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.