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

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

2005-09-27

arxiv.org/abs/q-bio/0509037v1

Biology

Quantitative Biology

Populations and Evolution

Scientific paper

10.1007/11732990_18

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+hM^2) time and O(N+M^2) 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 Preoteobacteria using the gene families in the COG (Clusters of Orthologous Groups) database.

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