Genetic structure of the world's polar bear populations

Impact of Holocene environmental change on the evolutionary ecology of an Arctic top predator

The Arctic is among the most climatically sensitive environments on Earth, and the disappearance of multiyear sea ice in the Arctic Ocean is predicted within decades. As apex predators, polar bears are sentinel species for addressing the impact of environmental variability on Arctic marine ecosystems. By integrating genomics, isotopic analysis, morphometrics, and ecological modeling, we investigate how Holocene environmental changes affected polar bears around Greenland. We uncover reductions in effective population size coinciding with increases in annual mean sea surface temperature, reduction in sea ice cover, declines in suitable habitat, and shifts in suitable habitat northward. Furthermore, we show that west and east Greenlandic polar bears are morphologically, and ecologically distinct, putatively driven by regional biotic and genetic differences. Together, we provide insights into the vulnerability of polar bears to environmental change and how the Arctic marine ecosystem plays a vital role in shaping the evolutionary and ecological trajectories of its inhabitants.

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.

Polar Bear Harvest Patterns Across the Circumpolar Arctic

Wildlife harvest remains a conservation concern for many species and assessing patterns of harvest can provide insights on sustainability and inform management. Polar bears (Ursus maritimus) are harvested over a large part of their range by local people. The species has a history of unsustainable harvest that was largely rectified by an international agreement that required science-based management. The objective of our study was to examine the temporal patterns in the number of polar bears harvested, harvest sex ratios, and harvest rates from 1970 to 2018. We analyzed data from 39,049 harvested polar bears (annual mean 797 bears) collected from 1970 to 2018. Harvest varied across populations and times that reflect varying management objectives, episodic events, and changes based on new population estimates. More males than females were harvested with an overall M:F sex ratio of 1.84. Harvest varied by jurisdiction with 68.0% of bears harvested in Canada, 18.0% in Greenland, 11.8% in the USA, and 2.2% in Norway. Harvest rate was often near the 4.5% target rate. Where data allowed harvest rate estimation, the target rate was exceeded in 11 of 13 populations with 1–5 populations per year above the target since 1978. Harvest rates at times were up to 15.9% of the estimated population size suggesting rare episodes of severe over-harvest. Harvest rate was unrelated to a proxy for ecosystem productivity (area of continental shelf within each population) but was correlated with prey diversity. In the last 5–10 years, monitored populations all had harvest rates near sustainable limits, suggesting improvements in management. Polar bear harvest management has reduced the threat it once posed to the species. However, infrequent estimates of abundance, new management objectives, and climate change have raised new concerns about the effects of harvest.

A novel mark-recapture-recovery survey using genetic sampling for polar bears Ursus maritimus in Baffin Bay

Changes in sea-ice dynamics are affecting polar bears Ursus maritimus across their circumpolar range, which highlights the importance of periodic demographic assessments to inform management and conservation. We used genetic mark-recapture-recovery to derive estimates of abundance and survival for the Baffin Bay (BB) polar bear subpopulation—the first time this method has been used successfully for this species. Genetic data from tissue samples we collected via biopsy darting were combined with historical physical capture and harvest recovery data. The combined data set consisted of 1410 genetic samples (2011-2013), 914 physical captures (1993-1995, 1997), and 234 harvest returns of marked bears (1993-2013). The estimate of mean subpopulation abundance was 2826 (95% CI = 2284-3367) in 2012-2013. Estimates of annual survival (mean ± SE) were 0.90 ± 0.05 and 0.78 ± 0.06 for females and males age ≥2 yr, respectively. The proportion of total mortality of adult females and males that was attributed to legal harvest was 0.16 ± 0.05 and 0.26 ± 0.06, respectively. Remote sensing sea-ice data, telemetry data, and spatial distribution of onshore sampling indicated that polar bears were more likely to use offshore sea-ice habitat during the 1990s sampling period compared to the 2010s. Furthermore, in the 1990s, sampling of deep fjords and inland areas was limited, and no offshore sampling occurred in either time period, which precluded comparisons of abundance between the 1993-1997 and 2011-2013 study periods. Our findings demonstrate that genetic sampling can be a practical method for demographic assessment of polar bears over large spatial and temporal scales.

Sea ice reduction drives genetic differentiation among Barents Sea polar bears

Loss of Arctic sea ice owing to climate change is predicted to reduce both genetic diversity and gene flow in ice-dependent species, with potentially negative consequences for their long-term viability. Here, we tested for the population-genetic impacts of reduced sea ice cover on the polar bear (Ursus maritimus) sampled across two decades (1995-2016) from the Svalbard Archipelago, Norway, an area that is affected by rapid sea ice loss in the Arctic Barents Sea. We analysed genetic variation at 22 microsatellite loci for 626 polar bears from four sampling areas within the archipelago. Our results revealed a 3-10% loss of genetic diversity across the study period, accompanied by a near 200% increase in genetic differentiation across regions. These effects may best be explained by a decrease in gene flow caused by habitat fragmentation owing to the loss of sea ice coverage, resulting in increased inbreeding of local polar bears within the focal sampling areas in the Svalbard Archipelago. This study illustrates the importance of genetic monitoring for developing adaptive management strategies for polar bears and other ice-dependent species.

Are tissue samples obtained via remote biopsy useful for fatty acid-based diet analyses in a free-ranging carnivore?

Fundamental knowledge on free-ranging animals has been obtained through capture-based studies; however, these may be logistically intensive, financially expensive, and potentially inconsistent with local cultural values. Genetic mark–recapture using remote tissue sampling has emerged as a less invasive alternative to capture-based population surveys but provides fewer opportunities to collect samples and measurements for broader ecological studies. We compared lipid content, fatty acid (FA) composition, and diet estimates from adipose tissue of polar bears (Ursus maritimus) obtained from two collection methods: remote biopsies (n = 138) sampled from helicopters and hunter-collected tissue (n = 499) from bears harvested in Davis Strait and Gulf of Boothia, Nunavut, 2010 – 2018. Lipid content of adipose tissue was lower in remote biopsies than harvest samples likely because remote biopsies removed only the outermost layer of subcutaneous tissue, rather than the more metabolically dynamic innermost tissue obtained from harvest samples. In contrast, FA composition was similar between the two collection methods with relatively small proportional differences in individual FAs. For diet estimates in Davis Strait, collection method was not a predictor of prey contribution to diet. In Gulf of Boothia, collection method was a predictor for some prey types, but the differences were relatively minor; the rank order of prey types was similar (e.g., ringed seal; Pusa hispida was consistently the primary prey in diets) and prey proportions differed by < 6% between the collection methods. Results from both methods showed that diets varied by geographic area, season, year, age class, and sex. Our study demonstrates that adipose tissue from remote biopsy provides reliable estimates of polar bear diet based on FA analysis and can be used to monitor underlying ecological changes in Arctic marine food webs.

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.

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, β-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.

UK rare breeds: population genetic analyses and implications for applied conservation

Since the establishment of the Rare Breeds Survival Trust (RBST) in 1973, rare breed genetic conservation has only gradually emerged as a major key to the continued success and survival of populations. Thus, although basic population and demographic data have been recorded for all breeds listed by the Trust and most rare breeds have kept detailed pedigrees, there is still little information available about current population genetic structure and dynamics over time. Consequently, the majority of rare breed population meta-analyses based upon pedigree data are yet to be carried out. Transfer of rare breed records onto a computer database is therefore a current priority for the RBST, in addition to making available software to provide rare breed organisations with breed profiles to describe founder effects, effective population size (Ne), rate of inbreeding (ΔF), and kinship patterns. Results from rare breed pedigree analyses using this software can now be used to a) illustrate where and how loss of genetic diversity has taken place in rare breeds and b) enable decision processes concerning conservation strategy in future. Conservation strategy informed by such analyses can only be successfully implemented if due regard is given to the realities imposed by the need to maintain rare breed populations within an agricultural context, however. In light of these recent improvements to data recording and access to studies of population genetic structure, some of the traditional limitations to advances to rare breed conservation strategy may now need to be re-examined.

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.

Circumpolar contaminant concentrations in polar bears (Ursus maritimus) and potential population-level effects

Polar bears (Ursus maritimus) currently receive much attention in the context of global climate change. However, there are other stressors that might threaten the viability of polar bear populations as well, such as exposure to anthropogenic pollutants. Lipophilic organic compounds bio-accumulate and bio-magnify in the food chain, leading to high concentrations at the level of top-predators. In Arctic wildlife, including the polar bear, various adverse health effects have been related to internal concentrations of commercially used anthropogenic chemicals like PCB and DDT. The extent to which these individual health effects are associated to population-level effects is, however, unknown. In this study we assembled data on adipose tissue concentrations of ∑PCB, ∑DDT, dieldrin and ∑PBDE in individual polar bears from peer-reviewed scientific literature. Data were available for 14 out of the 19 subpopulations. We found that internal concentrations of these contaminants exceed threshold values for adverse individual health effects in several subpopulations. In an exploratory regression analysis we identified a clear negative correlation between polar bear population density and sub-population specific contaminant concentrations in adipose tissue. The results suggest that adverse health effects of contaminants in individual polar bears may scale up to population-level consequences. Our study highlights the need to consider contaminant exposure along with other threats in polar bear population viability analyses.

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.

Circumpolar Genetic Structure and Recent Gene Flow of Polar Bears: A Reanalysis

Recently, an extensive study of 2,748 polar bears (Ursus maritimus) from across their circumpolar range was published in PLOS ONE, which used microsatellites and mitochondrial haplotypes to apparently show altered population structure and a dramatic change in directional gene flow towards the Canadian Archipelago-an area believed to be a future refugium for polar bears as their southernmost habitats decline under climate change. Although this study represents a major international collaborative effort and promised to be a baseline for future genetics work, methodological shortcomings and errors of interpretation undermine some of the study's main conclusions. Here, we present a reanalysis of this data in which we address some of these issues, including: (1) highly unbalanced sample sizes and large amounts of systematically missing data; (2) incorrect calculation of FST and of significance levels; (3) misleading estimates of recent gene flow resulting from non-convergence of the program BayesAss. In contrast to the original findings, in our reanalysis we find six genetic clusters of polar bears worldwide: the Hudson Bay Complex, the Western and Eastern Canadian Arctic Archipelago, the Western and Eastern Polar Basin, and-importantly-we reconfirm the presence of a unique and possibly endangered cluster of bears in Norwegian Bay near Canada's expected last sea-ice refugium. Although polar bears' abundance, distribution, and population structure will certainly be negatively affected by ongoing-and increasingly rapid-loss of Arctic sea ice, these genetic data provide no evidence of strong directional gene flow in response to recent climate change.

Population structure of two rabies hosts relative to the known distribution of rabies virus variants in Alaska

For pathogens that infect multiple species, the distinction between reservoir hosts and spillover hosts is often difficult. In Alaska, three variants of the arctic rabies virus exist with distinct spatial distributions. We tested the hypothesis that rabies virus variant distribution corresponds to the population structure of the primary rabies hosts in Alaska, arctic foxes (Vulpes lagopus) and red foxes (Vulpes vulpes) to possibly distinguish reservoir and spillover hosts. We used mitochondrial DNA (mtDNA) sequence and nine microsatellites to assess population structure in those two species. mtDNA structure did not correspond to rabies virus variant structure in either species. Microsatellite analyses gave varying results. Bayesian clustering found two groups of arctic foxes in the coastal tundra region, but for red foxes it identified tundra and boreal types. Spatial Bayesian clustering and spatial principal components analysis identified 3 and 4 groups of arctic foxes, respectively, closely matching the distribution of rabies virus variants in the state. Red foxes, conversely, showed eight clusters comprising two regions (boreal and tundra) with much admixture. These results run contrary to previous beliefs that arctic fox show no fine-scale spatial population structure. While we cannot rule out that the red fox is part of the maintenance host community for rabies in Alaska, the distribution of virus variants appears to be driven primarily by the arctic fox. Therefore, we show that host population genetics can be utilized to distinguish between maintenance and spillover hosts when used in conjunction with other approaches.

Conflict bear translocation: investigating population genetics and fate of bear translocation in Dachigam National Park, Jammu and Kashmir, India

The Asiatic black bear population in Dachigam landscape, Jammu and Kashmir is well recognized as one of the highest density bear populations in India. Increasing incidences of bear-human interactions and the resultant retaliatory killings by locals have become a serious threat to the survivorship of black bears in the Dachigam landscape. The Department of Wildlife Protection in Jammu and Kashmir has been translocating bears involved in conflicts, henceforth 'conflict bears' from different sites in Dachigam landscape to Dachigam National Park as a flagship activity to mitigate conflicts. We undertook this study to investigate the population genetics and the fate of bear translocation in Dachigam National Park. We identified 109 unique genotypes in an area of ca. 650 km2 and observed bear population under panmixia that showed sound genetic variability. Molecular tracking of translocated bears revealed that mostly bears (7 out of 11 bears) returned to their capture sites, possibly due to homing instincts or habituation to the high quality food available in agricultural croplands and orchards, while only four bears remained in Dachigam National Park after translocation. Results indicated that translocation success was most likely to be season dependent as bears translocated during spring and late autumn returned to their capture sites, perhaps due to the scarcity of food inside Dachigam National Park while bears translocated in summer remained in Dachigam National Park due to availability of surplus food resources. Thus, the current management practices of translocating conflict bears, without taking into account spatio-temporal variability of food resources in Dachigam landscape seemed to be ineffective in mitigating conflicts on a long-term basis. However, the study highlighted the importance of molecular tracking of bears to understand their movement patterns and socio-biology in tough terrains like Dachigam landscape.

Population substructure and space use of Foxe Basin polar bears

Climate change has been identified as a major driver of habitat change, particularly for sea ice-dependent species such as the polar bear (Ursus maritimus). Population structure and space use of polar bears have been challenging to quantify because of their circumpolar distribution and tendency to range over large areas. Knowledge of movement patterns, home range, and habitat is needed for conservation and management. This is the first study to examine the spatial ecology of polar bears in the Foxe Basin management unit of Nunavut, Canada. Foxe Basin is in the mid-Arctic, part of the seasonal sea ice ecoregion and it is being negatively affected by climate change. Our objectives were to examine intrapopulation spatial structure, to determine movement patterns, and to consider how polar bear movements may respond to changing sea ice habitat conditions. Hierarchical and fuzzy cluster analyses were used to assess intrapopulation spatial structure of geographic position system satellite-collared female polar bears. Seasonal and annual movement metrics (home range, movement rates, time on ice) and home-range fidelity (static and dynamic overlap) were compared to examine the influence of regional sea ice on movements. The polar bears were distributed in three spatial clusters, and there were differences in the movement metrics between clusters that may reflect sea ice habitat conditions. Within the clusters, bears moved independently of each other. Annual and seasonal home-range fidelity was observed, and the bears used two movement patterns: on-ice range residency and annual migration. We predict that home-range fidelity may decline as the spatial and temporal predictability of sea ice changes. These new findings also provide baseline information for managing and monitoring this polar bear population.

Genetic Variation, Structure, and Gene Flow in a Sloth Bear (Melursus ursinus) Meta-Population in the Satpura-Maikal Landscape of Central India

Sloth bears (Melursus ursinus) are endemic to the Indian subcontinent. As a result of continued habitat loss and degradation over the past century, sloth bear populations have been in steady decline and now exist only in isolated or fragmented habitat across the entire range. We investigated the genetic connectivity of the sloth bear meta-population in five tiger reserves in the Satpura-Maikal landscape of central India. We used noninvasively collected fecal and hair samples to obtain genotypic information using a panel of seven polymorphic loci. Out of 194 field collected samples, we identified 55 individuals in this meta-population. We found that this meta-population has moderate genetic variation, and is subdivided into two genetic clusters. Further, we identified five first-generation migrants and signatures of contemporary gene flow. We found evidence of sloth bears in the corridor between the Kanha and Pench Tiger Reserves, and our results suggest that habitat connectivity and corridors play an important role in maintaining gene flow in this meta-population. These corridors face several anthropogenic and infrastructure development threats that have the potential to sever ongoing gene flow, if policies to protect them are not put into action immediately.

Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears

Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed a remarkable episode of polar bear gene flow into the population of brown bears that colonized the Admiralty, Baranof and Chichagof islands (ABC islands) of Alaska. Here, we present an analysis of data from a large panel of polar bear and brown bear genomes that includes brown bears from the ABC islands, the Alaskan mainland and Europe. Our results provide clear evidence that gene flow between the two species had a geographically wide impact, with polar bear DNA found within the genomes of brown bears living both on the ABC islands and in the Alaskan mainland. Intriguingly, while brown bear genomes contain up to 8.8% polar bear ancestry, polar bear genomes appear to be devoid of brown bear ancestry, suggesting the presence of a barrier to gene flow in that direction.

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.

Implications of the circumpolar genetic structure of polar bears for their conservation in a rapidly warming Arctic

We provide an expansive analysis of polar bear (Ursus maritimus) circumpolar genetic variation during the last two decades of decline in their sea-ice habitat. We sought to evaluate whether their genetic diversity and structure have changed over this period of habitat decline, how their current genetic patterns compare with past patterns, and how genetic demography changed with ancient fluctuations in climate. Characterizing their circumpolar genetic structure using microsatellite data, we defined four clusters that largely correspond to current ecological and oceanographic factors: Eastern Polar Basin, Western Polar Basin, Canadian Archipelago and Southern Canada. We document evidence for recent (ca. last 1–3 generations) directional gene flow from Southern Canada and the Eastern Polar Basin towards the Canadian Archipelago, an area hypothesized to be a future refugium for polar bears as climate-induced habitat decline continues. Our data provide empirical evidence in support of this hypothesis. The direction of current gene flow differs from earlier patterns of gene flow in the Holocene. From analyses of mitochondrial DNA, the Canadian Archipelago cluster and the Barents Sea subpopulation within the Eastern Polar Basin cluster did not show signals of population expansion, suggesting these areas may have served also as past interglacial refugia. Mismatch analyses of mitochondrial DNA data from polar and the paraphyletic brown bear (U. arctos) uncovered offset signals in timing of population expansion between the two species, that are attributed to differential demographic responses to past climate cycling. Mitogenomic structure of polar bears was shallow and developed recently, in contrast to the multiple clades of brown bears. We found no genetic signatures of recent hybridization between the species in our large, circumpolar sample, suggesting that recently observed hybrids represent localized events. Documenting changes in subpopulation connectivity will allow polar nations to proactively adjust conservation actions to continuing decline in sea-ice habitat.

Giant pandas are not an evolutionary cul-de-sac: evidence from multidisciplinary research

The giant panda (Ailuropoda melanoleuca) is one of the world's most endangered mammals and remains threatened by environmental and anthropogenic pressure. It is commonly argued that giant pandas are an evolutionary cul-de-sac because of their specialized bamboo diet, phylogenetic changes in body size, small population, low genetic diversity, and low reproductive rate. This notion is incorrect, arose from a poor understanding or appreciation of giant panda biology, and is in need of correction. In this review, we summarize research across morphology, ecology, and genetics to dispel the idea, once and for all, that giant pandas are evolutionary dead-end. The latest and most advanced research shows that giant pandas are successful animals highly adapted to a specialized bamboo diet via morphological, ecological, and genetic adaptations and coadaptation of gut microbiota. We also debunk misconceptions around population size, population growth rate, and genetic variation. During their evolutionary history spanning 8 My, giant pandas have survived diet specialization, massive bamboo flowering and die off, and rapid climate oscillations. Now, they are suffering from enormous human interference. Fortunately, continued conservation effort is greatly reducing impacts from anthropogenic interference and allowing giant panda populations and habitat to recover. Previous ideas of a giant panda evolutionary cul-de-sac resulted from an unsystematic and unsophisticated understanding of their biology and it is time to shed this baggage and focus on the survival and maintenance of this high-profile species.

Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears

Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyper-lipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show that the species diverged only 479-343 thousand years BP. We find that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization of the cardiovascular system. One of the genes showing the strongest evidence of selection, APOB, encodes the primary lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain how polar bears are able to cope with life-long elevated LDL levels that are associated with high risk of heart disease in humans.

Brown and polar bear Y chromosomes reveal extensive male-biased gene flow within brother lineages

Brown and polar bears have become prominent examples in phylogeography, but previous phylogeographic studies relied largely on maternally inherited mitochondrial DNA (mtDNA) or were geographically restricted. The male-specific Y chromosome, a natural counterpart to mtDNA, has remained underexplored. Although this paternally inherited chromosome is indispensable for comprehensive analyses of phylogeographic patterns, technical difficulties and low variability have hampered its application in most mammals. We developed 13 novel Y-chromosomal sequence and microsatellite markers from the polar bear genome and screened these in a broad geographic sample of 130 brown and polar bears. We also analyzed a 390-kb-long Y-chromosomal scaffold using sequencing data from published male ursine genomes. Y chromosome evidence support the emerging understanding that brown and polar bears started to diverge no later than the Middle Pleistocene. Contrary to mtDNA patterns, we found 1) brown and polar bears to be reciprocally monophyletic sister (or rather brother) lineages, without signals of introgression, 2) male-biased gene flow across continents and on phylogeographic time scales, and 3) male dispersal that links the Alaskan ABC islands population to mainland brown bears. Due to female philopatry, mtDNA provides a highly structured estimate of population differentiation, while male-biased gene flow is a homogenizing force for nuclear genetic variation. Our findings highlight the importance of analyzing both maternally and paternally inherited loci for a comprehensive view of phylogeographic history, and that mtDNA-based phylogeographic studies of many mammals should be reevaluated. Recent advances in sequencing technology render the analysis of Y-chromosomal variation feasible, even in nonmodel organisms.

Molecular phylogeny and SNP variation of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) derived from genome sequences

We assessed the relationships of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) with high throughput genomic sequencing data with an average coverage of 25× for each species. A total of 1.4 billion 100-bp paired-end reads were assembled using the polar bear and annotated giant panda (Ailuropoda melanoleuca) genome sequences as references. We identified 13.8 million single nucleotide polymorphisms (SNP) in the 3 species aligned to the polar bear genome. These data indicate that polar bears and brown bears share more SNP with each other than either does with black bears. Concatenation and coalescence-based analysis of consensus sequences of approximately 1 million base pairs of ultraconserved elements in the nuclear genome resulted in a phylogeny with black bears as the sister group to brown and polar bears, and all brown bears are in a separate clade from polar bears. Genotypes for 162 SNP loci of 336 bears from Alaska and Montana showed that the species are genetically differentiated and there is geographic population structure of brown and black bears but not polar bears.

Estimating Allee dynamics before they can be observed: polar bears as a case study

Allee effects are an important component in the population dynamics of numerous species. Accounting for these Allee effects in population viability analyses generally requires estimates of low-density population growth rates, but such data are unavailable for most species and particularly difficult to obtain for large mammals. Here, we present a mechanistic modeling framework that allows estimating the expected low-density growth rates under a mate-finding Allee effect before the Allee effect occurs or can be observed. The approach relies on representing the mechanisms causing the Allee effect in a process-based model, which can be parameterized and validated from data on the mechanisms rather than data on population growth. We illustrate the approach using polar bears (Ursus maritimus), and estimate their expected low-density growth by linking a mating dynamics model to a matrix projection model. The Allee threshold, defined as the population density below which growth becomes negative, is shown to depend on age-structure, sex ratio, and the life history parameters determining reproduction and survival. The Allee threshold is thus both density- and frequency-dependent. Sensitivity analyses of the Allee threshold show that different combinations of the parameters determining reproduction and survival can lead to differing Allee thresholds, even if these differing combinations imply the same stable-stage population growth rate. The approach further shows how mate-limitation can induce long transient dynamics, even in populations that eventually grow to carrying capacity. Applying the models to the overharvested low-density polar bear population of Viscount Melville Sound, Canada, shows that a mate-finding Allee effect is a plausible mechanism for slow recovery of this population. Our approach is generalizable to any mating system and life cycle, and could aid proactive management and conservation strategies, for example, by providing a priori estimates of minimum conservation targets for rare species or minimum eradication targets for pests and invasive species.

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.

Genetic relationships of North American bears (Ursus) inferred from amplified fragment length polymorphisms and mitochondrial DNA sequences

The three species of bears in North America, polar bears (Ursus maritimus Phipps, 1774), brown bears (Ursus arctos L., 1758), and black bears (Ursus americanus Pallas, 1780), have differentiated morphologies and nuclear and mitochondrial genomes. An exception is a paraphyletic mitochondrial DNA relationship and some nuclear gene lineages common to polar bears and a population of brown bears from islands in southeast Alaska. In this study, we quantified the genetic relationships of extant brown bears and black bears from Alaska and Montana, and polar bears from Alaska, with amplified fragment length polymorphisms (AFLP) and mtDNA cytochrome-b sequences. Bayesian cluster analyses of the AFLP data show each species is distinct. All brown bears, including those from the islands in southeast Alaska, cluster separately from polar bears, and black bears cluster separately from brown bears and polar bears. The mtDNA of polar bears and southeast Alaska island brown bears is paraphyletic as reported previously, but the species have different haplotypes. These data indicate that extant populations of brown bears and polar bears have separate nuclear and mitochondrial gene pools and are supported as species under the genetic species concept.

A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes)

BACKGROUND

Many boreo-temperate mammals have a Pleistocene fossil record throughout Eurasia and North America, but only few have a contemporary distribution that spans this large area. Examples of Holarctic-distributed carnivores are the brown bear, grey wolf, and red fox, all three ecological generalists with large dispersal capacity and a high adaptive flexibility. While the two former have been examined extensively across their ranges, no phylogeographic study of the red fox has been conducted across its entire Holarctic range. Moreover, no study included samples from central Asia, leaving a large sampling gap in the middle of the Eurasian landmass.

RESULTS

Here we provide the first mitochondrial DNA sequence data of red foxes from central Asia (Siberia), and new sequences from several European populations. In a range-wide synthesis of 729 red fox mitochondrial control region sequences, including 677 previously published and 52 newly obtained sequences, this manuscript describes the pattern and timing of major phylogeographic events in red foxes, using a Bayesian coalescence approach with multiple fossil tip and root calibration points. In a 335 bp alignment we found in total 175 unique haplotypes. All newly sequenced individuals belonged to the previously described Holarctic lineage. Our analyses confirmed the presence of three Nearctic- and two Japan-restricted lineages that were formed since the Mid/Late Pleistocene.

CONCLUSIONS

The phylogeographic history of red foxes is highly similar to that previously described for grey wolves and brown bears, indicating that climatic fluctuations and habitat changes since the Pleistocene had similar effects on these highly mobile generalist species. All three species originally diversified in Eurasia and later colonized North America and Japan. North American lineages persisted through the last glacial maximum south of the ice sheets, meeting more recent colonizers from Beringia during postglacial expansion into the northern Nearctic. Both brown bears and red foxes colonized Japan's northern island Hokkaido at least three times, all lineages being most closely related to different mainland lineages. Red foxes, grey wolves, and brown bears thus represent an interesting case where species that occupy similar ecological niches also exhibit similar phylogeographic histories.