Reconstructing the spatiotemporal patterns of admixture during the European Holocene using a novel genomic dating method

Abstract

Recent studies have shown that gene flow or admixture has been pervasive throughout human history. While several methods exist for dating admixture in contemporary populations, they are not suitable for sparse, low coverage data available from ancient specimens. To overcome this limitation, we developed DATES that leverages ancestry covariance patterns across the genome of a single individual to infer the timing of admixture. By performing simulations, we show that DATES provides reliable results under a range of demographic scenarios and outperforms available methods for ancient DNA applications. We apply DATES to ~1,100 ancient genomes to reconstruct gene flow events during the European Holocene. Present-day Europeans derive ancestry from three distinct groups, local Mesolithic hunter-gatherers, Anatolian farmers, and Yamnaya Steppe pastoralists. These ancestral groups were themselves admixed. By studying the formation of Anatolian farmers, we infer that the gene flow related to Iranian Neolithic farmers occurred no later than 9,600 BCE, predating agriculture in Anatolia. We estimate the early Steppe pastoralist groups genetically formed more than a millennium before the start of steppe pastoralism, providing new insights about the history of proto-Yamnaya cultures and the origin of Indo-European languages. Using ancient genomes across sixteen regions in Europe, we provide a detailed chronology of the Neolithization across Europe that occurred from ~6,400-4,300 BCE. This movement was followed by a rapid spread of steppe ancestry from ~3,200-2,500 BCE. Our analyses highlight the power of genomic dating methods to elucidate the legacy of human migrations, providing insights complementary to archaeological and linguistic evidence. SignificanceThe European continent was subject to two major migrations during the Holocene: the movement of Near Eastern farmers during the Neolithic and the migration of Steppe pastoralists during the Bronze Age. To understand the timing and dynamics of these movements, we developed DATES that leverages ancestry covariance patterns across the genome of a single individual to infer the timing of admixture. Using ~1,100 ancient genomes spanning ~8,000-350 BCE, we reconstruct the chronology of the formation of the ancestral populations and the fine-scale details of the spread of Neolithic farming and Steppe pastoralist-related ancestry to Europe. Our analysis demonstrates the power of genomic dating methods to provide an independent and complementary timeline of population origins and movements using genetic data.