Algorithms for Rapid Error Correction for the Gene Duplication Problem

Abstract

AbstractGene tree - species tree reconciliation problems infer the patterns and processes of gene evolution within the context of an organismal phylogeny. In one example, the gene duplication problem seeks the evolutionary scenario that implies the minimum number of gene duplications needed to reconcile a gene tree and a species tree. While the gene duplication problem can effectively link gene and species evolution, error in gene trees can profoundly bias the results. We describe novel algorithms that rapidly search local Subtree Prune and Regraft (SPR) or Tree Bisection and Reconnection (TBR) neighborhoods of a gene tree to find a topology that implies the fewest duplications. These algorithms improve on the current solutions by a factor of n for searching SPR neighborhoods and n 2 for searching TBR neighborhoods, where n is the number of vertices in the given gene tree. They provide a fast error correction protocol for gene trees, in which we allow small gene tree rearrangements to improve the reconciliation cost. We tested the SPR tree rearrangement algorithm on a collection of 1201 plant gene trees, and in every case, the SPR algorithm identified an alternate topology that implied at least one fewer duplication. We also demonstrate a simple method to use the gene rearrangement algorithm to improve gene tree parsimony phylogenetic analyses, which infer a species tree based on the gene duplication problem.KeywordsSpecies TreeGene TreeTree ReconciliationNear Neighbor InterchangeGene Tree TopologyThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.