Isometric gene tree reconciliation revisited

Broňa Brejová,Tomáš Vinař,Michal Sabo,Askar Gafurov,Dana Pardubská

doi:10.1186/s13015-017-0108-x

Broňa Brejová, Tomáš Vinař + Show 3 more

Open Access

https://doi.org/10.1186/s13015-017-0108-x

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Journal: Algorithms for Molecular Biology	Publication Date: Jun 13, 2017
Citations: 16	License type: open-access

Affiliation: Comenius University Bratislava

Abstract

BackgroundIsometric 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. in 2008 in the context of reconstructing evolutionary histories of genomes in the infinite sites model.ResultsIn this paper, we show that the original algorithm by Ma et al. is incorrect, and we propose a modified algorithm that addresses the problems that we discovered. We have also improved the running time from O(N^2) to O(Nlog N), where N is the total number of nodes in the two input trees. Finally, we examine two new variants of the problem: reconciliation of two unrooted trees and scaling of branch lengths of the gene tree during reconciliation of two rooted trees.ConclusionsWe provide several new algorithms for isometric reconciliation of trees. Some questions in this area remain open; most importantly extensions of the problem allowing for imprecise estimates of branch lengths.

Highlights

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
In this paper, we revisit the problem of isometric gene tree reconciliation introduced by Ma et al [1, 2]
The evolutionary history starts with a single ancestral gene which evolves by a series of duplications, speciations, and losses, resulting in several present-day species, each carrying some number of copies of the studied gene

Summary

Introduction

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. Definition 4 An input partial history is a triple (GI , SI , μ) such that GI and SI are rooted or unrooted phylogenetic trees with positive edge weights, μ is a mapping from leaves of GI to leaves of SI, and each internal node v in both GI and SI satisfies the following:

Results

Conclusion