference samples analyzed whereas PC1 accounted for ~16% of total variability.