Introduction to tree diagrams

There are four types of tree diagrams or ‘dendrograms‘:

Fundamentally they all display hierarchical relationships through branching order where each branch is split into two more branches. The point at which each branch splits in two is called a node.

So, what’s the difference?

Cladogram

A cladogram is a tree like diagram that shows branching order only, this type of diagram does not represent real evolutionary relatedness, instead it represents hypothesised relationships based on the pattern of ancestral and derived traits.

Ancestral traits, also called ‘primitive traits’, are traits that are shared through common ancestry.

Derived traits are traits that developed some time after primitive traits, these traits only appear in a few members of a group. A node in a cladogram represents a change in character trait.

The cladrogram below in Fig 1. illustrates the hypothesised relationships between different groups of vertebrates.

The hierarchy and branching pattern of this cladogram is based on the following character traits of the different groups of species:

• All the groups are vertebrates.

• Sharks are vertebrates but they do not have a bony skeleton like the other vertebrates (they have cartilage skeletons instead of bone).

• Ray-finned fish have a bony skeleton but they do not have four limbs.

• Amphibians have four limbs but they do not have an amniotic egg.

• Primates, rodents, crocodiles, dinosaurs and birds all have an amniotic egg.

• Primates, rodents and rabbits have an amniotic egg but they don’t have two post-orbital fenestrae (these are openings in the skull behind the eye).

• Crocodiles, dinosaurs and birds have an amniotic egg but they don’t have hair.

Phenogram

A phenogram is a tree like diagram that shows branching order that is not related to evolutionary relationships. Unlike the other tree building methods phenograms use phenetic information.

Phenetic information comes from morphological or observable character traits similar to those used to construct a cladogram.

These types of trees rarely come up in the literature but they can be useful to illustrate clustering of morphological similarities.

A phenogram does not try to represent evolutionary relationships, instead it represents relationships based on the overall similarities of shared character traits.

This information is collected by counting the presence or absence of character traits shared between pairs of organisms and then clustering by similarity.

Phylogram

A phylogram is a tree like diagram that shows branching order and evolutionary relationships based on both similarities and differences in DNA sequence data. These are the most common type of trees you will see in the literature.

There is a lot of information in a phylogram and tree branches here are proportional to the amount of evolutionary change for example, the longer the branch the more evolutionary change has occurred.

A node in a phylogram represents a point in evolutionary time where two lineages diverged from a shared common ancestor.

Phylograms can be rooted or unrooted. If a phylogram is rooted, where the ancestral lineage of the organisms is defined, the tree will have a direction of evolutionary change.

This means that in a phylogram we can trace the order of evolutionary descent from the root and quantify how much evolutionary change has occurred after each node.

In phylograms evolutionary change is most commonly measured through the number of substitutions per site, these values are calculated from sequence alignment data (we will cover this in a later post).

It is important to remember that with phylograms we can only compare the evolutionary change in a single ancestral lineage at a time, we cannot make comparisons between different lineages.

For example, in Fig 4 below, nodes x and y are on separate branches of the tree. The branch that leads to node x is longer than the branch leading to node y.

We might at first assume that node y is younger than node x based on the amount of evolutionary change, however, we cannot tell whether the ancestral organisms in node y lived before or after those in node x.

This is because evolutionary change in a phylogram is not directly proportional to time.

In different lineages we can, and often see, different rates of evolutionary change.

As a result the scale of the branch lengths becomes incomparable across different lineages in the tree.

Chronogram

A chronogram is a tree like diagram that shows branching order and evolutionary relationships where the tips in the tree are all equidistant from the root of the tree.

If your data is ultrametric branch lengths are directly proportional to time (we will talk more about what ultrametric means in a future post).

Chronograms can be built using DNA sequence data where the rate of evolutionary change can be converted into time (usually in Millions of years – Mya) using a known historical date and/or a mutation rate for calibration.

In a chronogram nodes have ages. A node represents the time when two lineages diverged from their last common ancestor.

Chronograms are valuable for evolutionary analyses, unlike phylograms you can compare the ages of nodes across different lineages.

With this information you can make hypotheses about past evolutionary events based on historical dates.