Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European

Abstract

Ancient genomic sequences have started revealing the origin and the demographic impact of Neolithic farmers spreading into Europe1–3. 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 precludes an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. By sequencing a ~7,000-year-old Mesolithic skeleton discovered at the La Braña-Arintero site in León (Spain), we retrieved the first 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. Hence, these genomic variants cannot represent novel mutations that occurred during the adaptation to the farming lifestyle.

Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction

“…This latter finding was unexpected given the archaeological evidence of a long-term occupation of Neanderthals in [47,48]. High-coverage genomes of Late Pleistocene Europeans-and also from other populations-will be needed to estimate accurately if other admixture events could have occured with Neanderthals or Denisovans.…”

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

“…This high similarity of modern Basques to El Portalón individuals was surprising because Basques have been posited as a remnant isolated population with a close relationship to the Mesolithic inhabitants of the region, based on classical genetic markers (26) and mtDNA haplogroup data (8), although the level of continuity has been unclear (12,13). The Basque language (Euskara) is a linguistic isolate, with no proven relationships with any languages now spoken in Europe or elsewhere (11), and it has commonly been concluded that the Basque language is a relict of the ancient, preagricultural linguistic diversity of Europe, with roots as far back as the Paleolithic (SI Appendix, section S12) (9).…”

“…The relationship of early Iberian farmers to their Central European counterparts and HG groups in Iberia, as well as their contribution to the present-day genomic variation in Iberia, is crucial to understanding the demographic history of the region. Of particular interest is the connection of Basques to different ancient groups in Iberia, to shed light on their long-debated origins (6)(7)(8)(9)(10)(11)(12)(13).…”

Tracing the genetic origin of Europe's first farmers reveals insights into their social organization

“…I2a has indeed been found in Mesolithic and Neolithic Central and North European hunter-gatherers [33,34,40,41], as well as in Neolithic remains of southwestern Europe [44,45]. Haplogroup I2a (and possibly I1) might represent a pre-farming legacy of the NRY variation in Europe, alongside the recently described pre-Neolithic C (M130) haplogroups in Russia and Spain [35,42]. Y chromosome haplogroups from STA and LBKT samples, such as haplogroups G2a2b and F*, have also been reported from the Central European LBK [38], and support a homogeneity of paternal lineages among early farmers.…”

“…Ancient genomic studies have described the early farmers as genetically most similar to extant populations of southern Europe [31,33,40,41]. Y chromosome data from prehistoric Europeans is still scarce but relevant for our study (electronic supplementary material, dataset S20), including hunter-gatherers [33][34][35]40,42], and early farmers from Germany [38,40], eastern Hungary [41], Austria [43] and southwest Europe [40,44,45].…”