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Research Article

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, and Mattias Jakobsson
PNAS first published September 8, 2015; https://doi.org/10.1073/pnas.1509851112
Torsten Günther
aDepartment of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden;
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Cristina Valdiosera
aDepartment of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden;
bDepartment of Archaeology and History, La Trobe University, Melbourne, VIC 3086, Australia;
cCentro Mixto, Universidad Complutense de Madrid–Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain;
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Helena Malmström
aDepartment of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden;
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Irene Ureña
cCentro Mixto, Universidad Complutense de Madrid–Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain;
dDepartamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain;
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Ricardo Rodriguez-Varela
cCentro Mixto, Universidad Complutense de Madrid–Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain;
dDepartamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain;
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Óddny Osk Sverrisdóttir
aDepartment of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden;
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Evangelia A. Daskalaki
aDepartment of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden;
eDepartment of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden;
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Pontus Skoglund
aDepartment of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden;
eDepartment of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden;
fDepartment of Genetics, Harvard Medical School, Boston, MA 02115;
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Thijessen Naidoo
aDepartment of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden;
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Emma M. Svensson
aDepartment of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden;
gDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden;
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José María Bermúdez de Castro
hCentro Nacional de Investigación sobre la Evolución Humana, 09002 Burgos, Spain;
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Eudald Carbonell
iInstitut Català de Paleoecologia Humana i Evolució Social, CEIP Marcel·lí Domingo, 43007 Tarragona, Spain;
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Michael Dunn
jDepartment of Linguistics and Philology, Uppsala University, 75238 Uppsala, Sweden;
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Jan Storå
eDepartment of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden;
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Eneko Iriarte
kLaboratorio de Evolución Humana, Departamento de Ciencias Históricas y Geografía, Universidad de Burgos, 09001 Burgos, Spain;
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Juan Luis Arsuaga
cCentro Mixto, Universidad Complutense de Madrid–Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain;
dDepartamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain;
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José-Miguel Carretero
cCentro Mixto, Universidad Complutense de Madrid–Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain;
kLaboratorio de Evolución Humana, Departamento de Ciencias Históricas y Geografía, Universidad de Burgos, 09001 Burgos, Spain;
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Anders Götherström
eDepartment of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden;
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Mattias Jakobsson
aDepartment of Evolutionary Biology, Uppsala University, 75236 Uppsala, Sweden;
lScience for Life laboratory, Uppsala University, 75123 Uppsala, Sweden
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  • For correspondence: mattias.jakobsson@ebc.uu.se
  1. Edited by Eske Willerslev, University of Copenhagen, Copenhagen, Denmark, and approved July 29, 2015 (received for review May 21, 2015)

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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.

  • Ancient DNA
  • human prehistory
  • population genomics

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.

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Ancient genomes link early farmers to 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
Proceedings of the National Academy of Sciences Sep 2015, 201509851; DOI: 10.1073/pnas.1509851112

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Ancient genomes link early farmers to 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
Proceedings of the National Academy of Sciences Sep 2015, 201509851; DOI: 10.1073/pnas.1509851112
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