Ancient human genomes suggest three ancestral populations for present-day Europeans

Abstract

We sequenced genomes from a ~7,000 year old early farmer from Stuttgart in Germany, an ~8,000 year old hunter-gatherer from Luxembourg, and seven ~8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had ~44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.

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

“…Recent studies using ancient genomic data of Central and North European early farmers have shown an affinity to South European rather than Near Eastern populations [33,40,41]. Of note, the proportion of western hunter-gatherer ancestry is higher in all modern-day Europeans and the early farmer ancestry being comparably best preserved in, for example, Sardinians [33,40].…”

“…Sub-haplogroup U5b has been shown to be common in hunter-gatherer communities across Europe [28][29][30]32,33,47,48]. Contrary to the low mtDNA diversity observed in Central/North European hunter-gatherers [28][29][30], we identify a higher variability in early farming communities of the Carpathian Basin including haplogroups N1a, T1, T2, J, K, H, HV, V, W, X, U2, U3, U4 and U5a (electronic supplementary material, table S1).…”

“…Intriguingly, populations of the northeast Caucasus show greater distances to the STA-LBK samples due to lower abundance of haplogroup G/G2a [55]. Genomic data from early farmers have been shown to be the most similar to modern-day Sardinians [33,40,41], which could be explained by the geographical isolation of Sardinia, having led to a conservation of the Neolithic genetic signature. Interestingly, our mtDNA population genetic analyses did not highlight the NeolithicSardinian affinity, but was observed on our genetic distance map.…”

“…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].…”