Evolutionary history and seascape genomics of Harbour porpoises (Phocoena phocoena) across environmental gradients in the North Atlantic and adjacent waters.

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.

Effect of formic acid treatment on carbon and nitrogen stable isotope ratios in sperm whale teeth dentine.

RATIONALE: Stable isotope analysis of growth layers in sperm whale teeth dentine can provide valuable insight into individual long-distance displacements and diet. Although treating teeth half-sections with formic acid and rubbing their surface with a graphite pencil improves growth layer visibility and reduces sampling error, previous studies mostly used untreated half-sections as the effect that this treatment may have on stable isotope ratios in dentine is unknown. The present study investigates the treatment effect on stable C and N isotope ratios in sperm whale teeth dentine. METHODS: In the teeth of 30 sperm whales, we analysed and compared samples of powdered dentine obtained from (a) untreated half-sections, (b) half-sections etched with formic acid and rubbed with a graphite pencil and (c) half-sections etched with formic acid from which the graphite pencil rubbing had been cleansed off. δ 13 $$ {\delta}^{13} $$ C and δ 15 $$ {\delta}^{15} $$ N values were compared between the three sample groups. RESULTS: We found significant differences in values of both elements between untreated and etched samples, with a mean increase of 0.2% in δ13 C and δ15 N values in the etched samples. No significant differences were found between etched samples with graphite rubbing versus those without it. Significant linear regression models were calculated to predict untreated δ13 C and δ15 N values from the values obtained in the etched half-sections with limited precision. CONCLUSIONS: We show for the first time that formic acid etching has a clear effect on δ 13 $$ {\delta}^{13} $$ C and δ 15 $$ {\delta}^{15} $$ N values in sperm whale teeth dentine. The developed models permit the estimation of untreated values from etched half-sections, thus enabling the use of the latter in stable isotope analysis. However, as treatment procedures may vary between studies, it is advisable that similar predictive models are developed case-by-case to ensure comparability of results.

Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise.

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-by-distance. 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.

Legacy and emerging organic pollutants in liver and plasma of long-finned pilot whales (Globicephala melas) from waters surrounding the Faroe Islands.

Concentrations of PCBs, organochlorine pesticides (OCPs), brominated flame retardants and a suite of relevant metabolites of these POPs, in all 175 different compounds, were determined in liver and plasma of traditionally hunted pilot whales (n=14 males and n=13 females of different age groups) from the Faroe Islands. The main objectives of this study were to determine differences in the presence and concentrations of the compounds in the liver and plasma, how they depend on developmental stage (calves, sub adults, and adult females), and to assess maternal transfer of the compounds to suckling calves. Generally, the lipid weight (lw) concentrations of quantified POPs in the liver and plasma of pilot whales were positively correlated, and lw concentrations of most POPs did not differ between these matrices. However, concentrations of some individual POPs differed significantly (p<0.05) between plasma and liver; CB-153 (p=0.044), CB-174 (p=0.027) and BDE-47 (p=0.017) were higher in plasma than in liver, whereas p,p'-DDE (p=0.004) and HCB (p<0.001) were higher in liver than in plasma. POP concentrations differed between age/gender groups with lower levels in adult females than in juveniles. The relative distribution of compounds also differed between the age groups, due to the influence of the maternal transfer of the compounds. The results indicated that larger, more hydrophobic POPs were transferred to the offspring less efficiently than smaller or less lipid soluble compounds. Very low levels of both OH- and/or MeSO2-PCB and PBDE metabolites were found in all age groups, with no significant (p>0.05) differences between the groups, strongly suggesting a very low metabolic capacity for their formation in pilot whales. The lack of difference in the metabolite concentrations between the age groups also indicates less maternal transfer of these contaminant groups compared to the precursor compounds.

Stable isotopes provide insight into population structure and segregation in eastern North Atlantic sperm whales.

In pelagic species inhabiting large oceans, genetic differentiation tends to be mild and populations devoid of structure. However, large cetaceans have provided many examples of structuring. Here we investigate whether the sperm whale, a pelagic species with large population sizes and reputedly highly mobile, shows indication of structuring in the eastern North Atlantic, an ocean basin in which a single population is believed to occur. To do so, we examined stable isotope values in sequential growth layer groups of teeth from individuals sampled in Denmark and NW Spain. In each layer we measured oxygen- isotope ratios (δ(18)O) in the inorganic component (hydroxyapatite), and nitrogen and carbon isotope ratios (δ(15)N: δ(13)C) in the organic component (primarily collagenous). We found significant differences between Denmark and NW Spain in δ(15)N and δ(18)O values in the layer deposited at age 3, considered to be the one best representing the baseline of the breeding ground, in δ(15)N, δ(13)C and δ(18)O values in the period up to age 20, and in the ontogenetic variation of δ(15)N and δ(18)O values. These differences evidence that diet composition, use of habitat and/or migratory destinations are dissimilar between whales from the two regions and suggest that the North Atlantic population of sperm whales is more structured than traditionally accepted.

PFAS profiles in three North Sea top predators: metabolic differences among species?

Profiles of seven compounds of perfluoro-alkyl substances (PFASs) were compared among three species of top predators from the Danish North Sea: the white-beaked dolphin (Lagenorhynchus albirostris), the harbor porpoise (Phocoena phocoena), and the harbor seal (Phoca vitulina). The seals had higher total burdens (757.8 ng g(-1) ww) than the dolphins (439.9 ng g(-1) ww) and the porpoises (355.8 ng g(-1) ww), probably a reflection of feeding closer to the shore and thus contamination sources. The most striking difference among the species was the relative contribution of perfluorooctanesulfonamide (PFOSA) to the profiles; the seals (0.1%) had much lower levels than porpoises (8.3%) and dolphins (26.0%). In combination with the values obtained from the literature, this result indicates that Carnivora species including Pinnipedia have a much higher capacity of transforming PFOSA to perfluorooctane sulfonic acid (PFOS) than cetacean species. Another notable difference among the species was that the two smaller species (seals and porpoises) with supposedly higher metabolic rates had lower concentrations of the perfluorinated carboxylic acids, which are generally more easily excreted than perfluorinated sulfonamides. Species-specific characteristics should be recognized when PFAS contamination in marine mammals is investigated, for example, several previous studies of PFASs in cetaceans have not quantified PFOSA.

Temporal and life history related trends of perfluorochemicals in harbor porpoises from the Danish North Sea.

Eighty-five stranded or bycaught harbor porpoises collected from the Danish North Sea between 1980 and 2005 were analyzed for perfluorochemicals in the liver. PFOS was the predominant compound, making up on average 88.9% of the ∑PFC, followed by PFOSA (7.8%). PFUnA (1.9%) and PFDA (1.2%) were detected in most samples. PFHxS, PFNA and PFOA were only found in a minority of the samples. We found substantial differences in PFC concentrations among life history stages, the highest concentrations were found in neonates, suckling juveniles and lactating females. Such differences should be considered when PFC levels in wildlife are evaluated. The high concentrations found in young porpoises are of concern as PFCs have known toxic effects on the development of the central nervous system and reproductive organs. Despite efforts to reduce PFC emissions, a decreasing temporal trend of concentrations was not detected for any compound. PFCA concentrations were found to be increasing.

Harbour porpoises respond to climate change.

The effects of climate change on marine ecosystems and in particular on marine top predators are difficult to assess due to, among other things, spatial variability, and lack of clear delineation of marine habitats. The banks of West Greenland are located in a climate sensitive area and are likely to elicit pronounced responses to oceanographic changes in the North Atlantic. The recent increase in sea temperatures on the banks of West Greenland has had cascading effects on sea ice coverage, residency of top predators, and abundance of important prey species like Atlantic cod (Gadus morhua). Here, we report on the response of one of the top predators in West Greenland; the harbour porpoise (Phocoena phocoena). The porpoises depend on locating high densities of prey species with high nutritive value and they have apparently responded to the general warming on the banks of West Greenland by longer residence times, increased consumption of Atlantic cod resulting in improved body condition in the form of larger fat deposits in blubber, compared to the situation during a cold period in the 1990s. This is one of the few examples of a measurable effect of climate change on a marine mammal population.

Organochlorine contaminant and retinoid levels in blubber of common dolphins (Delphinus delphis) off northwestern Spain.

The effect of age, sex, nutritive condition and organochlorine concentration on blubber retinoid concentrations was examined in 74 common dolphins incidentally caught off northwestern Spain. Age and blubber lipid content were strong determinants of the retinoid concentrations in males, while these variables did not account for the variation found in females. Retinoids were positively correlated with organochlorines in males and negatively in females. However, pollution levels were moderate and likely to be below threshold levels above that a toxicological response is to be expected. Thus, a cause-effect relationship between organochlorine and retinoid concentrations could not be properly established, and the observed correlation may be the result of an independent association of the two variables with age. Further research on the influence of the best predictor variables on retinoid dynamics is required to implement the use of retinoids as biomarkers of pollutant exposure in cetaceans.

Accumulation of organotin compounds and mercury in harbour porpoises (Phocoena phocoena) from the Danish waters and West Greenland.

The concentrations of butyltin (summation operatorBT=TBT+DBT+MBT) and mercury (Hg) were determined in the liver of 35 harbour porpoises (Phocoena phocoena), which were found dead along the coastlines or caught as by-catch in the Danish North Sea and the Inner Danish waters. In addition, three harbour porpoises hunted in West Greenland were analysed. High levels of butyltin and mercury, within the range of 68-4605 mg BT/kg ww and 0.22-92 mg Hg/kg ww, were found in the liver of the Danish harbour porpoises and both substances tend to accumulate with age. The levels in the harbour porpoise from West Greenland were 2.0-18 mg BT/kg ww and 6.3-6.9 mg Hg/kg ww, respectively. The concentrations of butyltin and mercury were both found to be higher in stranded than in by-caught harbour porpoises but only the butyltin concentration was significantly higher in stranded porpoises in the age group 1-5 years. These substances are suspected of inducing adverse effects on immune and endocrine systems in mammals and they may thereby pose a threat to the animals. This study suggests that organotin compounds are also important, when assessing the risks of contaminants on the health and viability of harbour porpoises in Danish waters.

Organochlorine residues in harbour porpoises from Southwest Greenland.

During the 1995 hunting season, 75 harbour porpoises (Phocoena phocoena) were sampled in three locations in West Greenland: Maniitsoq, Nuuk, and Paamiut. Sex, age, morphometrics, reproductive condition, and organochlorine compound (OC) levels in blubber were determined for each individual. OC levels were extremely low and, therefore considered unlikely to affect the population adversely: mean blubber concentrations, expressed on lipid weight basis were 1.98 (S.D.=1.1) mg/kg for PCBs, 2.76 (S.D.=1.66) mg/kg for tDDT and 0.21 (S.D.=0.11) mg/kg for HCB. No statistical differences were observed among individuals caught in the various locations. OC concentrations showed statistically significant positive associations with age in males but negative in females; consequently, mature females presented lower pollutant loads than their male counterparts. Juveniles did not show differences between sexes. A higher proportion of less chlorinated and more metabolizable polychlorinated biphenyls (PCBs) compared to tPCBs was found in calves (age< or =1) than in mature females, indicating that the feeding habits of these two groups differ and that a greater transfer of less chlorinated compounds is passed from females to their pups through lactation and parturition. Harbour porpoises significantly contribute to the dietary intake of OCs by local Inuit populations. This contribution could be reduced if mature males were selectively avoided; however, current hunting procedures make this selection impracticable.