Insights into the genomics of clownfish adaptive radiation: the genomic substrate of the diversification

ABSTRACT Clownfishes are an iconic group of coral reef fishes that evolved a mutualistic interaction with sea anemones, which triggered the rapid diversification of the group. We investigated the genomic architecture underlying this process to determine the genomic characteristics associated with the adaptive radiation of the group and assess the mechanisms of parallel evolution in clownfishes. We took advantage of the available genomic data of five pairs of closely related but ecologically divergent clownfish species to perform comparative genomic analyses. We found that clownfish genomes show two bursts of transposable elements, overall accelerated coding evolution, and topology inconsistencies potentially resulting from hybridization events. These characteristics possibly facilitated the rapid diversification of the group. We also detected a signature of positive selection throughout the radiation in 5.4 % of the clownfish genes. Among them, five presented functions associated with social behavior and ecology. They could have potentially played a role in the evolution of size-based hierarchical social structure so particular to clownfishes. Finally, we found genes with patterns of either relaxation or intensification of purifying selection and signals of positive selection linked with clownfish ecological divergence, suggesting some level of parallel evolution during the diversification of the group. Altogether, these results provide the first insights into the genomic substrate of clownfish adaptive radiation. This work integrates the growing collection of studies investigating the genomic mechanisms governing species diversification, which brings us a step closer to understanding how biodiversity on Earth is created