2.3 Whole genome sequencing
Present-day (from whales after 2010) and historic (from blue whales that
died during 1900-1975) samples were included in our analyses to explore
the effects of whaling. The reference-based alignments of the 12 blue
whales (11 sequenced here and the genomic blue whale sequences from
Árnason et al., (2018) represented here as NE-Ar) from present-day were
performed to the masked autosomal scaffolds of the assembled NA blue
whale genome and used in the population structure, heterozygosity
estimation and introgression analyses. DNA from historical blue whale
bone samples were collected from: the ROM; Canadian Museum of Nature,
Ottawa, Ontario; Smithsonian National Museum of Natural History,
Washington D.C.; Slottsfjells Museum, Tønsberg, Norway; and The Whaling
Museum, Sandefjord, Norway (Fig. 1, Table 1). DNA extraction was carried
out in an ancient DNA facility at ROM following the methodology detailed
in Supplemental Information. The paired-end reads were sequenced on an
Illumina HiSeq X sequencer at TCAG and the adapter sequences were
trimmed and paired-end reads were merged using Seqprep v 1.1
(https://github.com/jstjohn/SeqPrep) with default settings and quality
score cut-off for mismatches in overlap >20 (-q 20). The
first and last two bases of the merged reads were trimmed to remove DNA
damage in historical bone samples. The paired-end reads were aligned
using BWA 0.7.17 (Li & Durbin, 2009) and variant discovery was
conducted as described in the Supplementary Information.