The Beaker phenomenon and the genomic transformation of northwest Europe

Abstract

From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain's gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.

Extended Data Figure 1. Beaker complex artefacts

a, ‘All-Over-Cord’ Beaker from Bathgate, West Lothian, Scotland. Photo: ãNational Museums Scotland. b, Beaker Complex grave goods from La Sima III barrow, Soria, Spain. The set includes Beaker pots of the so-called ‘Maritime style’. Photo: Junta de Castilla y León, Archivo Museo Numantino, Alejandro Plaza.

Extended Data Figure 2. Ancient individuals with previously published genome-wide data used in this study

a, Sampling locations. b, Time ranges. W/E/S/CHG, Western/Eastern/Scandinavian/Caucasus hunter-gatherers; E, Early; M, Middle; L, Late; N, Neolithic; CA, Copper Age; BA, Bronze Age. Map data from the R package maps.

Extended Data Figure 3. Population structure

a, Principal component analysis of 990 present-day West Eurasian individuals (grey dots), with previously published (pale yellow) and new ancient samples projected onto the first two principal components. b, ADMIXTURE clustering analysis with k=8 showing ancient individuals. W/E/S/CHG, Western/Eastern/Scandinavian/Caucasus hunter-gatherers; E, Early; M, Middle; L, Late; N, Neolithic; CA, Copper Age; BA, Bronze Age.

Extended Data Figure 4. Hunter-gatherer affinities in Neolithic/Copper Age Europe

Differential affinity to hunter-gatherer individuals (LaBraña1 from Spain and KO1 from Hungary) in European populations before the emergence of the Beaker Complex. See Supplementary Information, section 8 for mixture proportions and standard errors computed with qpAdm. E, Early; M, Middle; L, Late; N, Neolithic; CA, Copper Age; BA, Bronze Age; N_Iberia, Northern Iberia; C_Iberia, Central Iberia.

Extended Data Figure 5. Modelling the relationships between Neolithic populations

a, Admixture graph fitting a Test population as a mixture of sources related to both Iberia_EN and Hungary_EN. b, Likelihood distribution for models with different proportions of the source related to Iberia_EN (green admixture edge in (a)) when Test is England_N, Scotland_N or France_MLN. E, Early; M, Middle; L, Late; N, Neolithic.

Extended Data Figure 6. Genetic affinity between Beaker Complex-associated individuals from southern England and the Netherlands

a, f-statistics of the form f₄(Mbuti, Test; BK_Netherlands_Tui, BK_England_SOU). Negative values indicate that Test is closer to BK_Netherlands_Tui than to BK_England_SOU, and the opposite for positive values. Error bars represent ±3 standard errors. b, Outgroup-f₃ statistics of the form f₃(Mbuti; BK_England_SOU, Test) measuring shared genetic drift between BK_England_SOU and other Beaker Complex-associated groups. Error bars represent ±1 standard errors. Number of individuals for each group is given in parentheses. BK_Netherlands_Tui, Beaker-associated individuals from De Tuithoorn, Oostwoud, the Netherlands; BK_England_SOU, Beaker-associated individuals from southern England. See Supplementary Table 1 for individuals associated to each population label.

Extended Data Figure 7. Derived allele frequencies at three SNPs of functional importance

Error bars represent 1.9-log-likelihood support interval. The red dashed lines show allele frequencies in the 1000 Genomes GBR population (present-day people from Great Britain). Sample sizes are 50, 98, and 117 for Britain Neolithic, Britain CA-BA and Central European BC, respectively. BC, Beaker Complex; CA, Copper Age; BA, Bronze Age.

Figure 1. Spatial, temporal, and genetic structure of individuals in this study

a, Geographic distribution of samples with new genome-wide data. Random jitter was added for sites with multiple individuals. Map data from the R package maps. b, Approximate time ranges for samples with new genome-wide data. Sample sizes are given next to each bar. c, Principal component analysis of 990 present-day West Eurasian individuals (grey dots), with previously published (pale yellow) and new ancient samples projected onto the first two principal components. This figure is a zoom of Extended Data Fig. 3a. See Methods for abbreviations of population names.

Figure 2. Investigating the genetic makeup of Beaker Complex individuals

a, Proportion of Steppe-related ancestry (shown in black) in Beaker Complex-associated groups, computed with qpAdm under the model Steppe_EBA + Anatolia_N + WHG. The area of the pie is proportional to the number of individuals (shown inside the pie if more than one). Map data from the R package maps. b, f-statistics of the form f₄(Mbuti, Test; Iberia_EN, LBK_EN) computed for European populations (number of individuals for each group is given in parentheses) before the emergence of the Beaker Complex (Supplementary Information section 7). Error bars represent ±1 standard errors. c, Testing different populations as a source for the Neolithic ancestry component in Beaker Complex individuals. The table shows the P-values (highlighted if >0.05) for the fit of the model: Steppe_EBA + Neolithic/Copper Age source population.

Figure 3. Population transformation in Britain associated with the arrival of the Beaker Complex

Modelling Neolithic, Copper and Bronze Age (including Beaker Complex-associated) individuals from Britain as a mixture of continental Beaker Complex-associated individuals (red) and the Neolithic population from Britain (blue). Each bar represents genome-wide mixture proportions for one individual. Individuals are ordered chronologically and included in the plot if represented by more than 100,000 SNPs. Circles indicate the Y-chromosome haplogroup for male individuals.