# Genomic basis of the evolution of vertical bars in clownfishes

## TL;DR

This study explores how clownfish evolved different numbers of vertical color bars by examining genetic changes linked to pigmentation and selection pressures.

## Contribution

The study identifies pigmentation-related genes under selection that correlate with the gain or loss of vertical bars in clownfish evolution.

## Key findings

- Pigmentation-related genes like gch2, oca2, and vps11 show changes in selective pressure linked to vertical bar evolution.
- The pmel gene, important for melanin production, was found under positive selection, suggesting a role in bar patterning.
- Both gains and losses of vertical bars occurred in clownfish evolution, with genetic evidence of selection driving these changes.

## Abstract

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 (\documentclass[12pt]{minimal}
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\begin{document}$$d_{\text {N}} / d_{\text {S}}$$\end{document} 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.

The online version contains supplementary material available at 10.1186/s12864-026-12570-9.