Manuel Lafond1, Marc Hellmuth2. 1. Department of Computer Science, Université de Sherbrooke, 2500 Boul. de l'Université, Sherbrooke, J1K 2R1 Canada. 2. School of Computing, University of Leeds, E C Stoner Building, Leeds, LS2 9JT UK.
Abstract
BACKGROUND: The history of gene families-which are equivalent to event-labeled gene trees-can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The question then arises as whether inferred event-labeled gene trees are "biologically feasible" which is the case if one can find a species tree with which the gene tree can be reconciled in a time-consistent way. RESULTS: In this contribution, we consider event-labeled gene trees that contain speciations, duplications as well as horizontal gene transfer (HGT) and we assume that the species tree is unknown. Although many problems become NP-hard as soon as HGT and time-consistency are involved, we show, in contrast, that the problem of finding a time-consistent species tree for a given event-labeled gene can be solved in polynomial-time. We provide a cubic-time algorithm to decide whether a "time-consistent" species tree for a given event-labeled gene tree exists and, in the affirmative case, to construct the species tree within the same time-complexity.
BACKGROUND: The history of gene families-which are equivalent to event-labeled gene trees-can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The question then arises as whether inferred event-labeled gene trees are "biologically feasible" which is the case if one can find a species tree with which the gene tree can be reconciled in a time-consistent way. RESULTS: In this contribution, we consider event-labeled gene trees that contain speciations, duplications as well as horizontal gene transfer (HGT) and we assume that the species tree is unknown. Although many problems become NP-hard as soon as HGT and time-consistency are involved, we show, in contrast, that the problem of finding a time-consistent species tree for a given event-labeled gene can be solved in polynomial-time. We provide a cubic-time algorithm to decide whether a "time-consistent" species tree for a given event-labeled gene tree exists and, in the affirmative case, to construct the species tree within the same time-complexity.
Authors: Manuela Geiß; Edgar Chávez; Marcos González Laffitte; Alitzel López Sánchez; Bärbel M R Stadler; Dulce I Valdivia; Marc Hellmuth; Maribel Hernández Rosales; Peter F Stadler Journal: J Math Biol Date: 2019-04-09 Impact factor: 2.259
Authors: Marcus Lechner; Sven Findeiss; Lydia Steiner; Manja Marz; Peter F Stadler; Sonja J Prohaska Journal: BMC Bioinformatics Date: 2011-04-28 Impact factor: 3.169
Authors: Manuela Geiß; Marcos E González Laffitte; Alitzel López Sánchez; Dulce I Valdivia; Marc Hellmuth; Maribel Hernández Rosales; Peter F Stadler Journal: J Math Biol Date: 2020-01-30 Impact factor: 2.259
Authors: Nikolai Nøjgaard; Manuela Geiß; Daniel Merkle; Peter F Stadler; Nicolas Wieseke; Marc Hellmuth Journal: Algorithms Mol Biol Date: 2018-02-06 Impact factor: 1.405
Authors: Adrian M Altenhoff; Brigitte Boeckmann; Salvador Capella-Gutierrez; Daniel A Dalquen; Todd DeLuca; Kristoffer Forslund; Jaime Huerta-Cepas; Benjamin Linard; Cécile Pereira; Leszek P Pryszcz; Fabian Schreiber; Alan Sousa da Silva; Damian Szklarczyk; Clément-Marie Train; Peer Bork; Odile Lecompte; Christian von Mering; Ioannis Xenarios; Kimmen Sjölander; Lars Juhl Jensen; Maria J Martin; Matthieu Muffato; Toni Gabaldón; Suzanna E Lewis; Paul D Thomas; Erik Sonnhammer; Christophe Dessimoz Journal: Nat Methods Date: 2016-04-04 Impact factor: 28.547