Detection of 40 bp tandem repeat motif and associated insertions and deletions (INDEL) in the mitochondrial DNA control region of Sambar deer (Rusa unicolor)

Sambar (Rusa unicolor) is the largest oriental deer and has a wide distribution across South and Southeast Asia. Despite its wide distribution range, little information on the genetics of this species is available to date. We examined the genetic variability of Sambar populations using a partial fragment of the mtDNA control region and reconstructed the phylogeographic association of Sambar populations across India. We detected 56 haplotypes with an overall haplotype diversity, Hd = 0.939 +/- 0.012 and nucleotide diversity, Pi = 0.029 +/- 0.002 in Sambar populations across India. The Sambar populations of Northeast India exhibits 30 localized mtDNA control region haplotypes with no haplotype sharing with other populations of India. We identified a 40 bp tandem repeat motif in the mtDNA control region with variable copy numbers ranging between three to six duplications. The Sambar populations across India exhibited phylogeographic differentiation based on the observed insertion and deletion patterns in the mtDNA control region. The 40 bp tandem repeat motif was associated with patterns of insertions and deletions among different populations of Sambar in India. The findings of this study provide baseline information on the mtDNA genetic variability of Sambar populations across India, which is crucial for future population genetic studies.