Mitochondrial haplogroup N1a phylogeography, with implication to the origin of European farmers (original) (raw)

0 0 M o n t h 2 0 1 7 | V o L 0 0 0 | n A t U R E | 1 LEttER Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants 1-8 who received a limited amount of admixture from resident hunter-gatherers 3-5,9. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Here we investigate the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples, of which 130 are newly reported here, from the Neolithic and Chalcolithic periods of Hungary (6000-2900 bc, n = 100), Germany (5500-3000 bc, n = 42) and Spain (5500-2200 bc, n = 38). We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways in which gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modelling approaches to elucidate multiple dimensions of historical population interactions. The population dynamics of the Neolithization process are of great importance for understanding European prehistory 10-13. The first quantitative model of the Neolithic transition to integrate archaeological and genetic data was the demic diffusion hypothesis 10 , which posited that growing population densities among Near Eastern farmers led to a range expansion that spread agriculture to Europe. Ancient DNA analysis has validated major migrations from populations related to Neolithic Anatolians as driving the introduction of farming in Europe 1-8 , but the demic diffusion model does not account for the complexities of the interactions between farmers and hunter-gatherers in Europe throughout the Neolithic period 11-16. For example, ancient DNA analyses have shown that farmers traversed large portions of Europe with limited initial admixture from hunter-gatherers 3,5,7,8 and, furthermore, that farmers and hunter-gatherers lived in close proximity in some locations long after the arrival of agriculture 15,16. However, genetic data have not been used systematically to model population interactions and transformations during the course of the Neolithic period. Key open questions include whether migrating farmers mixed with hunter-gatherers at each stage of the expansion (and, if so, how soon after arriving this occurred) and whether the previously observed increase in hunter-gatherer ancestry among farmers in several parts of Europe by the Middle Neolithic period 5-9 represented a continuous versus discrete process and a continent-wide phenomenon versus a collection of parallel, local events. We compiled a high-resolution dataset of 180 Neolithic and Chalcolithic European genomes (pre-dating the arrival of steppe ancestry in the third millennium bc (ref. 5)) from what are now Hungary, Germany and Spain, of which 130 individuals are newly reported here, 45 with new direct radiocarbon dates (Table 1, Fig. 1a, b, Extended Data Tables 1, 2, Supplementary Tables 1, 2 and Supplementary Information sections 1-3). We enriched for DNA fragments covering a set of approximately 1.23 million single-nucleotide polymorphism (SNP) targets 7 and called one allele at random per site, obtaining mostly high-quality data, with at least 100,000 SNPs hit at least once (average coverage around 0.1 or higher) for 90 of the 130 samples (Methods). Most (90) of our new samples comprise an approximately 3,000-year transect of the prehistory of the Carpathian Basin (Supplementary Information section 1), from both the eastern (Great Hungarian Plain or Alföld) and western (Transdanubia) regions of present-day