A phylogenetic tree is a diagram that summarizes the true evolutionary relationships among a group of organisms.

Phylogenetic systematics is based on common ancestry; groups of organisms are hypothesized to be related if they share a common ancestor not shared by any other group. Another way of saying this is that for the purpose of constructing phylogenetic trees we recognize only monophyletic groups – groups that include an ancestor and all of its descendants (see diagram at right).

Phylogenetic trees as we use them are branching, treelike diagrams called cladograms. The vertical axis is always an implied time scale and organisms are classified according to the order in time that branches arose along a dichotomous (made up of paired branches) phylogenetic tree. Only similarities due to descent (ancestry) are considered in cladistic analysis. For more on why similarity due to common ancestry is so important see the page on homology and analogy.

How does one construct a phylogenetic tree?

First of all you have to distinguish those organisms that are more ancestral from the more recently derived organisms. Systematists use a technique called outgroup analysis to recognize ancestral characters for all members of the study group and to establish a starting point for a phylogenetic tree. An outgroup is a species or group of species that is relatively closely related to the study group (ingroup), but not as closely related as any study-group members are to each other. All members of the study group are compared as a group to the outgroup. Characters present in the ingroup that are also present in the outgroup are considered ancestral; those characters present in the ingroup but lacking in the outgroup are derived.

For example (see diagram at right), suppose you were classifying six animals: lancelet, turtle, tuna, lamprey, leopard, and salamander, using five characteristics: vertebrae, jaws, amniotic egg, hair, and tetrapody (many more characters would be used in an actual analysis). If you set this up in chart form, it would look like the matrix below, with 1 indicating presence of the character and 0 meaning absence.

In this analysis, the lancelet (a cephalochordate) is the outgroup, and the leopard has the most derived characters, with the lamprey, tuna, and salamander, and turtle in between. Note how the characteristics used to build the tree can be mapped onto the tree before each successive node indicating that all animals above that point share that characteristic. Also note that all the characters we chose are expected to be homologous among the animals studied. What would happen if we used characters that were analogous? See the diagrams below for an answer.