Parallel palaeogenomic transects reveal complex genetic history of early European farmers

Abstract

Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants1–8 who received a limited amount of admixture from resident hunter-gatherers3–5,9. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Using the highest-resolution genome-wide ancient DNA data set assembled to date—a total of 180 samples, 130 newly reported here, from the Neolithic and Chalcolithic of Hungary (6000–2900 BCE, n = 100), Germany (5500–3000 BCE, n = 42), and Spain (5500–2200 BCE, n = 38)—we investigate the population dynamics of Neolithization across Europe. 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 that gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modeling approaches to elucidate multiple dimensions of historical population interactions.

The Beaker phenomenon and the genomic transformation of northwest Europe

“…2b). These regional patterns could be partially explained by differential genetic affinities to pre-Neolithic hunter-gatherer individuals from different regions 22 (Extended Data Fig. 4).…”

The genomic history of southeastern Europe

“…We report, but do not analyze, nine individuals that were first-degree relatives of others in the dataset, resulting in an analysis dataset of 216 individuals. We analyzed these data together with 274 previously reported ancient individuals, 9–11,15–27 777 present-day individuals genotyped on the Illumina “Human Origins” array, 23 and 300 high coverage genomes from the Simons Genome Diversity Project (SGDP). 28 We used principal component analysis (PCA; Figure 1B, Extended Data Figure 1), supervised and unsupervised ADMIXTURE (Figure 1D, Extended Data Figures 2&3), 29 D- statistics, qpAdm and qpGraph , 30 along with archaeological and chronological information (including 137 newly reported AMS 14 C dates) to cluster the individuals into populations and investigate the relationships among them.…”

“…Seven samples were processed 27 at the Institute of Archaeology RCH HAS, Budapest, Hungary, and amplified libraries were sent to Boston for screening, 1240k capture and sequencing.…”

“…Thus, there is only a single allele from each individual at each site, but adjacent alleles might come from either of the two haplotypes of the individual. We merged the newly reported data with previously reported data from 274 other ancient individuals 9–11,15–27 , making pseudo-haploid calls in the same way at the 1240k sites for individuals that were shotgun sequenced rather than captured.…”

The Beaker Phenomenon and the Genomic Transformation of Northwest Europe

“…1a Neolithic populations (Fig. 2b), which could be explained by differential affinities to hunter-208 gatherer individuals from different regions 42 (Extended Data Fig. 2).…”