Phylogenetic tree construction MCQs With Answer

Phylogenetic tree construction MCQs With Answer

This short quiz collection is designed for M.Pharm students studying Bioinformatics and Computational Biotechnology. It focuses on phylogenetic tree construction principles and practices relevant to pharmaceutical research — including methods for inferring evolutionary relationships, model selection, tree rooting, interpretation of branch lengths, and impacts of alignment and substitution models on tree accuracy. Questions emphasize conceptual understanding and applied skills used in analyzing pathogen evolution, drug resistance emergence, and comparative genomics of drug targets. Use these MCQs to test and deepen your understanding of key algorithms (UPGMA, Neighbor-Joining, Maximum Likelihood, Bayesian inference), statistical support (bootstrapping), and common pitfalls (long-branch attraction, model misspecification).

Q1. Which tree construction method assumes a constant rate of evolution (molecular clock) across all lineages and produces ultrametric trees?

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

Correct Answer: UPGMA

Q2. Which distance correction model accounts for multiple substitutions at the same site and is commonly used to correct observed nucleotide distances?

• Jukes-Cantor model
• Poisson model
• Kimura two-parameter model (K2P)
• HKY85 model

Correct Answer: Jukes-Cantor model

Q3. Which approach infers phylogenies by searching for the tree topology that minimizes the total number of character-state changes?

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

Correct Answer: Maximum Parsimony

Q4. Bootstrapping in phylogenetics is used to estimate which of the following?

• Absolute divergence time between species
• Statistical support for tree clades
• Best-fit substitution model
• Sequence alignment quality directly

Correct Answer: Statistical support for tree clades

Q5. Which of these models allows different transition and transversion rates when modeling nucleotide substitution?

• Jukes-Cantor
• Kimura two-parameter (K2P)
• Poisson
• Dayhoff

Correct Answer: Kimura two-parameter (K2P)

Q6. In a phylogenetic tree, what does a long branch length typically indicate?

• A recent common ancestor
• A high number of substitutions per site
• An ultrametric relationship
• Guaranteed greater statistical support

Correct Answer: A high number of substitutions per site

Q7. Which tree-building algorithm constructs a tree by consecutively joining the pair of operational taxonomic units (OTUs) that minimizes the total branch length?

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

Correct Answer: Neighbor-Joining

Q8. Which statement about Maximum Likelihood (ML) phylogenetic methods is TRUE?

• ML methods do not require an explicit substitution model.
• ML methods are deterministic and do not need tree-search heuristics for many taxa.
• ML methods evaluate the probability of the data given a tree and substitution model.
• ML always produces an ultrametric tree.

Correct Answer: ML methods evaluate the probability of the data given a tree and substitution model.

Q9. When selecting a substitution model for phylogenetic analysis, which information criterion balances model fit and complexity?

• p-value
• Bootstrap proportion
• Akaike Information Criterion (AIC)
• Bayes factor only

Correct Answer: Akaike Information Criterion (AIC)

Q10. Which of the following is a primary advantage of Bayesian phylogenetic inference over Maximum Likelihood?

• Bayesian methods never require model selection.
• Bayesian inference provides a posterior probability distribution for trees and parameters.
• Bayesian methods are always faster for large datasets.
• Bayesian trees cannot incorporate prior information.

Correct Answer: Bayesian inference provides a posterior probability distribution for trees and parameters.

Q11. Why is accurate multiple sequence alignment crucial before phylogenetic tree construction?

• Because tree algorithms require sequences of different lengths to be input.
• Because misaligned homologous sites can mislead tree topology and branch length estimation.
• Because alignment directly computes bootstrap values.
• Because unaligned sequences improve ML performance.

Correct Answer: Because misaligned homologous sites can mislead tree topology and branch length estimation.

Q12. What is ‘long-branch attraction’ in phylogenetic inference?

• When short branches are incorrectly merged due to low substitution rates.
• When distantly related lineages with high substitution rates artifactually group together.
• When bootstrap values are artificially high for small datasets.
• When neighbor-joining always outperforms maximum likelihood.

Correct Answer: When distantly related lineages with high substitution rates artifactually group together.

Q13. Which tree type represents only the branching order (relationships) without proportional branch lengths?

• Phylogram
• Ultrametric tree
• Cladogram
• Additive tree

Correct Answer: Cladogram

Q14. In phylogenetic analysis, an outgroup is primarily used to:

• Increase bootstrap support for internal nodes.
• Root the tree and infer the direction of character change.
• Guarantee an ultrametric tree output.
• Remove gaps from the alignment automatically.

Correct Answer: Root the tree and infer the direction of character change.

Q15. Which software is commonly used for Maximum Likelihood phylogenetic inference and is scalable to large genomic datasets?

• ClustalW
• RAxML
• EMBOSS
• BLAST

Correct Answer: RAxML

Q16. When combining gene trees into a consensus species tree, which problem describes discordance due to different gene histories (e.g., incomplete lineage sorting)?

• Long-branch attraction
• Homoplasy
• Gene tree/species tree discordance
• Bootstrap inconsistency

Correct Answer: Gene tree/species tree discordance

Q17. Which substitution model family explicitly accounts for unequal base frequencies and different rates for all nucleotide substitutions (i.e., most general time-reversible form)?

• Jukes-Cantor
• Kimura 2-parameter
• GTR (General Time Reversible)
• Poisson

Correct Answer: GTR (General Time Reversible)

Q18. In likelihood-based hypothesis testing of phylogenetic trees, which test compares nested models or trees?

• Chi-square test for alignment length
• Likelihood Ratio Test (LRT)
• Bootstrap proportion test
• Mantel test

Correct Answer: Likelihood Ratio Test (LRT)

Q19. How are gaps (indels) commonly treated in phylogenetic analyses to avoid misleading signals?

• Always treat gaps as fifth nucleotide with equal weight.
• Ignore gaps or code them as missing data, or treat indels as separate binary characters depending on analysis.
• Replace gaps with random nucleotides to avoid bias.
• Automatically remove any sequence that contains gaps.

Correct Answer: Ignore gaps or code them as missing data, or treat indels as separate binary characters depending on analysis.

Q20. Which metric is most appropriate for comparing fit of non-nested phylogenetic models while penalizing complexity?

• Sum of branch lengths
• Posterior probability only
• Bayesian Information Criterion (BIC)
• Bootstrap percentage

Correct Answer: Bayesian Information Criterion (BIC)

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