We investigate the evolutionary relationships between photosynthetic reaction center proteins (D1, D2, L and M) and demonstrate that the pattern of nucleotide substitution in these is more complicated than has been assumed in previous phylogenetic analyses. We show that there are serious violations of methodological assumptions in previous published studies. We conclude that there is equal support for hypotheses indicating (i) a single gene duplication of an ancestral reaction center protein followed by diversification and (ii) two independent gene duplications giving rise to proteins in oxygenic and anoxygenic systems.
