Molecular approaches to the study of plant biosystematics

Genetic relationships among organisms can be estimated from the pattern of DNA sequence change between hereditary molecules. The methods of molecular biology are increasingly being employed in systematic and evolutionary research to study genetic relationships and phylogeny. The investigator is faced with a variety of choices in initiating research in 'molecular biosystematics'. First, a gene or genome that provides a level of genetic resolution appropriate for the materials under study must be selected. Common choices in plants include the chloroplast genome (cpDNA) or components of the chloroplast genome, the nuclear ribosomal RNA genes (rDNA), or nuclear-encoded, single-copy genes. A second consideration is that several methods can be employed to provide direct or indirect measures of DNA sequence divergence. One widely used method determines genetic divergence based on restriction site changes. Restriction site analyses typically require some knowledge of the physical map of the DNA molecule under study. Empirical studies indicate that restriction site analyses of cpDNA provide good resolution for systematic investigations at or below the family level. A second method that is increasing in importance is DNA sequencing. Until quite recently, DNA sequencing required the molecular cloning of the gene or DNA fragment of interest and the implementation of a 'sequencing strategy' for the production of overlapping sequence runs. Two related technological developments have overcome both of these requirements, when the goal is the repetitive sequencing of a specific gene from a number of taxa. It is now possible to synthesise synthetic oligonucleotides that can be used to prime dideoxy sequencing at virtually any point in the gene of interest, based on previously determined sequence information. The second major innovation is the invention of the polymerase chain reaction technique (PCR). The PCR method permits the direct amplification of DNA fragments from heterogeneous DNA mixtures and thereby circumvents the molecular cloning requirement. Application of the PCR method to chloroplast genes, together with direct primer-mediated sequencing, provides a method for obtaining large data sets. CpDNA sequence data are especially valuable at or above the family level and provide a powerful means of resolving genetic relationships at the deepest levels of plant evolution.