Phylogenetic Tree | Construction and Overview

A phylogenetic tree is a visual diagram that represents the history of the evolutionary descent of different species or genes from a common ancestor. The relationships are developed over time between different biological species based on the similarities and differences in their physical or genetic traits.

A phylogenetic tree is also known as an “Evolutionary tree” or “Dendrogram”. In this article, we will read about phylogenetic tree examples and construction in detail.

History of Phylogenetic Tree

Ancient beliefs of a ladder-like evolution from lower to higher life forms gave rise to the concept of a “tree of life”. A “paleontological chart” outlining the geological relationships between plants and animals can be found in Edward Hitchcock’s book Elementary Geology as one of the earliest examples of “branching” phylogenetic trees (first edition: 1840).

In his book ‘The Origin of Species’, Charles Darwin created one of the first pictures and played a significant role in popularising the idea of an evolutionary “tree.” The concept that speciation occurs through the adaptive and semi-random splitting of lineages is successfully communicated by tree diagrams, which are still used by evolutionary biologists to represent evolution more than a century after they were first used.

Examples of Phylogenetic Tree

Every species or person (in this example) has a common ancestor, as shown in the diagram, and that person is your grandparent. Then it separates into your parent’s and your aunt’s branches (sibling of your parent). Because you were born to different parents yet have a similar ancestor to your grandparents, you, your sibling, and your cousins have a special history.

Parts of Phylogenetic Tree

A phylogenetic tree consists of the following components:

• Every branch denotes a lineage (single line of descent).
• Each node on a branch (also known as a branch point) reflects the split in two or more evolutionary lineages from a common ancestor.
• A taxon, which might be a species or a group at any hierarchical level, is represented by each leaf, also known as a terminal node.
  • Sister taxa are groups of related taxa that diverge from a single node. They stand for species that have a more recent common ancestor than other groups. Sister taxa have the closest relationships among their members.
  • Taxa close to the root are called basal taxa. They are examples of species or groups that, early in the course of their evolutionary histories, diverge from the other members of the group.
• The most recent common ancestor of all taxa is shown as the tree’s root. Some phylogenetic trees do not have roots.

Phylogenetic Tree Construction

The phylogenetic tree construction is created using one of two different approaches:

Character-Based Approach

This method is also known as the discrete method because it is based solely on the sequence characters. Aligned characters are used in the character-based technique to build the phylogenetic tree. During the tree inference, these aligned characters either include DNA or protein sequences. Maximum parsimony and Character based approaches are the two most prevalent.

Distance-Based Approach

This approach is based on how dissimilar or how far apart the two aligned sequences are from one another. The pairwise distances from the sequence data are then utilized to create a matrix, which is subsequently used to generate the phylogenetic tree in this method.

What are the Steps for Constructing a Phylogenetic Tree?

Any phylogenetic study starts with the following fundamental steps:

• Select Organisms: Choose a set of organisms you want to analyze their evolutionary relationships.
• Gather Data: Collect data on the organisms, typically DNA sequences (e.g., genes) or morphological characteristics.
• Align Sequences: If using DNA data, align the sequences to ensure they are comparable.
• Choose a Method: Select a phylogenetic analysis method, such as:
  • Distance-based methods
  • Character-based methods
• Run the Analysis: Use specialized software (e.g., MEGA, PAUP, RAxML) to perform the chosen phylogenetic analysis with your data.
• Evaluate the Tree: Analyze the resulting tree for:
  • Branching patterns: Consistency with known evolutionary relationships.
  • Bootstrap support: Strength of the branching pattern based on resampling data.
• Refine the Analysis (Optional): If necessary, adjust parameters or repeat steps with different data or methods to improve the tree.
• Interpret the Tree: Analyze the branching patterns and visualize the evolutionary relationships between the organisms.
• Present the Results: Create a clear presentation of the phylogenetic tree with explanations and relevant information.

Types of Phylogenetic Tree

Distinct phylogenetic trees are divided into varied groups based on their different traits, such as whether they are rooted, non-rooted, bifurcating, or multifurcating.

Rooted Tree

A phylogenetic tree with a common ancestor on each node is referred to as a rooted tree. As a result, the categorization comes to a stop at one point, typically at the node that serves as the common ancestor of all the tree branches.

Unrooted Tree

The non-rooted tree does not share a common ancestor with the rooted tree. The common ancestor or the tree node is always left out while creating the unrooted phylogenetic tree from the rooted tree.

Bifurcating Tree

Phylogenetic trees that only have two branches or leaves are referred to as bifurcating trees. Additionally, it can be divided into rooted and unrooted bifurcating trees.

Multifurcating Tree

Multiple branches can be found on a single node in a multifurcating tree, as the name suggests. Both a rooted multifurcating tree and an unrooted multifurcating tree are categories for it once more.

Special Types of the Phylogenetic Trees

• Dendrogram – A phylogenetic tree’s diagrammatic representation is also known as a dendrogram because a dendrogram is a broad term for any tree, phylogenetic or not.
• Cladogram – A cladogram solely depicts a branching pattern; as a result, its interior nodes do not represent ancestors and its branch lengths do not correspond to time or the relative degree of character change.
• Chronogram – A Chronogram is a particular kind of Phylogenetic tree that uses the length of its branches to represent time.
• Phylogram – A phylogenetic tree with branch lengths according to character change is called a phylogram. A phylogenetic tree called a chronogram explicitly displays time by the lengths of its branches.
• Dahlgrenogram – A Dahlgrenogram is a diagram that shows a phylogenetic tree in cross-section.

What does Phylogenetic Tree of Life Shows?

The phylogenetic tree of life shows the evolutionary relationships among different organisms, depicting their shared ancestry and divergence over time. It showcases the branching patterns representing the evolutionary history of species, with each branch point indicating a common ancestor. By analyzing the tree’s structure and branching patterns, scientists can infer evolutionary processes such as speciation and divergence. Also, the tree highlights the diversity of life on Earth, revealing the vast range of organisms and their interconnectedness through evolutionary history. Ultimately, the phylogenetic tree serves as a visual representation of the evolutionary relationships that shape the biodiversity of our planet.

Why is Phylogenetic Tree Important?  

The most important data from the disciplines of anatomy, paleontology, molecular genetics, and embryology, may be derived using this essential method. The evolutionary tree also has the following significance:

• To illustrate the relationships between organisms thought to share some evolutionary origin.
• Researching the shared ancestors of extinct and surviving species.
• Employed to research the evolutionary past.
• Employed in the hunt for new species.
• The evolutionary histories of pathogenic bacteria can be tracked with the use of the phylogenetic tree.
• Research the global dispersal of the species
• It is used to determine the most recent shared ancestors and how closely related different species are to one another.
• To connect the important turning points in the development of life to the tree of life.

Phylogenetic Tree vs Cladogram

Phylogenetic trees and cladograms are frequently used interchangeably; however, they differ in some ways.

Feature	Phylogenetic Tree	Cladogram
Purpose	Shows evolutionary relationships and estimated time between divergences	Shows ancestral relationships and shared characteristics
Time Scale	Often incorporates time scale on branches (represents evolutionary distance)	Does not depict time scale on branches
Branch Length	Branch length may reflect time elapsed since divergence	Branch lengths are typically all the same length
Ancestral Information	May depict ancestral characteristics at nodes	Does not depict ancestral characteristics
Complexity	Can be more complex with detailed branching patterns	Generally simpler with fewer branches
Information Source	Uses various data sources like DNA sequences, morphology, fossils	Primarily uses morphological data
Evolutionary Certainty	Suggests relative evolutionary distances, but not necessarily exact timelines	Indicates shared ancestry but not the degree of evolutionary change

Applications of Phylogenetic Tree

Application of Phlyogenetic Tree are given below:

• The goal of the phylogenetic tree is to establish an evolutionary connection between distinct creatures. By doing this, we can learn more about the evolutionary processes and sources of various creatures.
• It is useful to investigate evolution-related occurrences and classify species according to how their structures and functions have diverged.
• Additionally, it is useful to organize organisms and species according to their DNA sequences and morphological similarities and differences.
• Studying the impacts of evolution and the traits of various organisms is also helpful.

Limitations of Phylogenetic Tree

Limitation of Phlyogenetic Tree are given below:

• This evolutionary tree of craniates, which resembles a progressing ladder, evolved from an organism without a spinal column.
• Therefore, depending only on the traits they share, various groupings of organisms, objects, or units are situated at the tips of each branch.
• A phylogenetic tree illustrates the theories regarding the evolution and development of life.
• They are only as accurate as the facts that they are based on and are supported by.
• The information is derived from research and studies, which may contain some bias.
• As a result, phylogenetic trees constructed using data from research and studies may always be erroneous, biased, or subject to manipulation.

Conclusion – Phylogenetic Tree

Phylogenetic tree is defined as the diagrammatic representation of evolutionary relationships among living organisms. It visually represents how different specie have evolved from a series of common ancestors. There are two approaches of construction of phylogenetic tree- character based and distance based approach. Based on different traits, phylogenetic tree is divided into various groups like rooted, non-rooted, bifurcating, or multifurcating.

FAQs – Phylogenetic Tree

Define Phylogenetic Tree.

Phylogenetic Tree is a visual representation of the evolutionary relationships that have developed over time between different biological species.

What is the Difference Between a Cladogram and a Phylogenetic Tree?

A cladogram shows evolutionary relationships based on shared characteristics, while a phylogenetic tree includes genetic data to depict evolutionary history more accurately.

What is a Spindle Diagram?

A spindle diagram is a visual representation of evolutionary relationships among species, resembling a branching tree, commonly used by evolutionary biologists to illustrate speciation and lineage splitting.

What is a Cladogram?

A cladogram solely depicts a branching pattern; as a result, its interior nodes do not represent ancestors and its branch lengths do not correspond to time or the relative degree of character change.

What are the 4 Parts of a Phylogenetic Tree?

The four parts of a phylogenetic tree are branches, nodes, tips, and the root.

What are the Steps in the Phylogenetic Tree?

Steps in constructing a phylogenetic tree include data gathering, species comparison, tree building, and result interpretation.

What is Phylogenetic Tree Analysis in Bioinformatics?

Phylogenetic tree analysis in bioinformatics involves computationally studying evolutionary relationships among biological entities to reconstruct their evolutionary history.

What are the 3 Types of Phylogenetic Tree?

The three types of phylogenetic trees are rooted trees, unrooted trees, and bifurcating trees.