What does electrophoretic variation tell us about protein variation?

Abstract

MCZ Laboratories, Harvard University Before the introduction of DNA sequencing meth- ods into population genetics by Kreitman (1983), the major source of information about genetic variation among organisms in natural populations came from electrophoretic studies of proteins. The amount of in- formation acquired during 25 years of major electro- phoretic activity is staggering and, for purely technical reasons, is likely to remain orders of magnitude greater in number of genes, number of individuals, and number of species examined than can be acquired from nucle- otide sequence data. It would be extremely desirable if this mass of data on electrophoretic phenotypes could be translated into data on patterns of amino acid varia- tion, using the information now available for a handful of cases where amino acid variation in natural popula- tions has been definitively ascertained from DNA se- quence variation. It is the purpose of this paper to show that while the total amount of amino acid variability can be inferred from electrophoretic data, the different pat- terns of electrophoretic class frequency distributions do not allow any other inferences, because those patterns can be generated by the simplest null model of the gen- eration of electrophoretic variation from amino acid variation, without the need to make any assumptions about selection or population structure. The charge-state model (or the stepwise mutation model) was originally proposed by Ohta and Kimura (1973) to deal with electrophoretic data. This model as- sumes that only amino acid changes resulting in signif- icant charge changes are clearly detectable. Hence gel electrophoresis ideally detects changes in net (integer) charge in a protein but not in fractions of charge. Al- though the model is somewhat simplistic, Brown, Mar- shall, and Weir (198 1) concluded after a review of the existing evidence that there was general support for the model, which can be considered at one end of the spec- trum of models describing electrophoretic variation. *