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Sequeira JJ, Vinuthalakshmi K, Das R, van Driem G, Mustak MS. The maternal U1 haplogroup in the Koraga tribe as a correlate of their North Dravidian linguistic affinity. Front Genet 2024; 14:1303628. [PMID: 38384360 PMCID: PMC10880486 DOI: 10.3389/fgene.2023.1303628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/31/2023] [Indexed: 02/23/2024] Open
Abstract
Introduction: The Koraga tribe are an isolated endogamous tribal group found in the southwest coastal region of India. The Koraga language shares inherited grammatical features with North Dravidian languages. To seek a possible genetic basis for this exceptionality and understand the maternal lineage pattern, we have aimed to reconstruct the inter-population and intra-population relationships of the Koraga tribal population by using mtDNA markers for the hypervariable regions along with a partial coding region sequence analysis. Methods and Results: Amongst the 96 individuals studied, we observe 11 haplogroups, of which a few are shared and others are unique to the clans Soppu, Oṇṭi and Kuṇṭu. In addition to several deep rooted Indian-specific lineages of macrohaplogroups M and U, we observe a high frequency of the U1 lineage (∼38%), unique to the Koraga. A Bayesian analysis of the U1 clade shows that the Koraga tribe share their maternal lineage with ancestral populations of the Caucasus at the cusp of the Last Glacial Maximum. Discussion: Our study suggests that the U1 lineage found in the Indian subcontinent represents a remnant of a post-glacial dispersal. The presence of West Asian U1 when viewed along with historical linguistics leads us to hypothesise that Koraga represents a mother tongue retained by a vanquished population group that fled southward at the demise of the Indus civilisation as opposed to a father tongue, associated with a particular paternal lineage.
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Affiliation(s)
| | | | - Ranajit Das
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland
| | - Mohammed S. Mustak
- Department of Applied Zoology, Mangalore University, Mangalore, Karnataka, India
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2
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Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q. Forensic Sci Int Genet 2022; 59:102708. [DOI: 10.1016/j.fsigen.2022.102708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/18/2022]
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3
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Contrasting maternal and paternal genetic histories among five ethnic groups from Khyber Pakhtunkhwa, Pakistan. Sci Rep 2022; 12:1027. [PMID: 35046511 PMCID: PMC8770644 DOI: 10.1038/s41598-022-05076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 12/10/2021] [Indexed: 11/24/2022] Open
Abstract
Northwest Pakistan has served as a point of entry to South Asia for different populations since ancient times. However, relatively little is known about the population genetic history of the people residing within this region. To better understand human dispersal in the region within the broader history of the subcontinent, we analyzed mtDNA diversity in 659 and Y-chromosome diversity in 678 individuals, respectively, from five ethnic groups (Gujars, Jadoons, Syeds, Tanolis and Yousafzais), from Swabi and Buner Districts, Khyber Pakhtunkhwa Province, Pakistan. The mtDNAs of all individuals were subject to control region sequencing and SNP genotyping, while Y-chromosomes were analyzed using 54 SNPs and 19 STR loci. The majority of the mtDNAs belonged to West Eurasian haplogroups, with the rest belonging to either South or East Asian lineages. Four of the five Pakistani populations (Gujars, Jadoons, Syeds, Yousafzais) possessed strong maternal genetic affinities with other Pakistani and Central Asian populations, whereas one (Tanolis) did not. Four haplogroups (R1a, R1b, O3, L) among the 11 Y-chromosome lineages observed among these five ethnic groups contributed substantially to their paternal genetic makeup. Gujars, Syeds and Yousafzais showed strong paternal genetic affinities with other Pakistani and Central Asian populations, whereas Jadoons and Tanolis had close affinities with Turkmen populations from Central Asia and ethnic groups from northeast India. We evaluate these genetic data in the context of historical and archeological evidence to test different hypotheses concerning their origins and biological relationships.
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4
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Genetic insights into the paternal admixture history of Chinese Mongolians via high-resolution customized Y-SNP SNaPshot panels. Forensic Sci Int Genet 2021; 54:102565. [PMID: 34332322 DOI: 10.1016/j.fsigen.2021.102565] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/10/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
Abstract
The Mongolian people, one of the Mongolic-speaking populations, are native to the Mongolian Plateau in North China and southern Siberia. Many ancient DNA studies recently reported extensive population transformations during the Paleolithic to historic periods in this region, while little is known about the paternal genetic legacy of modern geographically different Mongolians. Here, we genotyped 215 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) and 37 Y-chromosomal short tandem repeats (Y-STRs) among 679 Mongolian individuals from Hohhot, Hulunbuir, and Ordos in North China using the AGCU Y37 kit and our developed eight Y-SNP SNaPshot panels (including two panels first reported herein). The C-M130 Y-SNP SNaPshot panel defines 28 subhaplogroups, and the N/O/Q complementary Y-SNP SNaPshot panel defines 30 subhaplogroups of N1b-F2930, N1a1a1a1a3-B197, Q-M242, and O2a2b1a1a1a4a-CTS4658, which improved the resolution our developed Y-SNP SNaPshot panel set and could be applied for dissecting the finer-scale paternal lineages of Mongolic speakers. We found a strong association between Mongolian-prevailing haplogroups and some observed microvariants among the newly generated Y-STR haplotype data, suggesting the possibility of haplogroup prediction based on the distribution of Y-STR haplotypes. We identified three main ancestral sources of the observed Mongolian-dominant haplogroups, including the local lineage of C2*-M217 and incoming lineages from other regions of southern East Asia (O2*-M122, O1b*-P31, and N1*-CTS3750) and western Eurasia (R1*-M173). We also observed DE-M145, D1*-M174, C1*-F3393, G*-M201, I-M170, J*-M304, L-M20, O1a*-M119, and Q*-M242 at relatively low frequencies (< 5.00%), suggesting a complex admixture history between Mongolians and other incoming Eurasians from surrounding regions. Genetic clustering analyses indicated that the studied Mongolians showed close genetic affinities with other Altaic-speaking populations and Sinitic-speaking Hui people. The Y-SNP haplotype/haplogroup-based genetic legacy not only revealed that the stratification among geographically/linguistically/ethnically different Chinese populations was highly consistent with the geographical division and language classification, but also demonstrated that patrilineal genetic materials could provide fine-scale genetic structures among geographically different Mongolian people, suggesting that our developed high-resolution Y-SNP SNaPshot panels have the potential for forensic pedigree searches and biogeographical ancestry inference.
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5
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Yang XY, Rakha A, Chen W, Hou J, Qi XB, Shen QK, Dai SS, Sulaiman X, Abdulloevich NT, Afanasevna ME, Ibrohimovich KB, Chen X, Yang WK, Adnan A, Zhao RH, Yao YG, Su B, Peng MS, Zhang YP. Tracing the Genetic Legacy of the Tibetan Empire in the Balti. Mol Biol Evol 2021; 38:1529-1536. [PMID: 33283852 PMCID: PMC8042757 DOI: 10.1093/molbev/msaa313] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The rise and expansion of Tibetan Empire in the 7th to 9th centuries AD affected the course of history across East Eurasia, but the genetic impact of Tibetans on surrounding populations remains undefined. We sequenced 60 genomes for four populations from Pakistan and Tajikistan to explore their demographic history. We showed that the genomes of Balti people from Baltistan comprised 22.6–26% Tibetan ancestry. We inferred a single admixture event and dated it to about 39–21 generations ago, a period that postdated the conquest of Baltistan by the ancient Tibetan Empire. The analyses of mitochondrial DNA, Y, and X chromosome data indicated that both ancient Tibetan males and females were involved in the male-biased dispersal. Given the fact that the Balti people adopted Tibetan language and culture in history, our study suggested the impact of Tibetan Empire on Baltistan involved dominant cultural and minor demic diffusion.
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Affiliation(s)
- Xing-Yan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wei Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Juzhi Hou
- Key Laboratory of Alpine Ecology (LAE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Xue-Bin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Quan-Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Shan-Shan Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Xierzhatijiang Sulaiman
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Manilova Elena Afanasevna
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, Tajikistan
| | | | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Wei-Kang Yang
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Atif Adnan
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, China
| | - Ruo-Han Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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6
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Zadran SK, Rahman G, Ilyas M, ShamsiaDawari. Genetic characterization of the Afghan population: Analysis of mitochondrial DNA control region variation. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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7
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Zubair M, Hemphill BE, Schurr TG, Tariq M, Ilyas M, Ahmad H. Mitochondrial DNA diversity in the Khattak and Kheshgi of the Peshawar Valley, Pakistan. Genetica 2020; 148:195-206. [PMID: 32607672 DOI: 10.1007/s10709-020-00095-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/12/2020] [Indexed: 11/29/2022]
Abstract
The strategic location of Pakistan and its presence at the crossroads of Asia has resulted in it playing a central role in both prehistoric and historic human migratory events, thereby linking and facilitating contacts between the inhabitants of the Middle East, Central Asia, China and South Asia. Despite the importance of this region and its inhabitants for our understanding of modern human origins and population dispersals, the nature of mitochondrial DNA (mtDNA) variation among members of the myriad populations of this area has largely been unexplored. Here, we report mtDNA control region sequences in 58 individuals from the Khattak and the Kheshgi, two major Pakhtun tribes residing within the Peshawar Valley of northwestern Pakistan. The results reveal that these ethnic groups are genetically heterogeneous, having 55.7% West Eurasian, 33.9% South Asian and 10.2% East Asian haplogroups. The genetic diversity observed for the Kheshgi was somewhat higher than that of the Khattak. A multidimensional scaling plot based on haplogroup frequencies for the Khattak, Kheshgi and neighboring populations indicates that the Khattak have close affinities with Baluch, Uzbek and Kazak populations but are only distantly related to the Kheshgi and other Pakistani populations. By contrast, the Kheshgi cluster closely with other Pakhtun or Pathan populations of Pakistan, suggesting a possible common maternal gene pool shared amongst them. These mtDNA data allow us to begin reconstructing the origins of the Khattak and Kheshgi and describe their complex interactions with populations from the surrounding regions.
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Affiliation(s)
- Muhammad Zubair
- Department of Zoology, Hazara University Mansehra, Mansehra, 21120, Pakistan.,Department of Genetics, Hazara University Mansehra, Mansehra, 21120, Pakistan
| | - Brian E Hemphill
- Department of Anthropology, University of Alaska, Fairbanks, AK, 99775, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Muhammad Tariq
- Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan
| | - Muhammad Ilyas
- Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan
| | - Habib Ahmad
- Department of Genetics, Hazara University Mansehra, Mansehra, 21120, Pakistan. .,Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan.
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8
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Syama A, Arun VS, ArunKumar G, Subhadeepta R, Friese K, Pitchappan R. Origin and identity of the Brokpa of Dah-Hanu, Himalayas – an NRY-HG L1a2 (M357) legacy. Ann Hum Biol 2019; 46:562-573. [DOI: 10.1080/03014460.2019.1694700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Adikarla Syama
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
- Department of Biotechnology, Faculty of Engineering and Technology, Manav Rachana, International University, Faridabad, India
| | | | - GaneshPrasad ArunKumar
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
- Human Genomics Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thirumalaisamudram, India
| | | | | | - Ramasamy Pitchappan
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
- Nilgiri Adivasi Welfare Association, Kotagiri, India
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9
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Luis JR, Lacau H, Fadhlaoui-Zid K, Alfonso-Sanchez MA, Garcia-Bertrand R, Herrera RJ. Afghanistan: conduits of human migrations identified using AmpFlSTR markers. Int J Legal Med 2019; 133:1659-1666. [DOI: 10.1007/s00414-019-02018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/05/2019] [Indexed: 10/27/2022]
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10
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Pigeyre M, Saqlain M, Turcotte M, Raja GK, Meyre D. Obesity genetics: insights from the Pakistani population. Obes Rev 2018; 19:364-380. [PMID: 29265593 DOI: 10.1111/obr.12644] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/10/2017] [Accepted: 10/15/2017] [Indexed: 01/26/2023]
Abstract
The Pakistani population is extensively diverse, indicating a genetic admixture of European and Central/West Asian migrants with indigenous South Asian gene pools. Pakistanis are organized in different ethnicities/castes based on cultural, linguistic and geographical origin. While Pakistan is facing a rapid nutritional transition, the rising prevalence of obesity is driving a growing burden of health complications and mortality. This represents a unique opportunity for the research community to study the interplay between obesogenic environmental changes and obesity predisposing genes in the time frame of one generation. This review recapitulates the ancestral origins of Pakistani population, the societal determinants of the rise in obesity and its governmental management. We describe the contribution of syndromic, monogenic non-syndromic and polygenic obesity genes identified in the Pakistani population. We then discuss the utility of gene identification approaches based on large consanguineous families and original gene × environment interaction study designs in discovering new obesity genes and causal pathways. Elucidation of the genetic basis of obesity in the Pakistani population may result in improved methods of obesity prevention and treatment globally.
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Affiliation(s)
- M Pigeyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Department of Nutrition, CHRU Lille, University of Lille, Lille, France
| | - M Saqlain
- Department of Biochemistry, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - M Turcotte
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - G K Raja
- Department of Biochemistry, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - D Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
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11
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Huang YZ, Pamjav H, Flegontov P, Stenzl V, Wen SQ, Tong XZ, Wang CC, Wang LX, Wei LH, Gao JY, Jin L, Li H. Dispersals of the Siberian Y-chromosome haplogroup Q in Eurasia. Mol Genet Genomics 2018; 293:107-117. [PMID: 28884289 PMCID: PMC5846874 DOI: 10.1007/s00438-017-1363-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 08/27/2017] [Indexed: 12/17/2022]
Abstract
The human Y-chromosome has proven to be a powerful tool for tracing the paternal history of human populations and genealogical ancestors. The human Y-chromosome haplogroup Q is the most frequent haplogroup in the Americas. Previous studies have traced the origin of haplogroup Q to the region around Central Asia and Southern Siberia. Although the diversity of haplogroup Q in the Americas has been studied in detail, investigations on the diffusion of haplogroup Q in Eurasia and Africa are still limited. In this study, we collected 39 samples from China and Russia, investigated 432 samples from previous studies of haplogroup Q, and analyzed the single nucleotide polymorphism (SNP) subclades Q1a1a1-M120, Q1a2a1-L54, Q1a1b-M25, Q1a2-M346, Q1a2a1a2-L804, Q1a2b2-F1161, Q1b1a-M378, and Q1b1a1-L245. Through NETWORK and BATWING analyses, we found that the subclades of haplogroup Q continued to disperse from Central Asia and Southern Siberia during the past 10,000 years. Apart from its migration through the Beringia to the Americas, haplogroup Q also moved from Asia to the south and to the west during the Neolithic period, and subsequently to the whole of Eurasia and part of Africa.
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Affiliation(s)
- Yun-Zhi Huang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Horolma Pamjav
- National Center of Forensic Experts and Research, Budapest, 1087, Hungary
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 71000, Ostrava, Czech Republic
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russian Federation
| | - Vlastimil Stenzl
- Institute of Criminalistics, Police of the Czech Republic, 17089, Prague, Czech Republic
| | - Shao-Qing Wen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xin-Zhu Tong
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, 361005, China
| | - Ling-Xiang Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lan-Hai Wei
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Institut National des Langues et Civilisations Orientales, 75013, Paris, France
| | - Jing-Yi Gao
- Faculty of Arts and Humanities, University of Tartu, 50090, Tartu, Estonia
- Faculty of Central European Studies, Beijing International Studies University, Beijing, 100024, China
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hui Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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12
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Balanovsky O, Gurianov V, Zaporozhchenko V, Balaganskaya O, Urasin V, Zhabagin M, Grugni V, Canada R, Al-Zahery N, Raveane A, Wen SQ, Yan S, Wang X, Zalloua P, Marafi A, Koshel S, Semino O, Tyler-Smith C, Balanovska E. Phylogeography of human Y-chromosome haplogroup Q3-L275 from an academic/citizen science collaboration. BMC Evol Biol 2017; 17:18. [PMID: 28251872 PMCID: PMC5333174 DOI: 10.1186/s12862-016-0870-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background The Y-chromosome haplogroup Q has three major branches: Q1, Q2, and Q3. Q1 is found in both Asia and the Americas where it accounts for about 90% of indigenous Native American Y-chromosomes; Q2 is found in North and Central Asia; but little is known about the third branch, Q3, also named Q1b-L275. Here, we combined the efforts of population geneticists and genetic genealogists to use the potential of full Y-chromosome sequencing for reconstructing haplogroup Q3 phylogeography and suggest possible linkages to events in population history. Results We analyzed 47 fully sequenced Y-chromosomes and reconstructed the haplogroup Q3 phylogenetic tree in detail. Haplogroup Q3-L275, derived from the oldest known split within Eurasian/American haplogroup Q, most likely occurred in West or Central Asia in the Upper Paleolithic period. During the Mesolithic and Neolithic epochs, Q3 remained a minor component of the West Asian Y-chromosome pool and gave rise to five branches (Q3a to Q3e), which spread across West, Central and parts of South Asia. Around 3–4 millennia ago (Bronze Age), the Q3a branch underwent a rapid expansion, splitting into seven branches, some of which entered Europe. One of these branches, Q3a1, was acquired by a population ancestral to Ashkenazi Jews and grew within this population during the 1st millennium AD, reaching up to 5% in present day Ashkenazi. Conclusions This study dataset was generated by a massive Y-chromosome genotyping effort in the genetic genealogy community, and phylogeographic patterns were revealed by a collaboration of population geneticists and genetic genealogists. This positive experience of collaboration between academic and citizen science provides a model for further joint projects. Merging data and skills of academic and citizen science promises to combine, respectively, quality and quantity, generalization and specialization, and achieve a well-balanced and careful interpretation of the paternal-side history of human populations. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0870-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oleg Balanovsky
- Vavilov Institute of General Genetics, Moscow, Russia. .,Research Centre for Medical Genetics, Moscow, Russia.
| | | | - Valery Zaporozhchenko
- Vavilov Institute of General Genetics, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia
| | | | | | - Maxat Zhabagin
- National Laboratory Astana, Nazarbayev University, Astana, Republic of Kazakhstan
| | - Viola Grugni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | | | - Nadia Al-Zahery
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Shao-Qing Wen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shi Yan
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xianpin Wang
- Department of Criminal Investigation, Xuanwei Public Security Bureau, Xuanwei, China
| | | | | | - Sergey Koshel
- Faculty of Geography, Lomonosov Moscow State University, Moscow, Russia
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elena Balanovska
- Vavilov Institute of General Genetics, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia
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13
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Molecular Genealogy of a Mongol Queen's Family and Her Possible Kinship with Genghis Khan. PLoS One 2016; 11:e0161622. [PMID: 27627454 PMCID: PMC5023095 DOI: 10.1371/journal.pone.0161622] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 07/12/2016] [Indexed: 11/28/2022] Open
Abstract
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.
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Bhatti S, Aslamkhan M, Abbas S, Attimonelli M, Aydin HH, de Souza EMS. Genetic analysis of mitochondrial DNA control region variations in four tribes of Khyber Pakhtunkhwa, Pakistan. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:687-697. [PMID: 27159729 DOI: 10.3109/24701394.2016.1174222] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Due to its geo strategic position at the crossroad of Asia, Pakistan has gained crucial importance of playing its pivotal role in subsequent human migratory events, both prehistoric and historic. This human movement became possible through an ancient overland network of trails called "The Silk Route" linking Asia Minor, Middle East China, Central Asia and Southeast Asia. This study was conducted to analyze complete mitochondrial control region samples of 100 individuals of four major Pashtun tribes namely, Bangash, Khattak, Mahsuds and Orakzai in the province of Khyber Pakhtunkhwa, Pakistan. All Pashtun tribes revealed high genetic diversity which is comparable to the other Central Asian, Southeast Asian and European populations. The configuration of genetic variation and heterogeneity further unveiled through Multidimensional Scaling, Principal Component Analysis and phylogenetic analysis. The results revealed that Pashtun are the composite mosaic of West Eurasian ancestry of numerous geographic origin. They received substantial gene flow during different invasive movements and have a high element of the Western provenance. The most common haplogroups reported in this study are: South Asian haplogroups M (28%) and R (8%); whereas, West Asians haplogroups are present, albeit in high frequencies (67%) and widespread over all; HV (15%), U (17%), H (9%), J (8%), K (8%), W (4%), N (3%) and T (3%). Moreover, we linked the unexplored genetic connection between Ashkenazi Jews and Pashtun. The presence of specific haplotypes J1b (4%) and K1a1b1a (5%) pointed to a genetic connection of Jewish conglomeration in Khattak tribe. This was a result of an ancient genetic influx in the early Neolithic period that led to the formation of a diverse genetic substratum in present day Pashtun.
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Affiliation(s)
- Shahzad Bhatti
- a Department of Human Genetics and Molecular Biology , University of Health Sciences Lahore , Pakistan.,b Institute of Molecular Biology and Biotechnology, University of Lahore , Lahore , Pakistan
| | - M Aslamkhan
- a Department of Human Genetics and Molecular Biology , University of Health Sciences Lahore , Pakistan
| | - Sana Abbas
- b Institute of Molecular Biology and Biotechnology, University of Lahore , Lahore , Pakistan
| | - Marcella Attimonelli
- c Department of Biosciences, Biotechnologies and Biopharmaceutics , University of Bari , Italy
| | - Hikmet Hakan Aydin
- d Department of Medical Biochemistry , Ege University School of Medicine , Bornova Izmir , Turkey
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Genetic and Cultural Reconstruction of the Migration of an Ancient Lineage. BIOMED RESEARCH INTERNATIONAL 2015; 2015:651415. [PMID: 26491681 PMCID: PMC4605215 DOI: 10.1155/2015/651415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 08/24/2015] [Accepted: 08/25/2015] [Indexed: 11/17/2022]
Abstract
A rare R1a1 Y-haplogroup (Y-HG) L657 clade subtype designated as LPKSTR is found in most male members of a clan of "founder" families within the Goud Saraswat Brahmin community in Lotli town in Western India. TMRCA calculations using pairwise comparisons to control cohorts suggested a probable migration history distinct from the canonical narrative for medieval migration of orthodox Brahmin families to South India. Using Y-HG centroid analysis, chi-square analysis of TMRCA distributions and archeological find-spots, and discriminant function analysis we show that the parental Z93 L342.2 subclade in which LPKSTR occurs originated in West Asia and that LPKSTR individuals migrated toward the southeast by a Bolan Pass route distinct from the traditionally presumed route of Brahmin ingress into the Indian subcontinent. The proposed migration route is supported by archeological, toponymic, numismatic, linguistic, iconographic, and literary data. Lastly, we present cultural metrics demonstrating that these LPKSTR lineages retained distinct family practices with respect to literacy, religious practice, and emigration not shared with orthodox Brahmins of canonical geographic origin within the same community, despite centuries of intermarriage. Long-term transmission of differentiated family practices within a patrilineal endogamous community has rarely been documented.
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Ladakh, India: the land of high passes and genetic heterogeneity reveals a confluence of migrations. Eur J Hum Genet 2015; 24:442-9. [PMID: 25966630 DOI: 10.1038/ejhg.2015.80] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 03/18/2015] [Accepted: 03/20/2015] [Indexed: 01/26/2023] Open
Abstract
Owing to its geographic location near the longitudinal center of Asia, Ladakh, the land of high passes, has witnessed numerous demographic movements during the past millenniums of occupation. In an effort to view Ladakh's multicultural history from a paternal genetic perspective, we performed a high-resolution Y-chromosomal survey of Ladakh, within the context of Y haplogroup and haplotype distributions of 41 Asian reference populations. The results of this investigation highlight the rich ethnic and genetic diversity of Ladkah which includes genetic contributions from disparate regions of the continent including, West, East, South and Central Asia. The phylogenetic signals from Ladakh are consistent with the Indo-Aryans' occupation during the Neolithic age and its historic connection with Tibet, as well as the East-West gene flow associated with the Silk Road.
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Zeng YW, Du J, Pu XY, Yang JZ, Yang T, Yang SM, Yang XM. Coevolution between Human's Anticancer Activities and Functional Foods from Crop Origin Center in the World. Asian Pac J Cancer Prev 2015; 16:2119-28. [DOI: 10.7314/apjcp.2015.16.6.2119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Ralf A, van Oven M, Zhong K, Kayser M. Simultaneous analysis of hundreds of Y-chromosomal SNPs for high-resolution paternal lineage classification using targeted semiconductor sequencing. Hum Mutat 2014; 36:151-9. [PMID: 25338970 DOI: 10.1002/humu.22713] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 10/08/2014] [Indexed: 11/06/2022]
Abstract
SNPs from the non-recombining part of the human Y chromosome (Y-SNPs) are informative to classify paternal lineages in forensic, genealogical, anthropological, and evolutionary studies. Although thousands of Y-SNPs were identified thus far, previous Y-SNP multiplex tools target only dozens of markers simultaneously, thereby restricting the provided Y-haplogroup resolution and limiting their applications. Here, we overcome this shortcoming by introducing a high-resolution multiplex tool for parallel genotyping-by-sequencing of 530 Y-SNPs using the Ion Torrent PGM platform, which allows classification of 432 worldwide Y haplogroups. Contrary to previous Y-SNP multiplex tools, our approach covers branches of the entire Y tree, thereby maximizing the paternal lineage classification obtainable. We used a default DNA input amount of 10 ng per reaction but preliminary sensitivity testing revealed positive results from as little as 100 pg input DNA. Furthermore, we demonstrate that sample pooling using barcodes is feasible, allowing increased throughput for lower per-sample costs. In addition to the wetlab protocol, we provide a software tool for automated data quality control and haplogroup classification. The unique combination of ultra-high marker density and high sensitivity achievable from low amounts of potentially degraded DNA makes this new multiplex tool suitable for a wide range of Y-chromosome applications.
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Affiliation(s)
- Arwin Ralf
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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19
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Di Cristofaro J, Pennarun E, Mazières S, Myres NM, Lin AA, Temori SA, Metspalu M, Metspalu E, Witzel M, King RJ, Underhill PA, Villems R, Chiaroni J. Afghan Hindu Kush: where Eurasian sub-continent gene flows converge. PLoS One 2013; 8:e76748. [PMID: 24204668 PMCID: PMC3799995 DOI: 10.1371/journal.pone.0076748] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 08/29/2013] [Indexed: 01/09/2023] Open
Abstract
Despite being located at the crossroads of Asia, genetics of the Afghanistan populations have been largely overlooked. It is currently inhabited by five major ethnic populations: Pashtun, Tajik, Hazara, Uzbek and Turkmen. Here we present autosomal from a subset of our samples, mitochondrial and Y- chromosome data from over 500 Afghan samples among these 5 ethnic groups. This Afghan data was supplemented with the same Y-chromosome analyses of samples from Iran, Kyrgyzstan, Mongolia and updated Pakistani samples (HGDP-CEPH). The data presented here was integrated into existing knowledge of pan-Eurasian genetic diversity. The pattern of genetic variation, revealed by structure-like and Principal Component analyses and Analysis of Molecular Variance indicates that the people of Afghanistan are made up of a mosaic of components representing various geographic regions of Eurasian ancestry. The absence of a major Central Asian-specific component indicates that the Hindu Kush, like the gene pool of Central Asian populations in general, is a confluence of gene flows rather than a source of distinctly autochthonous populations that have arisen in situ: a conclusion that is reinforced by the phylogeography of both haploid loci.
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Affiliation(s)
| | - Erwan Pennarun
- Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Stéphane Mazières
- Aix Marseille Université, ADES UMR7268, CNRS, EFS-AM, Marseille, France
| | - Natalie M. Myres
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | - Alice A. Lin
- Department of Psychiatry, Stanford University School of Medicine, Stanford, California, United States of America
| | - Shah Aga Temori
- Department of Biochemistry, Kabul Medical University, Kabul, Afghanistan
| | - Mait Metspalu
- Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Ene Metspalu
- Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Michael Witzel
- Department of South Asian Studies, Harvard University. Cambridge, Massachusetts, United States of America
| | - Roy J. King
- Department of Psychiatry, Stanford University School of Medicine, Stanford, California, United States of America
| | - Peter A. Underhill
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Richard Villems
- Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
| | - Jacques Chiaroni
- Aix Marseille Université, ADES UMR7268, CNRS, EFS-AM, Marseille, France
- * E-mail:
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20
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Y-chromosome diversity in the Kalmyks at the ethnical and tribal levels. J Hum Genet 2013; 58:804-11. [DOI: 10.1038/jhg.2013.108] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/16/2013] [Accepted: 09/27/2013] [Indexed: 01/15/2023]
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21
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Indigenous and foreign Y-chromosomes characterize the Lingayat and Vokkaliga populations of Southwest India. Gene 2013; 526:96-106. [DOI: 10.1016/j.gene.2013.04.074] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 04/25/2013] [Accepted: 04/26/2013] [Indexed: 11/21/2022]
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Grugni V, Battaglia V, Hooshiar Kashani B, Parolo S, Al-Zahery N, Achilli A, Olivieri A, Gandini F, Houshmand M, Sanati MH, Torroni A, Semino O. Ancient migratory events in the Middle East: new clues from the Y-chromosome variation of modern Iranians. PLoS One 2012; 7:e41252. [PMID: 22815981 PMCID: PMC3399854 DOI: 10.1371/journal.pone.0041252] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 06/19/2012] [Indexed: 11/18/2022] Open
Abstract
Knowledge of high resolution Y-chromosome haplogroup diversification within Iran provides important geographic context regarding the spread and compartmentalization of male lineages in the Middle East and southwestern Asia. At present, the Iranian population is characterized by an extraordinary mix of different ethnic groups speaking a variety of Indo-Iranian, Semitic and Turkic languages. Despite these features, only few studies have investigated the multiethnic components of the Iranian gene pool. In this survey 938 Iranian male DNAs belonging to 15 ethnic groups from 14 Iranian provinces were analyzed for 84 Y-chromosome biallelic markers and 10 STRs. The results show an autochthonous but non-homogeneous ancient background mainly composed by J2a sub-clades with different external contributions. The phylogeography of the main haplogroups allowed identifying post-glacial and Neolithic expansions toward western Eurasia but also recent movements towards the Iranian region from western Eurasia (R1b-L23), Central Asia (Q-M25), Asia Minor (J2a-M92) and southern Mesopotamia (J1-Page08). In spite of the presence of important geographic barriers (Zagros and Alborz mountain ranges, and the Dasht-e Kavir and Dash-e Lut deserts) which may have limited gene flow, AMOVA analysis revealed that language, in addition to geography, has played an important role in shaping the nowadays Iranian gene pool. Overall, this study provides a portrait of the Y-chromosomal variation in Iran, useful for depicting a more comprehensive history of the peoples of this area as well as for reconstructing ancient migration routes. In addition, our results evidence the important role of the Iranian plateau as source and recipient of gene flow between culturally and genetically distinct populations.
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Affiliation(s)
- Viola Grugni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | | | - Silvia Parolo
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Nadia Al-Zahery
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Massoud Houshmand
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohammad Hossein Sanati
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
- Centro Interdipartimentale “Studi di Genere”, Università di Pavia, Pavia, Italy
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