Accurate species classification of Arctic toothed whale echolocation clicks using one-third octave ratios.

Passive acoustic monitoring has been an effective tool to study cetaceans in remote regions of the Arctic. Here, we advance methods to acoustically identify the only two Arctic toothed whales, the beluga (Delphinapterus leucas) and narwhal (Monodon monoceros), using echolocation clicks. Long-term acoustic recordings collected from moorings in Northwest Greenland were analyzed. Beluga and narwhal echolocation signals were distinguishable using spectrograms where beluga clicks had most energy >30 kHz and narwhal clicks had a sharp lower frequency limit near 20 kHz. Changes in one-third octave levels (TOL) between two pairs of one-third octave bands were compared from over one million click spectra. Narwhal clicks had a steep increase between the 16 and 25 kHz TOL bands that was absent in beluga click spectra. Conversely, beluga clicks had a steep increase between the 25 and 40 kHz TOL bands that was absent in narwhal click spectra. Random Forest classification models built using the 16 to 25 kHz and 25 to 40 kHz TOL ratios accurately predicted the species identity of 100% of acoustic events. Our findings support the use of echolocation TOL ratios in future automated click classifiers for acoustic monitoring of Arctic toothed whales and potentially for other odontocete species.

Quantifying the effect of ship noise on the acoustic environment of the Bering Strait.

The narrow Bering Strait provides the only gateway between the Pacific Ocean and the Arctic, bringing migrating marine mammals in close proximity to ships transiting the strait. We characterized ship activity in the Bering Strait during the open-water season (July-November) for 2013-2015 and quantified the impact of ship noise on third-octave sound levels (TOLs) for bands used by baleen whales (25-1000 Hz). Peak ship activity occurred in July-September with the greatest overlap in ship noise and whale vocalizations observed in October. Ships elevated sound levels by ∼4 dB on average for all TOL bands combined, and 250-Hz TOLs exceeding 100 dB re 1 µPa were recorded from two large vessels over 11 km away from the hydrophones. Our results show that ship noise has the potential to impact baleen whales in the Bering Strait and serve as a baseline for measuring future changes in ship activity in the region.

Glacial ice supports a distinct and undocumented polar bear subpopulation persisting in late 21st-century sea-ice conditions.

Polar bears are susceptible to climate warming because of their dependence on sea ice, which is declining rapidly. We present the first evidence for a genetically distinct and functionally isolated group of polar bears in Southeast Greenland. These bears occupy sea-ice conditions resembling those projected for the High Arctic in the late 21st century, with an annual ice-free period that is >100 days longer than the estimated fasting threshold for the species. Whereas polar bears in most of the Arctic depend on annual sea ice to catch seals, Southeast Greenland bears have a year-round hunting platform in the form of freshwater glacial mélange. This suggests that marine-terminating glaciers, although of limited availability, may serve as previously unrecognized climate refugia. Conservation of Southeast Greenland polar bears, which meet criteria for recognition as the world's 20th polar bear subpopulation, is necessary to preserve the genetic diversity and evolutionary potential of the species.

A polar bear paleogenome reveals extensive ancient gene flow from polar bears into brown bears.

Polar bears (Ursus maritimus) and brown bears (Ursus arctos) are sister species possessing distinct physiological and behavioural adaptations that evolved over the last 500,000 years. However, comparative and population genomics analyses have revealed that several extant and extinct brown bear populations have relatively recent polar bear ancestry, probably as the result of geographically localized instances of gene flow from polar bears into brown bears. Here, we generate and analyse an approximate 20X paleogenome from an approximately 100,000-year-old polar bear that reveals a massive prehistoric admixture event, which is evident in the genomes of all living brown bears. This ancient admixture event was not visible from genomic data derived from living polar bears. Like more recent events, this massive admixture event mainly involved unidirectional gene flow from polar bears into brown bears and occurred as climate changes caused overlap in the ranges of the two species. These findings highlight the complex reticulate paths that evolution can take within a regime of radically shifting climate.

Passive acoustic monitoring reveals year-round marine mammal community composition off Tasiilaq, Southeast Greenland.

Climate-driven changes are affecting sea ice conditions off Tasiilaq, Southeast Greenland, with implications for marine mammal distributions. Knowledge about marine mammal presence, biodiversity, and community composition is key to effective conservation and management but is lacking, especially during winter months. Seasonal patterns of acoustic marine mammal presence were investigated relative to sea ice concentration at two recording sites between 2014 and 2018, with one (65.6°N, 37.4°W) or three years (65.5°N, 38.0°W) of passive acoustic recordings. Seven marine mammal species were recorded. Bearded seals were acoustically dominant during winter and spring, whereas sperm, humpback, and fin whales dominated during the sea ice-free summer and autumn. Narwhals, bowhead, and killer whales were recorded only rarely. Song-fragments of humpback whales and acoustic presence of fin whales in winter suggest mating-associated behavior taking place in the area. Ambient noise levels in 1/3-octave level bands (20, 63, 125, 500, 1000, and 4000 Hz), ranged between 75.6 to 105 dB re 1 µPa. This study provides multi-year insights into the coastal marine mammal community composition off Southeast Greenland and suggests that the Tasiilaq area provides suitable habitat for various marine mammal species year-round.

An on-ice aerial survey of the Kane Basin polar bear (Ursus maritimus) subpopulation.

There is an imminent need to collect information on distribution and abundance of polar bears (Ursus maritimus) to understand how they are affected by the ongoing decrease in Arctic sea ice. The Kane Basin (KB) subpopulation is a group of high-latitude polar bears that ranges between High Arctic Canada and NW Greenland around and north of the North Water polynya (NOW). We conducted a line transect distance sampling aerial survey of KB polar bears during 28 April-12 May 2014. A total of 4160 linear kilometers were flown in a helicopter over fast ice in the fjords and over offshore pack ice between 76° 50' and 80° N'. Using a mark-recapture distance sampling protocol, the estimated abundance was 190 bears (95% lognormal CI: 87-411; CV 39%). This estimate is likely negatively biased to an unknown degree because the offshore sectors of the NOW with much open water were not surveyed because of logistical and safety reasons. Our study demonstrated that aerial surveys may be a feasible method for obtaining abundance estimates for small subpopulations of polar bears.

Distinct gut microbiomes in two polar bear subpopulations inhabiting different sea ice ecoregions.

Gut microbiomes were analyzed by 16S rRNA gene metabarcoding for polar bears (Ursus maritimus) from the southern Beaufort Sea (SB), where sea ice loss has led to increased use of land-based food resources by bears, and from East Greenland (EG), where persistent sea ice has allowed hunting of ice-associated prey nearly year-round. SB polar bears showed a higher number of total (940 vs. 742) and unique (387 vs. 189) amplicon sequence variants and higher inter-individual variation compared to EG polar bears. Gut microbiome composition differed significantly between the two subpopulations and among sex/age classes, likely driven by diet variation and ontogenetic shifts in the gut microbiome. Dietary tracer analysis using fatty acid signatures for SB polar bears showed that diet explained more intrapopulation variation in gut microbiome composition and diversity than other tested variables, i.e., sex/age class, body condition, and capture year. Substantial differences in the SB gut microbiome relative to EG polar bears, and associations between SB gut microbiome and diet, suggest that the shifting foraging habits of SB polar bears tied to sea ice loss may be altering their gut microbiome, with potential consequences for nutrition and physiology.

Soundscape and ambient noise levels of the Arctic waters around Greenland.

A longer Arctic open water season is expected to increase underwater noise levels due to anthropogenic activities such as shipping, seismic surveys, sonar, and construction. Many Arctic marine mammal species depend on sound for communication, navigation, and foraging, therefore quantifying underwater noise levels is critical for documenting change and providing input to management and legislation. Here we present long-term underwater sound recordings from 26 deployments around Greenland from 2011 to 2020. Ambient noise was analysed in third octave and decade bands and further investigated using generic detectors searching for tonal and transient sounds. Ambient noise levels partly overlap with previous Arctic observations, however we report much lower noise levels than previously documented, specifically for Melville Bay and the Greenland Sea. Consistent seasonal noise patterns occur in Melville Bay, Baffin Bay and Greenland Sea, with noise levels peaking in late summer and autumn correlating with open water periods and seismic surveys. These three regions also had similar tonal detection patterns that peaked in May/June, likely due to bearded seal vocalisations. Biological activity was more readily identified using detectors rather than band levels. We encourage additional research to quantify proportional noise contributions from geophysical, biological, and anthropogenic sources in Arctic waters.

Acoustic differentiation and classification of wild belugas and narwhals using echolocation clicks.

Belugas (Delphinapterus leucas) and narwhals (Monodon monoceros) are highly social Arctic toothed whales with large vocal repertoires and similar acoustic profiles. Passive Acoustic Monitoring (PAM) that uses multiple hydrophones over large spatiotemporal scales has been a primary method to study their populations, particularly in response to rapid climate change and increasing underwater noise. This study marks the first acoustic comparison between wild belugas and narwhals from the same location and reveals that they can be acoustically differentiated and classified solely by echolocation clicks. Acoustic recordings were made in the pack ice of Baffin Bay, West Greenland, during 2013. Multivariate analyses and Random Forests classification models were applied to eighty-one single-species acoustic events comprised of numerous echolocation clicks. Results demonstrate a significant difference between species' acoustic parameters where beluga echolocation was distinguished by higher frequency content, evidenced by higher peak frequencies, center frequencies, and frequency minimums and maximums. Spectral peaks, troughs, and center frequencies for beluga clicks were generally > 60 kHz and narwhal clicks < 60 kHz with overlap between 40-60 kHz. Classification model predictive performance was strong with an overall correct classification rate of 97.5% for the best model. The most important predictors for species assignment were defined by peaks and notches in frequency spectra. Our results provide strong support for the use of echolocation in PAM efforts to differentiate belugas and narwhals acoustically.

Vertical sonar beam width and scanning behavior of wild belugas (Delphinapterus leucas) in West Greenland.

Echolocation signals of wild beluga whales (Delphinapterus leucas) were recorded in 2013 using a vertical, linear 16-hydrophone array at two locations in the pack ice of Baffin Bay, West Greenland. Individual whales were localized for 4:42 minutes of 1:04 hours of recordings. Clicks centered on the recording equipment (i.e. on-axis clicks) were isolated to calculate sonar parameters. We report the first sonar beam estimate of in situ recordings of wild belugas with an average -3 dB asymmetrical vertical beam width of 5.4°, showing a wider ventral beam. This narrow beam width is consistent with estimates from captive belugas; however, our results indicate that beluga sonar beams may not be symmetrical and may differ in wild and captive contexts. The mean apparent source level for on-axis clicks was 212 dB pp re 1 µPa and whales were shown to vertically scan the array from 120 meters distance. Our findings support the hypothesis that highly directional sonar beams and high source levels are an evolutionary adaptation for Arctic odontocetes to reduce unwanted surface echoes from sea ice (i.e., acoustic clutter) and effectively navigate through leads in the pack ice (e.g., find breathing holes). These results provide the first baseline beluga sonar metrics from free-ranging animals using a hydrophone array and are important for acoustic programs throughout the Arctic, particularly for acoustic classification between belugas and narwhals (Monodon monoceros).

Transient benefits of climate change for a high-Arctic polar bear (Ursus maritimus) subpopulation.

Kane Basin (KB) is one of the world's most northerly polar bear (Ursus maritimus) subpopulations, where bears have historically inhabited a mix of thick multiyear and annual sea ice year-round. Currently, KB is transitioning to a seasonally ice-free region because of climate change. This ecological shift has been hypothesized to benefit polar bears in the near-term due to thinner ice with increased biological production, although this has not been demonstrated empirically. We assess sea-ice changes in KB together with changes in polar bear movements, seasonal ranges, body condition, and reproductive metrics obtained from capture-recapture (physical and genetic) and satellite telemetry studies during two study periods (1993-1997 and 2012-2016). The annual cycle of sea-ice habitat in KB shifted from a year-round ice platform (~50% coverage in summer) in the 1990s to nearly complete melt-out in summer (<5% coverage) in the 2010s. The mean duration between sea-ice retreat and advance increased from 109 to 160 days (p = .004). Between the 1990s and 2010s, adult female (AF) seasonal ranges more than doubled in spring and summer and were significantly larger in all months. Body condition scores improved for all ages and both sexes. Mean litter sizes of cubs-of-the-year (C0s) and yearlings (C1s), and the number of C1s per AF, did not change between decades. The date of spring sea-ice retreat in the previous year was positively correlated with C1 litter size, suggesting smaller litters following years with earlier sea-ice breakup. Our study provides evidence for range expansion, improved body condition, and stable reproductive performance in the KB polar bear subpopulation. These changes, together with a likely increasing subpopulation abundance, may reflect the shift from thick, multiyear ice to thinner, seasonal ice with higher biological productivity. The duration of these benefits is unknown because, under unmitigated climate change, continued sea-ice loss is expected to eventually have negative demographic and ecological effects on all polar bears.

Interrelated ecological impacts of climate change on an apex predator.

Climate change has broad ecological implications for species that rely on sensitive habitats. For some top predators, loss of habitat is expected to lead to cascading behavioral, nutritional, and reproductive changes that ultimately accelerate population declines. In the case of the polar bear (Ursus maritimus), declining Arctic sea ice reduces access to prey and lengthens seasonal fasting periods. We used a novel combination of physical capture, biopsy darting, and visual aerial observation data to project reproductive performance for polar bears by linking sea ice loss to changes in habitat use, body condition (i.e., fatness), and cub production. Satellite telemetry data from 43 (1991-1997) and 38 (2009-2015) adult female polar bears in the Baffin Bay subpopulation showed that bears now spend an additional 30 d on land (90 d in total) in the 2000s compared to the 1990s, a change closely correlated with changes in spring sea ice breakup and fall sea ice formation. Body condition declined for all sex, age, and reproductive classes and was positively correlated with sea ice availability in the current and previous year. Furthermore, cub litter size was positively correlated with maternal condition and spring breakup date (i.e., later breakup leading to larger litters), and negatively correlated with the duration of the ice-free period (i.e., longer ice-free periods leading to smaller litters). Based on these relationships, we projected reproductive performance three polar bear generations into the future (approximately 35 yr). Results indicate that two-cub litters, previously the norm, could largely disappear from Baffin Bay as sea ice loss continues. Our findings demonstrate how concurrent analysis of multiple data types collected over long periods from polar bears can provide a mechanistic understanding of the ecological implications of climate change. This information is needed for long-term conservation planning, which includes quantitative harvest risk assessments that incorporate estimated or assumed trends in future environmental carrying capacity.

The polar regions in a 2°C warmer world.

Over the past decade, the Arctic has warmed by 0.75°C, far outpacing the global average, while Antarctic temperatures have remained comparatively stable. As Earth approaches 2°C warming, the Arctic and Antarctic may reach 4°C and 2°C mean annual warming, and 7°C and 3°C winter warming, respectively. Expected consequences of increased Arctic warming include ongoing loss of land and sea ice, threats to wildlife and traditional human livelihoods, increased methane emissions, and extreme weather at lower latitudes. With low biodiversity, Antarctic ecosystems may be vulnerable to state shifts and species invasions. Land ice loss in both regions will contribute substantially to global sea level rise, with up to 3 m rise possible if certain thresholds are crossed. Mitigation efforts can slow or reduce warming, but without them northern high latitude warming may accelerate in the next two to four decades. International cooperation will be crucial to foreseeing and adapting to expected changes.

Depletion of Hemoglobin Transcripts and Long-Read Sequencing Improves the Transcriptome Annotation of the Polar Bear (Ursus maritimus).

Transcriptome studies evaluating whole blood and tissues are often confounded by overrepresentation of highly abundant transcripts. These abundant transcripts are problematic, as they compete with and prevent the detection of rare RNA transcripts, obscuring their biological importance. This issue is more pronounced when using long-read sequencing technologies for isoform-level transcriptome analysis, as they have relatively lower throughput compared to short-read sequencers. As a result, long-read based transcriptome analysis is prohibitively expensive for non-model organisms. While there are off-the-shelf kits available for select model organisms capable of depleting highly abundant transcripts for alpha (HBA) and beta (HBB) hemoglobin, they are unsuitable for non-model organisms. To address this, we have adapted the recent CRISPR/Cas9-based depletion method (depletion of abundant sequences by hybridization) for long-read full-length cDNA sequencing approaches that we call Long-DASH. Using a recombinant Cas9 protein with appropriate guide RNAs, full-length hemoglobin transcripts can be depleted in vitro prior to performing any short- and long-read sequencing library preparations. Using this method, we sequenced depleted full-length cDNA in parallel using both our Oxford Nanopore Technology (ONT) based R2C2 long-read approach, as well as the Illumina short-read based Smart-seq2 approach. To showcase this, we have applied our methods to create an isoform-level transcriptome from whole blood samples derived from three polar bears (Ursus maritimus). Using Long-DASH, we succeeded in depleting hemoglobin transcripts and generated deep Smart-seq2 Illumina datasets and 3.8 million R2C2 full-length cDNA consensus reads. Applying Long-DASH with our isoform identification pipeline, Mandalorion, we discovered ∼6,000 high-confidence isoforms and a number of novel genes. This indicates that there is a high diversity of gene isoforms within U. maritimus not yet reported. This reproducible and straightforward approach has not only improved the polar bear transcriptome annotations but will serve as the foundation for future efforts to investigate transcriptional dynamics within the 19 polar bear subpopulations around the Arctic.

Vulnerability of Arctic marine mammals to vessel traffic in the increasingly ice-free Northwest Passage and Northern Sea Route.

The fabled Northwest Passage and Northern Sea Route that were once the quests of early Western explorers are now increasingly sea ice-free, with routine vessel transits expected by midcentury. The potential impacts of this novel vessel traffic on endemic Arctic marine mammal (AMM) species are unknown despite their critical social and ecological roles in the ecosystem and widely recognized susceptibility to ice loss. We developed a vulnerability assessment of 80 subpopulations of seven AMM species to vessel traffic during the ice-free season. Vulnerability scores were based on the combined influence of spatially explicit exposure to the sea routes and a suite of sensitivity variables. More than half of AMM subpopulations (42/80) are exposed to open-water vessel transits in the Arctic sea routes. Narwhals (Monodon monoceros) were estimated to be most vulnerable to vessel impacts, given their high exposure and sensitivity, and polar bears (Ursus maritimus) were estimated to be the least vulnerable because of their low exposure and sensitivity. Regions with geographic bottlenecks, such as the Bering Strait and eastern Canadian Arctic, were characterized by two to three times higher vulnerability than more remote regions. These pinch points are obligatory pathways for both vessels and migratory AMMs, and so represent potentially high conflict areas but also opportunities for conservation-informed planning. Some of the species and regions identified as least vulnerable were also characterized by high uncertainty, highlighting additional data and monitoring needs. Our quantification of the heterogeneity of risk across AMM species provides a necessary first step toward developing best practices for maritime industries poised to advance into this rapidly changing seascape.

Sea surface temperature predicts the movements of an Arctic cetacean: the bowhead whale.

The effects of climate change constitute a major concern in Arctic waters due to the rapid decline of sea ice, which may strongly alter the movements and habitat availability of Arctic marine mammals. We tracked 98 bowhead whales by satellite over an 11-year period (2001-2011) in Baffin Bay - West Greenland to investigate the environmental drivers (specifically sea surface temperature and sea ice) involved in bowhead whale's movements. Movement patterns differed according to season, with aggregations of whales found at higher latitudes during spring and summer likely in response to sea-ice retreat and increasing sea temperature (SST) facilitated by the warm West Greenland Current. In contrast, the whales moved further south in response to sea temperature decrease during autumn and winter. Statistical models indicated that the whales targeted a narrow range of SSTs from -0.5 to 2 °C. Sea surface temperatures are predicted to undergo a marked increase in the Arctic, which could expose bowhead whales to both thermal stress and altered stratification and vertical transport of water masses. With such profound changes, bowhead whales may face extensive habitat loss. Our results highlight the need for closer investigation and monitoring in order to predict the extent of future distribution changes.

Range contraction and increasing isolation of a polar bear subpopulation in an era of sea-ice loss.

Climate change is expected to result in range shifts and habitat fragmentation for many species. In the Arctic, loss of sea ice will reduce barriers to dispersal or eliminate movement corridors, resulting in increased connectivity or geographic isolation with sweeping implications for conservation. We used satellite telemetry, data from individually marked animals (research and harvest), and microsatellite genetic data to examine changes in geographic range, emigration, and interpopulation connectivity of the Baffin Bay (BB) polar bear (Ursus maritimus) subpopulation over a 25-year period of sea-ice loss. Satellite telemetry collected from n = 43 (1991-1995) and 38 (2009-2015) adult females revealed a significant contraction in subpopulation range size (95% bivariate normal kernel range) in most months and seasons, with the most marked reduction being a 70% decline in summer from 716,000 km2 (SE 58,000) to 211,000 km2 (SE 23,000) (p < .001). Between the 1990s and 2000s, there was a significant shift northward during the on-ice seasons (2.6° shift in winter median latitude, 1.1° shift in spring median latitude) and a significant range contraction in the ice-free summers. Bears in the 2000s were less likely to leave BB, with significant reductions in the numbers of bears moving into Davis Strait (DS) in winter and Lancaster Sound (LS) in summer. Harvest recoveries suggested both short and long-term fidelity to BB remained high over both periods (83-99% of marked bears remained in BB). Genetic analyses using eight polymorphic microsatellites confirmed a previously documented differentiation between BB, DS, and LS; yet weakly differentiated BB from Kane Basin (KB) for the first time. Our results provide the first multiple lines of evidence for an increasingly geographically and functionally isolated subpopulation of polar bears in the context of long-term sea-ice loss. This may be indicative of future patterns for other polar bear subpopulations under climate change.

The commercial harvest of ice-associated seals in the Sea of Okhotsk, 1972-1994.

Sealing log books from 75 out of 79 commercial harvest cruises carried out between 1972 and 1994 in the Sea of Okhotsk, Russia, were analyzed to describe spatial and temporal allocation of ice-associated seal harvest effort, species composition of catches, total harvest rates, and related parameters for species including ringed (Pusa hispida), ribbon (Histriophoca fasciata), bearded (Erignathus barbatus) and spotted (Phoca largha) seal. Variations in catch per unit effort were explored in relation to year, sea ice conditions, day of the year, and geographic location. In most years, the harvest was predominantly represented by ringed seals (mean = 0.43, range 0.25-0.67), followed by ribbon (mean = 0.31, range 0.15-0.43), spotted (mean = 0.19, range 0.11-0.35) and bearded seals (mean = 0.07, range 0.03-0.14). The struck-and-lost percentages were as high as 30-35% for ringed, bearded and spotted seals and 15-20% for ribbon seals. Catch per unit effort (number of seals/skiff*day) for ringed, ribbon, and spotted seals had a similar seasonal pattern with a distinct spike in catches for spotted seals in the first week of May, for ribbon seals in the last week of May, and for ringed seals in the second week of June. Catches of bearded seals showed a less pronounced temporal structure with a gradual increase toward the end of the harvest season in the majority of years. Spatial distribution of harvest effort followed closely with seal distribution obtained from aerial surveys. These data could be used as a source of information on seal herd location throughout the breeding and molting seasons and for more complex demographic or life-table models. We did not find any evidence of the decline of catch per unit effort over the study period. Timely introduction of state regulations and efficient harvest management apparently prevented severe depletion of ice-associated seal populations in the Sea of Okhotsk during the periods of their intense exploitation.

Correlated velocity models as a fundamental unit of animal movement: synthesis and applications.

BACKGROUND: Continuous time movement models resolve many of the problems with scaling, sampling, and interpretation that affect discrete movement models. They can, however, be challenging to estimate, have been presented in inconsistent ways, and are not widely used. METHODS: We review the literature on integrated Ornstein-Uhlenbeck velocity models and propose four fundamental correlated velocity movement models (CVM's): random, advective, rotational, and rotational-advective. The models are defined in terms of biologically meaningful speeds and time scales of autocorrelation. We summarize several approaches to estimating the models, and apply these tools for the higher order task of behavioral partitioning via change point analysis. RESULTS: An array of simulation illustrate the precision and accuracy of the estimation tools. An analysis of a swimming track of a bowhead whale (Balaena mysticetus) illustrates their robustness to irregular and sparse sampling and identifies switches between slower and faster, and directed vs. random movements. An analysis of a short flight of a lesser kestrel (Falco naumanni) identifies exact moments when switches occur between loopy, thermal soaring and directed flapping or gliding flights. CONCLUSIONS: We provide tools to estimate parameters and perform change point analyses in continuous time movement models as an R package (smoove). These resources, together with the synthesis, should facilitate the wider application and development of correlated velocity models among movement ecologists.