Microsatellite Variation in Human Populations of the Indian Subcontinent

Abstract

An analysis of microsatellite variation among individuals of Indian origin was performed to compare the genetic diversity between different regions within India that are divided by spoken language and geographical distance. In addition, the relationship between the Indian and other human populations was examined. Six microsatellite loci -CSF1PO, TPOX, TH01, F13A01, FESFPS and vWA were amplified and typed in a total of 149 individuals representing a broad geographical distribution within the Indian subcontinent. Contingency analyses of allele frequency distributions between North and South Indian populations revealed a significant difference at the vWA locus. The lack of significant differences at the other five loci may indicate a considerable amount of gene flow between these two populations or that these polymorphisms existed before the split between Northern and Southern populations. The South Indian population (n = 37) revealed the presence of an allele at the vWA locus that was not detected in either the North Indian (n = 103) or Caucasian (n = 212) populations. The absence of this allele in the North and the presence in the South may indicate a population specific allele and gives support to the hypothesis that India was occupied by an earlier Dravidian population before the more recent arrival of the Aryans who lacked this allele. Genetic distance failed to reveal any significant distances between North and South Indian populations. Phylogenetic analyses, although not significant, indicated that the two populations were not monophyletic. A correlation between genetic and geographic distance between the Northeast, Northcentral, Southeast and Southwest regions of India revealed a correlation coefficient of r = -0.53 which was not significant. The negative correlation is solely due to the fact that the two most geographically closest populations, Salem and Cochin, show the greatest genetic distance (0.442) between them. This is consistent with the fact that social factors play an important role in the genetic structuring of Indian populations. Genetic distance analyses revealed significant distance values between the Indian, Caucasian and African populations and showed the Indian population to be genetically closer to the Caucasian population. These results are consistent with earlier studies using gene frequency data and mitochondrial DNA. Overall, the results of the genetic distance and phylogenetic analyses showed that six microsatellite loci were able to distinguish between African and non-African populations, but more loci need to be utilized to differentiate between non-African populations.