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).