2.5 Population structure analysis
To study if blue whales in the NWA represent a separate population from
the NEA, genomic population structure analyses were conducted on
present-day tissue samples of four NWA (NW-M6, NW-B7, NW7, NW9) and
eight NEA (NE1, NE2, NE3, NE4, NE71, NE72, NE73, NE-Ar) blue whales. One
sample (NW-M6) with high coverage of short read (99X) was adjusted to
~ 30X for this analysis to help SNP filtering and avoid
any bias due to large differences in depth of coverage. To deduce the
population structure of the NA blue whales prior to whaling and contrast
it to present-day population structure, six NWA (NWa-R4, NWa3, NWa4,
NWa5, NWa6, NWa-CM1) blue whales dating from the early days of blue
whale whaling through to post-whaling and one Antarctic blue whale
(Table 1) were included in the analyses. Population structure was
investigated using principal component analysis (PCA) and other
population structure analyses such as TREEMIX (Pickrell & Pritchard,
2012). and NGSADMIX (Skotte et al., 2013).