A Linear-Time Algorithm for the Isometric Reconciliation of Unrooted Trees

In the reconciliation problem, we are given two phylogenetic trees. A species tree represents the evolutionary history of a group of species, and a gene tree represents the history of a family of related genes within these species. A reconciliation maps nodes of the gene tree to the corresponding points of the species tree, and thus helps to interpret the gene family history. In this paper, we study the case when both trees are unrooted and their edge lengths are known exactly. The goal is to root them and to find a reconciliation that agrees with the edge lengths. We show a linear-time algorithm for finding the set of all possible root locations, which is a significant improvement compared to the previous O(N3logN) algorithm.

[1]  S. Kelly,et al.  STRIDE: Species Tree Root Inference from Gene Duplication Events , 2017, bioRxiv.

[2]  Oliver Eulenstein,et al.  Maximum likelihood models and algorithms for gene tree evolution with duplications and losses , 2011, BMC Bioinformatics.

[3]  Dana Pardubská,et al.  Isometric gene tree reconciliation revisited , 2017, Algorithms for Molecular Biology.

[4]  Manolis Kellis,et al.  Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss , 2012, Bioinform..

[5]  Vincent Berry,et al.  Models, algorithms and programs for phylogeny reconciliation , 2011, Briefings Bioinform..

[6]  J. Lagergren,et al.  Probabilistic orthology analysis. , 2009, Systematic biology.

[7]  Robert E. Tarjan,et al.  Fast Algorithms for Finding Nearest Common Ancestors , 1984, SIAM J. Comput..

[8]  G. Moore,et al.  Fitting the gene lineage into its species lineage , 1979 .

[9]  David Haussler,et al.  The infinite sites model of genome evolution , 2008, Proceedings of the National Academy of Sciences.

[10]  Louxin Zhang,et al.  On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies , 1997, J. Comput. Biol..

[11]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[12]  Jian Ma,et al.  DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications , 2008, J. Comput. Biol..

[13]  Jerzy Tiuryn,et al.  Inferring phylogeny from whole genomes , 2007, Bioinform..

[14]  Cédric Chauve,et al.  An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[15]  Jerzy Tiuryn,et al.  Unrooted Tree Reconciliation: A Unified Approach , 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.