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 migrants who received a limited amount of admixture from resident hunter-gatherers. 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.

Extended Data Figure 1. First two principal components from PCA

We computed PCs for a set of 782 present-day western Eurasian individuals genotyped on the Affymetrix Human Origins array (background gray points) and then projected ancient individuals onto these axes. Shown is a closeup omitting the present-day Bedouin population.

Extended Data Figure 2. Scaffold admixture graph used for modeling European Neolithic populations

Dotted lines denote admixture events. Neolithic Anatolians, LB1, and KO1 are modeled as admixed, with Basal Eurasian ancestry, deeper European hunter-gatherer ancestry, and FEF ancestry, respectively. European test populations are fit as a mixture of FEF and ancestry related to one or two of the four WHG individuals (here VIL-related as an example). See Supplementary Information section 6 for full details.

Extended Data Figure 3. Examples of ALDER weighted LD decay curves

Weighted LD is shown as a function of genetic distance d, using Neolithic Anatolians and WHG as references, for four individuals: BAM17b (Starčevo EN), CB13 (Iberia EN), Bla8 (Blätterhöhle hunter-gatherer), and KO1. The results shown here use helper individuals M11–363 (Neolithic Anatolian), L11–322 (Neolithic Anatolian), BIC, and LB1, respectively, and have fitted dates (blue curves) of 3.8±1.2, 18.3±6.0, 13.1±2.7, and 21.6±8.8 generations (compared to final individual-level dates of 4.5±1.9, 17.5±3.5, 12.1±2.9, and 21.0±7.0 generations; see Supplementary Information section 7). Note different x-axis scales for the four individuals.

Extended Data Figure 4. Hunter-gatherer ancestry as a function of latitude and longitude for Neolithic individuals

a, b, EN/MN Hungary. c, d, LN/CA Hungary. e, f, Iberia. Protob., Protoboleráz.

Extended Data Figure 5. Germany and Iberia time series and simulated data

a, Dates of admixture. b, Hunter-gatherer ancestry proportions, normalized by the total in the most recent (rightmost) population. Symbols are as in Figs 1 and 2, here showing population-level averages plus or minus two standard errors. Yellow dashed lines represent continuous admixture simulations: from top to bottom, diminishing 5% per generation, diminishing 3%, diminishing 1%, and uniform. Green solid lines represent pulse-plus-continuous admixture simulations: from top to bottom, all hunter-gatherer ancestry in a pulse at time zero; 3/4 of final hunter-gatherer ancestry in an initial pulse, followed by uniform continuous gene flow; half in initial pulse and half continuous; and 1/4 in initial pulse.

Figure 1. Spatial and temporal contexts of European Neolithic samples

a, b, Locations of samples used for analyses, with close-up of Hungary (orange shading for Alföld and light blue for Transdanubia). c, Sample dates arranged by longitude. d, Hunter-gatherer genetic cline (derived from MDS analysis; Supplementary Information section 5) as a function of longitude. The four primary WHG individuals are shown together with “BIC” (Bichon, ~11,700 BCE from Switzerland), “EHG” (eastern hunter-gatherers, ~7000–5000 BCE from Russia^,), and “ElM” (El Mirón, ~17,000 BCE from Spain). Random jitter is added to separate overlapping positions in a–c. GerMN, Germany MN; Blatt., Blätterhöhle; Protob., Protoboleráz.

Figure 2. Admixture parameters for test individuals and populations

a, Estimated individual hunter-gatherer ancestry versus sample date, with best-fitting regression lines for each region (excluding Blätterhöhle). Standard errors are around 2% for hunter-gatherer ancestry and 100 years for dates (Methods; Extended Data Tables 1, 2). b, Relative affinity of hunter-gatherer ancestry in Neolithic individuals, measured as f₄(LB1+LOS, KO1+VIL; Anatolia, X) (positive, more similar to eastern WHG; negative, more similar to western WHG; standard errors ~5×10⁻⁴), with best-fitting regression line (|Z| > 3 for aggregate differences among the three regions). c, Population-level average sample ages and dates of admixture, plus or minus two standard errors. Colored fill indicates the inferred primary hunter-gatherer ancestry component, with darker shades corresponding to higher confidence (all admixed populations except LBK and Tisza significant at p < 0.05; see Extended Data Table 3 and Supplementary Information section 6). Dashed lines denote the approximate date of arrival of farming in each region.

Figure 3. Hungary time series and simulated data

a, Dates of admixture. b, Hunter-gatherer ancestry proportions, normalized by the total in the most recent (rightmost) population. Symbols are as in Figs 1 and 2, here showing population-level averages plus or minus two standard errors. Yellow dashed lines represent continuous admixture simulations: from top to bottom, diminishing 5% per generation, diminishing 3%, diminishing 1%, and uniform. Green solid lines represent pulse-plus-continuous admixture simulations: from top to bottom, all hunter-gatherer ancestry in a pulse at time zero; 3/4 of final hunter-gatherer ancestry in an initial pulse, followed by uniform continuous gene flow; half in initial pulse and half continuous; and 1/4 in initial pulse.