Research Article

Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees

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Science  29 Mar 2013:
Vol. 339, Issue 6127, pp. 1578-1582
DOI: 10.1126/science.1234070

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Balancing Humans with Apes

Shared ancestral polymorphisms between species tend to be relatively rare, and studies of trans-species polymorphisms have focused on just a few regions known for balancing selection. Leffler et al. (p. 1578, published online 14 February) performed genome-wide scans among humans and great apes and found shared polymorphisms between chimps and humans. Many of the identified variants seem to be associated with genes involved in pathogen response or defense, suggesting that this widespread balancing selection may reflect the ongoing arms race between pathogens and hosts.


Instances in which natural selection maintains genetic variation in a population over millions of years are thought to be extremely rare. We conducted a genome-wide scan for long-lived balancing selection by looking for combinations of SNPs shared between humans and chimpanzees. In addition to the major histocompatibility complex, we identified 125 regions in which the same haplotypes are segregating in the two species, all but two of which are noncoding. In six cases, there is evidence for an ancestral polymorphism that persisted to the present in humans and chimpanzees. Regions with shared haplotypes are significantly enriched for membrane glycoproteins, and a similar trend is seen among shared coding polymorphisms. These findings indicate that ancient balancing selection has shaped human variation and point to genes involved in host-pathogen interactions as common targets.

  • § These authors co-supervised this work.

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