The mosaic nature of the eukaryotic nucleus

The phylogenies for each of the protein-coding genes from the Methanococcusjannaschii genome were surveyed to determine the history of the majorgroups of life. For each gene, homologous sequences from other archaea,eucarya, and Gram-positive and Gram-negative bacteria were collected andaligned, and a phylogeny was reconstructed with a maximum-likelihoodalgorithm. The majority of significant phylogenies favor the eucarya andthe archaca as sister groups. A smaller, but still substantial, portion ofthese significant phylogenies favor an eucarya/Gram-negative clade. Theseresults indicate that support for the early history of life is notunequivocal. A chimeric origin of eukaryotes or an ancient, massivehorizontal transfer of genes from Gram-negative bacteria to eucarya canexplain many of the observed phylogenies.