DNA barcoding and phylogenetic relationship for Aedes aegypti on Java Island, Indonesia

Objective: This study aimed to identify Aedes ( Ae. ) aegypti mosquitoes in four areas on Java Island, Indonesia, and to characterize their phylogenetic relationship based on the cytochrome oxidase subunit I (COI) gene. Methods: Mosquito specimens were collected from four geographical locations on Java Island using oviposition traps based on dengue outbreaks. Ae. aegypti larvae were morphologically identified and analyzed for their COI sequence. Sequences polymorphism was measured using DnaSP. Kimura two-parameter was used in MEGA X to estimate pairwise genetic distances. The median-joining haplotype network was generated using PopART, and the maximum likelihood tree was constructed using iTOL. Results: A total of 40 Ae. aegypti specimens were identified, with 13 haplotypes and 10 polymorphic sites detected. The number of haplotypes was higher in Jakarta (H=6) and lower in Bandung (H=2). The mean intraspecific genetic distance ranged from 0.1% to 1.0%, while the mean inter-specific distance varied between 0.3% to 0.9%. The phylogenetic tree revealed two clades and significant genetic differentiation occurred between Ae. aegypti populations, with a fixation index ranging from 0.00 to 0.50. The greatest genetic distance was found between Ae. aegypti populations in Bandung and Semarang. Conclusions: A significant genetic difference was observed among Ae. aegypti populations, suggesting that human activities and ecological conditions may affect the genetic differentiation of this species.