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MBE Advance Access published online on September 8, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh257
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted August 30, 2004

Research Article

Comparative Methods for the Analysis of Gene Expression Evolution: An Example Using Yeast Functional Genomic Data

Todd H. Oakley 1*, Zhenglong Gu 2, Ehab Abouheif 3, Nipam H. Patel 3, and Wen-Hsiung Li 2

1 Ecology and Evolution, University of Chicago, IL; Howard Hughes Medical Institute, University of Chicago, IL
2 Ecology and Evolution, University of Chicago, IL
3 Howard Hughes Medical Institute, University of Chicago, IL

* To whom correspondence should be addressed. E-mail: oakley{at}lifesci.ucsb.edu.


  Abstract

Understanding the evolution of gene function is a primary challenge of modern evolutionary biology. Despite an expanding database from genomic and developmental studies, we are lacking quantitative methods for analyzing the evolution of some important measures of gene function, such as gene expression patterns. Here we introduce phylogenetic comparative methods to compare different models of gene expression evolution in a maximum likelihood framework. We find that expression of duplicated genes has evolved according to a non-phylogenetic model, where closely related genes are no more likely than more distantly related genes to share common expression patterns. These results are consistent with previous studies that found rapid evolution of gene expression during the history of yeast. The comparative methods presented here are general enough to test a wide range of evolutionary hypotheses using genomic-scale data from any organism.


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