Isometric Gene Tree Reconciliation Revisited

Abstract

Isometric gene tree reconciliation is a gene tree/species tree reconciliation problem where both the gene tree and the species tree include branch lengths, and these branch lengths must be respected by the reconciliation. The problem was introduced by Ma et al. (2008a) in the context of reconstructing evolutionary histories of genomes in the infinite sites model. In this paper, we show that the original algorithm by Ma et al. (2008a) is incorrect, and we propose a modified algorithm that addresses the problems that we discovered. Moreover, by adapting a data structure by Amir et al. (2007), we were able to improve the running time from O(mn) to \(O(n+m\log m)\), where n is the size of the species tree, and m is the size of the gene tree.