Genome-wide SNP analysis of genetic differentiation between co-existing morphotypes of Aedes aegypti in India

We conducted a genomic differentiation analysis of two co-occurring Aedes aegypti morphotypes, the type form Aedes aegypti aegypti (normal) and its morphological variant Ae. aegypti var. luciensis. Across eight samples, ∼24.6 million high-quality biallelic SNPs were identified. All the eight samples were found unrelated based on kinship analysis. Multivariate analyses including PCA, redundancy analysis, DAPC, and phylogenetic clustering revealed subtle but consistent genome-wide differentiation between morphotypes. Whereas, fastSTRUCTURE analysis indicated weak clustering. Overall genome-wide Fst was low (Fst = 0.039), yet 11% SNPs (0.039 million) showed relatively high differentiation (Fst > 0.25). Among these, 1012 SNPs showed alternate alleles between morphotypes in the present dataset. These SNPs mapped to 348 genes, majority of which were enriched for neuronal and synapse-associated pathways. These results indicate modest but localized genomic divergence, which may reflect variation at specific functional loci rather than genome-wide divergence. The findings provide a preliminary genomic framework for future studies exploring the functional, behavioral, and epidemiological significance of morphotype variation in Ae. aegypti.