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.

Garden Warblers Sylvia borin were studied during autumn stopover in Crete before

crossing the barrier of theMediterranean Sea and the Sahara Desert. Birds followed

with transmitters show extensive stopover periods, which were longer in first-year

birds, 16 days, compared with adult birds, 14 days. The distribution of body masses

frombirds trapped in fig trees were used to estimate the departure body mass and the

results found indicate that both age categories on average depart with a fuel load close

to 100% of lean body mass. The movement of transmitter birds shows di

fferences between

first-year and adult birds. Adult birds move further away from the release site

and many also left the study area. Several were found settled outside the study area,

up to 17 km away, indicating that they regularly make longer stopover movements. It

is suggested that this might be a result of that they return to a place where they stayed

during an earlier migration. It was shown that stopover site fidelity exists and nine

garden warblers were recaptured in the area during a following autumn. The results

found highlights the importance of stopover areas close to the SaharaDesert.

In spring, long-distance migrants are considered to adopta time-minimizing strategy to promote early arrival atbreeding sites. The phenology of spring migration wasexamined and compared between two insular stopoversites in Greece and Sweden for Icterine Warbler, WoodWarbler, Spotted Flycatcher and Collared Flycatcher. All  of them migrate due north which means that some proportion of birds that pass through Greece are headingto Scandinavia. The Collared Flycatcher had the earliestand the Icterine Warbler the latest arrival time. Thedifferences in median dates between Greece and Swedenwere 3–4 weeks and the passages in Sweden weregenerally more condensed in time. The average overallspeed estimates were very similar and varied between129 and 137 km/d. In most of the species higher speedestimates were associated with years when birds arrivedlate in Greece. After crossing continental Europe birdsarrive at the Swedish study site with significantly higherbody masses compared to when they arrive in Greece andthis might indicate a preparation for arriving at breedinggrounds with some overload.

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.

Mercury (Hg) is a pollutant of global concern. Due to anthropogenic emissions, the atmospheric and surface ocean Hg burden has increased substantially since preindustrial times. Hg emitted into the atmosphere gets transported on a global scale and ultimately reaches the oceans. There it is transformed into highly toxic methylmercury (MeHg) that effectively accumulates in the food web. The international community has recognized this serious threat to human health and in 2017 regulated Hg use and emissions under the UN Minamata Convention on Mercury. Currently, the first effectiveness evaluation of the Minamata Convention is being prepared, and, in addition to observations, models play a major role in understanding environmental Hg pathways and in predicting the impact of policy decisions and external drivers (e.g., climate, emission, and land-use change) on Hg pollution. Yet, the available model capabilities are mainly limited to atmospheric models covering the Hg cycle from emission to deposition. With the presented model MERCY v2.0 we want to contribute to the currently ongoing effort to improve our understanding of Hg and MeHg transport, transformation, and bioaccumulation in the marine environment with the ultimate goal of linking anthropogenic Hg releases to MeHg in seafood.

Here, we present the equations and parameters implemented in the MERCY model and evaluate the model performance for two European shelf seas, the North and Baltic seas. With the model evaluation, we want to establish a set of general quality criteria that can be used for evaluation of marine Hg models. The evaluation is based on statistical criteria developed for the performance evaluation of atmospheric chemistry transport models. We show that the MERCY model can reproduce observed average concentrations of individual Hg species in water (normalized mean bias: HgT 17 %, Hg0 2 %, MeHg −28 %) in the two regions mentioned above. Moreover, it is able to reproduce the observed seasonality and spatial patterns. We find that the model error for HgT(aq) is mainly driven by the limitations of the physical model setup in the coastal zone and the availability of data on Hg loads in major rivers. In addition, the model error in calculating vertical mixing and stratification contributes to the total HgT model error. For the vertical transport we find that the widely used particle partitioning coefficient for organic matter of log(kd)=5.4 is too low for the coastal systems. For Hg0 the model performance is at a level where further model improvements will be difficult to achieve. For MeHg, our understanding of the processes controlling methylation and demethylation is still quite limited. While the model can reproduce average MeHg concentrations, this lack of understanding hampers our ability to reproduce the observed value range. Finally, we evaluate Hg and MeHg concentrations in biota and show that modeled values are within the range of observed levels of accumulation in phytoplankton, zooplankton, and fish. The model performance demonstrates the feasibility of developing marine Hg models with similar predictive capability to established atmospheric chemistry transport models. Our findings also highlight important knowledge gaps in the dynamics controlling methylation and bioaccumulation that, if closed, could lead to important improvements of the model performance.

Identifying Hg sources to aquatic ecosystems and processes controlling the levels of monomethylmercury (MMHg) is critical for developing efficient policies of Hg emissions reduction. Here we measured Hg concentrations and stable isotopes in sediment, seston, and fishes from the various basins of the Baltic Sea, a large brackish ecosystem presenting extensive gradients in salinity, redox conditions, dissolved organic matter (DOM) composition, and biological activities. We found that Hg mass dependent fractionation (Hg-MDF) values in sediments mostly reflect a mixing between light terrestrial Hg and heavier industrial sources, whereas odd Hg isotope mass independent fractionation (odd Hg-MIF) reveals atmospheric inputs. Seston presents intermediate Hg-MDF and odd Hg-MIF values falling between sediments and fish, but in northern basins, high even Hg-MIF values suggest the preferential accumulation of wet-deposited Hg. Odd Hg-MIF values in fish indicate an overall low extent of MMHg photodegradation due to limited sunlight exposure and penetration but also reveal large spatial differences. The photodegradation extent is lowest in the central basin with recurrent algal blooms due to their shading effect and is highest in the northern, least saline basin with high concentrations of terrestrial DOM. As increased loads of terrestrial DOM are expected in many coastal areas due to global changes, its impact on MMHg photodegradation needs to be better understood and accounted for when predicting future MMHg concentrations in aquatic ecosystems.

Since the 1970s, grey seals (Halichoerus grypus), harbour seals (Phoca vitulina) and ringed seals (Phoca hispida) have been collected and necropsied at the Swedish Museum of Natural History. Mostly have grey seals been examined. The effect of hunting during 19^th century and reproductive failure during the latter half of the century decreased Baltic seal populations. In the 1970s and 1980s, pathological changes found mostly in grey seals was called the Baltic Seal Disease Complex and was thought to be related to high levels of PCB and DDT. Since then several pathological changes have decreased in prevalence as well as levels of PCB and DDT. Since then in grey seals, the prevalence of intestinal ulcers has increased and then decreased, blubber thickness has decreased and the prevalence of a zoonotic biliary trematode infection increased.

In 2015, whole bodies and samples from 137 grey seals, 44 harbour seals and 27 ringed seals were examined at the museum. The public reported 196 seals found dead along the Swedish coast. At present, the Baltic grey seal population increases with 8% each year and 85% of the examined females 6-24 years old were pregnant during the pregnant period (August-February) in 2015. The harbour seal populations presently increase with 7-9 % per year, although the numbers of examined harbour seals are much lower than the number of grey seals, the proportion of examined pregnant harbour seals in corresponding age group was only 57%. The ringed seal population in the Gulf of Bothnia presently increase with 4,5% per year. One mature female examined from the period of pregnancy was pregnant. Of the examined 27 ringed seals, 20 of them were younger than 4 years. Two two-year old females showed malformations as diaphragmatic hiatus in one of them and the other female lacked one of the uterine horns.

In conclusion, the health situation for examined Baltic grey seals is better and the increase in the population during the last 15 years is stable. The number of examined harbour seals and ringed seals is small for presenting trends but harbour seals showed a tendency to low pregnancy rate that needs further studies. The populations of harbour seals on the Swedish west coast were affected by epidemics in 1988, 2002 and 2014 and the development rate of these populations have decreased since 2002. The development of the harbour seal population on the Swedish east coast has a steady increase since the 1970s. The population of ringed seals has a low increase in the Gulf of Bothnia

The Arctic terrestrial environment harbors a complex mosaic of mercury (Hg) and carbon (C) reservoirs, some of which are rapidly destabilizing in response to climate warming. The sources of riverine Hg across the Mackenzie River basin (MRB) are uncertain, which leads to a poor understanding of potential future release. Measurements of dissolved and particulate mercury (DHg, PHg) and carbon (DOC, POC) concentration were performed, along with analyses of Hg stable isotope ratios (incl. ∆199Hg, d202Hg), radiocarbon content (∆14C) and optical properties of DOC of river water. Isotopic ratios of Hg revealed a closer association to terrestrial Hg reservoirs for the particulate fraction, while the dissolved fraction was more closely associated with atmospheric deposition sources of shorter turnover time. There was a positive correlation between the ∆14C-OC and riverine Hg concentration for both particulate and dissolved fractions, indicating that waters transporting older-OC (14C-depleted) also contained higher levels of Hg. In the dissolved fraction, older DOC was also associated with higher molecular weight, aromaticity and humic content, which are likely associated with higher Hg-binding potential. Riverine PHg concentration increased with turbidity and SO4 concentration. There were large contrasts in Hg concentration and OC age and quality among the mountain and lowland sectors of the MRB, which likely reflect the spatial distribution of various terrestrial Hg and OC reservoirs, including weathering of sulfate minerals, erosion and extraction of coal deposits, thawing permafrost, forest fires, peatlands, and forests. Results revealed major differences in the sources of particulate and dissolved riverine Hg, but nonetheless a common positive association with older riverine OC. These findings reveal that a complex mixture of Hg sources, supplied across the MRB, will contribute to future trends in Hg export to the Arctic Ocean under rapid environmental changes.

The Mackenzie River Basin (MRB) delivers large quantities of organic carbon (OC) into the Arctic Ocean, with significant implications for the global C budgets and ocean biogeochemistry. The amount and properties of OC in the Mackenzie River's delta have been well monitored in the last decade, but the spatial variability in OC sources transported by its different tributaries is still unclear. Here we present new data on the radiocarbon (14C) content of dissolved and particulate OC (Δ14C‐DOC and Δ14C‐POC) across the mainstem and major tributaries of the MRB, comprising 19 different locations, to identify factors controlling spatial patterns in riverine OC sources. The Δ14C‐DOC and Δ14C‐POC varied across a large range, from −179.9‰ to 62.9‰, and −728.8‰ to −9.0‰, respectively. Our data reveal a positive spatial coupling between the Δ14C of DOC and POC across the MRB, whereby the most 14C‐depleted waters were issued from the mountainous west bank of the MRB. This 14C‐depleted DOC and POC likely originates from a combination of petrogenic sources, connected with the presence of kerogens in the bedrock, and biogenic sources, mobilized by thawing permafrost. Our analysis also reveals intriguing relationships between Δ14C of DOC and POC with turbidity, water stable isotope ratio and catchment elevation, indicating that hydrology and geomorphology are key to understanding riverine OC sources in this landscape. A closer examination of the specific mechanisms giving rise to these relationships is recommended. For now, this study provides a road map of the key OC sources in this rapidly changing river basin.

Methylmercury (MeHg), a neurotoxic compound biomagnifying in aquatic food webs, can be a threat to human health via fish consumption. However, the compositionand distribution of the microbial communities mediating the methylation of mercury (Hg) to MeHg in marine systems remain largely unknown. In order to fill this knowledge gap, we used the Baltic Sea Reference Metagenome (BARM) dataset to study the abundance and distribution of the genes involved in Hg methylation (the hgcAB gene cluster). We determined the relative abundance of the hgcAB genes and their taxonomic identity in 81 brackish metagenomes that cover spatial,seasonal and redox variability in the Baltic Sea water column. The hgcAB genes were predominantly detected in anoxic water, but some hgcAB genes were alsodetected in hypoxic and normoxic waters. Phylogenetic analysis identified putative Hg methylators within Deltaproteobacteria, in oxygen-deficient water layers, but also Spirochaetes-like and Kiritimatiellaeota-like bacteria. Higher relative quantities of hgcAB genes were found in metagenomes from marine particles compared to free-living communities in anoxic water, suggesting that such particles are hotspot habitats for Hg methylators in oxygen-depleted seawater. Altogether, our work unveils the diversityof the microorganisms with the potential to mediate MeHg production in the BalticSea and pinpoint the important ecological niches for these microorganisms within themarine water column.

Human-induced expansion of oxygen-deficient zones can have dramatic impacts on marine systems and itsresident biota. One example is the formation of the potent neurotoxic methylmercury (MeHg) that is mediated bymicrobial methylation of inorganic divalent Hg (HgII) under oxygen-deficient conditions. A negative consequenceof the expansion of oxygen-deficient zones could be an increase in MeHg production due to shifts in microbialcommunities in favor of microorganisms methylating Hg. There is, however, limited knowledge about Hg-methylatingmicrobes, i.e., those carrying hgc genes critical for mediating the process, from marine sediments. Here, weaim to study the presence of hgc genes and transcripts in metagenomes and metatranscriptomes from four surfacesediments with contrasting concentrations of oxygen and sulfide in the Baltic Sea. We show that potential Hgmethylators differed among sediments depending on redox conditions. Sediments with an oxygenated surface featuredhgc-like genes and transcripts predominantly associated with uncultured Desulfobacterota (OalgD group)and Desulfobacterales (including Desulfobacula sp.) while sediments with a hypoxic-anoxic surface included hgccarryingVerrucomicrobia, unclassified Desulfobacterales, Desulfatiglandales, and uncharacterized microbes. Ourdata suggest that the expansion of oxygen-deficient zones in marine systems may lead to a compositional changeof Hg-methylating microbial groups in the sediments, where Hg methylators whose metabolism and biology havenot yet been characterized will be promoted and expand.

Neurotoxic methylmercury (MeHg) is formed by microbial methylation of inorganic divalent Hg (HgII) and constitutes severe environmental and human health risks. The methylation is enabled by hgcA and hgcB genes, but it is not known if the associated molecular-level processes are rate-limiting or enable accurate prediction of MeHg formation in nature. In this study, we investigated the relationships between hgc genes and MeHg across redox-stratified water columns in the brackish Baltic Sea. We showed, for the first time, that hgc transcript abundance and the concentration of dissolved HgII-sulfide species were strong predictors of both the HgII methylation rate and MeHg concentration, implying their roles as principal joint drivers of MeHg formation in these systems. Additionally, we characterized the metabolic capacities of hgc+ microorganisms by reconstructing their genomes from metagenomes (i.e., hgc+ MAGs), which highlighted the versatility of putative HgII methylators in the water column of the Baltic Sea. In establishing relationships between hgc transcripts and the HgII methylation rate, we advance the fundamental understanding of mechanistic principles governing MeHg formation in nature and enable refined predictions of MeHg levels in coastal seas in response to the accelerating spread of oxygen-deficient zones.

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.

Worldwide, incidental bycatch in fisheries is a conservation threat to many seabird species. Although knowledge on bycatch of seabirds has increased in the last decade, most stems from longline fisheries and the impacts of coastal gillnet fisheries are poorly understood. Gillnet fishing for North Atlantic lumpsucker (Cyclopterus lumpus) is one such fishery. We collated and synthesized the available information on seabird bycatch in lumpsucker gillnet fisheries across the entire geographical range to estimate and infer the magnitude of their impact on the affected seabird populations. Most birds killed were diving ducks, cormorants and auks, and each year locally high numbers of seabirds were taken as bycatch. We found large differences in bycatch rates among countries. The estimated mean bycatch in Iceland was 2.43 birds/trip, while the estimates in Norway was 0.44 and 0.39 birds/trip, respectively. The large disparities between estimates might reflect large spatial differences in bycatch rates, but could partly also arise due to distinctions in data recorded by onboard inspectors (Iceland), self-administered registration (Norway) and direct observations by cameras (Denmark). We show that lumpsucker gillnet fisheries might pose a significant risk to some populations of diving seabirds. However, a distinct data deficiency on seabird bycatch in terms of spatio-temporal coverage and the age and origins of the birds killed, limited our abilities to fully assess the extent and population consequences of the bycatch. Our results highlight the need for a joint effort among countries to standardize monitoring methods to better document the impact of these fisheries on seabirds.

In the eutrophicated Baltic Sea, several naturally produced hydroxylated polybrominated diphenyl ethers (OH-PBDEs) have been found in marine biota. OH-PBDEs are toxic to adult and developing zebrafish and shown to be potent disruptors of oxidative phosphorylation (OXPHOS). Disturbed OXPHOS can result in altered energy metabolism and weight loss. In herring, the concentration of OH-PBDEs (i.e. 2'-OH-BDE68 and 6-OH-BDE47) has increased during the period 1980-2010 in the Baltic Proper. Over the same time period, the condition and fat content in Baltic herring have decreased. Given the toxicity and increasing trends of OH-PBDEs in Baltic herring it is important to further assess the exposure to OH-PBDEs in Baltic herring. In this study, the concentrations of OH-PBDEs and related brominated substances i.e. polybrominated phenols (PBPs), polybrominated anisoles (PBAs), methoxylated polybrominated diphenyl ethers (MeO-PBDEs) and polybrominated diphenyl ethers (PBDEs) were measured in herring sampled in the northern Baltic Proper (Askö, n = 12) and the southern Bothnian Sea (Ängskärsklubb, n = 12). The geometric mean (GM) concentrations (ng/g l.w.) at Askö and Ängskärsklubb were; Σ2PBPs: 4.3 and 9.6, Σ(2)PBAs: 34 and 20, Σ(6)OH-PBDEs: 9.4 and 10, Σ(7)MeO-PBDEs: 42 and 150, Σ(6)PBDEs: 54 and 27, respectively. 6-OH-BDE47 dominated the OH-PBDE profile and comprised 87% (Askö) and 91% (Ängskärsklubb) of the ΣOH-PBDEs. At Ängskärsklubb the mean concentration of ΣMeO-PBDEs (150 ng/g l.w.) was 15 times higher than ΣOH-PBDEs. As other fish species are known to metabolically transform MeO-PBDEs to OH-PBDEs, high levels of MeO-PBDEs can be of concern as a precursor for more toxic OH-PBDEs in herring and their roe.

Predation is an ecologically important process, and intra-guild interactions may substantially influence the ecological effects of predator species. Despite a rapid expansion in the use of mathematical graph theory to describe trophic relations, network approaches have rarely been used to study interactions within predator assemblages. Assemblages of diurnal raptors are subject to substantial intra- and interspecific competition. Here we used the novel approach of applying analyzes based on network topology to species-specific data on the stable isotopes 13C and 15N in feathers to evaluate patterns of relative resource utilization within a guild of diurnal raptors in northern Sweden. Our guild consisted of the golden eagle (Aquila chrysaetos), the gyrfalcon (Falco rusticolus), the peregrine falcon (Falco peregrinus) and the rough-legged buzzard (Buteo lagopus). We found a modular trophic interaction structure within the guild, but the interactions were less nested than expected by chance. These results suggest low redundancy and hence a strong ecological importance of individual species. Our data also suggested that species were less connected through intra-guild interactions than expected by chance. We interpret our results as a convergence on specific isotope niches, and that body size and different hunting behaviour may mediate competition within these niches. We finally highlight that generalist predators could be ecologically important by linking specialist predator species with disparate dietary niches.

Anthropogenic mercury (Hg) emissions have driven marked increases in Arctic Hg levels, which are now being impacted by regional warming, with uncertain ecological consequences. This Review presents a comprehensive assessment of the present-day total Hg mass balance in the Arctic. Over 98% of atmospheric Hg is emitted outside the region and is transported to the Arctic via long-range air and ocean transport. Around two thirds of this Hg is deposited in terrestrial ecosystems, where it predominantly accumulates in soils via vegetation uptake. Rivers and coastal erosion transfer about 80 Mg year−1 of terrestrial Hg to the Arctic Ocean, in approximate balance with modelled net terrestrial Hg deposition in the region. The revised Arctic Ocean Hg mass balance suggests net atmospheric Hg deposition to the ocean and that Hg burial in inner-shelf sediments is underestimated (up to >100%), needing seasonal observations of sediment-ocean Hg exchange. Terrestrial Hg mobilization pathways from soils and the cryosphere (permafrost, ice, snow and glaciers) remain uncertain. Improved soil, snowpack and glacial Hg inventories, transfer mechanisms of riverine Hg releases under accelerated glacier and soil thaw, coupled atmosphere–terrestrial modelling and monitoring of Hg in sensitive ecosystems such as fjords can help to anticipate impacts on downstream Arctic ecosystems.