Geographic patterns of human allele frequency variation: a variant-centric perspective

Genetic variation is often described by showing relationships among populations or individuals. Here, we present an alternative representation of genetic variation that reveals the relative abundance of different allele frequency patterns across populations. Applied to human data, this approach allows viewers to easily see several key features of human genetic variation: (1) most variants are rare and geographically localized, (2) variants that are common in any single region are likely to be shared across the globe, and (3) where two individuals differ, it is most often due to variants that are common globally, regardless of whether the individuals are from the same region or different regions. To guide interpretation, we show results for theoretical scenarios with varying levels of divergence and gene flow. Our variant-centric visualization clarifies the geographic patterns of human variation and can be used to help correct misconceptions about the extent of genetic differentiation among populations.