Natural selection is expected to eliminate genetic incompatibilities from interbreeding populations. We have identified a globally distributed incompatibility in the primarily selfing species Caenorhabditis elegans that has been maintained despite its negative consequences for fitness. Embryos homozygous for a naturally occurring deletion of the zygotically acting gene, zeel-1, arrest if their sperm parent carries an incompatible allele of a second, paternal effect locus, peel-1. The two interacting loci are tightly linked, with incompatible alleles occurring in linkage disequilibrium in two common haplotypes. These haplotypes exhibit elevated sequence divergence, and population genetic analyses of this region indicate that natural selection is preserving both haplotypes in the population. Our data suggest that long-term maintenance of a balanced polymorphism has permitted the incompatibility to persist despite gene flow across the rest of the genome.Caenorhabditis elegans is a globally distributed species of free-living, bacteria-eating nematode. Although rare males contribute at a low rate to outcrossing, C. elegans occurs primarily as inbred, self-fertilizing hermaphrodites (1-4). A wild isolate from Hawaii, CB4856, has been identified among well-studied isolates as the most divergent at the sequence level from the standard laboratory strain, N2, derived from an isolate from Bristol, England (5-7). As a result of this sequence divergence, the Hawaiian strain is widely used to map mutations induced in the Bristol background.
Genetic incompatibility between Bristol and HawaiiWe generated recombinant inbred lines (RILs) from the tenth generation of an advanced intercross between Bristol and Hawaii to study natural genetic variation in C. elegans, and we genotyped the RILs at 1450 single nucleotide polymorphism markers (8). We noted that a region on the left arm of chromsome I exhibited a dramatic deficit of Hawaii alleles among the RILs. Of 239 RILs, only five carried the Hawaii allele at the most skewed marker, and simulations of the intercross pedigree indicated that this allele frequency skew could not have arisen by drift, suggesting that selection had acted during construction of the RILs (Fig. S1). We then crossed Hawaii to a Bristol strain carrying a visible marker located 10cM from the most skewed RIL marker, and we examined F2 progeny produced by self-fertilizing F1 hermaphrodites. Surprisingly, approximately 25% of F2 progeny arrested as embryos, and embryonic lethality segregated opposite the visible marker (Table 1). F2 lethality was not an effect of the marker: self-fertilizing F1 hermaphrodites derived from reciprocal crosses between Hawaii and wildtype Bristol produced 25% dead embryos, as did F1 hermaphrodites mated to F1 males (Fig. 1).