Phylogenetic Tree

How do modern species emerge from ancestral species? Can we trace the evolutionary changes that distinguish one lineage from another? At what point in time do these changes occur? In the following article, we will discuss how organisms are named and classified, how their evolutionary history and relationship are illustrated through phylogenetic trees, and how phylogenetic trees differ from cladograms.

What are phylogenetic trees?

Before we discuss the concepts of phylogeny and its visual representation, phylogenetic trees, we must first discuss how organisms are classified.

How are organisms classified?

Scientists use an analytical approach called systematics to classify organisms and determine their evolutionary relationships. An approach to systematics, taxonomy refers to how organisms and groups are named and classified.

Taxonomy uses a hierarchical classification where species that share similar traits and features are grouped together in increasingly broader categories. For example, the leopard (Panthera pardus), the jaguar (P. onca) the African lion (P. leo), and the tiger (P. tigris) are species that belong to Panthera, a genus that includes all true "big cats".

These categories are (from least to most inclusive):

• Species

• Genus (plural: genera)

• Family

• Order

• Class

• Phylum

• Kingdom

• Domain

A unit at any hierarchical level is called a taxon. For example, Panthera is a taxon at the genus level, while Felidae is a taxon at the family level.

A species is named using the binomial nomenclature, a two-part format that consists of the genus and the specific epithet. For example, the binomial nomenclature for the leopard is Panthera pardus: Panthera is the genus to which it belongs, and pardus is the specific epithet (species) that distinguishes it from other members of the genus.

Species are often placed in the same taxonomic category due to similarities, but the name and classification of species may change if it does not reflect their actual evolutionary relationship and history.

What is a phylogenetic tree?

Parts of a phylogenetic tree

The parts of a phylogenetic tree are as follows:

• Each branch represents a lineage (single line of descent).

• Each branch point (called node) represents the divergence of two or more evolutionary lineages from a common ancestor.

• Each leaf (called terminal node) represents a taxon (plural: taxa) which can be a species or a group at any hierarchical level.

  • Sister taxa are pairs of taxa that branch off from a common node. They represent species that share a recent common ancestor that is not shared by other groups. Members of sister taxa are most closely related to each other.

  • Basal taxa are taxa close to the root. They represent species or groups that diverge from the other members of the group early in their evolutionary history.

• The root indicates the most recent common ancestor of all taxa within the tree. Not all phylogenetic trees are rooted.

Phylogenetic tree example

Let’s use an animal phylogenetic tree to elaborate. The phylogenetic tree below (Fig. 1) shows the evolutionary history and relationships of the members of the family Felidae. The branches indicate the different lineages that diverged from a common ancestral species. The taxa represent the various genera under the family Felidae that evolved from a common ancestor.

Figure 1. The evolutionary history and relationships of Felidae are illustrated in this phylogenetic tree. Source: Various, Public domain, via Wikimedia Commons.

The first branch from the top represents the Panthera lineage, the oldest lineage to diverge from a common ancestor. The descendants evolved into the species belonging to the genus Neofelis (which includes various species of clouded leopards) and the genus Panthera (which includes lions and tigers). Because Neofelis and Panthera branch off from a common node, they are considered sister taxa; meaning these genera are most closely related to each other.

The second branch from the top represents the Bay cat lineage, the second oldest lineage to diverge, which evolved into the genus Pardofelis which includes the marbled cat. The third branch from the top represents the Caracal lineage, the third oldest lineage to diverge. The succeeding lineages can be interpreted accordingly.

Some important things to note:

1. Phylogenetic trees are intended to reflect patterns of descent and do not necessarily show phenotypic similarity or the absolute ages of organisms or groups.

2. A taxon in a phylogenetic tree did not evolve from the taxon next to it; instead, both of them evolved from a common ancestor.

3. Phylogenies and phylogenetic trees are not definitive–they are hypotheses that can be revised or updated based on available evidence.

Different types of phylogenetic trees

Phylogenetic trees can also come in different shapes. Figures 2-5 are examples of phylogenetic trees that look very different from each other.

• Figure 2 (top left) is a phylogenetic tree of Mammalia summarized at the family level. Some of the nodes on this tree correspond to a location on a map of Earth, indicating the origin of the group.

• Figure 3 (bottom left) is a phylogenetic tree of Hexapoda. Some of its branches are curved, making this tree appear circular.

• Figure 4 (top right) is a phylogenetic tree that traces the evolutionary history and relationship of seven dog breeds (Canis lupus familiaris) to their common ancestor the wolf (C. lupus).

• Figure 5 (bottom right) is a phylogenetic tree that shows the evolutionary relationship of the three domains to the Last Universal Common Ancestor, the common ancestor of all life forms.

Figures 2-5. Phylogenetic trees come in different types and shapes. Figure 2 (top left) source: Graphodatsky et al., CC BY 2.0, via Wikimedia Commons. Figure 3 (bottom left) source: James L. Rainford , Michael Hofreiter, David B. Nicholson, Peter J. Mayhew, CC BY 2.5, via Wikimedia Commons. Figure 4 (top right) source: Roy E. Plotnick, Jessica M. Theodor & Thomas R. Holtz Jr., CC BY 4.0, via Wikimedia Commons. Figure 5 (bottom right) source: Maulucioni, CC BY-SA 3.0, via Wikimedia Commons.

When interpreting phylogenetic trees, the shape and position of branches do not matter. It is as valid to draw the root at the leftmost (Figure 4) as it is to draw the root at the center (Figure 3). Likewise, it does not matter if lines are bent or curved. What is important is how the branches are connected. Bending, twisting, or rotating the branches should not change the interpretation of the tree.

What is a cladogram?

Another approach to systematics is cladistics, where organisms and groups are classified into clades, which consist of a common ancestor and its descendant species. Figure 6 is a cladogram, an illustration showing the relationship between organisms and their common ancestor.

Figure 6. This Cladogram shows the evolutionary relationship among primates. Source: Petter Bøckman, CC BY-SA 3.0, via Wikimedia Commons.

Clades that have the ancestral species and all of its descendant species are called monophyletic. When information is incomplete, clades could either be paraphyletic or polyphyletic:

• Clades that do not include all of the descendant species are paraphyletic.

• Clades that do not include a common ancestor are polyphyletic.

Species that evolve share some, but not all, traits with their ancestors. To establish phylogeny, scientists must distinguish shared derived characters from shared ancestral characters.

• Shared derived characters are unique to a specific clade.

• Shared ancestral characters are found in the clade under study as well as older clades.

For example, hair is a shared derived character of mammals. It can be used to distinguish mammals from other vertebrates. On the other hand, the backbone is a shared ancestral character because it is a trait that is found in the common ancestor shared by all vertebrates.

Shared derived characters can be used to establish phylogeny while shared ancestral characters cannot, but whether a trait is a shared derived character or a shared ancestral character may depend on what level is being analyzed.

How is an outgroup used in constructing a cladogram?

Outgroup comparison can be used to distinguish between shared derived characters and shared ancestral characters. An outgroup is a species or group of species closely related to but not a part of the group of species being classified. The species being classified are the ingroup. The outgroup and ingroup of a simple cladogram are shown in Figure 7.

Figure 7. This diagram shows the outgroup and ingroup in a simple cladogram. Source: Ngilbert202, CC BY-SA 4.0, via Wikimedia Commons.

Any homologies present in both the ingroup and the outgroup are assumed to be ancestral characters that came from a common ancestor shared by both ingroup and outgroup. Homologies present in some or all of the ingroup are assumed to be derived characters that emerged with the divergence of the ingroup and the outgroup.

Cladogram vs phylogenetic tree

Cladogram and phylogenetic tree are often used interchangeably, but they have some differences.

• Cladograms show how different organisms are related through a common ancestor, without showing evolutionary changes that have occurred over time.

• Phylogenetic trees show how different organisms are related through the evolutionary changes that have occurred between an ancestor and its descendant species or group of species.