Cladistics: Basic Vocabulary

Taxonomy (also called Classification) refers to putting organisms into groups based on their evolutionary relationships. The taxonomic system provides a common set of names for all organisms, to help communication within the scientific community.

Phylogeny is the relationship between different taxa (groups of related species). These relationships are represented by a cladogram or phylogenetic tree, like the one below.

In a cladogram, the relationships between living species are shown by lines representing extinct ancestors (paleospecies), and junctions representing their last common ancestor (LCA), where different "branches" of a phylogenetic tree come together. In the example above, the LCA of a chimpanzee and a mouse is represented by the point where the lines leading to those species join together. A clade, then, is a group of taxa that includes all the descendants from a common ancestor. In other words, it is a full "branch" of a tree, which includes all descendants and doesn't leave any out. In the example above, the mouse and a chimpanzee are a clade. The mouse, the chimpanzee, and the pigeon are also a clade. But the pigeon and the chimpanzee are not a clade by themselves, since leaving out the mouse would leave out one of the descendants from their common ancestor.

Cladograms are built around specific types of traits, some of which are more important than others:

analogies: analogies are traits that are shared between two (or more) species because they are both adapted to the same environment, and not because those traits were passed down from a common ancestor. For example, jerboas and kangaroo rats look very similar. (Seriously, click those links. These are two incredibly cute rodents). They are both medium-sized, sandy-colored rodents, with long tufted tails and similar markings. They both have large back feet, short front feet, and can hop bipedally. But these species are not closely related, and these traits were not handed down from their common ancestor. Instead, all of these traits reflect their common adaptation to desert environments. This is a process known as convergent evolution: the development of similar traits to adapt to similar environments. Analogous traits cannot be used to create cladograms because they tell us about shared adaptations, not shared ancestry.

homologies: homologies are traits that are shared by two (or more) species because those species descended from a common ancestor. This trait was found in that common ancestor, and was passed down to some or all of its descendants. For example, very early mammals arms had three major bones: the humerus, the ulna, and the radius. Humans and dogs both have a humerus, an ulna, and a radius. This is a homology. We share those bones because we both inherited them from our common ancestor. Because homologies tell us about our evolutionary history, they can be used to determine the relationship between species.

Some homologies are more useful than others for creating cladograms. Primitive traits, also known as pleisiomorphies are ancestral traits shared by so many organisms that they are not useful for determining the relationships between the species that have them. Having four limbs, for example, is a pleisiomorph for mammals (as well as for reptiles, amphibians, and birds). Although having four limbs reflects our common ancestry, it doesn't give us much information beyond the fact that all mammals are related.

Derived traits, or apomorphies, are characteristics found only in some descendants. For example, one apomorphy of humans is bipedal (two-legged) walking. This is a derived trait, which separates us from close relatives, like chimpanzees and gorillas, who are quadrupeds (four-legged walkers). If the derived trait is shared by more than one group of organisms, then it is a synapomorphy, a shared derived trait. Chimpanzees, gorillas, and humans all have large bodies relative to other primates. This large body is a synapomorphy, showing that we are more closely related to each other than to gibbons, because we share a common ancestor with that derived trait. In the cladogram above, the derived traits that were used to distinguish the different groups of animals are labeled on each branch of the tree. Those labels show where a common ancestor first developed that trait, which is then shared by all its descendants (all species to the right of that line).

Cladograms are built on the principle of parsimony. Parsimony, essentially, is the idea that the simplest explanation is the best. Specifically, this means that the cladogram that requires the fewest evolutionary changes is the one that best fits the evidence. Consider the example of apes. All large apes (chimpanzees, gorillas, and humans) are members of the same clade. We share a common ancestor. Our large body size is one clue to our close relationship; our common ancestor had a larger body, so we do, too. If we tried to argue that chimpanzees, gorillas, and humans did not share a common ancestor, then we would be suggesting that large body size had evolved independently in three separate groups of animals. That is a more complicated scenario, involving more evolutionary changes, than just assuming that large body size evolved once. Recognizing our common ancestry is the most parsimonious explanation. (There are a lot of other reasons we know that chimpanzees, gorillas, and humans are closely related, but this example serves to illustrate the concept.)