Molecular systematics is the use of molecules to determine classification systems and relationships. For hundreds of years botanists used morphology, or overall appearance, to identify and classify plants. Morphological systematics has been important for the basic understanding of plant evolution and relationships; however, it has limitations. One limitation to morphology in plants is homology. Homology assumes that two similar structures have the same evolutionary origin. In other words, the trait arose in an ancestor and was passed down to its descendants. Homology in plant morphology is frequently very difficult to resolve since plant structures can become modified into other forms (e.g., spines of cacti are modified leaves).

Just as a botanist may compare the shape of a leaf between two different plants, molecular systematists compare molecules. Molecules have an advantage over morphology in two aspects. First, homology is usually much easier to determine in molecules...