Abstract
Studies of the apportionment of human genetic variation have long established that most human variation is within population groups and that the additional variation between population groups is small but greatest when comparing different continental populations. These studies often used Wright’s F ST that apportions the standardized variance in allele frequencies within and between population groups. Because local adaptations increase population differentiation, high-F ST may be found at closely linked loci under selection and used to identify genes undergoing directional or heterotic selection. We re-examined these processes using HapMap data. We analyzed 3 million SNPs on 602 samples from eight worldwide populations and a consensus subset of 1 million SNPs found in all populations. We identified four major features of the data: First, a hierarchically F ST analysis showed that only a paucity (12%) of the total genetic variation is distributed between continental populations and even a lesser genetic variation (1%) is found between intra-continental populations. Second, the global F ST distribution closely follows an exponential distribution. Third, although the overall F ST distribution is similarly shaped (inverse J), F ST distributions varies markedly by allele frequency when divided into non-overlapping groups by allele frequency range. Because the mean allele frequency is a crude indicator of allele age, these distributions mark the time-dependent change in genetic differentiation. Finally, the change in mean-F ST of these groups is linear in allele frequency. These results suggest that investigating the extremes of the F ST distribution for each allele frequency group is more efficient for detecting selection. Consequently, we demonstrate that such extreme SNPs are more clustered along the chromosomes than expected from linkage disequilibrium for each allele frequency group. These genomic regions are therefore likely candidates for natural selection.
Highlights
Knowledge about population genetic structure is central to the study of human origins, DNA forensics, and complex diseases
The post-Darwinian perception was that variation between individuals is the outcome of evolutionary processes that act differently on different individuals, but the extent of the genetic differentiation remained under debate [2,6,35,51]
The comprehensive high-quality HapMap singlenucleotide polymorphism (SNPs) catalog genotyped over eight worldwide populations is the best approximation to the global genetic diversity available
Summary
Knowledge about population genetic structure is central to the study of human origins, DNA forensics, and complex diseases. The present-day genetic diversity observed among human populations was shaped by biological and demographic events that marked their signatures in the genome Processes such as selection and genetic drift increased the frequency of rare alleles and the genetic diversity among populations [1]. As with most reconstructions, the only recoverable events are those that involved a reasonably large number of individuals and occurred before local migration exchange balanced their effect Before these genetic signatures can be deciphered and used to unravel the forces responsible for the genetic diversity at each locus, several key questions should be answered: how does geography affect the distribution of genetic information, what is the amount of genetic diversity among human populations, and how does genetic diversity distribute within and between populations?
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