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The agricultural transition started in a region comprising the Ancient Near East and Anatolia ~12,000 years ago with the first Pre-Pottery Neolithic villages and the first domestication of cereals and legumes1,2. Archaeological evidence suggests a complex scenario of multiple domestications in a number of areas3, coupled with examples of trade4. Ancient DNA (aDNA) has revealed that this cultural package was later brought into Europe by dispersing farmers from Anatolia (so called ‘demic’ diffusion, as opposed to non-demic cultural diffusion5,6) ~8,400 years ago. However a lack of aDNA from early Neolithic individuals from the Near East leaves a key question unanswered: was the agricultural transition developed by one major population group spanning the Near East, including Anatolia and the Central Zagros Mountains; or was the region inhabited by genetically diverse populations, as is suggested by the heterogeneous mode and timing of the appearance of early domesticates at different localities?
To answer this question, we sequenced the genome of an early Neolithic female from Ganj Dareh, GD13a, from the Central Zagros (Western Iran), dated to 10000-9700 cal BP7, a region located at the eastern edge of the Near East. Ganj Dareh is well known for providing the earliest evidence of herd management of goats beginning at 9,900 BP7,8,9. It is a classic mound site at an altitude of ~1400 m in the Gamas-Ab Valley of the High Zagros zone in Kermanshah Province, Western Iran. It was discovered in the 1960s during survey work and excavated over four seasons between 1967 and 1974. The mound, ~40 m in diameter, shows 7 to 8 m of early Neolithic cultural deposits. Five major levels were found, labelled A through E from top to bottom. Extended evidence showed a warren of rooms with evidence of under-floor inhumations within what may be burial chambers and/or disused houses10. The current Minimum Number of Individuals is 116, with 56 catalogued as skeletons that had four or more bones recovered11. The individual analysed here was part of burial 13, which contained three individuals, and was recovered in level C in 1971 from the floor of a brick-walled structure. The individual sampled, 13A (referred to as GD13a throughout the text), was a 30–50 year old female; the other individuals in the burial unit were a second adult (13B) and an adolescent (13).
The site has been directly dated to 9650–9950 cal BP7, and shows intense occupation over two to three centuries. The economy of the population was that of pastoralists with an emphasis on goat herding7. Archaeobotanical evidence is limited12 but the evidence present is for two-row barley with no evidence for wheat, rye or other domesticates. This implies that the overall economy was at a much earlier stage in the development of cereal agriculture than that found in the Levant, Anatolia and Northern Mesopotamian basin.
The petrous bone of GD13a yielded sequencing libraries comprising 18.57% alignable human reads that were used to generate 1.39-fold genome coverage. The sequence data showed read lengths and nucleotide misincorporation patterns indicative of post-mortem damage, and had low contamination estimates (<1%, see Supplementary Fig. S3). The mitochondrion of GD13a (91.74X) was assigned to haplogroup X, most likely to the subhaplogroup X2, which has been associated with an early expansion from the Near East13,14 and has been found in early Neolithic samples from Anatolia5, Hungary15 and Germany16.
We compared GD13a with a number of other ancient genomes and modern populations6,15,16,17,18,19,20,21,22,23,24,25,26,27, using principal component analysis (PCA)28, ADMIXTURE29 and outgroup f3 statistics30 (Fig. 1). GD13a did not cluster with any other early Neolithic individual from Eurasia in any of the analyses. ADMIXTURE and outgroup f3 statistics identified Caucasus Hunter-Gatherers of Western Georgia, just north of the Zagros mountains, as the group genetically most similar to GD13a (Fig. 1B,C), whilst PCA also revealed some affinity with modern Central South Asian populations such as Balochi, Makrani and Brahui (Fig. 1A and Fig. S4). Also genetically close to GD13a were ancient samples from Steppe populations (Yamanya & Afanasievo) that were part of one or more Bronze age migrations into Europe, as well as early Bronze age cultures in that continent (Corded Ware)16,21, in line with previous relationships observed for the Caucasus Hunter-Gatherers24.
To better understand the history of the population to which GD13a belonged, we investigated the distribution of lengths of runs of homozygosity (ROH) (Fig. 2A). A bias towards a high frequency of both long and short ROH is indicative of past strong bottlenecks followed by population re-expansion. GD13a has a distribution with few long ROH (>2 Mb), similar to that of the descendants of Anatolian early farmers (represented by the European farmers NE115 and Stuttgart17). In contrast, both Western17 and Caucasus Hunter-Gatherers24 have relatively more long as well as short ROH. Thus, GD13a is the descendant of a group that had relatively stable demography and did not suffer the bottlenecks that affected more northern populations.
The phenotypic attributes of GD13a are similar to the neighbouring Anatolian early farmers and Caucasus Hunter-Gatherers. Based on diagnostic SNPs, she had dark, black hair and brown eyes (see Supplementary). She lacked the derived variant (rs16891982) of the SLC45A2 gene associated with light skin pigmentation but likely had at least one copy of the derived SLC24A5 allele (rs1426654) associated with the same trait. The derived SLC24A5 variant has been found in both Neolithic farmer and Caucasus Hunter-Gatherer groups5,15,24 suggesting that it was already at appreciable frequency before these populations diverged. Finally, she did not have the most common European variant of the LCT gene (rs4988235) associated with the ability to digest raw milk, consistent with the later emergence of this adaptation5,15,21.
There is more to this study and I had to delete a paragraph to meet the character quota.
To answer this question, we sequenced the genome of an early Neolithic female from Ganj Dareh, GD13a, from the Central Zagros (Western Iran), dated to 10000-9700 cal BP7, a region located at the eastern edge of the Near East. Ganj Dareh is well known for providing the earliest evidence of herd management of goats beginning at 9,900 BP7,8,9. It is a classic mound site at an altitude of ~1400 m in the Gamas-Ab Valley of the High Zagros zone in Kermanshah Province, Western Iran. It was discovered in the 1960s during survey work and excavated over four seasons between 1967 and 1974. The mound, ~40 m in diameter, shows 7 to 8 m of early Neolithic cultural deposits. Five major levels were found, labelled A through E from top to bottom. Extended evidence showed a warren of rooms with evidence of under-floor inhumations within what may be burial chambers and/or disused houses10. The current Minimum Number of Individuals is 116, with 56 catalogued as skeletons that had four or more bones recovered11. The individual analysed here was part of burial 13, which contained three individuals, and was recovered in level C in 1971 from the floor of a brick-walled structure. The individual sampled, 13A (referred to as GD13a throughout the text), was a 30–50 year old female; the other individuals in the burial unit were a second adult (13B) and an adolescent (13).
The site has been directly dated to 9650–9950 cal BP7, and shows intense occupation over two to three centuries. The economy of the population was that of pastoralists with an emphasis on goat herding7. Archaeobotanical evidence is limited12 but the evidence present is for two-row barley with no evidence for wheat, rye or other domesticates. This implies that the overall economy was at a much earlier stage in the development of cereal agriculture than that found in the Levant, Anatolia and Northern Mesopotamian basin.
The petrous bone of GD13a yielded sequencing libraries comprising 18.57% alignable human reads that were used to generate 1.39-fold genome coverage. The sequence data showed read lengths and nucleotide misincorporation patterns indicative of post-mortem damage, and had low contamination estimates (<1%, see Supplementary Fig. S3). The mitochondrion of GD13a (91.74X) was assigned to haplogroup X, most likely to the subhaplogroup X2, which has been associated with an early expansion from the Near East13,14 and has been found in early Neolithic samples from Anatolia5, Hungary15 and Germany16.
We compared GD13a with a number of other ancient genomes and modern populations6,15,16,17,18,19,20,21,22,23,24,25,26,27, using principal component analysis (PCA)28, ADMIXTURE29 and outgroup f3 statistics30 (Fig. 1). GD13a did not cluster with any other early Neolithic individual from Eurasia in any of the analyses. ADMIXTURE and outgroup f3 statistics identified Caucasus Hunter-Gatherers of Western Georgia, just north of the Zagros mountains, as the group genetically most similar to GD13a (Fig. 1B,C), whilst PCA also revealed some affinity with modern Central South Asian populations such as Balochi, Makrani and Brahui (Fig. 1A and Fig. S4). Also genetically close to GD13a were ancient samples from Steppe populations (Yamanya & Afanasievo) that were part of one or more Bronze age migrations into Europe, as well as early Bronze age cultures in that continent (Corded Ware)16,21, in line with previous relationships observed for the Caucasus Hunter-Gatherers24.
To better understand the history of the population to which GD13a belonged, we investigated the distribution of lengths of runs of homozygosity (ROH) (Fig. 2A). A bias towards a high frequency of both long and short ROH is indicative of past strong bottlenecks followed by population re-expansion. GD13a has a distribution with few long ROH (>2 Mb), similar to that of the descendants of Anatolian early farmers (represented by the European farmers NE115 and Stuttgart17). In contrast, both Western17 and Caucasus Hunter-Gatherers24 have relatively more long as well as short ROH. Thus, GD13a is the descendant of a group that had relatively stable demography and did not suffer the bottlenecks that affected more northern populations.
The phenotypic attributes of GD13a are similar to the neighbouring Anatolian early farmers and Caucasus Hunter-Gatherers. Based on diagnostic SNPs, she had dark, black hair and brown eyes (see Supplementary). She lacked the derived variant (rs16891982) of the SLC45A2 gene associated with light skin pigmentation but likely had at least one copy of the derived SLC24A5 allele (rs1426654) associated with the same trait. The derived SLC24A5 variant has been found in both Neolithic farmer and Caucasus Hunter-Gatherer groups5,15,24 suggesting that it was already at appreciable frequency before these populations diverged. Finally, she did not have the most common European variant of the LCT gene (rs4988235) associated with the ability to digest raw milk, consistent with the later emergence of this adaptation5,15,21.
There is more to this study and I had to delete a paragraph to meet the character quota.