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.     

Introgressive hybridization: brown bears as vectors for polar bear alleles

The dynamics and consequences of introgression can inform about numerous evolutionary processes. Biologists have therefore long been interested in hybridization. One challenge, however, lies in the identification of nonadmixed genotypes that can serve as a baseline for accurate quantification of admixture. In this issue of Molecular Ecology, Cahill et al. (2015) analyse a genomic data set of 28 polar bears, eight brown bears and one American black bear. Polar bear alleles are found to be introgressed into brown bears not only near a previously identified admixture zone on the Alaskan Admiralty, Baranof and Chichagof (ABC) Islands, but also far into the North American mainland. Elegantly contrasting admixture levels at autosomal and X chromosomal markers, Cahill and colleagues infer that male‐biased dispersal has spread these introgressed alleles away from the Late Pleistocene contact zone. Compared to a previous study on the ABC Island population in which an Alaskan brown bear served as a putatively admixture‐free reference, Cahill et al. (2015) utilize a newly sequenced Swedish brown bear as admixture baseline. This approach reveals that brown bears have been impacted by introgression from polar bears to a larger extent (up to 8.8% of their genome), than previously known, including the bear that had previously served as admixture baseline. No evidence for introgression of brown bear into polar bear is found, which the authors argue could be a consequence of selection. Besides adding new exciting pieces to the puzzle of polar/brown bear evolutionary history, the study by Cahill and colleagues highlights that wildlife genomics is moving from analysing single genomes towards a landscape genomics approach.     

Ancestral Polymorphisms and Sex-Biased Migration Shaped the Demographic History of Brown Bears and Polar Bears

Recent studies have reported discordant gene trees in the evolution of brown bears and polar bears. Genealogical histories are different among independent nuclear loci and between biparentally inherited autosomal DNA (aDNA) and matrilineal mitochondrial DNA (mtDNA). Based on multi-locus genomic sequences from aDNA and mtDNA, we inferred the population demography of brown and polar bears and found that brown bears have 6 times (aDNA) or more than 14 times (mtDNA) larger population sizes than polar bears and that polar bear lineage is derived from within brown bear diversity. In brown bears, the effective population size ratio of mtDNA to aDNA was at least 0.62, which deviated from the expected value of 0.25, suggesting matriarchal population due to female philopatry and male-biased migration. These results emphasize that ancestral polymorphisms and sex-biased migration may have contributed to conflicting branching patterns in brown and polar bears across aDNA genes and mtDNA.     

Phylogeography of mitochondrial DNA variation in brown bears and polar bears

We analyzed 286 nucleotides of the middle portion of the mitochondrial cytochrome b gene of 61 brown bears from three locations in Alaska and 55 polar bears from Arctic Canada and Arctic Siberia to test our earlier observations of paraphyly between polar bears and brown bears as well as to test the extreme uniqueness of mitochondrial DNA types of brown bears on Admiralty, Baranof, and Chichagof (ABC) islands of southeastern Alaska. We also investigated the phylogeography of brown bears of Alaska's Kenai Peninsula in relation to other Alaskan brown bears because the former are being threatened by increased human development. We predicted that: (1) mtDNA paraphyly between brown bears and polar bears would be upheld, (2) the mtDNA uniqueness of brown bears of the ABC islands would be upheld, and (3) brown bears of the Kenai Peninsula would belong to either clade II or clade III of brown bears of our earlier studies of mtDNA. All of our predictions were upheld through the analysis of these additional samples.     

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.     

Admixture and Gene Flow from Russia in the Recovering Northern European Brown Bear (Ursus arctos)

Large carnivores were persecuted to near extinction during the last centuries, but have now recovered in some countries. It has been proposed earlier that the recovery of the Northern European brown bear is supported by migration from Russia. We tested this hypothesis by obtaining for the first time continuous sampling of the whole Finnish bear population, which is located centrally between the Russian and Scandinavian bear populations. The Finnish population is assumed to experience high gene flow from Russian Karelia. If so, no or a low degree of genetic differentiation between Finnish and Russian bears could be expected. We have genotyped bears extensively from all over Finland using 12 validated microsatellite markers and compared their genetic composition to bears from Russian Karelia, Sweden, and Norway. Our fine masked investigation identified two overlapping genetic clusters structured by isolation-by-distance in Finland (pairwise F_ST = 0.025). One cluster included Russian bears, and migration analyses showed a high number of migrants from Russia into Finland, providing evidence of eastern gene flow as an important driver during recovery. In comparison, both clusters excluded bears from Sweden and Norway, and we found no migrants from Finland in either country, indicating that eastern gene flow was probably not important for the population recovery in Scandinavia. Our analyses on different spatial scales suggest a continuous bear population in Finland and Russian Karelia, separated from Scandinavia.     

Gene flow between insular, coastal and interior populations of brown bears in Alaska

The brown bears of coastal Alaska have been recently regarded as comprising from one to three distinct genetic groups. We sampled brown bears from each of the regions for which hypotheses of genetic uniqueness have been made, including the bears of the Kodiak Archipelago and the bears of Admiralty, Baranof and Chichagof (ABC) Islands in southeast Alaska. These samples were analysed with a suite of nuclear microsatellite markers. The 'big brown bears' of coastal Alaska were found to be part of the continuous continental distribution of brown bears, and not genetically isolated from the physically smaller 'grizzly bears' of the interior. By contrast, Kodiak brown bears appear to have experienced little or no genetic exchange with continental populations in recent generations. The bears of the ABC Islands, which have previously been shown to undergo little or no female-mediated gene flow with mainland populations, were found not to be genetically isolated from mainland bears. The data from the four insular populations indicate that female and male dispersal can be reduced or eliminated by water barriers of 2–4 km and 7km in width, respectively.     

Could brown bears (Ursus arctos) have survived in Ireland during the Last Glacial Maximum?

Brown bears are recorded from Ireland during both the Late Pleistocene and early–mid Holocene. Although most of the Irish landmass was covered by an ice sheet during the Last Glacial Maximum (LGM), Irish brown bears are known to have hybridized with polar bears during the Late Pleistocene, and it is suggested that the Irish brown bear population did not become extinct but instead persisted in situ through the LGM in a southwestern ice-free refugium. We use historical population modelling to demonstrate that brown bears are highly unlikely to have survived through the LGM in Ireland under any combination of life-history parameters shown by living bear populations, but instead would have rapidly become extinct following advance of the British–Irish ice sheet, and probably recolonized Ireland during the end-Pleistocene Woodgrange Interstadial from a closely related nearby source population. The time available for brown bear–polar bear hybridization was therefore restricted to narrow periods at the beginning or end of the LGM. Brown bears would have been extremely vulnerable to extinction in Quaternary habitat refugia and required areas substantially larger than southwestern Ireland to survive adverse glacial conditions.     

Bear-hybrids: behaviour and phenotype

The behaviour of a female and a male bear hybrid (brown bear Ursus arctos x polar bear Ursus maritimus) was studied. Behavioural and morphological comparisons between the hybrids and the two parent-species were made.The observation period covered July to November 2007. Different objects were offered to the bears to evoke new patterns of behaviour. While manipulating the offered objects, both bears showed elements of behaviour also found in polar bears, though the male performed those to a larger extend. Not only in the way of manipulating objects but also in the male's type of stereotype parallels to polar bears can be drawn. Phenotypically both bears possess features of both species, brown bear and polar bear. Concerning it lighter colour of fur and the structure of hair the female hybrid resembles more a polar bear than the male. Summarising, the female appears phenotypically more like a polar bear, the male with respect to the behaviour.     

MOLECULAR GENETIC-DISTANCE ESTIMATES AMONG THE URSIDAE AS INDICATED BY ONE- AND TWO-DIMENSIONAL PROTEIN ELECTROPHORESIS

Evolutionary relationships among eight species of Ursidae (including the giant panda) relative to two Procyonidae species (raccoon and red panda) were estimated based on the extent of electrophoretic variation of 289 radiolabelled fibroblast proteins resolved by two-dimensional gel electrophoresis and among 44 isozyme loci resolved by one-dimensional electrophoresis. Allelic differences among these species were converted to genetic distances, and phenetic trees were constructed. In addition, the electrophoretic data were coded as unit characters, and minimum-length trees were derived based on the Wagner method using maximum parsimony. Regardless of the tree-building method employed, the data sets agreed on the following branching sequence: between 22.4 and 32.3 million years (MY) ago, the ancestors of the procyonids and the ursids split into two lineages. Within 10 MY, the red panda split from the line that led to the raccoon. An ancestor of the giant panda split from the ursid line 18–22 MY ago, and the South American spectacled bear split from the line leading to ursine bears 10.5–15.0 MY B.P. A group of six closely related ursine bears (brown bear, polar bear, Asiatic black bear, Malayan sun bear, American black bear, and sloth bear) diverged from a common ancestor during the past 4–8 MY. Much of this ursine radiation was not resolved by our results, with the exception of a recent (2–3 MY B.P.) divergence of brown bear and polar bear. The topological concordance of the data sets from one- and two-dimensional electrophoresis supports the usefulness of these procedures for evolutionary inference and provides additional precision to the reconstruction of divergence nodes of this carnivore group.     

Phylogeography and mitochondrial diversity of extirpated brown bear (Ursus arctos) populations in the contiguous United States and Mexico

The fossil record indicates that the brown bear (Ursus arctos) colonized North America from Asia over 50 000 years ago. The species historically occupied the western United States and northern Mexico but has been extirpated from over 99% of this range in the last two centuries. To evaluate colonization hypotheses, subspecific classifications, and historical patterns and levels of genetic diversity in this region, we sequenced 229 nucleotides of the mitochondrial DNA control region in 108 museum specimens. The work was set in a global context by synthesizing all previous brown bear control region sequences from around the world. In mid-latitude North America a single moderately diverse clade is observed, represented by 23 haplotypes with up to 3.5% divergence. Only eight of 23 haplotypes (35%) are observed in the extensively sampled extant populations suggesting a substantial loss of genetic variability. The restriction of all haplotypes from mid-latitude North America to a single clade suggests that this region was founded by bears with a similar maternal ancestry. However, the levels and distributions of diversity also suggest that the colonizing population was not a small founder event, and that expansion occurred long enough ago for local mutations to accrue. Our data are consistent with recent genetic evidence that brown bears were south of the ice prior to the last glacial maximum. There is no support for previous subspecies designations, although bears of the southwestern United States may have had a distinctive, but recent, pattern of ancestry.     

Microsatellite diversity and structure of Carpathian brown bears (Ursus arctos): consequences of human caused fragmentation

The formerly large, continuous brown bear population of the Carpathians has experienced a radical decrease in population size due to human activities which have resulted in splitting the population into the larger Eastern Carpathian and the smaller Western Carpathian subpopulations. In the Western Carpathians, brown bears came close to extinction at the beginning of 1930s, but thanks to both conservation and management efforts the bear population has begun to recover. In contrast, the Eastern Carpathian subpopulation in Romania has never dropped below 800 individuals, potentially preserving the original amount of genetic variation. In this paper we present results of a genetic study of brown bear subpopulations distributed in the Slovak and Romanian sections of the Carpathians using 13 nuclear microsatellites. The documented level of genetic differentiation between the Western and Eastern Carpathian subpopulations reflects the isolation which lasted almost 100 years. Furthermore, the existence of two, different, genetic clusters within the Western Carpathians despite close geographic proximity indicates that human-caused fragmentation and isolation have resulted in significant genetic divergence. Although the subpopulations display an indication of genetic bottleneck, the level of genetic diversity is within the range commonly observed in different brown bear populations. The results presented here point out the significance of human exploitation to the population structure of this large carnivore species. Future management efforts should be aimed at securing and restoring the connectivity of forested habitats, in order to preserve the genetic variation of the Carpathian brown bear subpopulations and to support the gene flow between them.     

Noninvasive genetic assessment of brown bear population structure in Bulgarian mountain regions

The Balkans are one of the last large refugia for brown bear (Ursus arctos) populations in Europe, and Bulgaria, in particular, contains relatively large areas of suitable brown bear habitat and a potential population of more than 600 individuals. Despite this, the majority of brown bear research remains focused on bear populations in Central and Western Europe. We provide the first assessment of genetic population structure of brown bears in Bulgaria by analysing tissue samples (n = 16) as well as samples collected with noninvasive genetic methods, including hair and faecal samples (n = 189 and n = 163, respectively). Sequence analysis of a 248 base pair fragment of the mitochondrial control region showed that two highly divergent mitochondrial European brown bear lineages form a contact zone in central Bulgaria. Furthermore, the analysis of 13 polymorphic microsatellite markers identified 136 individuals and found substantial genetic variability (H_e = 0.74; N_A = 8.9). The combination of both genetic markers revealed the presence of weak genetic substructure in the study area with considerable degrees of genetic admixture and the likely presence of migration corridors between the two subpopulation in the Rhodope Mountains and Stara Planina as evidenced from the genetic detection of two male long-distance dispersers. A detailed assessment from densely collected samples in the Rhodope Mountains resulted in a population size estimate of 315 (95% CI = 206–334) individuals, indicating that not all available habitat is presently occupied by bears in this region. Efficient management plans should focus on preserving connectivity of suitable habitats in order to maintain gene flow between the two Bulgarian brown bear subpopulations.     

Molecular evidence for historic long-distance translocations of brown bears in the Balkan region

We tested the hypothesis that brown bears were translocated from the Romanian Carpathians to Bulgaria via air transportation during the communist regime in the 1970s and 1980s. Microsatellite analysis was performed on 199 bear samples from Bulgaria and Romania. Assignment and admixture tests revealed the existence of seven genotypes (=2.8 %) in Bulgaria that were assigned with high probabilities to the Romanian population, supporting the translocation and successful establishment of Carpathian bears in Bulgaria. While we cannot rule out the possibility that active long-distance dispersal contributed to the observed pattern, the spatial distribution and sex ratio of the detected Romanian genotypes strongly favor the translocation hypothesis.     

Y chromosome haplotype distribution of brown bears (Ursus arctos) in Northern Europe provides insight into population history and recovery

High‐resolution, male‐inherited Y‐chromosomal markers are a useful tool for population genetic analyses of wildlife species, but to date have only been applied in this context to relatively few species besides humans. Using nine Y‐chromosomal STRs and three Y‐chromosomal single nucleotide polymorphism markers (Y‐SNPs), we studied whether male gene flow was important for the recent recovery of the brown bear (Ursus arctos) in Northern Europe, where the species declined dramatically in numbers and geographical distribution during the last centuries but is expanding now. We found 36 haplotypes in 443 male extant brown bears from Sweden, Norway, Finland and northwestern Russia. In 14 individuals from southern Norway from 1780 to 1920, we found two Y chromosome haplotypes present in the extant population as well as four Y chromosome haplotypes not present among the modern samples. Our results suggested major differences in genetic connectivity, diversity and structure between the eastern and the western populations in Northern Europe. In the west, our results indicated that the recovered population originated from only four male lineages, displaying pronounced spatial structuring suggestive of large‐scale population size increase under limited male gene flow within the western subpopulation. In the east, we found a contrasting pattern, with high haplotype diversity and admixture. This first population genetic analysis of male brown bears shows conclusively that male gene flow was not the main force of population recovery.     

Exploring Population Admixture Dynamics via Empirical and Simulated Genome-wide Distribution of Ancestral Chromosomal Segments

The processes of genetic admixture determine the haplotype structure and linkage disequilibrium patterns of the admixed population, which is important for medical and evolutionary studies. However, most previous studies do not consider the inherent complexity of admixture processes. Here we proposed two approaches to explore population admixture dynamics, and we demonstrated, by analyzing genome-wide empirical and simulated data, that the approach based on the distribution of chromosomal segments of distinct ancestry (CSDAs) was more powerful than that based on the distribution of individual ancestry proportions. Analysis of 1,890 African Americans showed that a continuous gene flow model, in which the African American population continuously received gene flow from European populations over about 14 generations, best explained the admixture dynamics of African Americans among several putative models. Interestingly, we observed that some African Americans had much more European ancestry than the simulated samples, indicating substructures of local ancestries in African Americans that could have been caused by individuals from some particular lineages having repeatedly admixed with people of European ancestry. In contrast, the admixture dynamics of Mexicans could be explained by a gradual admixture model in which the Mexican population continuously received gene flow from both European and Amerindian populations over about 24 generations. Our results also indicated that recent gene flows from Sub-Saharan Africans have contributed to the gene pool of Middle Eastern populations such as Mozabite, Bedouin, and Palestinian. In summary, this study not only provides approaches to explore population admixture dynamics, but also advances our understanding on population history of African Americans, Mexicans, and Middle Eastern populations.     

Geographic and genetic boundaries of brown bear (Ursus arctos) population in the Caucasus

The taxonomic status of brown bears in the Caucasus remains unclear. Several morphs or subspecies have been identified from the morphological (craniological) data, but the status of each of these subspecies has never been verified by molecular genetic methods. We analysed mitochondrial DNA sequences (control region) to reveal phylogenetic relationships and infer divergence time between brown bear subpopulations in the Caucasus. We estimated migration and gene flow from both mitochondrial DNA and microsatellite allele frequencies, and identified possible barriers to gene flow among the subpopulations. Our suggestion is that all Caucasian bears belong to the nominal subspecies of Ursus arctos. Our results revealed two genetically and geographically distinct maternal haplogroups: one from the Lesser Caucasus and the other one from the Greater Caucasus. The genetic divergence between these haplogroups dates as far back as the beginning of human colonization of the Caucasus. Our analysis of the least‐cost distances between the subpopulations suggests humans as a major barrier to gene flow. The low genetic differentiation inferred from microsatellite allele frequencies indicates that gene flow between the two populations in the Caucasus is maintained through the movements of male brown bears. The Likhi Ridge that connects the Greater and Lesser Caucasus mountains is the most likely corridor for this migration.     

Sudden expansion of a single brown bear maternal lineage across northern continental Eurasia after the last ice age: a general demographic model for mammals?

The brown bear has proved a useful model for studying Late Quaternary mammalian phylogeography. However, information is lacking from northern continental Eurasia, which constitutes a large part of the species' current distribution. We analysed mitochondrial DNA sequences (totalling 1943 bp) from 205 bears from northeast Europe and Russia in order to characterize the maternal phylogeography of bears in this region. We also estimated the formation times of the sampled brown bear lineages and those of its extinct relative, the cave bear.
Four closely related haplogroups belonging to a single mitochondrial subclade were identified in northern continental Eurasia. Several haplotypes were found throughout the whole study area, while one haplogroup was restricted to Kamchatka. The haplotype network, estimated divergence times and various statistical tests indicated that bears in northern continental Eurasia recently underwent a sudden expansion, preceded by a severe bottleneck. This brown bear population was therefore most likely founded by a small number of bears that were restricted to a single refuge area during the last glacial maximum. This pattern has been described previously for other mammal species and as such may represent one general model for the phylogeography of Eurasian mammals. Bayesian divergence time estimates are presented for different brown and cave bear clades. Moreover, our results demonstrate the extent of substitution rate variation occurring throughout the phylogenetic tree, highlighting the need for appropriate calibration when estimating divergence times.     

Genetics and conservation of European brown bears Ursus arctos

• 1 We review the genetics research that has been conducted on the European brown bear Ursus arctos, one of the genetically best‐studied mammalian species.
• 2 The first genetics studies on European brown bears were on phylogeography, as a basis for proposed population augmentations. Two major mitochondrial DNA lineages, western and eastern, and two clades within the western lineage were found. This led to a hypothesis that brown bears had contracted to southern refugia during the last glacial maximum. More recent results suggest that gene flow among brown bears blurred this structure and they survived north of these putative refugia. Thus, today's structure might be a result of population fragmentation caused by humans.
• 3 The nuclear diversity of European brown bears is similar in range to that in North American bears: low levels occur in the small populations and high levels in the large populations.
• 4 Many non‐invasive genetic methods, developed during research on brown bears, have been used for individual identification, censusing populations, monitoring migration and gene flow, and testing methods that are easier to use in endangered populations and over large areas.
• 5 Genetics has been used to study many behavioural and population ecological questions that have relevance for the conservation and management of brown bears.
• 6 The European brown bear has served, and will continue to serve, as a model for the development of methods, analyses and hypotheses in conservation genetics.