Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques

Torsten Günther; Cristina Valdiosera; Helena Malmström; Irene Ureña; Ricardo Rodriguez-Varela; Óddny Osk Sverrisdóttir; Evangelia A. Daskalaki; Pontus Skoglund; Thijessen Naidoo; Emma M. Svensson; José María Bermúdez de Castro; Eudald Carbonell; Michael Dunn; Jan Storå; Eneko Iriarte; Juan Luis Arsuaga; José-Miguel Carretero; Anders Götherström; Mattias Jakobsson

doi:10.1073/pnas.1509851112

New Research In

Edited by Eske Willerslev, University of Copenhagen, Copenhagen, Denmark, and approved July 29, 2015 (received for review May 21, 2015)

Significance

The transition from a foraging subsistence strategy to a sedentary farming society is arguably the greatest innovation in human history. Some modern-day groups—specifically the Basques—have been argued to be a remnant population that connect back to the Paleolithic. We present, to our knowledge, the first genome-wide sequence data from eight individuals associated with archaeological remains from farming cultures in the El Portalón cave (Atapuerca, Spain). These individuals emerged from the same group of people as other Early European farmers, and they mixed with local hunter–gatherers on their way to Iberia. The El Portalón individuals showed the greatest genetic affinity to Basques, which suggests that Basques and their language may be linked with the spread of agriculture across Europe.

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.

Footnotes

↵¹T.G. and C.V. contributed equally to this work.
↵²To whom correspondence should be addressed. Email: mattias.jakobsson{at}ebc.uu.se.

Author contributions: T.G., C.V., A.G., and M.J. designed research; C.V. organized and coordinated the experiments; C.V., Ó.O.S., and E.M.S. extracted DNA; C.V. and E.M.S. built libraries; C.V., H.M., I.U., R.R.-V., E.A.D., and E.M.S. conducted post PCR work; T.G., C.V., H.M., P.S., T.N., and M.J. analyzed genetic data with the following contributions: processing the data and population genomic analyses (T.G.), mtDNA (T.G. and H.M.), Y-chromosome (T.G. and T.N.); M.D., J.S., E.I., J.L.A., and J.-M.C. analyzed archaeological, linguistic, and anthropological data; C.V., I.U., R.R.-V., E.I., J.L.A., and J.-M.C. conducted field work; C.V., J.M.B.d.C., E.C., E.I., J.L.A., and J.-M.C. provided samples; and T.G., C.V., and M.J. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The sequences reported in this paper have been deposited in the European Nucleotide Archive (accession no. PRJEB9783).
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1509851112/-/DCSupplemental.

Freely available online through the PNAS open access option.