Was the Maikop culture the PIE homeland?

Between 10,000-9,000 BCE, humans began practicing agriculture in the Near East1. In the ensuing five millennia, plants and animals domesticated in the Near East spread throughout West Eurasia (a vast region that also includes Europe) and beyond. The relative homogeneity of present-day West Eurasians in a world context2 suggests the possibility of extensive migration and admixture that homogenized geographically and genetically disparate sources of ancestry. The spread of the world's first farmers from the Near East would have been a mechanism for such homogenization. To date, however, due to the poor preservation of DNA in warm climates, it has been impossible to study the population structure and history of the first farmers and to trace their contribution to later populations.

In order to overcome the obstacle of poor DNA preservation, we took advantage of two methodological developments. First, we sampled from the inner ear region of the petrous bone3,4 that can yield up to ~100 times more endogenous DNA than other skeletal elements4. Second, we used in-solution hybridization5 to enrich extracted DNA for about 1.2 million single nucleotide polymorphism (SNP) targets6,7, making efficient sequencing practical by filtering out microbial and non-informative human DNA. We merged all sequences extracted from each individual, and randomly sampled a single sequence with minimum mapping and sequence quality to represent each SNP, restricting to individuals with at least 9,000 SNPs covered at least once (Methods). We obtained genome-wide data passing quality control for 45 individuals on whom we had a median coverage of 172,819 SNPs. We assembled radiocarbon dates for 26 individuals (22 new generated for this study) (Supplementary Data Table 1).

The newly reported ancient individuals date to ~12,000-1,400 BCE and come from the southern Caucasus (Armenia), northwestern Anatolia (Turkey), Iran, and the southern Levant (Israel and Jordan) (Supplementary Data Table 1, Fig. 1a). (One individual had a radiocarbon date that was not in agreement with the date of its archaeological context and was also a genetic outlier.) The samples include Epipaleolithic Natufian hunter-gatherers from Raqefet Cave in the Levant (12,000-9,800 BCE); a likely Mesolithic individual from Hotu Cave in the Alborz mountains of Iran (probable date of 9,100-8,600 BCE); Pre-Pottery Neolithic farmers from ‘Ain Ghazal and Motza in the southern Levant (8,300-6,700 BCE); and early farmers from Ganj Dareh in the Zagros mountains of western Iran (8,200-7,600 BCE). The samples also include later Neolithic, Chalcolithic (~4,800-3,700 BCE), and Bronze Age (~3,350-1,400 BCE) individuals (Supplementary Information, section 1). We combined our data with previously published ancient data7,8,9,10,8,10-15 to form a dataset of 281 ancient individuals. We then further merged with 2,583 present-day people genotyped on the Affymetrix Human Origins array13,16 (238 new) (Supplementary Data Table 2; Supplementary Information, section 2). We grouped the ancient individuals based on archaeological culture and chronology (Fig. 1a; Supplementary Data Table 1). We refined the grouping based on patterns evident in Principal Components Analysis (PCA)17 (Fig. 1b; Extended Data Fig. 1), ADMIXTURE model-based clustering18 (Extended Data Fig. 2a), and ‘outgroup’ f3-analysis (Extended Data Fig. 3). We used f4-statistics to identify outlier individuals and to cluster phylogenetically indistinguishable groups into ‘Analysis Labels’ (Supplementary Information, section 3).


Figure 1
Genetic structure of ancient West Eurasia
(a) Sampling locations and times in six regions. Sample sizes for each population are given below each bar. Abbreviations used: E: Early, M: Middle, L: Late, HG: Hunter-Gatherer, N: Neolithic, ChL: Chalcolithic, BA: Bronze Age, IA: Iron Age. (b) Principal components analysis of 991 present-day West Eurasians (grey points) with 278 projected ancient samples (excluding the Upper Paleolithic Ust’-Ishim, Kostenki14, and MA1). To avoid visual clutter, population labels of present-day individuals are shown in Extended Data Fig. 1.

We analyzed these data to address six questions. (1) Previous work has shown that the first European farmers harboured ancestry from a Basal Eurasian lineage that diverged from the ancestors of north Eurasian hunter-gatherers and East Asians before they separated from each other13. What was the distribution of Basal Eurasian ancestry in the ancient Near East? (2) Were the first farmers of the Near East part of a single homogeneous population, or were they regionally differentiated? (3) Was there continuity between late pre-agricultural hunter-gatherers and early farming populations, or were the hunter-gatherers largely displaced by a single expansive population as in early Neolithic Europe?8 (4) What is the genetic contribution of these early Near Eastern farmers to later populations of the Near East? (5) What is the genetic contribution of the early Near Eastern farmers to later populations of mainland Europe, the Eurasian steppe, and to populations outside West Eurasia? (6) Do our data provide broader insights about population transformations in West Eurasia?


Figure 2
Basal Eurasian ancestry explains the reduced Neanderthal admixture in West Eurasians
Basal Eurasian ancestry estimates are negatively correlated to a statistic measuring Neanderthal ancestry f4(Test, Mbuti; Altai, Denisovan).

West Eurasians harbour significantly less Neanderthal ancestry than East Asians19-21, which could be explained if West Eurasians (but not East Asians) have partial ancestry from a source diluting their Neanderthal inheritance22. Supporting this theory, we observe a negative correlation between Basal Eurasian ancestry and the rate of shared alleles with Neanderthals19 (Supplementary Information, section 5; Fig. 2). By extrapolation, we infer that the Basal Eurasian population had lower Neanderthal ancestry than non-Basal Eurasian populations and possibly none (ninety-five percent confidence interval truncated at zero of 0-60%; Fig. 2; Methods). The finding of little if any Neanderthal ancestry in Basal Eurasians could be explained if the Neanderthal admixture into modern humans 50,000-60,000 years ago11 largely occurred after the splitting of the Basal Eurasians from other non-Africans.

It is striking that the highest estimates of Basal Eurasian ancestry are from the Near East, given the hypothesis that it was there that most admixture between Neanderthals and modern humans occurred19,23. This could be explained if Basal Eurasians thoroughly admixed into the Near East before the time of the samples we analyzed but after the Neanderthal admixture. Alternatively, the ancestors of Basal Eurasians may have always lived in the Near East, but the lineage of which they were a part did not participate in the Neanderthal admixture.

A population without Neanderthal admixture, basal to other Eurasians, may have plausibly lived in Africa. Craniometric analyses have suggested an affinity between the Natufians and populations of north or sub-Saharan Africa24,25, a result that finds some support from Y chromosome analysis which shows that the Natufians and successor Levantine Neolithic populations carried haplogroup E, of likely ultimate African origin, which has not been detected in other ancient males from West Eurasia (Supplementary Information, section 6) 7,8. However, no affinity of Natufians to sub-Saharan Africans is evident in our genome-wide analysis, as present-day sub-Saharan Africans do not share more alleles with Natufians than with other ancient Eurasians (Extended Data Table 1). (We could not test for a link to present-day North Africans, who owe most of their ancestry to back-migration from Eurasia26,27.) The idea of Natufians as a vector for the movement of Basal Eurasian ancestry into the Near East is also not supported by our data, as the Basal Eurasian ancestry in the Natufians (44±8%) is consistent with stemming from the same population as that in the Neolithic and Mesolithic populations of Iran, and is not greater than in those populations (Supplementary Information, section 4). Further insight into the origins and legacy of the Natufians could come from comparison to Natufians from additional sites, and to ancient DNA from north Africa.

Figure 1: Genetic structure of ancient Europe.

Deep coalescence of early Holocene lineages
The geographical proximity of the Southern Caucasus to the Levant begs the question of whether CHG might be related to early Neolithic farmers with Near Eastern heritage. To address this question formally we reconstructed the relationship among WHG, CHG and EF using available high-quality ancient genomes1,3. We used outgroup f3-statistics14 to compare the three possible topologies, with the correct relationship being characterized by the largest amount of shared drift between the two groups that form a clade with respect to the outgroup (Fig. 2a; Supplementary Note 4). A scenario in which the population ancestral to both CHG and EF split from WHG receives the highest support, implying that CHG and EF form a clade with respect to WHG. We can reject a scenario in which CHG and WHG form a distinct clade with respect to EF. The known admixture of WHG with EF1,3,4,5 implies that some shared drift is found between WHG and EF with respect to CHG, but this is much smaller than the shared drift between CHG and EF. Thus, WHG split first, with CHG and EF separating only at a later stage.


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

We next dated the splits among WHG, CHG and EF using a coalescent model implemented with G-PhoCS15 based on the high-coverage genomes in our data set (Fig. 2b for a model using the German farmer Stuttgart1 to represent EF; and Supplementary Table 5 for models using the Hungarian farmer NE1 (ref. 3)) and taking advantage of the mutation rate recently derived from Ust’-Ishim10. G-Phocs dates the split between WHG and the population ancestral to CHG and EF at ∼40–50 kya (range of best estimates depending on which genomes are used; see Supplementary Table 5 and Supplementary Note 5 for details), implying that they diverged early on during the colonisation of Europe16, and well before the LGM. On the WHG branch, the split between Bichon and Loschbour1 is dated to ∼16–18 kya (just older than the age of Bichon), implying continuity in western Europe, which supports the conclusions from our previous analyses. The split between CHG and EF is dated at ∼20–30 kya emerging from a common basal Eurasian lineage1 (Supplementary Fig. 2) and suggesting a possible link with the LGM, although the broad confidence intervals require some caution with this interpretation. In any case, the sharp genomic distinctions between these post-LGM populations contrasts with the comparative lack of differentiation between the earlier Eurasian genomes, for example, as visualized in the ADMIXTURE analysis (Fig. 1a), and it seems likely that this structure emerged as a result of ice age habitat restriction. Like EF, but in contrast to WHG, CHG carry a variant of the SLC24A5 gene17 associated with light skin colour (rs1426654, see Supplementary Note 6). This trait, which is believed to have risen to high frequency during the Neolithic expansion18, may thus have a relatively long history in Eurasia, with its origin probably predating the LGM.

A partial genome from a 24,000-year-old individual (MA1) from Mal’ta, Siberia6 had been shown to be divergent from other ancient samples and was shown by Lazaridis et al.1, using f4 statistics, to have more shared alleles with nearly all modern Europeans than with an EF genome. This allowed inference of an ANE component in European ancestry, which was subsequently shown to have an influence in later eastern hunter-gatherers and to have spread into Europe via an incursion of Steppe herders beginning ∼4,500 years ago5,7. Several analyses indicate that CHG genomes are not a subset of this ANE lineage. First, MA1 and CHG plot in distinct regions of the PCA and also have very different profiles in the ADMIXTURE analysis (Fig. 1). Second, when we test if CHG shows any evidence of excess allele sharing with MA1 relative to WHG using tests of the form D(Yoruba, CHG; MA1, WHG) no combinations were significantly positive (Supplementary Table 6). Last, we also tested whether the ancestral component inferred in modern Europeans from MA1 was distinct from any that may have been donated from CHG using tests of the form D(Yoruba, MA1; CHG, modern North European population) (Supplementary Table 7). All northern Europeans showed a significant sharing of alleles with MA1 separate to any they shared with CHG.