relates population size to genetic relatedness, and provides a model which focuses on the time at which two alleles last shared a common ancestor to describe their relationship in more informative, genetic terms. In support of such models, the last decade has seen the emergence of genetic markers and reproducible techniques of DNA fingerprinting. Both have contributed greatly to a clearer understanding of how variation occurs in clonal populations. Most DNA fingerprinting techniques examine the polymorphism sequences in only the chromosome or in the plasmids or only a single gene fragment (22). In many studies, actual variation can be revealed by amplified fragment length polymorphism (AFLP) or restriction fragment length polymorphism (RFLP) or by electrophoresis, with the use of various combinations of techniques revealing the greatest levels of taxonomic differences.
Many of these techniques have revealed significant levels of variation within clonal populations. This has proven especially useful in bacterial studies. Gray and Herwig (8) successfully extracted microbial DNA from marine sediments, yielding high molecular weight DNA for amplification and analysis. In studies of clonal pathogens where clonal identity may be critical to the creation of successful vaccine, fingerprinting techniques have made significant contributions. In the case of the clonal pathogen Borrelia burgdorferi, which causes Lyme borreliosis in man, an examination of genetic trees of plasmid sequences taken from fifteen isolates, no evidence was seen for genetic exchange between chromosomal genes and clones rarely exchanged plasmids between themselves. This indicated that of the clones examined, all were so highly divergent that vaccines developed to combat one would be highly unlikely to effectively immunize against any of the others, with serious implications for control (16).
In a study using polymorphic GC-rich repetitive sequences (PGRS), hybri...