Reconciliation Revisited: Handling Multiple Optima When Reconciling with Duplication, Transfer, and Loss

Phylogenetic tree reconciliation is a powerful approach for inferring evolutionary events like gene duplication, horizontal gene transfer, and gene loss, which are fundamental to our understanding of molecular evolution. While Duplication-Loss (DL) reconciliation leads to a unique maximum-parsimony solution, Duplication-Transfer-Loss (DTL) reconciliation yields a multitude of optimal solutions, making it difficult the infer the true evolutionary history of the gene family. Here, we present an effective, efficient, and scalable method for dealing with this fundamental problem in DTL reconciliation. Our approach works by sampling the space of optimal reconciliations uniformly at random and aggregating the results. We present an algorithm to efficiently sample the space of optimal reconciliations uniformly at random in O(mn2) time, where m and n denote the number of genes and species, respectively. We use these samples to understand how different optimal reconciliations vary in their node mapping and event assignments, and to investigate the impact of varying event costs.

[1]  E. Koonin.  Orthologs, Paralogs, and Evolutionary Genomics 1 , 2005 .

[2]  Fredrik Ronquist,et al.  Parsimony analysis of coevolving species associa-tions , 2002 .

[3]  R. Page.  Maps between trees and cladistic analysis of historical associations among genes , 1994 .

[4]  Daniel Merkle,et al.  Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information , 2005, Theory in Biosciences.

[5]  Vincent Berry,et al.  Representing a Set of Reconciliations in a Compact Way , 2013, J. Bioinform. Comput. Biol..

[6]  Dannie Durand,et al.  A hybrid micro-macroevolutionary approach to gene tree reconstruction. , 2006 .

[7]  Dannie Durand,et al.  Notung: dating gene duplications using gene family trees , 2000, RECOMB '00.

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

[9]  Ping Xu,et al.  Isolation and characterization of an ABC-transporter cDNA clone from wheat (Triticum aestivum L.) , 2009, Molecular Biology.

[10]  Ali Tofigh,et al.  Using Trees to Capture Reticulate Evolution , 2009 .

[11]  Berend Snel,et al.  Keeping Afloat: A Strategy for Small Island Nations , 2005, BMC Bioinformatics.

[12]  Oliver Eulenstein,et al.  Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees. , 2011, Systematic biology.

[13]  J. G. Burleigh,et al.  Heuristics for the Gene-duplication Problem : A Θ ( n ) Speed-up for the Local Search , 2007 .

[14]  Lawrence A. David,et al.  Rapid evolutionary innovation during an Archaean genetic expansion , 2011, Nature.

[15]  Oliver Eulenstein,et al.  Heuristics for the Gene-Duplication Problem: A Theta ( n ) Speed-Up for the Local Search , 2007, RECOMB.

[16]  Frank Rutschmann,et al.  Molecular dating of phylogenetic trees : A brief review of current methods that estimate divergence times , 2022 .

[17]  Erik L. L. Sonnhammer,et al.  Automated ortholog inference from phylogenetic trees and calculation of orthology reliability , 2002, Bioinform..

[18]  Paola Bonizzoni,et al.  Reconciling a gene tree to a species tree under the duplication cost model , 2005, Theor. Comput. Sci..

[19]  Anushya Muruganujan,et al.  PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium , 2009, Nucleic Acids Res..

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

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

[22]  Ali Tofigh,et al.  Using Trees to Capture Reticulate Evolution : Lateral Gene Transfers and Cancer Progression , 2009 .

[23]  Vincent Berry,et al.  An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers , 2010, RECOMB-CG.

[24]  Albert J. Vilella,et al.  EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. , 2009, Genome research.

[25]  M. Charleston,et al.  Jungles: a new solution to the host/parasite phylogeny reconciliation problem. , 1998, Mathematical biosciences.

[26]  Ilya B. Muchnik,et al.  A Biologically Consistent Model for Comparing Molecular Phylogenies , 1995, J. Comput. Biol..

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

[28]  Ran Libeskind-Hadas,et al.  The Cophylogeny Reconstruction Problem Is NP-Complete , 2011, J. Comput. Biol..

[29]  Gorbunov KIu,et al.  Reconstructing genes evolution along a species tree , 2009 .

[30]  Dannie Durand,et al.  A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction , 2005, RECOMB.

[31]  Ran Libeskind-Hadas,et al.  Jane: a new tool for the cophylogeny reconstruction problem , 2010, Algorithms for Molecular Biology.

[32]  Zhi-Zhong Chen,et al.  Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[33]  Daniel Merkle,et al.  A parameter-adaptive dynamic programming approach for inferring cophylogenies , 2010, BMC Bioinformatics.

[34]  K. Gorbunov,et al.  [Reconstructing genes evolution along a species tree]. , 2009, Molekuliarnaia biologiia.

[35]  Dannie Durand,et al.  Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees , 2012, Bioinform..

[36]  Martin Vingron,et al.  On the Equivalence of Two Tree Mapping Measures , 1998, Discret. Appl. Math..

[37]  Jerzy Tiuryn,et al.  DLS-trees: A model of evolutionary scenarios , 2006, Theor. Comput. Sci..

[38]  Michael T. Hallett,et al.  Simultaneous Identification of Duplications and Lateral Gene Transfers , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[39]  Nadia El-Mabrouk,et al.  Gene Family Evolution by Duplication, Speciation and Loss , 2022 .

[40]  E. Koonin.  Orthologs, paralogs, and evolutionary genomics. , 2005, Annual review of genetics.

[41]  Ran Libeskind-Hadas,et al.  On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem , 2009, J. Comput. Biol..

[42]  Manolis Kellis,et al.  A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction , 2010, Molecular biology and evolution.

[43]  N. Friedman,et al.  Natural history and evolutionary principles of gene duplication in fungi , 2007, Nature.