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.