Maximum Gene-Support Tree

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

Interconnecting bilayer networks

A typical complex system should be described by a supernetwork or a network of networks, in which the networks are coupled to some other networks. As the first step to understanding the complex systems on such more systematic level, scientists studied interdependent multilayer networks. In this letter, we introduce a new kind of interdependent multilayer networks, i.e., interconnecting networks, for which the component networks are coupled each other by sharing some common nodes. Based on the empirical investigations, we revealed a common feature of such interconnecting networks, namely, the networks with smaller averaged topological differences of the interconnecting nodes tend to share more nodes. A very simple node sharing mechanism is proposed to analytically explain the observed feature of the interconnecting networks.Comment: 9 page