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Author Arvestad, Lars ♦ Lagergren, Jens ♦ Sennblad, Bengt
Source ACM Digital Library
Content type Text
Publisher Association for Computing Machinery (ACM)
File Format PDF
Copyright Year ©2009
Language English
Subject Domain (in DDC) Computer science, information & general works ♦ Data processing & computer science
Subject Keyword Phylogeny ♦ Duplication ♦ Evolution ♦ Gene ♦ Loss ♦ Probability ♦ Reconciliation
Abstract Phylogeny is both a fundamental tool in biology and a rich source of fascinating modeling and algorithmic problems. Today's wealth of sequenced genomes makes it increasingly important to understand evolutionary events such as duplications, losses, transpositions, inversions, lateral transfers, and domain shuffling. We focus on the gene duplication event, that constitutes a major force in the creation of genes with new function [Ohno 1970; Lynch and Force 2000] and, thereby also, of biodiversity. We introduce the probabilistic gene evolution model, which describes how a gene tree evolves within a given species tree with respect to speciation, gene duplication, and gene loss. The actual relation between gene tree and species tree is captured by a reconciliation, a concept which we generalize for more expressiveness. The model is a canonical generalization of the classical linear birth-death process, obtained by replacing the interval where the process takes place by a tree. For the gene evolution model, we derive efficient algorithms for some associated probability distributions: the probability of a reconciled tree, the probability of a gene tree, the maximum probability reconciliation, the posterior probability of a reconciliation, and sampling reconciliations with respect to the posterior probability. These algorithms provides the basis for several applications, including species tree construction, reconciliation analysis, orthology analysis, biogeography, and host-parasite co-evolution.
ISSN 00045411
Age Range 18 to 22 years ♦ above 22 year
Educational Use Research
Education Level UG and PG
Learning Resource Type Article
Publisher Date 2009-04-01
Publisher Place New York
e-ISSN 1557735X
Journal Journal of the ACM (JACM)
Volume Number 56
Issue Number 2
Page Count 44
Starting Page 1
Ending Page 44


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Source: ACM Digital Library