Correlates of seasonal change in the body condition of an Arctic top predator.

Climate-driven sea ice loss has led to changes in the timing of key biological events in the Arctic, however, the consequences and rate of these changes remain largely unknown. Polar bears (Ursus maritimus) undergo seasonal changes in energy stores in relation to foraging opportunities and habitat conditions. Declining sea ice has been linked to reduced body condition in some subpopulations, however, the specific timing and duration of the feeding period when bears acquire most of their energy stores and its relationship to the timing of ice break-up is poorly understood. We used community-based sampling to investigate seasonality in body condition (energy stores) of polar bears in Nunavut, Canada, and examined the influence of sea ice variables. We used adipose tissue lipid content as an index of body condition for 1,206 polar bears harvested from 2010-2017 across five subpopulations with varying seasonal ice conditions: Baffin Bay (October-August), Davis Strait and Foxe Basin (year-round), Gulf of Boothia and Lancaster Sound (August-May). Similar seasonal patterns were found in body condition across subpopulations with bears at their nadir of condition in the spring, followed by fat accumulation past break-up date and subsequent peak body condition in autumn, indicating that bears are actively foraging in late spring and early summer. Late season feeding implies that even minor advances in the timing of break-up may have detrimental effects on foraging opportunities, body condition, and subsequent reproduction and survival. The magnitude of seasonal changes in body condition varied across the study area, presumably driven by local environmental conditions. Our results demonstrate how community-based monitoring of polar bears can reveal population-level responses to climate warming in advance of detectable demographic change. Our data on the seasonal timing of polar bear foraging and energy storage should inform predictive models of the effects of climate-mediated sea ice loss.

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.

Penile density and globally used chemicals in Canadian and Greenland polar bears.

Industrially produced chemicals have been a major environmental concern across our entire Globe since the onset of rapid industrial development around the early 1900. Many of the substances being used are known to be endocrine disrupting chemicals (EDCs) and are also known to be long-range dispersed and to biomagnify to very high concentrations in the tissues of Arctic apex predators such as polar bears (Ursus maritimus). A major concern relating to EDCs is their effects on vital organ-tissues such as bone and it is possible that EDCs represent a more serious challenge to the species' survival than the more conventionally proposed prey reductions linked to climate change. We therefore analyzed penile bone mineral density (BMD) as a key phenotype for reproductive success in 279 polar bear samples born 1990-2000 representing eight polar bear subpopulations. Since EDC concentrations were not available from the same specimens, we compared BMD with published literature information on EDC concentrations. Latitudinal and longitudinal BMD and EDC gradients were clearly observed, with Western Hudson bears having the highest BMD and lowest EDCs, and North East Greenland polar bears carrying the lowest BMD and highest EDCs. A BMD vs. polychlorinated biphenyls (PCB) regression analysis showed that BMD decreased as a function of the eight subpopulations' PCB concentrations and this relationship was close to being significant (p=0.10, R(2)=0.39). Risk quotient (RQ) estimation demonstrated that PCBs could be in a range that may lead to disruption of normal reproduction and development. It is therefore likely that EDCs directly affect development and bone density in polar bears. Canadian bears had in general the best health and the North East Greenland subpopulation being at the highest risk of having negative health effects. While reductions in BMD is in general unhealthy, reductions in penile BMD could lead to increased risk of species extinction because of mating and subsequent fertilization failure as a result of weak penile bones and risk of fractures. Based on this, future studies should assess how polar bear subpopulations respond upon EDC exposure since information and understanding about their circumpolar reproductive health is vital for future conservation.

Non-invasive biomonitoring of polar bear feces can be used to estimate concentrations of metals of concern in traditional food.

The Arctic faces increasing exposure to environmental chemicals such as metals, posing health risks to humans and wildlife. Biomonitoring of polar bears (Ursus maritimus) can be used to quantify chemicals in the environment and in traditional foods consumed by the Inuit. However, typically, these samples are collected through invasive or terminal methods. The biomonitoring of feces could be a useful alternative to the current metal monitoring method within the Arctic. Here, we aim to 1) quantify the relationship between concentrations of metals in the feces and tissues (muscle, liver, and fat) of polar bears using predictive modeling, 2) develop an easy-to-use conversion tool for use in community-based monitoring programs to non-invasively estimate contaminant concentrations in polar bears tissues and 3) demonstrate the application of these models by examining potential exposure risk for humans from consumption of polar bear muscle. Fecal, muscle, liver, and fat samples were harvested from 49 polar bears through a community-based monitoring program. The samples were analyzed for 32 metals. Exploratory analysis indicated that mean metal concentrations generally did not vary by age or sex, and many of the metals measured in feces were positively correlated with the internal tissue concentration. We developed predictive linear regression models between internal (muscle, liver, fat) and external (feces) metal concentrations and further explored the mercury and methylmercury relationships for utility risk screening. Using the cross-validated regression coefficients, we developed a conversion tool that contributes to the One Health approach by understanding the interrelated health of humans, wildlife, and the environment in the Arctic. The findings support using feces as a biomonitoring tool for assessing contaminants in polar bears. Further research is needed to validate the developed models for other regions in the Arctic and assess the impact of environmental weathering on fecal metal concentrations.

The geographic distribution, and the biotic and abiotic predictors of select zoonotic pathogen detections in Canadian polar bears.

Increasing Arctic temperatures are facilitating the northward expansion of more southerly hosts, vectors, and pathogens, exposing naïve populations to pathogens not typical at northern latitudes. To understand such rapidly changing host-pathogen dynamics, we need sensitive and robust surveillance tools. Here, we use a novel multiplexed magnetic-capture and droplet digital PCR (ddPCR) tool to assess a sentinel Arctic species, the polar bear (Ursus maritimus; n = 68), for the presence of five zoonotic pathogens (Erysipelothrix rhusiopathiae, Francisella tularensis, Mycobacterium tuberculosis complex, Toxoplasma gondii and Trichinella spp.), and observe associations between pathogen presence and biotic and abiotic predictors. We made two novel detections: the first detection of a Mycobacterium tuberculosis complex member in Arctic wildlife and the first of E. rhusiopathiae in a polar bear. We found a prevalence of 37% for E. rhusiopathiae, 16% for F. tularensis, 29% for Mycobacterium tuberculosis complex, 18% for T. gondii, and 75% for Trichinella spp. We also identify associations with bear age (Trichinella spp.), harvest season (F. tularensis and MTBC), and human settlements (E. rhusiopathiae, F. tularensis, MTBC, and Trichinella spp.). We demonstrate that monitoring a sentinel species, the polar bear, could be a powerful tool in disease surveillance and highlight the need to better characterize pathogen distributions and diversity in the Arctic.

A new multiplexed magnetic capture-Droplet digital PCR tool for monitoring wildlife population health and pathogen surveillance.

Anthropogenic stressors are exacerbating the emergence and spread of pathogens worldwide. In regions like the Arctic, where ecosystems are particularly susceptible, marked changes are predicted in regional diversity, intensity, and patterns of infectious diseases. To understand such rapidly changing host-pathogen dynamics and mitigate the impacts of novel pathogens, we need sensitive disease surveillance tools. We developed and validated a novel multiplexed, magnetic capture, and ddPCR tool for the surveillance of multiple pathogens in polar bears, a sentinel species that is considered susceptible to climate change and other stressors with a pan-Arctic distribution. Through sequence-specific magnetic capture, we concentrated five target template sequences from three zoonotic bacteria (Erysipelothrix rhusiopathiae, Francisella tularensis, and Mycobacterium tuberculosis complex) and two parasitic (Toxoplasma gondii and Trichinella spp.) pathogens from large quantities (<100 g) of host tissue. We then designed and validated two multiplexed probe-based ddPCR assays for the amplification and detection of the low-concentration target DNA. Validations used 48 polar bear tissues (muscle and liver). We detected 14, 1, 3, 4, and 22 tissue positives for E. rhusiopathiae, F. tularensis, M. tuberculosis complex, T. gondii, and Trichinella spp., respectively. These multiplexed assays offer a rapid, specific tool for quantifying and monitoring the changing geographical and host distributions of pathogens relevant to human and animal health.

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.

Genotyping-in-thousands by sequencing (GT-seq) of noninvasive faecal and degraded samples: A new panel to enable ongoing monitoring of Canadian polar bear populations.

Genetic monitoring using noninvasive samples provides a complement or alternative to traditional population monitoring methods. However, next-generation sequencing approaches to monitoring typically require high quality DNA and the use of noninvasive samples (e.g., scat) is often challenged by poor DNA quality and contamination by nontarget species. One promising solution is a highly multiplexed sequencing approach called genotyping-in-thousands by sequencing (GT-seq), which can enable cost-efficient genomics-based monitoring for populations based on noninvasively collected samples. Here, we develop and validate a GT-seq panel of 324 single nucleotide polymorphisms (SNPs) optimized for genotyping of polar bears based on DNA from noninvasively collected faecal samples. We demonstrate (1) successful GT-seq genotyping of DNA from a range of sample sources, including successful genotyping (>50% loci) of 62.9% of noninvasively collected faecal samples determined to contain polar bear DNA; and (2) that we can reliably differentiate individuals, ascertain sex, assess relatedness, and resolve population structure of Canadian polar bear subpopulations based on a GT-seq panel of 324 SNPs. Our GT-seq data reveal spatial-genetic patterns similar to previous polar bear studies but at lesser cost per sample and through use of noninvasively collected samples, indicating the potential of this approach for population monitoring. This GT-seq panel provides the foundation for a noninvasive toolkit for polar bear monitoring and can contribute to community-based programmes - a framework which may serve as a model for wildlife conservation and management for species worldwide.

Canadian polar bear population structure using genome-wide markers.

Predicting the consequences of environmental changes, including human-mediated climate change on species, requires that we quantify range-wide patterns of genetic diversity and identify the ecological, environmental, and historical factors that have contributed to it. Here, we generate baseline data on polar bear population structure across most Canadian subpopulations (n = 358) using 13,488 genome-wide single nucleotide polymorphisms (SNPs) identified with double-digest restriction site-associated DNA sequencing (ddRAD). Our ddRAD dataset showed three genetic clusters in the sampled Canadian range, congruent with previous studies based on microsatellites across the same regions; however, due to a lack of sampling in Norwegian Bay, we were unable to confirm the existence of a unique cluster in that subpopulation. These data on the genetic structure of polar bears using SNPs provide a detailed baseline against which future shifts in population structure can be assessed, and opportunities to develop new noninvasive tools for monitoring polar bears across their range.

The use of hair as a proxy for total and methylmercury burdens in polar bear muscle tissue.

Polar bears (Ursus maritimus) are an ecologically important species in the Arctic, whose health, and that of the people whose livelihoods depend on them, are increasingly affected by climate change and the bioaccumulation of contaminants such as mercury (Hg). Although methylmercury (MeHg) is the toxic form of Hg that biomagnifies up food webs, risk assessment studies typically only report on total Hg (THg) concentrations because it is cheaper to quantify. Furthermore, hair is commonly analysed for THg in polar bear as well as human risk assessment studies because it is relatively non-invasive to collect, yet we know little of how THg and MeHg concentrations differ between hair and muscle tissues. In this study, we quantified THg and MeHg concentrations in hair and muscle from 44 polar bears (24 sub-adults: 9 females, 15 males; 18 adults: 5 females, 13 males, and 2 males of unknown age group), harvested in 2015 and 2016 from four subpopulations in Nunavut, Canada (Davis Strait, n = 3; Gulf of Boothia, n = 8; Baffin Bay, n = 15; Foxe Basin, n = 18). We found only moderately positive correlations (0.4 ≤ r ≤ 0.5) between THg concentrations in hair and THg and MeHg concentrations in muscle. Further, 75% and 88% of THg was MeHg in hair and muscle, respectively. High concentrations of THg in hair - 71% of the samples were above the suggested neurochemical no observed effect level for polar bears - suggest some of the bears may be adversely affected by Hg-related health effects. Despite this, all MeHg concentrations in muscle (0.1 to 0.4 mg/kg (wet weight, ww)) were below the consumption maximum Hg concentration of 0.5 mg/kg (ww) set by Canadian health authorities.

High contributions of sea ice derived carbon in polar bear (Ursus maritimus) tissue.

Polar bears (Ursus maritimus) rely upon Arctic sea ice as a physical habitat. Consequently, conservation assessments of polar bears identify the ongoing reduction in sea ice to represent a significant threat to their survival. However, the additional role of sea ice as a potential, indirect, source of energy to bears has been overlooked. Here we used the highly branched isoprenoid lipid biomarker-based index (H-Print) approach in combination with quantitative fatty acid signature analysis to show that sympagic (sea ice-associated), rather than pelagic, carbon contributions dominated the marine component of polar bear diet (72-100%; 99% CI, n = 55), irrespective of differences in diet composition. The lowest mean estimates of sympagic carbon were found in Baffin Bay bears, which were also exposed to the most rapidly increasing open water season. Therefore, our data illustrate that for future Arctic ecosystems that are likely to be characterised by reduced sea ice cover, polar bears will not only be impacted by a change in their physical habitat, but also potentially in the supply of energy to the ecosystems upon which they depend. This data represents the first quantifiable baseline that is critical for the assessment of likely ongoing changes in energy supply to Arctic predators as we move into an increasingly uncertain future for polar ecosystems.

Persistent organic pollutants and penile bone mineral density in East Greenland and Canadian polar bears (Ursus maritimus) during 1996-2015.

Persistent organic pollutants (POPs) are long-range transported to the Arctic via atmospheric and oceanic currents, where they biomagnify to high concentrations in the tissues of apex predators such as polar bears (Ursus maritimus). A major concern of POP exposure is their physiological effects on vital organ-tissues posing a threat to the health and survival of polar bears. Here we examined the relationship between selected POPs and baculum bone mineral density (BMD) in the East Greenland and seven Canadian subpopulations of polar bears. BMD was examined in 471 bacula collected between years 1996-2015 while POP concentrations in adipose tissue were determined in 67-192 of these individuals collected from 1999 to -2015. A geographical comparison showed that baculum BMD was significantly lowest in polar bears from East Greenland (EG) when compared to Gulf of Boothia (GB), Southern Hudson (SH) and Western Hudson (WH) Bay subpopulations (all p < 0.05). The calculation of a T-score osteoporosis index for the EG subpopulation using WH bears as a reference group gave a T-score of -1.44 which indicate risk of osteopenia. Concentrations of ΣPCB74 (polychlorinated biphenyls), ΣDDT3 (dichlorodiphenyltrichloroethanes), p,p'-DDE (dichlorodiphenyldichloroethylene), ΣHCH3 (hexachlorohexane) and α-HCH was significantly highest in EG bears while ΣPBDE (polybrominated diphenyl ethers), BDE-47 and BDE-153 was significantly highest in SH bears (all p < 0.04). Statistical analyses of individual baculum BMD vs. POP concentrations showed that BMD was positively correlated with ΣPCB74, CB-153, HCB (hexachlorobenzene), ΣHCH, ß-HCH, ClBz (chlorobenzene), ΣPBDE and BDE-153 (all p < 0.03). In conclusion, baculum density was significantly lowest in East Greenland polar bears despite the positive statistical correlations of BMD vs. POPs. Other important factors such as nutritional status, body mass and body condition was not available for the statistical modelling. Since on-going environmental changes are known to affect these, future studies need to incorporate nutritional, endocrine and genetic parameters to further understand how POP exposure may disrupt bone homeostasis and affect baculum BMD across polar bear subpopulations.

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.

Dietary habits of polar bears in Foxe Basin, Canada: possible evidence of a trophic regime shift mediated by a new top predator.

Polar bear (Ursus maritimus) subpopulations in several areas with seasonal sea ice regimes have shown declines in body condition, reproductive rates, or abundance as a result of declining sea ice habitat. In the Foxe Basin region of Nunavut, Canada, the size of the polar bear subpopulation has remained largely stable over the past 20 years, despite concurrent declines in sea ice habitat. We used fatty acid analysis to examine polar bear feeding habits in Foxe Basin and thus potentially identify ecological factors contributing to population stability. Adipose tissue samples were collected from 103 polar bears harvested during 2010-2012. Polar bear diet composition varied spatially within the region with ringed seal (Pusa hispida) comprising the primary prey in northern and southern Foxe Basin, whereas polar bears in Hudson Strait consumed equal proportions of ringed seal and harp seal (Pagophilus groenlandicus). Walrus (Odobenus rosmarus) consumption was highest in northern Foxe Basin, a trend driven by the ability of adult male bears to capture large-bodied prey. Importantly, bowhead whale (Balaena mysticetus) contributed to polar bear diets in all areas and all age and sex classes. Bowhead carcasses resulting from killer whale (Orcinus orca) predation and subsistence harvest potentially provide an important supplementary food source for polar bears during the ice-free period. Our results suggest that the increasing abundance of killer whales and bowhead whales in the region could be indirectly contributing to improved polar bear foraging success despite declining sea ice habitat. However, this indirect interaction between top predators may be temporary if continued sea ice declines eventually severely limit on-ice feeding opportunities for polar bears.

Assessing polar bear (Ursus maritimus) population structure in the Hudson Bay region using SNPs.

Defining subpopulations using genetics has traditionally used data from microsatellite markers to investigate population structure; however, single-nucleotide polymorphisms (SNPs) have emerged as a tool for detection of fine-scale structure. In Hudson Bay, Canada, three polar bear (Ursus maritimus) subpopulations (Foxe Basin (FB), Southern Hudson Bay (SH), and Western Hudson Bay (WH)) have been delineated based on mark-recapture studies, radiotelemetry and satellite telemetry, return of marked animals in the subsistence harvest, and population genetics using microsatellites. We used SNPs to detect fine-scale population structure in polar bears from the Hudson Bay region and compared our results to the current designations using 414 individuals genotyped at 2,603 SNPs. Analyses based on discriminant analysis of principal components (DAPC) and STRUCTURE support the presence of four genetic clusters: (i) Western-including individuals sampled in WH, SH (excluding Akimiski Island in James Bay), and southern FB (south of Southampton Island); (ii) Northern-individuals sampled in northern FB (Baffin Island) and Davis Strait (DS) (Labrador coast); (iii) Southeast-individuals from SH (Akimiski Island in James Bay); and (iv) Northeast-individuals from DS (Baffin Island). Population structure differed from microsatellite studies and current management designations demonstrating the value of using SNPs for fine-scale population delineation in polar bears.

Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales.

As global warming accelerates the melting of Arctic sea ice, polar bears (Ursus maritimus) must adapt to a rapidly changing landscape. This process will necessarily alter the species distribution together with population dynamics and structure. Detailed knowledge of these changes is crucial to delineating conservation priorities. Here, we sampled 361 polar bears from across the center of the Canadian Arctic Archipelago spanning the Gulf of Boothia (GB) and M'Clintock Channel (MC). We use DNA microsatellites and mitochondrial control region sequences to quantify genetic differentiation, estimate gene flow, and infer population history. Two populations, roughly coincident with GB and MC, are significantly differentiated at both nuclear (F ST = 0.01) and mitochondrial (ΦST = 0.47; F ST = 0.29) loci, allowing Bayesian clustering analyses to assign individuals to either group. Our data imply that the causes of the mitochondrial and nuclear genetic patterns differ. Analysis of mtDNA reveals the matrilineal structure dates at least to the Holocene, and is common to individuals throughout the species' range. These mtDNA differences probably reflect both genetic drift and historical colonization dynamics. In contrast, the differentiation inferred from microsatellites is only on the scale of hundreds of years, possibly reflecting contemporary impediments to gene flow. Taken together, our data suggest that gene flow is insufficient to homogenize the GB and MC populations and support the designation of GB and MC as separate polar bear conservation units. Our study also provide a striking example of how nuclear DNA and mtDNA capture different aspects of a species demographic history.