A Linear Time Algorithm for Error-Corrected Reconciliation of Unrooted Gene Trees

摘要

Evolutionary methods are increasingly challenged by the fast growing resources of genomic sequence information. Fundamental evolutionary events, like gene duplication, loss, and deep coalescence, account more then ever for incongruence between gene trees and the actual species tree. Gene tree reconciliation is addressing this fundamental problem by invoking the minimum number of gene-duplication and losses that reconcile a gene tree with a species tree. Despite its promise, gene tree reconciliation assumes the gene trees to be correctly rooted and free of error, which severely limits its application in practice. Here we present a novel linear time algorithm for error-corrected gene tree reconciliation of unrooted gene trees. Furthermore, in an empirical study on yeast genomes we successfully demonstrate the ability of our algorithm to (i) reconcile (cure) error-prone gene trees, and (ii) to improve on more advanced evolutionary applications that are based on gene tree reconciliation.