both are transcribed, with the nuclear-encoded protein being targeted to the complex plastid. We can speculate that it is the fusion of Psb28 with the ribosomal protein S4 that prevents the elimination of psb28 from the plastid genome. Phylogenetic analyses show that nuclear psb28 is a duplicate of the plastid homologue, although this relationship only became apparent when appropriate methods were used. The reason lies in the compositional bias of the analyzed sequences, which causes LBA and substantially affects the topology of the tree. Molecular Phylogeny Nucleotide sequences coding for Psb28 from various photoautotrophs including cyanobacteria, glaucophytes, plants, chlorophytes, rhodophytes, cryptophytes, haptophytes, and stramenopiles, were downloaded from GenBankT and other sources (see Table S1 ). The nucleotide sequence dataset was translated to amino acids in BioEdit [33] and either aligned using ClustalW algorithm (BioEdit) and retranslated back into nucleotides or aligned using Mafft-6.717 [34] . Both amino acid and nucleotide alignments were used for further phylogenetic analyses. Both alignments were manually edited (BioEdit), and ambiguously aligned regions and gaps were excluded from further analyses. A specific nucleotide dataset was made by exclusion of the third nucleotide codon positions. Nucleotide datasets were used to construct Maximum parsimony (MP) [35] and Maximum likelihood trees (ML with GTR+? 4 +I model) [36] . Because the third codon position appeared to be saturated, we excluded this position prior to the analysis (trees not shown). Amino acid alignments were used to construct MP [35] , Neighbor joining (AsaturA [25] ; method designed to deal with