Abstract
When long-lasting, balancing selection can lead to “trans-species” polymorphisms that are shared by two or more species identical by descent. In such cases, the gene genealogy at the selected site clusters by allele instead of by species, and nearby neutral sites also have unusual genealogies because of linkage. While this scenario is expected to leave discernible footprints in genetic variation data, the specific patterns remain poorly characterized. Motivated by recent findings in primates, we focus on the case of a biallelic polymorphism under ancient balancing selection and derive approximations for summaries of the polymorphism data from two species. Specifically, we characterize the length of the segment that carries most of the footprints, the expected number of shared neutral single nucleotide polymorphisms (SNPs), and the patterns of allelic associations among them. We confirm the accuracy of our approximations by coalescent simulations. We further show that for humans and chimpanzees—more generally, for pairs of species with low genetic diversity levels—these patterns are highly unlikely to be generated by neutral recurrent mutations. We discuss the implications for the design and interpretation of genome scans for ancient balanced polymorphisms in primates and other taxa.
Highlights
Balancing selection is a mode of adaptation that leads to the presence of more than one allele in the population at a given time
Throughout, we consider T much larger than Ne. This condition is needed for trans-species polymorphisms to be a clear-cut manifestation of balancing selection, as otherwise a considerable proportion of the trans-species polymorphisms in the genome will be due to neutral incomplete lineage sorting (ILS; Wiuf et al 2004)
A neutral trans-species polymorphism will occur if three conditions are met: (1) at least two lineages from each species do not coalesce by the time of the split; (2) the first coalescent event in the ancestral species is not between lineages from the same descendant species; (3) there is a mutation in the appropriate lineage(s) to give rise to a shared polymorphism
Summary
THE MODEL We consider a simple demographic scenario in which an ancestral species splits into two species T generations ago, with no subsequent gene flow between them. We assume panmixia and constant population sizes for the ancestral (Na) and
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