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Post by Admin on Apr 6, 2020 21:30:41 GMT
The Sintashta culture is thought to represent an eastward migration of peoples from the Corded Ware culture. It is widely regarded as the origin of the Indo-Iranian languages. The earliest known chariots have been found in Sintashta burials, and the culture is considered a strong candidate for the origin of the technology, which spread throughout the Old World and played an important role in ancient warfare.  Some of the Sintashta samples are outliers from the main Sintashta cluster, and that's because they harbor elevated levels of ancestry related to Mesolithic and Neolithic Eastern Europe and Western Siberia. This is especially true of a pair of individuals who belong to Y-haplogroup Q. Archaeological data suggest that the Sintashta community may have been multi-cultural and multi-lingual. Indeed, it's generally accepted based on historical linguistics data that there were fairly intense contacts in North Eurasia between the speakers of Proto-Indo-Iranian, Proto-Uralic and Yeniseian languages. However, a sample from a Sredny Stog II culture burial on the North Pontic steppe, known as Ukraine_Eneolithic I6561, not only clusters very strongly with the most typical Sintashta samples, but also belongs to Y-haplogroup R1a-Z93. On the other hand, none of the CWC remains sequenced to date belong to this particular subclade of R1a, which casts a doubt on the thesis that the Sintashta culture derives directly from an eastward migration of Corded Ware people. A male buried in Ukraine ca. 4000 BC was found to be carrying R1a-Z93, the earliest sample of this clade (Mathieson et al. 2018). The Ukrainian site is ascribed to the Sredny Stog culture and the Sintashta culture may be its descendant culture along with the Andronovo culture. The Sintashta people were genetically almost indistinguishable from ancient samples from the Andronovo culture and both cultures are partially derived from the preceding Corded Ware culture.  In the 2015 study published in Nature (Allentoft et al. 2015), the remains of four individuals ascribed to the Sintastha culture were analyzed. One male carried haplogroup R1a and J1c1b1a, while the other carried R1a1a1b and J2b1a2a. The two females carried U2e1e and U2e1h respectively. The study found a close autosomal genetic relationship between peoples of Corded Ware culture and Sintashta culture, which "suggests similar genetic sources of the two," and may imply that "the Sintashta derives directly from an eastward migration of Corded Ware peoples." Sintashta individuals and Corded Ware individuals both had a relatively higher ancestry proportion derived from Central Europe, and both differed markedly in such ancestry from the population of the Yamnaya Culture and most individuals of the Poltavka Culture that preceded Sintashta in the same geographic region. The Bell Beaker culture, the Unetice culture and contemporary Scandinavian cultures were also found to be closely genetically related to Corded Ware. A particularly high lactose tolerance was found among Corded Ware and the closely related Nordic Bronze Age. In addition, the study found the Sintashta culture to be closely genetically related to the succeeding Andronovo culture.  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. Ancient DNA has not yet been found for the ANI and ASI, so for these the range is inferred statistically. In a genetic study published in Science (Narasimhan et al. 2018), the remains of several members of the Sintashta culture was analyzed. mtDNA was extracted from two females buried at the Petrovka settlement. They were found to be carrying subclades of U2 and U5. The remains of fifty individuals from the fortified Sintastha settlement of Kamennyi Ambar was analyzed. This was the largest sample of ancient DNA ever sampled from a single site. The Y-DNA from thirty males was extracted. Eighteen carried R1a and various subclades of it (particularly subclades of R1a1a1), five carried subclades of R1b (particularly subclades of R1b1a1a), three carried R1, two carried Q1a and a subclade of it, one carried I2a1a1a, and one carried P1. The majority of mtDNA samples belonged to various subclades of U, while W, J, T, H and K also occurred. A Sintashta male buried at Samara was found to be carrying R1b1a1a2 and J1c1b1a. The authors of the study found the Sintashta people to be closely genetically related to the people of the Corded Ware culture, the Srubnaya culture, the Potapovka culture, and the Andronovo culture. These were found to harbor mixed ancestry from the Yamnaya culture and peoples of the Central European Middle Neolithic. Sintashta people were deemed "genetically almost indistinguishable" from samples taken from the northwestern areas constituting the core of the Andronovo culture, which were "genetically largely homogeneous". The genetic data suggested that the Sintashta culture was ultimately derived of a remigration of Central European peoples with steppe ancestry back into the steppe. Some Sintastha individuals displayed similarites with earlier samples collected at Khvalynsk. The formation of human populations in South and Central Asia Vagheesh M. Narasimhan1,*,†, Nick Patterson2,3,*,†, Priya Moorjani4,5,‡, Nadin Rohland1,2,‡, David Reich1,2,6,81,† Science 06 Sep 2019: Vol. 365, Issue 6457, eaat7487 DOI: 10.1126/science.aat7487 Ancient human movements through Asia Ancient DNA has allowed us to begin tracing the history of human movements across the globe. Narasimhan et al. identify a complex pattern of human migrations and admixture events in South and Central Asia by performing genetic analysis of more than 500 people who lived over the past 8000 years (see the Perspective by Schaefer and Shapiro). They establish key phases in the population prehistory of Eurasia, including the spread of farming peoples from the Near East, with movements both westward and eastward. The people known as the Yamnaya in the Bronze Age also moved both westward and eastward from a focal area located north of the Black Sea. The overall patterns of genetic clines reflect similar and parallel patterns in South Asia and Europe. Science, this issue p. eaat7487; see also p. 981 Structured Abstract 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 The movement 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 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 also mixed with southeastern groups to form the “Ancestral South Indians” (ASI), whose direct descendants today live 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 Eurasian Steppe into Europe early in the third 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 Apr 7, 2020 1:33:54 GMT
Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe Choongwon Jeong, Shevan Wilkin, Tsend Amgalantugs, Abigail S. Bouwman, William Timothy Treal Taylor PNAS November 27, 2018 115 (48) E11248-E11255; first published November 5, 2018 doi.org/10.1073/pnas.1813608115Significance Since the Bronze Age, pastoralism has been a dominant subsistence mode on the Western steppe, but the origins of this tradition on the Eastern steppe are poorly understood. Here we investigate a putative early pastoralist population in northern Mongolia and find that dairy production was established on the Eastern steppe by 1300 BCE. Milk proteins preserved in dental calculus indicate an early focus on Western domesticated ruminants rather than local species, but genetic ancestry analysis indicates minimal admixture with Western steppe herders, suggesting that dairy pastoralism was introduced through adoption by local hunter-gatherers rather than population replacement.  Fig. 1. Map of the Eurasian steppes. (A) Distribution of the Western (brown) and Eastern (green) steppes and the locations of ancient (red) and modern (black) populations discussed in the text. Population codes are provided in the Dataset S1. A box indicates the location of the LBA burial mounds surveyed in the Arbulag soum of Khövsgöl aimag. (B) Enhanced view of LBA burial mounds (white circles) and burial clusters selected for excavation (boxes a–f) with the number of analyzed individuals in parentheses (SI Appendix, Table S1). (C) Photograph of burial 2009-52 containing the remains of ARS026, a genetic outlier with Western steppe ancestry. Abstract Recent paleogenomic studies have shown that migrations of Western steppe herders (WSH) beginning in the Eneolithic (ca. 3300–2700 BCE) profoundly transformed the genes and cultures of Europe and central Asia. Compared with Europe, however, the eastern extent of this WSH expansion is not well defined. Here we present genomic and proteomic data from 22 directly dated Late Bronze Age burials putatively associated with early pastoralism in northern Mongolia (ca. 1380–975 BCE). Genome-wide analysis reveals that they are largely descended from a population represented by Early Bronze Age hunter-gatherers in the Baikal region, with only a limited contribution (∼7%) of WSH ancestry. At the same time, however, mass spectrometry analysis of dental calculus provides direct protein evidence of bovine, sheep, and goat milk consumption in seven of nine individuals. No individuals showed molecular evidence of lactase persistence, and only one individual exhibited evidence of >10% WSH ancestry, despite the presence of WSH populations in the nearby Altai-Sayan region for more than a millennium. Unlike the spread of Neolithic farming in Europe and the expansion of Bronze Age pastoralism on the Western steppe, our results indicate that ruminant dairy pastoralism was adopted on the Eastern steppe by local hunter-gatherers through a process of cultural transmission and minimal genetic exchange with outside groups. Archaeogenetic studies provide evidence that the Eurasian Eneolithic–Bronze Age transition was associated with major genetic turnovers by migrations of peoples from the Pontic-Caspian steppe both in Europe and in central Asia (1⇓⇓⇓–5). The migration of these Western steppe herders (WSH), with the Yamnaya horizon (ca. 3300–2700 BCE) as their earliest representative, contributed not only to the European Corded Ware culture (ca. 2500–2200 BCE) but also to steppe cultures located between the Caspian Sea and the Altai-Sayan mountain region, such as the Afanasievo (ca. 3300–2500 BCE) and later Sintashta (2100–1800 BCE) and Andronovo (1800–1300 BCE) cultures. Although burials typologically linked to the Afanasievo culture have been occasionally reported in Mongolia (6), the genetic profile of Eastern steppe populations, as well as the timing and nature of WSH population expansion and the rise of dairy pastoralism in Mongolia, remain unclear. The remarkable demographic success of WSH populations has been linked to mobile pastoralism with dairying (7), a system that efficiently converts cellulose-rich wild grasses into protein- and fat-rich dairy products. Dairy foods provide a rich source of nutrients and fresh water, and function as an adaptive subsistence strategy in cold, dry steppe environments where most crop cultivation is highly challenging. Dairy pastoralism became widely practiced in the eastern Eurasian steppe, the homeland from which subsequent historical nomadic dairying empires, such as the Xiongnu (ca. 200 BCE to 100 CE) and the Mongols (ca. 1200–1400 CE) expanded; however, it is not fully understood when, where, and how this subsistence strategy developed. At Botai, in central Kazakhstan, evidence for Eneolithic dairying has been reported through the presence of ruminant and equine dairy lipids in ceramic residues as early as 3500 BCE (8, 9). In the Altai and Tarim basin, where WSH populations have left strong genetic footprints (1, 3, 10, 11), archaeological evidence supports the presence of dairy products by the early second Millennium BCE and later (8, 12, 13). In the Eastern steppe, however, no direct observations of dairy consumption have been made for a comparable time period, despite the fact that skeletal remains of domestic livestock (such as sheep, goats, cattle, and horses) have been found at Mongolian ritual sites and in midden contexts as early as the 14th century BCE (14⇓⇓–17). In the absence of direct evidence for Bronze Age milk production or consumption on the Eastern steppe, it remains unclear whether these animals are merely ritual in nature or signify a major shift in dietary ecology toward dairy pastoralism, and whether their appearance is connected to possible WSH migrations onto the Eastern steppe. To understand the population history and context of dairy pastoralism in the eastern Eurasian steppe, we applied genomic and proteomic analyses to individuals buried in Late Bronze Age (LBA) burial mounds associated with the Deer Stone-Khirigsuur Complex (DSKC) in northern Mongolia (SI Appendix, Figs. S1–S3 and Table S1). To date, DSKC sites contain the clearest and most direct evidence for animal pastoralism in the Eastern steppe before ca. 1200 BCE (18). Focusing on six distinct burial clusters in Arbulag soum, Khövsgöl aimag, Mongolia (Fig. 1 and SI Appendix, Figs. S1–S3), we produced genome-wide sequencing data targeting ∼1.2M single nucleotide polymorphisms (SNPs) for 22 DSKC-associated individuals directly dated to ca. 1380–975 calibrated BCE (SI Appendix, Fig. S4 and Table S2), as well as sequenced whole genomes for two individuals (>3× coverage). Nine of the individuals in this group yielded sufficient dental calculus for proteomic analysis, and we tested these deposits for the presence of milk proteins using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Overall, our results find that DSKC subsistence strategy included dairying of Western domesticated ruminants, but that there was minimal gene flow between analyzed DSKC populations and WSH groups during the LBA. Thus, in contrast to patterns observed in western Europe where, for example, the arrival of WSH is associated with population replacement and continental-level genetic turnover (5), contact between WSH and Eastern steppe populations is characterized by transcultural transmission of dairy pastoralism in the near absence of demic diffusion. |
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Post by Admin on Apr 7, 2020 5:08:00 GMT
Results Ancient DNA Sequencing and Quality Assessment. We built and sequenced uracil-DNA-glycosylase–half (19), double-indexed Illumina libraries for genomic DNA extracted from teeth or femora from DSKC-associated burials in Khövsgöl, Mongolia. Twenty of 22 libraries exhibited good human DNA preservation, with a mean host endogenous content of 14.9% (range 0.2–70.0%); two libraries yielded very little human DNA (<0.05%) and were excluded from further analysis (SI Appendix, Table S2). Libraries were then enriched for 1.2 million variable sites in the human genome (1240K) using in-solution hybridization (2, 3). All individuals (12 males, 8 females) showed characteristic patterns of chemical modifications typical of ancient DNA (SI Appendix, Fig. S5), and 18 individuals yielded both low estimates of modern DNA contamination (≤1% mitochondrial and nuclear contamination) and sufficient genome coverage for subsequent analysis (0.11× to 4.87× mean coverage for target sites) (SI Appendix, Table S3). No close relative pairs were identified among the ancient individuals (SI Appendix, Fig. S6). Two individuals with high endogenous content on screening (ARS008, 70.0%; ARS026, 47.6%) were deeply sequenced to obtain whole genomes (∼3.3× coverage) (SI Appendix, Table S3). We intersected our ancient data with a published world-wide set of ancient and contemporary individuals (Dataset S1) whose genotypes are determined for 593,124 autosomal SNPs on the Affymetrix HumanOrigins 1 array (20). Characterization of the Genetic Profile of the Khövsgöl Gene Pool. To characterize the genetic profile of DSKC-associated LBA Khövsgöl individuals (Khövsgöls), we performed principal component analysis (PCA) of Eurasian populations (SI Appendix, Fig. S7). PC1 separates eastern and western Eurasian populations, with central and north Eurasian populations falling in an intermediate position (SI Appendix, Fig. S7). PC2 separates eastern Eurasian populations along a north–south cline, with northern Siberian Nganasans and the Ami and Atayal from Taiwan forming the northern and southern end points, respectively. Most LBA Khövsgöls are projected on top of modern Tuvinians or Altaians, who reside in neighboring regions. In comparison with other ancient individuals, they are also close to but slightly displaced from temporally earlier Neolithic and Early Bronze Age (EBA) populations from the Shamanka II cemetry (Shamanka_EN and Shamanka_EBA, respectively) from the Lake Baikal region (SI Appendix, Fig. S7) (4, 21). However, when Native Americans are added to PC calculation, we observe that LBA Khövsgöls are displaced from modern neighbors toward Native Americans along PC2, occupying a space not overlapping with any contemporary population (Fig. 2A and SI Appendix, Fig. S8). Such an upward shift on PC2 is also observed in the ancient Baikal populations from the Neolithic to EBA and in the Bronze Age individuals from the Altai associated with Okunevo and Karasuk cultures (1). These observations are consistent with LBA Khövsgöls and other ancient Siberians sharing more ancestry with Native American-related gene pools than modern populations in the region do.  Fig. 2. The genetic profile of LBA Khövsgöl individuals summarized by PCA and ADMIXTURE. (A) Khövsgöl (Kvs, ARS017, and ARS026) and other ancient individuals (colored symbols) are projected onto the top PCs of modern Eurasian and Native American individuals. Contemporary individuals are marked by gray circles. Mean coordinates for each of the contemporary populations are marked by three-letter codes and by colors assigned to the associated geographic regions. Population codes are provided in Dataset S1 and SI Appendix, Fig. S8. (B) ADMIXTURE results for Khövsgöl and other ancient individuals with K values 9 and 17. In K = 17, the Khövsgöls main cluster is mainly modeled as a mixture of components most enriched in modern northeast Asians (e.g., Nivh) and ancient Siberians (e.g., AG3, Botai, and Okunevo). Notably, two individuals fall on the PC space markedly separated from the others: ARS017 is placed close to ancient and modern northeast Asians, such as early Neolithic individuals from the Devil’s Gate archaeological site (22) and present-day Nivhs from the Russian far east, while ARS026 falls midway between the main cluster and western Eurasians (Fig. 2A). Genetic clustering with ADMIXTURE (23) further supports these patterns (Fig. 2B and SI Appendix, Fig. S9). We quantified the genetic heterogeneity between Khövsgöl individuals by calculating f4 symmetry statistics (24) in the form of f4(chimpanzee, outgroup; Khövsgöl1, Khövsgöl2) for all pairs against 18 outgroups representative of world-wide ancestries (SI Appendix, Fig. S10). As expected, the two outliers did not form a clade with the rest of individuals and therefore we treated each individual separately in subsequent analyses. For the remaining 16 individuals, 14 were merged into a single main cluster based on their minimal genetic heterogeneity. The other two individuals (ARS009 and ARS015) were excluded from this cluster because they broke symmetry with four and two individuals (maximum |Z| = 3.9 and 4.7 SE), respectively, and were also slightly displaced from the others in our PCA (Fig. 2A).  Fig. 3. The genetic affinity of the Khövsgöl clusters measured by outgroup-f3 and -f4 statistics. (A) The top 20 populations sharing the highest amount of genetic drift with the Khövsgöl main cluster measured by f3(Mbuti; Khövsgöl, X). (B) The top 15 populations with the most extra affinity with each of the three Khövsgöl clusters in contrast to Tuvinian (for the main cluster) or to the main cluster (for the two outliers), measured by f4(Mbuti, X; Tuvinian/Khövsgöl, Khövsgöl/ARS017/ARS026). Ancient and contemporary groups are marked by squares and circles, respectively. Darker shades represent a larger f4 statistic. Population codes are provided in Dataset S1; see also SI Appendix, Figs. S11–S14 for further details. Next, we quantified the genetic affinity between our Khövsgöl clusters and world-wide populations by calculating outgroup-f3 statistics with Central African Mbuti as an outgroup (25). For the main cluster, top signals were observed with earlier ancient populations from the Baikal region, such as the early Neolithic and EBA individuals from the Shamanka II cemetry (4), followed by present-day Siberian and northeast Asian populations, such as Negidals from the Amur River basin and Nganasans from the Taimyr peninsula (Fig. 3A and SI Appendix, Fig. S11 A and B). As expected based on their nonoverlapping positions on PCA, however, Khövsgöls do not form a cluster with these high-affinity groups, as shown by f4 symmetry tests in the form of f4(Mbuti, X; Siberian, Khövsgöls). Interestingly, Upper Paleolithic Siberians from nearby Afontova Gora and Mal’ta archaeological sites (AG3 and MA-1, respectively) (25, 26) have the highest extra affinity with the main cluster compared with other groups, including the eastern outlier ARS017, the early Neolithic Shamanka_EN, and present-day Nganasans and Tuvinians (Z > 6.7 SE for AG3) (red shades in Fig. 3B and SI Appendix, Fig. S11 C and D). This extra affinity with so-called “Ancient North Eurasian” (ANE) ancestry (27) may explain their attraction toward Native Americans in PCA, because Native Americans are known to have high proportion of ANE ancestry (20, 25). Main-cluster Khövsgöl individuals mostly belong to Siberian mitochondrial (A, B, C, D, and G) and Y (all Q1a but one N1c1a) haplogroups (SI Appendix, Table S4). |
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Post by Admin on Apr 7, 2020 21:20:18 GMT
Source of ANE Ancestry in the LBA Khövsgöl Population. Previous studies show a close genetic relationship between WSH populations and ANE ancestry, as Yamnaya and Afanasievo are modeled as a roughly equal mixture of early Holocene Iranian/Caucasus ancestry (IRC) and Mesolithic Eastern European hunter-gatherers, the latter of which derive a large fraction of their ancestry from ANE (20, 28). It is therefore important to pinpoint the source of ANE-related ancestry in the Khövsgöl gene pool: that is, whether it derives from a pre-Bronze Age ANE population (such as the one represented by AG3) or from a Bronze Age WSH population that has both ANE and IRC ancestry. To test these competing hypotheses, we systematically compared various admixture models of the main cluster using the qpAdm program (20). Ancient Baikal populations were chosen as a proxy based on both their spatiotemporal and genetic similarities with the Khövsgöl main cluster (Figs. 2 and 3). When the early Neolithic Shamanka_EN is used as a proxy, we find that Baikal+ANE provides a better fit to the main cluster than Baikal+WSH, although no two-way admixture model provides a sufficient fit (P ≥ 0.05) (SI Appendix, Table S5). Adding a WSH population as the third source results in a sufficient three-way mixture model of Baikal+ANE+WSH with a small WSH contribution to the main cluster (e.g., P = 0.180 for Shamanka_EN+AG3+Sintashta with 3.7 ± 2.0% contribution from Sintashta) (Fig. 4 and SI Appendix, Table S6).  Fig. 4. Admixture modeling of Altai populations and the Khövsgöl main cluster using qpAdm. For the archaeological populations, (A) Shamanka_EBA and (B and C) Khövsgöl, each colored block represents the proportion of ancestry derived from a corresponding ancestry source in the legend. Error bars show 1 SE. (A) Shamanka_EBA is modeled as a mixture of Shamanka_EN and AG3. The Khövsgöl main cluster is modeled as (B) a two-way admixture of Shamanka_EBA+Sintashta and (C) a three-way admixture Shamanka_EN+AG3+Sintashta. Details of the admixture models are provided in SI Appendix, Tables S5 and S6. Using the temporally intermediate EBA population Shamanka_EBA, we can narrow down the time for the introduction of WSH ancestry into the main cluster. Shamanka_EBA is modeled well as a two-way mixture of Shamanka_EN and ANE (P = 0.158 for Shamanka_EN+AG3) (Fig. 4) but not as a mixture of Shamanka_EN and WSH (P ≤ 2.91 × 10−4) (SI Appendix, Table S5), suggesting no detectable WSH contribution through the early Bronze Age. Similar results are obtained for other Late Neolithic and EBA populations from the Baikal region (SI Appendix, Table S5). In contrast, the Khövsgöl main cluster is modeled well by Shamanka_EBA+WSH but not by Shamanka_EBA+ANE (P ≥ 0.073 and P ≤ 0.038, respectively) (SI Appendix, Table S5). A three-way model of Shamanka_EBA+ANE+WSH confirms this by providing the ANE contribution around zero (SI Appendix, Table S6). The amount of WSH contribution remains small (e.g., 6.4 ± 1.0% from Sintashta) (Fig. 4 and SI Appendix, Table S5). Assuming that the early Neolithic populations of the Khövsgöl region resembled those of the nearby Baikal region, we conclude that the Khövsgöl main cluster obtained ∼11% of their ancestry from an ANE source during the Neolithic period and a much smaller contribution of WSH ancestry (4–7%) beginning in the early Bronze Age. Admixture Testing of Genetic Outliers. Using the same approach, we obtained reasonable admixture models for the two outliers, ARS017 and ARS026. The eastern outlier ARS017, a female, shows an extra affinity with early Neolithic individuals from the Russian far east (Devil’s Gate) (22) and in general with contemporary East Asians (e.g., Han Chinese) compared with the Khövsgöl main cluster (Fig. 3B and SI Appendix, Fig. S12). ARS017 is also similar to Shamanka_EN in showing no significant difference in qpAdm (SI Appendix, Fig. S12 and Table S7). Using contemporary East Asian proxies, ARS017 is modeled as a mixture of predominantly Ulchi and a minor component (6.1–9.4%) that fits most ancient western Eurasian groups (P = 0.064–0.863) (SI Appendix, Table S7). This minor Western component may result from ANE ancestry; however, given the minimal western Eurasian contribution, we do not have sufficient power to accurately characterize this individual’s western Eurasian ancestry. The Western outlier ARS026, a male dating to the end of the radiocarbon series, has the highest outgroup-f3 with the main LBA Khövsgöl cluster, with extra affinity toward Middle Bronze Age (MBA) individuals from the Sintashta culture (Fig. 3B and SI Appendix, Fig. S13) (1). DNA recovered from this individual exhibited expected aDNA damage patterns (SI Appendix, Fig. S5) but was otherwise excellently preserved with >47% endogenous content and very low estimated contamination (1% mitochondrial; 0.01% nuclear). ARS026 is well modeled as a two-way mixture of Shamanka_EBA and Sintashta (P = 0.307; 48.6 ± 2.0% from Sintashta) (SI Appendix, Table S7). Similar to ARS026, contemporaneous LBA Karasuk individuals from the Altai (1400–900 BCE) (1, 29) also exhibit a strong extra genetic affinity with individuals associated with the earlier Sintashta and Andronovo cultures (SI Appendix, Fig. S14). Although two-way admixture models do not fit (P ≤ 0.045) (SI Appendix, Table S8), the Karasuk can be modeled as a three-way mixture of Shamanka_EBA/Khövsgöl and AG3 and Sintashta, suggesting an eastern Eurasian source with slightly higher ANE ancestry than those used in our modeling (P ≥ 0.186) (SI Appendix, Table S8). Like ARS026, admixture coefficients for the Karasuk suggest that MBA/LBA groups like the Sintashta or Srubnaya are a more likely source of their WSH ancestry than the EBA groups, like the Yamnaya or Afanasievo. Notably, Karasuk individuals are extremely heterogeneous in their genetic composition, with the genetically easternmost Eurasian individual nearly overlapping with the EBA Baikal groups (Fig. 2A and SI Appendix, Figs. S7 and S8). Earlier groups, such as the Afanasievo, Sintashta, and Andronovo, are mostly derived from WSH ancestries, and this may suggest that admixture in the Altai-Sayan region only began during the LBA following a long separation since the Eneolithic. Although ARS026 exhibits substantial WSH ancestry, strontium isotopic values obtained from his M3 enamel resemble local fauna and fall within the range of the main Khövsgöl cluster (SI Appendix, Fig. S15 and Table S9); however, because the enamel this individual also exhibited elevated manganese levels, postmortem trace element alteration from soil could not be excluded. |
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Post by Admin on Apr 8, 2020 3:03:44 GMT
Dairy Subsistence and Lactase Persistence. Contemporary Mongolia has a dairy- and meat-based subsistence economy, and to more precisely understand the role of dairy products in the diets of present-day mobile pastoralists in Khövsgöl aimag, we conducted a detailed nutritional investigation of summer and winter diets. We find that dairy-based foods contribute a mean of 35% total dietary energy, 36–40% total carbohydrate, 24–31% total protein, and 39–40% total fat to rural summer diets in Khövsgöl aimag, with liquid milk and dairy product consumption of 216–283 and 172–198 g/d, respectively (SI Appendix, Table S10 and Dataset S2). Despite the importance of dairying today, its origins in Mongolia are poorly understood. Given the limited WSH ancestry of the main Khövsgöl cluster, we sought to determine if dairy pastoralism was practiced by this putatively pastoralist LBA population by testing for the presence of milk proteins (30) in the dental calculus of these individuals. We extracted proteins from 12 dental calculus samples representing 9 individuals (SI Appendix, Table S11) and analyzed tryptic peptides using LC-MS/MS (31). Observed modifications included deamidation (N, Q) and oxidation (P, M) (SI Appendix, Table S12). All protein identifications were supported by a minimum of two peptides across the dataset, and only peptides with an E value ≤ 0.001 were assigned; the estimated peptide false-discovery rate (FDR) across the full dataset was 1.0%, and protein FDR was 4.6%. Milk proteins were detected in seven of the nine individuals analyzed (SI Appendix, Table S13 and Dataset S3), confirming that dairy foods were consumed as early as 1456 BCE (1606–1298 BCE, 95% probability of the earliest directly dated individual) (SI Appendix, Fig. S4 and Table S2). Specifically, we detected the milk whey protein β-lactoglobulin (Fig. 5 A and B) and the curd protein α-S1-casein, with peptides matching specifically to sheep (Ovis), goat (Capra), Caprinae, Bovinae, and a subset of Bovidae (Ovis or Bovinae) (Fig. 5C, SI Appendix, Table S13, and Dataset S3). These peptides exhibited asparagine and glutamine deamidation, as expected for ancient proteins (32), and the frequency and distribution of recovered β-lactoglobulin (Fig. 5B) and α-S1-casein peptides closely matched that empirically observed for modern bovine milk (33), thereby providing additional protein identification support through appropriate proteotypic behavior.  Fig. 5. Presence of ruminant β-lactoglobulin and α-S1-casein milk protein in LBA Khövsgöl dental calculus. (A) B- and Y-ion series for one of the most frequently observed β-lactoglobulin peptides, TPEVD(D/N/K)EALEKFDK, which contains a genus-specific polymorphic residue: D, Bos; N, Ovis; K, Capra. See SI Appendix, Fig. S16 for peptide and fragment ion error distribution graphs. (B) Alignment of observed peptides to the 178 amino acid β-lactoglobulin protein, with peptide taxonomic source indicated by color. Trypsin cut sites are indicated by gray ticks. The position and empirically determined observation frequency of BLG peptides for bovine milk are shown as a heatmap scaled from least observed peptides (light gray) to most frequently observed peptides (dark red), as reported in the Bovine PeptideAtlas (34). Inset displays a 3D model of the β-lactoglobulin protein with observed peptide positions highlighted in black. (C) Taxonomically assigned β-lactoglobulin (black) and α-S1-casein (gray) peptides presented as scaled pie charts on a cladogram of Mongolian dairy domesticates. Bracketed numbers represent the number of peptides assigned to each node. Ruminant milk proteins were well supported, but no cervid, camelid, or equid milk proteins were identified. Given the evidence for dairy consumption by the LBA Khövsgöl population, we sought to determine if the dairy-adaptive -13910*T (rs4988235) lactase persistence (LP) allele found today in Western steppe (34) and European (35) populations was present among LBA Khövsgöls dairy herders, and we examined this position in our SNP-enriched dataset. The -13910*T LP allele was not found in the LBA Khövsgöls (SI Appendix, Fig. S17 and Table S14), and additionally all observed flanking sequences in the lactase transcriptional enhancer region contained only ancestral alleles. Discussion In this study, we find a clear genetic separation between WSH populations and LBA Mongolians more than a millennium after the arrival of WSH at the furthest edges of the Western steppe and the earliest appearance of the WSH Afanasievo cultural elements east of the Altai-Sayan mountain range. This genetic separation between Western and Eastern steppe populations appears to be maintained with very limited gene flow until the end of the LBA, when admixed populations, such as the Karasuk (1200–800 BCE), first appear in the Altai (1) and we observe the first individual with substantial WSH ancestry in the Khövsgöl population, ARS026, directly dated to 1130–900 BCE. Consistent with these observations, we find that the WSH ancestry introduced during these admixture events is more consistent with MBA and LBA steppe populations, such as the Sintashta (2100–1800 BCE), than with earlier EBA populations, such as the Afanasievo (3300–2500 BCE), who do not seem to have genetically contributed to subsequent populations. Despite the limited gene flow between the Western and Eastern steppes, dairy pastoralism was nevertheless adopted by local non-WSH populations on the Eastern steppe and established as a subsistence strategy by 1300 BCE. Ruminant milk proteins were identified in the dental calculus of most of the tested LBA Khövsgöl individuals, and all identified milk proteins originated from ruminants, specifically the Western dairy domesticates sheep, goat, and Bovinae. These findings suggest that neighboring WSH populations directly or indirectly introduced dairy pastoralism to local indigenous populations through a process of cultural exchange. Further research on other regional cultures in Mongolia, such as Chemurchek, Hemsteg, and Ulaanzuukh, is needed to determine if this pattern of cultural adoption observed among DSKC sites is broadly shared across other Bronze Age cultures throughout the Eastern steppe. Bronze Age trade and cultural exchange are difficult to observe on the Eastern steppe, where mobile lifestyles and ephemeral habitation sites combine to make household archaeology highly challenging. Burial mounds are typically the most conspicuous features on the landscape, and thus much of Mongolian archaeology is dominated by mortuary archaeology. However, unlike WSH, whose kurgans typically contain a range of grave goods, many LBA mortuary traditions on the Eastern steppe did not include grave goods of any kind other than ritually deposited animal bones from horse, deer, and bovids. Given that Mongolian archaeological collections are typically dominated by human remains with limited occupational materials, the ability to reconstruct technological exchange, human–animal interaction, and secondary product utilization through the analysis of proteins preserved in dental calculus represents an important advance. The 3,000-y legacy of dairy pastoralism in Mongolia poses challenging questions to grand narratives of human adaptation and natural selection (36). For example, despite evidence of being under strong natural selection (36), LP was not detected among LBA Khövsgöls, and it remains rare (<5%) in contemporary Mongolia even though levels of fresh and fermented dairy product consumption are high (35). Recent studies in Europe and the Near East have found that dairying preceded LP in these regions by at least 5,000 y, suggesting that LP may be irrelevant to the origins and early history of dairying (36). As a non-LP dairying society with a rich prehistory, Mongolia can serve as a model for understanding how other adaptations, such as cultural practices or microbiome alterations (37), may be involved in enabling the adoption and long-term maintenance of a dairy-based subsistence economy. Early herding groups in Mongolia present a historical counter-example to Europe in which WSH migrations resulted in cultural exchange rather than population replacement, and dairying was maintained for millennia without the introgression or selection of LP alleles. |
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