2.4 Mitochondrial genome assembly
For the comparisons of the mitochondrial genomes of present-day and historical blue whales, the trimmed and merged Illumina paired-end reads for all samples were aligned to a reference mitogenome (NC_00160136) using BOWTIE2 2.3.3.1 (Langmead & Salzberg, 2012). This was done for 25 of the blue whales sequenced herein (Table 1), including individuals for which DNA was too degraded for whole genome sequencing.