Phenotypic plasticity and local adaptation often interact to generate phenotypic variation, yet disentangling their respective contributions remains challenging. The yellowtail anemonefish (Amphiprion clarkii) exhibits remarkable geographical and within-population variation in melanism, making it an ideal system to investigate the relative roles of environmental and genetic drivers. We quantified black pigmentation in 260 individuals sampled across the Ryukyu Archipelago and combined ecological, phenotypic and genome-wide SNP data to investigate the mechanisms underlying colour variation.
Our analyses revealed that both ecological and genetic factors contribute to melanism, although their relative importance differed across spatial scales. Host anemone identity emerged as a major determinant of colour expression, while population genetic structure explained additional variation at broader geographical scales. Genomic analyses further suggest that genetic effects act through developmental pathways rather than directly controlling pigmentation.
These findings indicate that melanism in A. clarkii results from the interaction between phenotypic plasticity and genetic background, illustrating how ecological interactions and evolutionary processes jointly shape phenotypic diversity in coral reef fishes.