Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe1,2,3. The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet4. However, the limited data available from earlier hunter-gatherers preclude an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton discovered at the La Braña-Arintero site in León, Spain, to retrieve a complete pre-agricultural European human genome. Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer.
The authors thank L. A. Grau Lobo (Museo de León) for access to the La Braña specimen, M. Rasmussen and H. Schroeder for valid input into the experimental work, and M. Raghavan for early access to Mal'ta genome data. Sequencing was performed at the Danish National High-Throughput DNA-Sequencing Centre, University of Copenhagen. The POPRES data were obtained from dbGaP (accession number 2038). The authors are grateful for financial support from the Danish National Research Foundation, ERC Starting Grant (260372) to TM-B, and (310372) to M.G.N., FEDER and Spanish Government Grants BFU2012-38236, the Spanish Multiple Sclerosis Netowrk (REEM) of the Instituto de Salud Carlos III (RD12/0032/0011) to A.N., BFU2011-28549 to T.M.-B., BFU2012-34157 to C.L.-F., ERC (Marie Curie Actions 300554) to M.E.A., NIH NRSA postdoctoral fellowship (F32GM106656) to C.W.K.C., NIH (R01-HG007089) to J.N., NSF postdoctoral fellowship (DBI-1103639) to M.D., the Australian NHMRC to R.A.S. and a predoctoral fellowship from the Basque Government (DEUI) to I.O.
Extended data figures
This file contains Supplementary Text, additional references and Supplementary Tables 1-26 (see Contents for more details).