Cladograms are not ends in themselves: Missing Data and the Extant Phylogenetic Bracket: A nice thing about the parsimony method of phylogeny reconstruction is that it is robust to missing data. Indeed, the results of the analysis allow us to hypothesize about what that data might have been using a method called the extant phylogenetic bracket (EPB) - i.e. the bracket formed on either side of the taxon with the missing information by extant taxa in which the character state is known. Using it, we can make three types of inference, listed in order of decreasing confidence. Consider the distribution of a soft-tissue character - the four-chambered heart - among three fossil reptiles:
Phylogenies and Biostratigraphy: Traditional biostratigraphers - Geologists who use the fossil record to date sedimentary rock units tend to be literal-minded souls who think that either fossils of an organism or group are known to be present at a particular time, or they aren't. Hypotheses of phylogeny tell us when we ought to be cautious about such literal interpretations.
In 1984, when Jacques Gauthier performed the first major cladistic analysis of diapsid reptiles, he got a surprise. Choristodera, whose members were known from the Late Cretaceous and Paleocene, appeared to have branched off of the reptilian tree by the late Permian. Thus, they sat at the end of a ghost lineage that persisted for over 150 million years. This seemed highly improbable. Was the cladogram wrong or our understanding of the fossil record? As paleontologists began reexamining museum collections, it became apparent that some neglected partially preserved creatures were, in fact, choristoderes. Today, the choristodere record starts in the late Triassic. Some research suggests an alternate phylogenetic placement for choristoderes that further shortens their ghost lineage.
Statistical applications: Biologists are fond of performing statistical studies, looking for meaningful correlations between different parts of animals' anatomies. For instance, one might look at the ratio of the length and depth of birds' beaks vs. the length of their tarsals to see if larger birds have proportionately deeper beaks. Such studies require that all observations be made from the same underlying population.
However, when samples are being taken not from a single pool but from groups of populations nested in a heirarchical phylogeny, this assumption is violated. (BSCI393 students take note!!) The above example I showed of how misleading this can be. Fortunately, Joe Felsenstein of the University of Washington developed a statistical technique for adjusting data to account for the phylogeny of the taxa sampled, called independent contrasts. By applying it, meaningful correlation studies can be performed. Without it, they would be meaningless and misleading.