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Characterizing the genetic differences between two distinct migrant groups from Indo-European and Dravidian speaking populations in India.

Ali M, Liu X, Pillai EN, Chen P, Khor CC, Ong RT, Teo YY - BMC Genet. (2014)

Bottom Line: We implemented three population genetics measures to identify genomic regions that are significantly differentiated between the two Indian populations originating from the north and south of India.These measures singled out genomic regions with: (i) SNPs exhibiting significant variation in allele frequencies in the two Indian populations; and (ii) differential signals of positive natural selection as quantified by the integrated haplotype score (iHS) and cross-population extended haplotype homozygosity (XP-EHH).Our finding points to a gene-flow from Europe to north India that provides an explanation for the lighter skin tones present in North Indians in comparison to South Indians.

View Article: PubMed Central - HTML - PubMed

Affiliation: Life Sciences Institute, National University of Singapore, Singapore, Singapore. statyy@nus.edu.sg.

ABSTRACT

Background: India is home to many ethnically and linguistically diverse populations. It is hypothesized that history of invasions by people from Persia and Central Asia, who are referred as Aryans in Hindu Holy Scriptures, had a defining role in shaping the Indian population canvas. A shift in spoken languages from Dravidian languages to Indo-European languages around 1500 B.C. is central to the Aryan Invasion Theory. Here we investigate the genetic differences between two sub-populations of India consisting of: (1) The Indo-European language speaking Gujarati Indians with genome-wide data from the International HapMap Project; and (2) the Dravidian language speaking Tamil Indians with genome-wide data from the Singapore Genome Variation Project.

Results: We implemented three population genetics measures to identify genomic regions that are significantly differentiated between the two Indian populations originating from the north and south of India. These measures singled out genomic regions with: (i) SNPs exhibiting significant variation in allele frequencies in the two Indian populations; and (ii) differential signals of positive natural selection as quantified by the integrated haplotype score (iHS) and cross-population extended haplotype homozygosity (XP-EHH). One of the regions that emerged spans the SLC24A5 gene that has been functionally shown to affect skin pigmentation, with a higher degree of genetic sharing between Gujarati Indians and Europeans.

Conclusions: Our finding points to a gene-flow from Europe to north India that provides an explanation for the lighter skin tones present in North Indians in comparison to South Indians.

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Related in: MedlinePlus

Population structure of the Indians. Principal components analyses of the two Indian populations (HapMap Gujarati: GIH, SGVP Tamil Indians: INS) with other global populations across 112,925 SNPs. (A) The first two principal components (PCs) of GIH and INS with the remaining ten populations from Phase 3 of the International HapMap Project. (B) Second and third PCs of the PCA of GIH and INS with the ten HapMap3 populations. (C) First two PCs from the analysis of GIH, INS and the 45 Indo-European speaking samples and 46 Dravidian-language speaking samples from the paper by Reich and colleagues. (D) First two PCs from the analysis with only GIH and INS samples.
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Figure 2: Population structure of the Indians. Principal components analyses of the two Indian populations (HapMap Gujarati: GIH, SGVP Tamil Indians: INS) with other global populations across 112,925 SNPs. (A) The first two principal components (PCs) of GIH and INS with the remaining ten populations from Phase 3 of the International HapMap Project. (B) Second and third PCs of the PCA of GIH and INS with the ten HapMap3 populations. (C) First two PCs from the analysis of GIH, INS and the 45 Indo-European speaking samples and 46 Dravidian-language speaking samples from the paper by Reich and colleagues. (D) First two PCs from the analysis with only GIH and INS samples.

Mentions: Performing the PCA at a global scale where we compared GIH and INS with the remaining 10 populations in HapMap Phase 3, the GIH and INS samples were clustered together and were not immediately distinguishable with the first two principal components (Figure 2A), although a marginal separation between the two Indian populations was evident with the second and third principal components (Figure 2B). Comparing the two populations against the 132 samples from a survey of the population diversity of India by Reich and colleagues[1], we observed that GIH samples clustered closer to north Indian samples while INS samples were appropriately located with most of the south Indian samples (Figure 2C). An interesting pattern emerged from the PCA of only the GIH and INS samples (Figure 2D), where there were a group of 51 GIH samples that were more homogeneous among themselves and were clearly distinct from the INS samples; while the remaining 34 GIH samples were considerably more homogeneous to the INS samples.


Characterizing the genetic differences between two distinct migrant groups from Indo-European and Dravidian speaking populations in India.

Ali M, Liu X, Pillai EN, Chen P, Khor CC, Ong RT, Teo YY - BMC Genet. (2014)

Population structure of the Indians. Principal components analyses of the two Indian populations (HapMap Gujarati: GIH, SGVP Tamil Indians: INS) with other global populations across 112,925 SNPs. (A) The first two principal components (PCs) of GIH and INS with the remaining ten populations from Phase 3 of the International HapMap Project. (B) Second and third PCs of the PCA of GIH and INS with the ten HapMap3 populations. (C) First two PCs from the analysis of GIH, INS and the 45 Indo-European speaking samples and 46 Dravidian-language speaking samples from the paper by Reich and colleagues. (D) First two PCs from the analysis with only GIH and INS samples.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4120727&req=5

Figure 2: Population structure of the Indians. Principal components analyses of the two Indian populations (HapMap Gujarati: GIH, SGVP Tamil Indians: INS) with other global populations across 112,925 SNPs. (A) The first two principal components (PCs) of GIH and INS with the remaining ten populations from Phase 3 of the International HapMap Project. (B) Second and third PCs of the PCA of GIH and INS with the ten HapMap3 populations. (C) First two PCs from the analysis of GIH, INS and the 45 Indo-European speaking samples and 46 Dravidian-language speaking samples from the paper by Reich and colleagues. (D) First two PCs from the analysis with only GIH and INS samples.
Mentions: Performing the PCA at a global scale where we compared GIH and INS with the remaining 10 populations in HapMap Phase 3, the GIH and INS samples were clustered together and were not immediately distinguishable with the first two principal components (Figure 2A), although a marginal separation between the two Indian populations was evident with the second and third principal components (Figure 2B). Comparing the two populations against the 132 samples from a survey of the population diversity of India by Reich and colleagues[1], we observed that GIH samples clustered closer to north Indian samples while INS samples were appropriately located with most of the south Indian samples (Figure 2C). An interesting pattern emerged from the PCA of only the GIH and INS samples (Figure 2D), where there were a group of 51 GIH samples that were more homogeneous among themselves and were clearly distinct from the INS samples; while the remaining 34 GIH samples were considerably more homogeneous to the INS samples.

Bottom Line: We implemented three population genetics measures to identify genomic regions that are significantly differentiated between the two Indian populations originating from the north and south of India.These measures singled out genomic regions with: (i) SNPs exhibiting significant variation in allele frequencies in the two Indian populations; and (ii) differential signals of positive natural selection as quantified by the integrated haplotype score (iHS) and cross-population extended haplotype homozygosity (XP-EHH).Our finding points to a gene-flow from Europe to north India that provides an explanation for the lighter skin tones present in North Indians in comparison to South Indians.

View Article: PubMed Central - HTML - PubMed

Affiliation: Life Sciences Institute, National University of Singapore, Singapore, Singapore. statyy@nus.edu.sg.

ABSTRACT

Background: India is home to many ethnically and linguistically diverse populations. It is hypothesized that history of invasions by people from Persia and Central Asia, who are referred as Aryans in Hindu Holy Scriptures, had a defining role in shaping the Indian population canvas. A shift in spoken languages from Dravidian languages to Indo-European languages around 1500 B.C. is central to the Aryan Invasion Theory. Here we investigate the genetic differences between two sub-populations of India consisting of: (1) The Indo-European language speaking Gujarati Indians with genome-wide data from the International HapMap Project; and (2) the Dravidian language speaking Tamil Indians with genome-wide data from the Singapore Genome Variation Project.

Results: We implemented three population genetics measures to identify genomic regions that are significantly differentiated between the two Indian populations originating from the north and south of India. These measures singled out genomic regions with: (i) SNPs exhibiting significant variation in allele frequencies in the two Indian populations; and (ii) differential signals of positive natural selection as quantified by the integrated haplotype score (iHS) and cross-population extended haplotype homozygosity (XP-EHH). One of the regions that emerged spans the SLC24A5 gene that has been functionally shown to affect skin pigmentation, with a higher degree of genetic sharing between Gujarati Indians and Europeans.

Conclusions: Our finding points to a gene-flow from Europe to north India that provides an explanation for the lighter skin tones present in North Indians in comparison to South Indians.

Show MeSH
Related in: MedlinePlus