Most taxonomists today believe that biological classification systems should reflect evolutionary relationships and that taxonomic units should be monophyletic.
- A paraphyletic group contains some, but not all, of the descendants of a particular ancestor.
- A polyphyletic taxon contains members with more than one recent common ancestor.
- A monophyletic group contains all descendants of a particular ancestor and no other organisms.
Some systematists believe that classification systems should also reflect degrees of difference among organisms. Certain paraphyletic groups have undergone rapid evolutionary change and should be retained. The groups are called grades. Recent molecular evidence suggests, for example, that birds, turtles, and crocodilians share a more recent ancestor than crocodilians and turtles share with snakes and lizards.
The traditional class Reptilia is paraphyletic because it does not include all descendants of its common ancestor; birds are excluded. This emphasizes that birds have evolved unique derived traits since they separated from reptiles, and are thus a distinct grade. The current tendency is to change classifications to eliminate paraphyletic groups; however, some of the familiar taxonomic categories (such as gymnosperm and reptiles) are paraphyletic and will probably remain in use. Studies of a genus in the phlox family (Linanthus) illustrate how phylogenetic analyses can determine how many times a trait has evolved. Some species can reproduce by self-pollination (they are self-compatible). A nuclear ribosomal DNA sequence was used to construct the phylogeny of the Linanthus plants. Self-incompatibility is the ancestral state. Self-compatibility has evolved three times within the Linanthus lineage.