Genomic structure in Europeans dating back at least 36,200 years

Abstract

The origin of contemporary Europeans remains contentious. We obtained a genome sequence from Kostenki 14 in European Russia dating from 38,700 to 36,200 years ago, one of the oldest fossils of anatomically modern humans from Europe. We find that Kostenki 14 shares a close ancestry with the 24,000-year-old Mal'ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a metapopulation that at times stretched from Europe to central Asia.

Gradual decline in mobility with the adoption of food production in Europe

“…However, unlike craniometric variables (51), limb bone dimensions do not appear to track population history in Europe (52). Recent work also indicates that the general genetic pool from which all Holocene Europeans were derived is ancient, extending back before the earliest specimens in our sample (53) and implying overall continuity despite periodic migrational events.…”

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.…”

“…Recent ancient DNA (aDNA) studies have provided direct insights into the mtDNA and nuclear genomic diversity of hunter-gatherers in Europe [28][29][30][31][32][33][34][35] and the Central European LBK [33,[36][37][38][39][40], describing genetic discontinuity between local foragers and early farmers [28,31,38,40]. Comparative analyses with present-day populations have revealed Near Eastern affinities of the mitochondrial LBK ancestry, supporting the demic diffusion model and population replacement at the beginning of the Neolithic period [38,39].…”

“…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].…”

Ancient DNA and human history

“…This observation is consistent with admixture having taken place 7,000-13,000 before the Ust'-Ishim individual lived, as admixture tracts tend to become shorter the longer the time since the admixture event. A similar pattern was seen in the genome of Kostenki-14, a 37,000-y-old modern European (33).…”