Collaborative Research: A Paleogenetic Survey of Late Quaternary Mammal Biodiversity in Southeast Alaska

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The Pleistocene Epoch began approximately 1.8 million years before present and lasted until about 12 milennia ago, when the last Ice Age ended. Many large mammals succumbed to the harsh climatic conditions of this period, while others were confined to habitable ice-free areas, or refugia. During the peak of the last Ice Age, sheets of ice divided the Old and New Worlds, restricting movement of organisms across the Bering Land Bridge for thousands of years. Geological and biological evidence have suggested, however, that refugia along the North Pacific Coast may have played crucial roles as "stepping stones" for movements of species between the Old and New Worlds, forming an early postglacial corridor for the recolonization of North America. Building on an unparalleled vertebrate bone collection excavated from limestone caves in Southeast (SE) Alaska, this project will perform genetic analyses and radiocarbon dating of black and brown bear specimens from throughout the last 50,000 years to directly test if these caves were occupied by bears at the peak of the last Ice Age. By ensuring precise species determinations of these keystone mammal species in SE Alaska, and providing evolutionary links to extant populations, this research will elucidate species' responses to climate change and help circumscribe the extent and timing of viable coastal refugia in SE Alaska. As such, results from this project will provide important data for a deeper comprehension of the dynamic changes in trans-Beringian biota during the Late Pleistocene, the diversity and biogeographic history of the region, and its importance as a corridor for exchange between continents during and after the last Ice Age.An important outcome of this research is to recover genetic information from bear specimens that occupied SE Alaska during the late Wisconsin glaciation and into the Holocene, and provide calibrations for precise timings of demographic events. Focusing on brown bears (Ursus arctos) and black bears (Ursus americanus), which have developed into well-established systems for studies of Northern Hemisphere phylogeography, the project will test if the same bear populations inhabited this region continuously for the last 50,000 years, or if they were recolonized following the Last Glacial Maximum, and if they contributed to postglacial (modern) mainland populations. The project will take a highly integrative approach that leverages state-of-the-art ancient DNA analysis (including a targeted hybridization enrichment approach using custom-made biotinylated RNA baits designed from whole mitochondrial genome sequences), radiocarbon and molecular dating, reconstruction of paleodiets, and phylogenetic reconstruction. This research will have broad significance toward understanding past and present North American mammal diversity and for assessing the impact of late Pleistocene climate change on biotic diversification, colonization, and the historical biogeography of the region.