that employ standard population genetics tests to infer selection and thus the historical importance of a gene.
How, then, does one address the problem of demography? One way is to develop a demographic model that provides a reasonable fit to available data and then apply statistical tests of selection under that demographic model. The estimation of demographic history from DNA sequence data was first applied to maize (Eyre-Walker et al., 1998; Hilton and Gaut, 1998). In these early studies, sequence variation was assessed at a handful of loci from maize and its wild ancestor, teosinte. It was explicitly assumed that there had been no artificial selection on these genes. Observed polymorphism data were compared with data simulated under a historical coalescent model that included a population bottleneck. The size and duration of the bottleneck were varied via simulation, and bottleneck parameters that best fit the observed data were determined. For example, over a time frame of 2,800 years (an estimate of the duration of domestication based on archaeological data), the effective size of the population maintained through the bottleneck was estimated to be ≈2,900 individuals (Hilton and Gaut, 1998). This indicates that high genetic diversity in maize is not necessarily due to a large founding population. Taken further, such inferences can be applied to better understand the agricultural practices of early domesticators (Hillman and Davies, 1990).
Since these initial studies, it has become possible to gather sequence polymorphism data from hundreds of loci. With many loci, it is no longer necessary or appropriate to assume that none of the genes has been targeted by selection, and it becomes possible both to infer the proportion of genes under selection and to identify those genes. At the same time, coalescent models have improved and can now include demographic factors such as recombination, population growth, and introgression (Hudson, 2002).
The bottom-up approach should be especially powerful when applied to domesticated species, for three reasons. First, archaeological remains provide independent information about the timing of the domestication bottleneck, and its effects are relatively well understood. Second, artificial selection is strong and domestication is recent on an evolutionary time scale, so that the signature of selection should be highly detectable in patterns of genetic diversity (Przeworski, 2002; Olsen et al., 2006; Teshima et al., 2006). Third, polymorphism can be compared between a crop and its wild ancestor, greatly increasing inferential power (Voight et al., 2005) and helping to discriminate among evolutionary events before, during, or after domestication (Wright and Gaut, 2005). Examples of this demographic approach have appeared in the literature with increasing frequency (95) and have been incorporated into testing for selection in humans and Drosophila as well (Tenaillon et al., 2004). At present, however, the process