New perspectives on gene family evolution: Losses in reconciliation and a link with supertrees

Abstract

Reconciliation between a set of gene trees and a species tree is the most commonly used approach to infer the duplication and loss events in the evolution of gene families, given a species tree. When a species tree is not known, a natural algorithmic problem is to infer a species tree such that the corresponding reconciliation minimizes the number of duplications and/or losses. In this paper, we clarify several theoretical questions and study various algorithmic issues related to these two problems. (1) For a given gene tree T and species tree S, we show that there is a single history explaining T and consistent with S that minimizes gene losses, and that this history also minimizes the number of duplications. We describe a simple linear-time and space algorithm to compute this parsimonious history, that is not based on the Lowest Common Ancestor (LCA) mapping approach; (2) We show that the problem of computing a species tree that minimizes the number of gene duplications, given a set of gene trees, is in fact a slight variant of a supertree problem; (3) We show that deciding if a set of gene trees can be explained using only apparent duplications can be done efficiently, as well as computing a parsimonious species tree for such gene trees. We also characterize gene trees that can be explained using only apparent duplications in terms of compatible triplets of leaves.Reconciliation between a set of gene trees and a species tree is the most commonly used approach to infer the duplication and loss events in the evolution of gene families, given a species tree. When a species tree is not known, a natural algorithmic problem is to infer a species tree such that the corresponding reconciliation minimizes the number of duplications and/or losses. In this paper, we clarify several theoretical questions and study various algorithmic issues related to these two problems. (1) For a given gene tree T and species tree S, we show that there is a single history explaining T and consistent with S that minimizes gene losses, and that this history also minimizes the number of duplications. We describe a simple linear-time and space algorithm to compute this parsimonious history, that is not based on the Lowest Common Ancestor (LCA) mapping approach; (2) We show that the problem of computing a species tree that minimizes the number of gene duplications, given a set of gene trees, is in fact a slight variant of a supertree problem; (3) We show that deciding if a set of gene trees can be explained using only apparent duplications can be done efficiently, as well as computing a parsimonious species tree for such gene trees. We also characterize gene trees that can be explained using only apparent duplications in terms of compatible triplets of leaves. © Springer-Verlag Berlin Heidelberg 2009.