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

更新世开始于距今大约180万年之前，一直持续到大约1.2万年前，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恶劣的气候条件，而另一些则被限制在可居住的无冰地区，或避难所。在最后一个冰河时代的高峰时期，冰盖将旧世界和新世界分开，限制了生物在白令海峡大陆桥上的活动数千年。然而，地质和生物学证据表明，北太平洋沿岸的避难所可能在新旧世界之间的物种运动中扮演了至关重要的“垫脚石”角色，形成了北美重新殖民的早期后冰川走廊。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定年，以直接测试这些洞穴在最后一个冰河时代的高峰期是否被熊所占据。通过确保对阿拉斯加东南部这些重要哺乳动物物种的精确物种测定，并提供与现存种群的进化联系，本研究将阐明物种对气候变化的反应，并有助于确定阿拉斯加东南部可行的沿海避难所的范围和时间。因此，该项目的结果将为深入了解晚更新世跨白令陆桥生物群的动态变化，该地区的多样性和生物地理历史，以及它在最后一个冰河时期和之后作为大陆交流走廊的重要性提供重要数据。本研究的一个重要成果是恢复了威斯康辛冰期晚期至全新世居住在阿拉斯加东南部的熊标本的遗传信息，并为人口事件的精确时间提供了校准。该项目以棕熊和黑熊为研究对象，它们已经发展成为北半球系统地理学研究的成熟系统。该项目将测试相同的熊种群是否在过去的5万年里一直居住在这个地区，或者它们是否在末次冰期极大期之后重新定居，以及它们是否对冰期后（现代）大陆种群做出了贡献。该项目将采用高度综合的方法，利用最先进的古代DNA分析（包括使用定制的生物素化RNA诱饵，利用全线粒体基因组序列设计的靶向杂交富集方法）、放射性碳和分子定年、古饮食重建和系统发育重建。该研究对于了解北美过去和现在的哺乳动物多样性，以及评估晚更新世气候变化对该地区生物多样性、殖民化和历史生物地理学的影响具有广泛的意义。

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.