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Summary: Comparative Methods for the Analysis of Gene-Expression Evolution:
An Example Using Yeast Functional Genomic Data
Todd H. Oakley,* 1
Zhenglong Gu,* Ehab Abouheif, 3
Nipam H. Patel, 2
and Wen-Hsiung Li*
*Ecology and Evolution, and Howard Hughes Medical Institute, University of Chicago
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 nonphylogenetic 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.
Introduction
Since the Evolutionary Synthesis (Mayr and Provine
1980), which established genes as the primary source of
evolutionary variation, a major focus of biology has been to
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