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.