Genetical Research

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

a1 Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
a2 Laboratoire de Génétique et d'Ecologie Végétales, Université Libre de Bruxelles, 1850 ChausseUe de Wavre, B-1160 Brussels, Belgium


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.

(Received June 2 1999)
(Revised November 5 1999)

c1 Corresponding author. Department of Ecology and Genetics, University of Aarhus, Ny Munkegade, Building 540, DK-8000 Aarhus C., Denmark.