We investigate the evolutionary relationships between photosynthetic r
eaction center proteins (D1, D2, L and M) and demonstrate that the pat
tern 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 publishe
d studies, We conclude that there is equal support for hypotheses indi
cating (i) a single gene duplication of an ancestral reaction center p
rotein followed by diversification and (ii) two independent gene dupli
cations giving rise to proteins in oxygenic and anoxygenic systems.