Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms

Watkins, W. Scott; Rangaswamy, Thara; Mowry, Bryan; Zhang, Y; Witherspoon, DJ; Tolpinrud, Whitney L.; Bamshad, Mike; Srinivasan, T. N.; Padmavati, R.; Smith, Heather J.; Nancarrow, Derek J.; Filippich, Cheryl; Jorde, L. B.

doi:10.1186/1471-2156-9-86

Cited by 36 publications

(25 citation statements)

References 59 publications

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“…These differences are likely attributable to the well-known difficulties in sequencing homopolymeric regions on the Ion Torrent platform. Additionally, no differences were found between the EXL-WGS data and lineage-defining SNVs genotyped previously in a subset of the 185 samples using single-base extension genotyping [31]. Taken together, these results demonstrate that EXL-WGS produces high-quality complete mitochondrial genome sequence data.…”

Section: Resultssupporting

confidence: 50%

Extremely low-coverage whole genome sequencing in South Asians captures population genomics information

et al. 2017

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BackgroundThe cost of Whole Genome Sequencing (WGS) has decreased tremendously in recent years due to advances in next-generation sequencing technologies. Nevertheless, the cost of carrying out large-scale cohort studies using WGS is still daunting. Past simulation studies with coverage at ~2x have shown promise for using low coverage WGS in studies focused on variant discovery, association study replications, and population genomics characterization. However, the performance of low coverage WGS in populations with a complex history and no reference panel remains to be determined.ResultsSouth Indian populations are known to have a complex population structure and are an example of a major population group that lacks adequate reference panels. To test the performance of extremely low-coverage WGS (EXL-WGS) in populations with a complex history and to provide a reference resource for South Indian populations, we performed EXL-WGS on 185 South Indian individuals from eight populations to ~1.6x coverage. Using two variant discovery pipelines, SNPTools and GATK, we generated a consensus call set that has ~90% sensitivity for identifying common variants (minor allele frequency ≥ 10%). Imputation further improves the sensitivity of our call set. In addition, we obtained high-coverage for the whole mitochondrial genome to infer the maternal lineage evolutionary history of the Indian samples.ConclusionsOverall, we demonstrate that EXL-WGS with imputation can be a valuable study design for variant discovery with a dramatically lower cost than standard WGS, even in populations with a complex history and without available reference data. In addition, the South Indian EXL-WGS data generated in this study will provide a valuable resource for future Indian genomic studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3767-6) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 50%

Extremely low-coverage whole genome sequencing in South Asians captures population genomics information

et al. 2017

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“…Our analyses also shed additional light on the genetic structure of Indian populations, which has been the subject of much research and debate (Bamshad et al 1998(Bamshad et al , 2001Basu et al 2003;Vishwanathan et al 2004;Watkins et al 2005Watkins et al , 2008Rosenberg et al 2006;Chaubey et al 2007). Our results show relatively larger genetic distances between the caste and tribal populations than among caste populations (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Most samples were collected previously in our laboratory (Jorde et al 1995;Bamshad et al 1998Bamshad et al , 2001Watkins et al 1999Watkins et al , 2008Bulayeva et al 2003). DNA samples of Luhya from Webuye, Kenya and Tuscans from Italy are part of the International HapMap project and were purchased from the Coriell Cell Repositories (http://ccr.coriell.org/).…”

Section: Dna Samples and Whole-genome Amplificationmentioning

confidence: 99%

Fine-scaled human genetic structure revealed by SNP microarrays

Xing¹,

Watkins²,

Witherspoon³

et al. 2009

Genome Res.

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We report an analysis of more than 240,000 loci genotyped using the Affymetrix SNP microarray in 554 individuals from 27 worldwide populations in Africa, Asia, and Europe. To provide a more extensive and complete sampling of human genetic variation, we have included caste and tribal samples from two states in South India, Daghestanis from eastern Europe, and the Iban from Malaysia. Consistent with observations made by Charles Darwin, our results highlight shared variation among human populations and demonstrate that much genetic variation is geographically continuous. At the same time, principal components analyses reveal discernible genetic differentiation among almost all identified populations in our sample, and in most cases, individuals can be clearly assigned to defined populations on the basis of SNP genotypes. All individuals are accurately classified into continental groups using a model-based clustering algorithm, but between closely related populations, genetic and self-classifications conflict for some individuals. The 250K data permitted high-level resolution of genetic variation among Indian caste and tribal populations and between highland and lowland Daghestani populations. In particular, upper-caste individuals from Tamil Nadu and Andhra Pradesh form one defined group, lower-caste individuals from these two states form another, and the tribal Irula samples form a third. Our results emphasize the correlation of genetic and geographic distances and highlight other elements, including social factors that have contributed to population structure.

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“…Dendrogram and principal component (PC) analysis of mitochondrial haplogroup frequencies were compared with data that were previously published by the other groups including East Asians (Mongolian, Japanese, Chinese, and Korean), South Asian (Indian), Southwest Asia (Yemen), European (Swedish) and Central American (Cuban) populations (15,(20)(21)(22)(23)(24)(25)(26)(27). Dendrogram analysis suggests that the Nukdo population was closely related to East Asian populations, whereas they greatly deviated from Yemen, Swedish and Cuban (Fig.…”

Section: Dendrogram and Pc Map Analysis For Mtdna Haplogroupmentioning

confidence: 99%

“…Dendrogram analysis was performed using the SPSS 12.0 program. For comparison of the dendrogram and PC map analyses, the published data from modern Mongolian (22), Japanese (25), Chinese (15), Korean (24), Indian (27), Yemen (21), Swedish (23) and Cuban (26) populations were used.…”

Section: Data Analysis and Haplogroupingmentioning

confidence: 99%

Mitochondrial DNA analysis of ancient human bones excavated from Nukdo island, S.Korea

Kim

Kim²,

Choi³

et al. 2010

BMB Reports

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We have performed analyses using ancient DNA extracted from 25 excavated human bones, estimating around the 1 st century B.C. Ancient human bones were obtained from Nukdo Island, which is located off of the Korean peninsula of East Asia. We made concerted efforts to extract ancient DNA of high quality and to obtain reproducible PCR products, as this was a primary consideration for this extensive kind of undertaking. We performed PCR amplifications for several regions of the mitochondrial DNA, and could determine mitochondrial haplogroups for 21 ancient DNA samples. Genetic information from mitochondrial DNA belonged to super-haplogroup M, haplogroup D or its sub-haplogroups (D4 or D4b), which are distinctively found in East Asians, including Koreans or Japanese. The dendrogram and principal component analysis based on haplogroup frequencies revealed that the Nukdo population was close to those of the East Asians and clearly distinguished from populations shown in the other regions. Considering that Nukdo is geologically isolated in the southern part of the Korean peninsula and is a site of commercial importance with neighboring countries, these results may reflect genetic continuity for the habitation and migration of ethnic groups who had lived in a particular area in the past. Therefore, we suggest that phylogenetic analyses of ancient DNA have significant advantages for clarifying the origins and migrations of ethnic groups, or human races. [BMB reports 2010; 43(2): 133-139]

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Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms

Abstract: Background: Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations.

Cited by 36 publications

References 59 publications

Extremely low-coverage whole genome sequencing in South Asians captures population genomics information

Extremely low-coverage whole genome sequencing in South Asians captures population genomics information

Fine-scaled human genetic structure revealed by SNP microarrays

Mitochondrial DNA analysis of ancient human bones excavated from Nukdo island, S.Korea

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