DOCSLIB.ORG

Southern East Asian Origin and Coexpansion of Mycobacterium Tuberculosis Beijing Family with Han Chinese

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Southern East Asian Origin and Coexpansion of Mycobacterium Tuberculosis Beijing Family with Han Chinese Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese Tao Luoa,b,Iñaki Comasc,d,1, Dan Luoe,1, Bing Luf,g,1, Jie Wuh,1, Lanhai Weii,1, Chongguang Yanga, Qingyun Liua, Mingyu Gana, Gang Suna, Xin Shenh, Feiying Liue, Sebastien Gagneuxj,2, Jian Meih,2, Rushu Lane,2, Kanglin Wanf,k,2, and Qian Gaoa,2 aKey Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; bLaboratory of Infection and Immunity, School of Basic Medical Science, West China Center of Medical Sciences, Sichuan University, Chengdu, Sichuan 610041, China; cGenomics and Health Unit, FISABIO Public Health, Valencia 46020, Spain; dCIBER (Centros de Investigación Biomédica en Red) in Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid 28029, Spain; eDepartment of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, Guangxi 530028, China; fState Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; gBeijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Control and Prevention, Beijing 100013, China; hDepartment of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China; iMinistry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China; jDepartment of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel 4002, University of Basel, Basel CH-4003, Switzerland; and kCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China Edited by William R. Jacobs Jr., Howard Hughes Medical Institute, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, and approved May 14, 2015 (received for review December 23, 2014) The Beijing family is the most successful genotype of Mycobacterium great attentions due to its global emergence in recent decades tuberculosis and responsible for more than a quarter of the global (6, 7, 10–12), its tendency to cause disease outbreak (13–17), and tuberculosis epidemic. As the predominant genotype in East Asia, the its association with antibiotic resistance (12, 18). Experimental and Beijing family has been emerging in various areas of the world and is clinical evidences suggest a hypervirulent phenotype of Beijing often associated with disease outbreaks and antibiotic resistance. Re- strains (12, 19), and a higher mutation rate compared with other vealing the origin and historical dissemination of this strain family is strains (20). important for understanding its current global success. Here we char- According to genotyping data from previous molecular- acterized the global diversity of this family based on whole-genome epidemiology studies, most Beijing strains from widespread geo- sequences of 358 Beijing strains. We show that the Beijing strains graphic areas showed a remarkable degree of genetic similarity endemic in East Asia are genetically diverse, whereas the globally (6, 21), suggesting this strain family might have emerged from emerging strains mostly belong to a more homogenous subtype recent expansions. It was hypothesized that vaccination with “ ” known as modern Beijing. Phylogeographic and coalescent analy- Bacille Calmette Guerin (bacillus Calmette–Guérin) that has ses indicate that the Beijing family most likely emerged around been widely implemented in East Asian countries might be the 30,000 y ago in southern East Asia, and accompanied the early colo- force driving the dominance of this strain family in this area (21). nization by modern humans in this area. By combining the genomic Moreover, the global emergence of the Beijing family may have data and genotyping result of 1,793 strains from across China, we found the “modern” Beijing sublineage experienced massive expan- sions in northern China during the Neolithic era and subsequently Significance spread to other regions following the migration of Han Chinese. Our results support a parallel evolution of the Beijing family and Mycobacterium tuberculosis Beijing family is a group of glob- modern humans in East Asia. The dominance of the “modern” Beijing ally emerging bacterial strains that are responsible for more sublineage in East Asia and its recent global emergence are most than a quarter of the global tuberculosis epidemic. Here, we likely driven by its hypervirulence, which might reflect adaption to combine whole-genome sequencing and large-scale genotyp- increased human population densities linked to the agricultural tran- ing to map the temporal and spatial changes of the genetic sition in northern China. diversity within this strain family. We reveal a southern East Asia origin and a parallel evolution of this bacterial genotype MTBC Beijing family | origin | expansion | Han Chinese with modern humans in East Asia during the last 30,000 years. The recently globally emerged Beijing strains mainly belong to uberculosis has plagued human beings since ancient times and a hypervirulent subtype that most likely has initially been se- Tremains a leading cause of global morbidity and mortality. The lected for adaption to increased population densities during causative agent of human tuberculosis is the Mycobacterium tuber- the agricultural transition in northern China. culosis complex (MTBC), a group of organisms that harbor little Author contributions: T.L., F.L., S.G., J.M., R.L., K.W., and Q.G. designed research; T.L., D.L., genetic diversity compared with other bacteria (1). MTBC most B.L., J.W., C.Y., Q.L., M.G., G.S., and X.S. performed research; T.L., I.C., and L.W. analyzed likely originated in Africa, although its age is being debated (2–4). data; and T.L., I.C., L.W., S.G., and Q.G. wrote the paper. The human-adapted MTBC is highly clonal and is classified into The authors declare no conflict of interest. seven main phylogenetic groups, designated lineage 1 through This article is a PNAS Direct Submission. lineage 7 (2). These seven lineages show strong biogeographic as- Data deposition: The sequences in this paper have been deposited in the Sequence Read sociations that have been proposed to result from codiversification Archive database, www.ncbi.nlm.nih.gov/sra (accession no. SRP051093). with different human populations (2, 5). Lineage 2 that dominates 1I.C., D.L., B.L., J.W., and L.W. contributed equally to this work. in East Asia is one of the most successful MTBC variants; more 2To whom correspondence may be addressed. Email: [email protected], sebastien. than a quarter of the global tuberculosis epidemic is caused by this [email protected], [email protected], [email protected], or [email protected] lineage (6, 7). Lineage 2 contains strains that mostly belong to the This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. so-called Beijing family (8, 9). This strain family has attracted 1073/pnas.1424063112/-/DCSupplemental. 8136–8141 | PNAS | June 30, 2015 | vol. 112 | no. 26 www.pnas.org/cgi/doi/10.1073/pnas.1424063112 Downloaded by guest on September 28, 2021 been due to its hypervirulence and association with drug re- A East sistance (7, 18). However, there were discrepant results regarding Europe 1 the relative protective effect of bacillus Calmette–Guérin vaccina- tion against Beijing strains from animal infection experiments (19), East Europe 2 and many epidemiological studies failed to find any association between bacillus Calmette–Guérin vaccination and Beijing strains (22–25). The link between drug resistance and the Beijing family has Bj-MG3 primarily been observed in regions where this family has emerged Lineage 2.2 recently (e.g., Cuba, South Africa, countries of the former Soviet (Beijing) Union) but not in East Asian, where the Beijing family has been endemic for a long time (18, 26). Furthermore, more recent studies 7.8 kya (7.1-8.6) indicate that the expansion of the Beijing family may have started NTF::IS6110 long before the introduction of vaccination and antibiotic treatment B (2, 3, 27). 11.3 kya (10.1-12.4) With the increased availability of genotyping data, the Beijing Bj-MG2 strains were proved more heterogeneous than initially estimated, RD181 18.5 kya – (16.4-20.6) and several Beijing sublineages have been identified (28 31). 12.2 kya 27.8 kya RD207 (10.7-13.6) Bj-MG1 (24.8-30.8) However, a full understanding of the genetic diversity of Beijing (Beijing) RD105 Extended RD105 Lineage 2.1 family is constrained by the low amount of nucleotide variation (Lineage 2) (Proto-Beijing) (8, 32). Whole-genome sequencing provides an ideal tool to 1.0E8 NDT Ne study the genetic diversity of MTBC, and new insights into the expansion 1.0E7 – (6.5 kya) per generation origin and evolution of MTBC have been gained (2, 4, 20, 33 C Pre-NDT 1.0E6 expansion 35). The genomic diversity of Beijing family was initially studied (10 kya) in a most recent study, in which a general East Asian origin and 1.0E5 recent expansions of this strain family were suggested (36). However, 1.0E4 1.0E3 the details about the origin and primary dissemination of Beijing 25 20 15 10 5 0 family remain unclear. Answering of these questions is important to Time (Kya) better understand the virulence of this lineage and its global success. Fig. 1. Genetic and geographic structure and population dynamics of Here, we combined whole-genome sequencing of key strains with global MTBC lineage 2 strains. (A) Places of origin for the 358 MTBC lineage detailed single nucleotide polymorphism (SNP) typing of a large 2 strains. The size of dot corresponds to the number of strains in each place.
Load more

Recommended publications
  • Genetic Structure, Divergence and Admixture of Han Chinese, Japanese and Korean Populations Yuchen Wang1,2, Dongsheng Lu1,2, Yeun-Jun Chung3 and Shuhua Xu1,2,4,5,6*
    Wang et al. Hereditas (2018) 155:19 https://doi.org/10.1186/s41065-018-0057-5 RESEARCH Open Access Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations Yuchen Wang1,2, Dongsheng Lu1,2, Yeun-Jun Chung3 and Shuhua Xu1,2,4,5,6* Abstract Background: Han Chinese, Japanese and Korean, the three major ethnic groups of East Asia, share many similarities in appearance, language and culture etc., but their genetic relationships, divergence times and subsequent genetic exchanges have not been well studied. Results: We conducted a genome-wide study and evaluated the population structure of 182 Han Chinese, 90 Japanese and 100 Korean individuals, together with the data of 630 individuals representing 8 populations wordwide. Our analyses revealed that Han Chinese, Japanese and Korean populations have distinct genetic makeup and can be well distinguished based on either the genome wide data or a panel of ancestry informative markers (AIMs). Their genetic structure corresponds well to their geographical distributions, indicating geographical isolation played a critical role in driving population differentiation in East Asia. The most recent common ancestor of the three populations was dated back to 3000 ~ 3600 years ago. Our analyses also revealed substantial admixture within the three populations which occurred subsequent to initial splits, and distinct gene introgression from surrounding populations, of which northern ancestral component is dominant. Conclusions: These estimations and findings facilitate to understanding population history and mechanism of human genetic diversity in East Asia, and have implications for both evolutionary and medical studies. Keywords: Han Chinese, Japanese, Korean, Genetic ancestry, Population structure, Population divergence, Admixture, SNP Background existed in Korean until their recent abolition in the East Asia is one of the world’s most populated places, 1940s [1].
    [Show full text]
  • Growth and Decline of Muslim Hui Enclaves in Beijing
    EG1402.fm Page 104 Thursday, June 21, 2007 12:59 PM Growth and Decline of Muslim Hui Enclaves in Beijing Wenfei Wang, Shangyi Zhou, and C. Cindy Fan1 Abstract: The Hui people are a distinct ethnic group in China in terms of their diet and Islamic religion. In this paper, we examine the divergent residential and economic develop- ment of Niujie and Madian, two Hui enclaves in the city of Beijing. Our analysis is based on archival and historical materials, census data, and information collected from recent field work. We show that in addition to social perspectives, geographic factors—location relative to the northward urban expansion of Beijing, and the character of urban administrative geog- raphy in China—are important for understanding the evolution of ethnic enclaves. Journal of Economic Literature, Classification Numbers: O10, I31, J15. 3 figures, 2 tables, 60 refer- ences. INTRODUCTION esearch on ethnic enclaves has focused on their residential and economic functions and Ron the social explanations for their existence and persistence. Most studies do not address the role of geography or the evolution of ethnic enclaves, including their decline. In this paper, we examine Niujie and Madian, two Muslim Hui enclaves in Beijing, their his- tory, and recent divergent paths of development. While Niujie continues to thrive as a major residential area of the Hui people in Beijing and as a prominent supplier of Hui foods and services for the entire city, both the Islamic character and the proportion of Hui residents in Madian have declined. We argue that Madian’s location with respect to recent urban expan- sion in Beijing and the administrative geography of the area have contributed to the enclave’s decline.
    [Show full text]
  • Inner Mongolia Information Overview Inner Mongolia Is Located in The
    Inner Mongolia Information Overview Inner Mongolia is located in the northern region of China and shares an international border with Mongolia and the Russian Federation. Inner Mongolia is the third-largest subdivision of China and covers 12% of China's total land area. The main languages spoken here are Chinese and Mongolian. The province has a population of about 24 million people with the majority being the Han Chinese. The capital of Inner Mongolia is Hohhot and the largest city is Baotou. The region is known as “Inner” Mongolia, to distinguish itself from “Outer Mongolia”, or the independent state of Mongolia. Geography Inner Mongolia ties the province of Shaanxi in that is has the most neighboring provinces of any other Chinese province. Inner Mongolia borders Heilongjiang, Jilin, Liaoning, Hebei, Shanxi, Shaanxi, Ningxia, and Gansu. Due to the size of the province stretching from Northwest to Northeast, the region has a four-season climate to include long, cold, dry winters and very warm to hot summers. Economy Farming of crops such as wheat takes precedence along the river valleys. In the more arid grasslands, herding of goats, sheep and so on is a traditional method of subsistence. Inner Mongolia has an abundance of natural resources such as coal, cashmere, natural gas, and rare earth elements. The region also has more deposits of naturally occurring niobium, zirconium and beryllium than any other province in China. Demographics When the region was established in 1947, Han Chinese comprised about 83% of the population, while the Mongols made up about 14% of the population. The Han Chinese live mostly in the Hetao region as well as in central and eastern Inner Mongolia.
    [Show full text]
  • The Floating Community of Muslims in the Island City of Guangzhou
    Island Studies Journal, 12(2), 2017, pp. 83-96 The floating community of Muslims in the island city of Guangzhou Ping Su Sun Yat-sen University, Zhuhai, China [email protected] ABSTRACT: The paper explores how Guangzhou’s urban density and hub functions have conditioned its cultural dynamics by looking specifically at the city’s Muslim community. Guangzhou’s island spatiality has influenced the development of the city’s Muslim community both historically and in the contemporary era. As a historic island port city, Guangzhou has a long-standing tradition of commerce and foreign trade, which brought to the city the first group of Muslims in China. During the Tang and Song dynasties, a large Muslim community lived in the fanfang of Guangzhou, a residential unit designated by the government for foreigners. Later, in the Ming and Qing dynasties, Hui Muslims from northern China, who were mostly soldiers, joined foreign Muslims in Guangzhou to form an extended community. However, during the Cultural Revolution, Guangzhou’s Muslim community and Islamic culture underwent severe damage. It was not until China’s period of reform and opening-up that the Muslim community in Guangzhou started to revive, thanks to the city’s rapid economic development, especially in foreign trade. This is today a floating community, lacking geographical, racial, ethnic, and national boundaries. This paper argues that Guangzhou’s island spatiality as a major port at the mouth of the Pearl River has given rise to a floating Muslim community. Keywords: floating community, Guangzhou, island cities, Muslims, trading port, spatiality https://doi.org/10.24043/isj.18 © 2017 – Institute of Island Studies, University of Prince Edward Island, Canada.
    [Show full text]
  • Glycosylation of Igg Associates with Hypertension and Type 2 Diabetes Mellitus Comorbidity in the Chinese Muslim Ethnic Minorities and the Han Chinese
    Journal of Personalized Medicine Article Glycosylation of IgG Associates with Hypertension and Type 2 Diabetes Mellitus Comorbidity in the Chinese Muslim Ethnic Minorities and the Han Chinese Xiaoni Meng 1 , Manshu Song 1,2,* , Marija Vilaj 3, Jerko Štambuk 3, Mamatyusupu Dolikun 4, Jie Zhang 1, Di Liu 1, Hao Wang 5 , Xiaoyu Zhang 1, Jinxia Zhang 1, Weijie Cao 1, Ana Momˇcilovi´c 3, Irena Trbojevi´c-Akmaˇci´c 3 , Xingang Li 2,6 , Deqiang Zheng 1, Lijuan Wu 1, Xiuhua Guo 1, Youxin Wang 1,2 , Gordan Lauc 3,7 and Wei Wang 1,2,6 1 Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; [email protected] (X.M.); [email protected] (J.Z.); [email protected] (D.L.); [email protected] (X.Z.); [email protected] (J.Z.); [email protected] (W.C.); [email protected] (D.Z.); [email protected] (L.W.); [email protected] (X.G.); [email protected] (Y.W.); [email protected] (W.W.) 2 School of Medical and Health Sciences, Edith Cowan University, Perth, WA 6027, Australia; [email protected] 3 Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia; [email protected] (M.V.); [email protected] (J.Š.); [email protected] (A.M.); [email protected] (I.T.-A.); [email protected] (G.L.) 4 College of the Life Sciences and Technology, Xinjiang University, Urumqi 830046, China; [email protected] Citation: Meng, X.; Song, M.; Vilaj, 5 Department of Clinical Epidemiology and Evidence-Based Medicine, M.; Štambuk, J.; Dolikun, M.; Zhang, National Clinical Research Center for Digestive Disease, Beijing Friendship Hospital, J.; Liu, D.; Wang, H.; Zhang, X.; Capital Medical University, Beijing 100050, China; [email protected] Zhang, J.; et al.
    [Show full text]
  • Three Cases in China on Hakka Identity and Self-Perception
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by NORA - Norwegian Open Research Archives Three cases in China on Hakka identity and self-perception Ricky Heggheim Master’s Thesis in Chinese Studie KIN 4592, 30 Sp Departement of Culture Studies and Oriental Languages University of Oslo 1 Summary Study of Hakka culture has been an academic field for only a century. Compare with many other studies on ethnic groups in China, Hakka study and research is still in her early childhood. This despite Hakka is one of the longest existing groups of people in China. Uncertainty within the ethnicity and origin of Hakka people are among the topics that will be discussed in the following chapters. This thesis intends to give an introduction in the nature and origin of Hakka identity and to figure out whether it can be concluded that Hakka identity is fluid and depending on situations and surroundings. In that case, when do the Hakka people consider themselves as Han Chinese and when do they consider themselves as Hakka? And what are the reasons for this fluidness? Three cases in China serve as the foundation for this text. By exploring three different areas where Hakka people are settled, I hope this text can shed a light on the reasons and nature of changes in identity for Hakka people and their ethnic consciousness as well as the diversities and sameness within Hakka people in various settings and environments Conclusions that are given here indicate that Hakka people in different regions do varies in large degree when it comes to consciousness of their ethnicity and background.
    [Show full text]
  • Elites in Between Ethnic Mongolians and the Han in China 39
    Elites in Between Ethnic Mongolians and the Han in China 39 Chelegeer Contents Introduction ...................................................................................... 696 MINZU in China at a Glance ................................................................ 696 Mongolian Elites Before 1949 .................................................................. 699 The Old Nobility ............................................................................. 700 From Old House to New Elite ............................................................... 702 Mongol MINZU from 1949 to 1979 ............................................................ 704 Economic and Cultural Reforming .......................................................... 705 MINZU as Social Transformation ........................................................... 707 Ongoing Generations from the 1980s ........................................................... 709 Conclusion ....................................................................................... 711 References ....................................................................................... 712 Abstract Whether an ethnicity or a nationality is a natural and historical entity with clear self-consciousness, or a constructed identity as one of the consequences of modernity, there are always academic debates in sociology. By concerning Mongolian elites, this chapter argues their essential role in interacting with Han, the dominant population of China, through history and informing their
    [Show full text]
  • Conflict, Community and Crime in Fin-De-Siècle Sichuan
    CONFLICT, COMMUNITY AND CRIME IN FIN-DE-SIÈCLE SICHUAN A DISSERTATION SUBMITTED TO THE DEPARTMENT OF HISTORY AND THE COMMITTEE ON GRADUATE STUDIES OF STANFORD UNIVERSITY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY QUINN DOYLE JAVERS MAY 2012 © 2012 by Quinn Doyle Javers. All Rights Reserved. Re-distributed by Stanford University under license with the author. This work is licensed under a Creative Commons Attribution- Noncommercial 3.0 United States License. http://creativecommons.org/licenses/by-nc/3.0/us/ This dissertation is online at: http://purl.stanford.edu/gr339jp1011 ii I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Matthew Sommer, Primary Adviser I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Karen Wigen I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Christian Henriot Approved for the Stanford University Committee on Graduate Studies. Patricia J. Gumport, Vice Provost Graduate Education This signature page was generated electronically upon submission of this dissertation in electronic format. An original signed hard copy of the signature page is on file in University Archives. iii Abstract The 350 legal cases from the ming’an [“cases of unnatural death”] category of the Ba County archive that survive from the final decade of the nineteenth century create a textured picture of social life and state-society relations at the grassroots near the end of the Qing Dynasty (1644-1912).
    [Show full text]
  • The Reunification of China: Peace Through War Under the Song Dynasty Peter Lorge Index More Information
    Cambridge University Press 978-1-107-08475-9 - The Reunification of China: Peace through War under the Song Dynasty Peter Lorge Index More information Index Alexander the Great, 281 Changzhou, 82 An Lushan Rebellion, 41 Chanyuan, 4, 6–7, 9, 11–12, 15, 17–20, Ancestral Rules, 38 153, 238–9, 244–5, 247, 262–4, Anguozhen, 235 266–75, 277, 286 Anyang River, 99 Chanyuan Covenant, 4, 6–7, 9, 11, 15, 18–20, autumn defense, 256, 262 30–3, 41, 43, 225, 238–9, 244–5, 247, 269–70, 272–5, 277 Bagongyuan, 51 Chen Feng, 38–9 Bai Jiyun, 233 Chen Hongjin, 190 Bai River, 204 Chen Qiao, 173, 176 Bai Zhongzan, 51 Chen Shiqing, 230 Baidimiao, 145 Chen Yaosou, 264 Baigou River, 217 Chengdu, 146, 225, 227–32, 234 Baitian, 161 Chengtian, 18 Baozhou, 245, 265 Chengzhou, 63 Battle of Gaoping, 32, 38, 48, 71, 100 Chiang Kai-shek, 35 Battle of Wangdu, 257 Chinese Ways in War,41 Bazhou, 231 Chizhou, 170–1 Beiping Fort, 265 Chu, 119, 121–4, 126, 128, 131, Beizhou, 266 236, 265 Bi Shi’an, 264 Chu Zhaofu, 166–7 Bian Canal, 92 Chuzhou, 79, 84, 93 Bian Hao, 89 Cizhou, 50 Bian River, 90–1, 98 Clausewitz, 271 Biankou, 95 Comprehensive Mirror Bozhou, 221 Comprehensive Mirror for Aid in Governing, 26–8, 34 Cai River, 118 Caishi, 168, 172, 175 Dahui Fort, 109 Caishiji, 171 Daizhou, 60, 219, 221 Cangzhou, 98, 244 Daming, 156, 197 Cao Bin, 137, 145–6, 149, 169–72, Damingfu, 197 174–5, 179, 186, 190, 193, 208–9, Dangtu, 171 214–19 David Curtis Wright, 42, 272, 274, 276 Cao Han, 87, 179, 203 Davis, Richard, 31, 40 Cao Keming, 226 Dechong, 209 Cao Liyong, 268–9, 271 Defang, 182–3,
    [Show full text]
  • Fine-Scale Population Structure and Demographic History of Han Chinese Inferred from Haplotype Network of 111,000 Genomes
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.03.166413; this version posted July 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Fine-scale Population Structure and Demographic History of Han Chinese Inferred from Haplotype Network of 111,000 Genomes Ao Lan1,†, Kang Kang2,1,†, Senwei Tang1,2,†, Xiaoli Wu1,†, Lizhong Wang1, Teng Li1, Haoyi Weng2,1, Junjie Deng1, WeGene Research Team1,2, Qiang Zheng1,2, Xiaotian Yao1,* & Gang Chen1,2,3,* 1 WeGene, Shenzhen Zaozhidao Technology Co., Ltd., Shenzhen 518042, China 2 Shenzhen WeGene Clinical Laboratory, Shenzhen 518118, China 3 Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China † These authors contributed equally to this work. * Correspondence: Xiaotian Yao: [email protected] & Dr. Gang Chen: [email protected] ABSTRACT Han Chinese is the most populated ethnic group across the globe with a comprehensive substructure that resembles its cultural diversification. Studies have constructed the genetic polymorphism spectrum of Han Chinese, whereas high-resolution investigations are still missing to unveil its fine-scale substructure and trace the genetic imprints for its demographic history. Here we construct a haplotype network consisted of 111,000 genome-wide genotyped Han Chinese individuals from direct-to-consumer genetic testing and over 1.3 billion identity-by-descent (IBD) links. We observed a clear separation of the northern and southern Han Chinese and captured 5 subclusters and 17 sub-subclusters in haplotype network hierarchical clustering, corresponding to geography (especially mountain ranges), immigration waves, and clans with cultural-linguistic segregation.
    [Show full text]
  • From Warhorses to Ploughshares: the Later Tang Reign of Emperor Mingzong
    《中國文化研究所學報》 Journal of Chinese Studies No. 61 – July 2015 Book Reviews 353 From Warhorses to Ploughshares: The Later Tang Reign of Emperor Mingzong. By Richard L. Davis. Hong Kong: Hong Kong University Press, 2014. Pp. xiii + 219. $60.00. Within the emerging field of Five Dynasties and Ten States studies, starting with 1 Edward H. Schafer, Brigitte Amthor, and Wang Hongjie, biographies of rulers have played an important part. The present study of Emperor Mingzong 明宗 (r. 926–933) of the Later Tang 後唐 by Richard L. Davis is thus a most welcome addition. Davis conveniently summarizes the history of the Shatuo 沙陀 and Shatuo rule in northern China until the end of the Later Tang dynasty. Previous studies have examined Shatuo rule in the general context of Five Dynasties history whereas Davis singles out the reign of one ruler, that of the second Later Tang ruler Mingzong, whom he clearly sees as an exemplary “good” ruler in terms of his adoption of cultural policies and leanings towards peaceful policies. The writing style is fluid, and the contents covers much more than just the life of Mingzong. This book starts with a preface (pp. xi–xvi), followed by Chapter 1 “People and Places” (pp. 1–31), an introduction to Shatuo history, family relations, and the main political actors. Chapter 2 “Royal Passage” (pp. 33–61) describes the rise of Li Siyuan 李嗣源, the later Mingzong, to the throne of the Later Tang. Chapters 3 and 4 “Political Events” look at Mingzong’s reign according to his reign titles Tiancheng 天 成 (pp.
    [Show full text]
  • The Family of Chinese Character-Type Scripts (Twenty Members and Four Stages of Development)
    SINO-PLATONIC PAPERS Number 28 September, 1991 The Family of Chinese Character-Type Scripts (Twenty Members and Four Stages of Development) by ZHOU Youguang Victor H. Mair, Editor Sino-Platonic Papers Department of East Asian Languages and Civilizations University of Pennsylvania Philadelphia, PA 19104-6305 USA [email protected] www.sino-platonic.org SINO-PLATONIC PAPERS is an occasional series edited by Victor H. Mair. The purpose of the series is to make available to specialists and the interested public the results of research that, because of its unconventional or controversial nature, might otherwise go unpublished. The editor actively encourages younger, not yet well established, scholars and independent authors to submit manuscripts for consideration. Contributions in any of the major scholarly languages of the world, including Romanized Modern Standard Mandarin (MSM) and Japanese, are acceptable. In special circumstances, papers written in one of the Sinitic topolects (fangyan) may be considered for publication. Although the chief focus of Sino-Platonic Papers is on the intercultural relations of China with other peoples, challenging and creative studies on a wide variety of philological subjects will be entertained. This series is not the place for safe, sober, and stodgy presentations. Sino-Platonic Papers prefers lively work that, while taking reasonable risks to advance the field, capitalizes on brilliant new insights into the development of civilization. The only style-sheet we honor is that of consistency. Where possible, we prefer the usages of the Journal of Asian Studies. Sinographs (hanzi, also called tetragraphs [fangkuaizi]) and other unusual symbols should be kept to an absolute minimum.
    [Show full text]