PASCAL - Pattern Analysis, Statistical Modelling and Computational Learning

Estimating the tempo and mode of gene family evolution from comparative genomic data
Matthew Hahn, Tijl De Bie, Jason Stajich, Chi Nguyen and Nello Cristianini
Genome Research Volume 15, pp. 1153-1160, 2005. ISSN 1088-9051


Comparison of whole genomes has revealed that changes in the size of gene families among organisms is quite common. However, there are as yet no models of gene family evolution that make it possible to estimate ancestral states or to infer upon which lineages gene families have contracted or expanded. In addition, large differences in family size have generally been attributed to the effects of natural selection, without a strong statistical basis for these conclusions. Here we use a model of stochastic birth and death for gene family evolution and show that it can be efficiently applied to multispecies genome comparisons. This model takes into account the lengths of branches on phylogenetic trees, as well as duplication and deletion rates, and hence provides expectations for divergence in gene family size among lineages. The model offers both the opportunity to identify large-scale patterns in genome evolution and the ability to make stronger inferences regarding the role of natural selection in gene family expansion or contraction. We apply our method to data from the genomes of five yeast species to show its applicability.

EPrint Type:Article
Project Keyword:Project Keyword UNSPECIFIED
Subjects:Computational, Information-Theoretic Learning with Statistics
ID Code:2208
Deposited By:Tijl De Bie
Deposited On:23 September 2006