Identify the character based method(s) used for the construction of a phylogenetic tree.
P. Maximum parsimony
Q. Neighbor joining
R. Maximum likelihood
S. Bootstrapping
Options:
(A) Q only
(B) P and R only
(C) Q and S only
(D) S only
Official Answer Key:
B
Step-by-Step Solution & Explanation
### **Official Solution & Step-by-Step Derivation (GATE BT 2018 Q.28)**
**1. Governing Concept & Question Classification**:
- **Section**: BT
- **Question Type**: **MCQ** (1 Mark)
- **Topic**: Bioinformatics / Phylogenetics (Tree Reconstruction Algorithms)
**2. Detailed Step-by-Step Analysis**:
- Phylogenetic tree construction algorithms are divided into two main categories:
1. **Character-based (discrete) methods**: Operate directly on individual aligned character positions (nucleotide or amino acid states) in a multiple sequence alignment.
- **Maximum Parsimony (MP)** (P): Seeks the tree topology that minimizes the total number of evolutionary character-state changes.
- **Maximum Likelihood (ML)** (R): Computes the tree that maximizes the probability of observing the sequence data given an explicit evolutionary model of substitution.
- Bayesian inference methods (e.g., MrBayes) are also character-based.
2. **Distance-based methods**: Convert character data into a pairwise genetic distance matrix and build trees using clustering algorithms.
- **Neighbor-Joining (NJ)** (Q) and UPGMA are distance-based methods.
- **Bootstrapping** (S) is a statistical resampling procedure used to assess clade branch support/confidence, not a tree construction method itself.
- Thus, the character-based methods among the choices are **Maximum parsimony (P)** and **Maximum likelihood (R)**.
- **Option-by-Option Evaluation**:
- **Option (A) [INCORRECT]**: Neighbor-joining is distance-based.
- **Option (B) [CORRECT]**: P (Maximum parsimony) and R (Maximum likelihood) are classical character-based phylogenetic methods.
- **Option (C) [INCORRECT]**: Neighbor-joining is distance-based, and bootstrapping is a resampling test.
- **Option (D) [INCORRECT]**: Bootstrapping is a statistical validation method.
**3. Final Answer / Verification Summary**:
- **Official GATE Answer Key**: **B**
- **Scoring Criteria**: +1.0 Mark (Negative marking: -0.33 marks).
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