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.
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Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska
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 (
- Award ID(s):
- 1854550
- NSF-PAR ID:
- 10408921
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Molecular Ecology
- Volume:
- 32
- Issue:
- 13
- ISSN:
- 0962-1083
- Page Range / eLocation ID:
- p. 3641-3656
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Larix laricina (eastern larch, tamarack) is a transcontinental North American conifer with a prominent disjunction in the Yukon isolating the Alaskan distribution from the rest of its range. We investigate whether in situ persistence during the last glacial maximum (LGM) or long‐distance postglacial migration from south of the ice sheets resulted in the modern‐day Alaskan distribution. We analyzed variation in three chloroplast DNA regions of 840 trees from a total of 69 populations (24 new sampling sites situated on both sides of the Yukon range disjunction pooled with 45 populations from a published source) and conducted ensemble species distribution modeling (SDM) throughout Canada and United States to hindcast the potential range ofL. laricina during the LGM. We uncovered the genetic signature of a long‐term isolation of larch populations in Alaska, identifying three endemic chlorotypes and low levels of genetic diversity. Range‐wide analysis across North America revealed the presence of a distinct Alaskan lineage. Postglacial gene flow across the Yukon divide was unidirectional, from Alaska toward previously glaciated Canadian regions, and with no evidence of immigration into Alaska. Hindcast SDM indicates one of the broadest areas of past climate suitability forL. laricina existed in central Alaska, suggesting possible in situ persistence of larch in Alaska during the LGM. Our results provide the first unambiguous evidence for the long‐term isolation ofL. laricina in Alaska that extends beyond the last glacial period and into the present interglacial period. The lack of gene flow into Alaska along with the overall probability of larch occurrence in Alaska being currently lower than during the LGM suggests that modern‐day Alaskan larch populations are isolated climate relicts of broader glacial distributions, and so are particularly vulnerable to current warming trends. -
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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.
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Abstract Quaternary climate fluctuations restructured biodiversity across North American high latitudes through repeated episodes of range contraction, population isolation and divergence, and subsequent expansion. Identifying how species responded to changing environmental conditions not only allows us to explore the mode and tempo of evolution in northern taxa, but also provides a basis for forecasting future biotic response across the highly variable topography of western North America. Using a multilocus approach under a Bayesian coalescent framework, we investigated the phylogeography of a wide‐ranging mammal, the long‐tailed vole,
Microtus longicaudus . We focused on populations along the North Pacific Coast to refine our understanding of diversification by exploring the potentially compounding roles of multiple glacial refugia and more recent fragmentation of an extensive coastal archipelago. Through a combination of genetic data and species distribution models (SDM s), we found that historical climate variability influenced contemporary genetic structure, with multiple isolated locations of persistence (refugia) producing multiple divergent lineages (Beringian or northern, southeast Alaska or coastal, and southern or continental) during glacial advances. These vole lineages all occur along the North Pacific Coast where the confluence of numerous independent lineages in other species has produced overlapping zones of secondary contact, collectively a suture zone. Finally, we detected high levels of neoendemism due to complex island geography that developed in the last 10,000 years with the rising sea levels of the Holocene. -
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Abstract Although islands are of long‐standing interest to biologists, only a handful of studies have investigated the role of climatic history in shaping evolutionary diversification in high‐latitude archipelagos. In this study of the Alexander Archipelago (AA) of Southeast Alaska, we address the impact of glacial cycles on geographic genetic structure for three mammals co‐distributed along the North Pacific Coast. We examined variation in mitochondrial and nuclear loci for long‐tailed voles (
Microtus longicaudus ), northwestern deermice (Peromyscus keeni ), and dusky shrews (Sorex monticola ), and then tested hypotheses derived from Species Distribution Models, reconstructions of paleoshorelines, and island area and isolation. In all three species, we identified paleoendemic clades that likely originated in coastal refugia, a finding consistent with other paleoendemic lineages identified in the region such as ermine. Although there is spatial concordance at the regional level for endemism, finer scale spatial and temporal patterns are less clearly defined. Demographic expansion across the region for these distinctive clades is also evident and highlights the dynamic history of Late Quaternary contraction and expansion that characterizes high‐latitude species.
