We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter–gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter–gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter–gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.
European Nucleotide Archive
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Extended data figures and tables
Extended Data Figures
- Extended Data Figure 1: Principal components analysis of 991 present-day West Eurasians. (385 KB)
The PCA analysis is performed on the same set of individuals as are reported in Fig. 1b, using EIGENSOFT. Here, we colour the samples by population (to highlight the present-day populations) instead of using grey points as in Fig. 1b (where the goal is to highlight ancient samples).
- Extended Data Figure 2: Genetic structure in ancient West Eurasian populations across time and decline of genetic differentiation over time. (333 KB)
a, ADMIXTURE model-based clustering analysis of 2,583 present-day humans and 281 ancient samples; we show the results only for ancient samples for K = 11 clusters. b, Pairwise FST between 19 Ancient West Eurasian populations (arranged in approximate chronological order), and select present-day populations.
- Extended Data Figure 3: Outgroup f3(Mbuti; X, Y) for pairs of ancient populations. (296 KB)
The dendrogram is plotted for convenience and should not be interpreted as a phylogenetic tree. Areas of high shared genetic drift are ‘yellow’ and include from top-right to bottom-left along the diagonal: early Anatolian and European farmers; European hunter–gatherers, Steppe populations and populations admixed with steppe ancestry; populations from the Levant from the Epipalaeolithic (Natufians) to the Bronze Age; populations from Iran from the Mesolithic to the Late Neolithic.
- Extended Data Figure 4: Reduction of genetic differentiation in West Eurasia over time. (177 KB)
We measure differentiation by FST. Each column of the 5 × 5 matrix of plots represents a major region and each row the earliest population with at least two individuals from each major region.
- Extended Data Figure 5: West Eurasian related admixture in East Africa, Eastern Eurasia and South Asia. (315 KB)
a, Levantine ancestry in Eastern Africa in the Human Origins dataset. b, Levantine ancestry in different Eastern African population in the dataset from Pagani et al. (2012); the remainder of the ancestry is a clade with Mota, a ~4,500 year old sample from Ethiopia49. c, EHG ancestry in Eastern Eurasians. d, Afontova Gora (AG2)-related ancestry in Eastern Eurasians; the remainder of their ancestry is a clade with Onge. e, Mixture proportions for South Asian populations showing that they can be modelled as having West Eurasian-related ancestry similar to that in populations from both the Eurasian steppe and Iran.
- Extended Data Figure 7: Admixture from ghost populations using ‘cline intersection’. (246 KB)
a–f, We model each Test population (purple) as a mixture (pink) of a fixed reference population (blue) and a ghost population (orange) residing on the cline defined by two other populations (red and green) according to the visualization method of Supplementary Information, section 10. a, Early/Middle Bronze Age steppe populations are a mixture of Iran_ChL and a population on the WHG→SHG cline. b, Scandinavian hunter–gatherers (SHG) are a mixture of WHG and a population on the Iran_ChL→Steppe_EMBA cline. c, Caucasus hunter–gatherers (CHG) are a mixture of Iran_N and both WHG and EHG. d, Late Neolithic/Bronze Age Europeans are a mixture of the preceding Europe_MNChL population and a population with both EHG and Iran_ChL ancestry. e, Somali are a mixture of Mota49 and a population on the Iran_ChL→Levant_BA cline. f, Eastern European hunter–gatherers (EHG) are a mixture of WHG and a population on the Onge→Han cline.
- Extended Data Figure 8: Admixture from a ‘ghost’ ANE population into both European and Eastern Eurasian ancestry. (118 KB)
EHG, and Upper Palaeolithic Siberians Mal’ta 1 (MA1) and Afontova Gora 2 (AG2) are positioned near the intersection of clines formed by European hunter–gatherers (WHG, SHG, EHG) and Eastern non-Africans in the space of outgroup f3-statistics of the form f3(Mbuti; Papuan, Test) and f3(Mbuti; Switzerland_HG, Test).
Extended Data Tables
- Supplementary Table 1 (65 KB)
This file contains Supplementary Data Table 1.
- Supplementary Table 2 (23 KB)
This file contains Supplementary Data Table 2.
- Supplementary Table 3 (60 KB)
This file contains Supplementary Data Table 3.
- Supplementary Information (9.8 MB)
This file contains Supplementary Text, Data and References – see contents page for details.