Methods for Fish Biology

Chapter 5: Starch Gel Electrophoresis and Species Distinctions

Robb F. Leary and Henry E. Booke


Taxonomists and systematists attempt to distinguish species and hypothesize lineages by conducting studies of genetically based differences and similarities among populations. Historically, genetic differentiation has usually been inferred from a comparison of morphological characters. There is, however, an increasing trend in taxonomy to supplement morphological analyses with comparisons of physiological, ecological, ethological, biochemical, or karyotypic characters among populations as a means of detecting genetic divergence. In this chapter, we consider the electrophoretic analysis of proteins as a means of detecting genetic differences among populations and the application of these data to species problems. We hope to provide the reader with a basic understanding of the technical aspects of electrophoresis, the information content of the data, and the ways this information can be used to address certain issues that concern fish biologists.

We do not believe that one can gain a basic understanding of the taxonomic usefulness of proteins without some knowledge of protein chemistry. Amino acids are the basic components from which proteins are constructed. Many amino acids exist in nature but only 20 are common. Each of the common amino acids is found in practically all proteins in all organisms. The general structure of these amino acids is the differences among them stem from the chemical composition of the variable R-group or side chain.

Construction of a protein molecule begins with the binding of amino acids into a linear chain. The bonds link the carboxyl group (-COOH) of one amino acid to the amino group (-NH2) of the adjacent amino acid. This bond is called a peptide bond and the resulting molecule is a polypeptide (Figure 5.1). The composition of a polypeptide (i.e., the type and position of each amino acid) is determined by the nucleotide sequence of a particular gene in the organism (see Chapter 2 for details).