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Dabas P, Nayak BP, Khajuria H, Jain S, Dutt S, Saraswathy KN. A Cross-Sectional Assessment of Quantitative Epidermal Melanin and Erythema Indices among North Indians. Indian Dermatol Online J 2023; 14:366-370. [PMID: 37266078 PMCID: PMC10231713 DOI: 10.4103/idoj.idoj_400_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/05/2022] [Accepted: 11/30/2022] [Indexed: 06/03/2023] Open
Abstract
Background Remarkable diversity of skin tones among Indians ranging from pale pinkish to dark brown appears to be an ideal choice for the assessment of skin pigment variation. Aim The present study was designed to assess the variation observed in melanin and erythema indices among north Indians. Material and Methods Skin reflectance data (n = 574) was collected from six diverse populations of north India using DermaSpectrometer (DSM II ColorMeter) followed by statistical analysis to investigate the impact of geographical location and gender on constitutive skin pigmentation. Results The melanin index (MI) varied between 17.93 and 56.92 (Mean (M) = 35.80 ± 6.26) whereas the erythema index (EI) varied between 4.92 and 18.82 (M = 10.48 ± 2.68). MI and EI of females were found to be significantly lower than males (P < 0.001). Geographical location exhibited a significant association with MI and EI (P < 0.001). Furthermore, we have noted a positive correlation between MI and EI (P < 0.001). Conclusion The study has refined our understanding of skin pigmentation variation among north Indians in terms of significant association with geographical location {MI: F (5,568) = 31.07, P < 0.001; EI: F (5,568) = 73.37, P < 0.001} and gender {MI: t (386) = -4.06, P < 0.001; EI: t (386) = -11.96, P < 0.001} and rendered opportunities for further studies.
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Affiliation(s)
- Prashita Dabas
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
| | - Biswa P. Nayak
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
| | - Himanshu Khajuria
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
| | - Sonal Jain
- Dept. of Anthropology, University of Delhi, Delhi, India
| | - Sarjana Dutt
- Molecular Biology & Cytogenetics Division, National Reference Labs Pathkind, Udyog Vihar, Gurugram, India
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2
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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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3
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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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4
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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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5
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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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6
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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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7
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Quillen EE, Norton HL, Parra EJ, Lona-Durazo F, Ang KC, Illiescu FM, Pearson LN, Shriver MD, Lasisi T, Gokcumen O, Starr I, Lin YL, Martin AR, Jablonski NG. Shades of complexity: New perspectives on the evolution and genetic architecture of human skin. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 168 Suppl 67:4-26. [PMID: 30408154 DOI: 10.1002/ajpa.23737] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 02/06/2023]
Abstract
Like many highly variable human traits, more than a dozen genes are known to contribute to the full range of skin color. However, the historical bias in favor of genetic studies in European and European-derived populations has blinded us to the magnitude of pigmentation's complexity. As deliberate efforts are being made to better characterize diverse global populations and new sequencing technologies, better measurement tools, functional assessments, predictive modeling, and ancient DNA analyses become more widely accessible, we are beginning to appreciate how limited our understanding of the genetic bases of human skin color have been. Novel variants in genes not previously linked to pigmentation have been identified and evidence is mounting that there are hundreds more variants yet to be found. Even for genes that have been exhaustively characterized in European populations like MC1R, OCA2, and SLC24A5, research in previously understudied groups is leading to a new appreciation of the degree to which genetic diversity, epistatic interactions, pleiotropy, admixture, global and local adaptation, and cultural practices operate in population-specific ways to shape the genetic architecture of skin color. Furthermore, we are coming to terms with how factors like tanning response and barrier function may also have influenced selection on skin throughout human history. By examining how our knowledge of pigmentation genetics has shifted in the last decade, we can better appreciate how far we have come in understanding human diversity and the still long road ahead for understanding many complex human traits.
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Affiliation(s)
- Ellen E Quillen
- Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina.,Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Heather L Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, Ohio
| | - Esteban J Parra
- Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada
| | - Frida Lona-Durazo
- Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada
| | - Khai C Ang
- Department of Pathology and Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania
| | - Florin Mircea Illiescu
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.,Centro de Estudios Interculturales e Indígenas - CIIR, P. Universidad Católica de Chile, Santiago, Chile
| | - Laurel N Pearson
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Mark D Shriver
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Tina Lasisi
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Izzy Starr
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Yen-Lung Lin
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nina G Jablonski
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
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8
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Iliescu FM, Chaplin G, Rai N, Jacobs GS, Basu Mallick C, Mishra A, Thangaraj K, Jablonski NG. The influences of genes, the environment, and social factors on the evolution of skin color diversity in India. Am J Hum Biol 2018; 30:e23170. [PMID: 30099804 DOI: 10.1002/ajhb.23170] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/18/2018] [Accepted: 07/09/2018] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES Skin color is a highly visible and variable trait across human populations. It is not yet clear how evolutionary forces interact to generate phenotypic diversity. Here, we sought to unravel through an integrative framework the role played by three factors-demography and migration, sexual selection, and natural selection-in driving skin color diversity in India. METHODS Skin reflectance data were collected from 10 diverse socio-cultural populations along the latitudinal expanse of India, including both sexes. We first looked at how skin color varies within and between these populations. Second, we compared patterns of sexual dimorphism in skin color. Third, we studied the influence of ultraviolet radiation on skin color throughout India. Finally, we attempted to disentangle the interactions between these factors in the context of available genetic data. RESULTS We found that the relative importance of these forces varied between populations. Social factors and population structure have played a stronger role than natural selection in shaping skin color diversity across India. Phenotypic overprinting resulted from additional genetic mutations overriding the skin lightening effect of variants such as the SLC24A5 rs1426654-A allele in some populations, in the context of the variable influence of sexual selection. Furthermore, specific genotypes are not associated reliably with specific skin color phenotypes. This result has relevance for DNA forensics and ancient DNA research. CONCLUSIONS India is a crucible of macro- and micro-evolutionary forces, and the complex interactions of physical and social forces are visible in the patterns of skin color seen today in the country.
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Affiliation(s)
- Florin Mircea Iliescu
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.,Centro de Estudios Interculturales e Indígenas - CIIR, P. Universidad Católica de Chile, Santiago, Chile
| | - George Chaplin
- Department of Anthropology, The Pennsylvania State University, University Park, State Park, Pennsylvania
| | - Niraj Rai
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Birbal Sahni Institute of Palaeosciences, Lucknow, India
| | - Guy S Jacobs
- Complexity Institute, Nanyang Technological University, Singapore
| | - Chandana Basu Mallick
- Estonian Biocentre, Tartu, Estonia.,The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Anshuman Mishra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Nina G Jablonski
- Department of Anthropology, The Pennsylvania State University, University Park, State Park, Pennsylvania
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9
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Crawford NG, Kelly DE, Hansen MEB, Beltrame MH, Fan S, Bowman SL, Jewett E, Ranciaro A, Thompson S, Lo Y, Pfeifer SP, Jensen JD, Campbell MC, Beggs W, Hormozdiari F, Mpoloka SW, Mokone GG, Nyambo T, Meskel DW, Belay G, Haut J, Rothschild H, Zon L, Zhou Y, Kovacs MA, Xu M, Zhang T, Bishop K, Sinclair J, Rivas C, Elliot E, Choi J, Li SA, Hicks B, Burgess S, Abnet C, Watkins-Chow DE, Oceana E, Song YS, Eskin E, Brown KM, Marks MS, Loftus SK, Pavan WJ, Yeager M, Chanock S, Tishkoff SA. Loci associated with skin pigmentation identified in African populations. Science 2017; 358:eaan8433. [PMID: 29025994 PMCID: PMC5759959 DOI: 10.1126/science.aan8433] [Citation(s) in RCA: 198] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 10/03/2017] [Indexed: 12/13/2022]
Abstract
Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2, and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in South Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of ultraviolet response genes under selection in Eurasians.
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Affiliation(s)
- Nicholas G Crawford
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Derek E Kelly
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcia H Beltrame
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shaohua Fan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shanna L Bowman
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine and Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ethan Jewett
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94704, USA
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94704, USA
| | - Alessia Ranciaro
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simon Thompson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yancy Lo
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Susanne P Pfeifer
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Michael C Campbell
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - William Beggs
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Farhad Hormozdiari
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | | | - Gaonyadiwe George Mokone
- Department of Biomedical Sciences, University of Botswana School of Medicine, Gaborone, Botswana
| | - Thomas Nyambo
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | - Gurja Belay
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jake Haut
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Harriet Rothschild
- Stem Cell Program, Division of Hematology and Oncology, Pediatric Hematology Program, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Leonard Zon
- Stem Cell Program, Division of Hematology and Oncology, Pediatric Hematology Program, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yi Zhou
- Stem Cell Program, Division of Hematology and Oncology, Pediatric Hematology Program, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Michael A Kovacs
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mai Xu
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongwu Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Bishop
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Sinclair
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cecilia Rivas
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eugene Elliot
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiyeon Choi
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shengchao A Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Shawn Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christian Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elena Oceana
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Yun S Song
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94704, USA
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94704, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Mathematics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eleazar Eskin
- Department of Computer Science and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine and Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
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10
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Jonnalagadda M, Bharti N, Patil Y, Ozarkar S, K SM, Joshi R, Norton H. Identifying signatures of positive selection in pigmentation genes in two South Asian populations. Am J Hum Biol 2017; 29. [PMID: 28439965 DOI: 10.1002/ajhb.23012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/14/2017] [Accepted: 04/01/2017] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVES Skin pigmentation is a polygenic trait showing wide phenotypic variations among global populations. While numerous pigmentation genes have been identified to be under positive selection among European and East populations, genes contributing to phenotypic variation in skin pigmentation within and among South Asian populations are still poorly understood. The present study uses data from the Phase 3 of the 1000 genomes project focusing on two South Asian populations-GIH (Gujarati Indian from Houston, Texas) and ITU (Indian Telugu from UK), so as to decode the genetic architecture involved in adaptation to ultraviolet radiation in South Asian populations. METHODS Statistical tests included were (1) tests to identify deviations of the Site Frequency Spectrum (SFS) from neutral expectations (Tajima's D, Fay and Wu's H and Fu and Li's D* and F*), (2) tests focused on the identification of high-frequency haplotypes with extended linkage disequilibrium (iHS and Rsb), and (3) tests based on genetic differentiation between populations (LSBL). RESULTS Twenty-two pigmentation genes fall in the top 1% for at least one statistic in the GIH population, 5 of which (LYST, OCA2, SLC24A5, SLC45A2, and TYR) have been previously associated with normal variation in skin, hair, or eye color. In comparison, 17 genes fall in the top 1% for at least one statistic in the ITU population. Twelve loci which are identified as outliers in the ITU scan were also identified in the GIH population. CONCLUSIONS These results suggest that selection may have affected these loci broadly across the region.
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Affiliation(s)
- Manjari Jonnalagadda
- Symbiosis School for Liberal Arts (SSLA), Symbiosis International University (SIU), Pune, 411014, India
| | - Neeraj Bharti
- HPC-MBA Group, Centre for Development of Advanced Computing, Pune, 411007, India
| | - Yatish Patil
- HPC-MBA Group, Centre for Development of Advanced Computing, Pune, 411007, India
| | - Shantanu Ozarkar
- Department of Anthropology, Savitribai Phule Pune University, Pune, 411007, India
| | - Sunitha Manjari K
- HPC-MBA Group, Centre for Development of Advanced Computing, Pune, 411007, India
| | - Rajendra Joshi
- HPC-MBA Group, Centre for Development of Advanced Computing, Pune, 411007, India
| | - Heather Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, Ohio
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Mishra A, Nizammuddin S, Mallick CB, Singh S, Prakash S, Siddiqui NA, Rai N, Carlus SJ, Sudhakar DVS, Tripathi VP, Möls M, Kim-Howard X, Dewangan H, Mishra A, Reddy AG, Roy B, Pandey K, Chaubey G, Das P, Nath SK, Singh L, Thangaraj K. Genotype-Phenotype Study of the Middle Gangetic Plain in India Shows Association of rs2470102 with Skin Pigmentation. J Invest Dermatol 2016; 137:670-677. [PMID: 27866970 DOI: 10.1016/j.jid.2016.10.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 10/15/2016] [Accepted: 10/17/2016] [Indexed: 02/06/2023]
Abstract
Our understanding of the genetics of skin pigmentation has been largely skewed towards populations of European ancestry, imparting less attention to South Asian populations, who behold huge pigmentation diversity. Here, we investigate skin pigmentation variation in a cohort of 1,167 individuals in the Middle Gangetic Plain of the Indian subcontinent. Our data confirm the association of rs1426654 with skin pigmentation among South Asians, consistent with previous studies, and also show association for rs2470102 single nucleotide polymorphism. Our haplotype analyses further help us delineate the haplotype distribution across social categories and skin color. Taken together, our findings suggest that the social structure defined by the caste system in India has a profound influence on the skin pigmentation patterns of the subcontinent. In particular, social category and associated single nucleotide polymorphisms explain about 32% and 6.4%, respectively, of the total phenotypic variance. Phylogeography of the associated single nucleotide polymorphisms studied across 52 diverse populations of the Indian subcontinent shows wide presence of the derived alleles, although their frequencies vary across populations. Our results show that both polymorphisms (rs1426654 and rs2470102) play an important role in the skin pigmentation diversity of South Asians.
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Affiliation(s)
- Anshuman Mishra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Chandana Basu Mallick
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia; Estonian Biocentre, Tartu, Estonia
| | - Sakshi Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Satya Prakash
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Niraj Rai
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - S Justin Carlus
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Vishnu P Tripathi
- Department of Biotechnology, V.B.S. Purvanchal University, Jaunpur, India
| | - Märt Möls
- Estonian Biocentre, Tartu, Estonia; Insitute of Mathematical Statistics, University of Tartu, Tartu, Estonia
| | - Xana Kim-Howard
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma, USA
| | | | | | - Alla G Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Biswajit Roy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Krishna Pandey
- Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | | | - Pradeep Das
- Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | - Swapan K Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma, USA
| | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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12
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Jonnalagadda M, Norton H, Ozarkar S, Kulkarni S, Ashma R. Association of genetic variants with skin pigmentation phenotype among populations of west Maharashtra, India. Am J Hum Biol 2016; 28:610-8. [PMID: 26918427 DOI: 10.1002/ajhb.22836] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/23/2015] [Accepted: 01/07/2016] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVES South Asians exhibit extensive variation in skin melanin index (MI) which is observed across the broader region of South Asia as well as within restricted geographic regions. However, the genetic variants associated with variation in the skin pigmentation phenotype are poorly understood in these populations. The present study examines the association between MI measures and genetic variants from 5 candidate pigmentation genes among 533 individuals representing 6 populations of West Maharashtra. METHODS Associations between five single nucleotide polymorphisms (SNPs) known to play a role in pigmentation (rs1426654-SLC24A5, rs1042602-TYR, rs16891982-SLC45A2, rs6058017-ASIP, and rs642742-KITLG) and MI measures were tested using standard one-way analysis of variance (ANOVA) within each population. Multiple linear regression was used to test the effects of these SNPs in the full West Maharashtra sample using sex, age, and population or social group as covariates. RESULTS rs1426654 showed significant association with MI in all six study populations (P < 0.01). Association tests using sex, age, and population as covariates showed rs1426654 and rs1042602 to be significantly (P < 0.01) associated with lighter skin pigmentation in West Maharashtra as a whole. By contrast, when social group was added as a covariate instead of population, rs1426654, rs1042602, and rs16891982 were significantly (P < 0.01) associated with lighter skin pigmentation. CONCLUSIONS Only rs1426654 is significantly associated with MI in each individual population; however, rs1426654, rs1042602, and rs16891982 are significantly associated with pigmentation in the broader West Maharashtra region after controlling for population and social group, with rs1426654 (SLC24A5) explaining the majority of the observed variation. Am. J. Hum. Biol. 28:610-618, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Manjari Jonnalagadda
- Department of Anthropology, Savitribai Phule Pune University (Formerly University of Pune), Pune, Maharashtra, India
| | - Heather Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, Ohio
| | - Shantanu Ozarkar
- Department of Anthropology, Savitribai Phule Pune University (Formerly University of Pune), Pune, Maharashtra, India
| | - Shaunak Kulkarni
- Department of Anthropology, Savitribai Phule Pune University (Formerly University of Pune), Pune, Maharashtra, India
| | - Richa Ashma
- Department of Zoology, Savitribai Phule Pune University (Formerly University of Pune), Pune, Maharashtra, India.
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13
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Norton HL, Edwards M, Krithika S, Johnson M, Werren EA, Parra EJ. Quantitative assessment of skin, hair, and iris variation in a diverse sample of individuals and associated genetic variation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 160:570-81. [PMID: 27435525 DOI: 10.1002/ajpa.22861] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/27/2015] [Accepted: 08/25/2015] [Indexed: 11/06/2022]
Abstract
OBJECTIVES The main goals of this study are to 1) quantitatively measure skin, hair, and iris pigmentation in a diverse sample of individuals, 2) describe variation within and between these samples, and 3) demonstrate how quantitative measures can facilitate genotype-phenotype association tests. MATERIALS AND METHODS We quantitatively characterize skin, hair, and iris pigmentation using the Melanin (M) Index (skin) and CIELab values (hair) in 1,450 individuals who self-identify as African American, East Asian, European, Hispanic, or South Asian. We also quantify iris pigmentation in a subset of these individuals using CIELab values from high-resolution iris photographs. We compare mean skin M index and hair and iris CIELab values among populations using ANOVA and MANOVA respectively and test for genotype-phenotype associations in the European sample. RESULTS All five populations are significantly different for skin (P <2 × 10(-16) ) and hair color (P <2 × 10(-16) ). Our quantitative analysis of iris and hair pigmentation reinforces the continuous, rather than discrete, nature of these traits. We confirm the association of three loci (rs16891982, rs12203592, and rs12913832) with skin pigmentation and four loci (rs12913832, rs12203592, rs12896399, and rs16891982) with hair pigmentation. Interestingly, the derived rs12203592 T allele located within the IRF4 gene is associated with lighter skin but darker hair color. DISCUSSION The quantitative methods used here provide a fine-scale assessment of pigmentation phenotype and facilitate genotype-phenotype associations, even with relatively small sample sizes. This represents an important expansion of current investigations into pigmentation phenotype and associated genetic variation by including non-European and admixed populations. Am J Phys Anthropol 160:570-581, 2016. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Heather L Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, OH, 45238
| | - Melissa Edwards
- Department of Anthropology, University of Toronto Mississauga, Toronto, ON, Canada
| | - S Krithika
- Department of Anthropology, University of Toronto Mississauga, Toronto, ON, Canada
| | - Monique Johnson
- Department of Anthropology, University of Toronto Mississauga, Toronto, ON, Canada
| | - Elizabeth A Werren
- Department of Anthropology, University of Cincinnati, Cincinnati, OH, 45238
| | - Esteban J Parra
- Department of Anthropology, University of Toronto Mississauga, Toronto, ON, Canada
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