Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment

Pere Gelabert,Susanna Sawyer,Anders Bergström,Ashot Margaryan,Thomas C Collin,Tengiz Meshveliani,Anna Belfer-Cohen,David Lordkipanidze,Nino Jakeli,Zinovi Matskevich,Guy Bar-Oz,Daniel M Fernandes,Olivia Cheronet,Kadir T Özdoğan,Victoria Oberreiter,Robin N.M Feeney,Mareike C Stahlschmidt,Pontus Skoglund,Ron Pinhasi

doi:10.1016/j.cub.2021.06.023

Abstract

SummaryCave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental “shotgun” genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.

Highlights

Ancient DNA fragments sequenced from bone,[1] teeth,[2] and hair[3] have revolutionized our understanding of natural history and the human past.[4,5] When skeletal material is not available, ancient environmental DNA has been used to determine the presence or absence of different species
We analyzed six sediment samples from different layers of areas A and B of Satsurblia cave (Figure 1A)[16] and performed shotgun sequencing to screen them for mammalian DNA (Data S1A)
SAT16 LS29 (SAT29) from layer BIII (Figure 1B), which is radiocarbon dated to 25.4–24.5 ka cal BP,[16] contained substantial amounts of DNA from humans as well as from other mammals and was sequenced to greater depth

Summary

Introduction

Ancient DNA fragments sequenced from bone,[1] teeth,[2] and hair[3] have revolutionized our understanding of natural history and the human past.[4,5] When skeletal material is not available, ancient environmental DNA has been used to determine the presence or absence of different species. A similar study recovered Denisovan mitochondrial DNA from sediments deposited $100 kya and $60 kya from Baishya Karst Cave on the Tibetan Plateau.[14] A recent study used targeted enrichment of 1.6 million loci to recover Neanderthal and Denisovan nuclear DNA from three Paleolithic sites. This yielded enough DNA to allow for some analyses of genome-wide ancestry, including the finding of a Neanderthal population replacement at one of the sites, thereby demonstrating the possibility of large-scale nuclear DNA recovery from sediments.[15]

Methods

Results

Discussion

Conclusion