Molecular Genetics Laboratory, Potato Research Centre, Agriculture and Agri-Food Canada, 850 Lincoln Rd, P.O. Box 20280, Fredericton, New Brunswick, E3B 4Z7, Canada.
Evol Bioinform Online. 2008 May 15;4:181-91. doi: 10.4137/ebo.s652.
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 finding. 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 reflects the phylogenetic relationship among species in comparison.
在进化过程中，基因组和基因会发生多样化；然而，基因在多大程度上仍然保留着物种间的关系尚不清楚。分子系统发育研究的模式物种包括已测序的酵母和病毒，以及具有化石支持的真实系统发育树的植物。在这项研究中，我们使用比较物种间所有同源基因，生成了七种酵母物种的单基因树和九种杆状病毒物种的单基因树。七个已知植物的同源基因用于验证该发现。使用了四种算法——最大简约法（MP）、最小进化法（ME）、最大似然法（ML）和邻接法（NJ）。在对基因间 DNA 和蛋白质序列长度进行加权之前和之后，重建了树。很少有一个基因总是可以通过所有四种算法生成“真实树”。然而，在酵母、杆状病毒或植物中，最常见的基因树，称为“最大基因支持树”（MGS 树，或加权的 WMGS 树），被一致地发现是物种间的“真实树”。结果提供了对所分析基因组的同源基因总体分化程度的深入了解，并提出以下观点：1）最大数量的同源基因仍然保持着物种间的真实树关系；2）在遗传上较近的物种之间，通常有更多具有更高相似性的同源基因，而在遗传上更远的物种之间则较少；3）最大基因支持树反映了物种间的系统发育关系。
