Protein-based phylogenies support a chimeric origin for the eukaryotic genome

The phylogenetic position of the archaebacteria and the place of eukaryotesin the history of life remain a question of debate. Recent studies based onsome protein-sequence data have obtained unusual phylogenies for theseorganisms. We therefore collected the protein sequences that were availablewith representatives from each of the major forms of life: thegram-negative bacteria, gram-positive bacteria, archaebacteria, andeukaryotes. Monophyletic, unrooted phylogenies based on these sequence datashow that seven of 24 proteins yield a significantgram-positive-archaebacteria clade/gram-negative- eukaryotic clade. Thephylogenies for these seven proteins cannot be explained by the traditionalthree-way split of the eukaryotes, archaebacteria, and eubacteria. Nine ofthe 24 proteins yield the traditional gram-positive-gram-negativeclade/archaebacteria-eukaryotic clade. The remaining eight proteins givephylogenies that cannot be statistically distinguished. These resultssupport the hypothesis of a chimeric origin for the eukaryotic cell nucleusformed from the fusion of an archaebacteria and a gram-negative bacteria.