The Tree Room : How to build a tree :
Any species can be described in terms of a seemingly infinite set of heritable traits. However, only some of these characters can actually inform us about evolutionary history. In order to be useful for building a phylogeny, a character must:
Be shared by some, but not all, of the species or groups being studied. For example, all pine species produce seeds housed in cones. Therefore, this character (whether the species has pinecones) can't help us understand which pine species are more closely related to one another. At the other extreme, Pinus monophylla is the only pine species with needles that grow individually on a branch, not in clusters. Therefore, this character (whether the species has individual or clustered needles) can't help us understand which species should be grouped with P. monophylla on an evolutionary tree.
Be evolving independently of other characters used to build the phylogeny. So, for example, if gene variant X produces protein variant X, the two traits are mechanistically tied to one another, and only one of them the gene variant or the protein variant (not both) should be used to build the tree. Traits that are evolutionarily linked represent the same evolutionary change and can bias a phylogenetic analysis.
Be shared among species because of inheritance from a common ancestor (i.e., the character states should be homologous, rather than arrived at independently or analogous to one another). For example, the maritime pine and the Scots pine each have two bundles of tissue in their needles that help move water and nutrients through the plant, while many other pine species (e.g., the white pines) have only one bundle. Maritime and Scots pines inherited the two-bundle trait from an ancestor that they have in common.4 Having two bundles of tissue is homologous in at least some species and can be used to help build the evolutionary tree of pines.
The maritime (left) and Scots pine (center) each have two vascular bundles (circled in all three images) within the central structure of their needles; this homologous structure was inherited from an ancestor they have in common. The white pine (right) has only one vascular bundle.
Using homologous traits is important for tree building because these traits are supporting evidence for common ancestry. Homologous morphological traits generally share basic structural similarity, develop through similar pathways, and have similar genetic underpinnings. Biologists do their best to exclude traits from phylogenetic analyses that do not meet these criteria and might appear similar to one another because of convergent evolution, as opposed to shared evolutionary history. For example, sharks and dolphins both have streamlined bodies with big dorsal fins, but the similarity in these traits is due to convergent evolution, not common ancestry, and so these traits cannot be used to argue that sharks and dolphins are closely related.
Sharks and dolphins both have big dorsal fins and streamlined body, but these traits evolved via convergent evolution and so should not be used to build a phylogeny involving sharks and dolphins.