Abstract

The temporal and spatial coarseness of megafaunal fossil records complicates attempts to to disentangle the relative impacts of climate change, ecosystem restructuring, and human activities associated with the Late Quaternary extinctions. Advances in the extraction and identification of ancient DNA that was shed into the environment and preserved for millennia in sediment now provides a way to augment discontinuous palaeontological assemblages. Here, we present a 30,000-year sedimentary ancient DNA (sedaDNA) record derived from loessal permafrost silts in the Klondike region of Yukon, Canada. We observe a substantial turnover in ecosystem composition between 13,500 and 10,000 calendar years ago with the rise of woody shrubs and the disappearance of the mammoth-steppe (steppe-tundra) ecosystem. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) at multiple sites persisting thousands of years after their supposed extinction from the fossil record.

. . .

The youngest signatures for Equus and Mammuthus (ca. 5700 cal BP) are of great interest because they imply local survival of these taxa long after the Pleistocene-Holocene transition. Aside from very late insular occurrences of mammoths from the Bering and Chukchi Seas41, there are no accepted radiocarbon dates on mammoth or horse fossils in mainland Beringia that fall anywhere close to the mid-Holocene (Figs. 2, 7, Supplementary Fig. 1). Although the authenticity of the identifications is not in question (Supplementary Fig. 57), the wide temporal gap between these sedaDNA molecules and dated bones is concerning. This difference needs to be evaluated in context. Palaeontological and archaeological records across much of the Arctic and Subarctic are notably sparse. Small refugial populations might have survived in remote pockets at sizes too small to be readily detected by macrofossil collections derived largely from a small set of resource extraction and development sites. The case of Mammuthus survival on St. Paul and Wrangel islands, until 5500 and 4000 cal years BP, respectively is interesting because until recent decades neither population was known to have persisted into the mid-Holocene. Bison priscus was likewise discovered to have survived throughout the Holocene in southern Yukon39,40. Conroy et al.165 observed the presence of coprophilous fungi in the Alaskan interior at Windmill and Jan Lakes until ~9000 cal BP and 4500 cal BP. This abundance of spores postdates the megafaunal turnover and is perhaps most likely related to a replacement with browsing cervids. Alternatively, it is also possible that cryptic, refugial populations of Pleistocene grazers were contributing sources. The way forward is through further testing and confirmation, which can be achieved through multiproxy sampling from a broader suite of high latitude sites where reworking is negligible, and conditions favour the widest possible metagenomic spectra.