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).