Maximum Gene-Support Tree

Abstract

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 (MP), minimum evolution (ME), maximum likelihood (ML), and neighbor-joining (NJ)-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.

43 genes support the lungfish-coelacanth grouping related to the closest living relative of tetrapods with the Bayesian method under the coalescence model

“…Another result from two genes supported lungfish and not the coelacanth as the closest living relative of the tetrapods [15]. In our previous study [22,23], tree II received significantly lower support than tree I or tree III and, evidently, lower taxon jackknife probabilities with all the phylogenetic methods and genome-scale approaches. The supports for tree III were significantly higher than those for tree I for only two out of 63 events, and taxon jackknife probabilities for tree III were slightly higher than those for tree I with MP, but the differences in supports and taxon jackknife probabilities between tree III and tree I are not as obvious as those between tree II and tree III/I.…”

“…Another from two recombination activating genes (Rag1 and Rag2) supported lungfish and not the coelacanth as the closest living relative of the tetrapods [ 15 ]. Our previous study provided strong evidence in favor of rejecting Hypothesis 2, but weak evidence to support Hypothesis 3 based on 43 genes with three common phylogenetic methods and three genome-scale approaches [ 22 , 23 ].…”

Genome-scale approach proves that the lungfish-coelacanth sister group is the closest living relative of tetrapods with the BEST program

“…Two recombination activation 3 genes supported lungfish and not the coelacanth as the closet living relative of the tetrapods . Our previous study provided strong evidence that hypothesis 2 is rejected, but hypothesis 1 or 3 could not be determined based on 43 genes with three common phylogenetic methods and three genome-scale approaches [23][24] .…”

Efficiency of Nuclear and Mitochondrial Markers Recovering and Supporting Known Amniote Groups

“…It is clear that different genes present distinct probabilities of efficiently recovering the correct tree and that a careful marker selection has been shown to be more important than the choice of a tree-building method 1,10. The longer the alignment, for instance, the lower is the sampling error 6,7. Also, a single gene tree may differ from the species tree, which is more likely the result of a multi-marker analysis.…”

“…In spite of the positive aspects, however, multiple markers inconsistency does represent a problem with actual data. 5–8 The overwhelming and rapidly accumulating amounts of molecular data have just scratched the surface of the problem. 9 It is clear that different genes present distinct probabilities of efficiently recovering the correct tree and that a careful marker selection has been shown to be more important than the choice of a tree-building method.…”