Data from: Strikingly high levels of heterozygosity despite 20 years of inbreeding in a clonal honey bee

Inbreeding (the mating between closely related individuals) has
detrimental effects that are associated with loss of heterozygosity at
overdominant loci, and the expression of deleterious recessive alleles.
However, determining which heterozygous loci are important for individual
fitness, and the extent of their phenotypic effects remains poorly
understood. Here, we utilise a unique inbred population of clonal
(thelytokous) honey bees, Apis mellifera capensis, to determine which
heterozygous loci are crucial for individual fitness. This population
arose from a common ancestor approximately 20 years ago and has persisted
for at least 100 generations. Thelytokous parthenogenesis results in a 1/3
of loss of heterozygosity with each generation. Yet, this clonal
population retains heterozygosity throughout its genome due to selection
against homozygotes. Deep sequencing of three sub-lineages of the
population revealed that 3,766 of 10,884 genes (34%) have retained
heterozygosity across all sub-lineages, suggesting that these genes have
heterozygote advantage. The maintenance of heterozygosity in the same
genes and genomic regions in all three sub-lineages suggests that nearly
every chromosome carries genes that show sufficient heterozygote advantage
to be selectively detrimental when homozygous.