PHYLOGENETIC TREE: TYPES AND THEIR CHARACTERISTICS, EXAMPLES - BIOLOGY - 2025

A phylogenetic tree is a mathematical graphical representation of the history and ancestor-descendant relationships of groups, populations, species, or any other taxonomic category. Theoretically, all phylogenetic trees can be grouped in the tree of life, constituting the universal tree.

These graphic representations have revolutionized the study of evolutionary biology, since they allow to establish and define a species, test various evolutionary hypotheses (such as endosymbiotic theory), evaluate the origin of diseases (such as HIV), etc.

Source: John Gould (14.Sep.1804 - 3.Feb.1881)

Trees can be reconstructed using morphological or molecular characters, or both. In the same way, there are various methods to build them, the most common being the cladist methodology. This seeks to identify shared derived characters, known as synapomorphy.

characteristics

One of the principles developed by Charles Darwin is the common ancestry of all living organisms - that is, we all share a remote ancestor.

In "The Origin of Species" Darwin raises the metaphor of the "tree of life." In fact, he uses a hypothetical graphical tree to develop his idea (curiously, it is the only illustration of the Origin).

The representation of this metaphor is what we know as phylogenetic trees, which allow us to graphically display the history and relationships of a specific group of organisms.

Anatomy of a phylogenetic tree

In phylogenetic trees, we can distinguish the following parts - continuing with the botanical analogy:

Branches: the lines of the tree are called "branches", and these represent the study populations over time. Depending on the type of tree (see below), the length of the branch may or may not have a meaning.

At the tips of the branches we find the organisms we want to evaluate. These can be entities that are currently alive, or extinct beings. The species would be the leaves of our tree.

Root: the root is the most ancient branch of the tree. Some have it and are called rooted trees, while others do not.

Nodes: The branch points of branches in two or more lineages are called nodes. The dot represents the most recent common ancestor of the descendant groups (note that these ancestors are hypothetical).

The existence of a node implies a speciation event - creation of new species. After this, each species follows its evolutionary course.

Additional terminology

In addition to these three basic concepts, there are other necessary terms when it comes to phylogenetic trees:

Politomy: when a phylogenetic tree has more than two branches in a node, it is said that there is a polytomy. In these cases, the phylogenetic tree is not fully resolved, because the relationships between the organisms involved are not clear. This often happens due to a lack of data, and can only be fixed when a researcher accumulates more.

External group: in phylogenetic issues it is common to hear the concept of external group - also called outgroup. This group is selected to be able to root the tree. It should be chosen as a taxon that previously diverged from the study group. For example, if I am studying echinoderms, you can outgroup sea squirts.

Types

There are three basic types of trees: cladograms, additive trees, and ultrametric trees.

Cladograms are the simplest trees and show the relationship of organisms in terms of common ancestry. The information of this type of tree resides in the branching patterns, since the size of the branches does not have any additional meaning.

The second type of tree is the additive, also called metric trees or phylograms. The length of the branches is related to the amount of evolutionary change.

Finally, we have ultrametric trees or dendograms, where all the tips of the trees are at the same distance (which is not the case in the phylogram, where a tip may appear lower or higher than its partner). The length of the branch is related to evolutionary time.

The choice of the tree is directly related to the evolutionary question that we want to answer. For example, if we are concerned only with the relationships between individuals, a cladogram will suffice for the study.

Most common mistakes when reading phylogenetic trees

Although phylogenetic trees are often widely used graphs in evolutionary biology (and general biology), there are many students and professionals who misinterpret the message that these apparently simple graphs are intended to deliver to the reader.

There is no trunk

The first mistake is to read them sideways, assuming that evolution implies progress. If we understand the evolutionary process correctly, there is no reason to think that the ancestral species are on the left and the more advanced species on the right.

Although the botanical analogy of a tree is very useful, there comes a point where it is no longer so exact. There is a crucial tree structure that is not present in the tree: the trunk. In phylogenetic trees we do not find any main branches.

Specifically, some people might consider man as the ultimate "goal" of evolution, and therefore the Homo sapiens species should always be located as the final entity.

However, this view is not consistent with evolutionary principles. If we understand that phylogenetic trees are mobile elements, we can place Homo in any terminal position of the tree, since this characteristic is not relevant in the representation.

Nodes can rotate

A vital feature that we must understand about phylogenetic trees is that they represent non-static graphs.

In them, all these branches can rotate - in the same way that a mobile can. We do not mean that we can move the branches at will, because some movements would involve changing the pattern or topology of the tree. What we can rotate are the nodes.

To interpret the message of a tree, we must not focus on the tips of the branches, we must focus on the branch points, which are the most important aspect of the graph.

In addition, we must bear in mind that there are several ways to draw a tree. Many times it depends on the style of the book or magazine and changes in the shape and position of the branches do not affect the information they want to convey to us.

We cannot deduce the existence of current ancestral or "old" species

When we are going to refer to current species, we should not apply ancestral connotations to them. For example, when we think about the relationships between chimpanzees and humans, we might misunderstand that chimpanzees are ancestral to our lineage.

However, the common ancestor of chimpanzees and humans was neither. To think that the chimpanzee is ancestral would be to assume that its evolution stopped once both lineages separated.

Following the same logic of these ideas, a phylogenetic tree does not tell us if there are young species either. As the allelic frequencies are constantly changing and there are new characters changing over time, it is difficult to determine the age of a species and, certainly, a tree does not give us such information.

The "change of allele frequencies over time" is how population genetics defines evolution.

They are unchangeable

When looking at a phylogenetic tree we must understand that this graph is simply a hypothesis generated from concrete evidence. It may be that if we add more characters to the tree, it will modify its topology.

The expertise of scientists in choosing the best characters to elucidate the relationships of the organisms in question is key. In addition, there are very powerful statistical tools that allow researchers to evaluate trees and choose the most plausible one.

Examples

The three domains of life: Archaea, Bacteria and Eukarya

In 1977, the researcher Carl Woese proposed grouping living organisms into three domains: Archaea, Bacteria and Eukarya. This novel classification system (previously there were only two categories, Eukaryota and Prokaryota) was based on the ribosomal RNA molecular marker.

Bacteria and eukaryotes are widely known organisms. Archaea are often mistaken for bacteria. However, these differ profoundly in the structure of their cellular components.

Therefore, although they are microscopic organisms like bacteria, the members of the Archaea domain are more closely related to eukaryotes - because they share a closer common ancestor.

Source: Prepared by Mariana Gelambi.

Phylogeny of primates

Within evolutionary biology, one of the most controversial topics is the evolution of man. For the opponents of this theory, an evolution starting from an apelike ancestor that gave rise to modern man is not logical.

A key concept is understanding that we did not evolve from current apes, but rather shared a common ancestor with them. In the tree of apes and humans, it stands out that what we know as "ape" is not a valid monophyletic group, since it excludes humans.

Source: Prepared by Mariana Gelambi.

Phylogeny of cetartiodactyls (Cetartiodactyla)

Evolutionarily speaking, cetaceans represented a group of vertebrates whose relationships with the rest of their fellow mammals were not very clear. Morphologically, whales, dolphins, and other members bear little resemblance to other mammals.

Currently, thanks to the study of different morphological and molecular characters, it has been possible to conclude that the sister group of the large cetaceans is formed by the artiodactyls - ungulates with even hoofs.

Source: Prepared by Mariana Gelambi.

References

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