  While much effort has focused on detecting positive and negative directional
selection in the human genome, relatively little work has been devoted to
balancing selection. This lack of attention is likely due to the paucity of
sophisticated methods for identifying sites under balancing selection. Here we
develop two composite likelihood ratio tests for detecting balancing selection.
Using simulations, we show that these methods outperform competing methods
under a variety of assumptions and demographic models. We apply the new methods
to whole-genome human data, and find a number of previously-identified loci
with strong evidence of balancing selection, including several HLA genes.
Additionally, we find evidence for many novel candidates, the strongest of
which is FANK1, an imprinted gene that suppresses apoptosis, is expressed
during meiosis in males, and displays marginal signs of segregation distortion.
We hypothesize that balancing selection acts on this locus to stabilize the
segregation distortion and negative fitness effects of the distorter allele.
Thus, our methods are able to reproduce many previously-hypothesized signals of
balancing selection, as well as discover novel interesting candidates.
