All living things have a pattern of relationship based on their evolutionary history. Thus, it is probably apparent to most people that, for instance, gorillas are more closely related to pigs than either are to turtles. Patterns of such relationship are termed "phylogenies" and in general can be most easily depicted with the use of tree-like branching diagrams. These phylogenetic diagrams will have species (or summarized groups of species) at the tips of the branches. The "nodes" or branching points in the diagrams are hypothetical, and are sometimes interpreted as representing our best estimation of what the common ancestor of descendant groups may have resembled.
While phylogenies are diagrammatic representations of evolutionary relationships among taxa, the methods by which we obtain such phylogenies are diverse. Since the time of Darwin and before, tree-like diagrams of living things, representing classifications, have often been presented. After Darwin, these diagrams were often interpreted as representative of evolutionary branching patterns. However, the basis for constructing such diagrams was more often than not anectdotal, and usually boiled down to authoritarian proclamation about the perceived relationships based on some subset of the evidence.
In the past 50 years, and especially in the past 25 years, numerical methods for analyzing taxonomic data have been developed which provide the basis for modern phylogenetic analysis. The most prominent and widely accepted of these methods has come to be known as "cladistics" from the Greek for "branching." While there exist many possible methods which have variously been termed "cladistic" the method that uses the criterion of parsimony is now the standard approach to phylogenetic reconstruction. Simply put, parsimony is a means of selecting among possible alternative trees which minimizes the need for hypotheses of "extra" unnecessary evolutionary steps. Alternatively, parsimony maximizes the overall information content of a tree (the data map more efficiently onto the tree) and thus is preferred even on non-evolutionary, purely classificatory, grounds.
Currently, the two major sources of data for cladistic analyses are molecular (such as DNA sequences) and morphological (e.g., structure and anatomy of parts of plants and animals). In the Bailey Hortorium, both kinds of data are used extensively, and more and more, the two types of data are combined together in simultaneous analyses. With large numbers of species, cladistic analyses require massive amounts of computer time. The best and fastest program currently available for such analyses is NONA (Goloboff, 1997). This program is several times faster than competing software, and was written by a former Cornell student, Pablo Goloboff, who began programming in the lab of Dr. Kevin Nixon in the Bailey Hortorium.
See the web site of the Willi Hennig Society for more information on cladistics.
Seed Plant Phylogeny This link is somewhat technical. You have been warned..