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.
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.
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.
Global patterns of skin pigmentation have evolved as an adaptation to local ultraviolet radiation (UVR). Indian populations exposed to intense UVR show great variation in skin pigmentation. The ...UVR-based selection model cannot satisfactorily address the high prevalence of light skin among these populations. Thus, the present study examines pigmentation variation among populations of West Maharashtra and the Indian subcontinent within the context of population structure and social hierarchy.
Melanin index (MI) was measured from 555 individuals representing six endogamous populations of West Maharashtra. Skin pigmentation was assessed in terms of variation between populations and differences between and among castes and tribes. A linear regression analysis was run to assess the relationship among MI, UVR, and social hierarchy using published MI data from 13 Indian endogamous populations.
Skin pigmentation differed significantly among populations of West Maharashtra. Significant pigmentation variation exists between castes and tribes of West Maharashtra as well as across the Indian subcontinent. We observe a significant negative relationship between social hierarchy and skin pigmentation, whereas the relationship between UVR and MI is weak.
Our results suggest that various factors may have contributed to pigmentation diversity across the Indian subcontinent. The lack of correlation between UVR and MI suggests that natural selection may not have played a significant role in shaping pigmentation variation across the subcontinent. We discuss other possible explanations, including metabolic conservation and cultural factors such as traditional social hierarchies and strict endogamy that have led to the development of population structure.
The gut microbiome has varied impact on the wellbeing of humans. It is influenced by different factors such as age, dietary habits, socio-economic status, geographic location, and genetic makeup of ...individuals. For devising microbiome-based therapies, it is crucial to identify population specific features of the gut microbiome. Indian population is one of the most ethnically, culturally, and geographically diverse, but the gut microbiome features remain largely unknown. The present study describes gut microbial communities of healthy Indian subjects and compares it with the microbiota from other populations. Based on large differences in alpha diversity indices, abundance of 11 bacterial phyla and individual specific OTUs, we report inter-individual variations in gut microbial communities of these subjects. While the gut microbiome of Indians is different from that of Americans, it shared high similarity to individuals from the Indian subcontinent i.e., Bangladeshi. Distinctive feature of Indian gut microbiota is the predominance of genus Prevotella and Megasphaera. Further, when compared with other non-human primates, it appears that Indians share more OTUs with omnivorous mammals. Our metagenomic imputation indicates higher potential for glycan biosynthesis and xenobiotic metabolism in these subjects. Our study indicates urgent need of identification of population specific microbiome biomarkers of Indian subpopulations to have more holistic view of the Indian gut microbiome and its health implications.
Access Denied? : Cultural Capital and Digital Access Kumbhojkar, Shraddha; Magar, Rahul; Ozarkar, Shantanu
Revista científica arbitrada de la Fundación MenteClara,
04/2019, Volume:
4, Issue:
1
Journal Article
Este artículo es un estudio cuantitativo a nivel micro de las percepciones de los estudiantes de ciencias sociales en la India sobre si el Wi-Fi gratuito les ha ayudado a aprender mejor. Se cree ...comúnmente que los recursos digitales son neutrales sobre las desigualdades sociales. Sin embargo, la encuesta revela que el capital sociocultural en forma de casta, género, idioma y ubicación tiene un impacto negativo en el acceso digital, incluso si es gratuito. El documento también infunde esperanza, ya que encuentra que casi todos los estudiantes en el campus de una Universidad Estatal en Western Maharashtra tienen acceso a Internet y la mayoría de estos estudiantes perciben que el acceso digital ha mejorado su rendimiento académico.
The paper is a micro-level quantitative study of perceptions of social science students in India whether Free Wi-Fi has helped them learn better. It is commonly believed that digital resources are ...neutral about social inequalities. However, the survey finds that socio-cultural capital in the form of Caste, Gender, Language and Location has a negative impact on digital access even if it is free. The paper also instills hope as it finds that almost every student on the campus of a State University in Western Maharashtra has access to the Internet and majority of these students perceive that the digital access has improved their academic performance.
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.
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).
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.
These results suggest that selection may have affected these loci broadly across the region.
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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