A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition

Abstract

Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and diet. We present 13 ancient genomes (c. 8500 to 7500 cal BCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Çayönü was a genetically diverse population, carrying mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organized along biological family lines. We document bodily interventions such as head shaping and cauterization among the individuals examined, reflecting Çayönü’s cultural ingenuity. Last, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesize that Upper Mesopotamia’s cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections.

Benchmarking kinship estimation tools for ancient genomes using pedigree simulations

“…In fact, in our own experience, READ results appear highly robust and reproducible compared to those of other tools (e.g. [2,29]). Another interesting observation was that KIN, which includes inference of both ROH and shared IBD segments using HMMs, did not perform much better than READ in accuracy.…”

Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean

“…This profile closely resembles that of ca. 8,500 BP Çatalhöyük, which suggests that putative eastern/southern gene flow into Central Anatolia 14 , 17 , 22 , 35 had taken place already by the late 10 th millennium BP, before the Ceramic Neolithic. Meanwhile, DATES 36 estimation of admixture times did not yield realistic or technically feasible results (Table IV in Document Z1).…”

“… 14 , 145 , 146 , 152 , 155 , 156 To model Anatolia Ottoman individuals, we also added Botai_EN to the right populations (Base12_Iran_Botai, Base12_CHG_Botai) (14 in total). In choosing “Right” populations we followed former studies 14 , 20 , 35 with some modifications to improve resolution.…”

Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria

“…For population genetics analyses, we used the following datasets: the Allen Ancient DNA Resource (AADR; Allen Ancient DNA Resource version 44.3); present-day Middle Easterners 20,32 , present-day worldwide populations from the Human Genome Diversity project (HGDP) 38 and from the Simons Genome Diversity Project 86 and previously published ancient individuals [10][11][12][13][14][15][16][17]30,[33][34][35]37,42,43,63,72, Where necessary, we converted the coordinates of the published data to the human genome assembly GRCh38 using CrossMapp v0.6.4 113 .…”

“…Around this time, an ancient Iranian-related component was introduced into the Levant 13,14 , followed by steppe/European-related ancestry in the Iron Age 15,16 . In the neighbouring region of Mesopotamia, the ancient DNA record is still sparse, and therefore the genetic composition of the local hunter-gatherers remains unknown, but recently published Pre-Pottery Neolithic (PPN) genomes from Upper Mesopotamia are genetically intermediate along the ancestry cline extending from ancient groups from Anatolia/Levant to Iran/Caucasus 12,17 .…”