The effect of hitch-hiking on genes linked to a balanced polymorphism in asubdivided population

The effect of multi-allelic balancing selection on nucleotide diversity at linked neutral sites was investigated by simulations of subdivided populati ons. The motivation is to understand the behaviour of self-recognition syst ems such as the MHC and plant self-incompatibility. For neutral sites, two types of subdivision are present: (1) into demes (connected by migration), and (2) into classes defined by different functional alleles at the selecte d locus (connected by recombination). Previous theoretical studies of each type of subdivision separately have shown that each increases diversity, an d decreases the relative frequencies of low-frequency variants, at neutral sites or loci. We show here that the two types of subdivision act non-addit ively when sampling is at the whole population level, and that subdivision produces some non-intuitive results. For instance, in highly subdivided pop ulations, genetic diversity at neutral sites may decrease with tighter link age to a selected locus or site. Another conclusion is that, if there is po pulation subdivision; balancing selection leads to decreased expected F-ST, values for neutral sites linked to the selected locus. Finally, we show th at the ability to detect balancing selection by its effects on linked varia tion, using tests such as Tajima's D, is reduced when genes in a subdivided population are sampled from the total population, rather than within demes .