Phylogenetic Trees and Reading Cladograms

A phylogenetic tree is a branching diagram that shows the evolutionary relationships among species, and a cladogram is a type of tree that groups organisms by shared derived characteristics, with each branching point representing a common ancestor. In brief: to read a tree, look at the branching points (nodes): two species that share a more recent node are more closely related. Order along the tips does not matter, because branches can be rotated like the parts of a mobile without changing the relationships.

Trees are the standard way biologists display the history of life. This guide explains the parts of a tree, how to read it correctly, how a cladogram is built from a table of characteristics, how clades differ from older groupings, works through a construction example and corrects common mistakes.

What is a phylogenetic tree?

Phylogeny is the evolutionary history of a group of organisms. A phylogenetic tree is a hypothesis about that history, built from evidence such as anatomy, DNA sequences and fossils. As new evidence is found, trees are revised. Darwin drew a simple tree in his notebook in 1837, with the words “I think” above it, and the tree is the only illustration in On the Origin of Species.

What are the parts of a tree?

• Root: the common ancestor of all the organisms in the tree.
• Branches: lines that represent lineages over time.
• Nodes (branching points): a point where a lineage splits in two, which represents the most recent common ancestor of the groups that arise from it.
• Tips (leaves): the species or groups being compared, usually living species.
• Clade: a group that consists of an ancestor and all its descendants. A clade is a branch that you could cut with a single cut.
• Outgroup: a species outside the group of interest, which is used to determine which characteristics are ancestral.

In some trees, the length of the branches is proportional to time or the amount of genetic change. In many simple school diagrams, length has no meaning.

How do you read a tree?

1. Find the most recent common ancestor of two species by tracing back from the tips until the lines join. The closer the junction to the tips, the more closely related the species.
2. Compare nodes, not the positions of tips. Species that are side by side in the diagram are not necessarily closer relatives than species that are further apart. In a tree, the branches can be flipped around any node.
3. Identify clades: choose a node and include all the tips from it.
4. Do not read the tree as a ladder. Modern species are all at the tips. No living species is “more evolved” than another. They have all been evolving for the same length of time since the root.

As an illustration, in a tree of vertebrates, mammals and birds are closer relatives of each other than of frogs, because their lineages share a more recent common ancestor. Crocodiles and birds, in fact, share a more recent ancestor with each other than crocodiles do with lizards, which is why modern classifications place birds with reptiles in a group called Sauropsida.

What is a cladogram, and how is it built?

A cladogram is a tree built from the distribution of derived characters (also called synapomorphies), which are novel features that appeared in an ancestor and are shared by its descendants. Ancestral features (plesiomorphies) are shared with more distant relatives and so are not useful for grouping. For example, having a backbone is ancestral for mammals, but having hair is a derived feature that defines mammals.

The method (cladistics) follows these principles:

• Groups should be defined by shared derived characters, not by general similarity.
• The tree that requires the fewest evolutionary changes is preferred (the principle of parsimony, a form of Occam’s razor).
• Only monophyletic groups (clades), which contain an ancestor and all its descendants, are recognized as natural groups. A group missing some descendants (paraphyletic), such as “reptiles” if birds are excluded, or a group of unrelated species (polyphyletic), is not.

Character table for a cladogram

A table of characters records whether each organism has a feature (+) or not (−). The table below is a simplified one for five animals.

Worked example: building a cladogram

1. Count the characters: the lamprey has only 1 (backbone), the frog has 2, the lizard has 3, and the cat and the human each have 4.
2. Order the groups by the number of shared characters: lamprey, then frog, then lizard, then cat and human.
3. Place nodes where characters first appear. Four limbs appear at the node leading to frog, lizard, cat and human (but not the lamprey). The amniotic egg appears at the node leading to the lizard, cat and human (not the frog). Hair appears at the node leading to the cat and human only.
4. Draw the tree. Notation using brackets: (lamprey, (frog, (lizard, (cat, human)))).

The interpretation: the cat and human form a clade defined by hair. The lizard shares a more recent ancestor with the cat and human than with the frog. Nothing in this data can resolve the relationship between the cat and the human, so a more detailed table would be needed to say which of them is closer to other mammals. The table uses characters that are consistent with each other, so parsimony needs only four changes in total: one for each character. Real data usually contain conflicts, which is why computer programs compare thousands of possible trees.

If a fifth character, such as “gills in adults”, were added and the lamprey and the frog both had it, it would be an ancestral feature that was lost in other groups. It would not be used to group the lamprey and the frog together, since it is not a derived feature shared only by them.

What data are used to build trees?

Early trees were built from morphological characters. Today, most trees are based on DNA or protein sequences, using computer programs that compare many possible trees and select the one that best fits the data by methods such as maximum likelihood or Bayesian inference. A tree may combine fossil evidence for dating the nodes. DNA data often resolve relationships that anatomy alone could not, for example showing that whales are most closely related to hippopotamuses among living mammals, and that fungi are more closely related to animals than to plants.

How did the method develop?

Willi Hennig, a German entomologist, developed the principles of phylogenetic systematics in 1950, and his book was translated into English in 1966. Carl Woese used ribosomal RNA sequences in the 1970s to build trees and proposed the three domains of life in 1990. The Tree of Life Web Project and similar databases attempt to map the relationships of all living species. The analysis of DNA is now a standard tool in conservation, medicine (tracking the evolution of viruses such as SARS-CoV-2) and forensics.

Which mistakes are common?

Mistake 1: Reading closeness on the page as closeness of relationship

Look at the nodes. The sequence of tips can be changed without altering the relationships.

Mistake 2: Saying that one living species evolved from another

Species at the tips share a common ancestor. Humans did not evolve from chimpanzees. Both evolved from a common ancestor.

Mistake 3: Grouping organisms by ancestral characters

Only shared derived characters define a clade. Having a backbone does not separate mammals from fish.

Mistake 4: Treating the tree as a fact

A tree is a hypothesis supported by the current evidence, and it can change.