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Post by Admin on Mar 1, 2022 1:33:19 GMT
Steppe Ancestry in South Asia is Primarily from Males and Disproportionately High in Brahmins In the Late Bronze Age and Iron Age individuals of the Swat Valley, we detect a significantly lower proportion of Steppe admixture on the Y chromosome (only 5% of the 44 Y chromosomes of the R1a-Z93 subtype that occurs at 100% frequency in the Central_Steppe_MLBA males) compared to 20% on the autosomes (Z = −3.9 for a deficiency from males under the simplifying assumption that all the Y chromosomes are unrelated to each other since admixture and thus statistically independent), documenting how Steppe ancestry was incorporated into these groups largely through females (Fig. 4). However, sex bias varied in different parts of South Asia, as in present-day South Asians we observe a reverse pattern of excess Central_Steppe_MLBA-related ancestry on the Y chromosome compared to the autosomes (Z = 2.7 for an excess from males) (13, 57) (Fig. 4). Thus, the introduction of lineages from Steppe pastoralists into the ancestors of present-day South Asians was mediated mostly by males. This bias is similar in direction to what has been documented for the introduction of Steppe ancestry into Iberia in far western Europe, although the bias is less extreme than reported in that case (58).
Our analysis of Steppe ancestry also identified 6 groups with a highly significantly elevated ratio of Central_Steppe_MLBA-to-Indus_Periphery_West-related ancestry compared to the expectation for the model at the Z < −4.5 level. The strongest two signals were in Brahmin_Tiwari (Z = −7.9) and Bhumihar_Bihar (Z = −7.0). More generally, there is a notable enrichment in groups that consider themselves to be of traditionally priestly status: 5 of the 6 groups with Z < −4.5 were Brahmins or Bhumihars even though they comprise only 7–11% of the 140 groups analyzed (p<10−12 by a χ2 test assuming all the groups evolved independently). We caution that this is not a formal test as there is an unknown degree of shared ancestry among groups since they formed by mixture, and because our decisions about which groups to include in the analysis was not made in a blinded way; for example, we excluded four “Catholic Brahmin” groups with strong evidence of substantial shared ancestry in the last millennium (10) which makes them not statistically independent (Table S5, Fig. 4 (13)). Nevertheless, the fact that traditional custodians of liturgy in Sanskrit (Brahmins) tend to have more Steppe ancestry than is predicted by a simple ASI-ANI mixture model provides an independent line of evidence, beyond the distinctive ancestry profile shared between South Asia and Bronze Eastern Europe mirroring the shared features of Balto-Slavic and Indo-Iranian languages (59), for a Steppe origin for South Asia’s Indo-European languages prior to ~2000 BCE.
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Post by Admin on Mar 1, 2022 3:06:46 GMT
Discussion Our analysis reveals that the ancestry of the greater South Asian region in the Holocene was characterized by at least three genetic gradients. Prior to ~2000 BCE, there was the Indus Periphery Cline consisting of people with different proportions of Iranian farmer- and AASI-related ancestry, which we hypothesize was a characteristic feature of many IVC people. The ASI formed after 2000 BCE as a mixture of a point along this cline with South Asians with higher proportions of AASI-related ancestry. Between about 2000 and 1000 BCE, people of largely Central_Steppe_MLBA ancestry expanded toward South Asia, mixing with people along the Indus Periphery Cline to form the Steppe Cline. Multiple points along the Steppe Cline are represented by individuals of the Swat Valley time transect and statistically we find that the ANI, one of the two primary source population of South Asia, can fit along the Steppe Cline. After 2000 BCE, mixtures of mixed populations—the ASI and ANI—mixed themselves to form the Modern Indian Cline, which is represented today in diverse groups in South Asia (Fig. 4).
Our finding based on admixture linkage disequilibrium ((13), Fig S59) that the mixture that formed the Indus Periphery Cline occurred by ~5400–3700 BCE—at least a millennium before the formation of the mature IVC—raises two possibilities. One is that Iranian farmer-related ancestry in this group was characteristic of the Indus Valley hunter-gatherers in the same way as it was characteristic of northern Caucasus and Iranian plateau hunter-gatherers. The presence of such ancestry in hunter-gatherers from Belt and Hotu Caves in northeastern Iran increases the plausibility that this ancestry could have existed in hunter-gatherers further east. An alternative is that this ancestry reflects movement into South Asia from the Iranian plateau of people accompanying the eastward spread of wheat and barley agriculture and goat and sheep herding as early as the 7th millennium BCE and forming early farmer settlements such as those at Mehrgarh in the hills flanking the Indus Valley (60, 61). However, this is in tension with the observation that the Indus Periphery Cline people had little if any Anatolian farmer-related ancestry, which is strongly correlated with the eastward spread of crop-based agriculture in our dataset. Thus, while our analysis supports the idea that eastward spread of Anatolian farmer-related ancestry was associated with the spread of farming to the Iranian plateau and Turan, our results do not support large-scale movements of ancestry from the Near East into South Asia following ~6000 BCE (the time after which all ancient individuals from Iran in our data have Anatolian farmer-related ancestry even though South Asians have very little). Languages in pre-state societies usually spread through movements of people (62), and thus the absence of much Anatolian farmer-related ancestry in the Indus Periphery Cline suggests that the Indo-European languages spoken in South Asia today are unlikely to owe their origin to the spread of farming from West Asia.
Our results not only provide negative evidence against an Iranian plateau origin for Indo-European languages in South Asia, but also positive evidence for the theory that these languages spread from the Steppe. While ancient DNA has documented westward movements of Steppe pastoralist ancestry providing a likely conduit for the spread of many Indo-European languages to Europe (7, 8), the chain-of-transmission into South Asia has been unclear because of a lack of relevant ancient DNA. Our observation of the spread of Central_Steppe_MLBA ancestry into South Asia in the first half of the 2nd millennium BCE provides this evidence, and is particularly striking as it provides a plausible genetic explanation for the linguistic similarities between the Balto-Slavic and Indo-Iranian sub-families of Indo-European, which despite their vast geographic separation, share the Satem innovation and Ruki sound laws (63). If the spread of people from the Steppe in this period was a conduit for the spread of South Asian Indo-European languages, then it is striking that there are so few material culture similarities between the central Steppe and South Asia in the Middle to Late Bronze Age (i.e. after the middle of the 2nd millennium BCE). Indeed, the material culture differences are so substantial that some archaeologists recognize no evidence of a connection. However, lack of material culture connections does not provide evidence against spread of genes, as has been demonstrated in the case of the Beaker Complex, which originated largely in western Europe, but in Central Europe was associated with skeletons that harbored ~50% ancestry related to Yamnaya Steppe pastoralists (18). Thus, in Europe we have an unambiguous example of people with ancestry from the Steppe making profound demographic impacts on the regions into which they spread while adopting important aspects of local material culture. Our findings document a similar phenomenon in South Asia, with the locally acculturated population harboring up to ~20% Western_Steppe_EMBA-derived ancestry according to our modeling (via Central_Steppe_MLBA groups) (Fig. 3). Our analysis also provides a second line of evidence for a linkage between Steppe ancestry and Indo-European languages. Steppe ancestry enrichment in groups that view themselves as being of traditionally priestly status is striking as some of these groups including Brahmins are traditional custodians of literature composed in early Sanskrit. A possible explanation is that the influx of Central_Steppe_MLBA ancestry into South Asia in the mid-2nd millennium BCE created a meta-population with varied proportions of Steppe ancestry, with people of more Steppe ancestry (or admixing less with Indus Periphery Cline groups) tending to be more strongly associated with Indo-European culture. Due to strong endogamy, which kept groups generally isolated from neighbors for thousands of years (7), some of this population substructure persists in South Asia among present-day custodians of Indo-European texts.
Our findings also shed light on the origin of its second-largest language group in South Asia, Dravidian. The strong correlation between ASI ancestry and present-day Dravidian languages suggests that the ASI, which we have shown formed as groups with ancestry typical of the Indus Periphery Cline moved south and east after the decline of the IVC to mix with groups with more AASI ancestry, most likely spoke an early Dravidian language. A possible scenario combining genetic data with archaeology and linguistics is that proto-Dravidian was spread by peoples of the IVC along with the Indus Periphery Cline ancestry component of the ASI. Non-genetic support for an IVC origin for Dravidian languages includes the present-day geographic distribution of these languages (in southern India and southwestern Pakistan), and a suggestion that some symbols on ancient Indus Valley seals denote Dravidian words or names (64, 65). An alternative possibility is that proto-Dravidian was spread by the approximately half of the ASI’s ancestry that was not from the Indus Periphery Cline, and instead derived from the south and the east (peninsular South Asia). The southern scenario is consistent with reconstructions of Proto-Dravidian terms for flora and fauna unique to peninsular India (66, 67).
We finally highlight a remarkable parallel between the prehistory of South Asia and Europe. In both regions there were exchanges between people related to Southwest Asian people and local people; mixtures of these groups led to the Indus Periphery Cline in South Asia and the European Cline in Europe. In both subcontinents, people arriving in the 3rd and 2nd millennia BCE who descended from mixtures of people related to Yamnaya Steppe pastoralists and European farmers mixed further with local populations: in South Asia forming the ANI, and in Europe forming groups like that of the Beaker Complex. In both cases, mixtures of these mixed populations—those with Steppe pastoralist-related admixture and those without—drive the modern ancestry clines in both regions (Fig. 3). However, there are also profound differences between the Bronze Age and Neolithic spreads of ancestry across the two subcontinents. One is that the maximum proportion of local ancestry is higher in South Asia (AASI ancestry of up to ~60%) than Europe (WEHG ancestry of up to ~30%) (7), which could reflect stronger ecological or cultural barriers to the spreads of people in South Asia than in Europe, allowing the previously established groups more time to adapt and mix with incoming groups. A second difference is the smaller proportion of Steppe pastoralist-related ancestry in South Asia than in Europe, its later arrival by ~500–1000 years, and a lower male sex bias in the admixture, factors that help to explain the continued persistence of a large fraction of non-Indo-European speakers amongst people of present-day South Asia today. The situation in South Asia is somewhat reminiscent of Mediterranean Europe where the proportion of Steppe ancestry is considerably lower than that of northern and central Europe (Fig. 3), and where many non-Indo European languages are attested in classical times (68). Further studies of ancient DNA from South Asia and the linguistically related Iranian world will extend and add nuance to the model presented here.
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Post by Admin on Mar 1, 2022 20:46:38 GMT
Genetic continuity of Indo-Iranian speakers since the Iron Age in southern Central Asia Perle Guarino-Vignon, Nina Marchi, Julio Bendezu-Sarmiento, Evelyne Heyer & Céline Bon Scientific Reports volume 12, Article number: 733 (2022)
Abstract Since prehistoric times, southern Central Asia has been at the crossroads of the movement of people, culture, and goods. Today, the Central Asian populations are divided into two cultural and linguistic groups: the Indo-Iranian and the Turko-Mongolian groups. Previous genetic studies unveiled that migrations from East Asia contributed to the spread of Turko-Mongolian populations in Central Asia and the partial replacement of the Indo-Iranian populations. However, little is known about the origin of the latters. To shed light on this, we compare the genetic data on two current-day Indo-Iranian populations — Yaghnobis and Tajiks — with genome-wide data from published ancient individuals. The present Indo-Iranian populations from Central Asia display a strong genetic continuity with Iron Age samples from Turkmenistan and Tajikistan. We model Yaghnobis as a mixture of 93% Iron Age individual from Turkmenistan and 7% from Baikal. For the Tajiks, we observe a higher Baikal ancestry and an additional admixture event with a South Asian population. Our results, therefore, suggest that in addition to a complex history, Central Asia shows a remarkable genetic continuity since the Iron Age, with only limited gene flow.
Introduction Central Asia is a large region stretching from the Caspian Sea in the west to Lake Baikal in the east, encompassing Tajikistan, Kazakhstan, Turkmenistan, Uzbekistan, Kyrgyzstan and north Afghanistan. This region has found itself at the crossroads of migration routes since modern humans left Africa1,2, leading to a long-term presence of humans, a rich history, and a high cultural diversity. For illustration, agropastoral communities present since the Djeitun culture3 6000 years BCE were replaced during the Chalcolithic (4800–3000 BCE) by the emergence of denser villages and the premises of irrigated agriculture. During the Middle Bronze Age, the Bactrio Margian Archaeological Complex (BMAC) civilization flourished in southern Central Asia with characteristic proto-urban cities, powerful irrigation techniques, and a marked social hierarchy4. A pastoral nomadic lifestyle emerged later in northern Central Asia around 3000 BCE and gained importance in this region during the late Bronze Age (2400–2000 BCE). At the end of the Bronze Age, from about 1800 BCE, the Oxus civilization underwent during its final phase important transformations: while remaining in the same tradition, the material culture was impoverished with some ceramic forms and artifacts disappearing; some habitat sites were abandoned, monumental architecture disappeared, the level of technological development seemed to decrease5; international trade, which had been flourishing during the previous peak phase, slowed down considerably, or even came to a halt, except for contacts with the steppes of northern Central Asia6; funerary practices changed with the appearance of new modes of burial, before the total disappearance of burials during the Early Iron Age, that can be linked to an ideological evolution7. The period between 1800 and 1500 BCE saw Andronovo-like culture take over, until the rise of Yaz culture8,9. Then, Central Asia was the scene of the eastwards conquests of Achaemenids, Greeks, Partho-Sassanians and Arabic people and of the westward movement of various Asian peoples like the Huns, the Xiongnus, and the Mongols10, before being a trade centre along the Silk Road, particularly during the Sassanid Empire and after the Islamic invasion.
Today, the complex demographic history of Central Asia results in a composite genetic diversity, with modern Central Asian populations being divided into two culturally distinct groups: a first group composed of Turkic and Mongolic-speaking populations (referred to later as Turko-Mongol populations including Kyrgyz, Kazakhs…), who are semi-nomadic herders10 and show genetic affinities with Eastern Asian and Siberian populations; and a second group formed by Tajiks and Yaghnobis who live in southern Central Asia, speak Indo-Iranian languages, practice agriculture, are sedentary and who are genetically more similar to present-day western Eurasian populations2,11 and Iranians12. Moreover, Yaghnobis are known to have been isolated for a long time with no evidence of recent admixture12. Modern DNA studies suggested that the Indo-Iranian group was present in Central Asia before the Turko-Mongol group11, maybe as early as Neolithic times; the Turko-Mongol group emerged later from the admixture between a group related to local Indo-Iranian and a South-Siberian or Mongolian group11,13,14 with a high East-Asian ancestry (around 60%). Turkmens, however, genetically stand out from the Turko-Mongol group, being intermediate with the Indo-Iranian group15, which suggests a recent language and culture shift16, possibly through a mostly elite dominance-driven linguistic replacement.
Paleogenetic studies confirmed that multiple migration waves and admixture events, in which steppe populations played an important role, have occurred in Eurasia in the last 10,000 years13,17,18,19,20. Although the settlement of Europe was extensively studied21,22,23,24,25,26, there have been only a few studies exploring the population history of Central Asia, and even fewer focusing on southern Central Asia. In northern Central Asia (Kazakhstan, Southern Russia), genetic studies evidenced eastward and westward movement of populations since the late Neolithic period13,17,18,27,28, leading to a gradient of western steppe genetic ancestry. In southern Central Asia where most of the ancient genomes date back to the late Neolithic and the Bronze Age, it was shown that populations from the BMAC were strongly related to southern Iranian ancient populations with some individuals displaying additional steppe-ancestry18.
However, the relation between modern Indo-Iranian speaking populations and ancient populations from southern Central Asia remains unclear: what are the genetic sources of modern Indo-Iranian speakers? Can they be traced back to the Iron or the Bronze Age? Is there one or several different population histories among a given linguistic group of populations? What is the role of the Turkmens in this story?
Paleogenetic studies brought additional tools to seek the origins of these populations. To explore the origins of modern Indo-Iranians in relationship with their Turko-Mongol neighbours, we jointly analyzed genome-wide data in 16 modern populations (one Yaghnobi and four Tajik populations, 11 from distinct Turko-Mongol ethnic groups from Central Asia, i.e. in Uzbekistan, Kyrgyzstan, Tajikistan and from West Mongolia and South Siberia) as well as 1501 present-day genomes from Eurasia and Africa29,30 and 3109 ancient published genomes from all Eurasia13,17,18,19,20,22,23,24,27,28,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45 (Table S1), including 126 ancient genomes from southern Central Asia17,18 (Fig. 1a).
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Post by Admin on Mar 1, 2022 22:03:59 GMT
Figure 1 Geographic and genetic structure of our dataset. (a) Map of the published ancient samples in our dataset (Map generated using ggmap46 and Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL). (b) PCA computed on a set of 236,566 SNPs for present-day Eurasians populations including 527 present-day Central Asian individuals genotyped on an 300k SNPs array15 and we projected the 3102 ancient genomes onto the two first Principal Components. Ancient genomes are represented with different colors by region, with density line to facilitate the reading. (c) Details of panel (b) focusing on Indo-Iranians individuals with ancient individuals from Neolithic, Bronze Age, Iron Age and Historical times. (Figures done with ggplot2 v. 3.3.3 R package cran.r-project.org/web/packages/ggplot2/index.html).
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Post by Admin on Mar 2, 2022 1:20:44 GMT
Results Modern Indo-Iranian genetic affinities with ancient samples To explore the relation between present-day Central Asian individuals and the Eurasian genomic diversity, ancient and modern, we first performed a Principal Component Analysis (PCA) (Fig. 1b, Supplementary fig. S1 and S2) on 1915 modern genomes and projected 3102 ancient genome-wide data onto it. Regarding the present-day Eurasian diversity, the three top Principal Components (PCs) roughly mimic the geographical repartition of modern populations: the PC1 (3% of variance) discriminates between Eastern and Western Eurasian individuals, the PC2 between South Asian and modern European individuals, and the PC3 discriminates against the Baikal populations from the East Asian cluster (see Supplementary fig. S1). Present-day Indo-Iranian individuals from Central Asia cluster together on the first three PCs while Turko-Mongol individuals form a gradient from the Indo-Iranian cluster to ancient Baikal samples on PC3, in agreement with cultural categorization instead of geography. However, a substructure appears within the Indo-Iranian group with the Yaghnobis (TJY) falling closely to the Western cluster, while the Tajiks populations (TJA, TJE, TAB) stretch toward the Baikal cluster, indicating some additional East Asian or Baikal Hunter-Gatherer (BHG) proximity. For the ancient individuals, Bronze Age, Iron Age, and historical steppe individuals fall on a cline stretching up from European to East Asian groups, with Western_Steppe individuals clustering on the bottom of the European cluster and Central_Steppe individuals spreading from the Western_Steppe cluster to the Okunevo_BA cluster close to Baikal and Siberian modern individuals. The ancient individuals of southern Central Asia (Neolithic, Bronze Age and Iron Age) follow a cline stretching from Neolithic Iranian individuals (Iran_N) to present-day Iranians and Yaghnobis. Contrastingly, the Iron Age samples (Turkmenistan_IA and Ksirov_Kushan individuals) are located close to modern Indo-Iranian populations, although slightly negative values on the first axis and positive values on the third axis suggest an addition of Baikal ancestry in the present-day Indo-Iranians. Finally, it appears from this PCA (Fig. 1c) that ancient and present-day Indo-Iranian populations from Central Asia form together a cline between Iranian Neolithic farmers and Central_Steppe Bronze Age, with a clear shift in ancestry toward Steppe between Bronze Age and Iron Age as observed before18, and a smaller shift toward eastern Asian ancestry between Iron Age and present-day. This shift is more pronounced for Tajiks than Yaghnobis. To confirm our initial observations and identify genetic structures, we performed an unsupervised clustering analysis using ADMIXTURE47 on the same dataset used for the PCA (see Supplementary fig. S4, S5 and S6). Consistently with the PCA, we evidenced in all modern Indo-Iranians the presence of a genetic component maximized in Iran Neolithic farmers (Iran_N, dark green; mean value for Yaghnobis: 37%; 25% for Tajiks), of another maximized in Eastern European Hunter-Gatherers (EEHG) and Western Scandinavian Hunter-Gatherers (WSHG) (pale green; mean value for Yaghnobis: 13%; for Tajiks: 10%) and of a third component (dark blue; mean value for Yaghnobis: 36%; for Tajiks: 29%) that is not completely maximized in any population of our dataset, but is found in present-day Europeans and in Anatolian Neolithic farmers (Anatolia_N). In addition, a fourth component maximized in Baikal Hunter-Gatherers (BHG: Shamanka_EN) and largely present in all modern Turko-Mongol populations (red; 50% on average) is also inferred to a lower extent in the modern Indo-Iranian populations, with a significantly smaller proportion in Yaghnobis than in Tajiks (mean value respectively 7% and 14%; t-test p-value = 2.10–16). Finally, the Tajiks present a small proportion (4%) of modern East Asian ancestry (pink component, maximized in the Han population), which is largely present in all Turko-Mongol populations from Central Asia (mean value 10%), and around 8% of the component maximized in present-day South Asian populations (orange), which are both absent in Yaghnobis. The ADMIXTURE analysis is also congruent with the PCA concerning the ancient groups (see Supplementary fig. S4 and S5). Indeed, Iron Age southern Central Asian individuals present a remarkably similar profile to Yaghnobis’ profile: for instance, the individual labelled as Turkmenistan_IA has a profile with about 25% of WSHG/EEHG component, 30% of Iran_N component and 35% of the Anatolian farmer ancestry component but missing BHG ancestry (Fig. 2). Bronze Age Central Steppe pastoralists show a similar profile except for a significant increase in Iranian ancestry, and Western Steppe pastoralists have the beige component maximized in Western European Hunter-Gatherers (WEHG), which is absent in modern Indo-Iranian populations. Figure 2 ADMIXTURE analysis of 5019 individuals (3102 ancient and 1915 modern). The results for a subset of the dataset (present-day Indo-Iranian individuals and ancient populations discussed in the main text) are displayed for K = 10, which has the lowest cross validation value (0.994). The full analysis is shown in SI. In the first column, the modern individuals from Central Asia; second column, the ancient individuals from southern Central Asia; third column, ancient individuals from the Steppe; last column, miscellaneous individuals discussed in the main text. (Figure done with ggplot2 v. 3.3.3 R package cran.r-project.org/web/packages/ggplot2/index.html). Thus, modern Indo-Iranian speaking populations appear as midway between Central Steppe and southern Central Asia Bronze Age populations, quite similarly to the Turkmenistan Iron Age individuals, with a limited impulse from eastern and southern Asian groups.
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