Gelabert (2021): Genome analysis of Upper Palaeolithic female from Satsurblia

Open access Genome-scale sequencing and analysis of human, wolf and bison DNA from 25,000 year-old sediment, by Gelabert et al. bioRxiv (2020).

Abstract:

Archaeological sediments have been shown to preserve ancient DNA, but so far have not yielded genome-scale information of the magnitude of skeletal remains. We retrieved and analysed human and mammalian low-coverage nuclear and high-coverage mitochondrial genomes from Upper Palaeolithic sediments from Satsurblia cave, western Georgia, dated to 25,000 years ago. First, a human female genome with substantial basal Eurasian ancestry, which was an ancestry component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe. Second, a wolf genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage that diverged from the ancestors of modern wolves and dogs before these diversified. Third, a bison 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 sediment DNA can be used not only for species identification, but also be a source of genome-wide ancestry information and genetic history.

Interesting excerpts:

We find that the SAT29 sample clusters with the Dzudzuana2 individual and not with the late Upper Paleolithic and Mesolithic genomes from the region, or with any of the other pre-LGM Eurasian genomes. Unsupervised ADMIXTURE clustering (Alexander and Lange, 2011) further supports a high similarity between SAT29 and Dzudzuana2.

Through targeted capture (Maricic et al., 2010) we recovered 4,953 human mitochondrial DNA (mtDNA) reads, providing 15-fold coverage of the mtDNA. The consensus sequence has 16 derived positions (Table S3) compared to the rCRS sequence and belongs to haplogroup N like individual Dzudzuana3 from Dzudzuana cave. We built a maximum parsimony (MP) tree with 68 ancient and 167 modern human mt genomes. The SAT29 sequence is positioned on a branch together with BK-CC7-355 (42450 ± 510 ka) and BK-BB7-240 (41850 ± 480 ka) from the Bacho-Kiro site in Bulgaria, the most ancient west-Eurasian mitochondrial sequences (Hublin et al., 2020) as well as Dzudzuana3 (Lazaridis et al., 2018).