Ancient genomes of Sitka black-tailed deer show evidence for postglacial stepping-stone dispersal along the Pacific Northwest Coast of North America

Background: The mule deer ( Odocoileus hemionus ) and its two distinct black-tailed deer (BTD) subspecies, Sitka and Columbian BTD, have a complex history in North America involving survival in Last Glacial Maximum (LGM) refugia, postglacial expansion along the Pacific Northwest Coast, evidence for incomplete lineage sorting and recent introgression between subspecies. Moreover, the differentiation process of the two black-tailed deer subspecies is poorly understood and could have been a consequence of the LGM. As such, they provide an exemplary system to explore patterns of population dynamics in response to climate change. Results: Here we analyzed genome-scale data from samples spanning the last 13,500 years to explore the evolutionary history of Sitka BTD in Southeast Alaska. Deer samples from Southeast Alaska older than 8,500 years ago shared a mitochondrial haplotype with mule deer, whereas samples younger than 6,000 years have the modern Sitka BTD haplotype. Discordantly, nuclear genomic data confirmed that all ancient individuals from Southeast Alaska are closely related to modern Sitka BTD, although the older group also shared ancestry with mule deer. Modern samples from Vancouver Island share more alleles with modern Sitka BTD than Columbian BTD. Our results support that they survived in the same glacial refugium south of the Cordilleran ice sheet, along today’s Oregon coast. Conclusion: The uneven deglaciation along the Northwest Pacific Coast following the LGM may have created temporary post-glacial refugia, or “stepping stones”, along the British Columbia Coast. Such dispersal, associated with genetic drift and isolation by distance, likely led to the emergence of the BTD subspecies, as well as the low genetic diversity observed in modern Sitka BTD.