Fig. 1

Nucleotide-based phylogeny of the analyzed fish species. We searched for positively selected genes on the last common ancestor of the clownfishes (Amphiprion, red). The two species A. clarkii and A. percula depicted in bold are those that were sequenced in this study. The phylogenetic tree was derived as part of the positive selection analysis with the PosiGene pipeline [79]. Briefly, during this process 8215 genes were concatenated and the resulting concatenated alignment split in 404 fragments each of which had a length of 15,000 nucleotides. From each fragment, a phylogeny was calculated via maximum likelihood and, from all resulting 404 trees, a consensus tree was determined using the Phylip package [83]. The scale bar represents 0.05 substitutions per site