ecoregion, diet, and subsistence. Much of this variation is related to major transitions that occurred during human evolutionary history, including the dispersal out of sub-Saharan Africa to regions with different climates and the adoption of more specialized—often less diverse—diets (i.e., farming and animal husbandry vs. foraging). Our results aim to clarify the genetics underlying the adaptive responses to these transitions.
Most human phenotypes, including adaptive traits like height and body proportions, are quantitative and highly polygenic (Manolio et al., 2009), and most human variation is shared across populations. Therefore, the same adaptive allele may often be independently selected in different geographic areas that share the same environment. The environmental aspects considered in this analysis changed dramatically over human evolutionary time. As a result, selection on standing—rather than new—alleles, which afford a faster adaptive response to environmental change (Hermisson and Pennings, 2005), may have played a prominent role in adaptation to new environments. This proposal is supported by expectations of selection models for quantitative traits (Falconer and MacKay, 1996), specifically that selection will generate small allele frequency shifts at many loci until the population reaches a new optimum (Pritchard et al., 2010). Whereas approaches that detect selection under a hard sweep model aim to identify loci that drove a new allele quickly to high frequency in the population (Pritchard et al., 2010), our approach is well suited to detect small shifts in the frequencies of beneficial alleles that have a broad geographic distribution [see Hancock et al. (2010) for a more detailed discussion]. For quantitative traits, the method we use may be particularly appropriate for understanding recent human adaptations. In this sense, our results fill an important gap and are useful for reconstructing the genetic architecture of human adaptations.
Some of our most interesting signals seem to be adaptations to dietary specializations. Although cultural adaptations certainly played an important role in our ability to diversify, there is strong evidence that genetic adaptations have been crucial as well. A previous genome-wide analysis of sequence divergence between species found evidence for ancient adaptations along the human lineage in the promoters of nutrition-related genes along the human lineage (Haygood et al., 2007). Examples of more recent genetic adaptations that were integral for dietary specializations include variants near the lactase gene, which confer the ability for adults to digest fresh milk in agropastoral populations, and an increase in the number of amylase gene copies in horticultural and agricultural populations (Bersaglieri et al., 2004; Perry et al., 2007; Tishkoff et al., 2007b; Enattah et al., 2008). Our results indicate that genetic adaptations to dietary specializations in human populations may be widespread. In particular, we find signals of adaptations in populations that heavily depend on roots and