Inferring gene duplications, transfers and losses can be done in a discrete framework.
In the field of phylogenetics, the evolutionary history of a set of organisms is commonly depicted by a species tree-whose internal nodes represent speciation events-while the evolutionary history of a gene family is depicted by a gene tree-whose internal nodes can also represent macro-evolutionary events such as gene duplications and transfers. As speciation events are only part of the events shaping a gene history, the topology of a gene tree can show incongruences with that of the corresponding species tree. These incongruences can be used to infer the macro-evolutionary events undergone by the gene family. This is done by embedding the gene tree inside the species tree and hence providing a reconciliation of those trees. In the past decade, several parsimony-based methods have been developed to infer such reconciliations, accounting for gene duplications ([Formula: see text]), transfers ([Formula: see text]) and losses ([Formula: see text]). The main contribution of this paper is to formally prove an important assumption implicitly made by previous works on these reconciliations, namely that solving the (maximum) parsimony [Formula: see text] reconciliation problem in the discrete framework is equivalent to finding a most parsimonious [Formula: see text] scenario in the continuous framework. In the process, we also prove several intermediate results that are useful on their own and constitute a theoretical toolbox that will likely facilitate future theoretical contributions in the field.
SupAgro, UMR-AGAP, 2 Place Pierre Viala, 34060, Montpellier, France.|Institut de Biologie Computationnelle, Montpellier, France.
Vincent
V
Ranwez
ISEM, UMR 5554 (Univ. Montpellier, CNRS, IRD, EPHE), Place Eugene Bataillon, Montpellier, France. celine.scornavacca@univ-montp2.fr.|Institut de Biologie Computationnelle, Montpellier, France. celine.scornavacca@univ-montp2.fr.
Celine
C
Scornavacca
ISEM, UMR 5554 (Univ. Montpellier, CNRS, IRD, EPHE), Place Eugene Bataillon, Montpellier, France.|LIRMM, CNRS, Univ. Montpellier, Montpellier, France.
Jean-Philippe
JP
Doyon
LIRMM, CNRS, Univ. Montpellier, Montpellier, France.|Institut de Biologie Computationnelle, Montpellier, France.
Vincent
V
Berry
D000465:Algorithms; D005075:Biological Evolution; D019143:Evolution, Molecular; D017353:Gene Deletion; D020440:Gene Duplication; D022761:Gene Transfer, Horizontal; D049810:Genetic Speciation; D008954:Models, Biological; D010802:Phylogeny
Equivalence; Gene evolution; Parsimony; Phylogenetics; Tree embedding; Tree reconciliation