Phylogenetic Analysis of Indian Dromedary Breeds Based on the Mitochondrial D-Loop Marker

The mitochondrial displacement loop (D-loop) region is a non-coding control region that plays a crucial role in replication and transcription, serving as an informative marker for evolutionary and demographic studies. In this study, the complete mitochondrial D-loop sequences from NCBI public database were analyzed across nine Indian and other dromedary populations. Evolutionary and pairwise sequence analysis indicate distinct separation from foreign populations and substantive clustering of Indian breeds within a monophyletic clade. Indian breeds showed greater than 99.4% sequence identity, minimal diversity (π ≈ 0.003), and limited divergence (k = 3-4), whereas Arabian and Iranian populations exhibited more prominent variability (π ≈ 0.004-0.0044; k ≈ 5). Nucleotide composition analyses corroborated the AT-rich nature of the D-loop with conserved sequence length and enrichment of CpG motifs. This suggests selective conservation of functional elements in the D-loop sequence region. Correlation and correspondence analyses highlighted non-random nucleotide usage and repeat dynamics consistent with replication-associated mutational pressures. Demographic structural diversity showed that nearly all genetic variation was distributed among populations (~99.9%), with minimal variation within breeds. Pairwise differentiation values indicated substantial divergence between Indian and foreign breeds, with Indian desert breeds displaying restricted differentiation, possibly due to shared maternal ancestry. Neutrality test results for the sequence dataset interpreted ongoing demographic expansion or bottleneck recovery for the Arabian, Iranian, Sindhi, and Kharai populations. In contrast, for other Indian desert breeds, the neutrality test values that were closing towards zero may express current population shrinkage. Conserved transcription factor binding motifs further support the role of purifying selection on sequence functional constraints. These findings highlight that Indian dromedaries bear highly conserved mitochondrial D-loop sequences, which are influenced by purifying selection and demographic stability. This low mitochondrial diversity in non-coding sequence can mirror the declining population size and emphasizes the urgent need for targeted conservation strategies.