Combined Analysis of Mitochondrial <i>Cytochrome c Oxidase</i> and <scp> <i>NADH</i> </scp> <i>Dehydrogenase Subunit 1</i> Genes Reveals <scp>SNPs</scp> Associated With Major Haplotypes and Genetic Structure of <scp> <i>Bactrocera dorsalis</i> </scp>

ABSTRACT The oriental fruit fly, Bactrocera dorsalis Hendel, is a major pest affecting mango and other fruit crops worldwide. Despite extensive research, genetic analysis across different locations and host plants remains limited in the Philippines. This study assessed the genetic diversity, population structure and demographic history of Philippine B. dorsalis populations using mitochondrial genes cox1 , cox2 and ND1 . A total of 109 fruit flies were collected from mango, guava and star fruit across multiple provinces. Analysis of cox1 (697 bp) and ND1 (597 bp) revealed more variation than cox2 (556 bp), which was more conserved. Two major haplotype groups, PHF‐A and PHF‐B, were identified, differentiated by SNPs at specific nucleotide positions in cox1 (603, 606, 619 and 663) and ND1 (354). Within PHF‐B, three subhaplotypes were resolved using ND1 . The two haplotype groups were widely distributed across provinces and host plants, showing no geographic isolation or host specialisation, with PHF‐A as the predominant lineage. PHF‐A displayed a star‐like haplotype network and significantly negative neutrality values (Tajima's D = −1.92 and Fu's F s = −10.74, p &lt; 0.05) consistent with recent expansion, while PHF‐B showed a linear network reflecting incipient expansion, gradual diversification and populaton substructure. Concatenated sequences (1850 bp) revealed moderate haplotype number, low genetic diversity and expansion signals across populations. Pairwise F ST values among provinces were low (0–0.022), indicating limited geographic structure, with most variation occurring within provinces (93.36% AMOVA), whereas differentiation between PHF‐A and PHF‐B was significant ( F ST = 0.108, p &lt; 0.001) with high sequence divergence (ΦST = 0.936, p &lt; 0.001). Global phylogeny indicated PHF‐A as a major Philippine lineage, whereas PHF‐B clustered with Asian populations. To our knowledge, this is the first combined analysis of cox and ND1 in the Philippines, which provides novel insights into the evolutionary history and population dynamics of B. dorsalis in the country and establishes a genetic baseline for future genomic, ecological and management studies that can inform biosecurity and sustainable pest management.