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

更新世开始于距今约180万年前，一直持续到大约1200万年前，最后一个冰河时代结束。许多大型哺乳动物屈服于这一时期的恶劣气候条件，而其他动物则被限制在适合居住的无冰地区或避难所。在最后一个冰河时代的高峰期，冰层将旧世界和新世界分开，限制了生物体在白令陆桥上的移动数千年。然而，地质学和生物学证据表明，北太平洋沿岸沿着的避难所可能在新旧世界之间的物种迁移中扮演了重要的“垫脚石”角色，形成了冰后期早期北美殖民化的走廊。在阿拉斯加东南部石灰岩洞穴中挖掘出的无与伦比的脊椎动物骨骼收藏的基础上，该项目将对过去5万年来的黑熊和棕熊标本进行遗传分析和放射性碳测年，以直接测试这些洞穴是否在最后一个冰河时代的高峰期被熊占据。通过确保这些关键的哺乳动物物种在阿拉斯加东南部的精确物种测定，并提供进化的联系，现存的人口，这项研究将阐明物种对气候变化的反应，并帮助限制在阿拉斯加东南部可行的沿海避难所的范围和时间。因此，该项目的结果将为更深入地了解晚更新世期间跨白令纪生物群的动态变化，该地区的多样性和地理历史提供重要数据，以及它在上一次冰河时代期间和之后作为大陆之间交流走廊的重要性。这项研究的一个重要成果是从阿拉斯加东南部的熊标本中恢复遗传信息。威斯康星州冰川和进入全新世，并提供人口事件的精确定时校准。该项目以棕熊（Ursus arctos）和黑熊（Ursus americanus）为重点，这两种熊已经发展成为研究北方大陆地理的成熟系统，该项目将测试相同的熊种群是否在过去5万年中持续居住在该地区，或者它们是否在末次冰期最大期之后被同化，以及它们是否对冰后期（现代）大陆种群做出了贡献。该项目将采取高度综合的方法，利用最先进的古代DNA分析（包括使用从整个线粒体基因组序列设计的定制生物素化RNA诱饵的靶向杂交富集方法），放射性碳和分子测年，古饮食重建和系统发育重建。这项研究将具有广泛的意义，了解过去和现在的北美哺乳动物的多样性，并评估晚更新世气候变化对生物多样性，殖民化和该地区的历史地理的影响。

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.