Genetic structure of Indian populations based on fifteen autosomal microsatellite loci

Abstract

Background: Indian populations endowed with unparalleled genetic complexity have received a great deal of attention from scientists world over. However, the fundamental question over their ancestry, whether they are all genetically similar or do exhibit differences attributable to ethnicity, language, geography or socio-cultural affiliation is still unresolved. In order to decipher their underlying genetic structure, we undertook a study on 3522 individuals belonging to 54 endogamous Indian populations representing all major ethnic, linguistic and geographic groups and assessed the genetic variation using autosomal microsatellite markers.

Results: The distribution of the most frequent allele was uniform across populations, revealing an underlying genetic similarity. Patterns of allele distribution suggestive of ethnic or geographic propinquity were discernible only in a few of the populations and was not applicable to the entire dataset while a number of the populations exhibited distinct identities evident from the occurrence of unique alleles in them. Genetic substructuring was detected among populations originating from northeastern and southern India reflective of their migrational histories and genetic isolation respectively.

Conclusion: Our analyses based on autosomal microsatellite markers detected no evidence of general clustering of population groups based on ethnic, linguistic, geographic or socio-cultural affiliations. The existence of substructuring in populations from northeastern and southern India has notable implications for population genetic studies and forensic databases where broad grouping of populations based on such affiliations are frequently employed.

Figure 1

Alleles with significant distribution among the different groups of India for the studied microsatellite markers. ○ represents alleles occurring at a high frequency and □ denotes unique alleles present in a population.

Figure 2

Bar plot of estimation of the membership coefficient (Q) for each individual of the Indian population grouped on geographic distribution. Each individual is represented by a thin vertical line, which is partitioned into K colored segments that represent the individual's estimated membership fractions in K clusters. Black lines separate individuals of different population groups based on geography. Population groups are labeled below the figure, with their geographical affiliations above it. The figure shown for K = 5 is based on the highest probability run at that K.

Figure 3

Estimated population structure in different geographic regions. Bar plot estimation figures for North, East, Northeast, South, West, and Central were based on the highest probability run at that K.