Genomic basis of the evolution of vertical bars in clownfishes

Clownfish exhibit striking color patterns, characterized primarily by the presence of zero to three vertical white bars, along with three main colors: orange, white, and/or black. The common ancestor of clownfish likely possessed three vertical bars, with several instances of gains and losses occurring throughout clownfish evolutionary history over the past 10 million years. However, the evolutionary genomic mechanisms underlying the gain or loss of vertical bars remain unknown. In this study, we tested whether vertical bar transitions across the clownfish phylogeny were associated with changes in non-synonymous to synonymous substitution rates ([Formula: see text] values). Our analyses identified pigmentation-related genes that underwent changes in selective pressure, including gch2, oca2, and vps11, which are linked to melanophores, iridophores, and visual function. Additionally, pmel, a key melanogenesis gene, was found under positive selection, suggesting its role in shaping bar patterning. These results provide new insights into the genomic basis of coloration in clownfish, highlighting how selection and genetic variation influence phenotypic evolution.Significance statement Clownfish are one of the most iconic groups of reef fish. Besides their mutualism with sea anemones, their conspicuous color patterns have fascinated evolutionary biologists and aquarium hobbyists alike. The number of vertical bars are variable between species and are thought to be used in species recognition, although little is known about how differences in their number of bars may have evolved. We have reconstructed the most likely evolution of number of vertical bars across the clownfish phylogeny finding both gain and loss events. We found that certain pigmentation-related genes underwent changes in selective pressures or positive selection alongside the gain or loss of vertical bars, providing evidence for selection driving the evolution of vertical bar patterns.