dorsal/arxiv
View SchemaMaximum-frequency gene tree: a simplified genome-scale approach to overcoming incongruence in molecular phylogenies
| Authors | Yunfeng Shan, Xiu-Qing Li |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0609003 |
| URL | https://arxiv.org/abs/q-bio/0609003 |
| License | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ |
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, 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
{
"annotation_id": "9230528d-c35a-4528-87b2-2e534a2cc375",
"date_created": "2026-03-02T18:01:34.978000Z",
"date_modified": "2026-03-02T18:01:34.978000Z",
"file_hash": "2883c6a8fa018375791986fc63ac62eff5f2e5cf3663df8b0f50d95c77ce8492",
"private": false,
"record": {
"abstract": "Genomes and genes diversify during evolution; however, it is unclear to what\nextent genes still retain the relationship among species. Model species for\nmolecular phylogenetic studies include yeasts and viruses whose genomes were\nsequenced as well as plants that have the fossil-supported true phylogenetic\ntrees available. In this study, we generated single gene trees of seven yeast\nspecies as well as single gene trees of nine baculovirus species using all the\northologous genes among the species compared. Homologous genes among seven\nknown plants were used for validation of the fi nding. Four algorithms: maximum\nparsimony, minimum evolution, maximum likelihood, and neighbor-joining, were\nused. Trees were reconstructed before and after weighting the DNA and protein\nsequence lengths among genes. Rarely a gene can always generate the \"true tree\"\nby all the four algorithms. However, the most frequent gene tree, termed\n\"maximum gene-support tree\" (MGS tree, or WMGS tree for the weighted one), in\nyeasts, baculoviruses, or plants was consistently found to be the \"true tree\"\namong the species. The results provide insights into the overall degree of\ndivergence of orthologous genes of the genomes analyzed and suggest the\nfollowing: 1) The true tree relationship among the species studied is still\nmaintained by the largest group of orthologous genes; 2) There are usually more\northologous genes with higher similarities between genetically closer species\nthan between genetically more distant ones; and 3) The maximum gene-support\ntree refl ects the phylogenetic relationship among species in comparison.\n Keywords: genome, gene evolution, molecular phylogeny, true tree",
"arxiv_id": "q-bio/0609003",
"authors": [
"Yunfeng Shan",
"Xiu-Qing Li"
],
"categories": [
"q-bio.GN"
],
"license": "http://arxiv.org/licenses/nonexclusive-distrib/1.0/",
"title": "Maximum-frequency gene tree: a simplified genome-scale approach to overcoming incongruence in molecular phylogenies",
"url": "https://arxiv.org/abs/q-bio/0609003"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "ffd938f1-6ca7-470e-93d7-5367add05e53",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}