Phylogenetic tree

A phylogenetic tree is a graphical representation of evolutionary history. It shows the relationships between a set of species, known as taxa. These diagrams use physical or genetic similarities and differences to map how organisms are related. In evolutionary biology, scientists believe all life on Earth is part of a single phylogenetic tree. This concept indicates that all living things share a common ancestry. The study of these trees is called phylogenetics.

To understand how these trees work, we must look at their structure. A rooted tree is a directed tree with a unique starting point called the root. This root represents the most recent common ancestor of all entities at the tips, or leaves, of the tree. The root node has no parent, but it acts as the parent to all other nodes. Internal nodes are called taxonomic units. Because we cannot observe these ancestors directly, they are often called hypothetical taxonomic units.

There are different ways to organize the branches of a tree. A rooted tree can be bifurcating or multifurcating. A bifurcating tree is a binary tree, meaning each internal node has exactly two descendants. In contrast, a multifurcating tree may have more than two children at certain nodes. Trees can also be labeled or unlabeled. A labeled tree assigns specific values to its leaves. An unlabeled tree, or tree shape, only defines the topology, which is the arrangement of the branches.

Scientists also use unrooted trees to show relatedness. An unrooted tree illustrates how leaf nodes are related without assuming a specific ancestral root. It does not require the ancestral root to be known or inferred. You can turn an unrooted tree into a rooted one by inserting a root. To do this, scientists often use an outgroup. An outgroup is a group that is close enough to provide data but far enough to be clearly distinct. Another method is midpoint rooting, which uses the molecular clock hypothesis to estimate evolution rates.

Different types of trees serve different scientific purposes. A cladogram only shows a branching pattern. Its branch lengths do not represent time or the amount of change. A phylogram is different because its branch lengths are proportional to the amount of character change. A chronogram is a specific type of phylogenetic tree that explicitly represents time. In a chronogram, the branch lengths are proportional to geological time.

Other specialized diagrams exist for specific uses. A dendrogram is a general name for any tree-like diagram. A phylogenetic network is used to overcome some tree limitations by acting as a more general graph. There are also spindle diagrams, or romerograms. These represent taxonomic diversity against geological time. The width of the spindle shows the number of families, while the vertical axis shows time.

Building these trees is a complex task handled by computational phylogenetics. This field uses algorithms to find the optimal tree within a phylogenetic landscape. Scientists use methods like neighbor-joining or UPGMA, which are distance-matrix methods. More advanced techniques use the maximum likelihood criterion, often within a Bayesian framework. Finding the best tree is often NP-hard, meaning it is a very difficult mathematical problem. Because of this, scientists use heuristic search and optimization methods to find a good fit for the data.

History shows how our understanding of these trees has changed. Ancient ideas often viewed life as a ladder, known as the Great Chain of Being. Later, branching ideas emerged. In 1840, Edward Hitchcock published a paleontological chart in his book, Elementary Geology. In 1859, Charles Darwin featured a diagrammatic tree in his book, On the Origin of Species. Today, these diagrams remain essential. They effectively convey how speciation occurs through the splitting of lineages.