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Genetic History of India Jan 6, 2022 1:14:47 GMT

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Introduction
The past ten thousand years have witnessed profound economic changes driven by the transition from foraging to food production, and have also witnessed dramatic changes in cultural practice evident from archaeology, the distribution of languages, and the written record. The extent to which these changes were associated with movements of people has been a mystery in Central Asia and South Asia in part because of a paucity of ancient DNA. We report genome-wide data from 523 individuals from Central Asia and northernmost South Asia from the Mesolithic period onward (1), and co-analyze them with previously published ancient DNA from across Eurasia and with data from diverse present-day people.

In Central Asia, we studied the extent to which the spread of farming and herding practices from the Iranian plateau to the desert oases south of the Steppe was accompanied by movements of people or adoption of ideas from neighboring groups (2–4). For the urban communities of the Bactria Margiana Archaeological Complex (BMAC) in the Bronze Age, we assessed whether the people buried in its cemeteries descended directly from earlier smaller scale food producers, and also documented their genetic heterogeneity (5). Further to the north and east, we showed that the Early Bronze Age spreads of crops and domesticated animals between southwest Asia and eastern Eurasia along the Inner Asian Mountain Corridor (6) was accompanied by movements of people. Finally, we examined when descendants of the Yamnaya, who spread across the Eurasian Steppe beginning around 3300 BCE (7–9), began to appear in Central Asia south of the Steppe.

In northernmost South Asia, we report a time transect of more than one hundred individuals beginning ~1200 BCE, which we co-analyze along with modern data from hundreds of present-day South Asian groups, as well as ancient DNA from neighboring regions (10). Previous analyses place the majority of present-day South Asians along a genetic cline (11) that can be modeled as having arisen from mixture of two highly divergent populations after 4000 years ago: the Ancestral North Indians (ANI) who harbor large proportions of ancestry related to West Eurasians, and the Ancestral South Indians (ASI) who are much less closely related to West Eurasians (12). We leveraged ancient DNA to place constraints on the genetic structure of the ANI and ASI and, in conjunction with other lines of evidence, to make inferences about when and where they formed. By modeling modern South Asians along with ancient individuals from sites in cultural contact with the IVC, we inferred a likely genetic signature for people of the Indus Valley Civilization (IVC) which reached its maturity in northwestern South Asia 2600–1900 CE. We also examined when Steppe pastoralist-derived ancestry (9) mixed with groups in South Asia, and placed constraints on whether Steppe-related ancestry or Iranian-related ancestry is more plausibly associated with the spread of Indo-European languages in South Asia.

Dataset and Analysis Strategy
We generated whole-genome ancient DNA data from 523 previously unsampled ancient individuals and increased the quality of data from 19 previously sequenced individuals. The individuals derive from three broad geographical regions: 182 from Iran and the southern part of Central Asia that we call Turan (present-day Turkmenistan, Uzbekistan, Tajikistan, Afghanistan and Kyrgyzstan), 209 from the Steppe and northern forest zone mostly in present-day Kazakhstan and Russia, and 132 from northern Pakistan. The ancient individuals are from 1) Mesolithic, Copper, Bronze and Iron Age Iran and Turan (12000–1 BCE from 19 sites) including the Bactria Margiana Archaeological Complex (BMAC); 2) early ceramic-using hunter-gatherers from the western Siberian forest zone who we show represent a point along an early Holocene cline of North Eurasians and who emerge as a valuable source population for modeling the ancestry of Central and South Asians (6400–3900 BCE from 2 sites); 3) Copper Age and Bronze Age pastoralists from the central Steppe, including from Bronze Age Kazakhstan (3400–800 BCE from 56 sites); and 4) northernmost South Asia, specifically Late Bronze Age, Iron Age and historical settlements in the Swat and Chitral districts of present-day Pakistan (~1200 BCE - 1700 CE from 12 sites) (Fig. 1, Table S1, (1, 13)). We prepared samples in dedicated clean rooms, extracted DNA (14, 15), and constructed libraries for Illumina sequencing (16, 17). We enriched the libraries for DNA overlapping around 1.2 million single nucleotide polymorphisms (SNPs) (7, 18, 19), sequenced the products on Illumina instruments, and performed quality control (Table S2) (7, 19, 20). Our final dataset after merging with previously reported data (7–9, 16, 18, 19, 21–31) spans 837 ancient individuals that passed all our analysis filters, which included removing individuals determined genetically to be first-degree relatives of other higher coverage individuals (Table S3), and restricting to the 92% of individuals (Table S1) that were represented by at least 15,000 of the targeted SNPs which we found was the number at which we began to be able to reliably estimate proportions of the deeply divergent ancestry sources. The median number of SNPs analyzed per individual was 617,000. We also merged with previously reported whole genome sequencing data from 686 present-day individuals (Table S1), and co-analyzed with 1,789 present-day people from 246 ethnographically-distinct groups in South Asia genotyped at ~600,000 SNPs (Table S5; (13)) (10, 32, 33).

Fig. 1
Overview of ancient DNA data.
(A) Distribution of sites and associated archeological or radiocarbon dates along with the number of individuals meeting our analysis thresholds from each site. (B) Locations of ancient individuals for whom we generated ancient DNA that passed our analysis thresholds along with the locations of individuals from 140 groups from present-day South Asia that we analyzed as forming the Modern Indian Cline. Shapes distinguish the individuals from different sites. Data from 106 South Asian groups that do not fit along the Modern Indian Cline as well as AHG are not shown. (C) PCA analysis of ancient and modern individuals projected onto a basis formed by 1,340 present day Eurasians reflects clustering of individuals that mirrors their geographical relationships. An interactive version of this figure is presented in the Online Data Visualizer.

We grouped individuals based on archaeological and chronological information, taking advantage of 269 direct radiocarbon dates generated on skeletal material from the individuals from whom we report DNA (Table S4). We further clustered individuals that were genetically indistinguishable within these groupings, and labeled outliers with ancestry that was significantly different from others at the same site and time period (13). For our primary analyses, we did not include individuals that were the sole representatives of their ancestry profiles, thereby reducing the chance that our conclusions were being driven by single individuals with contaminated DNA or misattributed archaeological context. This also ensured that each major analysis grouping was represented by many more SNPs that our minimum cutoff of 15,000 per individual. Thus, all but one analysis cluster included at least one individual covered by >200,000 SNPs, sufficient to support high resolution analysis of population history (19) (the exception is a pair of genetically similar outliers from the site of Gonur who are not the focus of any main analyses). We use Italic font to refer to genetic groupings and plain font to indicate archaeological cultures or sites.

To make inferences about population structure, we began by carrying out principal component analysis (PCA) projecting ancient individuals onto the patterns of genetic variation in present-day Eurasians, a procedure that allowed us to obtain meaningful constraints on ancestry even of ancient individuals with limited coverage because each SNP from each individual can be compared to a large reference data set (34–36). This revealed three major clusters strongly correlating to the geographic regions of the Forest Zone/Steppe, Iran/Turan, and South Asia (Fig. 1), a pattern we replicate in ADMIXTURE unsupervised clustering (37). To test if groups of ancient individuals were heterogeneous in their ancestry, we used f4-statistics to measure whether different partitions of these groups into two subgroups differed in their degree of allele sharing to a third group (using a distantly related outgroup as a baseline). We also used f3-statistics to test for admixture (33). To model the ancestry of each group, we used qpAdm, which evaluates whether a tested group is consistent with deriving from a pre-specified number of source populations (relative to a set of outgroups), and if so estimates proportions of ancestry (7). We first used qpAdm to attempt to model groups from the Copper Age and afterward as a mixture of seven “distal” sources related deeply to pre-Copper Age or distantly related modern populations for which we have data (Box 1). In this paper we use the term ‘farmers’ to refer to people who either cultivated crops, or herded animals, or both; this definition covers not only large settled communities but also smaller and probably less sedentary communities like the early herders of the Zagros Mountains of western Iran from the site of Ganj Dareh. The latter kept domesticated animals but did not cultivate crops, and are a key reference population for this study as they had a distinctive ancestry profile that spread widely after the Neolithic (9, 24, 38). We also identified “proximal” models for each group as mixtures of temporally preceding groups (10). We implemented an algorithm, DATES, for estimating the age of population mixtures by measuring the average size of segments of ancestry derive from the admixing populations, an approach whose reliability we verified by computer simulation (10) and that is an improvement relative to methods not optimized for analysis of ancient DNA (33, 39) (the approach’s robustness reflects the fact that it relies for its molecular clock on the accurately measured rate of meiotic recombination in humans (40)). In Box 2, we summarize the findings of these analyses (we use the same headings in Box 2 and the main text to allow cross-referencing), while the Online Data Visualizer (1) allows an interactive exploration of the data.

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Genetic History of India Jan 6, 2022 2:08:55 GMT

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Box 1.
Seven Source Populations Used for Distal Ancestry Modeling
Anatolia_N	Anatolian farmer-related: Represented by 7th millennium BCE western Anatolian farmers (19)
Ganj_Dareh_N	Iranian early farmer-related: Represented by 8th millennium BCE early goat herders from the Zagros Mountains of Iran (9, 24)
WEHG	Western European Hunter-Gatherer-related: represented by 9th millennium BCE Western Europeans (7, 19, 32, 69). (WEHG and EEHG discussed below were denoted WHG and EHG in previous studies, but as we co-analyze them with hunter-gatherers from Asia we modify the names to specify a European origin.)
EEHG	Eastern European Hunter-Gatherer-related: represented by 6th millennium BCE hunter-gatherers from Eastern Europe (19, 32)
WSHG	West Siberian Hunter-Gatherer-related: a previously undescribed deep source of Eurasian ancestry represented in this study by three individuals from the Forest Zone of Central Russia dated to the 6th millennium BCE.
ESHG	East Siberian Hunter-Gather-related: represented by 6th millennium BCE hunter-gatherers from the Lake Baikal region with ancestry deeply related to East Asians (26)
AHG	Andamanese Hunter-Gatherer-related: represented by present day indigenous Andaman Islanders (55) who we hypothesize are related to unsampled indigenous South Asians (Ancient Ancestral South Indians - AASI)

Box 2.
Summary of Key Findings
Iran and Turan
A West-to-East Cline of Decreasing Anatolian Farmer-Related Ancestry. There was a west-to-east gradient of ancestry across Eurasia in the Copper Age and Bronze Ages—the Southwest Asian Cline—with more Anatolian farmer-related ancestry in the west and more WSHG- or AASI-related ancestry in the east, superimposed on primary ancestry related to early Iranian farmers. The establishment of this gradient correlates in time to the spread of plant-based agriculture across this region, raising the possibility that people of Anatolian ancestry spread this technology east just as they helped spread it west into Europe.

People of the BMAC Were Not a Major Source of Ancestry for South Asians. The primary BMAC population largely derived from preceding local Copper Age peoples who were in turn closely related to people from the Iranian plateau, and had little of the Steppe ancestry that is ubiquitous in South Asia today.

Steppe Pastoralist-Derived Ancestry Arrived in Turan by 2100 BCE. We find no evidence of Steppe pastoralist-derived ancestry in groups at BMAC sites prior to 2100 BCE, but multiple outlier individuals buried at these sites show that by ~2100–1700 BCE, BMAC communities were regularly interacted with peoples carrying such ancestry.

An Ancestry Profile Widespread During the Indus Valley Civilization. We document a distinctive ancestry profile—45–82% Iranian farmer-related and 11–50% AASI (with negligible Anatolian farmer-related admixture)—that was present at two sites in cultural contact with the Indus Valley Culture (IVC). Combined with our detection of this same ancestry profile (in mixed form) about a millennium later in the post-IVC Swat Valley, this documents an Indus Periphery Cline during the flourishing of the IVC. Ancestors of this group formed by admixture ~5400–3700 BCE. There is little if any Anatolian farmer-related ancestry in the Indus Periphery Cline.

The Steppe and Forest Zone
Ancestry Clines in North Eurasia Established After the Advent of Farming. Prior to the spread of farmers and herders, northern Eurasia was characterized by a west-to-east gradient of very divergent hunter-gatherer populations with increasing proportions of relatedness to present-day East Asians: from Western European Hunter-Gatherers (WEHG), to Eastern European Hunter-Gatherers (EEHG), to West Siberian Hunter-Gatherers (WSHG), to Eastern Siberian Hunter-Gatherers (ESHG). Mixture of people along this ancestry gradient and its counterpart to the south formed five later clines following the advent of farming, the three northern ones of which are the European Cline, the Caucasus Cline, and the Central Asian Cline.

A Distinctive Ancestry Profile Stretching from Eastern Europe to Kazakhstan in the Bronze Age. We add more than one hundred samples from the previously described Western_Steppe_MLBA genetic cluster, including individuals associated with the Corded Ware, Srubnaya, Petrovka, and Sintashta archaeological complexes, and characterized by a mixture of about two-thirds ancestry related to Yamnaya Steppe pastoralists (from the Caucasus Cline), and European farmers (from the European Cline) suggesting that this population formed at the geographic interface of these two groups in Eastern Europe. Our analysis suggests that in the central Steppe and Minusinsk Basin in the Middle to Late Bronze Age, Western_Steppe_MLBA ancestry mixed with about 9% ancestry from previously established people from the region carrying WSHG-related to form a distinctive Central_Steppe_MLBA cluster that was the primary conduit for spreading Yamnaya Steppe pastoralist-derived ancestry to South Asia.

Bidirectional Mobility Along the Inner Asian Mountain Corridor. Beginning in the 3rd millennium BCE and intensifying in the 2nd millennium BCE, we observe multiple individuals in the Central Steppe who lived along the Inner Asian Mountain Corridor and who harbored admixture from Turan, documenting northward movement into the Steppe in this period. By the end of the 2nd millennium BCE, these people were later joined by numerous outlier individuals with East Asian-related admixture which become ubiquitous in the region by the Iron Age (25, 52). This ancestry is also seen in later groups with known cultural impacts on South Asia including Huns, Kushans and Sakas and is hardly present in the two primary ancestral populations of South Asia, suggesting that the Steppe ancestry widespread in South Asia derived from pre-Iron Age Central Asians.

South Asia
Three Ancestry Clines That Succeeded Each Other in Time in South Asia. We identify a unique trio of source populations that fits geographically and temporally diverse South Asians since the Bronze Age: a mixture of AASI, an Indus Periphery Cline group with predominantly Iranian farmer-related ancestry, and Central_Steppe_MLBA. Two-way clines driven more by populations that were mixtures of these three sources succeeded each other in time: prior to 2000 BCE the Indus Periphery Cline had no detectable Steppe ancestry, beginning after 2000 BCE the Steppe Cline, and finally the Modern Indian Cline.

The ASI and ANI Arose as Indus Periphery Cline People Mixed with Groups to the North and East. An ancestry gradient of which the Indus Periphery Cline individuals were a part played a pivotal role in the formation of both the two proximal sources of ancestry in South Asia: a minimum of ~55% Indus Periphery Cline ancestry for the ASI and ~70% for the ANI. Today there are groups in South Asia with very similar ancestry to the statistically reconstructed ASI suggesting that they have essentially direct descendants today. Much of the formation of both the ASI and ANI occurred in the 2nd millennium BCE. Thus, the events that formed both the ASI and ANI overlapped the time of the decline of the IVC.

Steppe Ancestry in South Asia is Primarily from Males and Disproportionately High in Brahmins. Most of the Steppe ancestry in South Asia derives from males, pointing to asymmetric social interaction between descendants of Steppe pastoralists and peoples of the Indus Periphery Cline. Groups that view themselves as being of traditionally priestly status, including traditional custodians of liturgical texts in the early Indo-European language Sanskrit, tend (with exceptions) to have more Steppe ancestry than expected based on ANI-ASI mixture, providing an independent line of evidence for a Steppe origin for South Asia’s Indo-European languages.

Last Edit: Jan 6, 2022 2:09:19 GMT by Admin

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Genetic History of India Jan 6, 2022 3:36:23 GMT

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Iran and Turan
A West-to-East Cline of Decreasing Anatolian Farmer-Related Ancestry
We studied the genetic transformations accompanying the spread of agriculture eastward from Iran beginning in the 7th millennium BCE (41, 42). We replicate previous findings that 9th to 8th millennium BCE herders from the Zagros Mountains of western Iran harbored a distinctive West Eurasian-related ancestry profile (9, 27), while later groups across a broad region were admixed between this ancestry and that related to early Anatolian farmers. Our analysis reveals a west-to-east cline of decreasing Anatolian farmer-related admixture in the Copper Age and Bronze Age ranging from ~70% in Anatolia to ~31% in eastern Iran, to ~7% in far eastern Turan (Fig. 1; (13), Fig. S10, Table S8–S16). This suggests that the archaeologically documented spread of a shared package of plants and animal domesticates from diverse locations across this region was accompanied by bi-directional spread of people and mixture with the local groups they encountered (3, 41, 43, 44). We call this the Southwest Asian Cline. In the far east of the Southwest Asian Cline (eastern Iran and Turan) in individuals from the 3rd millennium BCE, we detect not only the smallest proportions of Anatolian farmer-related admixture but also admixture related to West Siberian Hunter Gatherers (WSHG) (plausibly reflecting admixture from unsampled hunter-gatherer groups who inhabited this region prior to the spread of Iranian farmer-related ancestry into it). This shows that North Eurasian-related ancestry impacted Turan well before the spread of descendants of Yamnaya Steppe pastoralists into the region. We can exclude the possibility that the Yamnaya were the source of this North Eurasian-related ancestry, as they had more EEHG-than WSHG-related ancestry, and also carried high frequencies of mitochondrial DNA haplogroup type U5a as well as Y chromosome haplogroup types R1b or R1a not represented in Iran and Turan in this period ((13), Table S93-S94).

People of the BMAC Were Not a Major Source of Ancestry for South Asians
From Bronze Age Iran and Turan, we obtained genome-wide data for 84 ancient individuals (3000–1400 BCE) who lived in four urban sites of the Bactria Margiana Archaeological Complex (BMAC) and its immediate successors. The great majority of these individuals fall in a cluster genetically similar to the preceding groups in Turan, consistent with the hypothesis that the BMAC coalesced from preceding pre-urban populations (5). We infer three primary genetic sources: early Iranian farmer-related ancestry (~60–65%), and smaller proportions of Anatolian farmer- (~20–25%) and WSHG-related ancestry (~10%). Unlike preceding Copper Age individuals from Turan, people of the BMAC cluster also harbored an additional 2–5% ancestry related (deeply in time) to Andamanese Hunter-Gatherers (AHG). This evidence of north-to-south gene flow from South Asia is consistent with the archaeological evidence of cultural contacts between the Indus Valley Civilization and the BMAC and the existence of an IVC trading colony in northern Afghanistan (although we lack ancient DNA from that site) (45), and stands in contrast to our qpAdm analyses showing that a reciprocal north-to-south spread is undetectable. Specifically, our analyses reject the BMAC and the people who lived before them in Turan as plausible major sources of ancestry for diverse ancient and modern South Asians by showing that their ratio of Anatolian farmer-related to Iranian farmer-related ancestry is too high for them to be a plausible source for South Asians (p<0.0001, χ2 test; (13), Fig S50–S51). A previous study (26) fit a model in which a population from Copper Age Turan was used a source of the Iranian farmer-related ancestry in present-day South Asians, thus raising the possibility that the people of the BMAC whom the authors correctly hypothesized were primarily derived from the groups that preceded them in Turan were a major source population for South Asians. However, that study only had access to 2 samples from this period compared to the 36 we report with this study, and it lacked ancient DNA from individuals from the BMAC period or from any ancient South Asians. With additional samples, we have the resolution to show that none of the large number of Bronze and Copper Age populations from Turan for which we have ancient DNA fit as a source for the Iranian farmer-related ancestry in South Asia.

Steppe Pastoralist-Derived Ancestry Arrived in Turan by 2100 BCE
Our large sample sizes from Central Asia, including individuals from BMAC sites, are a particular strength of this study, allowing us to detect outlier individuals with ancestry different from those living at the same time and place, and revealing cultural contacts that would be otherwise difficult to appreciate (Fig. 2). Around ~2300 BCE, we observe three outliers in BMAC-associated sites carrying WSHG-related ancestry and we report data from the third millennium BCE from three sites in Kazakhstan and one in Kyrgyzstan that fit as sources for them (related ancestry has been found in ~3500 BCE Botai culture individuals (26)). Yamnaya-derived ancestry arrived by 2100 BCE, since from 2100–1700 BCE we observe outliers from three BMAC-associated sites carrying ancestry ultimately derived from Western_Steppe_EMBA pastoralists, in the distinctive admixed form typically carried by many Middle to Late Bronze Age Steppe groups (with roughly two thirds of the ancestry being of Western_Steppe_EMBA origin, and the rest consistent with deriving from European farmers). Thus, our data document a southward movement of ancestry ultimately descended from Yamnaya Steppe pastoralists that spread into Central Asia by the turn of the 2nd millennium BCE.

Fig. 2.
Outlier analysis reveals ancient contacts between sites.
We plot the average of Principal Component 1 (x-axis) and Principal Component 2 (y-axis) for the West Eurasian and All Eurasian PCA plots, as we found that this aids visual separation of the ancestry profiles. (A) In the Middle to Late Bronze Age Steppe, we observe in addition to the Western_Steppe_MLBA and Central_Steppe_MLBA clusters (indistinguishable in this projection), outliers admixed with other ancestries. The BMAC-related admixture in Kazakhstan documents northward gene flow onto the Steppe and confirms the Inner Asian Mountain Corridor as a conduit for movement of people. (B) At Shahr-i-Sokhta in eastern Iran, there are two primary groupings: one with ~20% Anatolian farmer-related ancestry and no detectable AHG-related ancestry, and the other with ~0% Anatolian farmer-related ancestry and substantial AHG-related ancestry (Indus Periphery Cline). (C) In individuals of the BMAC and successor sites, we observe a main cluster as well as numerous outliers: outliers >2000 BCE with admixture related to WSHG, outliers >2000 BCE on the Indus Periphery Cline (with an ancestral similar similar to the outliers at Shahr-i-Sokhta), and outliers after 2000 BCE that reveal how Central_Steppe_MLBA ancestry had arrived. (D) In the Late Bronze Age and Iron Age of northernmost South Asia, we observe a main cluster consistent with admixture between peoples of the Indus Periphery Cline and Central_Steppe_MLBA, and variable Steppe pastoralist-related admixture.

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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Genetic History of India Jan 7, 2022 3:45:09 GMT

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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.

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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Genetic History of India Jan 7, 2022 19:59:46 GMT

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Post by Admin on Jan 7, 2022 19:59:46 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.

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.