3. Results
To disentangle the evolutionary history and population structure of North Atlantic harbour porpoises we resequenced genomes of 74 specimens from 8 different regions (Figure 1). Sample biological information and sequencing statistics are provided in Table S1. After all filtering steps, one BES individual (Figure S1C) kept a small fraction of the raw reads (6.65%, 2.73X coverage) and was discarded from further analysis. Mean sequencing depth was 10.11X (Figure S1B), which is considered an intermediate coverage level (Bourgeouis & Warren, 2021; Fuentes-Pardo & Ruzzante, 2017), and similar depth levels were used in other population genomic studies on cetaceans based on whole genome resequencing (Cerca et al., 2022; de Greef et al., 2022; Zhou et al., 2018). Scaffold coverage comparisons between male and female sequencing data (Figure S2) identified 47 sex associated scaffolds (122.3 Mb), which were subsequently removed from downstream analysis. Relatedness analysis (Figure S3) identified one pair of first-degree relatives, thus we removed the individual (B41-14) with the lower coverage out of the pair, leading to a final sample size of 72 harbour porpoises. After SNP calling and filtering, we retained a set of 6,186,462 high quality SNPs, from which 1,320,367 were identified as unlinked.