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Post by Admin on Feb 26, 2022 20:28:40 GMT
An Ancestry Profile Widespread During the Indus Valley Civilization
We document 11 outliers—3 with radiocarbon dates between 2500–2000 BCE from the BMAC site of Gonur, and 8 with radiocarbon dates or archaeological context dates between 3300 BCE to 2000 BCE from the eastern Iranian site of Shahr-i-Sokhta—that harbored elevated proportions of AHG-related ancestry (range of 11–50%) and the remainder from a distinctive mixture of Iranian farmer- and WSHG-related ancestry (~50–89%). These outliers had no detectable Anatolian farmer-related ancestry, in contrast with the main BMAC (~20–25% Anatolian-related) and Shahr-i-Sokhta (~16–21%) clusters, allowing us to reject both the BMAC and Shahr-i-Sokhta main clusters as sources for them (p<10−7, χ2 test; (13), Table S83). Without ancient DNA from individuals buried in IVC cultural contexts, we cannot make a definitive statement that the genetic gradient represented by these 11 outlier individuals, which we call the Indus Periphery Cline, was also an ancestry profile common in the IVC. Nevertheless, our result provides six circumstantial lines of evidence for this hypothesis. (i) These individuals had no detectable Anatolian farmer-related ancestry suggesting they descend from groups further east along the Anatolia-to-Iran cline of decreasing Anatolian farmer-related ancestry than any individuals we sampled from this period. (ii) All 11 outliers had elevated proportions of AHG-related ancestry, and two carried Y chromosome haplogroup H1a1d2 which today is primarily found in southern India. (iii) At both Gonur and Shahr-i-Sokhta there is archaeological evidence of exchange with the IVC (46, 47), and all the outlier individuals we directly dated fall within the time frame of the mature IVC. (iv) Several outliers at Shahr-i-Sokhta were buried with artifacts stylistically linked to Baluchistan in South Asia whereas burials associated with the other ancestries did not have these linkages (13). (v) In our modeling, the 11 outliers fit as a primary source of ancestry for 86 ancient individuals from post-IVC cultures living near the headwaters of the Indus River ~1200–800 BCE as well as diverse present-day South Asians, whereas no other ancient genetic clusters from Turan fit as sources for all these groups ((13), Fig S50). (vi) The estimated date of admixture between Iranian farmer-related and AHG-related ancestry in the outliers is several millennia before the time they lived (71 ± 15 generations, corresponding to a 95% confidence interval of ~5400–3700 BCE assuming 28 years per generation (13, 48). Thus, AHG-and Iranian farmer-related groups were in contact well before the time of the mature IVC at ~2600–1900 BCE as might be expected if the ancestry gradient was a major feature of a group that was living in the Indus Valley during the IVC.
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Post by Admin on Feb 27, 2022 2:33:56 GMT
The Steppe and Forest Zone Ancestry Clines in Eurasia Established After the Advent of Farming The late hunter-gatherer individuals from northern Eurasia lie along a west-to-east hunter-gatherer gradient of increasing relatedness to East Asians (Fig. 3). In the Neolithic and Copper Ages, hunter-gatherers at different points along this cline mixed with people with ancestry at different points along a southern cline to form five later clines, two of which were in the south (the Southwest Asian Cline and the Indus Periphery Cline which are described in the previous section), and three of which were in northern Eurasia (Fig. 3). Furthest to the west in the Steppe and Forest Zone there was the European Cline, established by the spread of farmers from Anatolia after ~7000 BCE and mixture with Western European Hunter-Gatherers (19). In far eastern Europe at latitudes spanning the Black and Caspian Seas there was the Caucasus Cline, consisting of a mixture of Eastern European Hunter-Gatherers and Iranian farmer-related ancestry with additional Anatolian farmer-related ancestry in some groups (49). East of the Urals we detect a Central Asian Cline, with WSHG individuals at one extreme and Copper Age and Early Bronze Age individuals from Turan at the other.  Fig. 3. Ancestry Transformations in Holocene Eurasia. (A) Ancestry clines before and after the advent of farming. We document a South Eurasian Early Holocene Cline of increasing Iranian farmer- and West Siberian hunter-gatherer related ancestry moving west-to-east from Anatolia to Iran, and a North Eurasian Early Holocene Cline of increasing relatedness to East Asians moving west-to-east from Europe to Siberia. Mixtures of peoples along these two clines following the spread of farming formed five later gradients (shaded): moving west-to-east: the European Cline, the Caucasus Cline from which the Yamnaya formed, the Central Asian Cline which characterized much of Central Asia in the Copper and Bronze Ages, the Southwest Asian Cline established by spreads of farmers in multiple directions from several loci of domestication, and the Indus Periphery Cline. (B) Following the appearance of the Yamnaya Steppe pastoralists, Western_Steppe_EMBA (Yamnaya-like) ancestry then spread across this vast region. We use arrows to show plausible directions of spread of increasingly diluted ancestry (the arrows are not meant as exact routes which we do not have enough sampling to determine at present). Rough estimates of the timing of the arrival of this ancestry and estimated ancestry proportions are shown. A Distinctive Ancestry Profile Stretching from Eastern Europe to Kazakhstan in the Bronze Age Beginning around 3000 BCE, the ancestry profiles of many groups in Eurasia were transformed by the spread of Yamnaya Steppe pastoralist ancestry (Western_Steppe_EMBA) from its source in the Caucasus Cline (9, 49) to a vast region stretching from Hungary in the west to the Altai mountains in the east (7, 8) (Fig. 3). Over the next two millennia this ancestry spread further while admixing with local groups, eventually reaching the Atlantic shores of Europe in the west and South Asia in the southeast. The source of the Western_Steppe_EMBA ancestry that eventually reached Central Asia and South Asia was not the initial eastward expansion but instead a secondary expansion, which involved a group that had ~67% Western_Steppe_EMBA ancestry and ~33% ancestry from a point on the European Cline (8) (Fig. 3). We replicate previous findings that this group included people of the Corded Ware, Srubnaya, Petrovka, and Sintashta archaeological complexes spreading over a vast region from the border of eastern Europe to northwestern Kazakhstan (8, 19, 21), and our dataset adds more than one hundred individuals from this Western_Steppe_MLBA cluster. We also detect a further cluster, Central_Steppe_MLBA, which is differentiated from Western_Steppe_MLBA (p=7×10−6 by qpAdm), due to carrying ~9% additional ancestry derived from Bronze Age pastoralists of the central Steppe of primarily of WSHG-related ancestry (Central_Steppe_EMBA). Thus, individuals with Western_Steppe_MLBA ancestry admixed with local populations as they integrated eastward and southward. |
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Post by Admin on Feb 27, 2022 20:06:04 GMT
Bidirectional Mobility Along the Inner Asian Mountain Corridor
As in Iran/Turan, the outlier individuals provide crucial information about human interaction.
First, our analysis of 50 individuals from the Sintashta culture cemetery of Kamennyi Ambar V reveals multiple groups of outliers whom we directly radiocarbon dated to be contemporaries of the main cluster but were genetically distinctive, indicating that this was a cosmopolitan site (Fig. 2). One set of outliers had elevated proportions of Central_Steppe_EMBA (largely WSHG-related) ancestry, another had elevated Western_Steppe_EMBA (Yamnaya-related), and a third had elevated EEHG-related ancestry.
Second, in the central Steppe (present-day Kazakhstan), an individual from one site dated to 2800–2500 BCE, and individuals from three sites dated to ~1600–1500 BCE, show significant admixture from Iranian farmer-related populations that is well-fit by the main BMAC cluster, demonstrating northward gene flow from Turan into the Steppe at the same time as there was southward movement of Central_Steppe_MLBA-related ancestry through Turan to South Asia. Thus, the archaeologically documented spreads of material culture and technology both north and south along the Inner Asian Mountain Corridor (50, 51), which began as early as the middle 3rd millennium BCE, were associated with substantial movements of people (Fig. 2).
Third, we observe individuals from Steppe sites (Krasnoyarsk) dated to ~1700–1500 BCE that derive up to ~25% ancestry from a source related to East Asians (well-modeled as ESHG), with the remainder best modeled as Western_Steppe_MLBA. By the Late Bronze Age, ESHG-related admixture became ubiquitous as documented by our time transect from Kazakhstan, and ancient DNA data from the Iron Age and from later periods in Turan and the central Steppe including Scythians, Sarmatians, Kushans, and Huns (25, 52). Thus, these 1st millennium BCE to 1st millennium CE archaeological cultures with documented cultural and political impacts on South Asia cannot be important sources for the Steppe pastoralist-related ancestry widespread in South Asia today (since present-day South Asians have too little East Asian-related ancestry to be consistent with deriving from these groups), providing an example of how genetic data can rule out scenarios that are plausible based on the archaeological and historical evidence alone ((13), Fig S52). Instead, our analysis shows that the only plausible source for the Steppe ancestry is Steppe Middle to Late Bronze Age groups, who not only fit as a source for South Asia but who we also document as having spread into Turan and mixed with BMAC-related individuals at sites in Kazakhstan in this period. Taken together, these results identify a narrow time window (first half of the second millennium BCE) when the Steppe ancestry that is widespread today in South Asia must have arrived.
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Post by Admin on Feb 28, 2022 2:38:58 GMT
The Genomic Formation of Human Populations in South Asia Three Ancestry Clines That Succeeded Each Other in Time in South Asia Previous work has shown that South Asians harbor ancestry from peoples related to ancient groups in northern Eurasia and Iran, East Asians, and Australasians (9). Here we document the process through which these deep sources of ancestry mixed to form later groups. We begin with the pre-2000 BCE Indus Periphery Cline, described in an earlier section and detected in 11 outliers from two sites in cultural contact with the Indus Valley Civilization (Fig. 4). We can jointly model all individuals in this cline as a mixture of two source populations: one end of the cline is consistent with being entirely AHG-related, and the other is consistent with being 90% Iranian farmer-related and 10% WSHG-related (Fig. 4, (13)). People fitting on the Indus Periphery Cline form the majority of the ancestors of present-day South Asians. Through formal modeling, we demonstrate that it is this contribution of Indus Periphery Cline people to later South Asians, rather than westward gene flow bringing an ancestry unique to South Asia onto the Iranian plateau, that explains the high degree of shared ancestry between present-day South Asians and early Holocene Iranians (9, 13, 27).  Fig. 4. The Genomic Formation of South Asia. (A) The degree of allele sharing with southern Asian hunter-gatherers (AASI) measured by f4(Ethiopia_4500BP, X; Ganj_Dareh_N, AHG) and with Steppe pastoralists measured by f4(Ethiopia_4500BP, X; Central_Steppe_MLBA, Ganj_Dareh_N) reveals three ancestry clines that succeeded each other in time: the Indus Periphery Cline prior to ~2000 BCE, the Steppe Cline represented by northern South Asian individuals after ~2000 BCE, and the Modern Indian Cline. (B) Modeling South Asians as a mixture of Central_Steppe_MLBA, AHG (as a proxy for AASI), and Indus_Periphery_West (the individual from the Indus Periphery Cline with the least AASI ancestry). Groups along the edges of the triangle fit a two-way model, and in the interior only fit a three-way model. The 140 present-day South Asian groups on the Modern Indian Cline are shown as small dots. (C) Groups that traditionally view themselves as being of priestly status in this and the preceding panel are shown in red (“Brahmin,” “Pandit,” and “Bhumihar” but excluding “Catholic Brahmins”), and tend to have a significantly higher ratio of Central_Steppe_MLBA to Indus_Periphery_Cline ancestry than other groups. (D) Plot of the proportion of Central_Steppe_MLBA ancestry on the autosomes (x-axis) and the Y chromosome (y-axis) shows that the source of this ancestry is primarily from females in Late Bronze Age and Iron Age individuals from the Swat District of northernmost South Asia, and primarily from males in most present-day South Asians. We next characterized the 2000 BCE Steppe Cline, represented in our analysis by 117 individuals dating to 1400 BCE - 1700 CE from the Swat and Chitral districts of northernmost South Asia (Fig. 2, Fig. 4). We found that we could jointly model all individuals on the Steppe Cline as a mixture of two sources albeit different from the two sources in the earlier cline. One end is consistent with a point along the Indus Periphery Cline. The other end is consistent with a mixture of about 41% Central_Steppe_MLBA ancestry and 59% from a subgroup of the Indus Periphery Cline with relatively high Iranian farmer-related ancestry ((13), Fig S50). To understand the formation of the Modern Indian Cline, we searched for triples of populations that could fit as sources for diverse present-day South Asians groups as well as peoples of the Steppe Cline. All fitting models include as sources Central_Steppe_MLBA (or a group with a similar ancestry profile), a group of Indus Periphery Cline individuals, and either AHG or a subgroup of Indus Periphery Cline individuals with relatively high AHG-related ancestry (13), Fig S51). Co-analyzing 140 diverse South Asian groups (10) that fall on a gradient in PCA (13), we show that while there are three deep sources, just as in the case of the earlier two clines the great majority of groups on the Modern Indian Cline can be jointly modeled as a mixture of two populations that are mixed from the earlier three. While we do not have ancient DNA data from either of the two statistically reconstructed source populations for the Modern Indian Cline, the ASI or the ANI, in what follows we co-analyze our ancient DNA data in conjunction with modern data to characterize the exact ancestry of the ASI, and to provide constraints on the ANI. |
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Post by Admin on Feb 28, 2022 20:15:00 GMT
The ASI and ANI Arose as Indus Periphery Cline People Mixed with Groups to the North & East To gain insight into the formation of the ASI, we extrapolated to the least West Eurasian-related theoretical extreme of the Modern Indian Cline by setting the Central_Steppe_MLBA ancestry proportion to zero in our model. We estimate a minimum of 55% ancestry from people on the Indus Periphery Cline (by representing the Indus Periphery Cline by the individual on it with the most Iranian farmer-related ancestry, which we call Indus_Periphery_West), and modeling the reminder of the ancestry as deriving from an AHG-related group (13). We find that several tribal groups from southern India are consistent with ~0% Central_Steppe_MLBA ancestry (13). The fact that these individuals match the most extreme possible position for the ASI not only reveals that nearly direct descendants of the ASI live today in South Asia, but also allows us to make a precise statement about the ancestry profile of the ASI. In particular, the fact that they harbor substantial Iranian farmer-related ancestry (via the Indus Periphery Cline), disproves earlier suggestions that the ASI might not have any ancestry related to West Eurasians (11). Using the DATES software, we estimate an average of 107 ± 11 generations since admixture of the Iranian farmer-related and AHG-related groups in one of these groups: Palliyar. This corresponds to a 95% confidence interval of 1700–400 BCE assuming 28 years per generation (53). Thus, the ASI were note fully formed at the time of the IVC, and instead must have continued to form through mixture after its decline as material culture typical of the IVC spread eastward (54) and Indus Periphery Cline ancestry mixed with people of less West Eurasian relatedness. We also obtained additional evidence for a late (Bronze Age) formation of the ASI by building an admixture graph using qpGraph, co-modeling Palliyar and Juang (an Austroasiatic-speaking group in India with low West Eurasian-relatedness) (Fig. 5). The graph fits the component of South Asian ancestry with no West Eurasian relatedness (AASI - “Ancestral Ancient South Asians”) as an Asian lineage that split off around the time that East Asian, Andaman Islander, and Australian aboriginal ancestors separated from each other, consistent with the hypothesis that eastern and southern Asian lineages derives from an eastward spread that in a short span gave rise to lineages leading to AASI, East Asians, Andamanese Hunter Gatherers, and Australians (55) (Fig. 5). The Juang cannot be fit through a mixture of ASI ancestry and ancestry related to Austroasiatic language speakers, and instead can only be fit by modeling additional ancestry from AASI, showing that at the time Austroasiatic groups formed in South Asia, groups with less Iranian farming-related ancestry than in the ASI were also present. Austroasiatic languages are hypothesized to have spread into South Asia in the 3rd millennium BCE (based on hill cultivation systems hypothesized to be associated with the spread of Austroasiatic languages (42), and thus the ancestry profile of the Juang provides an independent line of evidence for a late (Bronze Age and plausibly post-IVC) formation of the ASI.  Fig. 5. Admixture Graph Model. The largest deviation between empirical and theoretical f-statistics is |Z|=2.9, indicating a good fit considering the large number of f-statistics analyzed. Admixture events are shown as dotted lines labeled by proportions, with the minor ancestry in gray. The present-day groups are shown in orange ovals, the ancient ones in blue, and unsampled groups in white. (The ovals and admixture events are positioned according to guesses about their relative dates to help in visualization, although the dates are in no way meant to be exact.) In this graph we do not attempt to model the contribution of WSHG and Anatolian farmer-related ancestry, and thus cannot model Central_Steppe_EMBA, the proximal source of Steppe ancestry in South Asia (instead we model the Steppe ancestry in South Asia through the more distally related Yamnaya). However, the admixture graph does highlight several key findings of the study, including the deep separation of the AASI from other Eurasian lineages, and the fact that some Austroasiatic-speaking groups in South Asia (e.g. Juang) harbor ancestry from a South Asian group with a higher ratio of AASI-related to Iranian farmer-related ancestry than any groups on the Modern Indian Cline, thus revealing that groups with substantial Iranian farmer-related ancestry were not ubiquitous in peninsular South Asia in the 3rd millennium BCE when Austroasiatic languages likely spread across the subcontinent. To shed light on the formation of the statistically reconstructed ANI, we return to the Swat Valley time transect that formed the Steppe Cline after 2000 BCE. The Modern Indian Cline intersects the Steppe Cline at a position close to the position of the Kalash, the group in northwest South Asia with the highest ANI ancestry proportion (56) (Fig. 4). The DATES-based estimate of admixture in the Kalash is 110 ± 12 generations (56), suggesting a post-IVC date of formation of the ANI paralleling the post-IVC date of formation of the ASI. Further evidence for a post-IVC integration of Steppe ancestry into South Asia comes from ancient individuals on the Steppe Cline (along which the ANI could theoretically have formed) whose admixture date for Steppe ancestry is also post-IVC. Specifically, we estimate the date of admixture into the Late Bronze Age and Iron Age individuals from the Swat District of northernmost South Asia to be on average 26 generations before the date that they lived, corresponding to a 95% confidence interval of ~1900–1500 BCE. This time scale for the arrival of Steppe ancestry in the region is consistent with our observation of 6 outlier individuals in Turan who lived between ~2000–1500 BCE and who carry this ancestry in mixed form (Fig. 2), and with our finding that the R1a Y chromosome associated with Central_Steppe_MLBA ancestry in South Asia is also present in the Swat District Late Bronze and Iron Age individuals (2 copies). Taken together, these results show neither of the two primary source populations of the Modern Indian Cline, the ANI and ASI, was fully formed before the turn of the 2nd millennium BCE. |
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