A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer

Authors:
Miklós Csűrös;István Miklós
Affiliations:
Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, Canada;Department of Plant Taxonomy and Ecology, Eötvös Lóránd University, Hungary
Venue:
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
Year:
2006

Citing 3
Cited 5

Sequence - Evolution - Function: Computational Approaches in Comparative Genomics

Sequence - Evolution - Function: Computational Approaches in Comparative Genomics
Phylogenetic trees based on gene content

Bioinformatics
Likely scenarios of intron evolution

RCG'05 Proceedings of the 2005 international conference on Comparative Genomics

Ancestral Reconstruction by Asymmetric Wagner Parsimony over Continuous Characters and Squared Parsimony over Distributions

RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
The gene evolution model and computing its associated probabilities

Journal of the ACM (JACM)
Simultaneous Identification of Duplications and Lateral Gene Transfers

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Recovering the tree-like trend of evolution despite extensive lateral genetic transfer: a probabilistic analysis

RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology
Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

Quantified Score

Hi-index	0.00

Visualization

Abstract

We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The likelihood for the changes in the size of a gene family across different organisms can be calculated in O(N+hM2) time and O(N+M2) space, where N is the number of organisms, h is the height of the phylogeny, and M is the sum of family sizes. We apply the model to the evolution of gene content in Proteobacteria using the gene families in the COG (Clusters of Orthologous Groups) database.