Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe. The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet. 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 POPRES data were obtained from dbGaP (accession number # 2038). The Danish National Research Foundation, ERC Starting Grant (260372) to TM-B, and (310372) to MGN, FEDER and Spanish Government Grants BFU2009-13409-C02-02, BFU2012-38236 to AN, BFU2011-28549 to TM-B, BFU2012-34157 to CL-F, ERC (Marie Cure Actions) to MEA, NIH NRSA postdoctoral fellowship (F32GM106656) to CWKC, NIH (R01-HG007089) to JN, NSF postdoctoral fellowship (DBI-1103639) to MDG