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Mendes M, Jonnalagadda M, Ozarkar S, Lima Torres FC, Borda Pua V, Kendall C, Tarazona-Santos E, Parra EJ. Identifying signatures of natural selection in Indian populations. PLoS One 2022; 17:e0271767. [PMID: 35925921 PMCID: PMC9352006 DOI: 10.1371/journal.pone.0271767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/06/2022] [Indexed: 11/18/2022] Open
Abstract
In this study, we present the results of a genome-wide scan for signatures of positive selection using data from four tribal groups (Kokana, Warli, Bhil, and Pawara) and two caste groups (Deshastha Brahmin and Kunbi Maratha) from West of the Maharashtra State In India, as well as two samples of South Asian ancestry from the 1KG project (Gujarati Indian from Houston, Texas and Indian Telugu from UK). We used an outlier approach based on different statistics, including PBS, xpEHH, iHS, CLR, Tajima’s D, as well as two recently developed methods: Graph-aware Retrieval of Selective Sweeps (GRoSS) and Ascertained Sequentially Markovian Coalescent (ASMC). In order to minimize the risk of false positives, we selected regions that are outliers in all the samples included in the study using more than one method. We identified putative selection signals in 107 regions encompassing 434 genes. Many of the regions overlap with only one gene. The signals observed using microarray-based data are very consistent with our analyses using high-coverage sequencing data, as well as those identified with a novel coalescence-based method (ASMC). Importantly, at least 24 of these genomic regions have been identified in previous selection scans in South Asian populations or in other population groups. Our study highlights genomic regions that may have played a role in the adaptation of anatomically modern humans to novel environmental conditions after the out of Africa migration.
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Affiliation(s)
- Marla Mendes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Anthropology, University of Toronto—Mississauga Campus, Mississauga, ON, Canada
| | - Manjari Jonnalagadda
- Symbiosis School for Liberal Arts (SSLA), Symbiosis International University (SIU), Pune, India
| | - Shantanu Ozarkar
- Department of Anthropology, Savitribai Phule Pune University, Pune, India
| | - Flávia Carolina Lima Torres
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Victor Borda Pua
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Christopher Kendall
- Department of Anthropology, University of Toronto—Mississauga Campus, Mississauga, ON, Canada
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Esteban J. Parra
- Department of Anthropology, University of Toronto—Mississauga Campus, Mississauga, ON, Canada
- * E-mail:
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Jonnalagadda M, Bharti N, Kasibhatla SM, Wagh MA, Joshi R, Ozarkar S, Ashma R. MC1R diversity and its role in skin pigmentation variation in West Maharashtra, India. Am J Hum Biol 2022; 34:e23734. [PMID: 35188998 DOI: 10.1002/ajhb.23734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES MC1R polymorphisms have been reported to be under a selective constraint in populations inhabiting high UVR regions such as Africans; however, these patterns are not consistent. Here we analyze the MC1R gene in West Maharashtra, India to see if sequence diversity corresponds to their diverse pigmentary profiles and if MC1R is constrained in dark skinned tribal as compared to lighter skinned caste populations. METHODS A 2648 bp region of this gene was sequenced in 102 individuals and the data was compared for π, ϴ diversity indices. Tajima's D was assessed for signatures of purifying selection and MC1R variants were associated with MI measures using the additive, dominant, and recessive models. Pairwise FST was tested among study populations and between study populations and 1000 Genomes regional samples. RESULTS MC1R diversity was not uniquely patterned among castes and tribes. Non-synonymous variants rs2228479A, rs1805007_T, and rs885479_A showed low variability in these populations. Selection tests did not indicate any constraint on MC1R and pairwise FST were also low among the study populations (-0.0163 to 0.06112). The SNP rs3212359 was significantly associated with MI measures when tested using different association models. CONCLUSIONS We do not find evidence of a selective constraint on MC1R. The presence of a large number of unique haplotypes and low FST values at this locus suggests that MC1R polymorphisms may not be influencing pigmentation variation among castes and tribes in this region. Observed associations between rs3212359 and MI measures need to be validated through studies on larger samples and in-vitro functional studies.
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Affiliation(s)
- Manjari Jonnalagadda
- Symbiosis School for Liberal Arts, Symbiosis International (Deemed University), Pune, India
| | - Neeraj Bharti
- HPC-MBA Group, C-DAC Innovation Park, Centre for Development of Advanced Computing, Pune, India
| | | | - Mayur A Wagh
- Symbiosis School for Liberal Arts, Symbiosis International (Deemed University), Pune, India
| | - Rajendra Joshi
- HPC-MBA Group, C-DAC Innovation Park, Centre for Development of Advanced Computing, Pune, India
| | - Shantanu Ozarkar
- Department of Anthropology, Savitribai Phule Pune University, Pune, India
| | - Richa Ashma
- Department of Zoology, Savitribai Phule Pune University, Pune, India
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Goswami A, Bhuniya U, Chatterjee S, Mandal P. The influence of IL1RN VNTR polymorphism on HPV infection among some tribal communities. J Med Virol 2021; 94:752-760. [PMID: 34741549 DOI: 10.1002/jmv.27436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 01/28/2021] [Accepted: 11/04/2021] [Indexed: 12/09/2022]
Abstract
Persistent infection of human Papillomavirus is the main etiological factor for cervical cancer. Austro-Asiatic tribes are early settlers in India and they have unique genetic variations compared to other people. The immunological response is crucial for the prevention of viral associated diseases. Interleukin-1 receptor antagonist (IL-1RN) is considered being an important regulator of host immune surveillance. A total of 45 Santali tribal women and 10 Kora tribal women were enrolled in the present study and demographic variables were recorded during collection. Genomic DNA was extracted from cervical/vaginal swab samples. IL1RN variable number of tandem repeats (VNTR) polymorphisms and HPV types were determined by PCR-based assay. Association between IL1RN VNTR polymorphisms with the HPV infections among the tribal communities was determined by logistic regression analysis. HPV18 prevalence was significantly higher among tribal women. We observed that the polymorphism A2*A2 (p = 0.022; odds ratio [OR] (95% confidence interval [CI]) = 0.16 (0.03-0.86)] were more resistant to oncogenic HPV infection. Use of oral contraceptives was associated with higher relative risk (p = 0.008; OR [95% CI] = 5.39 [1.47-19.8]) for oncogenic HPV18 positivity among the tribal women. The A2 allele homozygosity of IL1RN VNTR was identified to be associated with the protection from oncogenic HPV infection among various tribal communities of West Bengal and therefore may be a useful marker of host immune response among them.
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Affiliation(s)
- Anindita Goswami
- Biomedical Genetics Laboratory, Department of Zoology, The University of Burdwan, Burdwan, West Bengal, India
| | - Utpal Bhuniya
- Chakdighi Primary Health Centre, Health and Family Welfare Department, Govt. of West Bengal, Burdwan, West Bengal, India
| | - Soumendranath Chatterjee
- Parasitology and Microbiology Research Laboratory, Department of Zoology, The University of Burdwan, Burdwan, West Bengal, India
| | - Paramita Mandal
- Biomedical Genetics Laboratory, Department of Zoology, The University of Burdwan, Burdwan, West Bengal, India
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Sarma A, Barman B, Das GC, Saikia H, Momin AD. Correlation between the arm-span and the standing height among males and females of the Khasi tribal population of Meghalaya state of North-Eastern India. J Family Med Prim Care 2021; 9:6125-6129. [PMID: 33681051 PMCID: PMC7928122 DOI: 10.4103/jfmpc.jfmpc_1350_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/13/2020] [Accepted: 10/02/2020] [Indexed: 11/07/2022] Open
Abstract
Introduction: The estimation of relationship between the arm span and the standing height has been an important tool in anthropometric measurements especially in cases where direct measurement of stature is not possible. Objective: To find the relationship between the arm-span and the standing height of both males and females in the population of Khasi tribal population of Meghalaya. Materials and Methods: The study involved 400 numbers (272 males and 128 females) of healthy human volunteer subjects belonging to Khasi tribe of Meghalaya. The standing height and arm-span were measured for each individual and analyzed. Result: Of the 400 healthy volunteers, 272 (68%) were males and 128 (32%) were females with age ranged from 25 to 45 years. Height and arm span in males (159.68 ± 4.12 cm and 166.30 ± 4.27 cm, respectively) werefound to be significantly (p < 0.001) higher than females (149.96 ± 3.04 cm and 155.77 ± 3.13 cm respectively). The Pearson correlation coefficient (r) between height (cm) and arm span (cm) showed significant positive correlation in both male (r = 0.988, P < 0.001) and female (r = 0.991, P < 0.001) study subjects. The regression equation was Height = 1.060 + 0.954 (Arm span); R2 = 0.976; SEE = 0.646 for male. For female subjects the regression equation was found as Height = 0.150 + 0.962 (Arm span); R2 = 0.983; SEE = 0.400. Conclusion: Arm-span can be used as one of the most reliable parameter in both males and females for obtaining the stature of an individual in alternative to the height.
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Affiliation(s)
- Amitav Sarma
- Department of Anatomy, North Eastern Indira Gandhi Regional Institute of Health and MedicalSciences (NEIGRIHMS), Shillong, Meghalaya, India
| | - Bhupen Barman
- Department of Medicine, North Eastern Indira Gandhi Regional Institute of Health and MedicalSciences (NEIGRIHMS), Shillong, Meghalaya, India
| | - Gautam C Das
- Department of Anatomy, Silchar Medical College, Silchar, Assam, India
| | - Hiranya Saikia
- Department of Community Medicine, Assam Medical College and Hospital, Dibrugarh, Assam, India
| | - Ambath D Momin
- Department of Anatomy, North Eastern Indira Gandhi Regional Institute of Health and MedicalSciences (NEIGRIHMS), Shillong, Meghalaya, India
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Badiye A, Kapoor N, Kumawat RK, Dixit S, Mishra A, Dixit A, Kathane P, Bag S, Thakre V, Kaitholia K, Srivastava A, Chaubey G, Shrivastava P. A study of genomic diversity in populations of Maharashtra, India, inferred from 20 autosomal STR markers. BMC Res Notes 2021; 14:69. [PMID: 33622409 PMCID: PMC7903603 DOI: 10.1186/s13104-021-05485-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 02/13/2021] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVE This study was planned to evaluate the genetic diversity in the admixed and Teli (a Hindu caste) populations of Maharashtra, India using 20 autosomal Short Tandem Repeat (STR) genetic markers. We further investigated the genetic relatedness of the studied populations with other Indian populations. RESULTS The studied populations showed a wide range of observed heterozygosity viz. 0.690 to 0.918 for the admixed population and 0.696 to 0.942 for the Teli population. This might be due to the multi-directional gene flow. The admixed and Teli populations also showed a high degree polymorphism which ranged from 0.652 to 0.903 and 0.644 to 0.902, respectively. Their combined value of matching probability for all the studied loci was 4.29 × 10-25 and 5.01 × 10-24, respectively. The results of Neighbor-Joining tree and Principal Component Analysis showed that the studied populations clustered with the general populations of Jharkhand, UttarPradesh, Rajasthan and Central Indian States, as well as with the specific populations of Maharashtra (Konkanastha Brahmins) and Tamil Nadu (Kurmans). Overall, the obtained data showed a high degree of forensic efficacy and would be useful for forensic applications as well as genealogical studies.
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Affiliation(s)
- Ashish Badiye
- Department of Forensic Science, Government Institute of Forensic Science, Nagpur, Maharashtra, India
| | - Neeti Kapoor
- Department of Forensic Science, Government Institute of Forensic Science, Nagpur, Maharashtra, India
| | - R K Kumawat
- DNA Division, State Forensic Science Laboratory, Jaipur, Rajasthan, India
| | - Shivani Dixit
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, M.P., 470001, India
| | - Aditi Mishra
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, M.P., 470001, India
| | - Akansha Dixit
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, M.P., 470001, India
- Dr. A.P.J. Abdul Kalam Institute of Forensic Science & Criminology, Bundelkhand University, Jhansi, U.P., 284128, India
| | - Prachi Kathane
- Department of Forensic Science, Government Institute of Forensic Science, Nagpur, Maharashtra, India
| | - Sudeshna Bag
- Department of Forensic Science, Government Institute of Forensic Science, Nagpur, Maharashtra, India
| | - Vaishnavi Thakre
- Department of Forensic Science, Government Institute of Forensic Science, Nagpur, Maharashtra, India
| | - Kamlesh Kaitholia
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, M.P., 470001, India
| | - Ankit Srivastava
- Dr. A.P.J. Abdul Kalam Institute of Forensic Science & Criminology, Bundelkhand University, Jhansi, U.P., 284128, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Dept of Zoology, Banaras Hindu University, Varanasi, India
| | - Pankaj Shrivastava
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, M.P., 470001, India.
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Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data. Sci Rep 2020; 10:10075. [PMID: 32572090 PMCID: PMC7308293 DOI: 10.1038/s41598-020-66953-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/27/2020] [Indexed: 12/14/2022] Open
Abstract
The South Asian subcontinent is characterized by a complex history of human migrations and population interactions. In this study, we used genome-wide data to provide novel insights on the demographic history and population relationships of six Indo-European populations from the Indian State of West Maharashtra. The samples correspond to two castes (Deshastha Brahmins and Kunbi Marathas) and four tribal groups (Kokana, Warli, Bhil and Pawara). We show that tribal groups have had much smaller effective population sizes than castes, and that genetic drift has had a higher impact in tribal populations. We also show clear affinities between the Bhil and Pawara tribes, and to a lesser extent, between the Warli and Kokana tribes. Our comparisons with available modern and ancient DNA datasets from South Asia indicate that the Brahmin caste has higher Ancient Iranian and Steppe pastoralist contributions than the Kunbi Marathas caste. Additionally, in contrast to the two castes, tribal groups have very high Ancient Ancestral South Indian (AASI) contributions. Indo-European tribal groups tend to have higher Steppe contributions than Dravidian tribal groups, providing further support for the hypothesis that Steppe pastoralists were the source of Indo-European languages in South Asia, as well as Europe.
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Jonnalagadda M, Faizan MA, Ozarkar S, Ashma R, Kulkarni S, Norton HL, Parra E. A Genome-Wide Association Study of Skin and Iris Pigmentation among Individuals of South Asian Ancestry. Genome Biol Evol 2019; 11:1066-1076. [PMID: 30895295 PMCID: PMC6456006 DOI: 10.1093/gbe/evz057] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2019] [Indexed: 12/14/2022] Open
Abstract
South Asia has a complex history of migrations and is characterized by substantial pigmentary and genetic diversity. For this reason, it is an ideal region to study the genetic architecture of normal pigmentation variation. Here, we present a meta-analysis of two genome-wide association studies (GWASs) of skin pigmentation using skin reflectance (M-index) as a quantitative phenotype. The meta-analysis includes a sample of individuals of South Asian descent living in Canada (N = 348), and a sample of individuals from two caste and four tribal groups from West Maharashtra, India (N = 480). We also present the first GWAS of iris color in South Asian populations. This GWAS was based on quantitative measures of iris color obtained from high-resolution iris pictures. We identified genome-wide significant associations of variants within the well-known gene SLC24A5, including the nonsynonymous rs1426654 polymorphism, with both skin pigmentation and iris color, highlighting the pleiotropic effects of this gene on pigmentation. Variants in the HERC2 gene (e.g., rs12913832) were also associated with iris color and iris heterochromia. Our study emphasizes the usefulness of quantitative methods to study iris color variation. We also identified novel genome-wide significant associations with skin pigmentation and iris color, but we could not replicate these associations due to the lack of independent samples. It will be critical to expand the number of studies in South Asian populations in order to better understand the genetic variation driving the diversity of skin pigmentation and iris color observed in this region.
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Affiliation(s)
- Manjari Jonnalagadda
- Symbiosis School for Liberal Arts, Symbiosis International (Deemed University), Pune, India
| | | | - Shantanu Ozarkar
- Department of Anthropology, Savitribai Phule Pune University, India
| | - Richa Ashma
- Department of Zoology, Savitribai Phule Pune University, India
| | - Shaunak Kulkarni
- Department of Anthropology, Savitribai Phule Pune University, India
| | | | - Esteban Parra
- Department of Anthropology, University of Toronto, Ontario, Canada
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