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The parameters of genetic variation, genetic distances and time of divergence in three Indian goat breeds were studied using 16 cattle microsatellite markers. The mean number of alleles and mean allele size (bp) per microsatellite marker in goats were 5.37 ± 0.78 and 143.9 ± 33.75 bp respectively. The average values of heterozygosity and polymorphism information content were 0.54 ± 0.2 and 0.48 ± 0.20, respectively. Five of the eight genetic distance methods were highly correlated, revealing a closer relationship between Jamnapari and Barbari goats. A phylogenetic tree constructed from inter-individual distances revealed that the individuals clustered according to the breed to which they belonged, and the Jamnapari and Barbari goats formed a cluster. The divergence times between Sirohi and Jamnapari, and Sirohi and Barbari were ∼2000 years, while its value between Barbari and Jamnapari goats was …