Population genetic structure of Chilo partellus (Swinhoe) (Lepidoptera: Crambidae) in India to unravel the genetic diversity: insights from multilocus mitochondrial DNA markers

Abstract Chilo partellus is a major stem borer of cereals in India, causing significant yield losses. Understanding its population genetic structure is critical for tracing origins, elucidating dispersal patterns, and informing sustainable pest management. The present study focused on 11 geographically distinct Indian populations (Akola, New Delhi, Hyderabad, Umiam, Parbhani, Solan, Surat, Udaipur, Raichur, Coimbatore, and Kovilpatti) using multilocus mitochondrial DNA markers, viz., cytochrome c oxidase subunits I and II ( COI and COII ), cytochrome b (Cytb), and 16S rRNA. Phylogenetic analyses revealed moderate genetic differentiation, with no strictly location-specific clades, indicating partial geographic structuring alongside widespread haplotype sharing. COI sequences showed minimal divergence, reflecting strong genetic cohesion and recent common ancestry, while COII and Cytb provided higher resolution for detecting regional variation. The 16S rRNA marker captured deeper evolutionary divergence, particularly among northern, central, and southern populations. Haplotype networks displayed starlike topologies with dominant central haplotypes and multiple low-frequency derivatives, consistent with recent population expansion and high gene flow. Nucleotide polymorphism analyses identified locus-specific hotspots contributing to haplotype differentiation but not to strong population-specific signatures. Overall, Indian C. partellus populations exhibit low-to-moderate mitochondrial diversity and weak phylogeographic structure, suggesting a common genetic origin with extensive contemporary gene flow likely facilitated by contiguous cropping systems, migratory behaviour, and anthropogenic movement. These findings underscore the importance of area-wide integrated pest management strategies and highlight the utility of multilocus mitochondrial markers in resolving both historical and recent population dynamics in migratory insect pests.