Phylogenetic trees

A phylogenetic tree is a graphical representation of the evolutionary relationship between taxonomic groups. The term phylogeny refers to the evolution or historical development of a plant or animal species, or even a human tribe or similar group. Taxonomy is the system of classifying plants and animals by grouping them into categories according to their similarities. A phylogenetic tree is a specific type of cladogram where the branch lengths are proportional to the predicted or hypothetical evolutionary time between organisms or sequences. Cladograms are branched diagrams, similar in appearance to family trees, that illustrate patterns of relatedness where the branch lengths are not necessarily proportional to the evolutionary time between related organisms or sequences. Bioinformaticians produce cladograms representing relationships between sequences, either DNA sequences or amino acid sequences. However, cladograms can rely on many types of data to show the relatedness of species. In addition to sequence homology information, comparative embryology, fossil records and comparative anatomy are all examples of the types of data used to classify species into phylogenic taxa. So, it is important to understand that the cladograms generated by bioinformatics tools are primarily based on sequence data alone. Given that, it is also true that sequence relatedness can be very powerful as a predictor of the relatedness of species.

Cladograms cannot be considered completely true and accurate descriptions of the evolutionary history of organisms, because in any cladogram there are a number of possible evolutionary pathways that could produce the pattern of relatedness illustrated in the cladogram. The cladogram only illustrates the probability that two organisms, or sequences, are more closely related to each other than to a third organism, it does not necessarily clarify the pathway that created the existing relationships. However, the cladogram can be used in the formulation of new hypotheses and to cast new light on existing data. One of the most ambitious cladograms produced to date can be viewed at the Tree of Life website, originated by David and Wayne Maddison at the University of Arizona (1) . Please take a moment to view the "Root of the Tree" link on the Tree of Life web site. In this phylogenetic tree, the root is at the far left, termed the root of the cladogram because it is at the base of the cladogram, opposite the branches. Return to the home page and click on the link entitled "Popular Pages", then select "Mammals". At the right side of this cladogram are the terminal nodes, located at the tip of the branches in any cladogram. In the Mammalia cladogram illustrated here, there are six terminal nodes, labeled Triconodonts, Monotremata, Multituberculata, Marsupialia, Palaeoryctoids, and Eutheria. An internal node is a hypothetical common ancestor. The branching points between the root and the terminal nodes are internal nodes. Each internal node is also at the base of a clade, which includes the common ancestral node plus all its descendents. Sample a few more links on the Tree of Life. Be sure to read Darwin's quote on the home page and ponder how difficult it would be to get published in a scientific journal today, if it were necessary to write this beautifully in order to succeed.