Genome-wide SNP analysis identifies population structure and genetic differentiation in Anopheles stephensi

Anopheles stephensi, a major urban malaria vector in South Asia and the Arabian Peninsula, has recently spread to several African countries, raising significant public health concerns. Understanding its genetic structure is important for tracing invasion pathways; however, population genetic studies have been limited by sparse genome-wide datasets particularly from India, its native range. Here, we sequenced five An. stephensi samples from southern India and integrated them with 33 publicly available genomic datasets from India and Ethiopia to enable a comparison across native and invasive populations. Genome-wide analysis across 38 samples, revealed higher genetic diversity and evidence of broad-scale population differentiation among Indian and Ethiopian samples. Genetic differentiation between regions was moderate (FST = 0.14). A total of 813 SNPs were fixed (FST = 1) between populations, with 586 fixed in Ethiopian samples and 227 in Indian samples. Several fixed SNPs were concentrated in genes involved in sensory perception, ion transport, development, and transcriptional regulation, highlighting candidate genomic regions associated with population-specific differentiation that warrant further investigation. Overall, the results provide evidence of genetic differentiation between native and invasive populations and highlight genomic regions that may contribute to population-specific divergence in An. stephensi.