Upper Palaeolithic genomes reveal deep roots of modern Eurasians

Abstract

We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

Figure 1. Genetic structure of ancient Europe.

(a). Principal component analysis. Ancient data from Bichon, Kotias and Satsurblia genomes were projected onto the first two principal components defined by selected Eurasians from the Human Origins data set. The percentage of variance explained by each component accompanies the titles of the axes. For context we included data from published Eurasian ancient genomes sampled from the Late Pleistocene and Holocene where at least 200 000 SNPs were called (Supplementary Table 1). Among ancients, the early farmer and western hunter-gatherer (including Bichon) clusters are clearly identifiable, and the influence of ancient north Eurasians is discernible in the separation of eastern hunter-gatherers and the Upper Palaeolithic Siberian sample MA1. The two Caucasus hunter-gatherers occupy a distinct region of the plot suggesting a Eurasian lineage distinct from previously described ancestral components. The Yamnaya are located in an intermediate position between CHG and EHG. (b). ADMIXTURE ancestry components for ancient genomes (K=17) showing a CHG component (Kotias, Satsurblia) which also segregates in in the Yamnaya and later European populations.

Figure 2. The relationship between Caucasus hunter-gatherers (CHG), western hunter-gatherers and early farmers.

(a). Alternative phylogenies relating western hunter-gatherers (WHG), CHG and early farmers (EF, highlighted in orange), with the appropriate outgroup f₃-statistics. (b). The best supported relationship among CHG (Kotias), WHG (Bichon, Loschbour), and EF (Stuttgart), with split times estimates using G-Phocs. Oxygen 18 values (per mile) from the NGRIP core provide the climatic context; the grey box shows the extent of the Last Glacial Maximum (LGM).

Figure 3. Distribution of ROH.

(a). The total length of short ROH (<1.6 Mb) plotted against the total length of long ROH (≥1.6 Mb) and (b) mean total ROH length for a range of length categories. ROH were calculated using a panel of 199,868 autosomal SNPs. For Kotias we analysed both high-coverage genotypes and genotypes imputed from downsampled data (marked in italics; see Supplementary Information). Diploid genotypes imputed from low-coverage variant calls were used for Satsurblia and high-coverage genotypes were used for all other samples. A clear distinction is visible between either WHG and CHG who display an excess of shorter ROH, akin to modern Oceanic and Onge populations, and EF who resemble other populations with sustained larger ancestral population sizes.

Figure 4. The relationship of Caucasus hunter-gatherers to modern populations.

(a). Genomic affinity of modern populations to Kotias, quantified by the outgroup f₃-statistics of the form f₃(Kotias, modern population; Yoruba). Kotias shares the most genetic drift with populations from the Caucasus with high values also found for northern Europe and central Asia. (b). Sources of admixture into modern populations: semicircles indicate those that provide the most negative outgroup f₃ statistic for that population. Populations for which a significantly negative statistic could not be determined are marked in white. Populations for which the ancient Caucasus genomes are best ancestral approximations include those of the Southern Caucasus and interestingly, South and Central Asia. Western Europe tends to be a mix of early farmers and western/eastern hunter-gatherers while Middle Eastern genomes are described as a mix of early farmers and Africans.

Figure 5. Lowest admixture f₃-statistics of the form f₃ (X, Y; Yamnaya).

These statistics represent the Yamnaya as a mix of two populations with a more negative result signifying the more likely admixture event. (a). All negative statistics found for the test f₃(X, Y; Yamnaya) with the most negative result f₃(CHG, EHG; Yamnaya) highlighted in purple. Lines bisecting the points show the standard error. (b). The most significantly negative statistics which are highlighted by the yellow box in a. Greatest support is found for Yamnaya being a mix of Caucasus hunter-gatherers (CHG) and Russian hunter-gatherers who belong to an eastern extension of the WHG clade (EHG).