A new test suggests that balancing selection maintains hundreds of non-synonymous polymorphisms in the human genome

Abstract

The role that balancing selection plays in the maintenance of genetic diversity remains unresolved. Here we introduce a new test, based on the McDonald-Kreitman test, in which the number of polymorphisms that are shared between populations is contrasted to those that are private at selected and neutral sites. We show that this simple test is robust to a variety of demographic changes, and that it can also give a direct estimate of the number of shared polymorphisms that are directly maintained by balancing selection. We apply our method to population genomic data from humans and conclude that more than a thousand non-synonymous polymorphisms are subject to balancing selection.