Phylogenetic analysis basics MCQs With Answer

Introduction: Phylogenetic analysis is a vital tool in modern pharmaceutical research, helping M.Pharm students understand evolutionary relationships among genes, proteins, and organisms that influence drug discovery, vaccine design, and antimicrobial resistance tracking. This set of MCQs focuses on foundational concepts—sequence alignment, models of molecular evolution, tree-building methods, branch interpretation, and reliability measures like bootstrapping—tailored to the depth required in an M.Pharm curriculum. Questions emphasize practical implications, such as choosing appropriate models, recognizing artifacts like long-branch attraction, and selecting software commonly used in research. Working through these questions will strengthen conceptual understanding and aid application of phylogenetics in pharmaceutical and biomedical contexts.

Q1. What is the primary purpose of multiple sequence alignment in phylogenetic analysis?

• To identify phylogenetic tree topology without considering sites
• To determine homologous positions across sequences for evolutionary inference
• To estimate absolute divergence times directly
• To calculate molecular weight of proteins

Correct Answer: To determine homologous positions across sequences for evolutionary inference

Q2. Which substitution model explicitly accounts for different rates of transitions and transversions?

• Jukes-Cantor (JC69)
• Kimura 2-parameter (K2P)
• Poisson model
• Dayhoff PAM

Correct Answer: Kimura 2-parameter (K2P)

Q3. Which tree-building method uses pairwise distances between sequences to construct a tree?

• Maximum Likelihood
• Neighbor-Joining
• Maximum Parsimony
• Bayesian Inference

Correct Answer: Neighbor-Joining

Q4. In maximum parsimony analysis, what criterion defines the best tree?

• The tree with the highest likelihood score given a model
• The tree with the fewest total character-state changes
• The tree with the longest total branch length
• The tree with the most congruence to a reference taxonomy

Correct Answer: The tree with the fewest total character-state changes

Q5. What does a bootstrap value on a phylogenetic tree indicate?

• The absolute age of the clade in millions of years
• The proportion of resampled datasets that support a particular clade
• The number of substitutions on that branch
• The posterior probability from a Bayesian analysis

Correct Answer: The proportion of resampled datasets that support a particular clade

Q6. Which problem is commonly caused by high substitution rates in long branches and can mislead phylogenetic inference?

• Homology erosion
• Long-branch attraction
• Polytomy inflation
• Rate constancy calibration

Correct Answer: Long-branch attraction

Q7. Which approach estimates phylogenies by maximizing the probability of observing the data under a specified model?

• Distance methods
• Maximum Likelihood
• Parsimony with weights
• Neighbor-Joining

Correct Answer: Maximum Likelihood

Q8. In Bayesian phylogenetic inference, what does the posterior probability represent?

• The best tree according to parsimony
• The prior distribution of models only
• The probability of a clade given the data and the prior
• The bootstrap support converted to a percentage

Correct Answer: The probability of a clade given the data and the prior

Q9. Which model parameter accounts for among-site rate variation commonly used in ML and Bayesian analyses?

• Proportion of invariant sites (I) and gamma distribution (Γ)
• Only transition/transversion ratio (kappa)
• Codon position matrix exclusively
• Uniform rate across sites (U)

Correct Answer: Proportion of invariant sites (I) and gamma distribution (Γ)

Q10. Why is model selection (e.g., using AIC or BIC) important before conducting likelihood-based phylogenetic analyses?

• To choose the shortest tree length
• To identify the substitution model that best balances fit and complexity
• To determine sequence alignment quality
• To set branch length units to time

Correct Answer: To identify the substitution model that best balances fit and complexity

Q11. What is the difference between orthologs and paralogs in evolutionary terms?

• Orthologs result from gene duplication; paralogs from speciation
• Orthologs result from speciation; paralogs from gene duplication
• Both are produced only by horizontal gene transfer
• There is no evolutionary difference; terms are interchangeable

Correct Answer: Orthologs result from speciation; paralogs from gene duplication

Q12. In the context of molecular clocks, which assumption is required to estimate divergence times directly from branch lengths?

• Rates of substitution are constant across all lineages
• All taxa have identical genome sizes
• No homoplasy is present
• Every gene evolves under the JC69 model

Correct Answer: Rates of substitution are constant across all lineages

Q13. Which software is commonly used for rapid maximum likelihood phylogenetic inference on large datasets?

• ClustalW
• RAxML
• EMBOSS
• BLAST

Correct Answer: RAxML

Q14. What does branch length typically represent in a phylogenetic tree inferred from molecular data?

• The number of morphological characters supporting the node
• The amount of evolutionary change (e.g., expected substitutions per site)
• The geographic distance between sampled taxa
• The sampling date of each taxon

Correct Answer: The amount of evolutionary change (e.g., expected substitutions per site)

Q15. Which alignment problem is most likely to distort phylogenetic inference if not corrected?

• Random base composition in coding regions
• Incorrectly aligned homologous positions (misalignment)
• Using amino acid sequences instead of nucleotides
• Low GC content across genomes

Correct Answer: Incorrectly aligned homologous positions (misalignment)

Q16. For protein-coding genes, why might codon-based substitution models be preferred over nucleotide models?

• They ignore synonymous substitutions
• They explicitly model synonymous and nonsynonymous changes and codon structure
• They assume equal rates among all codon positions
• They are computationally simpler than nucleotide models

Correct Answer: They explicitly model synonymous and nonsynonymous changes and codon structure

Q17. What is a consensus tree in phylogenetic analysis?

• A single tree produced by neighbor-joining only
• A tree that summarizes common clades from a set of trees, e.g., bootstrap replicates
• A tree with no branch lengths displayed
• A tree inferred without using sequence data

Correct Answer: A tree that summarizes common clades from a set of trees, e.g., bootstrap replicates

Q18. Which evidence best supports that two sequences are homologous rather than analogous?

• Similar function but no sequence similarity
• Significant sequence similarity and conserved motifs consistent with common ancestry
• Presence in organisms living in similar environments only
• Equal length of sequences irrespective of composition

Correct Answer: Significant sequence similarity and conserved motifs consistent with common ancestry

Q19. What is the primary advantage of Bayesian phylogenetic methods compared with traditional maximum likelihood?

• They never require model selection
• They provide direct probabilities for trees and parameters incorporating prior information
• They are always faster for large datasets
• They do not need an alignment

Correct Answer: They provide direct probabilities for trees and parameters incorporating prior information

Q20. When comparing models of sequence evolution, which criterion penalizes model complexity more heavily, potentially favoring simpler models?

• Akaike Information Criterion (AIC)
• Bayesian Information Criterion (BIC)
• Likelihood ratio test without correction
• Bootstrap proportion

Correct Answer: Bayesian Information Criterion (BIC)

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