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Update from new paper (behind paywall) Paternal origin of Paleo-Indians in Siberia: insights from Y-chromosome sequences by Wei et al., Eur. J. Hum. Genet. (2018) on the expansion of haplogroup C2-M217
DIFFERENTIATION AND DIFFUSION IN PALAEOLITHIC SIBERIA
Based on the phylogenetic analyses and the current distributions of relative sub-lineages, we propose that the prehistoric population differentiation in Siberia after the LGM (post-LGM) provided the genetic basis for the emergence of the Paleo-Indian, American aborigine, population. According to the phylogenetic tree of Y-chromosome haplogroup C2-M217 (Fig. 2 and Figure S1), eight sub-lineages emerged in a short period between 15.3 kya and 14.3 kya (Table S5). Within these sub-lineages, haplogroups C2-M48, C2-F1918, and C2- F1756 are predominant paternal lineages in modern Altaic-speaking populations [46, 51, 52]. Samples of haplogroups C2-F8535 and C2-P53.1 were found in two Turkic- and Mongolic-speaking minorities in China (Table S1). Both archeological and genetic data suggest that Altaic-speaking populations are results of population expansion in the past several thousand years in the Altai Mountain, Mongolia Plateau, and Amur River region [51–54].
By contrast, three other sub-lineages, C2-B79, C2-B77, and C2-P39, appear only in Koryaks and Native Americans [16, 35]. The latitude of the Altai Mountain, the Mongolia Plateau, and Amur River region are much lower than that of Beringia, where the ancestors of Native Americans finally separated from their close relatives in Siberia. Therefore, the phylogeographic patterns of sub-lineages of C2-M217 in this study reveal a major splitting event between populations in a lower latitude region of Siberia and ancestors of Koryaks and Native Americans during the post-LGM period.
Earlier paper: Genetic Legacy of the Mongols on the origin of C*(xC3c)
The origin was most likely in Mongolia, where the largest number of different star-cluster haplotypes is found (fig. 1). Thus, a single male line, probably originating in Mongolia, has spread in the last ∼1,000 years to represent ∼8% of the males in a region stretching from northeast China to Uzbekistan. If this spread were due to a general population expansion, we would expect to find multiple lineages with the same characteristics of high frequency and presence in multiple populations, but we do not (Zerjal et al. 2002). The star-cluster pattern is unique.
This rise in frequency, if spread evenly over ∼34 generations, would require an average increase by a factor of ∼1.36 per generation and is thus comparable to the most extreme selective events observed in natural populations, such as the spread of melanic moths in 19th-century England in response to industrial pollution (Edleston 1865). We evaluated whether it could have occurred by chance. If the population growth rate is known, it is possible to test whether the observed frequency of a lineage is consistent with its level of variation, assuming neutrality (Slatkin and Bertorelle 2001). Using this method, we estimated the chance of finding the low degree of variation observed in the star cluster, with a current frequency of ∼8%, under neutral conditions. Even with the demographic model most likely to lead to rapid increase of the lineage, double exponential growth, the probability was <10−237; if the mutation rate were 10 times lower, the probability would still be <10−10. Thus, chance can be excluded: selection must have acted on this haplotype.
Could biological selection be responsible? Although this possibility cannot be entirely ruled out, the small number of genes on the Y chromosome and their specialized functions provide few opportunities for selection (Jobling and Tyler-Smith 2000). It is therefore necessary to look for alternative explanations. Increased reproductive fitness, transmitted socially from generation to generation, of males carrying the same Y chromosome would lead to the increase in frequency of their Y lineage, and this effect would be enhanced by the elimination of unrelated males. Within the last 1,000 years in this part of the world, these conditions are met by Genghis (Chingis) Khan (c. 1162–1227) and his male relatives. He established the largest land empire in history and often slaughtered the conquered populations, and he and his close male relatives had many children. Although the Mongol empire soon disintegrated as a political unit, his male-line descendants ruled large areas of Asia for many generations. These included China, where the Yüan Dynasty emperors remained in power until 1368, after which the Mongols continued to dominate the country north of the Great Wall for several more centuries, and the region west to the Aral Sea, where the Chaghatai Khans ruled. Although their power diminished over time, they remained at Kashghar near the Kyrgyzstan/China border until the middle of the 17th century (Morgan 1986).
It is striking that the boundary of the Mongol empire when Genghis Khan died (fig. 2), which also corresponds to the boundaries of the regions controlled by later Khans, matches the distribution of star-cluster chromosomes closely, with one exception: the Hazaras. We, therefore, wished to compare Genghis Khan’s Y profile with the star cluster. It is not possible to examine his remains directly, but history provides an alternative. The Hazaras of Pakistan have a Mongol origin (Qamar et al. 2002), and many consider themselves to be direct male-line descendants of Genghis Khan. A genealogy documenting these links has been constructed from their oral history (Mousavi 1998). A large proportion of the Hazara profiles do indeed lie in the star cluster, which is not otherwise seen in Pakistan (fig. 2), thus supporting their oral tradition and suggesting that Genghis Khan carried the star-cluster haplotype.
The Y chromosome of a single individual has spread rapidly and is now found in ∼8% of the males throughout a large part of Asia. Indeed, if our sample is representative, this chromosome will be present in about 16 million men, ∼0.5% of the world’s total. The available evidence suggests that it was carried by Genghis Khan. His Y chromosome would obviously have had ancestors, and our best estimate of the TMRCA of star-cluster chromosomes lies several generations before his birth. Several scenarios, which are not mutually exclusive, could explain its rapid spread: (1) all populations carrying star-cluster chromosomes could have descended from a common ancestral population in which it was present at high frequency; (2) many or most Mongols at the time of the Mongol empire could have carried these chromosomes; (3) it could have been restricted to Genghis Khan and his close male-line relatives, and this specific lineage could have spread as a result of their activities. Explanation 1 is unlikely because these populations do not share other Y haplotypes, and explanation 2 is difficult to reconcile with the high Y-haplotype diversity of modern Mongolians (Zerjal et al. 2002). The historically documented events accompanying the establishment of the Mongol empire would have contributed directly to the spread of this lineage by Genghis Khan and his relatives, but perhaps as important was the establishment of a long-lasting male dynasty. This scenario shows selection acting on a group of related men; group selection has been much discussed (Wilson and Sober 1994) and is distinguished by the property that the increased fitness of the group is not reducible to the increased fitness of the individuals. It is unclear whether this is the case here. Our findings nevertheless demonstrate a novel form of selection in human populations on the basis of social prestige. A founder effect of this magnitude will have influenced allele frequencies elsewhere in the genome: mitochondrial DNAlineages will not be affected, since males do not transmit their mitochondrial DNA, but, in the simplest models, the founder male will have been the ancestor of each autosomal sequence in ∼4% of the population and X-chromosomal sequence in ∼2.7%, with implications for the medical genetics of the region. Large-scale changes to patterns of human genetic variation can occur very quickly. Although local influences of this kind may have been common in human populations, it is, perhaps, fortunate that events of this magnitude have been rare.
Y Haplogroup C2b-L1373 (highly rated in Mongolia & Kazakhstan, 40~70% appears).
– Liaoning Sibe(23%) > Heilungjiang Hezhen(18%) > Liaoning Mongolian (14%) > Liaoning Manchurian1 (8%) > Heilungjiang Han Chinese (5%) > Liaoning Manchurian2 (4%) > Jirin Korean (2%) > Liaoning Han Chinese (1%)
Y Haplogroup O1b2-M176 (highly rated in Japanese & Korean, 20~40% appears).
– Liaoning Manchurian2 (34%) > Jirin Korean (22~38%) > Heilungjiang Hezhen (8~12%) > Liaoning Mongolian (4%) > Heilungjiang Han Chinese (4%) > Liaoning Sibe (3%) > Liaoning Manchurian1 (2%) > Liaoning Han Chinese (1%)
Y Haplogroup O2-M122 (highly rated in Han Chinese & Butan, 48~80% appears).
– Heilungjiang Han Chinese (58%) > Liaoning Han Chinese (55%) > Liaoning Manchurian1 (54%) > Liaoning Manchurian2 (42%)
> Liaoning Sibe (42%) > Heilungjiang Hezhen (42%) > Jirin Korean (34~48%)
The dolmens represent burials of royal nobility in North Korea settlers of R1B from the bronze age. 43% of North Koreans are genetically proven to have R1B which is similar to the amount of 40~50% R1A in India and the Middle East. Source Korean nobility, Family TreeDNA
The following study is significant – To assess the present geographical distribution of the same mtDNA haplotypes found in the Tavan Tolgoi bodies – The 4 D4-carrying bodies (MN0104, MN0125, MN0126, and MN0127) were assigned to categories corresponding to modern Eastern Asians such as Japanese, Chinese and Mongolian in NJ trees, exhibiting 98–99% similarity in their mtDNA sequences spanning a total of 664–673 base pairs of HVR1 and HVR2 (Table 5 and S6 Fig)
R1b (Phylogenetic Tree)was once prevalent all over Eurasia. The results of mtDNA, Y-SNP, and Y-STR indicate that the Golden family members from Tavan Tolgoi had matrilineal (D4 and CZ) and patrilineal (R1b-M343) lines with genealogical origins in East Asia and West Eurasia, respectively. In addition, the Y-STR data were consistent with those of Y-SNP, demonstrating that male members of the Golden family, which showed identical Y-STR profiles, are affiliated with the Y-haplogroup R1b-M343 and that their direct descendants are distributed in West Eurasia from Poland to the western region of China.
(R1b-343 arose somewhere in Eurasia, perhaps Western Eurasia its earliest populations are found in Italy and Botai-Kazakhstan, but its subclades are most common today among W Europeans, although it was once common through Eastern Eurasia, including among East Asians. It arose from R1* 174 Source: Jeong, Choongwon. “Characterizing the genetic history of admixture across inner Eurasia“. bioRxiv e May. 23, 2018; doi: http://dx.doi.org/10.1101/327122.
Botai individual should belong to the 413 R1b-M73 branch which is frequent in the Eurasian steppe (Figure S9). This branch was also found in Mesolithic samples from Latvia67 414 as well as in numerous modern southern Siberian and Central Asian 415 groups….
The Botai genomes provide a critical snapshot of the genetic profile of pre-Bronze Age steppe 530 populations. Our admixture modeling positions Botai primarily on an ancient genetic cline of the pre531 Neolithic western Eurasian hunter-gatherers: stretching from the post-Ice Age western European hunter532
gatherers (e.g. WHG) to EHG in Karelia and Samara to the Upper Paleolithic southern Siberians (e.g. 533 AG3). Botai’s position on this cline, between EHG and AG3, fits well with their geographic location and 534 suggests that ANE-related ancestry in the East did have a lingering genetic impact on Holocene Siberian 535 and Central Asian populations at least till the time of Botai. A recent study reports 6,000 to 8,000 year old 536 genomes from a region slightly north of Botai, whose genetic profiles are similar to our Botai individuals.68 537 This ancient cline in Altai-Sayan region has now largely been overwritten by waves of 538 genetic admixtures. Starting from the Eneolithic Afanasievo culture, multiple migrations from the Pontic539 Caspian steppe to the east have significantly changed the western Eurasian ancestry during the Bronze Age.7; 8 The most recent clear connection with the Botai 543 ancestry can be found in the Middle Bronze Age Okunevo individuals (Figure S6C). In contrast,
544 additional EHG-related ancestry is required to explain the forest-tundra populations to the east of the 545 Urals (Figure 5 and Table S8). Their multi-way mixture model may in fact portrait a prehistoric two-way 546 mixture of a WSH population and a hypothetical eastern Eurasian one that has an ANE-related
547 contribution higher than that in Nganasans. Botai and Okunevo individuals prove the existence of such 548 ANE ancestry-rich populations. Pre-Bronze Age genomes from Siberia will be critical for testing this 549 hypothesis….(However,) . East Asians (EAS) are more 389 closely related to Botai than to AG3 as shown by significantly positive f4 symmetry statistics in the form 390 of f4(Mbuti, EAS; AG3, Botai), suggesting East Asian gene flow into Botai (Figure S6B). We estimated the proportion of East Asian ancestry in Botai using qpAdm. The two-way admixture model of AG3+Korean provides a good fit to Botai with 17.3% East Asian contribution.. However, we find that Botai 394 harbors an extra affinity with Mesolithic western European hunter-gatherers (“WHG”) unexplained by 395 this modelwe conclude that the ANE404 related ancestry in Botai is intermediate between EHG and AG3, which corresponds to its intermediate405 geographic position. This suggests a genetic cline of decreasing ANE-related ancestry stretching from406 AG3 in Siberia to WHG in Western Europe. A substantial East Asian contribution into Botai make them407 offset from the WHG-ANE cline. A strong genetic affinity between Botai and the Middle Bronze Age408 Okunevo individuals in the Altai-Sayan region also suggests a wide geographic and temporal distribution409 of Botai-related ancestry in central Eurasia (Figure S6C).410 The Y-chromosome of the male Botai individual (TU45) belongs to the haplogroup R1b (Table S6). However, it falls into neither a predominant European branch R1b-L5165 411 nor into a R1b-GG400 branch found in Yamnaya individuals.66 412 Thus, phylogenetically this Botai individual should belong to the 413 R1b-M73 branch which is frequent in the Eurasian steppe (Figure S9). This branch was also found in Mesolithic samples from Latvia67 414 as well as in numerous modern southern Siberian and Central Asian415 groups
Our results show that contemporary inner Eurasians form genetic clines distinct from the ancient420 WHG-ANE cline, from which a majority of the Botai ancestry is derived. To see if this ancient cline of421 “ANE” ancestry left any legacy in the genetic structure of inner Eurasians, we performed admixture
422 modeling of populations from the Altai-Sayan region and those belonging to the forest-tundra cline.423 Specifically, we investigated if an additional contribution from ANE-related ancestry is required to424 explain their gene pools beyond a simple mixture model of contemporary eastern Eurasians and ancient425 western Eurasian populations.
426 Contemporary Altai-Sayan populations are effectively modeled as a two-way mixture of ancient427 populations from the region with WSH ancestry and contemporary eastern Eurasians, either Afanasievo+Ulchi or Sintashta+Nganasan (χ2 428 p ≥ 0.05 for 8/12 and 5/12 Altai-Sayan groups, respectively; 429 Table S7). Among the ancient groups, Sintashta+EAS generally fits Andronovo individuals well with a 430 small eastern Eurasian contribution (6.4±1.4% for estimate ± 1 SE with Nganasans), while later Karasuk
431 or Iron Age individuals from the Altai are modeled better with the older Afanasievo as their WSH-related432 source (Table S7). If the pre-Bronze Age populations of the Altai-Sayan region were related to either433 Botai in the west or the Upper Paleolithic Siberians in the east, these results suggest that these pre-Bronze434 Age populations in southern Siberia did not leave a substantial genetic legacy in the present-day435 populations in the region. The Okunevo individuals are the only case that WSH+EAS mixture cannot explain (χ2
p ≤ 3.85×10-4); similar to Botai, a model of AG3+EAS provides a good fit (χ
2 436 p = 0.396 for437 AG3+Korean; Table S5).
The Botai genomes provide a critical snapshot of the genetic profile of pre-Bronze Age steppe530 populations. Our admixture modeling positions Botai primarily on an ancient genetic cline of the pre531Neolithic western Eurasian hunter-gatherers: stretching from the post-Ice Age western European hunter532 gatherers (e.g. WHG) to EHG in Karelia and Samara to the Upper Paleolithic southern Siberians (e.g. 533 AG3). Botai’s position on this cline, between EHG and AG3, fits well with their geographic location and534 suggests that ANE-related ancestry in the East did have a lingering genetic impact on Holocene Siberian535 and Central Asian populations at least till the time of Botai. A recent study reports 6,000 to 8,000 year old536 genomes from a region slightly north of Botai, whose genetic profiles are similar to our Botai individuals.68 537 This ancient cline in Altai-Sayan region has now largely been overwritten by waves of538 genetic admixtures. Starting from the Eneolithic Afanasievo culture, multiple migrations from the Pontic539 Caspian steppe to the east have significantly changed the western Eurasian ancestry during the Bronze Age.7; 8
The study of ancient genomes from inner Eurasia will be extremely important for going forward.551 Inner Eurasia has functioned as a conduit for human migration and cultural transfer since the first 552 appearance of modern humans in this region. As a result, we observe deep sharing of genes between553 western and eastern Eurasian populations in multiple layers: the Pleistocene ANE ancestry in Mesolithic554 EHG and contemporary Native Americans, Bronze Age steppe ancestry from Europe to Mongolia, and 555 Nganasan-related ancestry extending from western Siberia into Eastern Europe. More recent historical 556 migrations, such as the westward expansions of Turkic and Mongolic groups, further complicate genomic 557 signatures of admixture and have overwritten those from older events. Ancient genomes of Iron Age
steppe individuals, already showing signatures of west-east admixture in the 5th to 2nd century BCE,38 558559 provide further direct evidence for the hidden old layers of admixture, which is often difficult to 560 appreciate from present-day populations as shown in our finding of a discrepancy between the estimates
561 of admixture dates from contemporary individuals and those from ancient genomes.
Lkhagvasuren G, Shin H, Lee SE, Tumen D, Kim J-H, Kim K-Y, et al. (2016) Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan. PLoS ONE 11(9): e0161622. https://doi.org/10.1371/journal.pone.0161622
Members of the Mongol imperial family (designated the Golden family) are buried in a secret necropolis; therefore, none of their burial grounds have been found. In 2004, we first discovered 5 graves belonging to the Golden family in Tavan Tolgoi, Eastern Mongolia. To define the genealogy of the 5 bodies and the kinship among them, SNP and/or STR profiles of mitochondria, autosomes, and Y chromosomes were analyzed. Four of the 5 bodies were determined to carry the mitochondrial DNA haplogroup D4, while the fifth carried haplogroup CZ, indicating that this individual had no kinship with the others. Meanwhile, Y-SNP and Y-STR profiles indicate that the males examined belonged to the R1b-M343 haplogroup. Thus, their East Asian D4 or CZ matrilineal and West Eurasian R1b-M343 patrilineal origins reveal genealogical admixture between Caucasoid and Mongoloid ethnic groups, despite a Mongoloid physical appearance. In addition, Y chromosomal and autosomal STR profiles revealed that the four D4-carrying bodies bore the relationship of either mother and three sons or four full siblings with almost the same probability. Moreover, the geographical distribution of R1b-M343-carrying modern-day individuals demonstrates that descendants of Tavan Tolgoi bodies today live mainly in Western Eurasia, with a high frequency in the territories of the past Mongol khanates. Here, we propose that Genghis Khan and his family carried Y-haplogroup R1b-M343, which is prevalent in West Eurasia, rather than the Y-haplogroup C3c-M48, which is prevalent in Asia and which is widely accepted to be present in the family members of Genghis Khan. Additionally, Tavan Tolgoi bodies may have been the product of marriages between the lineage of Genghis Khan’s Borjigin clan and the lineage of either the Ongud or Hongirad clans, indicating that these individuals were members of Genghis Khan’s immediate family or his close relatives.
Temujin was born into the Borjigin clan as a son of Yesugei, who was a grandson of Khabul (or Qabul) Khan (King in the Mongolian language), the first khan of the Khamag Mongol confederation. In 1206, Temujin annexed and unified many Mongol-Turkic nomadic tribes of Northeast Asia, and was then crowned the “Genghis Khan (the supreme king in the Mongolian language)” at a Kurultai, a general council of Mongol chiefs . After founding the Mongol Empire, Genghis Khan invaded neighboring lands outward from the Mongolian plateau, ultimately conquering most of Eurasia. The Mongol Empire expanded to be the largest contiguous land empire in human history, covering the area from Eastern Europe to the East Sea/the Sea of Japan. The vast transcontinental empire allowed for the exchange of cultures and religions between Asia and Europe via the Silk Road. Thus, the Pax Mongolica greatly influenced many civilizations in Eurasia during the 13th and 14th centuries; indeed, its cultural, social, religious, and economic impact on the world remains today.
To solidify the foundation of the Mongol Empire, Genghis Khan employed two major strategies. First, because the Mongol Empire was too large to be controlled by a single ruler, he allocated the territories to his family members and let them rule their own independent territories [2, 3]. Because his wives were old and his sons were incompetent compared to his daughters, Genghis Khan bestowed upon his daughters, instead of his sons, the heavy responsibilities of shielding the inner territory of the Mongolian plateau and operating the outposts for his world conquest. He distributed the neighboring kingdoms surrounding the inner territory of the Mongolian plateau among his 4 daughters, including Alaqai Beki, “beki” meaning princess in the Mongolian language, who came to dominate the Ongud kingdom, Eastern Mongolia [2, 4]. His daughters faithfully ruled their own kingdoms throughout their lives on behalf of their father.
Genghis Khan’s second strategy was to use quda, the traditional marriage alliance system of Mongolia, to marry his sons and daughters into the ruling lineages of neighboring kingdoms such as the Ongud [3, 5]. Through this system, Genghis Khan expected his daughters to become regents of the kingdoms once dominated by their husbands (guregens; prince consorts in the Mongolian language); he forced guregens to go to war, leaving their wives (bekis) in charge of running the home according to Mongol tradition. In doing so, Genghis Khan conferred power to his daughters, and not to the guregens, to rule the kingdoms. Moreover, guregens could not return to their homeland for long periods of time, and were killed at a high rate in Genghis Khan’s war. Through these qudas, bekis, as authoritarian rulers, strengthened alliances among their kingdoms and provided Genghis Khan the solid foundation necessary to conquer many kingdoms outward from the Mongol steppe .
Thus, Genghis Khan could not have founded the Mongol Empire without his bekis dominating the kingdoms [2, 3]. Although Genghis Khan’s daughters wielded unprecedented political authority in several kingdoms of the Mongol Empire, their names and achievements in solidifying the Mongol Empire have disappeared from Mongol chronicles over generations. Their burial grounds have never been found because all members of the imperial family of the Mongol Empire, including khans, khatuns, meaning “empress” in Mongolian, bekis, and their descendants, were buried without identifying signs, according to the long-standing tradition of keeping the burial grounds of ancestors in a secret necropolis called “Lord’s Enclosure” [3–5]. Indeed, the geographical locations of the graves of the Mongol imperial family (designated the Golden family) members are unknown [1, 6, 7].
Many researchers believe that the discovery of graves of the ancients will undoubtedly reveal details of their genealogies and lives. Molecular archaeologists have developed scientific and systematic approaches to trace customs, diseases, and genealogies of the ancients as well as various activities during the lifetimes of ancient peoples. Accordingly, it is likely that direct molecular archaeological analysis of the human remains from Genghis Khan’s Golden family members who ruled Pax Mongolica will provide scientific clues to unveil their mysterious lives and genealogies.
In 2004, 7 graves were first excavated in the central hill of Tavan Tolgoi (“five hills” in the Mongolian language) by a Mongolian excavation team. Tavan Tolgoi lies within the Ongud province once dominated by Alaqai Beki and then Sorkhokhtani, a wife of Genghis Khan’s youngest son Tolui, during the early Mongolian era . Mongolian archaeologists who participated in the excavation of Tavan Tolgoi graves strongly suspected that 5 of 7 Tavan Tolgoi graves belonged to the Golden family [9–11], and one of those 5 graves was thought to be that of a Mongol Queen. Burial artifacts excavated from the Tavan Tolgoi graves have since been displayed in the National Museum of Mongolian History, recognized as important relics of the Mongol Empire.
In this study, we aimed to determine the matrilineal and patrilineal origins of the Golden family members from the Tavan Tolgoi burial site and to determine kinship among them and with Genghis Khan, through analysis of single nucleotide polymorphism (SNP) and short tandem repeat (STR) of mitochondria, autosomes, and Y chromosomes from ancient DNAs (aDNAs). In addition, we compared their mitochondrial DNA (mtDNA) and Y-STR haplotypes with those of modern-day individuals using neighbor-joining (NJ) and Y-chromosome STR Haplotype Reference Database (YHRD) analyses, respectively, to determine the current geographical distribution of female- and male-line descendants of the Golden family members. Moreover, the familial relationship of the Tavan Tolgoi bodies with Genghis Khan was also postulated based on molecular archaeological and historical evidence. This study, the first molecular archaeological analysis of several skeletons belonging to Genghis Khan’s Golden family, presents molecular data to reveal the identity and genealogy of Golden family members, including a Mongol Queen, thereby unlocking the door to mysterious lives of the Golden family.
Archaeological and physical anthropological analyses of the Tavan Tolgoi bodies
In 2004, a Mongolian excavation team from the Department of Anthropology and Archaeology, National University of Mongolia, discovered burial grounds scattered on the sunny slope of the center hill of five hills in Tavan Tolgoi. Tavan Tolgoi is geographically located near the Ongon district, Sukhbaatar province, Eastern Mongolia, 650 km away from the capital city of modern Mongolia, Ulan Bator (Fig 1A). It consists of a rocky hill slope amidst a huge plain that is 1,104 m above sea level and is located between Karakorum (present-day Kharkhorin), the capital city of the 13th century Mongol Empire, and Dadu (present-day Beijing), the capital city of the Yuan Dynasty. Archaeological monuments, the remnants of several ancient nomadic tribes who had inhabited the region over thousands of years from the Neolithic to Mongolian eras, have been identified in this region. Out of them, two headless stone statues called “Mongolian King and Queen” by local people are regarded as very important relics, indicating that Tavan Tolgoi is a sacred region from the traditional Mongolian perspective (Fig 1B).
A: A map of Tavan Tolgoi (top) and the relative geographical locations (bottom) of the graves excavated there. B: Two headless stone statues called Mongol King and Queen are located at the entrance of Tavan Tolgoi.
The 7 Tavan Tolgoi graves had similar exterior surface structures surrounded by a ring-shaped stone construction with a diameter of 6–8 m, reflecting a tomb style typical of the Xiongnu era (from about the 3rd century B.C. to the late 1st century C.E.) [11, 12]. However, the internal structure of the Tavan Tolgoi graves and the style of burial artifacts, instead, indicated graves from the medieval Mongolian era (Fig 2 and S1 Table) [11, 13]. This was confirmed by Youn and colleagues , who used 14C radiocarbon dating of their human remains or artifacts to show that the Tavan Tolgoi graves dated between 1130–1250 AD. Mongolian archaeologists demonstrated that the surface features of the Tavan Tolgoi graves were probably intended to protect the graves from looting and enemies from the contemporary or future world, implying that these individuals were important figures in the society at that time [10, 11]. Thus, archaeological and radiocarbon dating results strongly suggest that the 7 Tavan Tolgoi graves correspond to the early Mongolian era, when Genghis Khan and his close family members, including his sons, daughters, sons-in-law, and daughters-in-law, were in power.
A-D: MN0105; A-B: a golden ring engraved with a falcon image, C-D: another golden ring engraved with the same falcon image as in A. E-G: MN0125; E: a saddle sheathed in gold dragon-shaped artistic decoration, F: the same golden ornament of boqta as those of the boqtas of Mongol khatuns in the design and shape, G: a golden ornament inside the boqta. H: Jins of MN0124. I: a golden earring of MN0126. J-K: MN0127; J: a golden earring, K: a coffin made of cinnamon.
All physical anthropological parameters indicate that the skulls of the Tavan Tolgoi graves were all anthropologically Mongoloid (S2 Table). Unfortunately, not all of the cranial metric traits from the skulls of MN0125 and MN0127 were available because of significant breakage of the skeletons, including the skulls. The presumed height and weight of MN0104 and MN0105 were 169.8 cm and 78.1 kg and 165.6 cm and 68.1 kg, respectively. Particularly, MN0105 was more than 10 cm taller than other females of average height in the Mongolian era, indicating that she was well nourished and/or genetically superior [9, 15]. Estimation of height and weight failed in other Tavan Tolgoi bodies; the femurs of MN0124, MN0126, and MN0376 were badly broken and those of MN0125 and MN0127 were completely broken. In addition, their anatomical sex and presumed age at death, according to physical anthropological data obtained from osteometric and odontometric estimation of the skulls and/or pelvic bones, and teeth, respectively, are shown in Table 1 and S1 Table [16, 17]. Based on these data, it was estimated that the anatomical sex of MN0104, MN0126, MN0127, and MN0376 was male, while that of the other bodies (MN0105, MN0124, and MN0125) was female. The results of physical anthropological analysis were coincided with those of amelogenin sex determination by the conventional PCR analysis using X-Y primers. One Tavan Tolgoi body (MN0124) was estimated to have died in her 10s, 4 (MN0104, MN0125, MN0126, and MN0127) in their 20s, and 2 (MN0105 and MN0376) in their 40s or 50s.
Burial artifacts from the 5 Tavan Tolgoi graves were exceptional in quality and quantity, compared to those previously found in other graves from the Mongolian era; most artifacts from the Tavan Tolgoi graves, however, including MN0104, MN0126, and MN0127, had been looted a long time ago . In the female graves, MN0105 and MN0125, we unearthed golden rings engraved with the falcon image that symbolizes the Genghis Khan and the Borjigin clan, a saddle sheathed in gold dragon-shaped artistic decoration and golden ornaments for boqta, which are similar to those of Mongol khatuns in shape and decoration (Fig 2A–2G). In the male graves, MN0104 was unearthed holding an ornament, called “Jins” in Mongolia, consisting of a large pearl mounted on a flower-shaped golden base (Fig 2H). MN0126 and MN0127 were each wearing only a single earring that was found under the skull, indicating their higher social status (Fig 2I and 2J); Mongolian aristocratic men usually wore hats adorned with Jins and a single earring in their left ears, confirming that MN0104, MN0126 and MN0127 were all males. In addition, the coffin wood of MN0127 was not from trees native to the Mongolian Plateau; the wood was cinnamon (Cinnamomum sp.), which grows only in hot and humid Southeast Asia, at least several thousand kilometers away from Tavan Tolgoi. This finding suggests that he and his family had considerable financial and political power sufficient to bring the plant for his coffin from a far-off province. Taken together, these data clearly indicate that the 5 graves belong to the Golden family members who were contemporaries of Genghis Khan, including a Mongol Queen (MN0125), although their exact identities are ambiguous [9–11].
On the contrary, the internal structure and lack of notable artifacts, aside from a pair of small earrings, in the MN0124 grave containing the teenage female skeleton indicate that it belonged to a member of the general public of the Mongolian era. MN0376 was also believed to belong to a member of the general public, based on the artifacts excavated. The burial artifacts from this grave were all associated with war, including an arrow quiver and arrowheads; his physical anthropological characteristics, including several signs of injury during his lifetime, such as trauma of the left clavicle and a well-developed skeleton, indicate that he was a common warrior [9, 11].
Authenticity assessment of aDNA analysis
To prevent cross-contamination of DNA samples, bone samples were collected with extensive precautions according to previously published procedures [18–20]. We ensured that our data were derived from genuine aDNAs, and not from contaminated DNA samples, based on the following precautions. First, our data were obtained from at least 6 independent multiple extractions and amplifications per sample. In detail, aDNAs from Tavan Tolgoi bodies were independently extracted more than 3 times per sample in two independent laboratories, and then their haplotypes and haplogroups of mtDNA and Y chromosome were determined by independent PCR amplification more than two times per extract. DNA sequences obtained from at least 6 (3 extractions per sample × 2 PCR amplifications per extract) independent experiments per sample were compared to determine the similarity among the obtained nucleotide sequences, and the DNA sequences were confirmed to be identical in at least 5–6 experiments and were regarded as a consensus sequence for the specific sample. Second, our data were obtained from 2 independent laboratories located in different buildings and managed by different principal investigators; if the data obtained were not identical, all procedures were repeated beginning with the extraction step of aDNA. Third, we compared mtDNA data from aDNAs with these of all researchers who participated in the archaeological excavation, aDNA extraction, and PCR amplification of aDNA (Table 1); if the aDNA and modern DNA sequences matched, these samples were excluded from the analysis. Fourth, to support that our PCR products were derived from human aDNA, sequences of hypervariable region 1 (HVR1) of horse mtDNA were amplified using previously reported primer sets (S1 Fig). Ancient horse bones excavated together with MN0105 were subjected to mtDNA analysis. The D-loop HVR1 of horse mtDNA was successfully amplified and sequenced with no evidence of contamination by human aDNA. In addition, the DNA sequences of amplified horse aDNA were compared to human DNA sequences from the Tavan Tolgoi bodies and from researchers of the 2 laboratories, as well as to the revised Cambridge Reference Sequence (rCRS), using SeqMan II software [18, 21]. The results demonstrate that our data were sufficiently reproducible for selective analysis of aDNA from ancient human skeletons and were not contaminated by organelles or contemporary individuals. Fifth, uracil DNA glycosylase (UDG) treatment of purified aDNA reduces the risk of identifying incorrect DNA sequences by inhibiting the erroneous PCR amplifications and deamination of deoxycytidine residues in the aDNA template. Therefore, we compared DNA sequences obtained from direct PCR amplification with those from clones constructed after treating aDNA samples of 6 Tavan Tolgoi bodies, except for MN0127, with either active or inactive UDG (S3 and S4 Tables). The consensus nucleotide sequences from the direct PCR and the clones were identical, including the sites of haplogroup-defining SNPs, indicating that all data obtained from the 6 Tavan Tolgoi bodies were indeed from aDNA and did not contain significant base modifications. One exception was found at nucleotide position 16,250 of HVR1 in MN0376, which showed a transition from C to T when the clones were inserted by MN0376 aDNA treated with inactive UDG (S4 Table). However, the reversion of transition from T to C was observed when clones were inserted with MN0376 aDNA treated with active UDG, indicating that UDG effectively inhibits post-mortem DNA damage.
Identification of mtDNA haplogroups and haplotypes of the Tavan Tolgoi bodies and their matrilineal origins
Skeletons of 7 Tavan Tolgoi graves were analyzed for haplotypes and haplogroups of their mtDNAs through DNA sequencing of control regions, HVR1 and HVR2, and several coding regions. Their mtDNA haplotypes were determined by comparison of HVR1 and HVR2 DNA sequences with rCRS; mtDNA haplogroups were assigned by DNA sequence analysis of 10 additional coding regions and the control regions, HVR1 and HVR2, for obtaining unambiguous results [18, 22–25]. PCR amplification and DNA sequencing of the control and coding regions were successfully performed in all bodies examined by using primer sets presented in S5 Table; results obtained from the two laboratories were identical.
Overall, 4 haplotypes were identified in the 7 Tavan Tolgoi bodies and were assigned to 4 haplogroups (Table 1). Four bodies, MN0104, MN0125, MN0126, and MN0127, likely members of the Golden family according to archaeological and physical anthropological analyses, were identical in their mtDNA sequences and were assigned to the same haplogroup, D4, prevalent in Far Eastern Asia [26, 27]. Meanwhile, the other Golden family member, MN0105, was assigned to the CZ haplogroup, which is prevalent in Northeastern Asia (mostly in Siberia), implying that MN0105 had no kinship with the other Golden family members of Tavan Tolgoi. The haplogroups of the members of the general public, MN0124 and MN0376, were R and M9, occurring mostly in Arabian plate and South East Asia including Tibet, respectively [28–30].
Identification of Y-haplogroups and haplotypes of the Tavan Tolgoi bodies and their patrilineal origins
Patrilineal origins of Tavan Tolgoi bodies were first traced by Y-haplogrouping using 10 biallelic Y chromosome markers. Four (MN0104, MN0126, MN0127 and MN0376) of 7 Tavan Tologoi bodies were determined to be males based on physical anthropological estimation and molecular sex determination using amelogenin analysis (Table 1 and S1 Table). Unfortunately, MN0127, who was believed to belong to the Golden family, could not undergo Y-haplogroup analysis because the amount of DNA purified was insufficient for PCR amplification of the Y chromosome, which exists as only one copy within a cell.
MN0104 was positive only for R-M207 and was negative for O-M175, C-RPS4Y, N-M231, D-M174, J-M304, and Q-M242 (Table 2 and S2 Fig). In addition, MN0104 carried the R1-defining M173 and R1b-defining M343 biallelic markers, but not R1a1a-defining M17. MN0126 was also positive for the same biallelic markers (R-M207 and R1b-M343) as those carried by MN0104 and negative for O-M175 and C-RPS4Y (Table 2 and S3 Fig) [31, 32]. These data suggest that male members, MN0104 and MN0126, of the Golden family belong to haplogroup R1b-M343; however, only 4 biallelic markers were definable in MN0126 . In contrast, the Mongolian warrior MN0376 was positive for R-M207 and negative for O-M175, C-RPS4Y, N-M231, D-M174, J-M304, and Q-M242. MN0376 was affiliated with R1a1a-M17, a subclade of haplogroup R1, rather than R1b-M343 because he carried R-M207, R1-M173, and R1a1a-M17 but not R1b-M343 (Table 2 and S4 Fig) [31, 32].
To ascertain whether the R1b-M343-carrying males shared an identical haplotype, we determined their Y-allelotypes using 16 Y-STR markers (Table 3 and S5 Fig). Y-STR markers were examined in bodies MN0104, MN0126, and MN0376, but not MN0127, again due to PCR failure. Y-STR haplotypes of MN0104 and MN0376 were successfully identified in all of 16 marker loci examined, whereas only 8of 16 marker loci were determined in MN0126. Two Golden family members, MN0104 and MN0126, contained the consensus Y-STR allelotypes, which were identical in 7 of 8 definable loci and shared 1 of 2 alleles in a DYS385 marker locus. In contrast, 10 of the 16 marker loci that were definable were not identical in Y-STR allelotypes between MN0104 and MN0376, and 5 of 8 loci between MN0126 and MN0376 did not match in their Y-STR allelotypes. These results are fully consistent with the Y-SNP results, indicating that MN0104 and MN0126 had identical Y-haplotypes from the same patrilineal origin, whereas MN0376 shared no patrilineal origin with the two male members of the Golden family.
In addition, the Y-STR profiles from YHRD were screened to identify individuals with the same STR profile as that of MN0104. PowerPlex Y and Yfiler of YHRD, which enable comparison of a total of 11 and 16 Y-STR marker loci among samples, respectively, were compared with the Y-STR profile of MN0104 with Y-STR profiles from YHRD (S6 Table). Two individuals who perfectly matched MN0104 in all 16 Y-STR definable marker loci were identified as 1 Kalmyk (named Kalmyk 73) and Hui (Chinese) through Yfiler of YHRD. One individual, Uzbek (unnamed), was found to match MN0104 in all 11 Y-STR marker loci through PowerPlex Y of YHRD. Moreover, the Y-STR profiles of the 3 individuals (Hui, Kalmyk, and Uzbek) were applied to determine their Y-haplogroups using Yfiler or PowerPlex Y of YHRD; these individuals were not previously assigned to specific Y-haplogroups in the literature. They were all assigned to the same Y-haplogroup R1b as MN0104 with the highest probability, suggesting that male Golden family bodies carried the Y-haplogroup R1b.
Additionally, individuals with the Y-STR profile matching that of MN0104 in 16 definable marker loci were searched in the literature reporting Y-STR profiles associated with modern Eurasian populations (S6 Table) [33–35]. Two Russian (named Kalmyk 73 and Russian), 1 Uzbek (named 26), and 1 Tajik (named 134) individuals were found to match MN0104 in 14–16 definable Y-STR marker loci. One (named Kalmyk 73) of 2 Russians was confirmed to be the same individual as the Kalmyk described above and searched from YHRD. The other 3 individuals including Russian, Uzbek, and Tajik were previously assigned to the Y-haplogroups R1*-M173, R1b1a*-P297, and R1b1a*-P297, respectively, by Y-SNP analysis [34, 35], except for Kalmyk 73 which was not previously assigned to the specific Y-haplogroup in the literature . The Russian matched MN0104 in 15 of 16 marker loci, exhibiting a different allele from MN0104 in the DYS439 Y-STR marker locus. Two other individuals (Uzbek and Tajik) whose Y-STR profiles were identical in all 16 marker loci did not match MN0104 in 2 marker loci (DYS389II and DYS458). MN0104, Kalmyk, and the other Russian (named Russian) were also assigned to the Y- haplogroup R1b through Yfiler of YHRD, while the other individuals, Uzbek (named 26) and Tajik, were not assigned to the specific Y-haplogroup through Yfiler of YHRD.
In contrast, individuals with the same Y-STR profiles as that of MN0376 were screened through Yfiler and PowerPlex Y from YHRD and the literature (S7 Table). Individuals matching MN0376 in the Y-STR profiles defined through Yfiler of YHRD were not identified, whereas 8 individuals perfectly matched MN0376 in all 11 definable Y-STR marker loci through PowerPlex Y of YHRD. In addition, none were previously assigned to the specific Y-haplogroup based on Y-SNP analysis and were affiliated with a specific Y-haplogroup through PowerPlex Y of YHRD. However, 7 individuals who matched MN0376 in 13 of 16 marker loci were identified in the literature [34–38], including 1 Russian, 1 Hui (Chinese), 1 Croatian, and 4 Pashtun. Two individuals (Russian and Pashtun) were previously assigned to the Y-haplogroup R1a1a-M17 using Y-SNP analysis, and the 3 other Pashtuns were assigned to the Y-haplogroup R1a1a*-M198 (S7 Table). The Hui (Chinese) and Croatian were not previously assigned to the specific Y-haplogroup using Y-SNP analysis. All 7 individuals were affiliated with the Y-haplogroup R1a through Yfiler of YHRD, whereas MN0376 was not assigned to a specific Y-haplogroup.
Taking all data of Y-SNP and Y-STR into consideration, the male Golden family bodies (MN0104, MN0126, and MN0127) from Tavan Tolgoi were clearly assigned to the Y-haplogroup R1b with the identical Y-haplotype, whereas a male general public (MN0376) to the Y-haplogroup R1a1a showed a quite different Y-haplotype from that of male members of the Golden family.
Determination of autosomal STR (A-STR) allelotypes of the Tavan Tolgoi bodies
To define the exact kinship among 4 Golden family members (MN0104, MN0125, MN0126 and MN0127) who shared the same SNP and/or STR profiles of mtDNA and Y chromosome each other, their A-STR allelic profiles were further examined using a total of 9 A-STR markers, including amelogenin for sex determination, and estimated by GeneMapper software (Table 4). STR profiles of autosomal DNA and amelogenin were reproducible for 6 Tavan Tolgoi bodies, except for MN0127 due to failed PCR amplification. Consensus A-STR profiles were successfully determined for the 6 bodies based on results obtained from at least a total of 6 independent experiments carried out in 2 independent laboratories, except that MN0126 was not clearly determined for the consensus allelotypes in a D21S11 marker locus, showing 30/30 or 30/33.2.
The results of amelogenin-based sex identification in the Tavan Tolgoi bodies were consistent with physical anthropological analysis, confirming the validity of our A-STR profiling (Tables 1and 4). The A-STR profiles of the 6 bodies were defined by allelotypes for 8 loci as indicated in Table 4. Inconsistency among consensus A-STR profiles was found in 5 of 48 total consensus allelotypes detected in all 8 marker loci in 6 Tavan Tolgoi bodies. Despite these exceptions, all other A-STR profiles were perfectly consistent in the 43 consensus allelotypes. MN0125 shared at least one allele with either MN0104 or MN0126 in all 8 marker loci examined except for amelogenin. Nevertheless, MN0104 and MN0126 did not share both alleles in 2 marker loci (D21S11 and FGA), but they shared at least 1 of 2 alleles in the remaining 6 marker loci. On the contrary, other Tavan Tolgoi bodies (MN0105, MN0124, and MN0376) shared no alleles in 2 or more loci with the 3 Golden family members (MN0104, MN0125, and MN0126) and among themselves. These results strongly indicate that MN0104, MN0125 and MN0126 have some family ties, but no family relationship with other Tavan Tolgoi bodies (MN0105, MN0124 and Mn0376), although the exact kinship among them is ambiguous.
Present geographical distribution of modern-day individuals with the same mtDNA haplotypes or Y-STR haplotypes as those of Tavan Tolgoi bodies
To assess the present geographical distribution of the same mtDNA haplotypes found in the Tavan Tolgoi bodies, HVR1 and HVR2 DNA sequences were compared with those of 8,478 modern-day individuals from GenBank database, and were used to construct NJ trees using MEGA version 6.0.6 [18, 24, 39]. The 4 D4-carrying bodies (MN0104, MN0125, MN0126, and MN0127) were assigned to categories corresponding to modern Eastern Asians such as Japanese, Chinese and Mongolian in NJ trees, exhibiting 98–99% similarity in their mtDNA sequences spanning a total of 664–673 base pairs of HVR1 and HVR2 (Table 5 and S6 Fig). Meanwhile, the CZ-carrying body (MN0105) had a close genetic relationship with modern Northeastern Asians such as the Yukaghir, Yakut, Xibo, Szekely and Hezhen (Table 5 and S7 Fig). The R-carrying teenager (MN0124) exhibited high sequence similarity with East Europeans and Middle Eastern and South Asians, including populations of Slavs, Druze, Indians and Slovakians (Table 5 and S8 Fig). The M9-carrying warrior (MN0376) exhibited high sequence similarity with South East Asians including Indonesians and Taiwanese (Table 5 and S9 Fig).
MN0104, a male member of the Golden family, was tested using Yfiler and PowerPlex Y of YHRD to assess the geographical distribution of individuals with the same Y-STR profiles as the Tavan Tolgoi (S6 Table). A total of 6 modern-day individuals who matched MN0104 in at least 14 of 16 Y-STR marker loci were identified through YHRD and the literature. These individuals were mainly distributed in East Asia and Central Asia, including the territories (China, Kalmykia, Russia, Uzbekistan, and Tajikistan) associated with the past Mongol khanates.
By comparison, the Y-STR profile of MN0376 perfectly matched those of 8 individuals distributed across Eurasia including India, China, Pakistan, the Czech Republic, and Poland when 11 Y-STR marker loci were considered for matching MN0376 with individuals searched through the PowerPlex Y of YHRD (S7 Table). In addition, when we further examined published literature related to Y-STR profiles associated with modern Eurasian populations and compared the obtained data with the Y-STR profile of MN0376, 7 individuals who matched MN0376 in 13 of 16 definable Y-STR marker loci were identified. These individuals were distributed mainly in West Eurasia, including Russia, Croatia, Pashtun, and China.
Collectively, the results of mtDNA, Y-SNP, and Y-STR indicate that the Golden family members from Tavan Tolgoi had matrilineal (D4 and CZ) and patrilineal (R1b-M343) lines with genealogical origins in East Asia and West Eurasia, respectively. In addition, the Y-STR data were consistent with those of Y-SNP, demonstrating that male members of the Golden family, which showed identical Y-STR profiles, are affiliated with the Y-haplogroup R1b-M343 and that their direct descendants are distributed in West Eurasia from Poland to the western region of China.
Golden family members of Tavan Tolgoi reveal the genealogical admixture between Caucasoid and Mongoloid ethnic groups
So far, no molecular archaeological study of members of the Mongolian imperial family has been conducted; this is largely because no grave of imperial family, especially those of the Golden family, has been identified until the Tavan Tolgoi grave excavation. To the best of our knowledge, this study is the first molecular archeological attempt to define the genealogy of Genghis Khan’s Golden family members in the Mongolian era.
Evidence suggests that many Mongoloid and Caucasoid nomadic tribes inhabited the present-day Mongolian plateau over thousands of years . Since Genghis Khan’s era, the Mongolian population underwent rapid and considerable gene flow from Eurasia, resulting in additional genetic admixture . Likewise, the Mongolian population was formed by the continuous admixture of indigenous tribes who inhabited the Mongolian plateau, with European and other Asian populations who inhabited regions geographically distant from Mongolia. This admixture has deeply influenced the physical appearance of modern-day Mongolian people, exhibiting both Mongoloid and Caucasoid features.
The mixing between Mongoloid and Caucasoid ethnic groups inherent in the genetic structure of modern-day Mongolians was also observed in the Tavan Tolgoi bodies. The Golden family members carried mtDNA haplogroups D4 and CZ, mostly found in Far Eastern and Northeastern Asia, respectively, whereas male members of Golden family carried the Y-haplogroup R1b-M343, dominant in Western Europe [41–43]. That is, although members of Golden family were physically Mongoloid, their molecular genealogy revealed the admixture between Caucasoid and Mongoloid ethnic groups. Thus, it is likely that their Mongoloid appearance would have resulted from gradual changes in their appearance from Caucasoid to Mongoloid through generations from their ancestors. Their physical appearance was largely attributed to D4-carrying Mongoloid females who were indigenous peoples of the Mongolian plateau, rather than an R1b-M343-carrying Caucasoid male spouse who had initially moved from Europe to the Mongolian plateau and his male descendants; it is, however, uncertain how and when the admixture between Mongoloid and Caucasoid ethnic groups originated in the Mongolian plateau.
Y-haplogroup R1b-M343 of Tavan Tolgoi bodies may be another candidate for the Y-haplogroup of Genghis Khan and Genghis Khan’s Borjigin clan
Although many regard the portrait at the National Palace Museum in Taipei, Taiwan, as the depiction most closely resembles Genghis Khan, all existing portraits, including this one, are essentially arbitrary interpretations of Genghis Khan’s appearance by historians living generations after Genghis Khan’s era [2, 6]. Although the factual nature of the statement is controversial, Persian historian Rashid-al-Din reported in his “Jami’s al-tawarikh” written at the start of the 14th century that most Borjigin ancestors of Genghis Khan were tall, long-bearded, red-haired, and bluish green-eyed, suggesting that the Genghis Khan’s male lineage had some Caucasoid-specific genetic features . He also said that Genghis Khan looked just like his ancestors, but Kublai Khan, his grandson, did not inherit his ancestor’s red hair, implying that the addition of Mongoloid-specific alleles for determining hair color to the genetic makeup of Genghis Khan’s Borjigin clan was probably from the grandmother or mother of Kublai Khan, that is, the wife or daughter-in-law of Genghis Khan.
“On” and “gud” from Ongud mean West and plural in ancient Altaic language, respectively, implying that the Ongud is a tribe from Western Asia. In fact, the ancestors of the Ongud are the Shato Turks of the Western Göktürks Khaganate [45, 46]; they moved to Eastern Xinjiang in the 7th century, and were scattered over Northern China and Inner Mongolia in the 9th century . In the Mongolian era, many Ongud peoples were resettled in Khorazm of Western Central Asia, as governors for the Golden Horde Dynasty, and eventually formed part of the Kazakhs and the Mughals . In addition, they also fell under the Chagatai Khanate that was ruled by Chagatai Khan and his descendants and/or successors and extended from the Southern part of the Aral Sea to the Altai Mountains . These suggest the possibility that the Ongud clan may be anthropologically Caucasoid rather than Mongoloid, according to their geographical origin. Therefore, the male bodies carrying R1b-M343 (prevalent in Western Europe) from Tavan Tolgoi, which was located within the territory of the Ongud Kingdom during the early Mongolian era, could be related to the Ongud male lineage, implying that Tavan Tolgoi bodies are genealogically Caucasoid.
Eastern Russian Tatars, Bashkirs, and Pakistani Hazara were found to carry R1b-M343 at unusually high frequencies of 12.65%, 46.07%, and 32%, respectively, compared to other regions of Eastern Asia, which rarely have this haplotype (Fig 3) [40, 42, 43, 49–53]. Interestingly, ancestors of those 3 populations were all closely associated with the medieval Mongol Empire. That is, Russian Tatars and Bashkirs are descendants of the Golden Horde (also known as the Ulus of Jochi) that had been controlled by Jochi, the first son of Genghis Khan, and his descendants during the 12th–15th centuries. In addition, some of the Hazara tribes are believed to consist of descendants of Mongolian soldiers and their slave women after the 1221 siege of Bamiyan under the leadership of Genghis Khan [54, 55]. Through domination of Hazara, Mongolians strongly influenced the genetic makeup of the Hazara people, especially in Pakistan [49, 54, 56]. Some modern Hazara populations resemble Mongolians in their physical attributes including facial bone structure. Similarly, the high frequency of R1b-M343 in geographic regions associated with the past Mongol khanates including the Golden Horde (from Ural Mountain to Western Siberia, which includes Russia, Ukraine, Belarus, Poland, Azerbaijan, Kazakhstan, and Uzbekistan), Ilkhanate (Iran and neighboring territories including Armenia, Turkey, Georgia, Afghanistan, Syria, and Tajikistan), and Chagatai Khanate (from the Aral sea to the Altai mountain, including Pakistan (Hazara), Uzbekistan, Kazakhstan, Tajikistan, India, and China), strongly suggest a close association between the Y haplotype R1b-M343 and the past Mongol Empire (Fig 3) [42–44, 49–53].
Each circle represents a population sample; the area of the circle is proportional to the sample size. Black sectors denote the relative frequency of R1b-M343-carrying groups identified in the literature.
Thus, the appearance of R1b-M343 in Tavan Tolgoi bodies reflects that the genealogical structure of the Genghis Khan’s Golden family consisted largely of a Caucasoid paternal genetic pool, and the distribution of modern-day R1b-M343 carriers at a high frequency in the past Mongol khanates supports that they are direct descendants of Genghis Khan’s Borjigin clan. In contrast, considering that modern-day individuals with specific haplotypes such as C3c-M48 are largely distributed within the past Mongol Empire, Zerjal and colleagues  reported that Genghis Khan carried haplogroups C-RPS4Y711, and C3c-M48, which are common Mongoloid paternal markers. However, their results did not come directly from the remains of Genghis Khan. Accordingly, nobody can determine whether those haplogroups were indeed carried by Genghis Khan until human remains from Genghis Khan’s grave are excavated to obtain direct proof of the connection of those haplogroups with him.
Collectively, our results provide three possibilities about the high genetic affinity between Tavan Tolgoi bodies and the members of Genghis Khan’s Borjigin clan. First, Tavan Tolgoi bodies would be Golden family members from qudas between the female lineage of Borjigin clan and the male lineage of rulers who dominated Eastern Mongolia, including the Ongud Kingdom. Accordingly, R1b-M343 of Tavan Tolgoi bodies reveals the Y-haplogroup of rulers of Eastern Mongolia in the Mongolian era, not that of Genghis Khan’s Borjigin clan. Second, it is plausible that R1b-M343-carrying Tavan Tolgoi bodies are somehow related to Genghis Khan’s male lineage for a similar reason to C3c-M48 being assumed as the Y-haplogroup of Genghis Khan by Zerjal and colleagues . Thus, Genghis Khan may have carried Y-haplogroup R1b-M343, which is prevalent in West Eurasia, and not haplogroup C3c-M48, which is prevalent in Asia. This is based on Genghis Khan’s physical appearance, which exhibited some features of Caucasoid ethnic groups and the geographical distribution of modern-day R1b-M343 carriers. Third, we cannot entirely exclude the possibility that R1b-M343-carrying modern-day individuals are descendants of Genghis Khan’s generals or relatives who had no genetic relationship with Genghis Khan and his Borjigin clan, but exercised considerable influence throughout the past Mongol khanates including Golden Horde, Ilkhanate, and Chagatai Khanate, as the R1b-M343-carrying modern-day individuals are distributed across the 3 Mongol khanates and are not limited to specific areas, similarly to the Hazara of Pakistan.
Tavan Tolgoi bodies are members of a family with the relationship of mother-sons or full siblings
As shown in Table 1, mtDNA sequence data for 13 haplogroup-defining coding regions besides HVR1 and HVR2 control regions, in 4 members of the Golden family (MN0104, MN0125, MN0126 and MN0127) matched exactly, with a total of 2,761 base pairs being identical, strongly suggesting that they are immediate family members with the same matrilineal origin. In addition, male bodies, MN0104 and MN0126, were confirmed to be family members based on the results of Y-SNP, Y-STR, and A-STR analyses. MN0127 was also assumed to be their family member, because he shared mtDNA sequences with three other D4-carrying Golden family members; additionally, his burial artifacts and burial location clearly indicate that he was a male with the family relationship with other Golden family members (S1 Table). Additional direct molecular evidence to determine his kinship with other members of Golden family could not be obtained due to failure of PCR amplification for Y-SNP, Y-STR, and A-STR.
Taking these data into consideration, it is clear that 3 (MN0104, MN0125, and MN0126) of the 7 Tavan Tolgoi bodies are immediate family members. In addition, their exact relationship is expected to be 1) a mother (MN0125) and 2 sons (MN0104 and MN0126), 2) a father (1 of the 2 male bodies, MN0104 or MN0126) and 2 children (MN0125 and the other 1 of the 2 male bodies), or 3) 3 siblings. Allelotypes of 30/30 or 30/33.2 at D21S11 marker locus and 19/22 at FGA marker locus in MN0126 could not be obtained from MN0104, assuming that MN0104 is a father of the other 2 bodies (Table 4). Similarly, allelotypes of 29/29 at D21S11 marker locus and 21/27 at FGA marker locus in MN0104 could not come from MN0126, assuming that MN0126 is a father of the other 2 bodies. Due to these conflicting data, we completely ruled out the second possibility. However, the A-STR profiles of 8 marker loci in the 3 Tavan Tolgoi bodies could not rule out the possibility of assumptions 1 and 3. In addition, the results of the Kinship Index Calculation program used by the Korea National Forensic Service for personal identification of Koreans demonstrate that the probability of assumptions 1 and 3 between MN0104 and MN0125 or between MN0125 and MN0126 was nearly 100%. This indicates that the Golden family members, MN0104, MN0125, and MN0126, were either mother-son or had full sibling relationships, assuming that the allelotype of D21S11 was 30/33.2 in MN0126 (S8 Table). The probability of assumptions 1 and 3 between MN0104 and MN0126 was, however, found to be 0% and 64.2%, respectively, indicating no possibility of a parent-child relationship. The probability of assumption 3 decreased to 64.2% because of the small numbers of allelotypes compared, rather than the absence of a relationship between full siblings. In contrast, the probability of kinship among the other 3 Tavan Tolgoi bodies (MN0105, MN0124, and MN0376) and between each of these bodies and the Golden family members (MN0104, MN0125, and MN0126) indicated no family relationship between them. These data strongly suggest that the 3 Golden family members including MN0104, MN0125, and MN0126 are related as either mother-sons or full siblings with nearly the same probability, and have no kinship with the members of the other Golden family (MN0105) and the general public (MN0124 and MN0376).
In any case, it is certain that the grave of the father of the 3 Golden family members, or alternatively a husband of MN0125, was not found near their graves. Accordingly, if assumption 1 is the case, the husband of MN0125 and wives of her possible sons (MN0104 and MN0126) were not buried together with the Golden family members, implying that the Tavan Tolgoi graves were arranged according to the matriarchal, Golden family-dominated burial custom. We cannot exclude the possibility that the husband of MN0125, a guregen, was killed in Genghis Khan’s war and buried somewhere in his death place. This may explain why a Mongol Queen’s husband would not be buried together with his wife and sons. If assumption 3 is true, then it may have been customary for Golden family members to be buried together, far from the graves of their biological parents, particularly from that of their father (i.e., guregen).
Tavan Tolgoi bodies are Golden family members from marriages between the lineage of Genghis Khan’s Borjigin clan and either the lineage of Ongud clan as guregen or the lineage of Hongirad clan as khatun
Historically, Tavan Tolgoi was dominated by Golden family members, including Alaqai Beki, a daughter of Genghis Khan, Sorghaghtani, the wife of Tolui, Genghis Khan’s youngest son, and their descendants or successors . Taking into account all the data in this study, several scenarios could explain the identity of the Golden family members excavated in Tavan Tolgoi. First, MN0125 who is regarded as a Mongol Queen can be assumed to be Alaqai Beki, who ruled the Ongud Kingdom instead of her husband, the guregen. This scenario, however, can be easily refuted because Alaqai Beki had only one son and died approximately in her 50s; MN0125 was buried together with 3 sons or 3 full siblings and died in her 20s (S1 Table). In addition, if MN0125 is Alaqai Beki, a sister of other three males (MN0104, MN0126 and MN0127), her male siblings would be the Great Khans, including Ogodei, the 2nd Great Khan of the Mongol Empire. Of course, this assumption is not also acceptable. In the second scenario, MN0125 can be presumed to be Sorghaghtani. It is illogical, however, that the 3 male graves at Tavan Tolgoi are those of the Great Khans, her sons, Mongke and Kublai, the 4th and 5th Great Khans of the Mongol Empire, respectively. In addition, the presumed age at death of MN0125 is inconsistent with that of Sorghaghtani, who died in her late 60s . Moreover, Sorghoghtani was a Christian, and was buried in a church located in the Gansu province, Northwestern China, far from Tavan Tolgoi . Accordingly, the assumption that MN0125 is Sorghoghtani is excluded. Third, the Tavan Tolgoi bodies could be direct descendants of Alaqai or Sorghaghtani. This possibility, however, is also untenable because their descendants were died young or could not be Great Khans as mentioned above. Fourth, Tavan Tolgoi bodies may be successors of Alaqai. Alaqai invented a new marriage alliance system, quda, between women, probably her close relatives, of Genghis Khan’s Borjigin clan and men of the ruling lineages of the Ongud, to solidify her political power and to extend her rule over the Ongud Kingdom [2, 3]. Accordingly, it is possible that the Tavan Tolgoi graves belong to the ruling lineage newly formed by qudas, as successors of Alaqai Beki, who had no sons. Fifth, the Tavan Tolgoi graves may belong to the Hongirad clan. The homeland of the Hongirad clan was located near Hulun Lake, Northeastern Mongolia, which is not far from Tavan Tolgoi . During the Yuan dynasty, some Hongirads moved to the territory of modern Uzbekistan and Kazakhstan; today their descendants are widely distributed in the modern Kazakh, Western Mongolian, Uyghur, and Uzbek people. Women of the Hongirad clan married many Great Khans of the Borjigin clan, including Genghis Khan and his descendants, as well as his ancestors . The qudas between the male lineage of the Borjigin clan and the female lineage of the Hongirad clan continued in the Yuan Dynasty and the Golden Horde Dynasty, giving the Hongirad tribe enormous power in the Mongol Empire as a clan of Mongol khatuns including Genghis Khan’s grandmother, mother, and chief wife, Borte Khatun [2, 3, 8]. Accordingly, it is possible that some Golden family members from quads between the male lineage of Genghis Khan’s Borjigin clan and the female lineage of khatuns of the Hongirad clan were buried in a sacred burial site, such as Tavan Tolgoi.
MN0105 is presumed to be the most important figure among the Tavan Tolgoi bodies. The Mongolian archaeologist, Dr. Navaan D., who first excavated the Tavan Tolgoi graves suggested the possibility that MN0105 is a mother of MN0104, since MN0104 was buried near the foot of MN0105 and the presumed age of death of MN0104 was approximately his late 20s whereas that of MN0105 was around the age of 45–55 years [9, 10]. At the time of excavation, the archaeological importance of MN0105 was overlooked in favor of MN0125 because MN0105 was buried with only a modest amount of artifacts, including 2 golden rings and ornaments for boqta, whereas MN0125 was unearthed with numerous expensive and interesting artifacts. Nonetheless, MN0105’s burial artifacts, such as golden rings engraved with the falcon image, clearly indicate that she is closely related to Genghis Khan’s Borjigin clan. If we assume that MN0105 is Alaqai Beki or another female ruler from Genghis Khan’s Borjigin clan, then she should be related politically, not biologically, to the other Golden family members from Tavan Tolgoi as their stepmother, foster mother, or guardian. In other words, it is likely that they would be from a quda between the female lineage of Genghis Khan’s Borjigin clan and the male lineage of the Ongud clan, arranged by Alaqai Beki who had no direct descendants, or by a female ruler from Genghis Khan’s Borjigin clan.
Considering the historical, archaeological, physical anthropological, and molecular archaeological evidence obtained, it seems most likely that the Tavan Tolgoi bodies are members of Genghis Khan’s Golden family, including the lineage of bekis, Genghis Khan’s female lineage, and their female successors who controlled Eastern Mongolia in the early Mongolian era instead of guregens of the Ongud clan, or the lineage of khans, Genghis Khan’s male lineage, who married females of the Hongirad clan, including Genghis Khan’s grandmother, mother, chief wife, and some daughters-in-law.
The modern-day descendants of Tavan Tolgoi bodies have disappeared from the Mongolian plateau
We found that 27.8% (15/54) modern-day Mongolians carry the mtDNA haplogroup D4 at about (S9 and S10 Tables). Keyser-Tracqui and colleagues  and Kim and colleagues  also reported that D4 was found in about 36.96% among Northern Mongolian populations in the Xiongnu age, and in 2 of 3 Xiongnu bodies in the North Eastern Mongolia. This implies that the mtDNA haplogroup D4 is one of the most prevalent haplogroups across the Mongolian plateau from at least the Xiongnu era to the present. In comparison, our unpublished data demonstrated that the Y-haplogroups R1b-M343 and R1a1a-M17 are distributed at 0.0% (0/101) and 0.99% (1/101) in modern-day Mongolians across the Mongolian plateau, respectively (S10 Fig) [31, 32]. Zhong and Colleagues  also reported that the modern-day Mongolians who inhabit in the Inner and Outer Mongolia carry the R1b-M343 haplogroup at 8.3% (1/12) (only in Heilongjiang; the province located in the North Eastern part of China) and 0.0%, respectively. Meanwhile, Zhong and colleagues  and Katoh and colleagues  demonstrated that the R1a1a-M17 was found at 9.1% (2/22), 3.5% (3/85), 6.7% (4/60) and 13.3% (8/60) in modern-day Inner Mongolians, Khalkh, Uriankhai, and Zakhchin Mongolian tribes, respectively. Thus, R1b-M343 is scarcely found in the Mongolian plateau, whereas R1a1a-M17 is widely distributed, although at a relatively low frequency, having a maximum of 13.3% in the Zakhchin tribe . These results demonstrate that modern-day individuals carrying R1b-M343 are hard to find on the Mongolian Plateau, meaning that descendants of R1b-M343-carrying members of the Golden family disappeared from the Mongolian Plateau for unknown reasons.
Modern-day individuals with the same Y-STR profiles as members of the Golden family have been carefully screened in many studies and in YHRD from modern-day individuals, totaling approximately 154,329 individuals (searched on August 25, 2015). Modern-day individuals matching the Golden family members in Y-STR profiles from Yfiler and PowerPlex Y of YHRD and the literature are mainly distributed in Kalmykia, Russia, Uzbekistan, Tajikistan and China (Fig 3 and S6 Table).
Coincidentally, the geographical distribution of modern-day individuals matching the Y-haplogroup and haplotype of the Tavan Tolgoi bodies in the regions corresponding to the past Mongol khanates, including the Golden Horde Dynasty and Chagatai Khanate, implies that the modern-day individuals are direct descendants of the Golden family members. The ancestors of Kalmykia are the Oirats, the westernmost tribe of the Mongols. The Oirats also had strong ties with Chagatai Khanate and the Golden Horde, through marriage alliances between Mongol khans and Oirat khatuns, just like the Hongirads [2, 60]. These distributions imply the movement of descendants of the Golden family from Eastern Mongolia to West Eurasia, including Kalmykia, and a possible genealogical connection between Golden family members and the Oirats. By the 9th century, the Shato Turks of the Western Göktürks Khaganate, as ancestors of the Ongud, moved to modern-day Inner Mongolia and eventually were dominated by the Mongol Oirats, later known as Kalmyks, suggesting an anthropological connection of the Ongud with Kalmyks [33, 45, 46, 61, 62]. Taken together, Golden family members from Tavan Tolgoi may have been direct ancestors of R1b-M343-carrying modern-day individuals who live in the territories of the past Mongol khanates.
Why both R1b-M343 carriers and modern-day individuals with the same Y-STR profile as that of the Golden family members are rarely found in the Mongolian plateau could be explained by the following 2 hypotheses, which are not mutually exclusive. One is large-scale redeployment of descendants of our Golden family members from the Mongolian Plateau to Eastern Europe (Kalmykia and Russia) or Central Asia (Uzbekistan and Tajikistan). Many of the Onguds returned to the ancestral homeland near Central Asia from Eastern Mongolia; this turn of events resulted in a significant decrease in the number of their descendants, including R1b-M343 carriers, in Eastern Mongolia. The other possibility is internecine massacre among direct male descendants of Genghis Khan’s Borjigin clan and their wives (i.e., among the Golden family). As soon as Genghis Khan died, kingdoms of bekis, including the Ongud, were attacked and eventually toppled by the daughters-in-law and grandsons of Genghis Khan [2, 3]. Most bekis lost power and were killed in a horrendous manner by opponent factions including the Great Khans, such as Ogodei and Mongke . Under such political conditions, most Golden family members, including the lineages of the former rulers of the Ongud or the Hongirad, who were opposed to the faction in power, were likely exterminated [2, 3]. Meanwhile, Golden family members who lived in the Golden Horde, Ilkhanate and Chagatai Khanate where are far apart from the central area of the Mongol Empire were relatively safe from such horrendous massacre.
Thus, the large-scale movement and slaughter that occurred in the Mongolian plateau could explain at least in part why direct descendants of the Golden family are hard to find in modern-day Mongolia. However, further studies are needed to firmly conclude when and why R1b-M343 carriers, which are distributed mostly in Europe and Central Asia, appeared and then subsequently disappeared from the Mongolian Plateau region.
The ancestors of the Ongud were the Yueban who later intermixed with Turkic peoples, forming the Shatuo of the Western Turkic Khaganate. In the 7th century they moved to eastern Xinjiang under the protection of the Tang Dynasty. By the 9th century the Shato were scattered over North China and modern Inner Mongolia. A Shato warlord, Li, mobilized 10,000 Shato cavalrymen and served the Tang as ally. In 923 his son defeated the rebellious dynasty and became emperor of the Later Tang. After the overthrow of the Li family, Shatuo commanders established the Later Jin, the Later Han and the Northern Han.
In the 13th century a part of Shato probably included in the Mongol Empire as an Ongut tribe, another part as White Tatars. During Mongolian time, a part of the Chuy Onguts were resettled in Khorazm, to eventually become a part of Kazakhs, and another fraction remained in Mongolia, in the 15th century they became part of the Tumed.
The Ongud chief Alakush tegin revealed the Naimans plan to attack Genghis in 1205 and allied with the Mongols. When Genghis Khan invaded the Jin Dynasty in 1211, Alagush Tegin supported him. Genghis bestowed his daughter Alaga Bekhi on his son. However, the political opponents killed Alagush. Genghis put down the rebellion and took the family under his protection. Genghis Khan’s daughter Alaga ruled the Ongud people as regent for several underage princes until the reign of Güyük Khan (1246–48).
Many famous post-Genghis Mongols are of Ongud descent.
The Ongud, (Mongolian: Онгуд, Онход) were Mongols active in Mongolia around the time of Genghis Khan (1162–1227).Many members were members of the Church of the East. They lived in an area lining the Great Wall in the northern part of the Ordos Plateau and territories to the northeast of it. They appear to have had two capitals, a northern one at the ruin known as Olon Süme and another a bit to the south at a place called Koshang or Dongsheng. They acted as wardens of the marches for the Jin dynasty (1115–1234) to the north of Shanxi.
Archaeology, Ethnology and Anthropology of Eurasia
Volume 38, Issue 3, September 2010, Pages 99-110
Archaeology, Ethnology and Anthropology of Eurasia
THE WUSUN IN NORTHEASTERN CENTRAL ASIA
https://doi.org/10.1016/j.aeae.2010.10.010Get rights and content
Among the peoples mentioned in Chinese dynastic chronicles are the Xiongnu and other steppe nomads such as the Yuezhi and the Wusun. The Xiongnu forced both these peoples to abandon their camping grounds and move to Zhetysu. Numerous sites in Tuva of the Late Scythian period (those of the Uyuk–Sagly culture) reveal ties with the Xiongnu and suggest that they were associated with the Wusun. Artifacts from Suglug-Khem-1 and -2 and Khayirakan, Tuva, specifically mirrors with side handles, hairpins, wire earrings, small wooden four-legged tables, painted vessels, etc., are paralleled by finds from burials of the low-ranking Wusun in Zhetysu. Before arriving at Zhetysu, the Wusun crossed the Altai-Sayan highland and the Irtysh below Lake Zaisan, where their presence is attested by sites of the Kula-Zhurga type. The distinctive features of the latter are flexed burials in stone cists and vessels resembling those from Tuva in shape; other artifacts are extremely rare and similar to those from burials of the low-ranking Wusun in Zhetysu.
Discovery of ancient tomb was sacrificed to join noblewoman in death Ancient Origins 11 APRIL, 2015 – 01:33 APRILHOLLOWAY
Kazim Abdullaev, Nomad migration in Central Asia t: https://www.researchgate.net/publication/288957714 · July 2007
We report genome-wide data from two hunter-gatherers from Devil’s Gate, an early Neolithic cave site (dated to ~7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.
By analyzing genome-wide data from two early Neolithic East Asians
from Devil’s Gate, in the Russian Far East, we could demonstrate a
high level of genetic continuity in the region over at least the last
7700 years. The cold climatic conditions in this area, where modern
populations still rely on a number of hunter-gatherer-fisher practices,
likely provide an explanation for the apparent continuity and lack
of major genetic turnover by exogenous farming populations, as has
been documented in the case of southeast and central Europe. Thus,
it seems plausible that the local hunter-gatherers progressively
added food-producing practices to their original lifestyle. However,
it is interesting to note that in Europe, even at very high latitudes,
where similar subsistence practices were still important until very
recent times, the Neolithic expansion left a significant genetic signature,
albeit attenuated in modern populations, compared to the
southern part of the continent. Our ancient genomes thus provide
evidence for a qualitatively different population history during the
Neolithic transition in East Asia compared to western Eurasia, suggesting
stronger genetic continuity in the former region. These results
encourage further study of the East Asian Neolithic, which
would greatly benefit from genetic data from early agriculturalists
(ideally, from areas near the origin of wet rice cultivation in southern
East Asia), as well as higher-coverage hunter-gatherer samples
from different regions to quantify population structure before intensive
The presence of the two-rooted canines in East Asia may provide some clue as to the eastward migration of new populations into China and Mongolia. The largest numbers of individuals with this trait are concentrated along the western and northern frontiers of China and Mongolia. Archaeological excavations support the large scale movement of people into this area during the Bronze age (ca. 2200 BCE–400 BCE). Burial artifacts and settlement patterns suggest cultural and technological ties to the Afanasevo culture in Siberia, which in turn is linked archaeologically, linguistically, and genetically with the Indo-European Tocharian populations that appear to have migrated to the Tarim Basin ca. 4,000 years ago (Ma and Sun, 1992; Ma and Wang, 1992; Mallory and Mair, 2000; Romgard, 2008; Keyser et al., 2009; Li et al., 2010).
Haak et al. 2015, the Yamnaya samples are again from the eastern half of the Yamnaya horizon. This time, however, not all of the Yamnaya individuals carry Y-haplogroup R1b; one of the five samples belongs to Y-haplogroup I2a (see here).
Abstract: The Bronze Age of Eurasia (around 3000–1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.
Allentoft et al., Population genomics of Bronze Age Eurasia, Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507
Mathieson et al. 2017 has just been posted at BioRxiv (see here). It includes more samples. One of these new samples is a male from an Eneolithic Sredny Stog culture site on the North Pontic (Ukrainian) steppe who belongs to Y-haplogroup R1a-M417 (ID I6561 from Alexandria in the ADMIXTURE bar graph below). This is huge, obviously with major implications for the peopling of large parts of Eurasia. Why? Because of this. Here’s the new abstract:
Abstract: Farming was first introduced to southeastern Europe in the mid-7th millennium BCE – brought by migrants from Anatolia who settled in the region before spreading throughout Europe. To clarify the dynamics of the interaction between the first farmers and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient DNA data from 223 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document previously uncharacterized genetic structure, showing a West-East cline of ancestry in hunter-gatherers, and show that some Aegean farmers had ancestry from a different lineage than the northwestern Anatolian lineage that formed the overwhelming ancestry of other European farmers. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but that some groups mixed extensively, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West after farming arrived, with intermittent genetic contact from the Steppe up to 2000 years before the migration that replaced much of northern Europe’s population.
R1a was born somewhere in North Eurasia. More importantly, its R1a-M417 subclade, which encompasses almost 100% of modern-day R1a lineages, no doubt came into existence somewhere on the Pontic-Caspian (or Western) steppe in what is now Ukraine and southern Russia just 7,000-6,000 years ago.
And within a couple of thousand years it expanded in almost all directions, probably on the back of the early Indo-European dispersals (see here), to cover a massive range from Scandinavia to South Asia. The most common subclade of R1a-M417 in South Asia today is R1a-Z93, and, realistically, it couldn’t have arrived there earlier than about 2,000BC
Yinqiu Cui, Hongjie Li, Chao Ning, Ye Zhang, Lu Chen, Xin Zhao, Erika Hagelberg and Hui Zhou Y Chromosome analysis of prehistoric human populations in the West Liao River Valley, Northeast China BMC Evolutionary Biology201313:216
https://doi.org/10.1186/1471-2148-13-216© Cui et al.; licensee BioMed Central Ltd. : 30 September 2013
The West Liao River valley in Northeast China is an ecologically diverse region, populated in prehistory by human populations with a wide range of cultures and modes of subsistence. To help understand the human evolutionary history of this region, we performed Y chromosome analyses on ancient human remains from archaeological sites ranging in age from 6500 to 2700 BP.
47 of the 70 individuals provided reproducible results. They were assigned into five different Y sub-haplogroups using diagnostic single nucleotide polymorphisms, namely N1 (xN1a, N1c), N1c, C/C3e, O3a (O3a3) and O3a3c. We also used 17 Y short tandem repeat loci in the non-recombining portion of the Y chromosome. There appears to be significant genetic differences between populations of the West Liao River valley and adjacent cultural complexes in the prehistoric period, and these prehistoric populations were shown to carry similar haplotypes as present-day Northeast Asians, but at markedly different frequencies.
The most ancient populations of the West Liao River valley exhibited a high frequency (71%) of haplogroup N1-M231. Because of the short amplicons needed for the ancient samples, it was not possible to type the diagnostic site P43 of sub-haplogroup N1b, so samples that yielded negative M128 and TAT mutations were defined as N1 (xN1A, N1c). Besides being the only haplogroup in the Halahaigou site, N1 (x N1a, N1c) was also predominant in the Niuheliang and Dadianzi sites. In the Dashanqian site, there were two subtypes of N1-M231: N1 (xN1a, N1c) and N1c-TAT. One of the nine Dashaqian samples was N1 (xN1a, N1c), and three were N1c (Table 1). N1 is particularly widespread in northern Eurasia, from the Far East to Eastern Europe. Its subtype, N1c, is found at low frequency but has high STR variability in northern China, suggesting that this region was N1c’s centre of expansion .
A single instance of O3a (xO3a3) was observed in the Neolithic Hongshan and Xiaoheyan sites, although this haplogroup was observed in just under half of the Bronze Age individuals. The Upper Xiajiadian individuals of the late Bronze Age had different subtypes of O3a-M324, O3a3c-M117. O3a-M324 is found today in most East Asian populations, and its subtype O3a3c-M117 occurs at the highest frequency in modern Sino-Tibetan populations [12, 13].
C3-M217 is the most widespread haplogroup in Central Asia, South Asia, Southeast Asia, East Asia, Siberia and the Americas, but is absent in Oceania. Its sub-branch C3e-P53.1 is found only in Northeast Asia with low STR diversity, suggesting a recent origin in this region . All individuals with the haplogroup C3-M217 in the ancient populations of the West Liao River valley belonged to the sub-branch C3e, except one from the Niuheliang site, who had an unidentified subtype. One instance of C3e-P53.1 was found in the Dashanqian site, while all 12 individuals of the Jinggouzi site belonged to this subtype. The Jinggouzi people originated in the North China steppe, and our findings support the view that C3e originated in the north.
Y chromosome STR analysis
All ancient samples were analyzed at 17 Y chromosome STR loci. Due to DNA damage, only 21 of the 47 individuals yielded results for at least three loci in two independent extractions. Consensus data are reported in Additional file 1: Table S1. The DYS389II, DYS438 and DYS635 loci frequently failed to amplify, probably because of their longer length. The inverse relationship between amplification efficiency and PCR fragment is further support for the authenticity of the extracted DNA, as ancient DNA is presumably degraded while modern DNA contamination would exhibit longer fragment lengths.
There are only two Y-chromosome haplotypes in the Jinggouzi site suggesting that individuals are paternally closely related, despite being buried in separate tombs. In the other sites in our study, we detected no potential paternal relatives among ancient individuals of the same haplogroup.
Y chromosome characteristics of the prehistoric population
Previous analyses showed that there were different frequency distributions of the sub-haplogroups used in this study in both ancient and extant populations of adjacent regions. The Yellow River valley, located in the southwest region of the West Liao River valley, was one original centre of agriculture in China. O3-M122 is the most abundant haplogroup in both ancient (80%, n=5) and extant population (53%, n=304) of the region [8, 13], but the frequency of O3-M122 only began to rise in the West Liao River valley in the Bronze Age. The ancient West Liao River valley population is significantly different from both the ancient Yellow River Valley population (P<0.01), and the extant Yellow River Valley population (P<0.01). The Miaozigou site, about 500 km west of the West Liao River valley in the central/southern region of Inner Mongolia, was settled by people of the northern branch of the Yangshao culture, an important Neolithic farming culture along the Yellow River. Our analysis of three ancient Miaozigou individuals revealed that they all belong to haplogroup N1(xN1a, N1c), while the main lineage of the Yellow River valley culture is O3-M122 . The existence of N1(xN1a, N1c) in the Miaozigou site could be evidence for the expansion of the Hongshan culture during its heyday, a view supported by archaeological evidence of Hongshan influences at the Miaozigou site . However, the small sample size of our current ancient genetic material and the lack of data for earlier time periods means an alternate explanation , in which N1(xN1a, N1c) existed across the region prior to the Neolithic, is still a possibility.
The main haplogroups of Northern steppe nomad population were C3 (50.7% in the Mongolian, n=285) [8, 17, 18], and N1c (94% in the Yakut, n=184) . The ancient individuals from the Jinggouzi site, a Northern Steppe nomadic culture on the western fringes of the West Liao River valley, carry a single haplogroup, C3e, divided into two sub-types on the basis of Y chromosome STR analysis. Previous mtDNA data have shown that the Jinggouzi people have closely related mtDNA types , suggesting that the Jinggouzi site was settled by family groups migrating from the northern steppe within a short period, which is in agreement with archaeological results . Therefore, the prehistoric people of the West Liao River valley carried the characteristic N1 (x N1a, N1c) lineage, and appear both culturally and genetically distinct.
Prehistoric migrations in relation to cultural transitions
The Lower Xiajiadian culture (LXC) was an early Bronze Age culture with a highly developed agricultural society, with a subsistence strategy quite different from the hunting-gathering strategy typical of the Hongshan culture. However, the LXC people retained the microliths (tips of hunting weapons) and custom of dragon worship typical of the Hongshan culture. Most archaeologists agree that during the transition from the Neolithic to the Bronze Age, migrants carried farming technology from the Yellow River valley to surrounding areas including the West Liao River valley. In the Dadianzi people of the LXC, O3a is the main haplogroup after N1(xN1a, N1c). The former was previously shown to be the characteristic lineage for ancient populations along the Yellow River and Yangtze River valleys . Previous mitochondrial DNA analyses of the Dadianzi population showed that the LXC people probably included immigrants from the Central Plains . The archaeological analyses showed that farming tools and ceramic techniques can be traced to cultures from the Yellow River Basin . Both the ancient genetic and archaeological data suggest that immigrants from the Yellow River valley, of type O3a, may have migrated into the West Liao River valley and influenced changes to the existing culture, but genetic drift cannot be ruled out as the cause for the observed frequencies.
The Upper Xiajiadian culture (UXC) of the late Bronze Age succeeded the LXC but was completely different from the LXC. The UXC people mainly practiced animal husbandry and made bronze objects decorated with animal and other natural motifs in the style of the Eurasian steppes. The UXC individuals of the Dashaqian site had higher Y chromosome haplogroup diversity, with a lower frequency of the LXC lineage. Only one individual carried N1 (×N1a, N1c), the prevalent haplogroup before the UXC period. The O3-M122 type could have been inherited from LXC, but the existence of two different sub-types of O3, O3a (xO3a3) and O3a3c, implies continuous northward gene flow from the Yellow River valley. It is worth noting that the two northern haplogroups N1c and C3e first appeared in the ancient peoples of the Dashaqian site. N1c-TAT has the greatest frequency in populations from Northern Eurasia (see Table 2), and 94% of Yakuts belong to this haplogroup . 33.3% of Dashaqian samples were N1c, and the present-day distribution of the ancient haplotype based on one STR profile search is mainly Northern Asia. The presence of N1c in the UXC might suggest that there is immigration from the north Eurasian steppes during this period.
The Jinggouzi site is situated northwest of the West Liao River Valley, and was occupied by northern nomadic tribes during similar time periods (3000-2500BP) as the Dashanqian site. All ancient samples of the Jinggouzi site were assigned to C3e, suggesting northern nomads might have entered the West Liao River valley from the northwest. C3e is rare in modern populations, and is only found in Northeast Asia.
Because the farming LXC was replaced by the nomadic UXC and no transitional type has yet been found, it had been suggested that there might have been large-scale immigration or even population replacement by northern Asian nomads . Y chromosome data show immigration components from both northern steppe tribes and farmers from the Yellow River valley. However, because all original LXC lineages in this investigation were retained in the UXC gene pool, we tend to believe that while immigrant nomads from the north played an important part in the cultural transitions in this region, they probably did not replace the preceding populations in the West Liao River valley. Instead, the cultural transitions were more likely the result of adaptations to a new lifestyle caused by climate change.
Temporal continuity of paternal lineages in the West Liao River valley
The origin and development of the prehistoric populations of the West Liao River valley, a cross road of continuous migration events, is expected to involve complex processes and population admixture. Our prehistoric population data show that the principal lineages in the region remained relatively constant from the Neolithic to the Bronze Age. In the historic period, the region was controlled mainly by nomads, including the Nüzhen, Mongolians and Manchu. The genetic structure of this period can be deduced from data of Xibe, an extant minority in Xinjiang, from the northwestern region of China. The Xinjiang Xibe originated in Northeast China and were sent to Xinjiang in 1764 by the Qing emperor to defend the frontier . This population carries the original Y chromosome lineages of the prehistoric population of the West Liao River valley, with a high frequency of C3e (Table 2), whose genetic structure is similar to that of the Upper Xiajiadian.
In modern times, especially the last century, a massive number of immigrants from the south poured into this region. To investigate the extent of continuity in the paternal lineages, we examined the present-day patterns of distribution of the Y chromosome lineages observed in our ancient populations (Table 2). Except for O3a, the lineages of the prehistoric people are present today at low frequencies in the West Liao River valley. O3a continued to enter the West Liao River valley during the expansion of the Yellow River valley culture, displacing or replacing the original lineages. Today, N1 (xN1a, N1c) and C3e are mostly found in the northern Han and the northeast minority populations such as the Mongolians, Manchu, Oroqen, Xibe and Hezhe, although at low frequencies. Yi is the only population which has a relatively high frequency of N1 (xN1a,xN1c) in southern China. According to the archaeological record, one of the original branches of the ancestral Yi population was the Diqian, a nomadic ethnic group who lived in the northern steppes from 5000 to 3000 BP , which may explain the origin of N1(xN1a,xN1c) in the Yi people.
Our results suggest that the prehistoric cultural transitions were associated with immigration from the Yellow River valley and the northern steppe into the West Liao River valley. They reveal the temporal continuity of Y chromosome lineages in populations of the West Liao River valley over 5000 years, with a concurrent increase in lineage diversity caused by an influx of immigrants from other populations. During the cultural transitions occurring in this region, the immigration had an effect on the genetic structure of populations in this region, but no population replacement was found
Q: Donghu – Who were they? How were they related to the other nomads?
A: The study below finds that the Donghu are closest to the Xianbeis and the Oroqens.
Haijing Wang et al., Genetic characteristics of an ancient nomadicgroup in northern China, Available from : http://digitalcommons.wayne.edu/humbiol_preprints/1
Nomadic populations have played a significant role in the history of not only China but also in many nations worldwide. Because they had no written language, an important aspect in the study of these people is the discovery of their tombs. It has been generally accepted that Xiongnu was the first empire created by nomadic tribe in the 3rd century B.C. However, little population genetic information is available concerning the Donghu, another flourishing nomadic tribe at the same period because of the restriction of materials until Jinggouzi site was excavated. In order to test the genetic characteristics of ancient people in this site and explore the relationship between Jinggouzis and Donghus, two uniparentally inherited markers were analyzed from 42 human remains in this site, which located in northern China, dated approximately 2,500 years ago. With ancientDNA technology, four mtDNA haplogroups (D, G, C and M10) and one Y chromosome haplogroup (C) were identified using mitochondrial DNA and Y-chromosome single nucleotide polymorphisms (Y-SNPs). Those haplogroups are common in North Asia and
East Asia. And the Jinggouzi people were genetically closest to the Xianbeis in ancient populations and to the Oroqens among extant populations, who were all pastoralists. This might indicate that ancient Jinggouzi people were nomads. Meanwhile, according to the genetic data and the evidences in archaeology, we inferred that Jinggouzi people were associated with Donghu. It is of much value to trace the history of Donghu tribe and might show some insight into the ancient nomadic society.
It is acceptable by the worldwide that the Xiongnu was the first empire created by nomadic tribe in the 3rd century B.C. in history (Christine et al. 2003). Nonetheless few knew that there was another ancient nomadic
tribal union in the same period—the Donghu, located in the eastern of Xiongnus in the record of some ancient Chinese literature (Lin 1989), had been flourishing in North China for many years. After being defeated by Xiongnus in early western Han dynasty (about 206 BC), the underlings broke up to two new nomadic tribes– the Wuhuan and Xianbei (Lin 1989). And some later important tribes or ethnic groups such as the Khitan, Shiwei, Mongol, Daur and Xibo, among others, also belonged to the Donghu lineage (Lin 1989).
Because the Donghu tribe had neither writings nor buildings, and the record on it was scarcity, so that it couldn’t be known to the world. Some scholars try to find the remains of the Donghu to testify its existence and study the ancient tribe, but they didn’t obtain valuable clues for many years until the Jinggouzi site was excavated.
The Jinggouzi site consisted of diverse burial patterns (21 single burials, 12 double and 22 multiple burials). Many animal bones, such as those of horse, cattle, sheep, donkey, mule and dog, were found at this archaeological site, while no farming tools and farming products were discovered. This observation implied that stockbreeding was a dominant activity for their livelihood (Wang et al. 2010). The Jinggouzi site was estimated to have been used in the late Spring-Autumn period (770–476 BC) and the early War States period (475–221 BC) based on the associated funeral material and was corroborated by reasonable radiocarbon (14C) measurements (2485 ± 45 B.P.) (Wang et al. 2010).
MtDNA polymorphisms and haplogroup identification 42 mtDNA sequences were all successfully amplified from position 16017 to 16409 of the revised Cambridge Reference Sequence (rCRS). There were a total of 32
phylogenetically informative sites, and 26 mtDNA haplotypes were obtained, as presented in Table 2. A majority of the mtDNA of these specimens fully exhibited haplogroup motifs and therefore could be safely assigned to the relevant haplogroups, which were consistent with the APLP and sequencing results. The 26 different haplotypes were further assigned to 4 haplogroups: C, D, G and M10. Out of 42 obtained sequences, 6 were assigned to haplogroup C, 25 to haplogroup D, 10 to G and 1 to M10 (Table 2). The high frequency of the 16223-16362 motif was the main characteristic of the mtDNA sequences, and haplogroups D and G were dominant in the ancient Jinggouzi people
Moreover, almost all of the samples belonging to the mtDNA haplogroup D were in the sub-haplogroup D4, except for one (sample code 29) which was assigned to haplogroup D5 based on the mutation 16189 (Yao et al. 2002a) and another one (sample code 14) which could not be further classified. All of the haplogroup G samples were further divided into haplogroup G2 based on the mutation 16278 (Yao et al. 2002a). All of these results are shown in Table 2.
In this study, a set of Y-SNP markers was investigated, including M8-derived (Hg C1), M38-derived (Hg C2), PK2-derived (Hg C3) and M356-derived (Hg C5) markers, none of which matched our samples …[hence], these samples were assigned to the Hg C* group in this study.
Jinggouzi cemeteries were composed of relatively well-preserved skeletons. Indeed, the climatic conditions (cold and dry) and the archaeological context encountered at this site had undoubtedly protected the most recovered specimens against DNA degradation.
In the present article, strict precautions were taken to avoid the contamination of samples with modern DNA during sampling and laboratory analysis. With appropriate effort to exclude possible errors in the obtained sequences, genetic data were successfully obtained from a sample of 42 human skeletal remains in this site using maternal and paternal markers.
From the maternal standpoint, four mtDNA haplogroups (D, C, G and M10) were observed, which all belonging to the macrohaplogroup M and could be assigned to an Eastern Eurasian mtDNA gene pool. Some individuals sharing the same sequence (shown in Table 2) had close maternal genetic relationships (Vernesi et al. 2004, Ainhoa et al.
Regarding the paternal inheritance, only one Y-SNP haplogroup
(Hg C*) was detected. It indicated that ancient Jinggouzi people had simplex paternal genetic structure.
According to MDS, the results indicated some degree of genetic similarity between Jinggouzis and nomadic populations (Xiangbeis, Xiongnus, Oroqens and Mongols) rather than farming groups (Hengbeis, Taojiazhais, Nuheliangs, South Hans and North Hans) (Fig.2). Meanwhile, according to the excavation report, animal skulls, bronze swords, as well as daggers but no farming tools were found at the Jinggouzi burial site. These burial objects implied that the ancient Jinggouzi people lived by hunting and stockbreeding(Wang et al. 2010). Moreover, a high ratio of 15N isotopes in these bones of remains from
the Western zone of the Jinggouzi cemetery was found, indicating that the animal food intake in their daily nutrition was rather high(Zhang et al. 2008). This finding also suggests that activities related to animal raising and hunting played a significant role in the subsistence of the Jinggouzi people at the time. Combined with the genetic data, we inferred that ancient Jinggouzi people were nomads.
Mitochondrial DNA and Y-chromosome DNA diversity were comparable to that of ancient and contemporary populations. Jinggouzi people exhibited the nearest genetic distance with Xianbeis among ancient groups (Figure 2), indicating that Jinggouzi people had the closest relationship with Xianbeis, who were the descendants of Donghus.
Interestingly, both the mtDNA and Y-chromosome DNA frequency analyses indicate that Jinggouzis are most closely related to Oroqens (Fig. 3 and 4), who are originating from the north of Asia (Pu 1983). This result was consistent with that of MDS analysis And most scholars consider the Shiwei was the ancestor of Oroqens, who were also the Donghus’ descendants.
It can be inferred that Jinggouzis had some relationship with Donghus.
In addition, the location of the burial ground, Chifeng city of Inner Mongolia, was part of the Donghu territory, and the 14C analysis dated the site to 2485 ± 45 B.C., coinciding with the time in which the Donghu flourished according to the Chinese historical records (Wang et al. 2010). Based on these findings, we inferred that the ancient Jinggouzi people associated with the Donghu culture, they might belong to Donghu population. It is of much value to trace the history of Donghu and know more about the development and disappearance of this ancient nomadic tribe. Moreover, it might help us to explore the structure of the ancient nomadic society.