Two-Dimensional Protein Electrophoresis in Phylogenetic Studies

This chapter describes two-dimensional protein electrophoresis in phylogenetic studies. For molecular systematics, the 10-fold increase in number of typed protein loci as compared to allozyme methods normalizes the variance arising from differing evolutionary rates of proteins and the large number of sites screened reduces the variance in detected mutational divergence that is stochastically accumulated over evolutionary time scales. This chapter explains the preparation and labeling of cellular proteins. Autoradiograms of radiolabeled cellular proteins are more diverse and easily analyzable for molecular systematics than alternatives, such as silver-stained serum or erythrocyte protein patterns. Two-dimensional protein electrophoresis molecular distance measures are based on a large sample of randomly sampled proteins that are constrained only in that they fall within a certain range of isoelectric point, mass, and abundance. Improvements in two-dimensional electrophoresis methodology, such as threaded isoelectric focusing gels, ease the difficulty of obtaining high-quality gels. The major methodological difficulty remains the analysis of autoradiograms.