COMSATS University Islamabad

Department of Computer Science

Assignment # 3

Subject: Introduction to Bioinformatics

Submitted to:
Sir Afraz Ahmed Raja

Submitted by:
Abdul Wahab (SP19-BSE-004-8A)

Date: May 24, 2023

1. What is phylogenetics?
Answer: -
Phylogenetics is a field of biology that focuses on studying the evolutionary relationships
between organisms. It involves analyzing genetic, morphological, and behavioral
characteristics to understand the evolutionary history and relatedness of different species.

2. Why is studying phylogenetics significant?

Answer: -
Studying phylogenetics is important for several reasons. It provides insights into the
evolutionary processes that have shaped life on Earth, including species diversification,
adaptation to different environments, and the emergence of new traits. Phylogenetics also
helps in understanding the classification and taxonomy of organisms, assisting in species
identification, conservation efforts, and the development of evolutionary hypotheses.

3.What are rooted and unrooted phylogenetic trees? Can

you provide examples?
Answer: -
Rooted and unrooted phylogenetic trees represent different aspects of evolutionary
relationships. A rooted tree has a common ancestor at its base, indicating the direction of
evolution and the relative time of divergence. An unrooted tree represents the relationships
among species without specifying a common ancestor or the direction of evolution.

Example of a rooted phylogenetic tree: The Tree of Life, which illustrates the evolutionary
relationships among all living organisms and their common ancestry.

Example of an unrooted phylogenetic tree: A Neighbor-Joining tree based on genetic

distances between different populations of a species, where the focus is on understanding
relationships among different populations rather than a common ancestor.

4. List the main terminologies of phylogenetic trees.

Answer: -
The main terminologies of phylogenetic trees include:

- Node: Represents a common ancestor or a speciation event.

- Branch: Represents the evolutionary lineage or relationship between two nodes.
- Root: The starting point or common ancestor of the tree.
- Taxon: A group of organisms, such as a species or a genus, included in the tree.
- Clade: A monophyletic group that includes an ancestor and all of its descendants.
- Outgroup: A taxon used to root the tree and serve as a reference point for comparison.
- Sister Taxa: Two taxa that share a recent common ancestor.

5.What are monophyletic and paraphyletic trees? Can

you provide examples?
Answer: -
Monophyletic trees include all the descendants of a common ancestor and represent a
complete lineage. They are characterized by a single clade that includes the ancestor and all
its descendants.

Example: A phylogenetic tree showing the evolutionary relationships among different

species of cats, where all the species and their common ancestor are included in the same
clade.

Paraphyletic trees exclude some of the descendants of a common ancestor and do not
represent a complete lineage. They are characterized by a group that includes the common
ancestor but not all its descendants.

Example: A phylogenetic tree showing the relationships among different species of reptiles,
where birds (descendants of reptiles) are excluded from the reptile group.

6. What are the five steps involved in molecular

phylogenetic tree construction?
Answer: -
The five steps of molecular phylogenetic tree construction are as follows:

- Data Collection: Obtain molecular data (DNA or protein sequences) from the organisms of
interest.
- Sequence Alignment: Align the sequences to identify corresponding positions and account
for gaps or insertions.
- Phylogenetic Analysis: Use computational methods to analyze the aligned sequences and
infer evolutionary relationships.
- Tree Building: Construct a phylogenetic tree based on inferred relationships, using
algorithms and statistical models.
- Tree Evaluation: Assess the reliability and robustness of the tree through statistical tests,
bootstrap analysis, or other validation methods.

7. What are the two main methods used for building

phylogenetic trees? Can you provide examples?
Answer: -
The two main methods used for building phylogenetic trees are:

- Distance-based methods: These methods calculate genetic distances between sequences

and use these distances to construct trees.
Examples: Neighbor-Joining and UPGMA (Unweighted Pair Group Method with Arithmetic
Mean).

- Character-based methods: These methods analyze the characters or sites in sequences to

infer evolutionary relationships.
Examples: Maximum Likelihood (ML) and Bayesian Inference.

8. Define two evolution models commonly used in

phylogenetics. Can you provide examples?
Answer: -
Two commonly used evolution models in phylogenetics are:

- Molecular Clock Model: This model assumes a relatively constant rate of molecular
evolution over time, allowing estimation of divergence dates based on genetic differences.

Example: Estimating the time of divergence between human and chimpanzee based on
genetic data.

- Coalescent Model: This model describes the process of how genetic lineages coalesce or
merge backward in time to a common ancestor. It is used to study the evolutionary history of
populations and gene flow patterns.

Example: Inferring the historical population dynamics of a species based on genetic variation
among individuals.

9. Define maximum parsimony. Can you provide

examples?
Answer: -
Maximum parsimony is a principle used in phylogenetic tree construction. It states that the
tree requiring the fewest evolutionary changes or mutations is the most likely or accurate
representation of the evolutionary relationships. Maximum parsimony seeks to minimize the
number of inferred evolutionary events (such as nucleotide substitutions) to explain the
observed data.
Example: Constructing a phylogenetic tree for a group of bird species based on their genetic
sequences, where the tree with the least number of genetic changes would be favored
according to the principle of maximum parsimony.
10. Construct a phylogenetic tree using the example
provided in lecture 3,4,5.
Answer: -