A host of techniques to detect molecular variants are 

 available to assay intraspecif ic variability. For example, protein 

 polymorphisms detected by isozyme electrophoresis have been used to 

 describe allele frequency changes in time and space. Immunological 

 techniques can detect intraspecies antigenic variation at the level 

 of the single cell. The polymerase chain reaction will be 

 particularly useful to isolate and detect variants at the genetic 

 level, whether in the mitochondrial, chloroplastic, or nuclear 

 genomes. 



The genomes of eukaryotic organisms contain many repetitive 

 DNA sequences. In some cases (e.g., the human "Alu" sequence), 

 specific repetitive sequences are distributed throughout the 

 genome; in other cases, a specific repetitive sequence may be 

 confined to one or few loci. Chromosome-specific sequences in 

 humans have been used to identify and quantify specific chromosomes 

 from mixed populations. The "Alu" sequence has been used to 

 differentiate among human, hamster, and human-hamster hybrid 

 chromosomes. 



The same technique could be applied to identify and quantify 

 specific species of microbes within a population. The presence of 

 sequence repeats increases the sensitivity of the method; 

 therefore, expression of the gene is not necessary for success. 

 Moreover, there is no need to understand the function of the 

 sequence. Such sequence probes could, therefore, be isolated from 

 mixed populations of organisms, sequence specificity determined, 

 and the species containing a specific repetitive sequence 

 identified. Once this basic characterization is completed, the 

 repetitive DNA probe could be used to identify the presence and 

 number of the species within a larger, mixed population of 

 organisms. 



Molecular Determination of Mutation Rate and Evolutionary Origins 



The DNA preserved in some ancient materials is essentially a 

 "molecular fossil," providing a genetic record of the evolutionary 

 past. Molecular techniques, in particular the polymerase chain 

 reaction (PCR) , now allow reasonably straightforward access to this 

 "molecular fossil record." Via PCR amplification of ancient DNA, 

 both extinct and contemporary species have been compared using 

 molecular phylogenetic analyses (Paabo et al., 1989). A recent 

 example of this approach examined the historical epidemiology of 



III-5 



