The Harbour porpoise (Phocoena phocoena) is a highly mobile cetacean species which primarily occurs in coastal and shelf waters across the Northern hemisphere. It inhabits heterogeneous seascapes that vary broadly 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 support a genetic differentiation between three subspecies, 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 both Black Sea and Iberian porpoises while a population expansion in the P.p. phocoena populations. Phylogenetic trees indicate a post-glacial colonization of Harbour porpoises 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 and shows how strong environmental gradients and local adaptation may lead to population differentiation. The results have great conservation implications as we found major levels of inbreeding and low genetic diversity in the endangered Black Sea subspecies and identified the critically endangered Proper Baltic Sea porpoises as a separate population.

Knowing the abundance of a population is a crucial component to assess its conservation status and develop effective conservation plans. For most cetaceans, abundance estimation is difficult given their cryptic and mobile nature, especially when the population is small and has a transnational distribution. In the Baltic Sea, the number of harbour porpoises (Phocoena phocoena) has collapsed since the mid-20th century and the Baltic Proper harbour porpoise is listed as Critically Endangered by the IUCN; however, its abundance remains unknown. Here, one of the largest ever passive acoustic monitoring studies was carried out by eight Baltic Sea nations to estimate the abundance of the Baltic Proper harbour porpoise for the first time. By logging porpoise echolocation signals at 298 stations during May 2011-April 2013, calibrating the loggers’ spatial detection performance at sea, and measuring the click rate of tagged individuals, we estimated an abundance of 66-1,143 individuals (95% CI, point estimate 490) during May-October within the population’s proposed management border. The small abundance estimate strongly supports that the Baltic Proper harbour porpoise is facing an extremely high risk of extinction, and highlights the need for immediate and efficient conservation actions through international cooperation. It also provides a starting point in monitoring the trend of the population abundance to evaluate the effectiveness of management measures and determine its interactions with the larger neighbouring Belt Sea population. Further, we offer evidence that design-based passive acoustic monitoring can generate reliable estimates of the abundance of rare and cryptic animal populations across large spatial scales.