Mitochondrial and Nuclear DNA Analyses of Rhipicephalus microplus from Mizoram, Northeast India: Insights into Genetic Diversity and Endosymbiont

<b>Background/Objectives</b>: In this study, we conducted molecular identification of <i>R.microplus</i> and explored the genetic diversity of <i>R. microplus</i> for the first time in Mizoram, a Northeastern Hill (NEH) state of India bordering Myanmar. <b>Methods</b>: To assess genetic variation and evolutionary relationships, we employed phylogenetic analyses, genetic divergence metrics, and haplotype network construction based on mitochondrial (COX1 and 16S rDNA) and nuclear (ITS-2 and 18S rDNA) markers. Additionally, multivariate Principal Coordinate Analysis (PCoA) was used to visualize genetic differentiation among <i>R. microplus</i> populations. <b>Results</b>: Our analyses indicated that populations of <i>R. microplus sensu lato</i> from India, Bangladesh, and Pakistan form a closely related matrilineal lineage distinct from <i>R. microplus sensu stricto</i>, clustering within clade C of the COX1-based phylogeny. Globally, 24 COX1 haplotypes were recovered, with 1 haplotype identified in India. The Mizoram population exhibited a single 16S rDNA haplotype; however, intraspecific divergence was evident across India, with seven matrilineal haplotypes detected and nineteen globally. Further, five haplotypes were identified within <i>R. microplus</i> using the ITS-2 marker, while five haplotypes were observed within the <i>Rhipicephalus</i> genus using the 18S rDNA marker. Moreover, this study revealed the presence of <i>Coxiella-</i>like endosymbionts in 95% of the tick specimens analyzed. <b>Conclusions</b>: This study fills a critical knowledge gap by providing the first molecular documentation of tick diversity in Mizoram, a strategic region along the Indo-Myanmar border, and offers novel insights into the phylogeography and symbiotic associations of <i>R. microplus</i> and related tick taxa.