Demogenomic modeling of the timing and the processes of early European farmers differentiation

Abstract

SummaryWhile the Neolithic expansion in Europe is well described archaeologically, the genetic origins of European first farmers and their affinities with local hunter-gatherers (HGs) remain unclear. To infer the demographic history of these populations, the genomes of 15 ancient individuals located between Western Anatolia and Southern Germany were sequenced to high quality, allowing us to perform population genomics analyses formerly restricted to modern genomes. We find that all European and Anatolian early farmers descend from the merging of a European and a Near Eastern group of HGs, possibly in the Near East, shortly after the Last Glacial Maximum (LGM). Western and Southeastern European HG are shown to split during the LGM, and share signals of a very strong LGM bottleneck that drastically reduced their genetic diversity. Early Neolithic Central Anatolians seem only indirectly related to ancestors of European farmers, who probably originated in the Near East and dispersed later on from the Aegean along the Danubian corridor following a stepwise demic process with only limited (2-6%) but additive input from local HGs.Our analyses provide a time frame and resolve the genetic origins of early European farmers. They highlight the impact of Late Pleistocene climatic fluctuations that caused the fragmentation, merging and reexpansion of human populations in SW Asia and Europe, and eventually led to the world's first agricultural populations.

A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition

“…It is plausible that east-west admixture occurred in Upper Mesopotamia, giving rise to Çayönü's gene pool, and may have also influenced Central Anatolia by the PN (6). We note that the duration and timing of this putative admixture process remain unclear, and that alternative scenarios are also conceivable (30). Irrespective of the demographic mechanisms, though, Central Zagros appears to have been genetically the most distinct group in early Holocene Southwest Asia.…”

Human inbreeding has decreased in time through the Holocene

“…West Eurasian hunter-gatherers carry the highest total length of short ROHs among all historical groups, attesting to their small population size around the early Holocene, as recently inferred using high-quality ancient genomes. 58 However, this inbreeding signal is rapidly lost, and West Eurasian advanced agriculturalists carry the lowest average sum of short ROHs among all ancient groups studied. In Central Eurasia, the total length of short ROHs is also high in hunter-gatherers and decreases in agriculturalists, but at a more modest rate (SROH decreases from c.235.3 Mb to c.85.1 Mb in West Eurasia, and from c.168.3 Mb to c.115.5 Mb in Central Eurasia).…”

Paleolithic Gene Duplications Primed Adaptive Evolution of Human Amylase Locus Upon Agriculture

“…Overall, our results support the complex narrative of the transition to agriculture, which includes the replacement of western hunter-gatherers by Anatolian farmers in Europe (41), potentially bringing with them amylase haplotypes that harbor higher AMY1 gene copies. Similarly, transient interactions between hunter-gatherer and agricultural groups (42) could explain the similar copy numbers observed between these groups during the transition period.…”

“…We used the program GeneToCN (26) to determine amylase copy number in 73 ancient human and 8 archaic hominin genomes (fig. S33 and, tables S10 and S12) (27,42,. The raw sequencing FASTQ formatted files were obtained through the European Nucleotide Archive (https://www.ebi.ac.uk/ena/browser/).…”