Widespread Genetic Signals of Visual System Adaptation in Deepwater Cichlid Fishes

The light environment exerts a profound selection pressure on the visual system, driving morphological and molecular adaptations that may also contribute to species diversification. Here, we investigate the evolution and genetic basis of visual system diversification in deepwater cichlid fishes of the genus Diplotaxodon. We find that Diplotaxodon exhibit the greatest eye size variation among Lake Malawi cichlids and that this variation is largely uncoupled from phylogeny, with various nonsister species sharing similar eye sizes. Using a combination of genome-wide association analysis across nine Diplotaxodon species, haplotype-based selection scans, and transcriptome analysis, we uncover consistent and widespread signatures of evolution in visual pathways, centered on green-sensitive opsins and throughout the phototransduction cascade, suggesting coordinated evolution of eye size and visual molecular pathways. Our findings underscore the role of visual system diversification in niche specialization within deepwater habitats and offer new insights into visual system evolution within this extraordinary cichlid radiation.