Reconciling Gene Trees to a Species Tree
نویسندگان
چکیده
In this paper we deal with the general problem of recombining the information from evolutionary trees representing the relationships between distinct gene families. First we solve a problem from [8] regarding the construction of a minimum reconciled tree by giving an efficient algorithm. Then we show that the exemplar problem, arising from the exemplar analysis of multigene genomes [2], is NP-hard even when the number of copies of a given label is at most two. Finally we introduce two novel formulations for the problem of recombining evolutionary trees, extending the notion of the gene duplication problem studied in [8, 11, 9, 10, 6], and we give an exact algorithm (via dynamic programming) for one of the formulations given.
منابع مشابه
Quantitative Comparison of Tree Pairs Resulted from Gene and Protein Phylogenetic Trees for Sulfite Reductase Flavoprotein Alpha-Component and 5S rRNA and Taxonomic Trees in Selected Bacterial Species
Introduction: FAD is the cofactor of FAD-FR protein family. Sulfite reductase flavoprotein alpha-component is one of the main enzymes of this family. Based on applications of this enzyme in biotechnology and industry, it was chosen as the subject of evolutionary studies in 19 specific species. Method: Gene and protein sequences of sulfite reductase flavoprotein alpha-component, 5S rRNA sequence...
متن کاملReconciliation of Gene and Species Trees With Polytomies
Motivation: Millions of genes in the modern species belong to only thousands of gene families. Genes duplicate and are lost during evolution. A gene family includes instances of the same gene in different species and duplicate genes in the same species. Two genes in different species are ortholog if their common ancestor lies in the most recent common ancestor of the species. Because of complex...
متن کاملQuantitative Comparison of Tree Pairs Resulted from Gene and Protein Phylogenetic Trees for Sulfite Reductase Flavoprotein Alpha-Component and 5S rRNA and Taxonomic Trees in Selected Bacterial Species
Introduction: FAD is the cofactor of FAD-FR protein family. Sulfite reductase flavoprotein alpha-component is one of the main enzymes of this family. Based on applications of this enzyme in biotechnology and industry, it was chosen as the subject of evolutionary studies in 19 specific species. Method: Gene and protein sequences of sulfite reductase flavoprotein alpha-component, 5S rRNA sequence...
متن کاملReconciling Gene Trees with Apparent Polytomies
We consider the problem of reconciling gene trees with a species tree based on the widely accepted Gene Duplication model from Goodman et al. Current algorithms that solve this problem handle only binary gene trees or interpret polytomies in the gene tree as true. While in practice polytomies occur frequently, they are typically not true. Most polytomies represent unresolved evolutionary relati...
متن کاملInferring phylogeny from whole genomes
MOTIVATION Inferring species phylogenies with a history of gene losses and duplications is a challenging and an important task in computational biology. This problem can be solved by duplication-loss models in which the primary step is to reconcile a rooted gene tree with a rooted species tree. Most modern methods of phylogenetic reconstruction (from sequences) produce unrooted gene trees. This...
متن کاملAlgorithms for Unrooted Gene Trees with Polytomies
Gene tree reconciliation is a method to reconcile gene trees that are confounded by complex histories of gene duplications with a provided species tree. The trees involved are required to be rooted and full binary. Reconciling gene trees allows not only to identify and study such histories for gene families, but is also the base for several higher level applications including the estimation of ...
متن کامل