Browsing by Author "Rakesh Tamang"

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Complex genetic origin of Indian populations and its implications
(2012) Rakesh Tamang; Lalji Singh; Kumarasamy Thangaraj
Indian populations are classified into various caste, tribe and religious groups, which altogether makes them very unique compared to rest of the world. The long-term firm socio-religious boundaries and the strict endogamy practices along with the evolutionary forces have further supplemented the existing high-level diversity. As a result, drawing definite conclusions on its overall origin, affinity, health and disease conditions become even more sophisticated than was thought earlier. In spite of these challenges, researchers have undertaken tireless and extensive investigations using various genetic markers to estimate genetic variation and its implication in health and diseases. We have demonstrated that the Indian populations are the descendents of the very first modern humans, who ventured the journey of out-of-Africa about 65,000 years ago. The recent gene flow from east and west Eurasia is also evident. Thus, this review attempts to summarize the unique genetic variation among Indian populations as evident from our extensive study among approximately 20,000 samples across India. © Indian Academy of Sciences.
COVID-19: Impact on linguistic and genetic isolates of India
(Springer Nature, 2022) Prajjval Pratap Singh; Prashanth Suravajhala; Chandana Basu Mallick; Rakesh Tamang; Ashutosh Kumar Rai; Pratheusa Machha; Royana Singh; Abhishek Pathak; Vijay Nath Mishra; Pankaj Shrivastava; Keshav K. Singh; Kumarasamy Thangaraj; Gyaneshwer Chaubey
The rapid expansion of coronavirus SARS-CoV-2 has impacted various ethnic groups all over the world. The burden of infectious diseases including COVID-19 are generally reported to be higher for the Indigenous people. The historical knowledge have also suggested that the indigenous populations suffer more than the general populations in the pandemic. Recently, it has been reported that the indigenous groups of Brazil have been massively affected by COVID-19. Series of studies have shown that many of the indigenous communities reached at the verge of extinction due to this pandemic. Importantly, South Asia also has several indigenous and smaller communities, that are living in isolation. Till date, despite the two consecutive waves in India, there is no report on the impact of COVID-19 for indigenous tribes. Since smaller populations experiencing drift may have greater risk of such pandemic, we have analysed Runs of Homozygosity (ROH) among South Asian populations and identified several populations with longer homozygous segments. The longer runs of homozygosity at certain genomic regions may increases the susceptibility for COVID-19. Thus, we suggest extreme careful management of this pandemic among isolated populations of South Asia. © 2021, The Author(s), under exclusive licence to Springer Nature Limited.
Frogs from the Darjeeling Hill Region, India: Elucidation of their morphology and habitat
(Springer, 2025) Kumaresh Mandal; Shishir Tamang; Soni Subba; Divya Rai; Saptaparni De; Aditya Pradhan; Kaushik Deuti; G. Chaubey; Rakesh Tamang
The Darjeeling Hill Region (DHR) comprises the hilly areas of Darjeeling and Kalimpong districts in West Bengal, India. It’s an important part of the Himalayas biodiversity hotspot and is renowned for its enormous biodiversity and enchanting natural beauty. It has variations in altitude, vegetation, temperature, and rainfall. Mainly, the structure and composition of the habitat change along the altitudinal gradients. The enormous biodiversity in the DHR includes several frog species. Frogs play a vital role in the ecological food chain and are an efficient indicator of environmental health. Abundant information is available on the frogs from southern India, however, frogs from the DHR are less studied. Therefore, this study for the first time intends to enlist and examine major frog species from the DHR using morphological tools and documentary evidence. Additionally, detailed accounts of their habitat are elaborated. The survey was conducted from 2020 to 2023 mostly in rainy seasons. Nine species of frogs belonging to seven genera and four major families (Dicroglossidae, Ranidae, Rhachophoridae, and Megophryidae) were observed in the DHR. These frogs were mostly spotted in forests, hill streams, and bushes including tea plants. Interestingly, a well-segregated niche was observed for most of the frogs. Upon comparison, some frogs had slightly variable morphology that may be attributed to their adaptation to specific habitats and prey selection. This work serves as a baseline study and aims to bridge the existing gap in understanding the Indian frog diversity and is expected to aid in framing guidelines for their conservation. © Zoological Society, Kolkata, India 2025.
Genetic affinities of the central Indian tribal populations
(2012) Gunjan Sharma; Rakesh Tamang; Ruchira Chaudhary; Vipin Kumar Singh; Anish M. Shah; Sharath Anugula; Deepa Selvi Rani; Alla G. Reddy; Muthukrishnan Eaaswarkhanth; Gyaneshwer Chaubey; Lalji Singh; Kumarasamy Thangaraj
Background: The central Indian state Madhya Pradesh is often called as 'heart of India' and has always been an important region functioning as a trinexus belt for three major language families (Indo-European, Dravidian and Austroasiatic). There are less detailed genetic studies on the populations inhabited in this region. Therefore, this study is an attempt for extensive characterization of genetic ancestries of three tribal populations, namely; Bharia, Bhil and Sahariya, inhabiting this region using haploid and diploid DNA markers. Methodology/Principal Findings: Mitochondrial DNA analysis showed high diversity, including some of the older sublineages of M haplogroup and prominent R lineages in all the three tribes. Y-chromosomal biallelic markers revealed high frequency of Austroasiatic-specific M95-O2a haplogroup in Bharia and Sahariya, M82-H1a in Bhil and M17-R1a in Bhil and Sahariya. The results obtained by haploid as well as diploid genetic markers revealed strong genetic affinity of Bharia (a Dravidian speaking tribe) with the Austroasiatic (Munda) group. The gene flow from Austroasiatic group is further confirmed by their Y-STRs haplotype sharing analysis, where we determined their founder haplotype from the North Munda speaking tribe, while, autosomal analysis was largely in concordant with the haploid DNA results. Conclusions/Significance: Bhil exhibited largely Indo-European specific ancestry, while Sahariya and Bharia showed admixed genetic package of Indo-European and Austroasiatic populations. Hence, in a landscape like India, linguistic label doesn't unequivocally follow the genetic footprints. © 2012 Sharma et al.
Genetic and linguistic non-correspondence suggests evidence for collective social climbing in the Kol tribe of South Asia
(Nature Research, 2020) Anshika Srivastava; Prajjval Pratap Singh; Audditiya Bandopadhyay; Pooja Singh; Debashruti Das; Rakesh Tamang; Akhilesh Kumar Chaubey; Pankaj Shrivastava; George van Driem; Gyaneshwer Chaubey
Both classical and recent genetic studies have unanimously concluded that the genetic landscape of South Asia is unique. At long distances the ‘isolation-by-distance’ model appears to correspond well with the genetic data, whereas at short distances several other factors, including the caste, have been shown to be strong determinant factors. In addition with these, tribal populations speaking various languages add yet another layer of genetic complexity. The Kol are the third most populous tribal population in India, comprising communities speaking Austroasiatic languages of the Northern Munda branch. Yet, the Kol have not hitherto undergone in-depth genetic analysis. In the present study, we have analysed two Kol groups of central and western India for hundreds thousands of autosomal and several mitochondrial DNA makers to infer their fine genetic structure and affinities to other Eurasian populations. In contrast, with their known linguistic affinity, the Kol share their more recent common ancestry with the Indo-European and Dravidian speaking populations. The geographic-genetic neighbour tests at both the temporal and spatial levels have suggested some degree of excess allele sharing of Kol1 with Kol2, thereby indicating their common stock. Our extensive analysis on the Kol ethnic group shows South Asia to be a living genetics lab, where real-time tests can be performed on existing hypotheses. © 2020, The Author(s).
Genetic Diversity and Spatiotemporal Distribution of SARS-CoV-2 Alpha Variant in India
(Multidisciplinary Digital Publishing Institute (MDPI), 2023) Jahnavi Parasar; Rudra Kumar Pandey; Yashvant Patel; Prajjval Pratap Singh; Anshika Srivastava; Rahul Kumar Mishra; Bhupendra Kumar; Niraj Rai; Vijaya Nath Mishra; Pankaj Shrivastava; P. B. Kavi Kishor; Prashanth Suravajhala; Rakesh Tamang; Ajai Kumar Pathak; Gyaneshwer Chaubey
After the spill to humans, in the evolutionary timeline of SARS-CoV-2, several positively selected variants have emerged. A phylogeographic study on these variants can reveal their spatial and temporal distribution. In December 2020, the alpha variant of the severe acute respiratory syndrome coronavirus (SARS-CoV-2), which has been designated as a variant of concern (VOC) by the WHO, was discovered in the south-eastern United Kingdom (UK). Slowly, it expanded across India, with a considerable number of cases, particularly in North India. This study focuses on determining the prevalence and expansion of the Alpha variants in various parts of India mainly by using phylospatial analysis. The genetic diversity estimation has helped us to understand various evolutionary forces that have shaped the spatial distribution of this variant during its peak. Overall, our study paves the way to understanding the evolution and expansion of a virus variant, which may help to mitigate in the case of any future wave. © 2023 by the authors.
Genetic Structure of Tibeto-Burman Populations of Bangladesh: Evaluating the Gene Flow along the Sides of Bay-of-Bengal
(2013) Nurun Nahar Gazi; Rakesh Tamang; Vipin Kumar Singh; Ahmed Ferdous; Ajai Kumar Pathak; Mugdha Singh; Sharath Anugula; Pandichelvam Veeraiah; Subburaj Kadarkaraisamy; Brijesh Kumar Yadav; Alla G. Reddy; Deepa Selvi Rani; Syed Saleheen Qadri; Lalji Singh; Gyaneshwer Chaubey; Kumarasamy Thangaraj
Human settlement and migrations along sides of Bay-of-Bengal have played a vital role in shaping the genetic landscape of Bangladesh, Eastern India and Southeast Asia. Bangladesh and Northeast India form the vital land bridge between the South and Southeast Asia. To reconstruct the population history of this region and to see whether this diverse region geographically acted as a corridor or barrier for human interaction between South Asia and Southeast Asia, we, for the first time analyzed high resolution uniparental (mtDNA and Y chromosome) and biparental autosomal genetic markers among aboriginal Bangladesh tribes currently speaking Tibeto-Burman language. All the three studied populations; Chakma, Marma and Tripura from Bangladesh showed strikingly high homogeneity among themselves and strong affinities to Northeast Indian Tibeto-Burman groups. However, they show substantially higher molecular diversity than Northeast Indian populations. Unlike Austroasiatic (Munda) speakers of India, we observed equal role of both males and females in shaping the Tibeto-Burman expansion in Southern Asia. Moreover, it is noteworthy that in admixture proportion, TB populations of Bangladesh carry substantially higher mainland Indian ancestry component than Northeast Indian Tibeto-Burmans. Largely similar expansion ages of two major paternal haplogroups (O2a and O3a3c), suggested that they arose before the differentiation of any language group and approximately at the same time. Contrary to the scenario proposed for colonization of Northeast India as male founder effect that occurred within the past 4,000 years, we suggest a significantly deep colonization of this region. Overall, our extensive analysis revealed that the population history of South Asian Tibeto-Burman speakers is more complex than it was suggested before. © 2013 Gazi et al.
Most frequent South Asian haplotypes of ACE2 share identity by descent with East Eurasian populations
(Public Library of Science, 2020) Anshika Srivastava; Rudra Kumar Pandey; Prajjval Pratap Singh; Pramod Kumar; Avinash Arvind Rasalkar; Rakesh Tamang; George van Driem; Pankaj Shrivastava; Gyaneshwer Chaubey
It was shown that the human Angiotensin-converting enzyme 2 (ACE2) is the receptor of recent coronavirus SARS-CoV-2, and variation in this gene may affect the susceptibility of a population. Therefore, we have analysed the sequence data of ACE2 among 393 samples worldwide, focusing on South Asia. Genetically, South Asians are more related to West Eurasian populations rather than to East Eurasians. In the present analyses of ACE2, we observed that the majority of South Asian haplotypes are closer to East Eurasians rather than to West Eurasians. The phylogenetic analysis suggested that the South Asian haplotypes shared with East Eurasians involved two unique event polymorphisms (rs4646120 and rs2285666). In contrast with the European/American populations, both of the SNPs have largely similar frequencies for East Eurasians and South Asians, Therefore, it is likely that among the South Asians, host susceptibility to the novel coronavirus SARS-CoV-2 will be more similar to that of East Eurasians rather than to that of Europeans. Copyright: © 2020 Srivastava et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Outlier maternal haplogroups N5 and X2 and their potential role in elevated tuberculosis prevalence among the Sahariya tribe
(Elsevier B.V., 2025) Debashruti Das; Prajjval Pratap Singh; Shailesh Desai; Rahul Kumar Mishra; Pankaj Shrivastava; Prashanth N. Suravajhala; Rakesh Tamang; G. Chaubey
India bears the largest burden of tuberculosis (TB) cases in the world. Prior studies have highlighted significantly higher pulmonary TB among the Sahariya tribal population in Central India. The disease susceptibility of a population to disease may be influenced by genetic ancestry. In this context, we investigated the maternal genetic ancestry of the Sahariya in relation to their neighbouring tribal populations. For this study, we used the largest available dataset (n = 729), comprising 140 Sahariya individuals and 589 individuals from adjacent caste and tribal groups (including 50 newly sequenced samples). Our detailed mtDNA analysis revealed the exclusive presence of two rare haplogroups N5 and X2 which are completely absent in neighbouring tribal and caste populations. Further examination of the phylogeographic origins of the branches of haplogroups N5 and X2 suggests that these unique founder haplogroup branches (N5a and X2a) were likely introduced into the Sahariya from the western regions of the Indian subcontinent. The temporal expansion of these haplogroups indicates a gene flow from the western area to the Sahariya population during the early Iron Age. In addition to that, we have also analysed 33 SNPs for six TB-associated genes. We observed a single SNP (rs4958847-IRGM1) where the minor allele frequency was significantly different in Sahariya with their neighbouring populations. Consequently, our analysis of maternal genetic ancestry and known associated autosomal genes provides insights that may help explain the higher prevalence of TB among the Sahariya compared to their neighbouring populations. © 2025 Elsevier B.V. and Mitochondria Research Society
Prevalence of Low EPHX1 Activity-Associated Genotypes in Himalayan Populations of India
(John Wiley and Sons Inc, 2025) Divya Rai; Saptaparni De; Debashruti Das; Shishir Tamang; Kumaresh Mandal; Soni Subba; Lakkakula Suhasini Sahithi; Alla Govardhan Reddy; Periyasamy Govindaraj; Kumarasamy Thangaraj; G. Chaubey; Rakesh Tamang
Objectives: The EPHX1 gene encodes human microsomal epoxide hydrolase 1, which helps in biotransformation processes. Its activity is influenced by combinations of genotypes at its polymorphic sites. There are no data on the EPHX1 gene variants in the Indian Himalayan and adjoining populations (HAAPs). Therefore, this study aims to investigate the activity-associated genotypes of the EPHX1 gene variants in the HAAPs. Materials and Methods: The EPHX1 activity-associated variants, located in exon 3 (Tyr113His) and exon 4 (His139Arg), were analyzed among 607 samples from 16 different HAAPs. Genotype data from previously published 14 Indian populations were combined and evaluated for pan-India comparison. Results: We observed the prevalence of low EPHX1 activity-associated genotypes compared to the intermediate and high activity combinations in the HAAPs. There was a significant difference (p < 0.05) between the HAAPs and the reference Indian population based on variants in the EPHX1 gene. Comparison based on linguistic affiliation revealed that low EPHX1 activity-related genotypes were significantly higher in frequency among Tibeto-Burman speaking HAAPs (p < 0.001), followed by the other three major linguistic groups in India. Conclusion: Our study highlights the variations in both the studied loci among the HAAPs. We observed the widespread presence of low-activity-associated genotypes of the EPHX1 gene in the HAAPs. The pan-India comparison revealed the highest prevalence of low-activity-associated genotypes among the Tibeto-Burman speaking HAAPs compared to other linguistic groups. In the future, high-resolution genetic and molecular studies on EPHX1 are necessary to corroborate this finding and better understand human health holistically. © 2025 Wiley Periodicals LLC.
Reconstructing the demographic history of the Himalayan and adjoining populations
(Springer Verlag, 2018) Rakesh Tamang; Gyaneshwer Chaubey; Amrita Nandan; Periyasamy Govindaraj; Vipin Kumar Singh; Niraj Rai; Chandana Basu Mallick; Vishwas Sharma; Varun Kumar Sharma; Anish M. Shah; Albert Lalremruata; Alla G. Reddy; Deepa Selvi Rani; Pilot Doviah; Neetu Negi; Yarin Hadid; Veena Pande; Satti Vishnupriya; George van Driem; Doron M. Behar; Tikaram Sharma; Lalji Singh; Richard Villems; Kumarasamy Thangaraj
The rugged topography of the Himalayan region has hindered large-scale human migrations, population admixture and assimilation. Such complexity in geographical structure might have facilitated the existence of several small isolated communities in this region. We have genotyped about 850,000 autosomal markers among 35 individuals belonging to the four major populations inhabiting the Himalaya and adjoining regions. In addition, we have genotyped 794 individuals belonging to 16 ethnic groups from the same region, for uniparental (mitochondrial and Y chromosomal DNA) markers. Our results in the light of various statistical analyses suggest a closer link of the Himalayan and adjoining populations to East Asia than their immediate geographical neighbours in South Asia. Allele frequency-based analyses likely support the existence of a specific ancestry component in the Himalayan and adjoining populations. The admixture time estimate suggests a recent westward migration of populations living to the East of the Himalaya. Furthermore, the uniparental marker analysis among the Himalayan and adjoining populations reveal the presence of East, Southeast and South Asian genetic signatures. Interestingly, we observed an antagonistic association of Y chromosomal haplogroups O3 and D clines with the longitudinal distance. Thus, we summarise that studying the Himalayan and adjoining populations is essential for a comprehensive reconstruction of the human evolutionary and ethnolinguistic history of eastern Eurasia. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature.
Reconstructing the population history of the largest tribe of India: The Dravidian speaking Gond
(Nature Publishing Group, 2017) Gyaneshwer Chaubey; Rakesh Tamang; Erwan Pennarun; Pavan Dubey; Niraj Rai; Rakesh Kumar Upadhyay; Rajendra Prasad Meena; Jayanti R. Patel; George Van Driem; Kumarasamy Thangaraj; Mait Metspalu; Richard Villems
The Gond comprise the largest tribal group of India with a population exceeding 12 million. Linguistically, the Gond belong to the Gondi-Manda subgroup of the South Central branch of the Dravidian language family. Ethnographers, anthropologists and linguists entertain mutually incompatible hypotheses on their origin. Genetic studies of these people have thus far suffered from the low resolution of the genetic data or the limited number of samples. Therefore, to gain a more comprehensive view on ancient ancestry and genetic affinities of the Gond with the neighbouring populations speaking Indo-European, Dravidian and Austroasiatic languages, we have studied four geographically distinct groups of Gond using high-resolution data. All the Gond groups share a common ancestry with a certain degree of isolation and differentiation. Our allele frequency and haplotype-based analyses reveal that the Gond share substantial genetic ancestry with the Indian Austroasiatic (ie, Munda) groups, rather than with the other Dravidian groups to whom they are most closely related linguistically. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
Reconstructing the population history of the Nicobarese
(Springer Nature, 2024) Rahul Kumar Mishra; Prajjval Pratap Singh; Niraj Rai; Shailesh Desai; Pratik Pandey; Sachin Kr. Tiwary; Rakesh Tamang; Prashanth Suravajhala; Pankaj Shrivastava; Kumarasamy Thangaraj; George van Driem; Gyaneshwer Chaubey
The Nicobarese are the major tribal groups in the Nicobar district, situated south of the Andaman group of Islands. Linguistic phylogeny suggests that the linguistic ancestors of the Nicobarese settled the Nicobar archipelago in the early Holocene. So far, genetic research on them is low-resolution and restricted to the haploid DNA markers. Therefore, in the present analysis, we have used the high-resolution biparental (1554 published and 5 newly genotyped Nicobarese individuals) and uniparental genetic markers and looked at the genetic association of Nicobarese with the South and Southeast Asian populations. We report a common ancestral component shared among the Austroasiatic of South and Southeast Asia. Our analyses have suggested that the Nicobarese peoples retain this ancestral Austroasiatic predominant component in their genomes in the highest proportion. On the Southeast Asian mainland, the Htin Mal, who speak an Austroasiatic language of the Khmuic branch, represent a population that has preserved their ethnic distinctness from other groups over time and consequently shown the highest drift with the Nicobarese. The analysis based on haplotypes indicated a significant level of genomic segment sharing across linguistic groups, indicating an ancient broader distribution of Austroasiatic populations in Southeast Asia. Based on the temporal analyses of haploid DNA, it is suggested that the forebears of the Nicobarese people may have arrived on the Nicobar Islands in the last 5000 YBP. Therefore, among the modern populations, the Nicobarese peoples and the Htin Mal language community represent good genetic proxies for ancient Austroasiatics. © The Author(s), under exclusive licence to European Society of Human Genetics 2024.
Signatures of high altitude adaptation in Tibeto-Burman tribes of the Darjeeling Hill Region
(John Wiley and Sons Inc, 2023) Saptaparni De; Divya Rai; Shishir Tamang; Rinchen Doma Sherpa; Soni Subba; Dup Tshering Lepcha; Periyasamy Govindaraj; Kumarasamy Thangaraj; Gyaneshwer Chaubey; Rakesh Tamang
Objectives: The long-term isolation, endogamy practices, and environmental adaptations have shaped the enormous human diversity in India. The genetic and morphological variations in mainland Indians are well studied. However, the data on the Indian Himalayan populations are scattered. Thus, the present study attempts to understand variations in the selected parameter among four Tibeto-Burman speaking ethnic tribal populations from the Darjeeling Hill Region (DHR) in the Eastern Himalaya Biodiversity Hotspot region of India. Methods: A total of 178 healthy male individuals (Lepcha 98, Sherpa 31, Bhutia 27, and Tibetans 22) living at an altitudinal range of 1467–2258 m above the sea level were studied for the 10 parameters namely, weight (kg), height (cm), body mass index (BMI) (kg/m2) systolic and diastolic pressure (mm of Hg), pulse rate (per minute), saturation of peripheral oxygen (SPO2) (%), hemoglobin (g/dl), hematocrit (HCT) (%), and blood glucose (mg/dl). The data was statistically analyzed using analysis of variance and multiple linear regression methods. Results: Our analysis revealed comparatively lower hemoglobin and HCT levels, and higher systolic and diastolic blood pressure in the Sherpas followed by the Tibetans. This may be reflecting the persistence of high-altitude adaptation signatures even in lowlands. Interestingly, the Tibetans differed significantly from other populations in terms of their higher body weight, height, and BMI. Conclusion: Thus, our study showed the persistence of high altitude signatures in Tibetans and Sherpa inhabited the DHR. Additionally, we also observed significant differences in the anthropometric and physiological parameters among the Tibeto-Burman populations of the DHR. © 2023 Wiley Periodicals LLC.
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 matrilineal ancestry of Nepali populations
(Springer Science and Business Media Deutschland GmbH, 2023) Rajdip Basnet; Niraj Rai; Rakesh Tamang; Nagendra Prasad Awasthi; Isha Pradhan; Pawan Parajuli; Deepak Kashyap; Alla Govardhan Reddy; Gyaneshwer Chaubey; Krishna Das Manandhar; Tilak Ram Shrestha; Kumarasamy Thangaraj
The Tibetan plateau and high mountain ranges of Nepal are one of the challenging geographical regions inhabited by modern humans. While much of the ethnographic and population-based genetic studies were carried out to investigate the Tibetan and Sherpa highlanders, little is known about the demographic processes that enabled the colonization of the hilly areas of Nepal. Thus, the present study aimed to investigate the past demographic events that shaped the extant Nepalese genetic diversity using mitochondrial DNA (mtDNA) variations from ethnic Nepalese groups. We have analyzed mtDNA sequences of 999 Nepalese and compared data with 38,622 published mtDNA sequences from rest of the world. Our analysis revealed that the genomic landscapes of prehistoric Himalayan settlers of Nepal were similar to that of the low-altitude extant Nepalese (LAN), especially Newar and Magar population groups, but differ from contemporary high-altitude Sherpas. LAN might have derived their East Eurasian ancestry mainly from low-altitude Tibeto-Burmans, who likely have migrated from East Asia and assimilated across the Eastern Himalayas extended from the Eastern Nepal to the North-East of India, Bhutan, Tibet and Northern Myanmar. We also identified a clear genetic sub-structure across different ethnic groups of Nepal based on mtDNA haplogroups and ectodysplasin-A receptor (EDAR) gene polymorphism. Our comprehensive high-resolution mtDNA-based genetic study of Tibeto-Burman communities reconstructs the maternal origins of prehistoric Himalayan populations and sheds light on migration events that have brought most of the East Eurasian ancestry to the present-day Nepalese population. © 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
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.
Vaccine hesitancy for coronavirus SARS-CoV-2 in Varanasi India
(Frontiers Media S.A., 2022) Utkarsh Srivastava; Avanish Kumar Tripathi; Jagjeet Kaur; Sabita Devi; Shipra Verma; Vanya Singh; Debashruti Das; Prajjval Pratap Singh; Rahul Kumar Mishra; Nikhil A. Kumar; Vijaya Nath Mishra; Pradeep Kumar; Vandana Rai; Rakesh Tamang; Prashanth Suravajhala; Rakesh Pandey; Gyaneshwer Chaubey
With the rollout of the world's largest vaccine drive for SARS-CoV-2 by the Government of India on January 16 2021, India had targeted to vaccinate its entire population by the end of 2021. Struggling with vaccine procurement and production earlier, India overcome these hurdles, but the Indian population still did not seem to be mobilizing swiftly toward vaccination centers. The severe second wave has slowed the vaccination pace and was also one of the major contributing factors to vaccine hesitancy. To understand the nature of vaccine hesitancy and its underlying factors, we conducted extensive online and offline surveys in Varanasi and adjoining regions using structured questions. Most respondents were students (0.633). However, respondents from other occupations, such as government officials (0.10), have also participated in the study. Interestingly, most people (0.75) relied on fake news and did not take COVID-19 seriously. Most importantly, we noticed that a substantial proportion of respondents (relative frequency 0.151; mean age 24.8 years) reported that they were still not interested in vaccination. We observed a significant association between vaccine hesitancy and socioeconomic status (χ2 = 307.6, p < 0.001). However, we failed to detect any association between vaccine hesitancy and gender (χ2 = 0.007, p > 0.5). People who have neither been vaccinated nor have ever been infected may become the medium for spreading the virus and creating new variants, which may lead to the vaccine-resistant variant. We expect this extensive survey to help the Government upgrade their vaccination policies for COVID-19 in North India. Copyright © 2022 Srivastava, Tripathi, Kaur, Devi, Verma, Singh, Das, Singh, Mishra, Kumar, Mishra, Kumar, Rai, Tamang, Suravajhala, Pandey and Chaubey.