When large-effect damaging alleles enter small populations
Large-effect recessive damaging variants found at relatively high frequencies are common enough in domestic animals that they cause problems in breeding programs. There are several potential reasons. Deleterious variants may rise in frequency because of genetic drift, be driven to intermediate frequency by balancing selection by heterozygote advantage, or be spread by exceptionally influential parents, usually sires, that sometimes occur in animal breeding programs. Further, animal populations are often connected by migration. In this paper, we use a series of population genetic models to address how large-effect damaging alleles establish themselves in small populations, such as domestic animal populations or wild populations of mammals. The results confirm that a lethal allele under directional selection is fairly unlikely to become common, unless there are influential sire events with very large contributions or the population size is very small. On the other hand, a lethal allele under balancing selection can easily become common, especially if there are influential parents. When there is balancing selection, migration between connected populations effectively spreads alleles. The results accord with the many examples of recessive damaging alleles in domestic animals.