A phylogenetic tree, or cladogram, is a schematic diagram used as a visual illustration of proposed evolutionary relationships among taxa. Phylogenetic trees are diagrammed based on assumptions of cladistics, or phylogenetic systematics. The main assumptions of cladistics are:
All organisms descend from a common ancestor.
New organisms develop when existing populations split into two groups.
Over time, lineages experience changes in characteristics.
Phylogenetic tree structure is determined by shared traits among different organisms. Its tree-like branching shows diverging taxa from a common ancestor. Terms that are important to understand when interpreting a phylogenetic tree diagram include:
Nodes: These are points on a phylogenetic tree where branching occurs. A node represents the end of the ancestral taxon and the point where a new species splits from its predecessor.
Branches: These are the lines on a phylogenetic tree that represent ancestral and/or descendant lineages. Branches arising from nodes represent descendant species that split from a common ancestor. The pattern in which the branches connect represents our understanding of how the species in the tree evolved from a series of common ancestors. Each branch point (also called an internal node) represents a divergence event, or splitting apart of a single group into two descendant groups.
Monophyletic Group (Clade): This group is a single branch on a phylogenetic tree that represents a group of organisms that are descended from a most recent common ancestor.
Taxon (Taxa): Taxa are specific groupings or categories of living organisms. The tips of branches in a phylogenetic tree end in a taxon.
In building a tree, we organize species into nested groups based on shared derived traits (traits different from those of the group's ancestor). When we draw a phylogenetic tree, we are representing our best hypothesis about how a set of species (or other groups) evolved from a common ancestor.
A rooted phylogenetic tree is a directed tree with a unique node, the root that corresponds to the most recent common ancestor of all the entities at the leaves of the tree. The root node does not have a parent node, but serves as the parent of all other nodes in the tree. The root is therefore a node of degree 2 while other internal nodes have a minimum degree of 3.
The most common method for rooting trees is the use of an uncontroversial outgroup, close enough to allow inference from trait data or molecular sequencing, but far enough to be a clear outgroup.
Unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about ancestry. They do not require the ancestral root to be known or inferred. Unrooted trees can always be generated from rooted ones by simply omitting the root.
Both rooted and unrooted trees can be either bifurcating or multifurcating. A rooted bifurcating tree has exactly two descendants arising from each interior node (that is, it forms a binary tree), and an unrooted bifurcating tree takes the form of an unrooted binary tree, a free tree with exactly three neighbors at each internal node. In contrast, a rooted multifurcating tree may have more than two children at some nodes and an unrooted multifurcating tree may have more than three neighbors at some nodes.
Both rooted and unrooted trees can be either labeled or unlabeled. A labeled tree has specific values assigned to its leaves, while an unlabeled tree, sometimes called a tree shape, defines a topology only.
The number of possible trees for a given number of leaf nodes depend on the specific type of tree, but there are always more labeled than unlabeled trees, more multifurcating than bifurcating trees, and more rooted than unrooted trees. The last distinction is the most biologically relevant, it arises because there are many places on an unrooted tree to put the root.