Genomic insights into the origin of farming in the ancient Near East

Abstract

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.

Extended Data Figure 1. Principal components analysis of 991 present-day West Eurasians

The PCA analysis is performed on the same set of individuals as are reported in Fig. 1b, using EIGENSOFT. Here, we color 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

(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 F_ST 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

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 ones admixed with steppe ancestry; populations from the Levant from the Epipaleolithic (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

We measure differentiation by F_ST. 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

(a) Levantine ancestry in Eastern Africa in the Human Origins dataset, (b) Levantine ancestry in different Eastern African population in the dataset of Pagani et al. (2012); the remainder of the ancestry is a clade with Mota, a ~4,500 year old sample from Ethiopia. (c) EHG ancestry in Eastern Eurasians, or (d) Afontova Gora (AG2) 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 6

Inferred position of ancient populations in West Eurasian PCA according to the model of Fig. 4.

Extended Data Figure 7. Admixture from ghost populations using ‘cline intersection’

We model each Test population (purple) in panels (a-f) 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 Mota 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

EHG, and Upper Paleolithic 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).

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.

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).

Figure 3. Genetic differentiation and its dramatic decrease over time in West Eurasia

Pairwise F_ST distribution among populations belonging to four successive time slices in West Eurasia; the median (red) and range of F_ST is shown.

Figure 4. Modelling ancient West Eurasians, East Africans, East Eurasians and South Asians

(a) All the ancient populations can be modelled as mixtures of two or three other populations and up to four proximate sources (marked in colour). Mixture proportions inferred by qpAdm are indicated by the incoming arrows to each population. Clouds represent sets of more than one population. Multiple admixture solutions are consistent with the data for some populations, and while only one solution is shown here, Supplementary Information, section 7 presents the others. (b) A flat representation of the graph showing mixture proportions from the four proximate sources.