The effect of multi-allelic balancing selection on nucleotide diversity at linked neutral sites was
investigated by simulations of subdivided populations. The motivation is to understand the
behaviour of self-recognition systems 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 selected locus (connected by recombination).
Previous theoretical studies of each type of subdivision separately have shown that each increases
diversity, and decreases the relative frequencies of low-frequency variants, at neutral sites or loci.
We show here that the two types of subdivision act non-additively when sampling is at the whole
population level, and that subdivision produces some non-intuitive results. For instance, in highly
subdivided populations, genetic diversity at neutral sites may decrease with tighter linkage to a
selected locus or site. Another conclusion is that, if there is population subdivision, balancing
selection leads to decreased expected FST values for neutral sites linked to the selected locus.
Finally, we show that the ability to detect balancing selection by its effects on linked variation,
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.