Levels of neutral genetic diversity in populations subdivided into
two demes were studied by multi-locus stochastic simulations. The model
includes deleterious mutations at loci throughout the
genome, causing ‘background selection’, as well as a single
locus at which a polymorphism is
maintained, either by frequency-dependent selection or by local
selective differences. These
balanced polymorphisms induce long coalescence times at linked neutral
loci, so that sequence
diversity at these loci is enhanced at statistical equilibrium. We study
how
equilibrium neutral
diversity levels are affected by the degree of population subdivision,
the
presence or absence of
background selection, and the level of inbreeding of the population. The
simulation results are
compared with approximate analytical formulae, assuming the infinite
sites neutral model. We
discuss how balancing selection can be distinguished from local selection,
by determining whether
peaks of diversity in the region of the polymorphic locus are seen within
or between demes. The
width of such diversity peaks is shown to depend on the total species
population size, rather than
local deme sizes. We show that, with population subdivision, local
selection enhances between-deme diversity even at neutral sites distant
from
the polymorphic locus, producing higher FST
values than with no selection; very high values can be generated at sites
close to a selected locus.
Background selection also increases FST,
mainly because of decreased diversity within populations,
which implies that its effects may be distinguishable from those of local
selection. Both effects are
stronger in selfing than outcrossing populations. Linkage disequilibrium
between neutral sites is
generated by both balancing and local selection, especially in selfing
populations, because of
linkage disequilibrium between the neutral sites and the selectively
maintained alleles. We discuss
how these theoretical results can be related to data on genetic diversity
within and between local populations of a species.