Balancing selection maintains sex determining alleles in multiple‐locus complementary sex determination

Hymenopteran species in which sex is determined through a haplo‐diploid mechanism known as complementary sex determination (CSD) are vulnerable to a unique form of inbreeding depression. Diploids heterozygous at one or more CSD loci develop into females but diploids homozygous at all loci develop into diploid males, which are generally sterile or inviable. Species with multiple polymorphic CSD loci (ml‐CSD) may have lower rates of diploid male production than species with a single CSD locus (sl‐CSD), but it is not clear if polymorphism is consistently maintained at all loci. Here, we assess the rate of diploid male production in a population of Cotesia rubecula, a two‐locus CSD parasitoid wasp species, approximately 20 years after the population was introduced for biological control. We show that diploid male production dropped from 8–13% in 2005 and 2006 to 3–4% by 2015. We also show from experimental crosses that the population maintained polymorphism at both CSD loci in 2015. We use theory and simulations to show that balancing selection on all CSD alleles promotes polymorphism at several loci in ml‐CSD populations. Our study supports the hypothesis that ml‐CSD populations have lower diploid male production and are more likely to persist than comparable sl‐CSD populations.