More on selection outside Africa

I have a feeling I'll have many occasions to use that headline.

Here's the central part of Stajich and Hahn (2004) concerning selection in Europeans vs. Africans:

There is a highly significant, positive relationship between Tajima's D statistic from loci in the European-American data set and recombination rates across loci, even while controlling for (R2 = 0.09, F = 14.7, P = 0.0002). This relationship is not significant in the African-American data (R2 = 0.02, F = 3.1, P = 0.08). If we do not control for levels of polymorphism and use simply the Tajima's D statistic values alone, there is a marginally significant relationship between recombination and D statistic values in both populations (fig. 4) (EA, R = 0.10, F = 16.5, P < 0.0001; AA, R2 = 0.03, F = 4.9, P = 0.027). The positive relationship between the D statistic values and recombination in the European-American population suggests that multiple hitchhiking events have been associated with the migration out of Africa and colonization of novel habitats. Repeated fixation of advantageous mutations throughout the genome has caused a skew in linked variation towards lower frequencies, with more pronounced effects in regions of low recombination. The lack of a relationship in the African-American sample could be an effect of sampling from an admixed population, but the rank-order of D statistic values in this population is significantly correlated with the values in the European-American sample (Spearman's = 0.33, P < 0.0001). We believe that the significant correlation present only in the European-American sample is caused by the increased number and/or effect of advantageous alleles that are associated with migration into new habitats. This conclusion assumes that the environments in Africa are more similar to the ancestral human environments than those found outside of Africa, and that migration out of Africa brought humans into novel environments. These conclusions are consistent, however, with a number of recent studies also reporting a preponderance of evidence for selective sweeps in non-African human populations (Kayser, Brauer, and Stoneking 2003; Storz, Payseur, and Nachman 2004). Also, because we have controlled for levels of polymorphism, the relationship between recombination and the frequency spectrum in European-Americans should be independent of any mutagenic effect of recombination (Hellmann et al. 2003).

The paper ends this way:

Whereas demographic events such as population bottlenecks or expansions will affect all genes in a genome, natural selection is expected to have only locus-specific or region-specific effects on DNA variation. Our analyses have shown that the demographic histories of human populations can largely account for the level and frequency of variation across the genome. However, even working within a nonequilibrium framework, we were able to show deviations from neutral expectations at the ABO and TRPV6 loci and in many regions of low recombination. The results for this data set are consistent with the combined effects of a population bottleneck and repeated selective sweeps in the human migration out of Africain agreement with previous reports (Kayser, Brauer, and Stoneking 2003; Storz, Payseur, and Nachman 2004)and suggest that natural selection affects a relatively large proportion of the genome.

The evidence for widespread selection, in other words, is the association of Tajima's D and recombination rate; this association is significant in Europeans but not in African-Americans. The lack of such an association in the African-American sample may be partly explained by a dual ancestry among Africans and Europeans, since recent population mixture tends to inflate the number of rare alleles in a sample (and hence decrease Tajima's D).

This is not the greatest test for selection, since recent selection (i.e. new positively selected variants that are not yet near fixation) may not strongly affect Tajima's D. And the effect in Europeans is manifested as high-recombination loci having positive D values, not low-recombination loci having negative values. So clearly there is selection here, but it is not being picked up that strongly.

References:

Stajich JE, Hahn MW. 2004. Disentangling the effects of demography and selection in human history. Mol Biol Evol 22:63-73. <a href="http://mbe.oxfordjournals.org/cgi/content/full/22/1/63</a>