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.