Coral Fluorescent Proteins Figure 2. Bayesian phylogenetic tree of the cnidarian fluorescent proteins; Arthropoda FPs are shown as an outgroup. The edges with posterior probability less than 0.95 are collapsed. Black dots identify the proteins first described in this paper. Major clades and sub-clades are denoted, as well as the two reconstructed ancestral proteins (All-coral and All-Faviina). See legend for the color-coding of FP color classes. The position of meffGFP is tentative based on the short portion of its sequence that did not undergo gene conversion (see text for details). See Table S1 for the GenBank accession numbers corresponding to the protein names, and File S1 for the FASTA-formatted alignment of coding cDNA sequences. doi:10.1371/journal.pone.0002680.g002 within the remaining 198 nucleotides of the coding region, whereas the corresponding region in meffGFP is only 74% identical to amilRFP. This difference is highly significant (p,0.001) for the number of nucleotides involved. It can be concluded therefore that it was the portion of meffRFP gene that was copied into meffGFP via gene conversion and not the other way around. meffGFP was therefore excluded from the main phylogenetic analysis and its placement within clade C2 is tentatively based on the short unconverted portion of its coding sequence. Ancestral colors For this study we reconstructed two ancestral proteins: one was the common ancestor of all coral proteins and the other an ancestor of all Faviina proteins (‘‘all-coral’’ and ‘‘all-Faviina’’ respectively, Fig. 2). We applied a novel strategy of reconstruction to address the problem of uncertainty associated with the ancestral sequence prediction. Instead of synthesizing the protein having the most probable amino acid at each site, for each of the ancestral nodes we reconstructed five proteins in which the identity of the amino acid at a site was a result of random sampling from the PLoS ONE | www.plosone.org 6 July 2008 | Volume 3 | Issue 7 | e2680