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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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Sikdar M. Complete mitochondrial DNA sequence tries to settle hitherto putative history of Kayastha population of India. Am J Hum Biol 2022; 35:e23851. [PMID: 36571462 DOI: 10.1002/ajhb.23851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVES Indian caste system is unique as it has an inimitable type of class system where the social ordering is done based on birth. Within the caste system, there is a distinct endogamous population known as the Kayastha, who have had inconclusive stratification records due to unidentified historical records. METHODS To gain a more inclusive view on the history and genetic affinities of Kayastha people, complete mitochondrial genomes from 15 individuals of a Kayastha population from North-western India have been sequenced. RESULTS Interestingly, three novel sub-clades (U2b2a, M3d2, and M33a3b) have been identified that represent unique Kayastha motifs. CONCLUSION The haplotype-based analysis suggests that the Kayastha population shares genetic affinities with the Indo-European and Sino-Tibetan populations found in the trans-Himalayan region. The FST based population comparison and the MDS plot indicates that Kayastha people have close maternal genetic affinity with the available genetic database of Brahmins, Kashmiris, and Tharus. The maternal genetic lineages among Kayastha population shows deep in situ origin that emerged much before settled life developed on this sub-continent. Both mtDNA and Y-chromosome markers, trace the genetic lineages of Kayastha population with Tharus, who regard themselves Kshatriya, corroborated by the oral history of the Kayasthas for their Kshatriya affiliation. It also validates genetic heritage of earliest settlers of India in both indigenous tribal and caste populations.
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Affiliation(s)
- Mithun Sikdar
- DNA Laboratory Unit, Anthropological Survey of India, Southern Regional Center, Mysore, India
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3
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Panda M, Kumawat R, Dixit S, Sharma AN, Shankar H, Chaubey G, Shrivastava P. Forensic features and phylogenetic analyses of the population of Nayagarh (Odisha), India using 23 Y-STRs. Ann Hum Biol 2022; 49:54-68. [PMID: 35499241 DOI: 10.1080/03014460.2022.2039762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
AIM The present study was designed to explore the STR diversity and genomic history of the inhabitants of Nayagarh district of Odisha, India. We also tested the proficiency of the most recent, new generation PowerPlexR Y23 multiplex system for forensic characterisation and to decipher the phylogenetic affinities. SUBJECTS AND METHODS The genetic diversity and polymorphism among 236 healthy unrelated male volunteers from Nayagarh district of Odisha, India was investigated. This investigation was carried out via 23 Y-chromosomal STRs using capillary electrophoresis. RESULT A total 223 unique haplotypes were reported. Discrimination capacity (DC), gene diversity (GD) and power of discrimination (PD) were observed as 0.945, 0.999999999998333, and 0.99999999999794, respectively. Polymorphic information content (PIC) and matching probability (PM) were reported as 0.999999999925535 and 2.06 × 10-12, respectively. Simultaneously, the haplogroup analysis characterised with C2, E1b1a, E1b1b, G2a, H1, I2a, J2a, J2b, L, O, O1, O2, Q, R1a, R2, and T haplogroups, disclosing the possible geographical relatedness of the studied population to different areas of the world. CONCLUSION Phylogenetic analysis with previously reported Indian and Asian populations showed the genetic closeness of the studied population to different Indian populations and the Bangladeshi population of Dhaka, whereas the Bhotra population of Odisha and Han population of China showed much less genetic affinity.
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Affiliation(s)
- Muktikanta Panda
- Department of Home (Police), DNA Fingerprinting Unit, State Forensic Science Laboratory, Government of MP, Sagar, India.,Department of Anthropology, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, India
| | - Ramkishan Kumawat
- DNA Division, State Forensic Science Laboratory, Jaipur, Rajasthan, India
| | - Shivani Dixit
- Department of Home (Police), DNA Fingerprinting Unit, State Forensic Science Laboratory, Government of MP, Sagar, India
| | - Awdhesh Narayan Sharma
- Department of Anthropology, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, India
| | - Hari Shankar
- Department of Home (Police), DNA Fingerprinting Unit, State Forensic Science Laboratory, Government of MP, Sagar, India
| | - Gyaneshwer Chaubey
- Department of Zoology, Cytogenetics Laboratory, Banaras Hindu University, Varanasi, India
| | - Pankaj Shrivastava
- Department of Home (Police), DNA Fingerprinting Unit, State Forensic Science Laboratory, Government of MP, Sagar, India.,Department of Anthropology, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, India
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4
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Singh B, Chamlagai D, Gurung J. HLA Profile of Kami Population Refutes the Earlier Proposition of Exclusive Closer Genetic Affinity of All the Gorkhas to Mongoloids. Hum Hered 2021; 85:1-6. [PMID: 33592612 DOI: 10.1159/000514220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/23/2020] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Based on the HLA profile of Indian Gorkhas, Debnath and Chaudhuri (2006) proposed that Gorkhas are genetically closer to Mongoloids, and they may have originated from Mongolians or Tibetan stocks. However, the major limitation of the earlier study was that Gorkhas comprise 2 broad groups, i.e. Tibeto-Burmans and Indo-Aryans. Besides, Gorkhas have an assemblage of many sociocultural and linguistically distinct populations such as Rai, Magar, Limbu, Tamang, Newar, Bahun, Kami, and so on. Thus, the generalization of the findings on Gorkhas by considering them as a single homogenous population may not be free from biases. Therefore, the present study aims to understand the genetic affinity of a constituent population from the Gorkha community, i.e. Kami, based on HLA polymorphism. METHODS First field HLA typing was performed among 158 Kami individuals by PCR-SSP methods. RESULTS The most frequent genes observed were HLA-A*11, HLA-B*15, HLA-DRB1*15. The frequency of HLA-DRB1*15 reported here is the highest recorded among the North Indian population to date, which is a noteworthy finding of the study. The hierarchical cluster analysis and principal component analysis showed that the Kami population lies within the cluster of the Indian subcontinental population. CONCLUSION The study refutes the earlier proposition of exclusive belongingness of all the Gorkhas to Mongoloids.
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Affiliation(s)
- Bisu Singh
- Department of Zoology, School of Life Sciences, Sikkim University, Gangtok, India,
| | - Dependra Chamlagai
- Department of Zoology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Jiwan Gurung
- Department of Zoology, School of Life Sciences, Sikkim University, Gangtok, India
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Reconstructing the demographic history of the Himalayan and adjoining populations. Hum Genet 2018; 137:129-139. [PMID: 29356938 DOI: 10.1007/s00439-018-1867-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/06/2018] [Indexed: 12/19/2022]
Abstract
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.
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Bhatti S, Abbas S, Aslamkhan M, Attimonelli M, Trinidad MS, Aydin HH, de Souza EMS, Gonzalez GR. Genetic perspective of uniparental mitochondrial DNA landscape on the Punjabi population, Pakistan. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:714-726. [PMID: 28745560 DOI: 10.1080/24701394.2017.1350951] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
To investigate the uniparental genetic structure of the Punjabi population from mtDNA aspect and to set up an appropriate mtDNA forensic database, we studied maternally unrelated Punjabi (N = 100) subjects from two caste groups (i.e. Arain and Gujar) belonging to territory of Punjab. The complete control region was elucidated by Sanger sequencing and the subsequent 58 different haplotypes were designated into appropriate haplogroups according to the most recently updated mtDNA phylogeny. We found a homogenous dispersal of Eurasian haplogroup uniformity among the Punjab Province and exhibited a strong connotation with the European populations. Punjabi castes are primarily a composite of substantial South Asian, East Asian and West Eurasian lineages. Moreover, for the first time we have defined the newly sub-haplogroup M52b1 characterized by 16223 T, 16275 G and 16438 A in Gujar caste. The vast array of mtDNA variants displayed in this study suggested that the haplogroup composition radiates signals of extensive genetic conglomeration, population admixture and demographic expansion that was equipped with diverse origin, whereas matrilineal gene pool was phylogeographically homogenous across the Punjab. This context was further fully acquainted with the facts supported by PCA scatterplot that Punjabi population clustered with South Asian populations. Finally, the high power of discrimination (0.8819) and low random match probability (0.0085%) proposed a worthy contribution of mtDNA control region dataset as a forensic database that considered a gold standard of today to get deeper insight into the genetic ancestry of contemporary matrilineal phylogeny.
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Affiliation(s)
- Shahzad Bhatti
- a Department of Human Genetics and Molecular Biology , University of Health Sciences Lahore , Lahore , Pakistan.,b Institute of Molecular Biology and Biotechnology , University of Lahore , Lahore , Pakistan
| | - Sana Abbas
- b Institute of Molecular Biology and Biotechnology , University of Lahore , Lahore , Pakistan
| | - Muhammad Aslamkhan
- a Department of Human Genetics and Molecular Biology , University of Health Sciences Lahore , Lahore , Pakistan
| | - Marcella Attimonelli
- c Department of Biosciences, Biotechnologies and Biopharmaceutics , University of Bari , Bari , Italy
| | - Magali Segundo Trinidad
- d Universidad National Autonoma de Mexico , Facultad de Medicinia , Ciudad de Mexico , Mexico
| | - Hikmet Hakan Aydin
- e Department of Medical Biochemistry , Ege University School of Medicine , Izmir , Turkey
| | - Erica Martinha Silva de Souza
- f Instituto Nacional de Pesquisa, Manaus Programa de Pós Graduação em Genética , Conservação e Biologia Evolutiva , Manaus , Brazil
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7
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Negi N, Tamang R, Pande V, Sharma A, Shah A, Reddy AG, Vishnupriya S, Singh L, Chaubey G, Thangaraj K. The paternal ancestry of Uttarakhand does not imitate the classical caste system of India. J Hum Genet 2015; 61:167-72. [PMID: 26511066 DOI: 10.1038/jhg.2015.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/03/2015] [Accepted: 09/11/2015] [Indexed: 01/17/2023]
Abstract
Although, there have been rigorous research on the Indian caste system by several disciplines, it is still one of the most controversial socioscientific topic. Previous genetic studies on the subcontinent have supported a classical hierarchal sharing of genetic component by various castes of India. In the present study, we have used high-resolution mtDNA and Y chromosomal markers to characterize the genetic structuring of the Uttarakhand populations in the context of neighboring regions. Furthermore, we have tested whether the genetic structuring of caste populations at different social levels of this region, follow the classical chaturvarna system. Interestingly, we found that this region showed a high level of variation for East Eurasian ancestry in both maternal and paternal lines of descent. Moreover, the intrapopulation comparison showed a high level of heterogeneity, likely because of different caste hierarchy, interpolated on asymmetric admixture of populations inhabiting on both sides of the Himalayas.
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Affiliation(s)
- Neetu Negi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Rakesh Tamang
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Estonian Biocentre, Tartu, Estonia.,Department of Zoology, University of Calcutta, Kolkata, India.,Department of Genetics, Osmania University, Hyderabad, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Amrita Sharma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Anish Shah
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Alla G Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Genome Foundation, Hyderabad, India
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8
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Guha P, Das A, Dutta S, Bhattacharjee S, Chaudhuri TK. Study of genetic diversity of KIR and TLR in the Rabhas, an endogamous primitive tribe of India. Hum Immunol 2015; 76:789-94. [PMID: 26429322 DOI: 10.1016/j.humimm.2015.09.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 07/13/2015] [Accepted: 09/27/2015] [Indexed: 12/18/2022]
Abstract
The Rabha tribe is a little known small endogamous population belonging to Indo-mongoloid group of north-eastern India. We have analyzed 16 KIR and 5 TLR gene polymorphisms in the Rabha population of northern West Bengal, India for the first time. The observed frequencies of the KIR genes (except framework and pseudogene loci) ranged between 0.26 (KIR2DS3) and 0.96 (KIR2DL1). Comparisons based on KIR polymorphism have revealed that although the Rabhas are of Indian origin the presence of mongoloid component in their gene pool cannot be denied. The frequencies of the 5 TLR genes ranged between 0.90 (TLR4) and 0.46 (TLR5). TLR variations found in the Rabhas may play a synergistic role in fighting against the bacterial invasions. Our results may contribute to the understanding of (1) genetic background and extent of genetic admixture in the Rabhas, (2) population migration events and (3) KIR-disease-TLR interactions.
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Affiliation(s)
- Pokhraj Guha
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, Raja Rammohunpur, Siliguri, West Bengal 734013, India
| | - Avishek Das
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, Raja Rammohunpur, Siliguri, West Bengal 734013, India
| | - Somit Dutta
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, Raja Rammohunpur, Siliguri, West Bengal 734013, India
| | - Soumen Bhattacharjee
- Cell and Molecular Biology Laboratory, Department of Zoology, University of North Bengal, Raja Rammohunpur, Siliguri, West Bengal 734013, India
| | - Tapas Kumar Chaudhuri
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, Raja Rammohunpur, Siliguri, West Bengal 734013, India.
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9
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Abstract
CONTEXT India is considered a treasure for geneticists and evolutionary biologists due to its vast human diversity, consisting of more than 4500 anthropologically well-defined populations (castes, tribes and religious groups). Each population differs in terms of endogamy, language, culture, physical features, geographic and climatic position and genetic architecture. These factors contributed to India-specific genetic variations which may be responsible for various common diseases in India and its migratory populations. As a result, interpretations of the origins and affinities of Indian populations as well as health and disease conditions require complex and sophisticated genetic analysis. Evidence of ancient human dispersals and settlements is preserved in the genome of Indian inhabitants and this has been extensively analysed in conventional and genomic analyses. OBJECTIVE AND METHODS Using genomic analyses of STRs and Alu on a set of populations, this study estimates the level and extent of genetic variation and its implications. RESULTS The results show that Indian populations have a higher level of unique genetic diversity which is structured by many social processes and geographical attributes of the country. CONCLUSION This overview highlights the need to study the anthropological structure and evolutionary history of Indian populations while designing genomic and epigenomic investigations.
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Affiliation(s)
- Sarabjit S Mastana
- Human Genomics Lab, Centre for Global Health and Human Development, School of Sport, Exercise and Health Sciences, Loughborough University , Loughborough , UK
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10
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Guha P, Bhattacharjee S, Chaudhuri TK. Diversity of killer cell immunoglobulin-like receptor genes in the Bengali population of northern West Bengal, India. Scand J Immunol 2014; 80:441-51. [PMID: 25205074 DOI: 10.1111/sji.12239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 08/06/2014] [Indexed: 11/26/2022]
Abstract
The Indian Subcontinent exhibits extensive diversity in its culture, religion, ethnicity and linguistic heritage, which symbolizes extensive genetic variations within the populations. The highly polymorphic Killer cell Immunoglobulin-like Receptor (KIR) family plays an important role in tracing genetic differentiation in human population. In this study, we aimed to analyse the KIR gene polymorphism in the Bengali population of northern West Bengal, India. To our knowledge, this is the first report on the KIR gene polymorphism in the Bengalis of West Bengal, India. Herein, we have studied the distribution of 14 KIR genes (KIR3DL1-3DL3, KIR2DL1-2DL5, KIR2DS1-2DS5 AND KIR3DS1) and two pseudogenes (KIR3DP1 and 2DP1) in the Bengalis. Apart from the framework genes (KIR2DL4, 3DL2, 3DL3 and 3DP1), which are present in all the individuals, the gene frequencies of other KIR genes varied between 0.34 and 0.88. Moreover, upon comparing the KIR polymorphism of the Bengalis with the available published data of other world populations, it has been found that the Indo-European-speaking Bengalis from the region share both Dravidian and Indo-Aryan gene pool with considerable influences of mongoloid and European descents. Furthermore, evidences from previously published data on human leucocyte antigen and Y-chromosome haplogroup diversity support the view. Our results will help to understand the genetic background of the Bengali population, in illustrating the population migration events in the eastern and north-eastern part of India, in explaining the extensive genetic admixture amongst the different linguistic groups of the region and also in KIR-related disease researches.
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Affiliation(s)
- P Guha
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, Siliguri, India
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11
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Retrieving Y chromosomal haplogroup trees using GWAS data. Eur J Hum Genet 2013; 22:1046-50. [PMID: 24281365 DOI: 10.1038/ejhg.2013.272] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 10/06/2013] [Accepted: 10/25/2013] [Indexed: 11/09/2022] Open
Abstract
Phylogenetically informative Y chromosomal single-nucleotide polymorphisms (Y-SNPs) integrated in DNA chips have not been sufficiently explored in most genome-wide association studies (GWAS). Herein, we introduce a pipeline to retrieve Y-SNP data. We introduce the software YTool (http://mitotool.org/ytool/) to handle conversion, filtering, and annotation of the data. Genome-wide SNP data from populations in Myanmar are used to construct a haplogroup tree for 117 Y chromosomes based on 369 high-confidence Y-SNPs. Parallel genotyping and published resequencing data of Y chromosomes confirm the validity of our pipeline. We apply this strategy to the CEU HapMap data set and construct a haplogroup tree with 107 Y-SNPs from 39 individuals. The retrieved Y-SNPs can discern the parental genetic structure of populations. Given the massive quantity of data from GWAS, this method facilitates future investigations of Y chromosome diversity.
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12
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Guha P, Srivastava SK, Bhattacharjee S, Chaudhuri TK. Human migration, diversity and disease association: a convergent role of established and emerging DNA markers. Front Genet 2013; 4:155. [PMID: 23950760 PMCID: PMC3738866 DOI: 10.3389/fgene.2013.00155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/25/2013] [Indexed: 01/30/2023] Open
Abstract
With the gradual development of intelligence, human got curious to know his origin and evolutionary background. Historical statements and anthropological findings were his primary tool for solving the puzzles of his own origin, until came the golden era of molecular markers which took no time to prove it's excellence in unveiling answers to the questions regarding the migration pattern of human across different geographical regions. As a bonus these markers proved very much beneficial in solving criminal offenses and in understanding the etiology of many dreaded diseases and to design their prevention. In this review, we have aimed to throw light on some of the promising molecular markers which are very much in application now-a-days for not only understanding the evolutionary background and ancient migratory routes of humans but also in the field of forensics and human health.
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Affiliation(s)
- Pokhraj Guha
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, SiliguriWest Bengal, India
| | - Sanjeev K. Srivastava
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, SiliguriWest Bengal, India
- Department of Medical genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, LucknowUttar Pradesh, India
| | - Soumen Bhattacharjee
- Cell and Molecular Biology Laboratory, Department of Zoology, University of North BengalSiliguri, West Bengal, India
| | - Tapas K. Chaudhuri
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, SiliguriWest Bengal, India
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Isaacs S, Geduld-Ullah T, Benjeddou M. Reconstruction of major maternal and paternal lineages of the Cape Muslim population. Genet Mol Biol 2013; 36:167-76. [PMID: 23885197 PMCID: PMC3715281 DOI: 10.1590/s1415-47572013005000019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 03/12/2013] [Indexed: 11/28/2022] Open
Abstract
The earliest Cape Muslims were brought to the Cape (Cape Town - South Africa) from Africa and Asia from 1652 to 1834. They were part of an involuntary migration of slaves, political prisoners and convicts, and they contributed to the ethnic diversity of the present Cape Muslim population of South Africa. The history of the Cape Muslims has been well documented and researched however no in-depth genetic studies have been undertaken. The aim of the present study was to determine the respective African, Asian and European contributions to the mtDNA (maternal) and Y-chromosomal (paternal) gene pool of the Cape Muslim population, by analyzing DNA samples of 100 unrelated Muslim males born in the Cape Metropolitan area. A panel of six mtDNA and eight Y-chromosome SNP markers were screened using polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP). Overall admixture estimates for the maternal line indicated Asian (0.4168) and African mtDNA (0.4005) as the main contributors. The admixture estimates for the paternal line, however, showed a predominance of the Asian contribution (0.7852). The findings are in accordance with historical data on the origins of the early Cape Muslims.
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Affiliation(s)
- Shafieka Isaacs
- Department of Biotechnology, University of the Western Cape, Bellville, Cape Town, South Africa
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14
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Study of the KIR gene profiles and analysis of the phylogenetic relationships of Rajbanshi population of West Bengal, India. Hum Immunol 2013; 74:673-80. [DOI: 10.1016/j.humimm.2013.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 01/06/2013] [Accepted: 01/14/2013] [Indexed: 01/30/2023]
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15
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Rai N, Chaubey G, Tamang R, Pathak AK, Singh VK, Karmin M, Singh M, Rani DS, Anugula S, Yadav BK, Singh A, Srinivasagan R, Yadav A, Kashyap M, Narvariya S, Reddy AG, van Driem G, Underhill PA, Villems R, Kivisild T, Singh L, Thangaraj K. The phylogeography of Y-chromosome haplogroup h1a1a-m82 reveals the likely Indian origin of the European Romani populations. PLoS One 2012; 7:e48477. [PMID: 23209554 PMCID: PMC3509117 DOI: 10.1371/journal.pone.0048477] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 10/02/2012] [Indexed: 12/16/2022] Open
Abstract
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.
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Affiliation(s)
- Niraj Rai
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Gyaneshwer Chaubey
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- * E-mail: (GC); (KT)
| | - Rakesh Tamang
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Ajai Kumar Pathak
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Vipin Kumar Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Monika Karmin
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Manvendra Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Deepa Selvi Rani
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Sharath Anugula
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Brijesh Kumar Yadav
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Ashish Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | - Anita Yadav
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Manju Kashyap
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Sapna Narvariya
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Alla G. Reddy
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - George van Driem
- Himalayan Languages Project, Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland
| | - Peter A. Underhill
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Richard Villems
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
| | - Toomas Kivisild
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
- Genome Foundation, Hyderabad, India
- Banaras Hindu University, Varanasi, India
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
- * E-mail: (GC); (KT)
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Wei W, Ayub Q, Chen Y, McCarthy S, Hou Y, Carbone I, Xue Y, Tyler-Smith C. A calibrated human Y-chromosomal phylogeny based on resequencing. Genome Res 2012; 23:388-95. [PMID: 23038768 PMCID: PMC3561879 DOI: 10.1101/gr.143198.112] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We have identified variants present in high-coverage complete sequences of 36 diverse human Y chromosomes from Africa, Europe, South Asia, East Asia, and the Americas, representing eight major haplogroups. After restricting our analysis to 8.97 Mb of the unique male-specific Y sequence, we identified 6662 high-confidence variants, including single-nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs), and indels. We constructed phylogenetic trees using these variants, or subsets of them, and recapitulated the known structure of the tree. Assuming a male mutation rate of 1 × 10−9 per base pair per year, the time depth of the tree (haplogroups A3-R) was ∼101,000–115,000 yr, and the lineages found outside Africa dated to 57,000–74,000 yr, both as expected. In addition, we dated a striking Paleolithic male lineage expansion to 41,000–52,000 yr ago and the node representing the major European Y lineage, R1b, to 4000–13,000 yr ago, supporting a Neolithic origin for these modern European Y chromosomes. In all, we provide a nearly 10-fold increase in the number of Y markers with phylogenetic information, and novel historical insights derived from placing them on a calibrated phylogenetic tree.
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Affiliation(s)
- Wei Wei
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
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17
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Simms TM, Wright MR, Hernandez M, Perez OA, Ramirez EC, Martinez E, Herrera RJ. Y-chromosomal diversity in Haiti and Jamaica: Contrasting levels of sex-biased gene flow. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 148:618-31. [DOI: 10.1002/ajpa.22090] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 04/04/2012] [Indexed: 11/06/2022]
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18
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He JD, Peng MS, Quang HH, Dang KP, Trieu AV, Wu SF, Jin JQ, Murphy RW, Yao YG, Zhang YP. Patrilineal perspective on the Austronesian diffusion in Mainland Southeast Asia. PLoS One 2012; 7:e36437. [PMID: 22586471 PMCID: PMC3346718 DOI: 10.1371/journal.pone.0036437] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 04/02/2012] [Indexed: 01/22/2023] Open
Abstract
The Cham people are the major Austronesian speakers of Mainland Southeast Asia (MSEA) and the reconstruction of the Cham population history can provide insights into their diffusion. In this study, we analyzed non-recombining region of the Y chromosome markers of 177 unrelated males from four populations in MSEA, including 59 Cham, 76 Kinh, 25 Lao, and 17 Thai individuals. Incorporating published data from mitochondrial DNA (mtDNA), our results indicated that, in general, the Chams are an indigenous Southeast Asian population. The origin of the Cham people involves the genetic admixture of the Austronesian immigrants from Island Southeast Asia (ISEA) with the local populations in MSEA. Discordance between the overall patterns of Y chromosome and mtDNA in the Chams is evidenced by the presence of some Y chromosome lineages that prevail in South Asians. Our results suggest that male-mediated dispersals via the spread of religions and business trade might play an important role in shaping the patrilineal gene pool of the Cham people.
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Affiliation(s)
- Jun-Dong He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Huy Ho Quang
- Department of Immunology, Hanoi Medical University, Hanoi, Vietnam
| | - Khoa Pham Dang
- Department of Immunology, Hanoi Medical University, Hanoi, Vietnam
| | - An Vu Trieu
- Department of Immunology, Hanoi Medical University, Hanoi, Vietnam
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Robert W. Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms, 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
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China
- * E-mail:
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19
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Ayub Q. Male lineages in the Himalayan foothills: a commentary on Y-chromosome haplogroup diversity in the sub-Himalayan Terai and Duars populations of East India. J Hum Genet 2011; 56:813-4. [PMID: 21975650 DOI: 10.1038/jhg.2011.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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