Genotype likelihood (beagle file) and genotype (vcf) files of North Atlantic and Black Sea Harbour porpoises (Phocoena phocoena)

The Harbour porpoise (Phocoena phocoena) is a highly mobile cetacean
species primarily occurring in coastal and shelf waters across the
Northern hemisphere. It inhabits heterogeneous seascapes broadly varying
in salinity and temperature. Here we produced 74 whole genomes at
intermediate coverage to study Harbour porpoise’s evolutionary history and
investigate the role of local adaptation in the diversification into
subspecies and populations. We identified ~6 million high-quality SNPs
sampled at 8 localities across the North Atlantic and adjacent waters,
which we used for population structure, demographic, and
genotype-environment association analyses. Our results suggest a genetic
differentiation between three subspecies (P.p. relicta, P.p. phocoena, and
the recently proposed P.p meridionalis), and three distinct populations
within the subspecies P.p. phocoena: Atlantic, Belt Sea, and Proper Baltic
Sea. Effective population size and Tajima’s D levels suggest a population
contraction in Black Sea and Iberian porpoises, but a population expansion
in the P.p. phocoena populations. Phylogenetic trees indicate a
post-glacial colonization from a southern refugium. Genotype-environment
association analysis identified salinity as a major driver in genomic
variation and we identified candidate genes putatively underlying
adaptation to different salinity levels. Our study highlights the value of
whole genome resequencing to unravel subtle population structure in highly
mobile species, shows how strong environmental gradients and local
adaptation may lead to population differentiation and how neutral and
adaptive markers give different perspectives on population subdivision.
The results have great conservation implications as we found inbreeding
and low genetic diversity in the endangered Black Sea subspecies and
identified the critically endangered Proper Baltic Sea porpoises as a
separate population.