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Post by Admin on Nov 27, 2020 23:25:28 GMT
Finally, we fit all the ancient and modern Lebanese data into an admixture graph model showing their relationship with other ancient populations by using data in set 2. The graph supports the results reported here, showing substantial genetic continuity in Lebanon since the Bronze Age interrupted by three significant admixture events during the Iron Age, Hellenistic period, and Ottoman period, each contributing 3%–11% of non-local ancestry to the admixed population (Figures 3 and S13).  Figure 3. An Admixture Graph Model for Ancient Lebanon A graph model that fits our data showing the relationship between the ancient Lebanon populations and the admixture events that contributed to the population until modern times. Worst f4-statistics, Iran_N,Levant_N;EHG,Qed_LRoman; Z score = 3.0. See Figure S13 for alternative graph models. In this study, we present new whole-genome sequence data from ancient individuals who lived in the Near East between the Iron Age and the Roman period, spanning a time marked by major historical events and population movements. Our data capture the genetic outcome of some of these events but also show that the genetic composition of the general population was minimally affected and that great cultural transitions in the Near East were not in these cases matched by comparable genetic transitions. Yet, we show that the small genetic changes we detect when using ancient populations sampled from a time series have the power to provide information about past events with details that complement the available historical records. Declaration of Interests The authors declare no competing interests. Data and Code Availability Raw sequencing reads for the ancient individuals are available through the European Nucleotide Archive (ENA) under accession number ENA: ERP121575. Aligned sequences, genotypes, and imputed genotypes can be obtained from the corresponding author M.H. Acknowledgments We thank the Directorate General of Antiquities (DGA) in Lebanon for approving (reference: 3333) transfer and processing of bones from Lebanon. We thank Rui Martiniano for discussions related to the Y chromosome analysis. M.H., Y.X., and C.T.-S. were supported by The Wellcome Trust (098051). M.A.A. was supported by the government of Dubai (Dubai Police GHQ). The ancient DNA lab at the University of Tartu is supported by the European Union through the European Regional Development Fund (2014–2020.4.01.16–0030) (C.L.S., T.S., and S.J.G.) and the Estonian Research Council (PRG243) (C.L.S. and L.S.). |
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Post by Admin on May 7, 2022 17:27:19 GMT
A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition doi: doi.org/10.1101/2022.01.31.478487Abstract Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and foodways. We present thirteen ancient genomes (c.8500-7500 calBCE) 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 a mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organised along biological family lines. We document bodily interventions such as head-shaping and cauterization among the individuals examined, reflecting Çayönü’s cultural ingenuity. Finally, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesise 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. Introduction Located between the Euphrates and Tigris rivers, the hilly flanks of Upper Mesopotamia were home to the earliest sedentary hunter-gatherers who built the first monumental structures at Göbekli Tepe (1) and domesticated numerous local plant and animal species, including einkorn, emmer, sheep, goat, pig, and cattle (2–5). The innovative spirit and cultural dynamism of these societies during the Neolithic Transition in Southwest Asia (c. 9800-6500 BC) is well documented in the archaeological record, but their demographic history and social structures has remained unknown owing to the lack of genomes from North Mesopotamia. This stands in contrast with a significant number of recent archaeogenomic studies that focused on the three most distant corners of Neolithic Southwest Asia, namely South Levant, Central Zagros, and Central Anatolia (Fig. 1A, B) (6–12). This body of work has together revealed (a) genetically distinct populations in all three regions, (b) a dominant trend of population continuity between pre-Neolithic, Pre-Pottery Neolithic (PPN) and Pottery Neolithic (PN) communities, (c) an overlay of interregional gene flow through time, such as inferred “southern” and “eastern” gene flow events into Central Anatolia between the Early and Late Neolithic. Meanwhile, key questions about the possible roles of Upper Mesopotamia in interregional demographic and cultural change, e.g., whether Upper Mesopotamia influenced Late Neolithic Central Anatolia and whether it was the source of the post-Neolithic gene flow into Anatolia (6, 13), have remained open. With the exception of a single ancient DNA study reporting 15 mitochondrial DNA sequences from the Upper Euphrates (14), Upper Mesopotamia has remained genomically unexplored, mostly owing to low DNA preservation in the region. |
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Post by Admin on May 7, 2022 19:42:33 GMT
 Fig. 1. Spatio-temporal distribution of the samples and the population structure of Neolithic Southwest Asia. (A) Timeline of ancient Southwest Asian individuals used in the analyses. Colored rectangles at the bottom represent the sub-periods of the Neolithic Era in Southwest Asia. (B) The map shows Epi-Paleolithic (EP) and Neolithic populations from Southwest Asia. Shaded areas mark Pre-Pottery Neolithic (PPN) cultural zones. (C) Çayönü building types and their approximate dates of use, considered as evidence for Çayönü’s cultural openness and ingenuity. Adapted from (103). (D) First two dimensions of multidimensional scaling (MDS) plot of genetic distances. The MDS summarises the genetic distance matrix among ancient genomes calculated as (1 - outgroup f3) values. Outgroup f3-statistics were calculated as f3(Yoruba; individual1, individual2). The labels represent the following sites: Anatolia EP: Pınarbaşı; Anatolia PPN: Boncuklu and Aşıklı Höyük; Anatolia PN: Çatalhöyük and Barcın Höyük; Levant EP: Natufian; Levant PPN: Ain’ Ghazal, Kfar HaHoresh, Motza and Ba’ja; C Zagros N (Central Zagros Neolithic): Ganj Dareh, Tepe Abdul and Wezmeh Cave; S Caucasus EP (South Caucasus EP): Kotias and Satsurblia. We use “Anatolia” here following the traditional geographic definition, referring to the west of the Anatolian Diagonal. Here we address this gap by studying genomic data from Çayönü Tepesi (hereon Çayönü) of the Upper Tigris area (Fig. 1A), a settlement that presents one of the best examples of the transition from foraging to food production in Southwest Asia (15). Firstly, Çayönü’s uninterrupted stratigraphy extending from the Pre-Pottery Neolithic A (PPNA) (c. 9500 cal BCE) to the final PPN (c. 7000 cal BCE) is unparalleled in the region. Secondly, the Çayönü Neolithic community is recognized for its marked cultural dynamism, which is reflected (a) in evidence for intense plant cultivation (16) and animal management (pig, cattle, sheep and goat) (17), (b) in continuous innovation in architectural styles (Fig. 1C), (c) in technological experimentation, from pioneering lime burning techniques (15, 18) to the production of copper beads and reamer-like objects (19). Finally, both western (Levant-Euphrates) and eastern (Tigris-Zagros) influences and parallel developments are traceable in Çayönü’s material culture (20) (Supplementary Table 1). These observations suggest that Çayönü and contemporaneous Upper Mesopotamian communities could have acted as hubs of cultural interaction and innovation in Neolithic Southwest Asia. Our study presents genomic data from Çayönü, which we then use to describe (i) the structure of Fertile Crescent populations in comparison with interregional material culture affinities, (ii) the Neolithic demographic transition reflected in intraregional genomic diversity, (iii) genetic kinship among co-burials in domestic structures at Çayönü, and (iv) the potential role of Upper Mesopotamia in Neolithic and post-Neolithic human movements influencing Anatolia. We also detail the curious case of a Çayönü infant, whom we infer to be a migrant offspring, and whose skeletal material presents the earliest known examples of cauterization and head-shaping in the region. |
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Post by Admin on May 8, 2022 18:37:10 GMT
Results and Discussion We studied a total of 33 human remains from Çayönü (Fig. 1A, B, Supplementary Table 2). These were mainly found as subfloor burials located inside or within the proximity of six Pre-Pottery Neolithic B (PPNB) buildings (Table S1). We screened 33 aDNA libraries by shotgun sequencing, which revealed endogenous DNA proportions varying between 0.04% and 5% (median = 0.2%, Fig. S1). This was lower than aDNA preservation in a contemporaneous Central Anatolian settlement, Aşıklı (median = 1.4%, Wilcoxon rank sum test p < 0.05), but comparable to another Central Anatolian site, Boncuklu (median = 0.1%, Wilcoxon rank sum test p > 0.05, Fig. S2). Libraries from 14 individuals were chosen for deeper sequencing (Methods), from which we generated shotgun genomes with depths ranging from 0.016x to 0.49x. (Fig. S1, Supplementary Table 2). High rates of post-mortem damage (PMD) accumulation at read ends, short average fragment sizes (49-60 bps, median = 51.4 bps), and mitochondrial haplotype-based estimates suggested authenticity of all 14 libraries (Methods) (Supplementary Table 2). With this data we first estimated genetic kinship among all individual pairs (Methods). Two samples, both identified as female infants (cay018 and cay020), were genetically inferred to either belong to the same individual or to be identical twins. Anthropological evaluation also showed that both petrouses could belong to the same individual. We therefore merged their genomic data and treated this merged data as representing a single individual, reducing our sample size to 13 individuals (6 adult females, 2 adult males, 3 sub-adult females, 2 sub-adult males). We further identified four related pairs of 1st to 3rd degree (see below) and removed all but one individual among sets of closely related individuals in population genetic analyses (Methods). The east-west genetic structure of Neolithic Southwest Asia To obtain an overview of genetic affinities among human populations in Neolithic Southwest Asia we compared the 13 Çayönü genomes with published ancient genomes dating to c.15,000-5,500 BCE from the Fertile Crescent and neighbouring regions (Supplementary Table 3) (6–8, 11, 12, 21–24) using multidimensional scaling (MDS) of pairwise f3 results, D-statistics, and qpAdm analyses (25). These revealed a number of observations. In the MDS analysis, the Çayönü group occupied a distinct and intermediate position within the space of Southwest Asian genetic diversity bordered by early Holocene South Levant, Central Zagros and South Caucasus, and Central Anatolia (Fig. 1D, Fig. S3). Our sample of Çayönü genomes was internally homogeneous within this space, with the exception of an “outlier” individual, cay008, who appeared relatively closer to Zagros/Caucasus individuals. D-statistics likewise showed that the Çayönü group was genetically closer to western Southwest Asia (early Holocene Central Anatolia and South Levant) than to eastern Southwest Asia (Central Zagros) (Fig. 2A, Supplementary Table 4). At the same time, Central Zagros genomes showed higher genetic affinity to our Çayönü sample than to Central Anatolia or South Levant (Fig. 2B). Finally, we found that cay008 harbours higher Zagros contribution than other Çayönü individuals (Fig. 1D, Fig. 2C, Supplementary Table 5).  Fig. 2. Genetic affinities of Çayönü population with the neighbouring populations. Formal tests computed in the form of (A) D(Yoruba, Çayönü/cay008; pop2, test) D(Yoruba, pop1; Çayönü/cay008, Anatolia EP/PPN/PN). Z-scores were corrected with the Benjamini-Hochberg multiple testing correction (82). Horizontal bars represent ±2 standard errors. (C) qpAdm modelling of the Çayönü group and cay008. The “local” Çayönü group or outlier cay008 individual was the “target”; Central Anatolia Epi-Paleolithic, Central Zagros Neolithic and South Levant Neolithic samples were sources for both targets. The “local” Çayönü group was also used as “source” for modelling of cay008. Horizontal bars represent standard errors of the coefficients. All three models yielded p-values > 0.05. We also cannot reject a three-way model of Central Anatolia PPN, Central Zagros and South Levant at >0.01 p-value threshold (Supplemental Table 5). In all analyses shown in the figure, “Çayönü” represents the 9 genomes listed in Table 1, excluding relatives and cay008. |
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Post by Admin on May 8, 2022 20:39:03 GMT
Given these observations, we first investigated the origins of the genetic structure in Neolithic Southwest Asia. The higher genetic affinity among Upper Mesopotamia (represented by Çayönü), Central Anatolia, and South Levant populations relative to Central Zagros (Fig. 1D, Fig. S3) was intriguing, which led us to ask whether this affinity could be explained by an isolation-by-distance process (26, 27). We computed shared genetic drift between each pair of individuals in our Southwest Asia sample and compared these to geodesic geographic distance among settlements (Methods). To eliminate the effect of temporal genetic changes, we only included individual pairs separated by <1,000 years. We found a general correlation between spatial and genetic distances, as expected (Fig. 3A). However, we also found that Central Zagros genomes were significantly more differentiated compared to that expected from a linear isolation-by-distance model (Fig. 3B). We therefore infer a stark west-east genetic structure in the Fertile Crescent, where the lowest effective migration (28) appears to lie between Upper Mesopotamia and Central Zagros.  Fig. 3. Genetic isolation-by-distance in Southwest Asia. Panel (A) shows correlation between geographic (x-axis) and genetic (y-axis) distance for Southwest Asia Neolithic populations. The red regression line shows the linear fit with 95% confidence interval. Each point represents pairs of individuals from Southwest Asia Neolithic. Pairs from the same site, and pairs separated by >1,000 years time difference were not included. All regression lines were highly significant (p<0.001). Panel (B) shows the distribution of residuals which we calculated by subtracting observed values from predicted values obtained from the linear regression models in Panel A. In all analyses shown in the figure, “Çayönü” represents the 9 genomes listed in Table 1, excluding relatives and cay008. At face value, this result may seem to imply resistance to gene flow between Upper Mesopotamia and Central Zagros during the Neolithic. However, such resistance does not align with observed material culture affinities between the two regions (e.g., (29) Supplementary Table 1). We therefore suggest an alternative scenario to explain the observed genetic structure. During Last Glacial Maximum (LGM), the eastern regions of Southwest Asia (the ancestors of Central Zagros / South Caucasus) could have been isolated from the western regions (the ancestors of Central Anatolians/Levantines), with the east and west populations differentiating through drift or by admixture with third populations. Sometime after the LGM, these eastern and western regional populations could have re-expanded and partly admixed within Southwest Asia. It is plausible that east-west admixture occurred in Upper Mesopotamia, giving rise to Çayönü’s gene pool, and may have also influenced Central Anatolia by the PN (6). We note that the duration and timing of this putative admixture process remain unclear, and that alternative scenarios are also conceivable (30). Irrespective of the demographic mechanisms, though, Central Zagros appears to have been genetically the most distinct group in early Holocene Southwest Asia. Admixed ancestry and diverse material culture affinities in Çayönü We next investigated the demographic origins of Çayönü inhabitants. The D-statistics results mentioned above had suggested that the Çayönü sample carried mixed eastern and western ancestry (Fig. 2A, B), which is consistent with the site’s intermediate geographic position. Using qpAdm we could further model ancestry proportions in the Çayönü genome sample (excluding the cay008 individual) as three-way admixtures of Central Anatolia-(represented by Epi-Paleolithic (EP) Pınarbaşı; Anatolia_EP), South Levant- and Central Zagros-related ancestries (Fig. 2C; Supplemental Table 5) (Methods). Çayönü bears mainly Anatolian ancestry, complemented by 33% (SE ± 3%) of Zagros and 19% (SE ± 5%) of Southern Levant ancestry (p-value > 0.05). We then asked whether the genetic affinity of Çayönü individuals to regional populations could have changed over the 1,000 years covered by our sample (Fig. 4). We found no significant temporal effect (multiple testing corrected p>0.05). Still, this does not rule out immigration into Çayönü, as the cay008 “outlier” individual shows. With qpAdm we estimated that the cay008 genome carried 50% Anatolia_EP and 50% Zagros_N ancestry (SE ± 5%, p-value > 0.05) and lacked a significant South Levant component found in the rest of Çayönü genomes (Fig. 2C). We were also able to model cay008 as a mixture of the “local” Çayönü sample (79%, SE ± 8%) and Zagros-like (21%, SE ± 8%) ancestries (p-value > 0.05). We caution that “Zagros ancestry” here might actually represent Northwest Zagros ancestry (i.e., modern-day North Iraq, from where archaeogenomic data is not yet available) rather than Central Zagros ancestry, which would also be compatible with Çayönü’s material cultural affinities with Northwest Zagros (Fig. 1B; Supplementary Table 1). |
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