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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 eight 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 P.p. meridionalis), and three distinct populations within P.p. phocoena: Atlantic, Belt Sea and Proper Baltic Sea. Effective population size and Tajima's D suggest population contraction in Black Sea and Iberian porpoises, but expansion in the P.p. phocoena populations. Phylogenetic trees indicate post-glacial colonization from a southern refugium. Genotype–environment association analysis identified salinity as major driver in genomic variation and we identified candidate genes putatively underlying adaptation to different salinity. 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 can 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., Hälsoövervakning av marina däggdjur

Knowing the abundance of a population is a crucial component to assess its conservationstatus and develop effective conservation plans. For most cetaceans, abundanceestimation is difficult given their cryptic and mobile nature, especially when thepopulation is small and has a transnational distribution. In the Baltic Sea, the numberof harbour porpoises (Phocoena phocoena) has collapsed since the mid-20thcenturyand the Baltic Proper harbour porpoise is listed as Critically Endangered by the IUCNand HELCOM; however, its abundance remains unknown. Here, one of the largestever passive acoustic monitoring studies was carried out by eight Baltic Sea nationsto estimate the abundance of the Baltic Proper harbour porpoise for the first time. Bylogging porpoise echolocation signals at 298 stations during May 2011–April2013,calibrating the loggers’ spatial detection performance at sea, and measuring the clickrate of tagged individuals, we estimated an abundance of 71–1105individuals (95% CI,point estimate 491) during May–Octoberwithin the population's proposed managementborder. The small abundance estimate strongly supports that the Baltic Properharbour porpoise is facing an extremely high risk of extinction, and highlights theneed for immediate and efficient conservation actions through international cooperation.It also provides a starting point in monitoring the trend of the populationabundance to evaluate the effectiveness of management measures and determine itsinteractions with the larger neighboring Belt Sea population. Further, we offer evidencethat design-basedpassive acoustic monitoring can generate reliable estimatesof the abundance of rare and cryptic animal populations across large spatial scales.

The grey seal became locally extinct in the southern Baltic Sea, Danish Straits and Kattegat in the early 1900s after prolonged culling campaigns. Here, we combine national monitoring and anecdotal data from Denmark, Sweden, Germany and Poland to report on the grey seal's recolonisation of those areas and the initial reestablishment of breeding colonies. Grey seal occurrence has steadily increased since year 2003 as evidenced by the coordinated Baltic Sea moult censuses. At the first census in 2003, there were 146 grey seals along the southern Baltic coasts of Sweden and Denmark, ca 1% of the total Baltic Sea population count. Since 2015, this has increased to 2000–2600 grey seals, or ca 7% of the total population count. Since the local extinction, there have been sporadic breeding events in the 1940s on sea ice around Bornholm and in the 1980s and 1990s on haul-outs in Kattegat. In 2003, the first two pups in the southern Baltic Sea were recorded at Rødsand, Denmark. This is to date the only site in the southern Baltic Sea with regular annual pupping since the recolonisation. Since 2000, there have also been sporadic breeding events in Danish Kattegat, southern Sweden, Poland and Germany. At Rødsand, there have been at least 3–10 pups recorded every year since initiation of monitoring in 2011, with an increasing tendency until 2017 with 10 pups counted, which subsequently decreased to 5–6 pups annually in 2018–2020. Compared to recolonising events in the Atlantic, the numbers of pups are low. This may be caused by differences in population dynamics, recolonisation distances, habitat and mortality and effects of rehabilitation programmes. It is likely that the breeding distribution will spread throughout the southern Baltic, Danish Straits and Kattegat if appropriate protection measures of seals and haul-outs are installed.