Phylogenetic Tree

An evolutionary or phylogenetic tree both have the same names. It is a branching diagram or tree that represents the relationships that have developed over time between different biological species or other entities based on the similarities and differences in their physical or genetic traits. One phylogenetic tree, which shows a common ancestor for all life on Earth, is present.

Human 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 grandparent, you, your sibling, and your cousins have a special history.

History

Ancient beliefs of a ladder-like evolution from lower to higher life forms gave rise to the concept of a “tree of life” (such as in the Great Chain of Being). 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 ground-breaking book The Origin of Species, Charles Darwin (1859) also 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. The taxonomy of species has evolved to become more dynamic and less static.

Parts of a 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 (plural: taxa), 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.

Parts of a phylogenetic tree

Approaches to make Phylogenetic Tree

The phylogenetic tree 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.

Steps for Phylogenetic Analysis

Any phylogenetic study starts with the following fundamental steps:

Step 1: Setup and alignment of a dataset

• Finding an interesting protein or DNA sequence is the initial stage, followed by compiling a dataset of related sequences.
• Using NCBI BLAST or other comparable search engines, DNA sequences of interest can be located.
• Multiple sequence alignment is produced after the selection and recovery of sequences.
• To find homology regions, a set of sequences must be arranged in a matrix.
• ClustalW, MSA, MAFFT, and T-Coffee are just a few of the websites and software tools available for doing multiple sequencing on a given set of molecular data.

Step 2: Create (estimate) phylogenetic trees 

• From sequences using stochastic models and computational techniques.
• Statistical techniques are used to ascertain the tree topology and calculate the branch lengths that most accurately depict the phylogenetic relationships of the matched sequences in a dataset in order to construct phylogenetic trees.
• The most often used computational techniques are those that use distance matrices and discrete data, including maximum likelihood and parsimony.
• Many software programs, including Paup, PAML, and PHYLIP, use these most common techniques.

Step 3: Test and evaluate the estimated trees statistically.

• One or more ideal trees are produced via tree estimation techniques.
• A number of statistical tests are run on this set of potential trees to see which is the best option and whether the suggested phylogeny makes sense. 
• Jackknife Resampling techniques, as well as analytical techniques like parsimony, distance, and likelihood, are frequently used to evaluate trees.

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.

It was once thought that multicellular eukaryotic beings descended from ape-like prokaryotes. The evolution process is governed by several forces. One of them is genetic makeup.

Based on morphological, genotypic, and phylogenetic variances and similarities across species, a phylogenetic tree is created.
This means that to create an accurate phylogenetic tree, both observable alterations and changes in DNA sequences are taken into consideration.

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.

Importance 

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:

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

Applications

• 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

• 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.

Cladogram

A phylogeny, or hypothetical link between groups of creatures, is depicted in a diagram known as a cladogram. A phylogenetic systematics researcher will use a cladogram to depict the groups of organisms being compared, their relationships, and their most recent shared ancestors. A cladogram might be quite complicated and compare every known form of life, or it can be extremely simple and compare just two or three groups of creatures.

Difference between a Cladogram and a Phylogenetic Tree

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

Cladograms demonstrate the evolutionary relationships between various organisms without demonstrating the course of evolution. Through the evolutionary changes that have taken place between an ancestor and its descendant species or set of species, phylogenetic trees demonstrate how various organisms are connected.

FAQs on Phylogenetic Trees

Question 1: Define a phylogenetic tree.

Answer:

An evolutionary or phylogenetic tree both have the same names. It is a branching diagram or tree that represents the relationships that have developed over time between different biological species or other entities based on the similarities and differences in their physical or genetic traits

Question 2: Write the difference between a cladogram and a phylogenetic tree.

Answer:

Cladograms demonstrate the evolutionary relationships between various organisms without demonstrating the course of evolution. Through the evolutionary changes that have taken place between an ancestor and its descendant species or set of species, phylogenetic trees demonstrate how various organisms are connected.

Question 3: Write about the spindle diagram.

Answer:

A spindle diagram, with the breadth of the spindles denoting different families, illustrates the evolution of vertebrates at the class level. The usage of spindle diagrams in evolutionary taxonomy is common. After its popularisation by the American paleontologist Alfred Romer, a spindle diagram, also known as a bubble diagram, is frequently referred to as a Rome program. To reflect changes in taxon abundance across time, it plots taxonomic diversity (horizontal breadth) versus geological time (vertical axis).

Question 4: What is a cladogram?

Answer:

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.

Question 5: Write the importance of a phylogenetic tree.

Answer:

• 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.