Genetic divergence between rodent species assessed by using two-dimensional electrophoresis

O'Farrell's technique of two-dimensional gel electrophoresis (2-DGE) has previously been applied to the study of intrapopulation genetic variation. This approach assays a larger, and in part nonoverlapping, cohort of protein encoding loci compared to conventional one-dimensional electrophoretic procedures (SGE) and has revealed substantially lower levels of mean heterozygosity. Here we extend this approach to analyze levels and patterns of genetic differentiation between species. We have used 2-DGE to compare an average of 189 polypeptides between six species of wild mice representing levels of evolutionary divergence ranging from different subspecies to different families. The magnitude of protein divergence estimated by 2-DGE was on the average only about one-half that predicted by SGE. This discrepancy may result from differences in sensitivities between the techniques or differences in the mean level of variation and divergence between the sets of loci assayed by the two methods. Nonetheless, the ranking of genetic distances by 2-DGE was identical to that by SGE. Thus, these results support the use of the simpler SGE techniques to estimate relative levels of genetic divergence.