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Fay and Wu (1999) examine a historical model in which a population quickly shrinks, stays small for some time, and then suddenly recovers its original population size, at which it stays until samples are drawn from it. This is a bottleneck model of the kind traditionally used in population genetics (Nei, Maruyama, and Chakraborty 1975); however, it is not the model that is most commonly considered in the context of genetic evidence of human population size change. That model is one of population size expansion, and it pervades the literature on analysis of mitochondrial DNA (e.g., Rogers and Harpending 1992), as well as the more recent literature on microsatellites (e.g., Kimmel et al. 1998), some of which explicitly confounds ‘‘expansion’’ with ‘‘bottleneck.’’ Fay and Wu (1999) repeatedly cite Hey (1997), who showed that nuclear genes and mtDNA are not both consistent with simple historical models. However, Hey’s paper explored only models of constant population size and models of expansion. Both of these models are considerably simpler than a bottleneck model, and they were the models that had received most of the attention in the literature. However, Hey’s (1997) paper may have contributed to a confusion over models, for the final sentence did mention ‘‘bottleneck.’’ Fay and Wu (1999) bring up a valuable point, that the time over which the pattern of polymorphism responds to a change in population size will be greater for larger populations. This means that the polymorphism patterns of genes with inherently different population sizes (e.g., mtDNA and nuclear genes) may be out of phase with one another if the period of population size fluctuation is sufficiently short and the fluctuation has been recent. Fay and Wu’s letter is also timely in light of the increasing amount of nuclear gene data that are emerging. Since Hey’s (1997) paper, which focused mostly on a few small data sets, larger data sets from PDHA1 (Harris and Hey 1999), b-globin (Harding et al. 1997), dystrophin (Zietkiewicz et al. 1998), and lipoprotein lipase (Clark et al. 1998) have been published, and all reveal an abundance of intermediate frequency polymorphism and positive values for Tajima’s D (Tajima 1989b). Also recently, small samples from a series of X-linked loci revealed that five out of six loci had positive values of D (although three were just slightly positive) (Nachman et al. 1998). Thus, the overall im-

Population bottlenecks and patterns of human polymorphism