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 (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 brown 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.晚更新世（Late Pleistocene）时期，北美大部分区域曾周期性被冰盖覆盖。然而，针对末次冰盛期（Last Glacial Maximum, LGM）期间阿拉斯加东南沿海的亚历山大群岛（Alexander Archipelago）是否存在无冰避难所（ice-free refugia），学界仍存在争议。研究人员已从阿拉斯加东南部的洞穴中发掘出大量亚化石（subfossils），其中包括美洲黑熊（Ursus americanus）与棕熊（U. arctos）；现今这两种熊类均栖息于亚历山大群岛，但与大陆种群在遗传层面存在显著差异。因此，这两种熊类为研究长期定居、潜在避难所存续以及谱系更替（lineage turnover）提供了理想的研究体系。本研究基于覆盖近4.5万年的99条全新完整线粒体基因组（mitochondrial genomes），对古代与现代的棕熊和黑熊开展遗传分析。美洲黑熊形成两个阿拉斯加东南部亚支系（subclades），二者分化时间距今超10万年，分别对应冰期前与冰期后类群。所有冰期后的古代棕熊均与群岛现存棕熊亲缘关系紧密，而唯一的冰期前棕熊样本则属于一个亲缘关系较远的演化支。熊类亚化石记录在末次冰盛期前后存在一段记录空缺，且二者冰期前与冰期后亚支系存在深度分化，这两点均不支持两种熊类在末次冰盛期期间持续栖息于阿拉斯加东南部的假说。本研究结果与阿拉斯加东南沿海不存在无冰避难所的结论相符，同时表明冰川消退（deglaciation）后植被快速恢复，使得熊类能够在短暂的末次冰盛期峰值过后重新定居该区域。