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Post by Admin on May 9, 2022 18:06:17 GMT
Fig. 4. Testing temporal genetic change in Çayönü. Formal tests computed in the form of D(Yoruba, pop1; test, Boncuklu) where pop1 denotes CHG/Levant_N/Natufian/Zagros_N and test denotes radiocarbon-dated Çayönü individuals (Table 1), ordered from past to present in top to bottom direction, respectively. Horizontal bars represent ±2 standard errors. These observations overall support the notion that the Çayönü population had both historical and ongoing demographic connections with the neighbouring regions. Archaeologically, Çayönü shares a number of distinctive features with PPNA/PPNB settlements in the eastern wing of Neolithic Southwest Asia, particularly those in the Tigris and Euphrates basins and Northwest Zagros (Fig. 1B; Supplementary Table 1). These features include monumental architecture and/or special buildings, lithic types such as the “Çayönü tool”, and plain or winged marble bracelets (15, 20, 31, 32) (Supplementary Table 1). Another observation worth mentioning is the joint presence of both the pressure technique and bidirectional blade technologies at Çayönü, which were predominant in the eastern and western regions of Neolithic Southwest Asia, respectively (Supplementary Table 1). Obsidian network analyses further suggest close interactions between the Tigris and Zagros areas (29). We speculate that Çayönü’s east-west mixed ancestry and its possible openness to interregional human movement may have facilitated its observed wide-ranging material culture affinities and cultural dynamism. A pre-agriculture demographic shift in the “Fertile Crescent” Our dataset further allowed us to revisit a previous observation on the demographic impact of the Neolithic transition. It had been earlier reported that the Central Anatolian PPN (pre-agriculturalist) populations Aşıklı and Boncuklu had low levels of genetic diversity, similar to Upper Paleolithic and Mesolithic Europeans and Caucasians (8, 12). In comparison, Central Anatolian PN populations Tepecik-Çiftlik and Çatalhöyük, as well as West Anatolian and European Neolithic populations carried higher genetic diversity levels. This temporal increase in genetic diversity was attributed to the transition to farming and the consequent intensification of population movements and admixture ((8); also see (11)). Here we asked whether PPN populations of the “Fertile Crescent” sensu stricto, which comprises the main domestication centres of animals and plants in Southwest Asia, also had low genetic diversity levels similar to those of Central Anatolian PPN groups. Measuring genetic diversity using outgroup f3 values in genetic samples from Upper Mesopotamia (Çayönü), South Levant (Ain Ghazal) and Central Zagros (Ganj Dareh), we found that genetic samples from all three “Fertile Crescent” PPN settlements had high diversity levels, on a par with later-coming agriculturalists of Central and Western Anatolia PN, and significantly higher than those of Central Anatolia PPN (Fig. 5A, Supplementary Table 6).
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Post by Admin on May 9, 2022 20:02:35 GMT
Fig. 5. Genetic diversity in Neolithic Southwest Asia. (A) Small dots show pairwise genetic distance calculated as (1 - outgroup f3) values for all pairs of individuals, whereas large dots show the median values of each population. The vertical grey line represents the total median across the 8 populations. Deviation from the total median is shown with colored horizontal lines. Outgroup f3-statistics were computed as f3(Yoruba; ind1, ind2) where ind1 and ind2 represent individuals from the same archaeological site. (B) and (C) presents runs of homozygosity (ROH) in Southwest Asia. Sum of total ROH >4 cM and Number of total ROH >4 cM was shown on the x- and y-axes, respectively. The baseline (the red diagonal line) was computed using short ROH values (4-8 cM) in present-day West and Central Eurasian individuals to represent outbreed samples to determine the baseline. Panel is the zoomed version of Panel (B) in which we draw the zoomed area with grey rectangular. Red star point is the only Çayönü individual, namely cay007, that have more than 300,000 SNPs in the 1240K SNP Panel. The grey dots designate the ROH values for modern genomes. We further studied background population diversity through runs of homozygosity (ROH) analyses of one Çayönü genome (cay007) with sufficient coverage using the hapROH algorithm (33) and compared these with ROH distributions estimated in other early Holocene Southwest Asian genomes (Methods). As reported earlier (8, 12, 21, 23), Aşıklı, Boncuklu, and Caucasus pre-Neolithic genomes carried large numbers of ROH, indicative of small population size. Certain Neolithic genomes (e.g., WC1, Ash128) also showed a “right-shift” when plotting the number versus sum of ROHs, indicative of recent inbreeding (34) (Fig. 5B-C). In contrast, the cay007 genome had small and few ROHs, suggesting lack of recent inbreeding and a relatively large population size, respectively. Overall, these results suggest that the demographic transition observed in Central Anatolia between the PPN and the PN did not take place in the “Fertile Crescent”, at least at the same magnitude. This observation is in line with radiocarbon-based estimates of low population density on the Central Anatolian plateau relative to other Fertile Crescent regions in the early Holocene (35). This result would also be consistent with the “Hilly Flanks hypothesis”, according to which the fertile flanks of the Taurus and Zagros Mountains that supported both the large hunter-gatherer populations and the progenitors of plant and animal domesticates eventually became cradles of early domestication events (36–38).
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Post by Admin on May 10, 2022 17:49:08 GMT
Çayönü co-burials reflect nuclear and extended family structures Recent work suggested that in the Central Anatolian PPN communities, Aşıklı Höyük and Boncuklu Höyük, co-burials frequently included close genetic kin, suggesting that these earliest sedentary communities may have been organised around biological families (12), as hypothesised earlier (39, 40). In contrast, co-burials were rarely close kin in PN communities, Çatalhöyük and Barcın (12), implying distinct social organisation patterns in the latter. But the generality of these observations has remained uncertain as this single study included limited sample sizes. Here we investigated genetic kinship among Çayönü co-burials using two approaches. First, using methods that have sensitivity up to second- or third-degree relatedness (41, 42), we estimated genetic kinship levels among a total of 78 pairs, with 10 pairs representing co-burials in the same building. We identified 4 closely related pairs, including first-, second-, and third-degree relationships (Fig. 6A-B, Supplementary Table 7-8). These 4 pairs were interred in three buildings, and each pair shared the same building (Fig. 7). Kinship coefficient (θ) estimates among Çayönü individuals. Comparison of (A) autosomal and (B) X-chromosomal estimates of θ are shown. In both panels, NGSRelate θ estimates are shown on the x-axes and READ θ estimates, calculated as (1 - normalised P0), on the y-axes. Vertical bars represent ±2 standard errors of P0 values. Vertical dotted, dashed and straight grey lines intersect with expected θ values for first-, second- and third-degree relatives, respectively. Annotation with the grey label shows the pair cay008 and cay013. Fig. 7. Locations of Çayönü co-burials interred in domestic buildings. All three buildings belong to the Cell Building sub-phase. The figure shows plans of buildings coded (A) CA, (B) CL, and (C) CN. Red dots represent individuals analysed in this study; pink dots represent individuals screened for aDNA but with insufficient preservation, and blue dots represent burials of other individuals within the same buildings. Black curved lines show the closely related pairs in each building. We hypothesised that the 9 individuals who were co-buried with others but were not closely related, could still belong to the same extended biological families. We investigated this by testing whether each of these co-buried pairs were genetically closer to each other than to other Çayönü individuals, using outgroup f3-statistics. We indeed found that co-buried pairs who were not identified as close genetic kin were still slightly genetically closer to each other than pairs from distinct buildings (effect size = 0.03, permutation test p-value < 0.001) (Fig. S4). Our results are similar to observations from the contemporaneous Aşıklı and Boncuklu of Central Anatolian PPN (12), but not genetic kinship analyses of Upper Palaeolithic co-burials from Sunghir, Siberia (43). Hence, biological family-based co-burial cultures may belong to a diverse set of derived cultural traits shared among communities across Southwest Asia in this period. The social significance of Neolithic co-burials and whether they represented household members is yet ambiguous, though the observed patterns are consistent with the notion that biological family structures played a role in social organisation in Southwest Asia during the transition to sedentism (39, 40). Our results also render the reported deficiency of a genetic kinship signal in the later-coming Barcın and Çatalhöyük PN communities (44, 45) even more intriguing.
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Post by Admin on May 10, 2022 20:29:54 GMT
A toddler of migrant descent, with intentional head-shaping and cauterization Our genetic comparisons highlighted a 1.5-2-year-old female toddler, cay008, as an outlier, with higher genetic affinity to Zagros populations (Fig. 1D, Fig. 2, Fig. S3). Genetic kinship analysis using autosomal loci suggested a third-degree relationship between this individual and an adult female, cay013, interred in the same building (Fig. 6–7, Supplementary Table 7). In contrast, analysis of their X-chromosomal loci indicated a genetic relationship closer than third-degree (Fig. 6B, Supplementary Table 8). Such discrepancy would be expected if cay013 was the paternal kin of cay008. Pedigree analysis suggested cay013 being the paternal great-aunt of cay008 as a likely scenario (Methods; Fig. S5 and 6). In addition, the mtDNA haplogroup of cay008 (haplogroup T2g) was a clear outlier within the Çayönü sample, which consisted mostly of haplogroup K1 (Supplementary Table 2). These lines of evidence suggest that the Zagros-like ancestry of cay008 was inherited from her maternal side and her migrant ancestors bred with local individuals. This toddler further displayed two intriguing features in her cranium (Fig. 8A-F). First, cay008’s skull appears to be subject to intentional head-shaping, manifested as frontal flattening with a fronto-occipital groove and post-coronal depression (Fig. 8C). This could be produced by a double-bandaged circular head-shaping procedure. Three additional individuals in our sample also showed similar evidence, including cay013, the adult female relative of cay008 (Table S1). Although circular head-shaping with two bandages was previously documented in Neolithic Southwest Asia (46, 47), Çayönü presents one of the earliest known examples of this tradition. Fig. 8. Cranial features of the cay008 toddler. (A) Frontal flattening, post-coronal depression, bulging on the parietal tuber and fronto-occipital grooving suggest a double bandaged circular type cranial deformation. (B) Cauterisation with a circular depression found on the post-coronal area on the left parietal bone. The bone is very thin in the centre and the edge of the lesion is elevated. (C) An enlarged picture of a post-coronal depression and frontal flattening. (D-E) Endocranial lithic lesions similar to serpens endocrania symmetrica on occipital bone. (F) Slightly developed cribra orbitalia on the right orbital roof. This lesion together with porotic hyperostosis is mainly related to anaemia. (G) Cranial trepanation performed by drilling on the skull of Çayönü individual ÇT’78 KE 6-2/3a SK5 (not represented in our genetic sample). The cay008 skull also presents evidence of cauterization, i.e., the intentional burning of the cranium by an instrument (Fig. 8B). Cauterization marks were prevalent in Neolithic populations in Anatolia and Europe (47, 48), but to our knowledge, cay008 shows the earliest documented case of this treatment. Cauterization marks from Europe are usually associated with trepanation, performed to thin the cranial bone (49), but the cranium of cay008 lacks a trepanation signal. Instead, we observed endocranial lesions reminiscent of serpens endocrania symmetrica on the inner surface of the fragmented occipital of cay008, suggesting that the toddler suffered from an infection (Fig. 8D, E). The cranium also showed cribra orbitalia which can signal anaemia (Fig. 8F). We hypothesise that cauterization on the parietal bone might have been applied to treat the adverse effect of these diseases. The bone formation suggests the toddler lived for a period of time after cauterization. The evidence for cauterization, widespread head shaping, and additional reports of trepanation in Çayönü (Fig. 8G) altogether suggest a prominent culture of intentional body modification in this community (50). Body modifications may have developed in parallel with other aspects of cultural innovation in Çayönü, and could also be shared interregionally; indeed, cases of head-shaping and trepanation are also known from Neolithic sites in the Fertile Crescent (46, 51–53).
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Post by Admin on May 10, 2022 21:13:35 GMT
The demographic impact of Upper Mesopotamia on Neolithic and post-Neolithic Anatolia Finally, we investigated the possible role of Upper Mesopotamia as a source of post-7,000 BCE eastern gene flow into Anatolia. Eastern gene flow events have been inferred from increasing levels of early Holocene South Caucasus and/or Zagros ancestry in Anatolian populations, starting by the PN and continuing into the Bronze Age (8, 13, 54, 55). It was speculated that the original source of Caucasus/Zagros-related ancestry might be Upper Mesopotamia (13, 55). This could be plausible given our results above, specifically that our Çayönü sample included >25% Zagros ancestry relative to Central Anatolian PPN populations (Fig. 2C). We thus asked whether the post-7,000 BCE eastern admixture in Anatolian populations is better explained by gene flow from an early Holocene Caucasus-related group, or from Upper Mesopotamia, represented by Çayönü. We computed D-statistics in the form of D(Yoruba, CHG/Çayönü; X, Anatolia_EP/Anatolia_PPN), where X was a Neolithic to Bronze Age population from Anatolia/Aegean, CHG represents early Holocene Caucasus (the so-called “Caucasus hunter-gatherers”), and Anatolia_EP/Anatolia_PPN represents Epi-Palaeolithic Pınarbaşı and Central Anatolia PPN Boncuklu, respectively. This revealed two interesting results. First, we found that Çayönü genomes show higher genetic affinity to PN Anatolian populations Çatalhöyük, Tepecik-Çiftlik, and Barcın, than to pre-7000 BCE Anatolian genomes (Fig. 9A, B; Supplementary Table 4). Moreover, this affinity was weak or absent when using CHG instead of Çayönü (D-statistics ≈ 0). This result is consistent with Upper Mesopotamia, but not Caucasus, being the source of eastern gene flow into Central Anatolia and possibly Western Anatolia around 7,000 BCE. The finding also resonates with archaeological evidence from Çatalhöyük, where the mid-7th millennium BCE witnesses the first introduction of obsidian from the Bingöl area of Eastern Turkey, the appearance of lithic types akin to “Çayönü tools”, and an increasing use of the pressure technique in lithic industries (56–58). Fig. 9. Biplots of D-statistics illustrating excess allele sharing between Çayönü and post-7000 BCE populations from Central/Western Anatolia. D-statistics were computed in the form of D(Yoruba, pop1; pop2, X) where X represents Pottery Neolithic, Chalcolithic and Bronze Age populations from the Anatolian Plateau. Each population is represented by a dot and error bars representing ±2 standard errors. The list of populations and D-statistics can be found in Supplementary Table 4. In both panels, pop1 corresponds to CHG on the x-axes whereas on the y-axes pop1 corresponds to the Çayönü population. pop2 is represented by Boncuklu (Central Anatolian PPN) in panel (A) and Pınarbaşı (Central Anatolian EP) in panel (B) in both axes. The slope of the diagonal dashed line is 1 showing x = y and the intercept of both vertical and horizontal dotted lines are 0. Second, starting with early Chalcolithic in Anatolia, Çayönü genomes lose their affinity to post-Neolithic Anatolians while the CHG sample gains affinity to post-Neolithic Anatolians over pre-7000 BCE Anatolians (Fig. 9A-B). Hence, PPN Çayönü-related groups do not appear as the direct source of Caucasus-related ancestry in post-Neolithic Anatolia. This can be explained in two ways. One is that Caucasus-related influence in post-Neolithic populations emerged from another region than Upper Mesopotamia, such as North or East Anatolia. An alternative scenario is that the Upper Mesopotamian gene pool itself changed post-7000 BCE by Zagros/Caucasus-related gene flow. In this case, Upper Mesopotamia could have remained the source of eastern gene flow into Anatolia with its new profile. Conclusion Whereas the main driver behind European Neolithization has been recognized as mass population movements from Anatolia and/or Southeast Europe (9, 22, 24), the role of human movement in the multi-millennia process of Neolithization in Southwest Asia is less understood. Here, we described the formation of Upper Mesopotamian PPN populations, represented by PPNB Çayönü, as an admixture event between western and eastern populations of early Holocene Southwest Asia. The PPNB Çayönü community appears to have carried relatively high genetic diversity levels relative to PPN Central Anatolia and pre-Neolithic Europe which indicates that the site was open to interaction. Nearly half a century ago archaeologists Robert Braidwood and Halet Çambel described Çayönü as a perfect spot for the emergence of sedentism and agriculture, due its location along the Hilly Flanks of the Taurus and Zagros Mountains where progenitors of plant and domesticates naturally co-existed (59). We hypothesise that Çayönü was also a lively hub of interregional networks, potentially due to its location between the sources of the Tigris and the Euphrates rivers in Upper Mesopotamia. Recent discoveries and ongoing research at sites such as Göbekli Tepe and Karahan Tepe (60, 61) continue to demonstrate the significance of this region as a central node of cultural dynamism and social networks.
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