Genetic Structure of the World's First Farmers

Anatolian farmers first emerged in history in the Mesolithic era and they subsequently expanded in all directions from Europe and South Asia. The Göbekli Tepe site may be associated with Chalcolithic Anatolians who belonged to haplogroup L1a (Lazaridis et al. 2016). L1a, which is common in India and Pakistan (15%), also appears at low frequencies (2-4%) in the Northern part of the Middle East, where the Göbekli Tepe site is located. "The genetic structure of the world’s first farmers" was just published online last week. It concludes that the early farmers of mainland Europe were descended from a population related to Neolithic northwestern Anatolians, which is consistent with an Anatolian origin of farming in Europe.




Extreme regional differentiation in the ancient Near East PCA on present-day West Eurasian populations (Methods) (Extended Data Fig. 1) on which we projected the ancient individuals (Fig. 1b) replicates previous findings of a Europe-Near East contrast along the horizontal Principal Component 1 (PC1) and parallel clines (PC2) in both Europe and the Near East (Extended Data Fig. 1)7,8,13. Ancient samples from the Levant project at one end of the Near Eastern cline, and ancient samples from Iran at the other. The two Caucasus Hunter Gatherers (CHG)9 are less extreme along PC1 than the Mesolithic and Neolithic individuals from Iran, while individuals from Chalcolithic Anatolia, Iran, and Armenia, and Bronze Age Armenia occupy intermediate positions. Qualitatively, the PCA has the appearance of a quadrangle whose four corners are some of the oldest samples: bottom-left: Western Hunter Gatherers (WHG), top-left: Eastern Hunter Gatherers (EHG), bottom-right: Neolithic Levant and Natufians, top-right: Neolithic Iran.



Our data document continuity across the hunter-gatherer / farming transition, separately in the southern Levant and in the southern Caucasus-Iran highlands. The qualitative evidence for this is that PCA, ADMIXTURE, and outgroup f3 analysis cluster Levantine hunter-gatherers (Natufians) with Levantine farmers, and Iranian and Caucasus Hunter Gatherers with Iranian farmers (Fig. 1b; Extended Data Fig. 1; Extended Data Fig. 2). We confirm this in the Levant by showing that its early farmers share significantly more alleles with Natufians than with the early farmers of Iran: the statistic f4(Levant_N, Chimp; Natufian, Iran_N) is significantly positive (Z=13.6). The early farmers of the Caucasus-Iran highlands similarly share significantly more alleles with the hunter-gatherers of this region than with the early farmers from the Levant: the statistic f4(Iran_N, Chimp; Caucasus or Iran highland hunter-gatherers, Levant_N) is significantly positive (Z>6).



Among first farmers, those of the Levant trace ~2/3 of their ancestry to people related to Natufian hunter-gatherers and ~1/3 to people related to Anatolian farmers (Supplementary Information, section 7). Western Iranian first farmers cluster with the likely Mesolithic HotuIIIb individual and more remotely with hunter-gatherers from the southern Caucasus (Fig. 1b), and share alleles at an equal rate with Anatolian and Levantine early farmers (Supplementary Information, section 7), highlighting the long-term isolation of western Iran.



During subsequent millennia, the early farmer populations of the Near East expanded in all directions and mixed, as we can only model populations of the Chalcolithic and subsequent Bronze Age as having ancestry from two or more sources. The Chalcolithic people of western Iran can be modelled as a mixture of the Neolithic people of western Iran, the Levant, and Caucasus Hunter Gatherers (CHG), consistent with their position in the PCA (Fig. 1b). Admixture from populations related to the Chalcolithic people of western Iran had a wide impact, consistent with contributing ~44% of the ancestry of Levantine Bronze Age populations in the south and ~33% of the ancestry of the Chalcolithic northwest Anatolians in the west. Our analysis show that the ancient populations of the Chalcolithic Iran, Chalcolithic Armenia, Bronze Age Armenia and Chalcolithic Anatolia were all composed of the same ancestral components, albeit in slightly different proportions (Fig. 4b; Supplementary Information, section 7).



Admixture did not only occur within the Near East but extended towards Europe. To the north, a population related to people of the Iran Chalcolithic contributed ~43% of the ancestry of early Bronze Age populations of the steppe. The spread of Near Eastern ancestry into the Eurasian steppe was previously inferred7 268 without access to ancient samples, by hypothesizing a population related to present-day Armenians as a source7,8. To the west, the early farmers of mainland Europe were descended from a population related to Neolithic northwestern Anatolians8. This is consistent with an Anatolian origin of farming in Europe but does not reject other sources, since the spatial distribution of the Anatolian/European-like farmer populations is unknown. We can rule out the hypothesis that European farmers stem directly from a population related to the ancient farmers of the southern Levant30,31.



In South Asia, our dataset provides insight into the sources of Ancestral North Indians (ANI), a West Eurasian related population that no longer exists in unmixed form but contributes a variable amount of the ancestry of South Asians35,36 (Supplementary Information, section 9) (Extended Data Fig. 4). We show that it is impossible to model the ANI as being derived from any single ancient population in our dataset. However, it can be modelled as a mix of ancestry related to both early farmers of western Iran and to people of the Bronze Age Eurasian steppe; all sampled South Asian groups are inferred to have significant amounts of both ancestral types. The demographic impact of steppe related populations on South Asia was substantial, as the Mala, a south Indian population with minimal ANI along the ‘Indian Cline’ of such ancestry35,36 is inferred to have ~18% steppe-related ancestry, while the Kalash of Pakistan are inferred to have ~50%, similar to present-day northern Europeans7.



Applying this while withholding major populations, we validated some of our key inferences, successfully inferring mixture proportions consistent with those obtained when the populations are included in the analysis. Application of this methods highlights the impact of Ancient North Eurasian (ANE) ancestry related to the ~22,000 BCE Mal’ta 1 and ~15,000 BCE Afontova Gora 215 311 on populations living in Europe, the Americas, and Eastern Eurasia. Eastern Eurasians can be modelled as arrayed along a cline with different proportions of ANE ancestry (Supplementary Information, section 11; Extended Data Fig. 7), ranging from ~40% ANE in Native Americans matching previous findings13,15, to no less than ~5-10% ANE in diverse East 316 Asian groups including Han Chinese (Extended Data Fig. 4; Extended Data Fig. 6f). We also document a cline of ANE ancestry across the east-west extent of Eurasia. Eastern Hunter Gatherers (EHG) derive ~3/4 of their ancestry from the ANE (Supplementary Information,section 11); Scandinavian hunter-gatherers7,8,13 319 (SHG) are a mix of EHG and WHG; and WHG are a mix of EHG and the Upper Paleolithic Bichon from Switzerland (Supplementary Information, section 7). Northwest Anatolians—with ancestry from a population related to European hunter-gatherers (Supplementary Information, section 7)—are better modelled if this ancestry is taken as more extreme than Bichon (Supplementary Information, section 10).

doi: dx.doi.org/10.1101/059311