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East Asia harbors substantial genetic, physical, cultural and linguistic diversity, but the detailed structures and interrelationships of those aspects remain enigmatic. This question has begun to be addressed by a rapid accumulation of molecular anthropological studies of the populations in and around East Asia, especially by Y chromosome studies. The current Y chromosome evidence suggests multiple early migrations of modern humans from Africa via Southeast Asia to East Asia. After the initial settlements, the northward migrations during the Paleolithic Age shaped the genetic structure in East Asia. Subsequently, recent admixtures between Central Asian immigrants and northern East Asians enlarged the genetic divergence between southern and northern East Asia populations. Cultural practices, such as languages, agriculture, military affairs and social prestige, also have impacts on the genetic patterns in East Asia. Furthermore, application of Y chromosome analyses in the family genealogy studies offers successful showcases of the utility of genetics in studying the ancient history.
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... China, being a country of large geographic extent as well as of enormous cultural and demographic impact, has repeatedly been the subject of genetic studies to elucidate its prehistoric and historic demography (Chu et al. 1998;Piazza 1998). Many of the more contemporary studies concentrated on Y-linked polymorphisms (Deng et al. 2004;Li et al. 2007;Qi et al. 2013;Wang et al. 2012;Wang and Li 2013;Wen et al. 2004;Xu et al. 2015), whereas others used large sets of autosomal single-nucleotide polymorphisms Xu et al. 2009). While classical marker studies reported a genetic distinction between Northern and Southern China, with a boundary corresponding approximately to the Yangtze River (Chu et al. 1998;Xiao et al. 2000), Y chromosome and also autosomal surveys could not find a correspondence between this geographical pattern and the ethnic structure of contemporary China, although substantially different expansion time estimates were obtained for Northern and Southern populations (Xue et al. 2006 (Wen et al. 2004). ...
... We observed substantial differences in the distribution of Y chromosomal haplotypes between some ethnic groups, most notably Kazakhs and Tibetans, and most other ethnicities. The strong differentiation of the Kazakhs is explicable by a different ancestry as well as repeated migrations and admixture events along the Silk Road in the past 2000 years or so, as has been recently suggested (Mezzavilla et al. 2014), whereas Tibetans' Y-STR haplotype variation may mirror a deep ancestral root that is indicated by the high frequency of the D-M174 haplogroup in Tibetans (Shi et al. 2008;Wang and Li 2013). On a provincial level, however, differences were much less pronounced, with the exceptions of the Tibet and Qinghai provinces. ...
... The southern route is also supported by paternal evidence. Four Y-chromosome haplogroups, C, D, N, and O, accounting for 93% of the present East Asian males (Wang and Li 2013), all have southern origins. Males of haplogroup C went through the southern coastal route to Southeast Asia approximately 60,000 years ago and then spread to East Asia approximately 40,000 years ago (Zhong et al. 2010). ...
... These D-M174 populations surprisingly settled on the Tibetan Plateau, adapting to extreme environments, possibly benefitting from gene flow from Denisovans (Huerta-Sánchez et al. 2014). The younger haplogroups N and O migrated to East Asia in several waves 40,000 years ago (Wang and Li 2013). Furthermore, a previous study based on the autosomal single nucleotide polymorphisms (SNPs) also confirmed that Southeast Asian populations made more genetic contributions to East Asian populations than Central/South Asian populations did (HUGO Pan-Asian SNP Consortium 2009). ...
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East Asia, geographically extending to the Pamir Plateau in the west, to the Himalayan Mountains in the southwest, to Lake Baikal in the north and to the South China Sea in the south, harbors a variety of people, cultures, and languages. To reconstruct the natural history of East Asians is a mission of multiple disciplines, including genetics, archaeology, linguistics, and ethnology. Geneticists confirm the recent African origin of modern East Asians. Anatomically modern humans arose in Africa and immigrated into East Asia via a southern route approximately 50,000 years ago. Following the end of the Last Glacial Maximum approximately 12,000 years ago, rice and millet were domesticated in the south and north of East Asia, respectively, which allowed human populations to expand and linguistic families and ethnic groups to develop. These Neolithic populations produced a strong relation between the present genetic structures and linguistic families. The expansion of the Hongshan people from northeastern China relocated most of the ethnic populations on a large scale approximately 5300 years ago. Most of the ethnic groups migrated to remote regions, producing genetic structure differences between the edge and center of East Asia. In central China, pronounced population admixture occurred and accelerated over time, which subsequently formed the Han Chinese population and eventually the Chinese civilization. Population migration between the north and the south throughout history has left a smooth gradient in north–south changes in genetic structure. Observation of the process of shaping the genetic structure of East Asians may help in understanding the global natural history of modern humans.
... One question concerns the extent to which the peopling of East Asia by modern humans occurred via a coastal or interior route. Suggestive genetic evidence for a coastal route comes from Y chromosome data as Tibetan populations have a high frequency (around 50%) of the deeply branching haplogroup D-M174, which is shared with modern Japanese groups (and ancient Jomon hunter-gatherers of Japan) along with Indigenous Andaman islanders of the Bay of Bengal 15 . ...
... The contributions of the Onge-related lineage are concentrated in coastal groups: we estimate 100% in Andamanese, 44% in Jomon and 20% in ancient Taiwan farmers, consistent with the coastal route expansion hypothesized based on the Y-chromosomal haplogroup D-M174 that is found in both Andamanese and Japanese populations 15 . Although Tibet is not coastal, the relatively high inferred contribution of this lineage to ancient Tibetan populations (16%) and the presence of D-M174 with a frequency of around 50% in modern Tibetan individuals, provides a link between this Y-chromosomal haplogroup and Onge-related ancestry. ...
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The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people1,2. We report genome-wide data from 166 East Asians dating to 6000 BCE – 1000 CE and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan plateau are linked by a deeply-splitting lineage likely reflecting a Late Pleistocene coastal migration. We follow Holocene expansions from four regions. First, hunter-gatherers of Mongolia and the Amur River Basin have ancestry shared by Mongolic and Tungusic language speakers but do not carry West Liao River farmer ancestry contradicting theories that their expansion spread these proto-languages. Second, Yellow River Basin farmers at ~3000 BCE likely spread Sino-Tibetan languages as their ancestry dispersed both to Tibet where it forms up ~84% to some groups and to the Central Plain where it contributed ~59-84% to Han Chinese. Third, people from Taiwan ~1300 BCE to 800 CE derived ~75% ancestry from a lineage also common in modern Austronesian, Tai-Kadai and Austroasiatic speakers likely deriving from Yangtze River Valley farmers; ancient Taiwan people also derived ~25% ancestry from a northern lineage related to but different from Yellow River farmers implying an additional north-to-south expansion. Fourth, Yamnaya Steppe pastoralist ancestry arrived in western Mongolia after ~3000 BCE but was displaced by previously established lineages even while it persisted in western China as expected if it spread the ancestor of Tocharian Indo-European languages. Two later gene flows affected western Mongolia: after ~2000 BCE migrants with Yamnaya and European farmer ancestry, and episodic impacts of later groups with ancestry from Turan.
... Shannan Tibetan (42.31%), Luoba (30.77) and Danba Qiang (22.22%) (Kang et al., 2012;Qi et al., 2013;Wang and Li, 2013;Wang et al., 2014) and present-day Han Chinese (Yan et al., 2011) such as Shandong (24.2%), Beijing (18.5%) and Heilongjiang (16.6%) (Lang et al., 2019). ...
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The relationship between archeological culture and ethnicity is invariably complex. This is especially the case for periods of national division and rapid inter-ethnic exchange, such as China’s Sixteen Kingdoms (304–439 CE) and Northern and Southern Dynasties (420–589 CE). Going by tomb shape and grave goods, the Foyemiaowan cemetery at Dunhuang exhibits a typical third–tenth century Han style. Despite this, the ethnic makeup of the Foyemiaowan population has remained unclear. We therefore analyzed 485 Y-chromosomal SNPs and entire mitochondrial genomes of 34 Foyemiaowan samples. Our study yielded the following discoveries: (1) principal component analysis revealed that the Foyemiaowan population was closely clustered with Tibeto-Burman populations on the paternal side and close to Mongolic-speaking populations on the maternal side; (2) lineage comparisons at the individual level showed that the Foyemiaowan population consisted of primarily Tibeto-Burman and Han Chinese related lineages (Oα-M117, 25%;Oβ-F46, 18.75%), partially Altaic speaking North Eurasian lineages (N-F1206, 18.75%) and a slight admixture of southern East Asian lineages (O1b1a2-Page59, 6.25%; O1b1a1-PK4, 3.13%). Similarly, the maternal gene pool of Foyemiaowan contained northern East Asian (A, 4.17%; CZ, 16.67%; D, 20.83%; G, 4.17%; M9, 4.17%), southern East Asian (B, 12.51%; F, 20.83%) and western Eurasian (H, 4.17%; J, 4.17%) related lineages; (3) we discovered a relatively high genetic diversity among the Foyemiaowan population (0.891) in our ancient reference populations, indicating a complex history of population admixture. Archeological findings, stable isotope analysis and historical documents further corroborated our results. Although in this period China’s central government had relinquished control of the Hexi Corridor and regional non-Han regimes became the dominant regional power, Foyemiaowan’s inhabitants remained strongly influenced by Han culture.
... Furthermore, haplogroup D1a1 is widely distributed among the Tibetan, Sichuan Yi, Yunnan Yi (Tangut-Qiang) and Lolo populations [101], while D1a2 is most distributed in Tibetans [102]. Subhaplogroup D1a2a-P47 is unique to Tibetans and only appears in Tibetans and some Tibetan-Burman minorities close to Tibetans in Sichuan and Yunnan provinces, such as Pumi and Naxi [103]. Haplogroup D and its subhaplogroups found in the Yunnan population might be a result of the geographic "Tibet-Yi Corridor", which spans three Chinese provinces: Sichuan, Tibet, and Yunnan. ...
Article
Improving the resolution of the current widely used Y-chromosomal short tandem repeat (Y-STR) dataset is of great importance for forensic investigators, and the current approach is limited, except for the addition of more Y-STR loci. In this research, a regional Y-DNA database was investigated to improve the Y-STR haplotype resolution utilizing a Y-SNP Pedigree Tagging System that includes 24 Y-chromosomal single nucleotide polymorphism (Y-SNP) loci. This pilot study was conducted in the Chinese Yunnan Zhaoyang Han population, and 3,473 unrelated male individuals were enrolled. Based on data on the male haplogroups under different panels, the matched or near-matching (NM) Y-STR haplotype pairs from different haplogroups indicated the critical roles of haplogroups in improving the regional Y-STR haplotype resolution. A classic median-joining network analysis was performed using Y-STR or Y-STR/Y-SNP data to reconstruct population substructures, which revealed the ability of Y-SNPs to correct misclassifications from Y-STRs. Additionally, population substructures were reconstructed using multiple unsupervised or supervised dimensionality reduction methods, which indicated the potential of Y-STR haplotypes in predicting Y-SNP haplogroups. Haplogroup prediction models were built based on nine publicly accessible machine-learning (ML) approaches. The results showed that the best prediction accuracy score could reach 99.71% for major haplogroups and 98.54% for detailed haplogroups. Potential influences on prediction accuracy were assessed by adjusting the Y-STR locus numbers, selecting Y-STR loci with various mutabilities, and performing data processing. ML-based predictors generally presented a better prediction accuracy than two available predictors (Nevgen and EA-YPredictor). Three tree models were developed based on the Yfiler Plus panel with unprocessed input data, which showed their strong generalization ability in classifying various Chinese Han subgroups (validation dataset). In conclusion, this study revealed the significance and application prospects of Y-SNP haplogroups in improving regional Y-STR databases. Y-SNP haplogroups can be used to discriminate NM Y-STR haplotype pairs, and it is important for forensic Y-STR databases to develop haplogroup prediction tools to improve the accuracy of biogeographic ancestry inferences.
... The fact that numerous open-air Paleolithic sites have recently been found and excavated in south China implies that south China plays a pivotal role in understanding the origin and prehistory of humanity in East Asia (Liu et al., 2008;Zhu et al., 2008). In addition, according to genetic studies (Chu et al., 1998;Piazza 1998;Wang and Li, 2013), south China is also the possible gateway for hominin to migrate into the hinterland of China, and thereby more detailed analyses of Paleolithic sites in south China are of great archaeological significance. However, it is hard to construct their chronological framework, because an intensive chemical weathering of the deposits results in the lack of suitable materials for numerical dating such as radiocarbon dating. ...
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The Huxushan archaeological site in northern Hunan Province, China, was recently excavated, from which stone tools including handaxes were unearthed. The deposits of the site are chemically weathered, which makes it difficult to date the site using numerical dating techniques except for optically stimulated luminescence (OSL) method. Here, we used various luminescence procedures including single-aliquot regenerative-dose (SAR), sensitivity-corrected multiple-aliquot regenerative-dose (SMAR) and thermally transferred optically stimulated luminescence (TT-OSL) SAR procedures on fine-grained quartz, and two-step post-infrared infrared stimulated luminescence (pIRIR) and multi-elevated-temperature pIRIR (MET-pIRIR) procedures on fine polymineral fractions. The results show that the fine quartz grains have excellent luminescence properties and the quartz SAR-, SMAR- and TT-OSL ages for the samples agree with each other and in stratigraphical order except for one sample. The fine polymineral fractions exhibited relatively weak pIRIR and MET-pIRIR signals, resulting in difficulty in constructing the dose-response curve for MET-pIRIR signals and the stratigraphically inconsistent pIRIR(100, 275) ages. The seven samples yielded their quartz OSL ages ranging from about 62 ka to 133 ka. The two samples from the cultural layer was dated to 78 to 92 ka using different procedures on fine quartz . However, given the systematically older pIRIR ages obtained with the fine polymineral grains for the two samples, their quartz OSL ages are considered to represent the minimal ages of this layer, and their pIRIR(100, 275) ages of 118 and 110 ka represent the upper age limit, indicating that the site was occupied by hominins during Marine Isotope Stage 5.
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This paper attempts to discuss the convergence phenomena in the Amdo Sprachbund in the light of genetic and cultural/religious factors. As an ethnolinguistically diverse region, the Amdo Sprachbund constitutes a natural laboratory for the study of language contact and human interaction at large. Unsurprisingly, populations within the Amdo Sprachbund show considerable signs of genetic admixture which sometimes result in disagreement between genetic structure and linguistic affiliation. More remarkably, their languages appear to show varying degrees of structural convergence towards Amdo Tibetan depending on their religious practice. To wit, syllable-initial consonant clusters and a three-term evidential system, two features which are clearly attributable to Tibetic influence, are only found in languages whose speakers practise(d) Tibetan Buddhism. These observations suggest that genetic and various sociohistorical factors should be taken into account in the study of areal linguistics.
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Prehistoric Japan underwent rapid transformations in the past 3000 years, first from foraging to wet rice farming and then to state formation. A long-standing hypothesis posits that mainland Japanese populations derive dual ancestry from indigenous Jomon hunter-gatherer-fishers and succeeding Yayoi farmers. However, the genomic impact of agricultural migration and subsequent sociocultural changes remains unclear. We report 12 ancient Japanese genomes from pre- and postfarming periods. Our analysis finds that the Jomon maintained a small effective population size of ~1000 over several millennia, with a deep divergence from continental populations dated to 20,000 to 15,000 years ago, a period that saw the insularization of Japan through rising sea levels. Rice cultivation was introduced by people with Northeast Asian ancestry. Unexpectedly, we identify a later influx of East Asian ancestry during the imperial Kofun period. These three ancestral components continue to characterize present-day populations, supporting a tripartite model of Japanese genomic origins.
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东亚面积广阔、 环境多样, 有着占世界五分之一的人口,有阿尔泰、南亚、南岛、侗傣、苗瑶、汉藏和印欧等七个语系的 200 多种语言,是世界上研究人类进化、遗传多样性和基因与文化相互作用的最重要区域之一。近年来, 随着分子生物学技术的发展, 各类遗传标记系统被成功应用于人类群体历史的研究, 为解决东亚人群的起源、 演化、迁徙等诸多科学问题提供了新的证据和极有价值的信息。本文应用 Y 染色体、线粒体(mtDNA)和常染色体 STR 等遗传标记对东亚的汉藏、壮侗、回族人群进行遗传结构分析,与语言学、考古学和历史学相结合来理清这些复杂族群的起源、迁徙和融合历程。 本文还通过姓氏、家谱和 Y 染色体的关联研究并结合古 DNA 对曹操的 Y 染色体类型进行论证, 开创历史人类学研究的新篇章。另外,本文还应用语音多样性对全世界语言的起源地进行了探讨。 Y 染色体单倍群 O3a1c-002611, O3a2c1*-M134 和 O3a2c1a-M117 是汉族的三个主要类型,分别能占到汉族人群的 11-17%。通过 Y 染色体捕获测序,我们在上述三个O3单倍群下发现了三个在新石器时代有过剧烈人口扩张的支系Oα、Oβ和 Oγ,扩张时间分别是 5400、 6500 和 6800 年前,正好与中国北方全面转入农业阶段的时间相吻合。单倍群 O3a2c1*-M134 和 O3a2c1a-M117 在藏缅族群中也高频出现,是古氐羌族群的代表类型, 氐羌经由藏彝走廊南下,与 D-M174 混合形成了今天的藏缅族群。 单倍群 O3a1c-002611 及其下游分支在藏缅族群中的频率却很低,但在中东部地区显著高频分布,显示该父系类型并没有参与西南藏缅族群的形成,而很可能是东夷族群的代表类型。 藏缅族群的母系基因库也有大量北方族群的贡献,例如高频的单倍群 A、 C、 D 和 G 等。常染色体 STR 也支持汉藏族群的遗传近缘性,汉族的遗传组成与东亚的阿尔泰族群较相近,但藏族与阿尔泰族群有很大差异; 南西伯利亚的阿尔泰族群中有大量与欧洲人共享的遗传组分,但这在汉藏人群里是几乎观察不到的。 中国回族起源于宗教文化上的转变或是伴随着一定程度的基因流动是回族形成过程中的关键问题。 现代回族人群中确实有一定比例的欧亚西部和中东特有的 Y 染色体类型,平均约占到整个回族遗传构成的 30%。然而,由于回族长期以来与中国本土的民族特别是与汉族通婚, 其遗传构成上大部分是来自中国本土的成分, 例如, 相比于越南占城人和其他中南半岛的人群,回辉人的 Y 染色体和 mtDNA 却与海南原住民最为接近。回族与东亚族群的融合过程是有性别差异的, 我们通过常染色体 STR 位点几乎没有在回族中看到西方遗传成分,而西方成分在父系 Y 染色体上却能占到 30%, 因此回族的形成主要源于回回男性与汉族等人群的女子通婚。 本文还通过 Y 染色体和姓氏、家谱相结合的方法确定了赛典赤•赡思丁和郑和的 Y 染色体很可能是南亚西部特有支系 L1a-M76,证实了其波斯祖源。 壮侗族群的主要 Y 染色体类型是 O1a-M119 和 O2a1-M95,而 mtDNA 也主要是南方特异的 B4a, F1a, M7b1, B5a, M7b*, M*和 R9 等。 在以上研究的基础上,我们对广西仫佬族、 茶洞人(未识别人群)和海南黎族的五个分支侾黎、杞黎、润黎、美孚和加茂黎族进行遗传学调查。 Y 染色体和 mtDNA 都显示茶洞和仫佬族与南方人群特别是壮侗族群非常相近, 茶洞与仫佬族的母系遗传关系更近于毛南族。 海南黎族的 mtDNA 分析展现海南岛早期人类定居的三个阶段: 5 万年前出非洲群体的一部分到达东亚,成为到海南岛最早的定居者;在东南亚和东亚广泛分布的mtDNA 单倍群F*, B4a和 D4a记录了在末次冰川期之前亚洲大陆的人群回流进入海南岛(4 万-1.5 万年前),即海南原住民主要源于末次盛冰期前进入东亚的早期移民的回流; mtDNA 单倍群 F1b, M7b 和 R9b 则显示了在末次冰期之后及新石器时代(1.5 万年以内)海南岛的人口扩张。 姓氏与 Y 染色体有很好的平行对应关系,结合家谱,我们对曹氏家族进行了全国范围大规模遗传调查。单倍群 O2-M268 是唯一在宣称是曹操后代的家族中显著高频出现的类型,很有可能这就是曹操的 Y 染色体类型,而单倍群O3a1c-002611 却最可能是西汉丞相曹参的类型,由此得出曹操不太可能是曹参的后裔。 通过古 DNA 分析,曹操叔祖曹鼎的 Y 染色体类型也是 O2-M268,与曹操及其现代后裔一致,也说明了曹操的父亲应是从曹腾本宗室过继而非抱养自街头乞丐。 基因的进化和语言的演化有着很好的相关性,那么语言是不是也和人类一样起源于非洲而后经过一系列奠基者效应扩散至世界各地? 奥克兰大学的Atkinson 提出语音多样性支持语言从非洲扩张的系列奠基者效应,但他所选用的数据的分类太粗糙,不能反映元音、辅音和声调的真实多样性;他在数据标准化过程中未考虑到不同音素的权重不同,而是采用简单的求均值方法来计算总的语音多样性,这使得辅音的多样性难以体现在总的语音多样性中;语言的特征有很多,但他只选择了元音、辅音和声调这三项,而漏掉了其他许多重要特征对语言起源和演化的影响,另外,元音、辅音和声调是否可以保守到能反映数万年前人类出非洲迁徙事件还难确定。本文尽可能地完善了 Atkinson 的上述疏漏之后,发现欧亚大陆的语音的多样性倾向于最高, 语音多样性不支持语言从非洲扩张的系列奠基者效应。
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Concerns have been raised about my proposal that global phonemic diversity was shaped by a serial founder effect during the human expansion from Africa. I welcome this discussion of new data and alternative interpretations. Although this work highlights interesting questions for future research, it does not undermine support for a serial founder effect model of expansion of language from Africa.
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a b s t r a c t Neanderthals are an extinct hominid lineage that coexisted with modern humans in Eurasia. The Neanderthal's role in the evolutionary history of modern humans is a well concerned topic. Mito-chondrial DNA sequences from Neanderthal fossils support the "Out of Africa" theory of human evolu-tion, suggesting that modern human ancestors replaced Neanderthal populations in Eurasia. Recent analyses of Neanderthal genome draft sequences indicate minor gene flow between Neanderthals and modern humans in Eurasia but not in Africa. However, these conclusions are quite controversial due to data quality and insufficient sampling, especially about when and where the genetic admixture took place, and the direction of the assumed gene flow.