Xiu-Qing Li | Searcharxiv

arXiv2009

The hypothesis that coelacanth is the closest living relative of tetrapods 3 was rejected based on three genome-scale approaches

Since its discovery of the living fossil in 1938, the coelacanth (Latimeria chalumnae) has generally been considered to be the closest living relative of the land vertebrates, and this is still the prevailing opinion in most general biology textbooks. However, the origin of tetrapods has been the subject of intense debate for decades. The three principal hypothesis (lungfish-tetrapod, coelacanth-tetrapod, or lungfish-coelacanth sister group) have been proposed. We used the maximum gene-support tree approach to analyze 43 nuclear genes encoding amino acid residues, and compared the results of concatenation and majority-rule tree approaches. The results inferred with three common phylogenetic methods and three genome-scale approaches consistently rejected the hypothesis that the coelacanth is the closest living relative of tetrapods.

q-bio.PE↗

arXiv2009

GeneSupport Maximum Gene-Support Tree Approach to Species Phylogeny Inference

Summary: GeneSupport implements a genome-scale algorithm: Maximum Gene-Support Tree to estimate species tree from gene trees based on multilocus sequences. It provides a new option for multiple genes to infer species tree. It is incorporated into popular phylogentic program: PHYLIP package with the same usage and user interface. It is suitable for phylogenetic methods such as maximum parsimony, maximum likelihood, Baysian and neighbour-joining, which is used to reconstruct single gene trees firstly with a variety of phylogenetic inference programs.

q-bio.GN↗

arXiv2008

Maximum-frequency gene tree: a simplified genome-scale approach to overcoming incongruence in molecular phylogenies

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

q-bio.GN↗