title: Reconciliation of gene and species trees.
abstract: The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree.
authors.affiliation: Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny Pereulok 19, Moscow 127994, Russia ; Faculty of Biology, Moscow State University, Leninskie Gory 1-12, Moscow 119234, Russia.
authors.forename: L Y
authors.initials: LY
authors.lastname: Rusin
authors.affiliation: Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny Pereulok 19, Moscow 127994, Russia.
authors.forename: E V
authors.initials: EV
authors.lastname: Lyubetskaya
authors.affiliation: Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny Pereulok 19, Moscow 127994, Russia.
authors.forename: K Y
authors.initials: KY
authors.lastname: Gorbunov
authors.affiliation: Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny Pereulok 19, Moscow 127994, Russia.
authors.forename: V A
authors.initials: VA
authors.lastname: Lyubetsky
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D008957:Models, Genetic; D009154:Mutation; D010802:Phylogeny