Early Neolithic genomes from the eastern Fertile Crescent

Abstract

We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed substantially to the ancestry of modern Europeans. These people are estimated to have separated from Early Neolithic farmers in Anatolia some 46,000 to 77,000 years ago and show affinities to modern-day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians. We conclude that multiple, genetically differentiated hunter-gatherer populations adopted farming in southwestern Asia, that components of pre-Neolithic population structure were preserved as farming spread into neighboring regions, and that the Zagros region was the cradle of eastward expansion.

Fig 1. Map of prehistoric Neolithic and Iron Age Zagros genome locations.

Colors indicate isochrones with numbers giving approximate arrival times of the Neolithic culture in years BCE.

Fig 2. PCA plot of Zagros, European, and Near and Middle Eastern ancient genomes.

Comparing ancient and modern genomes, Neolithic Zagros genomes form a distinct genetic cluster close to modern Pakistani and Afghan genomes but distinct from other Neolithic farmers and European hunter-gatherers. See Animation S1 for an interactive 3D version of the PCA including the third principal component.

Fig 3. Level and structure of ancient genomic diversity.

(A) Total length of the genome in different ROH classes; shades indicate the range observed among modern samples from different populations and lines indicate the distributions for ancient samples. (B) The total length of short (<1.6Mb) vs long (≥1.6Mb) ROH. (C) Distribution of heterozygosity (θ) inferred in 1Mb windows along a portion of chromosome 3 showing the longest ROH segment in WC1. Solid lines represent the MLE estimate, shades indicate the 95% confidence intervals and dashed lines the genome-wide median for each sample. (D) Distribution of heterozygosity (θ) estimated in 1Mb windows across the autosomes for modern and ancient samples. (E) Similarity in the pattern of heterozygosity (θ) along the genome as obtained by a PCA on centered Spearman correlations. Ancient - Bich: Bichon, Upper Palaeolithic forager from Switzerland; KK1: Kotias, Mesolithic forager from Georgia; WC1: Wezmeh Cave, Early Neolithic farmer from Zagros; Mota: 4,500 year old individual from Ethiopia; BR2: Ludas-Varjú-dúló, Late Bronze Age individual from Hungary. Modern - YRI: Yoruban, W-Africa; TSI: Tuscans, Italy; PJL: Punjabi, Pakistan; GBR: British

Fig 4. Modern-day peoples with affinity to WC1.

Modern groups with an increasingly higher (respectively lower) inferred proportion of haplotype sharing with the Iranian Neolithic Wezmeh Cave (WC1, 7,455-7,082 cal BCE, blue triangle) compared to the Anatolian Neolithic Barcın genome (Bar8; 6,212–6,030 cal BCE, red triangle) are depicted with an increasingly stronger blue color (respectively red color). Circle sizes illustrate the relative absolute proportion of this difference between WC1 versus Bar8. The key for the modern group labels is provided in Table S24.