Population Genomics of Late Stone Age Western Eurasia

The later Stone Age in Eurasia (c. 11,000 to 5,000 cal. BP) witnessed several large-scale migration events. These include the transition from foraging to farming facilitated by the spread of Neolithic people from the Middle East, permanently changing the culture, lifestyle, and gene pools of the regions they settled in. To investigate cross-continental differences in impact of these major demographic processes we shotgun sequenced 317 genomes of primarily Mesolithic and Neolithic origin. These were imputed alongside published data to obtain diploid genotypes from >1,600 ancient human genomes. This dataset enabled fine-grained population genetic inferences of these prehistoric events across Northern and Western Eurasia. This revealed a 'Great Divide' genomic boundary zone extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers (HGs) were highly genetically differentiated east and west of this zone, and the impact of the neolithisation was equally disparate. Large-scale shifts in genetic ancestry occurred in the west, including an almost complete replacement of HGs in many areas, whereas no substantial shifts in ancestry happened east of the zone during the same period. Similarly, within-group genetic relatedness was reduced substantially in the west from the Neolithic transition onwards, while east of the Urals relatedness remained high until ~4,000 BP, consistent with a longer persistence of localised HG groups. The boundary dissolved when ancestry related to Yamnaya steppe pastoralists spread westwards into Europe and eastwards to Altai around 5,000 BP resulting in a second major cross-continental genetic turnover. This rapid transformation reached most parts of Europe within a 1,000-year span. The genetic origin and fate of Yamnaya have remained elusive but we demonstrate that HGs from the Middle Don region contributed ancestry to Yamnaya people. These later admixed with people from the Globular Amphora Culture to form the Corded Ware groups before expanding into Europe. Similar dramatic turnover-patterns occurred in western Siberia, where we report substantial new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe zones to the Lake Baikal region. The spatiotemporal dynamics of these prehistoric migrations were highly heterogeneous but each had profound and lasting effects on the genetic diversity of Eurasian populations.