Geographic allele frequency variation in the 1000 Genomes hg38 NYGC dataset

A key challenge in human genetics is to describe and understand the
distribution of human genetic variation. Often genetic variation is
described by showing rela tionships among populations or
individuals, in each case drawing inferences over a large number
of variants. Here, we present an alternative representation of human
genetic variation that reveals the relative abundance of different allele
frequency patterns across populations. This approach allows viewers to
easily see several features of human genetic structure: (1) most variants
are rare and geographically localized, (2) variants that are common in a
single geographic region are more likely to be shared across the globe
than to be private to that region, 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 of the results, we also apply the visualization to
contrasting theoretical scenarios with varying levels of divergence and
gene flow. Our variant-centric visualization clarifies the major
geographic patterns of human variation and can be used to help correct
potential misconceptions about the extent and nature of genetic
differentiation among populations.