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An appraisal on the usefulness of R-matrix analysis and the model of Harpending and Ward (1982) to study the population structure of Iudian populations is made in the light of prevalent marriage patterns, caste structure, and cultural specificity of the region. With the help of available data on the migration histories and geographical backgrounds of marine fishermen on the east coast of India, and through the historical analysis of marriage patterns, it is demonstrated that the routine inferences based on the regression plots of average heterozygosity versus genetic distance from the centroid may not generally be apt for the Indian situation. Increased heterozygosity among migrant fishermen seems to have resulted from mating patterns within this community rather than from external gene flow. In either case, the genetic implications are supposedly identical. Nevertheless, when making inferences regarding local population structure it is important to have detailed knowledge of mating patterns and the cultural context of the region under study.