Computing for Biologists Python Programming and Principles

Biologists are frequently interested in the relationships between species. To represent such relationships they use a diagram called a phylogenetic tree. The phylogenetic tree in Figure 9.2 consists of a set of nodes connected by branches. In this example, we have marked the nodes with dots. The ones on the right are called leaf nodes or simply leaves. They represent the species whose relationships we want to understand. In this example, the leaves are five currently living primate species, including great apes and humans. There are also internal nodes, which represent hypothesized ancestral species. For example, the node marked in red represents the most recent common ancestor of chimpanzees and humans, an animal that lived between 5 and 8 million years ago.

The tree provides information about the evolutionary relationships between species. We can use the internal nodes to define groups of closely related species called clades. All the species descended from a particular internal node form a clade, and are more closely related to each other than they are to other species. Thus the red dot in Figure 9.2 defines a clade that we might call the human-chimpanzee clade. This clade includes three living species: human, the common chimpanzee, and the pygmy chimpanzee. The fact that they are in a clade together tells us, for example, that chimpanzees are more closely related to humans than they are to gorillas.