Asexual reproduction often leads to loss of genetic diversity, but several mechanisms have evolved to maintain heterozygosity. The subterrestrial nematode, Halicephalobus mephisto, reproduces parthenogenetically, and here, we investigate how its genetic diversity \(-\) 1.15% SNP heterozygosity—is retained from generation to generation. To test for loss of heterozygosity, we PCR-typed 56 individual animals at two different loci; no homozygotes were observed in the population. Furthermore, whole-genome analysis of parent and progeny demonstrated no transition from heterozygote to homozygote across over 620,000 SNPs. Surprisingly, these SNPs are not uniformly distributed throughout the genome, as we find multiple tracts of loss of heterozygosity (LOH) where no variation exists. Covering 4.3 million base pairs (Mb) genome-wide, these LOH tracts are most consistent with a recent meiotic recombination event or an error of chromosomal segregation. Supporting this, we observed chromosomal associations during reproduction that may reflect some degree of synapsis, potentially enabling recombination. However, full-genome analysis of parent–progeny pairs shows the current state of the genome remains stable, with no new LOH detectable, suggesting that history of H. mephisto is more dynamic than previously appreciated, and that heterozygosity has not always been retained with perfect fidelity. The potential functional and evolutionary consequences of this observation are discussed along with potential mechanisms contributing to this unusual genomic history.
