Early evolution of eukaryotes inferred by combined phylogeny of multiple genes

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In order to elucidate a higher-order phylogeny of eukaryotes infer a root of the eukaryotic tree, combined phylogeny of multiple genes were carried out. For this purpose, several genes encoding cytosolic ribosomal RNAs and conservative proteins were isolated and sequenced from various organisms belonging to stramenopiles, alveolates, centrohelids, cryptomonads, rhodophytes, and fornicates. Including original sequence data obtained, various kinds of data sets with different taxon samplings and with different selections of genes were generated and these were analyzed by combined maximum likelihood analyses of the multiple genes. Until recently major outcomes listed below have been obtained:1. Optimal trees locating centrohelids at the outgroup position to bikont organisms and locating between the branches of amoebozoa and opisthokonts were independently obtained by different data sets, but these locations were not clearly supported with statistical confidence.2. No clear support was obtained for the monophyly of chromalveolates including cryptophytes, haptophytes, stramenopiles, and alveolates.3. Phylogenies of elongation factors 1 α and 2 demonstrated that Dysnectes brevis and a flagellate resemble to D. brevis (NY0173) were located between the branchings of trichomonads and diplomonads, supporting the previous results based on the SSUrRNA phylogeny.