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, 112 (38), 11917-22

Ancient Genomes Link Early Farmers From Atapuerca in Spain to Modern-Day Basques

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Ancient Genomes Link Early Farmers From Atapuerca in Spain to Modern-Day Basques

Torsten Günther et al. Proc Natl Acad Sci U S A.

Abstract

The consequences of the Neolithic transition in Europe--one of the most important cultural changes in human prehistory--is a subject of great interest. However, its effect on prehistoric and modern-day people in Iberia, the westernmost frontier of the European continent, remains unresolved. We present, to our knowledge, the first genome-wide sequence data from eight human remains, dated to between 5,500 and 3,500 years before present, excavated in the El Portalón cave at Sierra de Atapuerca, Spain. We show that these individuals emerged from the same ancestral gene pool as early farmers in other parts of Europe, suggesting that migration was the dominant mode of transferring farming practices throughout western Eurasia. In contrast to central and northern early European farmers, the Chalcolithic El Portalón individuals additionally mixed with local southwestern hunter-gatherers. The proportion of hunter-gatherer-related admixture into early farmers also increased over the course of two millennia. The Chalcolithic El Portalón individuals showed greatest genetic affinity to modern-day Basques, who have long been considered linguistic and genetic isolates linked to the Mesolithic whereas all other European early farmers show greater genetic similarity to modern-day Sardinians. These genetic links suggest that Basques and their language may be linked with the spread of agriculture during the Neolithic. Furthermore, all modern-day Iberian groups except the Basques display distinct admixture with Caucasus/Central Asian and North African groups, possibly related to historical migration events. The El Portalón genomes uncover important pieces of the demographic history of Iberia and Europe and reveal how prehistoric groups relate to modern-day people.

Keywords: Ancient DNA; human prehistory; population genomics.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Overview of samples. (A) Geographic locations of ancient individuals used in this study. The dataset includes individuals sequenced as part of this study (from El Portalón) as well as individuals from the literature (1, 2, 10, 12, 19). The map template is modified from www.primap.com. (B) Temporal and cultural context of the ancient individuals; individuals from a hunter–gatherer context are shown in italics. The symbols and colors denoting each individual are used consistently throughout this paper. (C) PCA of ancient individuals and modern-day individuals across Europe (1). Only those ancient samples with more than 20,000 transversion SNPs overlapping with the modern-day SNP data are plotted (see also SI Appendix, section S8 and Dataset S1). Colored areas show kernel densities of modern-day groups with more than eight individuals.
Fig. 2.
Fig. 2.
Admixture among ancient groups based on genome sequence data. (A) Admixture graph with four migration edges for the individual with the highest sequencing coverage for each geographic site, region, or time period. To improve clarity, branch lengths are not drawn to scale and represent only the hierarchical clustering (see SI Appendix, Fig. S10 for the topology drawn to scale). (B) Genetic affinity of the different early farmer individuals (f4-statistic) to a Central European Mesolithic individual (Loschbour, highest coverage Mesolithic genome), as a function of the dating of the early farmer individuals. A central European LBK individual is used as a baseline early Neolithic farmer (highest coverage early Neolithic individual, but the choice of reference individual does not affect the qualitative result) (SI Appendix, section S11). The Bronze Age, Chalcolithic, and Scandinavian farmers show greater levels of admixture with HG groups than the temporally older Neolithic Central European farmers (Pearson correlation R2 = 0.69, P = 0.001).
Fig. 3.
Fig. 3.
Population structure of ancient and modern-day individuals. (A) Admixture fractions among modern-day individuals from Eurasia and North Africa together with 16 ancient individuals. Only ancient and modern-day individuals from Southwestern Europe are shown (see Dataset S1 for the complete plot with all individuals). Admixture components are labeled based on the populations/geographic regions in which they are modal. (B) Genetic similarity (measured using outgroup f3 statistics) between Southwestern European groups and four El Portalón individuals. Error bars show ±1 SE. Higher values represent greater genetic similarity between the El Portalón farmers and the modern-day Southwestern populations in the legend.

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