Chemosensory evolution in the aquatic predator Drosophila enhydrobia

From the Wunderkammern of Renaissance Europe to the curated vaults of today's natural history museums, millions of insect specimens have been preserved, capturing an irreplaceable chronicle of biodiversity, including lineages that are rare, highly specialized, or already extinct. Yet their fragility has historically constrained genomic inquiry. Here, we apply museomic methodology to a >40-year-old specimen of Drosophila enhydrobia, a rarely collected member of the enigmatic simulivora group whose fully aquatic obligate predatory larvae develop in fast-flowing streams where they hunt black fly and midge larvae. Despite the specimen's age, we recovered a highly complete genome, enabling both phylogenetic and comparative analyses of one of the most ecologically unusual drosophilids. Phylogenomic inference places this African lineage within the subgenus Siphlodora, closely allied to Oriental riparian specialists, revealing that the simulivora lineage represents an extreme extension of an ancestral, water-associated niche rather than an isolated evolutionary departure. Comparative genomic analyses identify focused reductions in gene families associated with cuticle formation, detoxification, metabolism, and chemosensation, consistent with a highly specialized aquatic and carnivorous lifestyle. Expanding our framework to 30 additional species, sampled from within Siphlodora, including two more genomes recovered from museum specimens, we find that D. enhydrobia sits at the extreme of chemosensory reduction and simplification, even in comparison with other siphlodoran specialists, which display patterns of gain, loss, or stasis. Selection analyses reveal that these reductions are not accompanied by pervasive relaxation. Instead, a subset of retained chemosensory genes shows intensified selection, suggesting functional refinement rather than wholesale decay.