During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still open 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 that diverged >100,00 years ago, one preglacial and one postglacial. All postglacial ancient brown bears are closely related to modern 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 post-glacial 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.

Shared phylogenetic breaks across taxa, syntopic clusters of endemics, and paleogeographic reconstruction of isostatic and vegetation change over time suggest the existence of one or more ice-free glacial refugia off of North America’s North Pacific Coast. However, both an incomplete fossil record and cosmogenic 10Be exposure dating create uncertainty over whether hypothesized coastal refugia even existed. If refugia existed, then identifying the persistent species is critical to interpretation of the timing, duration, and paleoenvironment-reconstructions. We use whole-genome resequencing to assess the historical biogeography of these complex northern landscapes that span multiple archipelagos and mountain ranges. Unanticipated discovery of genomically-distinct insular and continental clades within forest-associated Pacific martens (M. caurina) is consistent with morphometric and parasitological investigations, and also with the Coastal Refugium Hypothesis. Our results support the persistence of forested refugial communities along the western edges of the Alexander Archipelago. We found no evidence of admixture on islands that received historical translocations of American pine martens (M. americana), but detected introgression in two zones of secondary contact: one insular, one continental. Evidence of early-generational hybrids across multiple hybrid zones, each backcrossed with M. americana, is consistent with a history of genetic dilution of M. caurina through outbreeding. Into the future, these hybrid zones will serve as instructive natural experiments for forecasting outcomes of genetic management initiatives, such as genetic rescue or restoration. Evidence of refugial divergence in a forest-associated, medium-sized carnivore along the North Pacific Coast suggests that genomic reevaluations may identify new perspectives on a suite of forest-associated species and provide new insight into refugial community composition.

Shared phylogenetic breaks across taxa, syntopic clusters of endemics, and paleogeographic reconstruction of isostatic and vegetation change over time suggest the existence of one or more ice-free glacial refugia off of North America’s North Pacific Coast. An incomplete fossil record, however, creates uncertainty over which species persisted in hypothesized refugia, obscuring interpretation of the timing, potential duration, and surrounding paleoenvironments. We use whole-genome resequencing to assess the historical biogeography of these complex northern landscapes that consist of multiple coastal archipelagos and mountain ranges. Discovery of distinct insular and continental clades within Pacific martens (M. caurina) is consistent with previous morphometric and parasitological studies and also with the Coastal Refugium Hypothesis, thereby supporting the persistence of diverse, potentially forested refugial communities along the western edges of the Alexander Archipelago. We found no evidence of admixture on islands that received translocations of American pine martens (M. americana) in the mid 1900s, but we detected introgression in two geographically distinct zones of secondary contact. Evidence of early-generational hybrids across multiple hybrid zones, each backcrossed with M. americana, is consistent with a history of genetic dilution of M. caurina through outbreeding with M. americana. Into the future, these hybrid zones will serve as iterative tests for the outcome of admixture, providing instructive natural experiments for forecasting outcomes of proactive measures such as genetic rescue by natural resource managers.