Browsing by Author "Toomas Kivisild"

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Ancient human genomes suggest three ancestral populations for present-day Europeans
(Nature Publishing Group, 2014) Iosif Lazaridis; Nick Patterson; Alissa Mittnik; Gabriel Renaud; Swapan Mallick; Karola Kirsanow; Peter H. Sudmant; Joshua G. Schraiber; Sergi Castellano; Mark Lipson; Bonnie Berger; Christos Economou; Ruth Bollongino; Qiaomei Fu; Kirsten I. Bos; Susanne Nordenfelt; Heng Li; Cesare De Filippo; Kay Prüfer; Susanna Sawyer; Cosimo Posth; Wolfgang Haak; Fredrik Hallgren; Elin Fornander; Nadin Rohland; Dominique Delsate; Michael Francken; Jean-Michel Guinet; Joachim Wahl; George Ayodo; Hamza A. Babiker; Graciela Bailliet; Elena Balanovska; Oleg Balanovsky; Ramiro Barrantes; Gabriel Bedoya; Haim Ben-Ami; Judit Bene; Fouad Berrada; Claudio M. Bravi; Francesca Brisighelli; George B.J. Busby; Francesco Cali; Mikhail Churnosov; David E.C. Cole; Daniel Corach; Larissa Damba; George Van Driem; Stanislav Dryomov; Jean-Michel Dugoujon; Sardana A. Fedorova; Irene Gallego Romero; Marina Gubina; Michael Hammer; Brenna M. Henn; Tor Hervig; Ugur Hodoglugil; Aashish R. Jha; Sena Karachanak-Yankova; Rita Khusainova; Elza Khusnutdinova; Rick Kittles; Toomas Kivisild; William Klitz; Vaidutis Kučinskas; Alena Kushniarevich; Leila Laredj; Sergey Litvinov; Theologos Loukidis; Robert W. Mahley; Béla Melegh; Ene Metspalu; Julio Molina; Joanna Mountain; Klemetti Näkkäläjärvi; Desislava Nesheva; Thomas Nyambo; Ludmila Osipova; Jüri Parik; Fedor Platonov; Olga Posukh; Valentino Romano; Francisco Rothhammer; Igor Rudan; Ruslan Ruizbakiev; Hovhannes Sahakyan; Antti Sajantila; Antonio Salas; Elena B. Starikovskaya; Ayele Tarekegn; Draga Toncheva; Shahlo Turdikulova; Ingrida Uktveryte; Olga Utevska; René Vasquez; Mercedes Villena; Mikhail Voevoda; Cheryl A. Winkler; Levon Yepiskoposyan; Pierre Zalloua; Tatijana Zemunik; Alan Cooper; Cristian Capelli; Mark G. Thomas; Andres Ruiz-Linares; Sarah A. Tishkoff; Lalji Singh; Kumarasamy Thangaraj; Richard Villems; David Comas; Rem Sukernik; Mait Metspalu; Matthias Meyer; Evan E. Eichler; Joachim Burger; Montgomery Slatkin; Svante Pääbo; Janet Kelso; David Reich; Johannes Krause
We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes1-4 with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians3, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages. ©2014 Macmillan Publishers Limited. All rights reserved.
Author Correction: The genetic legacy of continental scale admixture in Indian Austroasiatic speakers (Scientific Reports, (2019), 9, 1, (3818), 10.1038/s41598-019-40399-8)
(Nature Publishing Group, 2019) Kai Tätte; Luca Pagani; Ajai K. Pathak; Sulev Kõks; Binh Ho Duy; Xuan Dung Ho; Gazi Nurun Nahar Sultana; Mohd Istiaq Sharif; Md Asaduzzaman; Doron M. Behar; Yarin Hadid; Richard Villems; Gyaneshwer Chaubey; Toomas Kivisild; Mait Metspalu
This Article contains errors in the Methods section, under subsection ‘Samples collection and genotyping’. “All genotyped data will be made publicly available on the ebc.ee/free_data website and NCBI-GEO public repository (accession number XXXX)”. should read: “All genotyped data will be made publicly available on the ebc.ee/free_data website and NCBI-GEO public repository (accession number GSE126882)”. © 2019, The Author(s).
Dissecting the paternal founders of Mundari (Austroasiatic) speakers associated with the language dispersal in South Asia
(Springer Nature, 2021) Prajjval Pratap Singh; Shani Vishwakarma; Gazi Nurun Nahar Sultana; Arno Pilvar; Monika Karmin; Siiri Rootsi; Richard Villems; Mait Metspalu; Doron M. Behar; Toomas Kivisild; George van Driem; Gyaneshwer Chaubey
The phylogenetic analysis of Y chromosomal haplogroup O2a-M95 was crucial to determine the nested structure of South Asian branches within the larger tree, predominantly present in East and Southeast Asia. However, it had previously been unclear that how many founders brought the haplogroup O2a-M95 to South Asia. On the basis of the updated Y chromosomal tree for haplogroup O2a-M95, we analysed 1437 male samples from South Asia for various novel downstream markers, carefully selected from the extant phylogenetic tree. With this increased resolution of genetic markers, we were able to identify at least three founders downstream to haplogroup O2a-M95, who are likely to have been associated with the dispersal of Austroasiatic languages to South Asia. The fourth founder was exclusively present amongst Tibeto-Burman speakers of Manipur and Bangladesh. In sum, our new results suggest the arrival of Austroasiatic languages in South Asia during last 5000 years. © 2020, The Author(s), under exclusive licence to European Society of Human Genetics.
Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia
(2011) Mait Metspalu; Irene Gallego Romero; Bayazit Yunusbayev; Gyaneshwer Chaubey; Chandana Basu Mallick; Georgi Hudjashov; Mari Nelis; Reedik Mägi; Ene Metspalu; Maido Remm; Ramasamy Pitchappan; Lalji Singh; Kumarasamy Thangaraj; Richard Villems; Toomas Kivisild
South Asia harbors one of the highest levels genetic diversity in Eurasia, which could be interpreted as a result of its long-term large effective population size and of admixture during its complex demographic history. In contrast to Pakistani populations, populations of Indian origin have been underrepresented in previous genomic scans of positive selection and population structure. Here we report data for more than 600,000 SNP markers genotyped in 142 samples from 30 ethnic groups in India. Combining our results with other available genome-wide data, we show that Indian populations are characterized by two major ancestry components, one of which is spread at comparable frequency and haplotype diversity in populations of South and West Asia and the Caucasus. The second component is more restricted to South Asia and accounts for more than 50% of the ancestry in Indian populations. Haplotype diversity associated with these South Asian ancestry components is significantly higher than that of the components dominating the West Eurasian ancestry palette. Modeling of the observed haplotype diversities suggests that both Indian ancestry components are older than the purported Indo-Aryan invasion 3,500 YBP. Consistent with the results of pairwise genetic distances among world regions, Indians share more ancestry signals with West than with East Eurasians. However, compared to Pakistani populations, a higher proportion of their genes show regionally specific signals of high haplotype homozygosity. Among such candidates of positive selection in India are MSTN and DOK5, both of which have potential implications in lipid metabolism and the etiology of type 2 diabetes. © 2011 The American Society of Human Genetics.
The Genetic Ancestry of Modern Indus Valley Populations from Northwest India
(Cell Press, 2018) Ajai K. Pathak; Anurag Kadian; Alena Kushniarevich; Francesco Montinaro; Mayukh Mondal; Linda Ongaro; Manvendra Singh; Pramod Kumar; Niraj Rai; Jüri Parik; Ene Metspalu; Siiri Rootsi; Luca Pagani; Toomas Kivisild; Mait Metspalu; Gyaneshwer Chaubey; Richard Villems
The Indus Valley has been the backdrop for several historic and prehistoric population movements between South Asia and West Eurasia. However, the genetic structure of present-day populations from Northwest India is poorly characterized. Here we report new genome-wide genotype data for 45 modern individuals from four Northwest Indian populations, including the Ror, whose long-term occupation of the region can be traced back to the early Vedic scriptures. Our results suggest that although the genetic architecture of most Northwest Indian populations fits well on the broader North-South Indian genetic cline, culturally distinct groups such as the Ror stand out by being genetically more akin to populations living west of India; such populations include prehistorical and early historical ancient individuals from the Swat Valley near the Indus Valley. We argue that this affinity is more likely a result of genetic continuity since the Bronze Age migrations from the Steppe Belt than a result of recent admixture. The observed patterns of genetic relationships both with modern and ancient West Eurasians suggest that the Ror can be used as a proxy for a population descended from the Ancestral North Indian (ANI) population. Collectively, our results show that the Indus Valley populations are characterized by considerable genetic heterogeneity that has persisted over thousands of years. © 2018 American Society of Human Genetics
The genetic legacy of continental scale admixture in Indian Austroasiatic speakers
(Nature Publishing Group, 2019) Kai Tätte; Luca Pagani; Ajai K. Pathak; Sulev Kõks; Binh Ho Duy; Xuan Dung Ho; Gazi Nurun Nahar Sultana; Mohd Istiaq Sharif; Md Asaduzzaman; Doron M. Behar; Yarin Hadid; Richard Villems; Gyaneshwer Chaubey; Toomas Kivisild; Mait Metspalu
Surrounded by speakers of Indo-European, Dravidian and Tibeto-Burman languages, around 11 million Munda (a branch of Austroasiatic language family) speakers live in the densely populated and genetically diverse South Asia. Their genetic makeup holds components characteristic of South Asians as well as Southeast Asians. The admixture time between these components has been previously estimated on the basis of archaeology, linguistics and uniparental markers. Using genome-wide genotype data of 102 Munda speakers and contextual data from South and Southeast Asia, we retrieved admixture dates between 2000–3800 years ago for different populations of Munda. The best modern proxies for the source populations for the admixture with proportions 0.29/0.71 are Lao people from Laos and Dravidian speakers from Kerala in India. The South Asian population(s), with whom the incoming Southeast Asians intermixed, had a smaller proportion of West Eurasian genetic component than contemporary proxies. Somewhat surprisingly Malaysian Peninsular tribes rather than the geographically closer Austroasiatic languages speakers like Vietnamese and Cambodians show highest sharing of IBD segments with the Munda. In addition, we affirmed that the grouping of the Munda speakers into North and South Munda based on linguistics is in concordance with genome-wide data. © 2019, The Author(s).
The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent
(2013) Chandana Basu Mallick; Florin Mircea Iliescu; Märt Möls; Sarah Hill; Rakesh Tamang; Gyaneshwer Chaubey; Rie Goto; Simon Y. W. Ho; Irene Gallego Romero; Federica Crivellaro; Georgi Hudjashov; Niraj Rai; Mait Metspalu; C. G. Nicholas Mascie-Taylor; Ramasamy Pitchappan; Lalji Singh; Marta Mirazon-Lahr; Kumarasamy Thangaraj; Richard Villems; Toomas Kivisild
Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22-28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India. © 2013 Basu Mallick et al.
The Phylogeography of Y-Chromosome Haplogroup H1a1a-M82 Reveals the Likely Indian Origin of the European Romani Populations
(2012) Niraj Rai; Gyaneshwer Chaubey; Rakesh Tamang; Ajai Kumar Pathak; Vipin Kumar Singh; Monika Karmin; Manvendra Singh; Deepa Selvi Rani; Sharath Anugula; Brijesh Kumar Yadav; Ashish Singh; Ramkumar Srinivasagan; Anita Yadav; Manju Kashyap; Sapna Narvariya; Alla G. Reddy; George van Driem; Peter A. Underhill; Richard Villems; Toomas Kivisild; Lalji Singh; Kumarasamy Thangaraj
Linguistic and genetic studies on Roma populations inhabited in Europe have unequivocally traced these populations to the Indian subcontinent. However, the exact parental population group and time of the out-of-India dispersal have remained disputed. In the absence of archaeological records and with only scanty historical documentation of the Roma, comparative linguistic studies were the first to identify their Indian origin. Recently, molecular studies on the basis of disease-causing mutations and haploid DNA markers (i.e. mtDNA and Y-chromosome) supported the linguistic view. The presence of Indian-specific Y-chromosome haplogroup H1a1a-M82 and mtDNA haplogroups M5a1, M18 and M35b among Roma has corroborated that their South Asian origins and later admixture with Near Eastern and European populations. However, previous studies have left unanswered questions about the exact parental population groups in South Asia. Here we present a detailed phylogeographical study of Y-chromosomal haplogroup H1a1a-M82 in a data set of more than 10,000 global samples to discern a more precise ancestral source of European Romani populations. The phylogeographical patterns and diversity estimates indicate an early origin of this haplogroup in the Indian subcontinent and its further expansion to other regions. Tellingly, the short tandem repeat (STR) based network of H1a1a-M82 lineages displayed the closest connection of Romani haplotypes with the traditional scheduled caste and scheduled tribe population groups of northwestern India. © 2012 Rai et al.
Unravelling the distinct strains of Tharu ancestry
(Nature Publishing Group, 2014) Gyaneshwer Chaubey; Manvendra Singh; Federica Crivellaro; Rakesh Tamang; Amrita Nandan; Kamayani Singh; Varun Kumar Sharma; Ajai Kumar Pathak; Anish M. Shah; Vishwas Sharma; Vipin Kumar Singh; Deepa Selvi Rani; Niraj Rai; Alena Kushniarevich; Anne-Mai Ilumäe; Monika Karmin; Anand Phillip; Abhilasha Verma; Erik Prank; Vijay Kumar Singh; Blaise Li; Periyasamy Govindaraj; Akhilesh Kumar Chaubey; Pavan Kumar Dubey; Alla G. Reddy; Kumpati Premkumar; Satti Vishnupriya; Veena Pande; Jüri Parik; Siiri Rootsi; Phillip Endicott; Mait Metspalu; Marta Mirazon Lahr; George Van Driem; Richard Villems; Toomas Kivisild; Lalji Singh; Kumarasamy Thangaraj
The northern region of the Indian subcontinent is a vast landscape interlaced by diverse ecologies, for example, the Gangetic Plain and the Himalayas. A great number of ethnic groups are found there, displaying a multitude of languages and cultures. The Tharu is one of the largest and most linguistically diverse of such groups, scattered across the Tarai region of Nepal and bordering Indian states. Their origins are uncertain. Hypotheses have been advanced postulating shared ancestry with Austroasiatic, or Tibeto-Burman-speaking populations as well as aboriginal roots in the Tarai. Several Tharu groups speak a variety of Indo-Aryan languages, but have traditionally been described by ethnographers as representing East Asian phenotype. Their ancestry and intra-population diversity has previously been tested only for haploid (mitochondrial DNA and Y-chromosome) markers in a small portion of the population. This study presents the first systematic genetic survey of the Tharu from both Nepal and two Indian states of Uttarakhand and Uttar Pradesh, using genome-wide SNPs and haploid markers. We show that the Tharu have dual genetic ancestry as up to one-half of their gene pool is of East Asian origin. Within the South Asian proportion of the Tharu genetic ancestry, we see vestiges of their common origin in the north of the South Asian Subcontinent manifested by mitochondrial DNA haplogroup M43. © 2014 Macmillan Publishers Limited All rights reserved.