Protein phylogeny gives a robust estimation for early divergences of eukaryotes: phylogenetic place of a mitochondria-lacking protozoan, Giardia lamblia

A partial nucleotide sequence of the mRNA encoding a major part ofelongation factor 1 alpha (EF1 alpha) from a mitochondria-lackingprotozoan, Giardia lamblia, was reported, and the phylogenetic relationshipamong lower eukaryotes was inferred by the maximum- likelihood andmaximum-parsimony methods of protein phylogeny. Both the methodsconsistently demonstrated that, G. lamblia among the four protozoan speciesbeing analyzed, is the earliest offshoot of the eukaryotic tree. Althoughthe Giardia EF1 alpha gene showed an extremely high G+C content as comparedwith those of other protozoa, it was concentrated only at the third codonpositions, resulting in no remarkable differences of amino acid frequenciesvis-a-vis those of other species. This clearly suggests (a) that the aminoacid frequencies of conservative proteins are free from the drastic bias ofgenome G+C content, which is a serious problem in the widely used tree ofribosomal RNA, and (b) that protein phylogeny gives a robust estimation forthe early divergences in the evolution of eukaryotes.