The genetics of an early Neolithic pastoralist from the Zagros, Iran

Abstract

The agricultural transition profoundly changed human societies. We sequenced and analysed the first genome (1.39x) of an early Neolithic woman from Ganj Dareh, in the Zagros Mountains of Iran, a site with early evidence for an economy based on goat herding, ca. 10,000 BP. We show that Western Iran was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus, but distinct from the Neolithic Anatolian people who later brought food production into Europe. The inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, suggesting those of the Central Zagros were somewhat isolated from other populations of the Fertile Crescent. Runs of homozygosity are of a similar length to those from Neolithic farmers, and shorter than those of Caucasus and Western Hunter-Gatherers, suggesting that the inhabitants of Ganj Dareh did not undergo the large population bottleneck suffered by their northern neighbours. While some degree of cultural diffusion between Anatolia, Western Iran and other neighbouring regions is possible, the genetic dissimilarity between early Anatolian farmers and the inhabitants of Ganj Dareh supports a model in which Neolithic societies in these areas were distinct.

Figure 1. GD13a appears to be related to Caucasus Hunter Gatherers and to modern South Asian populations.

(A) PCA loaded on modern populations (represented by open symbols). Ancient individuals (solid symbols) are projected onto these axes. (B) Outgroup f₃(X, GD13a; Dinka), where Caucasus Hunter Gatherers (Kotias and Satsurblia) share the most drift with GD13a. Ancient samples have filled circles whereas modern populations are represented by empty symbols. (C) ADMIXTURE using K = 17, where GD13a appears very similar to Caucasus Hunter Gatherers, and to a lesser extent to modern south Asian populations.

Figure 2. GD13a did not undergo a recent large population bottleneck.

(A) GD13a has similar runs of homozygosity (ROH) lengths to Neolithic individuals, while Caucasus Hunter Gatherers (Kotias and Satsurblia), like European Hunter Gatherers (Loschbour and Bichon), underwent recent large population bottlenecks potentially associated withthe LGM. (B) Map showing geographical location of Anatolian Neolithic samples, Caucasus Hunter Gatherers (CHG) and GD13a. Background colours indicate mean temperature (°C) of coldest quarter during the LGM (data from the worldclim database60 generated by the CCSM4 model), with LGM sea levels. Map of populations was generated with MATLAB R2015b (Mathworks, http://www.mathworks.com/).