The polar bear ( Ursus maritimus ) has become a symbol of the threat to biodiversity from climate change. Understanding polar bear evolutionary history may provide insights into apex carnivore responses and prospects during periods of extreme environmental perturbations. In recent years, genomic studies have examined bear speciation and population history, including evidence for ancient admixture between polar bears and brown bears ( Ursus arctos ). Here, we extend our earlier studies of a 130,000- to 115,000-y-old polar bear from the Svalbard Archipelago using a 10× coverage genome sequence and 10 new genomes of polar and brown bears from contemporary zones of overlap in northern Alaska. We demonstrate a dramatic decline in effective population size for this ancient polar bear’s lineage, followed by a modest increase just before its demise. A slightly higher genetic diversity in the ancient polar bear suggests a severe genetic erosion over a prolonged bottleneck in modern polar bears. Statistical fitting of data to alternative admixture graph scenarios favors at least one ancient introgression event from brown bears into the ancestor of polar bears, possibly dating back over 150,000 y. Gene flow was likely bidirectional, but allelic transfer from brown into polar bear is the strongest detected signal, which contrasts with other published work. These findings may have implications for our understanding of climate change impacts: Polar bears, a specialist Arctic lineage, may not only have undergone severe genetic bottlenecks but also been the recipient of generalist, boreal genetic variants from brown bears during critical phases of Northern Hemisphere glacial oscillations.
more »
« less
Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher.
Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?
Some links on this page may take you to non-federal websites. Their policies may differ from this site.
-
-
more » « less
Abstract During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice‐free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (
Ursus americanus ) and brown (U. arctos ) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long‐term occupation, potential refugial survival and lineage turnover. Here, we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades, one preglacial and another postglacial, that diverged >100,000 years ago. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre‐ and postglacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast, but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short‐lived LGM peak. -
more » « less
Abstract Aim Refugial isolation during glaciation is an established driver of speciation; however, the opposing role of interglacial population expansion, secondary contact, and gene flow on the diversification process remains less understood. The consequences of glacial cycling on diversity are complex and especially so for archipelago species, which experience dramatic fluctuations in connectivity in response to both lower sea levels during glacial events and increased fragmentation during glacial recession. We test whether extended refugial isolation has led to the divergence of genetically and morphologically distinct species within Holarctic ermine (
Mustela erminea ), a small cosmopolitan carnivore species that harbours 34 extant subspecies, 14 of which are insular endemics.Location Holarctic.
Methods We use genetic sequences (complete mitochondrial genomes, four nuclear genes) from >100 ermine (stoats) and geometric morphometric data for >200 individuals (27 of the 34 extant subspecies) from across their Holarctic range to provide an integrative perspective on diversification and endemism across this complex landscape. Multiple species delimitation methods (
iBPP ,bPTP ) assessed congruence between morphometric and genetic data.Results Our results support the recognition of at least three species within the
M. erminea complex, coincident with three of four genetic clades, tied to diversification in separate glacial refugia. We found substantial geographic variation within each species, with geometric morphometric results largely consistent with historical infraspecific taxonomy.Main conclusions Phylogeographic structure mirrors patterns of diversification in other Holarctic species, with a major Nearctic‐Palearctic split, but with greater intraspecific morphological diversity. Recognition of insular endemic species
M. haidarum is consistent with a deep history of refugial persistence and highlights the urgency of mindful management of island populations along North America's North Pacific Coast. Significant environmental modification (e.g. industrial‐scale logging, mining) has been proposed for a number of these islands, which may elevate the risk of extinction of insular palaeoendemics. -
more » « less
Abstract Environmental conditions in the Chukchi Sea are changing rapidly and may alter the abundance and distribution of marine species and their benthic prey. We used a metabarcoding approach to identify potentially important prey taxa from Pacific walrus (
Odobenus rosmarus divergens ) fecal samples (n = 87). Bivalvia was the most dominant class of prey (66% of all normalized counts) and occurred in 98% of the samples. Polychaeta and Gastropoda occurred in 70% and 62% of the samples, respectively. The remaining nine invertebrate classes comprised <21% of all normalized counts. The common occurrence of these three prey classes is consistent with examinations of walrus stomach contents. Despite these consistencies, biases in the metabarcoding approach to determine diet from feces have been highlighted in other studies and require further study, in addition to biases that may have arisen from our opportunistic sampling. However, this noninvasive approach provides accurate identification of prey taxa from degraded samples and could yield much‐needed information on shifts in walrus diet in a rapidly changing Arctic. -
more » « less
Abstract Aim Numerous glacial refugia have been hypothesized along North America's North Pacific Coast that may have increased divergence of refugial taxa, leading to elevated endemism and subsequently clustered hybrid zones following deglaciation. The locations and community composition of these ice‐free areas remains controversial, but whole‐genome sequences now enable detailed analysis of the demographic and evolutionary histories of refugial taxa. Here, we use genomic data to test spatial and temporal processes of diversification among martens with respect to the Coastal Refugium Hypothesis, to understand the role of climate cycling in shaping diversity across complex landscapes.
Location North America and North Pacific Coast archipelagos.
Taxon North American martens (
Martes ).Methods Short‐read whole‐genome resequencing data were generated for 11 martens: four
M. americana , fourM. caurina , two hybrids, and one outgroup (Martes zibellina ). Sampling was representative of known genetic clades within New World martens, including sampling within insular and continental hybrid zones and along the North Pacific Coast (five island populations).ADMIXTURE , F‐statistics, andD ‐statistics (ABBA‐BABA) were used to identify introgression and infer directionality. Heterozygosity densities, estimated via PSMC, were used to characterize historical demography at and below the species level to infer refugial and colonization processes.Results Forest‐associated Pacific martens (
M. caurina ) are divided into distinct insular and continental clades consistent with the Coastal Refugium Hypothesis. There was no evidence of introgression on islands that received historical translocations of American pine martens (M. americana ), but introgression was detected in two active zones of secondary contact: one insular and one continental. Only early‐generational hybrids were identified across multiple hybrid zones, a pattern consistent with potential genetic swamping ofM. caurina byM. americana .Main conclusions Despite an incomplete fossil record, genomic evidence supports the persistence of forest‐associated martens, likely the insular Pacific marten lineage, along the western edges of the Alexander Archipelago during the Last Glacial Maximum. This discovery informs our understanding of refugial paleoenvironments, critical to interpreting refugial timing, duration, and community composition. Genomic reevaluations of other taxa along North America's North Pacific Coast may yield new and deeper perspectives on the history of refugial forest communities and the role of dynamic climate shifts in shaping high‐latitude diversity across complex insular landscapes.
