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Post by Admin on Jul 28, 2019 17:58:43 GMT
The dominant mtDNA lineages of the Shirenzigou people are commonly found in modern and ancient West Eurasian populations, such as U4, U5, and H, while they also have East Eurasian-specific haplogroups A, D4, and G3, preliminarily documenting admixed ancestry from eastern and western Eurasia. The admixture profile is also shown on the paternal Y chromosome side that 4 out of 6 males in Shirenzigou (Figure S2) belong to the West Eurasian-specific haplogroup R1b (n = 2) and East Eurasian-specific haplogroup Q1a (n = 2) (Table 1), the former is predominant in ancient Yamnaya and nearly 100% in Afanasievo [1, 19], different from the Middle and Late Bronze Age Steppe groups (Steppe_MLBA) such as Andronovo, Poltavka, Srubnaya, and Sintashta whose Y chromosomal haplogroup is mainly R1a [19, 20, 21]. Figure 2 PCA and ADMIXTURE Analysis for Shirenzigou Samples Autosomal DNA We called between 27 and 479 thousand SNPs (Table 1; Data S1A) from our ancient samples at 1,240k positions previously described [19]. We merged our newly generated data with published ancient and modern data [2, 3, 22]. We first carried out principal component analysis (PCA) [23] to assess the genetic affinities of the ancient individuals qualitatively by projecting them onto present-day Eurasian variation (Figure 2). We observed a distinct separation between East and West Eurasians. Our ancient Shirenzigou samples and present-day populations from Central Asia and northwestern China form a genetic cline from East to West in the first PC. The distribution of Shirenzigou samples on the cline is relatively scattered with two major clusters, one being closer to modern-day Uygurs and Kazakhs and the other being closer to recently published ancient Saka and Huns from the Tianshan in Kazakhstan [2]. We then carried out the model-based ADMIXTURE clustering analysis [24] to get a detailed overview of the ancestry composition (Figure 2). Consistent with the PCA, the Shirenzigou samples show a similar East-West admixed genetic profile with present-day populations from Central Asia and northwestern China, for example, Uygur, Kyrgyz, and Uzbek. But, interestingly, the Shirenzigou samples lack the green component that is enriched in Anatolian and European farmers when compared to the above present-day groups. The East Eurasian component in Shirenzigou looks more related to northern Asians such as Daur and Hezhen than to southern Asians as they do not have the pink component that is enriched in southern Asians (Figure 2). We applied a formal admixture test using f3 statistics [25] in the form of f3 (Shirenzigou; X, Y) where X and Y are worldwide populations that might be the genetic sources for the Shirenzigou individuals. We observed the most significant signals of admixture in the Shirenzigou samples when using Yamnaya_Samara or Srubnaya as the West Eurasian source and some Northern Asians or Koreans as the East Eurasian source (Table S1). We also plotted the outgroup f3 statistics in the form of f3 (Mbuti; X, Anatolia_Neolithic) and f3 (Mbuti; X, Kostenki14) to visualize the allele sharing between population X and Anatolian farmers. As shown in Figure S3, the Steppe_MLBA populations including Srubnaya, Andronovo, and Sintashta were shifted toward farming populations compared with Yamnaya groups and the Shirenzigou samples. This observation is consistent with ADMIXTURE analysis that Steppe_MLBA populations have an Anatolian and European farmer-related component that Yamnaya groups and the Shirenzigou individuals do not seem to have [1, 2, 3, 19, 26]. The analysis consistently suggested Yamnaya-related Steppe populations were the better source in modeling the West Eurasian ancestry in Shirenzigou. We continued to use qpAdm [4, 27] to estimate the admixture proportions in the Shirenzigou samples by using different pairs of source populations, such as Yamnaya_Samara, Afanasievo, Srubnaya, Andronovo, BMAC culture (Bustan_BA and Sappali_Tepe_BA) and Tianshan_Hun as the West Eurasian source and Han, Ulchi, Hezhen, Shamanka_EN as the East Eurasian source. In all cases, Yamnaya, Afanasievo, or Tianshan_Hun always provide the best model fit for the Shirenzigou individuals, while Srubnaya, Andronovo, Bustan_BA and Sappali_Tepe_BA only work in some cases [3] (Tables 2 and S2; Data S2A). The Yamnaya_Samara or Afanasievo-related ancestry ranges from ∼20% to 80% in different Shirenzigou individuals, consistent with the scattered distribution on the East-West cline in the PCA (Figure 2). In the PCA, ADMIXTURE, outgroup f3 statistics (Figure S4), as well as f4 statistics (Table S3), we observed the Shirenzigou individuals were closer to the present-day Tungusic and Mongolic-speaking populations in northern Asia than to the populations in central and southern China, suggesting the northern populations might contribute more to the Shirenzigou individuals. Based on this, we then modeled Shirenzigou as a three-way admixture of Yamnaya_Samara, Ulchi (or Hezhen) and Han to infer the source from the East Eurasia side that contributed to Shirenzigou. We found the Ulchi or Hezhen and Han-related ancestry had a complicated and unevenly distribution in the Shirenzigou samples. The most Shirenzigou individuals derived the majority of their East Eurasian ancestry from Ulchi or Hezhen-related populations, while the following two individuals M820 and M15-2 have more Han related than Ulchi/Hezhen-related ancestry (Data S2C1 and S2C2).
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Post by Admin on Jul 29, 2019 18:08:09 GMT
Table 2p Values and Ancestry Proportions in Modeling a Two-Way (p = rank 1) Admixture in Shirenzigou Samples Using the Following Set of Outgroups Populations: Dinka, Ust_Ishim, Kostenki14, Onge, Papuan, Australian, Iran_N, EHG, and LBK_EN Sample p = rank 1 Yamnaya_Samara Han Proportion SE Proportion SE All 5.996E−02 0.542 0.010 0.458 0.010 M819 8.479E−01 0.574 0.020 0.426 0.020 M820a 2.784E−03 0.731 0.022 0.269 0.022 M15-1 1.248E−01 0.695 0.026 0.305 0.026 M15-2 1.192E−01 0.803 0.029 0.197 0.029 M4 2.682E−01 0.773 0.041 0.227 0.041 M8R1 7.824E−01 0.493 0.047 0.507 0.047 X3 3.336E−01 0.261 0.023 0.739 0.023 M012 2.093E−01 0.400 0.025 0.600 0.025 M010 1.609E−01 0.463 0.020 0.537 0.020 F004 6.563E−01 0.480 0.022 0.520 0.022 a Individual failed in qpAdm modeling; models with a p ≥ 0.05 are considered as a good fit and the failed models have p ≤ 0.05
The origin and dating of the East and West Eurasian admixture in Xinjiang have been long debated. There is a discussion on when and how many times eastern and western Eurasian populations met and admixed in Xinjiang. Genomic studies estimated the admixture time in present-day Uygur people from Xinjiang ranging from ∼150 to 20 generations ago, about 4,200 to 560 years ago assuming a generation time of 28 years [6, 25, 28, 29]. However, due to the complex history of human populations that may suffer frequent population replacements and also potential gene flows, the dates inferred from present-day populations can only be approximations. By sequencing ancient DNA from archaeological excavations, we can directly infer population changes at various points in time. Here, we report genomic data of 10 Iron Age samples from the Shirenzigou site in the eastern Tianshan. We find the Shirenzigou people were genetically admixed deriving ancestry from both eastern and western Eurasians, tracing the East-West admixture in Xinjiang directly back to at least 2,000 years ago. The Shirenzigou individuals were found on a genetic cline from East Asians to Western Eurasians showing different East-West admixture proportions beside them being from the same time period and archaeological site. For example, the difference of Yamnaya-related ancestry between individuals from the Shirenzigou site reached up to 80%. One possible explanation is a recent admixture event between groups with Yamnaya-related ancestry and East Asian ancestry. It could furthermore indicate that the region was a corridor and meeting place for Eastern and Western populations or indicate a structured population with various ancestries that occupied the Iron Age Xinjiang region. We also cannot rule out that the genetic heterogeneity had already existed in the western source populations before they entered the eastern Tianshan region to form the Shirenzigou individuals, since the genomic composition of nomadic populations such as Scythian, Hun, and Saka at that period in the region were also highly dynamic [2]. The existing archaeological evidences suggest that the Shirenzigou site shows typical characteristics of the agro-pastoral Yanbulake Culture from the Bronze-Age Hami Basin located in the southern slope of the East Tianshan Mountains. The animal motifs such as the deer-shaped Griffin in the site also reflects the influences from the Pazyryk Culture from the Altai region. Besides the cultural exchange between the eastern Tianshan Mountains and the Altai region, a special funeral ritual appeared in the Shirenzigou site, whereby the upper torsos were disturbed. This was a common custom in the Neolithic Gansu corridor, in Northwestern China [18]. Furthermore, the chemical composition analysis of ancient glass beads excavated from the site indicated they were imported from the central region of China [17]. The diverse cultural elements observed in the same site provide evidence that different populations once came to this region and admixed with each other to form the genetic structure of the Shirenzigou people, which is well supported by the ancestry profile inferred in this study. We found most Shirenzigou individuals derived a large amount of their ancestry from Ulchi or Hezhen-related populations, which might be associated with ancient nomadic people in northern Asia. The Shirenzigou samples also harbor a Han Chinese-related component, which may be introduced into this region by the farming populations from surrounding regions, such as Gansu and Qinghai, who also contributed to present-day Han Chinese. Based on the ADMIXTURE and qpAdm analysis, we conclude that the western Eurasian ancestry in the Shirenzigou individuals was most likely related to Yamnaya without significant evidence of European farmer-related gene flow that is present in later Steppe_MLBA populations [19, 26]. The Yamnaya-related steppe ancestry has been described as a mixture of Eastern- and Caucasus hunter-gatherers from the Pontic-Caspian steppes, dating to 3,300–2,600 BCE, which eventually spread further to the Altai region in the East in the form of people associated to the Afanasievo Culture. The same population likely migrated to Europe in the West contributing substantially to present-day Europeans along with the spread of some of the Indo-European languages [1, 4]. In the following millennia, the Altai region was characterized by the local Bronze Age Andronovo culture. The Andronovo people were genetically closely related to Late Bronze Age Sintashta and Srubnaya people with significant evidence of European farmer-related ancestry [1]. Our results suggest that the Yamnaya and/or Afanasievo-related ancestry expanded further south through the Dzungarian Basin into the northern slope of the Tianshan Mountains in Xinjiang since at least the second millennium BCE and thus support the “Steppe hypothesis” for the early peopling of Xinjiang. A potential direction of future research is the generation of genome data from ancient individuals from the Tarim Basin to see whether the Steppe-related ancestry had come across the geographic barrier and spread to the south of the Tianshan mountains. Our analysis might thus provide direct evidence for the steppe-related eastern spread of Indo-European languages, notably the arrival of the Tocharian branch of Indo-European in the Tarim basin. The Tocharian languages are known from manuscripts from 500 to 800 CE, found south of the Tianshan Mountains, in the north central and eastern reaches of the Tarim Basin. The relationship between these languages is commonly explained by divergence from a common ancestor, Proto-Tocharian, which must have preceded the attested languages by more than a millennium, probably dating to the middle 1st millennium BCE [30]. Damgaard et al. [31] pointed out that proto-Tocharian is not more closely affiliated with Indo-Iranian than with any other branch of Indo-European and that it therefore cannot be related to the Indo-Iranian Sintashta and Andronovo cultures. As the homeland of Proto-Tocharian seems to be situated south of the Tianshan Mountains, future research should determine to what extent the Tianshan has served as a geographic barrier for the ancient Steppe gene flow. Combining both the genetic and archaeological evidence, we here provide the first direct evidence of an early stage of population admixture around 2,100 BP in Xinjiang in Western China. Our study supports the “Steppe hypothesis” over the “Bactrian Oasis hypothesis” for the peopling of the Xinjiang region. The high amount of Yamnaya or Afanasievo-related ancestry in the Iron Age Xinjiang individuals indirectly supports the introduction of Indo-European languages into the region that survived in the form of Tocharian until the late first millennium CE. We note that we need more individuals from different sites and time periods to shed more light on the genetic history of the Tarim basin and the whole Xinjiang region. Published:July 25, 2019 DOI:https://doi.org/10.1016/j.cub.2019.06.044
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Post by Admin on Jul 6, 2021 20:09:07 GMT
Ancient Xinjiang mitogenomes reveal intense admixture with high genetic diversity
Science Advances 31 Mar 2021: Vol. 7, no. 14, eabd6690 DOI: 10.1126/sciadv.abd6690
Abstract Xinjiang is a key region in northwestern China, connecting East and West Eurasian populations and cultures for thousands of years. To understand the genetic history of Xinjiang, we sequenced 237 complete ancient human mitochondrial genomes from the Bronze Age through Historical Era (41 archaeological sites). Overall, the Bronze Age Xinjiang populations show high diversity and regional genetic affinities with Steppe and northeastern Asian populations along with a deep ancient Siberian connection for the Tarim Basin Xiaohe individuals. In the Iron Age, in general, Steppe-related and northeastern Asian admixture intensified, with North and East Xinjiang populations showing more affinity with northeastern Asians and South Xinjiang populations showing more affinity with Central Asians. The genetic structure observed in the Historical Era of Xinjiang is similar to that in the Iron Age, demonstrating genetic continuity since the Iron Age with some additional genetic admixture with populations surrounding the Xinjiang region.
INTRODUCTION The Xinjiang region in northwestern China has served as a crossroads for East and West Eurasian migrations for thousands of years. As early as the Bronze Age (BA), Xinjiang hosted diverse cultures influenced by ancient Steppe, Siberian, Central Asian, and Northeast Asian populations (1–6). As suggested by many archaeological findings, these cultural influences on Xinjiang varied by region and time period (1–6). Archaeological studies of northern Xinjiang have revealed connections with the Afanasievo (~3300 to 2500 BCE) and Chemurchek (~2750 to 1900 BCE) cultures present in the Altai Mountains (1–3). BA cemeteries in western Xinjiang contain materials associated with mobile transportation and advanced metallurgy, which were likely derived from the Andronovo culture (~1700 to 1500 BCE) in the western Steppe and Tianshan region (7–11). There was a Central West Asian connection with Xinjiang in the BA through the Inner Asian Mountain Corridor (IAMC), which likely introduced agriculturally important crops, such as wheat and barley, and an East Asian connection through the Hexi Corridor, which introduced broomcorn millet in Xinjiang (12–14). In addition, BA populations in eastern Xinjiang share a cultural connection with East Asians from the Gansu and Qinghai (Gan-Qing) region of northern China (3, 13–17). Past studies on two BA sites (Xiaohe and Tianshanbeilu), using a limited number of Y-chromosomal single-nucleotide polymorphisms (SNPs) and the hypervariable region of mitochondrial DNA (mtDNA), could not resolve the past genetic history of Xinjiang (18–20).
During the Iron Age (IA; ~800 to 200 BCE), nomadic groups from the Eurasian Steppe affected different regions of Xinjiang. One such group was the Scythians who were a confederation of several populations, such as the Tagar, Pazyryk, and Sakas (18, 21). Some burial custom records suggest that the Middle BA southern Siberian Okunevo culture, which had a limited amount of Steppe ancestry, also influenced northern Xinjiang (22–25).
A recent genomic study of a single IA site reported Steppe-related ancestry in eastern Xinjiang (26). Ancient genomic studies in regions around Xinjiang, mostly in the Steppe region, further support the widespread population movement and admixture of western Steppe–related ancestry in the IA (21). However, the extent of Steppe-related ancestry across Xinjiang is unknown without more ancient DNA. Later, after 200 BCE, Xinjiang was dominated by many important nomadic confederations (such as the Xiongnu and Turkic Khaganates) and Han (21, 27). These groups notably influenced this region, and the frequent transitions of power suggest that the Historical Era (HE) was also a culturally mixed period, but whether Xinjiang population structure was affected by these cultural shifts is indeterminable without ancient DNA. Overall, the population genetic structure of ancient Xinjiang remains uncharacterized, as well as the genetic changes from the BA to IA and into the HE. Linguistically, the presence of Tocharian and Khotanese language is also an important question to explore (28). Genomic studies on present-day Xinjiang populations indicate a complex genetic structure with frequent migration and genetic admixture (29, 30). However, with ancient DNA from only a few Xinjiang sites, our ability to reconstruct a complete picture of past population structure and admixture is limited. Therefore, obtaining ancient genetic data from BA, IA, and Historical populations is critical for characterizing the spatiotemporal changes in Xinjiang’s population structure.
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Post by Admin on Jul 6, 2021 22:39:03 GMT
RESULTS Overview of data We captured mtDNA from 237 ancient individuals from 41 archaeological sites across Xinjiang (listed in table S1), with samples dating to ~4962 to 500 years before the present (BP). Of these 237 mtDNA samples, 235 of them have low contamination rates (≤4%), while for the other two samples with higher contamination rates (>4%), we only used fragments with damaged signatures characteristic of ancient DNA to avoid contamination. In total, we obtained complete mtDNA genomes from 237 individuals sequenced to between 31 and 5515× coverage (table S1). For the BA, we collected 63 samples spanning the time period of ~4962 to 2900 BP (table S1), including 24 individuals from North Xinjiang in the Early and Middle BA (EMBA; ~4800 to 4000 BP); among them, 18 individuals were associated with the Chemurchek culture (NChemur_EMBA, 4811 to 3965 BP), and two were associated with the Afanasievo culture (NAfana_EMBA; 4570 to 4426 BP). We obtained three samples associated with the Afanasievo culture from the Ili Valley in western Xinjiang (WAfana_EMBA; ~4962 to 4840 BP) and combined them with samples associated with the Afanasievo from North Xinjiang to form the NWAfana_EMBA group. The other sites, Songshugou (NSSG_EMBA; n = 3, 4237 to 4087 BP) and Habahe (n = 1, ~4500 BP), with no known information on their archaeological cultures were analyzed separately. From eastern Xinjiang, we collected one individual from the BA Nanwan site (E_BA; ~3600 to 3000 BP) and an additional 25 samples dating to the Late BA (E_LBA; ~3000 to 2900 BP). We merged the haplogroup information of our single Nanwan individual with 29 previously published Tianshanbeilu individuals to comprise the E_BA group, given the close archaeological relationship between the two sites (18). In addition, we collected 10 samples from the fourth to fifth layers of the Xiaohe archaeological site in the eastern Tarim Basin, southeastern Xinjiang (SEXiaohe_BA; ~3929 to 3572 BP) (figs. S1 and S2) (20). These groupings represent the eastern, western, northern, and southeastern Xinjiang populations during the BA, as indicated by the first letters of their labels (Fig. 1). Fig. 1 Geographic locations and haplogroups of ancient Xinjiang samples. (A) Geographic locations and haplogroups of BA and IA/HE samples from eastern (E), western (W), southern (S), and northern (N) Xinjiang (XJ). The different colored and shaped symbols overlaying Xinjiang represent different sites (group names in the map are consistent with those in the manuscript). We merged haplogroup information of our one Nanwan (NW) individual with 29 previously published Tianshanbeilu (TSBL) individuals to comprise the E_BA group. Colored bar plots represent the frequencies of various haplogroups, shown on the bottom right. (B) Timeline of Xinjiang sites with the number of individuals in parentheses. NS, NC, and NWA_EMBA are the abbreviations of NSSG_EMBA, NChemur_EMBA, and NWAfana_EMBA, respectively. For the IA, we collected 128 samples (~2900 to 2000 BP) across Xinjiang (Fig. 1), of which 27 were from eastern Xinjiang (E_IA), 15 from northern Xinjiang (N_IA), 55 from the Ili region in western Xinjiang (W_IA), and 31 from southern Xinjiang (S_IA). We did not merge the different S_IA archaeological sites into one large group because of their high cultural heterogeneity and wide geographic distribution (31–36); we analyzed them as separate groups. The S_IA groups SZGLK_IA (n = 19) and SWJEZKL_IA (n = 12) were from the Tarim Basin, while the SWJEZKL_IA was from the high-altitude region of southwestern Xinjiang, adjacent to the Pamir Plateau (Fig. 1). We also collected and analyzed the haplogroup information of 10 published IA individuals (~2200 BP) from the Shirenzigou site of eastern Tianshan (grouped as SRZG_IA) (26). In addition to the BA and IA mitogenomes, we also sequenced mtDNA from 46 HE (~2000 to 500 BP) individuals. Considering the sample size and highly mixed archaeological cultures of HE sites, we first grouped the samples based on their geographical locations and then additionally subdivided geographical groups based on their archaeological cultures. There are five groups in total, one from western Xinjiang (W_HE; n = 11), three from southern Xinjiang (SBZL_HE, n = 15; SSPL_HE, n = 10; and SHetian_HE, n = 9), and one individual from the Baiyanghe site in eastern Xinjiang (E_HE). In addition, we obtained the published ancient (n = 738) and present-day (n = 7085) mtDNA data from regions surrounding Xinjiang and grouped all these populations into several subgroups based on previous genetic studies (see Box 1 and table S1 for additional details).
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Post by Admin on Jul 7, 2021 3:46:10 GMT
In general, for all the sampled ancient Xinjiang populations, we find a positive and significant correlation coefficient between maternal genetic distance (FST) and geographic distance (R2 ≈ 0.0327, P ≈ 0.018) (fig. S3), using the Mantel test (37, 38). Thus, ancient Xinjiang populations were likely highly admixed and had low geographic structuring. The genetic comparison of BA, IA, and HE Xinjiang populations also revealed variation in nucleotide diversity (π) (fig. S4). IA and HE populations, generally, showed higher π compared to their BA populations, indicative of elevated population migration and admixture during the IA and HE relative to the BA. Among the IA and HE populations, W_HE (0.0024 ± 0.0013) showed the highest diversity, with the lowest diversity observed in southern Xinjiang populations (0.0015 ± 0.0008 to 0.0020 ± 0.0010) (fig. S4).
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