Mitogenomics and the genetic differentiation of contemporary <i>Balaena mysticetus</i> (Cetacea) from Svalbard

Full mitochondrial genomes were assembled for 12 recently sampled animals from the Svalbard bowhead whale (Balaena mysticetus) stock via high-throughput sequencing data, facilitating analysis of the demographic history of the population for the first time. The Svalbard population has retained noticeable amounts of mitochondrial genome diversity despite extreme historical harvest levels. Haplotype and nucleotide diversities were similar to those estimated earlier for other bowhead whale populations. The reconstructed demographic history was in accordance with a boom–bust scenario, combining a slight Pleistocene population growth 25 000–35 000 years ago and a Holocene decline. Employing a mutation rate of 3.418 × 10–8 substitutions per site per year, the time to the most recent common ancestor for the mitochondrial genomes of the contemporary Svalbard bowhead whales was estimated to be 68 782 (54 353–83 216) years before the present. Based on 370 bp fragments of the D-loop region, significant genetic differentiation was detected between all extant bowhead whale populations across the circumpolar Arctic. Thus, the Svalbard bowhead whales can be regarded as a population with its own genetic legacy

Best practice guidelines for cetacean tagging

Animal-borne electronic instruments (tags) are valuable tools for collecting information on cetacean physiology, behaviour and ecology, and for enhancing conservation and management policies for cetacean populations. Tags allow researchers to track the movement patterns, habitat use andother aspects of the behaviour of animals that are otherwise difficult to observe. They can even be used to monitor the physiology of a tagged animal within its changing environment. Such tags are ideal for identifying and predicting responses to anthropogenic threats, thus facilitating the development of robust mitigation measures. With the increasing need for data best provided by tagging and the increasing availability of tags, such research is becoming more common. Tagging can, however, pose risks to the health and welfare of cetaceans and to personnel involved in tagging operations. Here we provide ‘best practice’ recommendations for cetacean tag design, deployment and follow-up assessment of tagged individuals, compiled by biologists and veterinarians with significant experience in cetacean tagging. This paper is intended to serve as a resource to assist tag users, veterinarians, ethics committees and regulatory agency staff in the implementation of high standards of practice, and to promote the training of specialists in this area. Standardised terminology for describing tag design and illustrations of tag types and attachment sites are provided, along with protocols for tag testing and deployment (both remote and through capture-release), including training of operators. The recommendations emphasise the importance of ensuring that tagging is ethically and scientifically justified for a particular project and that tagging only be used to address bona fide research or conservation questions that are best addressed with tagging, as supported by an exploration of alternative methods. Recommendations are provided for minimising effects on individual animals (e.g. through careful selection of the individual, tag design and implant sterilisation) and for improving knowledge of tagging effects on cetaceans through increased post-tagging monitoring.Publisher PDFPeer reviewe

Marine mammal hotspots across the circumpolar Arctic

Aim: Identify hotspots and areas of high species richness for Arctic marine mammals. Location: Circumpolar Arctic. Methods: A total of 2115 biologging devices were deployed on marine mammals from 13 species in the Arctic from 2005 to 2019. Getis-Ord Gi* hotspots were calculated based on the number of individuals in grid cells for each species and for phyloge-netic groups (nine pinnipeds, three cetaceans, all species) and areas with high spe-cies richness were identified for summer (Jun-Nov), winter (Dec-May) and the entire year. Seasonal habitat differences among species’ hotspots were investigated using Principal Component Analysis. Results: Hotspots and areas with high species richness occurred within the Arctic continental-shelf seas and within the marginal ice zone, particularly in the “Arctic gateways” of the north Atlantic and Pacific oceans. Summer hotspots were generally found further north than winter hotspots, but there were exceptions to this pattern, including bowhead whales in the Greenland-Barents Seas and species with coastal distributions in Svalbard, Norway and East Greenland. Areas with high species rich-ness generally overlapped high-density hotspots. Large regional and seasonal dif-ferences in habitat features of hotspots were found among species but also within species from different regions. Gap analysis (discrepancy between hotspots and IUCN ranges) identified species and regions where more research is required. Main conclusions: This study identified important areas (and habitat types) for Arctic marine mammals using available biotelemetry data. The results herein serve as a benchmark to measure future distributional shifts. Expanded monitoring and teleme-try studies are needed on Arctic species to understand the impacts of climate change and concomitant ecosystem changes (synergistic effects of multiple stressors). While efforts should be made to fill knowledge gaps, including regional gaps and more com-plete sex and age coverage, hotspots identified herein can inform management ef-forts to mitigate the impacts of human activities and ecological changes, including creation of protected areas

Data from: Colonizing the wild west: low diversity of complete mitochondrial genomes in western North Pacific killer whales suggests a founder effect

In the North Pacific, fish-eating R-type ‘resident’ and mammal-eating T-type ‘transient’ killer whales do not interbreed and differ in ecology and behavior. Full-length mitochondrial genomes (about 16.4 kbp) were sequenced and assembled for 12 R-type and 14 T-type killer whale samples from different areas of the western North Pacific. All R-type individuals had the same haplotype, previously described for R-type killer whales from both eastern and western North Pacific. However, haplotype diversity of R-type killer whales was much lower in the western North Pacific than in the Aleutian Islands and the eastern North Pacific. T-type whales had three different haplotypes, including one previously undescribed. Haplotype diversity of T-type killer whales in the Okhotsk Sea was also much lower than in the Aleutian Islands and the eastern North Pacific. The highest haplotype diversity for both R- and T-type killer whales was observed in the Aleutian Islands. We discuss how the environmental conditions during the last glacial period might have shaped the history of killer whale populations in the North Pacific. Our results suggest the recent colonization or re-colonization of the western North Pacific by small groups of killer whales originating from the central or eastern North Pacific, possibly due to favorable environmental changes after the Last Glacial Maximum

High genomic diversity in the endangered East Greenland Svalbard Barents Sea stock of bowhead whales (Balaena mysticetus)

The East Greenland-Svalbard-Barents Sea (EGSB) bowhead whale stock (Balaena mysticetus) was hunted to near extinction and remains Endangered on the International Union of Conservation of Nature Red List. The intense, temporally extensive hunting pressure may have left the population vulnerable to other perturbations, such as environmental change. However, the lack of genomic baseline data renders it difficult to evaluate the impacts of various potential stressors on this stock. Twelve EGSB bowhead whales sampled in 2017/2018 were re-sequenced and mapped to a previously published draft genome. All individuals were unrelated and void of significant signs of inbreeding, with similar observed and expected homo- and heterozygosity levels. Despite the small population size, mean autosome-wide heterozygosity was 0.00102, which is higher than that of most mammals for which comparable estimates are calculated using the same parameters, and three times higher than a conspecific individual from the Eastern-Canada-West-Greenland bowhead whale stock. Demographic history analyses indicated a continual decrease of Ne from ca. 1.5 million to ca. 250,000 years ago, followed by a slight increase until ca. 100,000 years ago, followed by a rapid decrease in Ne between 50,000 and 10,000 years ago. These estimates are lower than previously suggested based on mitochondrial DNA, but suggested demographic patterns over time are similar

High genomic diversity in the endangered East Greenland Svalbard Barents Sea stock of bowhead whales (Balaena mysticetus)

Abstract The East Greenland-Svalbard-Barents Sea (EGSB) bowhead whale stock ( Balaena mysticetus ) was hunted to near extinction and remains Endangered on the International Union of Conservation of Nature Red List. The intense, temporally extensive hunting pressure may have left the population vulnerable to other perturbations, such as environmental change. However, the lack of genomic baseline data renders it difficult to evaluate the impacts of various potential stressors on this stock. Twelve EGSB bowhead whales sampled in 2017/2018 were re-sequenced and mapped to a previously published draft genome. All individuals were unrelated and void of significant signs of inbreeding, with similar observed and expected homo- and heterozygosity levels. Despite the small population size, mean autosome-wide heterozygosity was 0.00102, which is higher than that of most mammals for which comparable estimates are calculated using the same parameters, and three times higher than a conspecific individual from the Eastern-Canada-West-Greenland bowhead whale stock. Demographic history analyses indicated a continual decrease of N e from ca. 1.5 million to ca. 250,000 years ago, followed by a slight increase until ca. 100,000 years ago, followed by a rapid decrease in N e between 50,000 and 10,000 years ago. These estimates are lower than previously suggested based on mitochondrial DNA, but suggested demographic patterns over time are similar

Circumpolar phylogeography and demographic history of beluga whales reflect past climatic fluctuations

Several Arctic marine mammal species are predicted to be negatively impacted by rapid sea ice loss associated with ongoing ocean warming. However, consequences for Arctic whales remain uncertain. To investigate how Arctic whales responded to past climatic fluctuations, we analysed 206 mitochondrial genomes from beluga whales (Delphinapterus leucas) sampled across their circumpolar range, and four nuclear genomes, covering both the Atlantic and the Pacific Arctic region. We found four well-differentiated mitochondrial lineages, which were established before the onset of the last glacial expansion ~110 thousand years ago. Our findings suggested these lineages diverged in allopatry, reflecting isolation of populations during glacial periods when the Arctic sea-shelf was covered by multiyear sea ice. Subsequent population expansion and secondary contact between the Atlantic and Pacific Oceans shaped the current geographic distribution of lineages, and may have facilitated mitochondrial introgression. Our demographic reconstructions based on both mitochondrial and nuclear genomes showed markedly lower population sizes during the Last Glacial Maximum (LGM) compared to the preceding Eemian and current Holocene interglacial periods. Habitat modelling similarly revealed less suitable habitat during the LGM (glacial) than at present (interglacial). Together, our findings suggested the association between climate, population size, and available habitat in belugas. Forecasts for year 2100 showed that beluga habitat will decrease and shift northwards as oceans continue to warm, putatively leading to population declines in some beluga populations. Finally, we identified vulnerable populations which, if extirpated as a consequence of ocean warming, will lead to a substantial decline of species-wide haplotype diversity

Circumpolar phylogeography and demographic history of beluga whales reflect past climatic fluctuations

Several Arctic marine mammal species are predicted to be negatively impacted by rapid sea ice loss associated with ongoing ocean warming. However, consequences for Arctic whales remain uncertain. To investigate how Arctic whales responded to past climatic fluctuations, we analysed 206 mitochondrial genomes from beluga whales (Delphinapterus leucas) sampled across their circumpolar range, and four nuclear genomes, covering both the Atlantic and the Pacific Arctic region. We found four well-differentiated mitochondrial lineages, which were established before the onset of the last glacial expansion ~110 thousand years ago. Our findings suggested these lineages diverged in allopatry, reflecting isolation of populations during glacial periods when the Arctic sea-shelf was covered by multiyear sea ice. Subsequent population expansion and secondary contact between the Atlantic and Pacific Oceans shaped the current geographic distribution of lineages, and may have facilitated mitochondrial introgression. Our demographic reconstructions based on both mitochondrial and nuclear genomes showed markedly lower population sizes during the Last Glacial Maximum (LGM) compared to the preceding Eemian and current Holocene interglacial periods. Habitat modelling similarly revealed less suitable habitat during the LGM (glacial) than at present (interglacial). Together, our findings suggested the association between climate, population size, and available habitat in belugas. Forecasts for year 2100 showed that beluga habitat will decrease and shift northwards as oceans continue to warm, putatively leading to population declines in some beluga populations. Finally, we identified vulnerable populations which, if extirpated as a consequence of ocean warming, will lead to a substantial decline of species-wide haplotype diversity

Marine mammal hotspots in the Greenland and Barents Seas

Environmental change and increasing levels of human activity are threats to marine mammals in the Arctic. Identifying marine mammal hotspots and areas of high species richness are essential to help guide management and conservation efforts. Herein, space use based on biotelemetric tracking devices deployed on 13 species (ringed seal Pusa hispida, bearded seal Erignathus barbatus, harbour seal Phoca vitulina, walrus Odobenus rosmarus, harp seal Pagophilus groenlandicus, hooded seal Cystophora cristata, polar bear Ursus maritimus, bowhead whale Balaena mysticetus, narwhal Monodon monoceros, white whale Delphinapterus leucas, blue whale Balaenoptera musculus, fin whale Balaenoptera physalus and humpback whale Megaptera novaeangliae; total = 585 individuals) in the Greenland and northern Barents Seas between 2005 and 2018 is reported. Getis-Ord Gi* hotspots were calculated for each species as well as all species combined, and areas of high species richness were identified for summer/autumn (Jun-Dec), winter/spring (Jan-May) and the entire year. The marginal ice zone (MIZ) of the Greenland Sea and northern Barents Sea, the waters surrounding the Svalbard Archipelago and a few Northeast Greenland coastal sites were identified as key marine mammal hotspots and areas of high species richness in this region. Individual hotspots identified areas important for most of the tagged animals, such as common resting, nursing, moulting and foraging areas. Location hotspots identified areas heavily used by segments of the tagged populations, including denning areas for polar bears and foraging areas. The hotspots identified herein are also important habitats for seabirds and fishes, and thus conservation and management measures targeting these regions would benefit multiple groups of Arctic animals