The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.

Flame retardants are globally distributed contaminants that have been linked to negative health effects in humans and wildlife. As top predators, marine mammals bioaccumulate flame retardants and other contaminants in their tissues which is one of many human-imposed factors threatening population health. While some flame retardants, such as the polybrominated diphenyl ethers (PBDE), have been banned because of known toxicity and environmental persistence, limited data exist on the presence and distribution of current-use alternative flame retardants in marine mammals from many industrialized and remote regions of the world. Therefore, this study measured 44 legacy and alternative flame retardants in nine marine mammal species from three ocean regions: the Northwest Atlantic, the Arctic, and the Baltic allowing for regional, species, age, body condition, temporal, and tissue comparisons to help understand global patterns. PBDE concentrations were 100–1000 times higher than the alternative brominated flame retardants (altBFRs) and Dechloranes. 2,2′,4,5,5′-pentabromobiphenyl (BB-101) and hexabromobenzene (HBBZ) were the predominant altBFRs, while Dechlorane-602 was the predominant Dechlorane. This manuscript also reports only the second detection of hexachlorocyclopentadienyl-dibromocyclooctane (HCDBCO) in marine mammals. The NW Atlantic had the highest PBDE concentrations followed by the Baltic and Arctic which reflects greater historical use of PBDEs in North America compared to Europe and greater industrialization of North America and Baltic countries compared to the Arctic. Regional patterns for other compounds were more complicated, and there were significant interactions among species, regions, body condition and age class. Lipid-normalized PBDE concentrations in harbor seal liver and blubber were similar, but HBBZ and many Dechloranes had higher concentrations in liver, indicating factors other than lipid dynamics affect the distribution of these compounds. The health implications of contamination by this mixture of compounds are of concern and require further research.

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.

The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-bydistance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymorphisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis.

North American river otters (Lontra canadensis) aretop predators in riverine ecosystems and are vulnerable to per- andpolyfluoroalkyl substance (PFAS) exposure. Little is known aboutthe magnitude of exposure and tissue distribution of PFAS in riverotters. We measured 45 PFAS in various tissues of 42 river otterscollected from several watersheds in the state of West Virginia,USA. The median concentrations of ΣAll (sum concentration of45 PFAS) varied among tissues in the following decreasing order:liver (931 ng/g wet weight) > bile > pancreas > lung > kidney >blood > brain > muscle. Perfluoroalkylsulfonates (PFSAs) were thepredominant compounds accounting for 58−75% of the totalconcentrations, followed by perfluoroalkyl carboxylates (PFCAs;21−35%). 8:2 fluorotelomer sulfonate (8:2 FTS), 10:2 FTS, and 6:2 chlorinated polyfluoroalkyl ether sulfonate were frequentlyfound in the liver (50−90%) and bile (96−100%), whereas hexafluoropropylene oxide dimer acid (HFPO-DA) was rarely found.The hepatic concentrations of ΣAll in river otters collected downstream of a fluoropolymer production facility located along theOhio River were 2-fold higher than those in other watersheds. The median whole body burden of ΣAll was calculated to be 1580μg. PFOS and perfluorooctanoic acid (PFOA) concentrations in whole blood of some river otters exceeded the human toxicityreference values, which warrant further studies.

Denna rapport är den första delen av två i en pilotstudie om läkemedelsrester i utter. I den första delen ville vi undersöka om det gick att analysera rester av läkemedel i urin och blod från utter, samt att utvärdera vilken matris som är mest lämplig för ändamålet.    Vi har analyserat 30 olika läkemedelsrester i blod och urin från 20 poolade prover som innehöll blod respektive urin från 33 uttrar. Samtliga läkemedel fanns i blod och/eller urinprover, dock inte i alla prov. Ett flertal ämnen låg under kvantificerbar nivå (<LOQ). Det innebär att man kan se att de finns i provet men pga ”brus” inte kan kvantificera det.  Det antidepressiva medlet Venlafaxin fanns i samtliga tio blodprover (0,24-2,0 ng/g färskvikt) men inte alls i urinproverna. Risperidone som används vid behandling av bl.a. schitzofreni fanns i mätbara halter i 7 av de 10 blodproven (4,3-250 ng/g färskvikt) och 7 av 10 urinprov (0,12-46 ng/g färskvikt).   Högst antal läkemedelsrester i urinet hade en utter från Västervik (11 st + 4 st <LOQ). Den hade också mätbara halter från 7 olika läkemedelsrester i blodet (+ 4 st <LOQ).  Det fanns fler mätbara läkemedel i urinproverna jämfört med blodproverna, med ett undantag (Venlafaxin). Dessvärre är urin begränsande, de flesta uttrar som inkommer till museet har tom eller nästan tom urinblåsa. Att blodprov ändå fungerar bra är positivt. Det är oftast möjligt att ta blod från uttrarna som skickas in och därför föreslår vi att man i fortsättningen analyserar blod, och urin bara i de fall där det är möjligt.