Anonymous nuclear DNA markers in the American oyster and their implications for the heterozygote deficiency phenomenon in marine bivalves

A puzzling population-genetic phenomenon widely reported in allozymesurveys of marine bivalves is the occurrence of heterozygote deficitsrelative to Hardy-Weinberg expectations. Possible explanations for thispattern are categorized with respect to whether the effects should beconfined to protein-level assays or are genomically pervasive and expectedto be registered in both protein- and DNA-level assays. Anonymous nuclearDNA markers from the American oyster were employed to reexamine thephenomenon. In assays based on the polymerase chain reaction (PCR), twoDNA-level processes were encountered that can lead to artifactual genotypicscorings: (a) differential amplification of alleles at a target locus and(b) amplification from multiple paralogous loci. We describe symptoms ofthese complications and prescribe methods that should generally help toameliorate them. When artifactual scorings at two anonymous DNA loci in theAmerican oyster were corrected, Hardy-Weinberg deviations registered inpreliminary population assays decreased to nonsignificant values.Implications of these findings for the heterozygote-deficit phenomenon inmarine bivalves, and for the general development and use of PCR-basedassays, are discussed.