  Genomes and genes diversify during evolution; however, it is unclear to what
extent genes still retain the relationship among species. Model species for
molecular phylogenetic studies include yeasts and viruses whose genomes were
sequenced as well as plants that have the fossil-supported true phylogenetic
trees available. In this study, we generated single gene trees of seven yeast
species as well as single gene trees of nine baculovirus species using all the
orthologous genes among the species compared. Homologous genes among seven
known plants were used for validation of the fi nding. Four algorithms: maximum
parsimony, minimum evolution, maximum likelihood, and neighbor-joining, were
used. Trees were reconstructed before and after weighting the DNA and protein
sequence lengths among genes. Rarely a gene can always generate the "true tree"
by all the four algorithms. However, the most frequent gene tree, termed
"maximum gene-support tree" (MGS tree, or WMGS tree for the weighted one), in
yeasts, baculoviruses, or plants was consistently found to be the "true tree"
among the species. The results provide insights into the overall degree of
divergence of orthologous genes of the genomes analyzed and suggest the
following: 1) The true tree relationship among the species studied is still
maintained by the largest group of orthologous genes; 2) There are usually more
orthologous genes with higher similarities between genetically closer species
than between genetically more distant ones; and 3) The maximum gene-support
tree refl ects the phylogenetic relationship among species in comparison.
  Keywords: genome, gene evolution, molecular phylogeny, true tree
