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Methods

Estimating the tempo and mode of gene family evolution from comparative genomic data

¹ Center for Population Biology, University of California, Davis, California 95616, USA ² Department of Computer Science, University of California, Davis, California 95616, USA ³ Department of Statistics, University of California, Davis, California 95616, USA ⁴ ISIS Research Group, University of Southampton, Southampton, SO17 1BJ, United Kingdom ⁵ Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27708, USA

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.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.3567505.

⁶ These authors contributed equally to this work.

⁷ Corresponding author.
E-mail mwh{at}Indiana.edu; fax (812) 855-6705.

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