Models, algorithms and programs for phylogeny reconciliation

Gene sequences contain a gold mine of phylogenetic information. But unfortunately for taxonomists this information does not only tell the story of the species from which it was collected. Genes have their own complex histories which record speciation events, of course, but also many other events. Am...

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Bibliographic Details
Published in:Briefings in bioinformatics Vol. 12; no. 5; pp. 392 - 400
Main Authors: Doyon, Jean-Philippe, Ranwez, Vincent, Daubin, Vincent, Berry, Vincent
Format: Journal Article
Language:English
Published: England Oxford University Press 01.09.2011
Oxford Publishing Limited (England)
Oxford University Press (OUP)
Subjects:
Algorithms
Animals
Computer Science
Data Structures and Algorithms
Evolution
Evolution, Molecular
Gene Duplication
Gene Transfer, Horizontal
Genome
Genomics
Genomics - methods
Humans
Life Sciences
Mathematical models
Models, Genetic
Phylogenetics
Phylogeny
Speciation
Species Specificity
Taxonomy
loss
parsimony
gene duplication
probability
phylogeny
lateral gene transfer
reconciliation
ISSN:1467-5463, 1477-4054, 1477-4054
Online Access:Get full text
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Summary:Gene sequences contain a gold mine of phylogenetic information. But unfortunately for taxonomists this information does not only tell the story of the species from which it was collected. Genes have their own complex histories which record speciation events, of course, but also many other events. Among them, gene duplications, transfers and losses are especially important to identify. These events are crucial to account for when reconstructing the history of species, and they play a fundamental role in the evolution of genomes, the diversification of organisms and the emergence of new cellular functions. We review reconciliations between gene and species trees, which are rigorous approaches for identifying duplications, transfers and losses that mark the evolution of a gene family. Existing reconciliation models and algorithms are reviewed and difficulties in modeling gene transfers are discussed. We also compare different reconciliation programs along with their advantages and disadvantages.
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ISSN:1467-5463
1477-4054
1477-4054
DOI:10.1093/bib/bbr045