MBE Advance Access published online on November 3, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi035
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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1 Dept. of Ecology and Evolutionary Biology, U.C. Irvine, Irvine, CA 92697-2525; Dept. of Biology, York University, Toronto, ON Canada
* To whom correspondence should be addressed. The first papers on plant molecular population genetics were published
Review Article
Molecular Population Genetics and the Search for Adaptive Evolution in Plants
2 Dept. of Ecology and Evolutionary Biology, U.C. Irvine, Irvine, CA 92697-2525
Brandon S. Gaut, E-mail: bgaut{at}uci.edu
Abstract 
10 years ago. Since that time, well over 50 additional studies of plant nucleotide polymorphism have been published, and many of these focused on detecting the signature of balancing or positive selection at a locus. In this review, we discuss some of the theoretical and statistical issues surrounding the detection of selection, with focus on plant populations, and we also summarize the empirical plant molecular population genetics literature. At face value, the literature suggests that a history of balancing or positive selection in plant genes is rampant. In two well-studied taxa (maize and Arabidopsis) over 20% of studied genes have been interpreted as containing the signature of selection. We argue that this is probably an overstatement of the prevalence of natural selection in plant genomes, for two reasons. First, demographic effects are difficult to incorporate and have generally not been well integrated into the plant population genetics literature. Second, the genes studied to date are not a random sample, so selected genes may be overrepresented. The next generation of studies in plant molecular population genetics requires additional sampling of local populations, explicit comparisons among loci, and improved theoretical methods to control for demography. Eventually candidate loci should be confirmed by explicit consideration of phenotypic effects.
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