Originally published as Genetics Published Articles Ahead of Print on September 14, 2008.

Genetics, Vol. 180, 1379-1389, November 2008, Copyright © 2008
doi:10.1534/genetics.108.089623

Evolution of Primate Gene Expression: Drift and Corrective Sweeps?

R. Chaix^*,, M. Somel^,, D. P. Kreil^**, P. Khaitovich^, and G. A. Lunter^,1

^* Department of Statistics, University of Oxford, Oxford OX1 3TG, United Kingdom, Unité d'Eco-Anthropologie, CNRS UMR 5145, Musée de l'Homme, 75116 Paris, France, Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China, Max-Planck-Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany, ^** Chair of Bioinformatics, Boku University, AT-1190 Vienna, Austria and MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom

¹ Corresponding author: MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom.
E-mail: gerton.lunter{at}dpag.ox.ac.uk

Changes in gene expression play an important role in species' evolution. Earlier studies uncovered evidence that the effect of mutations on expression levels within the primate order is skewed, with many small downregulations balanced by fewer but larger upregulations. In addition, brain-expressed genes appeared to show an increased rate of evolution on the branch leading to human. However, the lack of a mathematical model adequately describing the evolution of gene expression precluded the rigorous establishment of these observations. Here, we develop mathematical tools that allow us to revisit these earlier observations in a model-testing and inference framework. We introduce a model for skewed gene-expression evolution within a phylogenetic tree and use a separate model to account for biological or experimental outliers. A Bayesian Markov chain Monte Carlo inference procedure allows us to infer the phylogeny and other evolutionary parameters, while quantifying the confidence in these inferences. Our results support previous observations; in particular, we find strong evidence for a sustained positive skew in the distribution of gene-expression changes in primate evolution. We propose a "corrective sweep" scenario to explain this phenomenon.

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