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Post by Admin on Jul 17, 2024 2:16:27 GMT
Genetically, the ancient Indus Valley people were composed of a primarily "Iranian" hunter-gatherers (or farmers) ancestry, with varying degrees of ancestry from local hunter-gatherer groups. The modern-day Dravidian-speakers are primarily composed of ASI ancestry formed by the admixture of indigenous South Asian hunter gatherer groups and the Indus Valley Civilisation people, but also carry a small portion of Western Steppe Herders due to minor admixture with Ancestral North Indian groups formed by admixture between the Steppe herders and the IVC people. ![](https://upload.wikimedia.org/wikipedia/commons/thumb/a/ac/Dravidian_map.svg/800px-Dravidian_map.svg.png) The Formation of Human Populations in South and Central Asia Abstract By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and southeast Asia. Following the Indus Valley Civilization’s decline, they mixed with people in the southeast to form one of the two main ancestral populations of South Asia whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who spread via Central Asia after 4000 years ago to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the unique shared features shared between Indo-Iranian and Balto-Slavic languages. ![](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6822619/bin/nihms-1053677-f0001.jpg) The Bronze Age spread of Yamnaya steppe pastoralist ancestry into two subcontinents, Europe and South Asia. Pie charts reflect the proportion of Yamnaya ancestry, and dates reflect the earliest available ancient DNA with Yamnaya ancestry in each region. There is no ancient DNA yet for the ANI and ASI, so for these the range is inferred statistically. www.ncbi.nlm.nih.gov/pmc/articles/PMC6822619/
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Post by Admin on Jul 18, 2024 1:16:08 GMT
Introduction and Rationale: To elucidate the extent to which the major cultural transformations of farming, pastoralism and shifts in the distribution of languages in Eurasia were accompanied by movement of people, we report genome-wide ancient DNA data from 523 individuals spanning the last 8000 years mostly from Central Asia and northernmost South Asia.
Results: Movements of people following the advent of farming resulted in genetic gradients across Eurasia that can be modeled as mixtures of seven deeply divergent populations. A key gradient formed in southwestern Asia beginning in the Neolithic and continuing into the Bronze Age, with more Anatolian farmer-related ancestry in the west and more Iranian farmer-related ancestry in the east. This cline extended to the desert oases of Central Asia and was the primary source of ancestry in peoples of the Bronze Age Bactria Margiana Archaeological Complex (BMAC). This supports the idea that the archaeologically documented dispersal of domesticates was accompanied by the spread of people from multiple centers of domestication.
The main population of the BMAC carried no ancestry from Steppe pastoralists and did not contribute substantially to later South Asians. However, Steppe pastoralist ancestry appeared in outlier individuals at BMAC sites by the turn of the second millennium BCE around the same time as it appeared on the southern Steppe. Using data from ancient individuals from the Swat Valley of northernmost South Asia, we show that Steppe ancestry then integrated further south in the first half of the second millennium BCE, contributing up to 30% of the ancestry of modern groups in South Asia. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the unique shared features shared between Indo-Iranian and Balto-Slavic languages.
The primary ancestral population of modern South Asians is a mixture of people related to early Holocene populations of Iran and South Asia that we detect in outlier individuals from two sites in cultural contact with the Indus Valley Civilization (IVC), making it plausible that it was characteristic of the IVC. After the IVC’s decline, this population mixed with northwestern groups with Steppe ancestry to form the “Ancestral North Indians” (ANI) and with southeastern groups to form the “Ancestral South Indians” (ASI) whose direct descendants live today in tribal groups in southern India. Mixtures of these two post-IVC groups--the ANI and ASI--drive the main gradient of genetic variation in South Asia today.
Conclusion: Earlier work recorded massive population movement from the Steppe into Europe early in the 3rd millennium BCE, likely spreading Indo-European languages. We reveal a parallel series of events leading to the spread of Steppe ancestry to South Asia, thereby documenting movements of people that were likely conduits for the spread of Indo-European languages.
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Post by Admin on Jul 19, 2024 13:35:09 GMT
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.
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Post by Admin on Jul 22, 2024 2:02:40 GMT
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). ![](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6822619/bin/nihms-1053677-f0002.jpg) 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.
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Post by Admin on Jul 24, 2024 2:21:00 GMT
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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