2.7 Pairwise sequentially Markovian coalescent (PSMC) model
The PSMC model was used to estimate changes in effective population size (Ne) through time (Li & Durbin, 2012). To infer population size history, whole genome sequences of an individual from the NWA (NW-B7) and whales from the NEA (NE2 and NE-Ar) were aligned to the masked NA blue whale assembly. The trimmed reads were aligned with BWA 0.7.17 and bam format files were generated following GATK best practices. A fin whale (~20X) was also included to infer its population history. The diploid consensus file for each individual was generated using SAMTOOLS MPILEUP version 1.5 following Li and Durbin (2012), and minimum and maximum depth of coverage thresholds were set to between 10X and 100X for all samples. The software PSMC v 0.6.5 was used with plots scaled by the mutation rates and generation times for the two different species of whales from Árnason et al., (2018).