MBE Advance Access originally published online on September 8, 2004
Molecular Biology and Evolution 2005 22(1):63-73; doi:10.1093/molbev/msh252
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Research Article |
Disentangling the Effects of Demography and Selection in Human History
* Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina; and Center for Population Biology, University of California, Davis
E-mail: mwhahn{at}ucdavis.edu.
Demographic events affect all genes in a genome, whereas natural selection has only local effects. Using publicly available data from 151 loci sequenced in both European-American and African-American populations, we attempt to distinguish the effects of demography and selection. To analyze large sets of population genetic data such as this one, we introduce "Perlymorphism," a Unix-based suite of analysis tools. Our analyses show that the demographic histories of human populations can account for a large proportion of effects on the level and frequency of variation across the genome. The African-American population shows both a higher level of nucleotide diversity and more negative values of Tajima's D statistic than does a European-American population. Using coalescent simulations, we show that the significantly negative values of the D statistic in African-Americans and the positive values in European-Americans are well explained by relatively simple models of population admixture and bottleneck, respectively. Working within these nonequilibrium frameworks, we are still able to show deviations from neutral expectations at a number of loci, including ABO and TRPV6. In addition, we show that the frequency spectrum of mutations—corrected for levels of polymorphism—is correlated with recombination rate only in European-Americans. These results are consistent with repeated selective sweeps in non-African populations, in agreement with recent reports using microsatellite data.
Key Words: hitchhiking • ABO • TRPV6 • bottleneck • admixture
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