Reconciliation of Gene and Species Trees

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, i...

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Vydáno v:BioMed research international Ročník 2014; číslo 2014; s. 1 - 22
Hlavní autoři: Rusin, L. Y., Lyubetskaya, E. V., Gorbunov, K. Y., Lyubetsky, Vassily
Médium: Journal Article
Jazyk:angličtina
Vydáno: Cairo, Egypt Hindawi Puplishing Corporation 01.01.2014
Hindawi Publishing Corporation
John Wiley & Sons, Inc
Témata:
Algorithms
Binding sites
Biology
Computational Biology - methods
Evolution
Evolution, Molecular
Gene Transfer, Horizontal
Genetic research
Genomes
Identification and classification
Methods
Models, Genetic
Mutation
Phenetics
Phylogenetics
Phylogeny
Reconciliation
ISSN:2314-6133, 2314-6141, 2314-6141
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Shrnutí: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.
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Academic Editor: William H. Piel
ISSN:2314-6133
2314-6141
2314-6141
DOI:10.1155/2014/642089