Disentangling the effects of demography and selection in human history.
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.
Stajich
Jason E
JE
Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA.
Hahn
Matthew W
MW
D000017:ABO Blood-Group System / Q000235:genetics; D001741:Black or African American / Q000235:genetics*; D015220:Calcium Channels / Q000235:genetics; D002877:Chromosomes, Human / Q000235:genetics; D003198:Computer Simulation; D003710:Demography; D019143:Evolution, Molecular; D005260:Female; D014644:Genetic Variation; D005828:Genetics, Population; D015894:Genome, Human; D006801:Humans; D008297:Male; D009154:Mutation; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic; D012641:Selection, Genetic; D050916:TRPV Cation Channels; D044465:White People / Q000235:genetics*
D000017:ABO Blood-Group System; D015220:Calcium Channels; D050916:TRPV Cation Channels; C120776:TRPV6 channel