M.Sc. DEGREE EXAMINATION, APRIL 2016
Second Semester
Bioinformatics
LAB IV — COMPUTATIONAL APPROACHES TO
TAXONOMY AND PHYLOGENY
(2013 onwards)
Time 3 Hours Maximum 75 Marks
Part A (10 2 20)
Answer all questions.
1. What is biological species concept to define species?
2. State allopatric speciation by natural selection.
3. Define convergent evolution.
4. Define various types of trees.
5. Define maximum parsimony and maximum likelihood.
6. What do you mean by topology and branch length of a
phylogenetic tree?
7. What are the limitations of phylogenetic algorithms?
8. Differentiate between rooted tree and unrooted tree with
suitable example.
9. What is Newick tree format? Give one example.
10. List any four phylogenetic tree construction tools.
Sub. Code
502206
RW-10869
2
Ws8
Part B 5 25)
Answer all questions.
11. Discuss briefly the role of natural selection in
evolution.
Or
Describe the five kingdom classification system.
12. Describe jackknife estimation method in statistical
re-sampling.
Or
Distinguish between the terms 'inferred 'true
'gene tree' and 'species tree'. Explain why gene
trees and species trees are not equivalent.
13. Define parsimony. Write in detail how parsimony is
used to infer phylogenetic relationships?
Or
Explain neighbor joining method in phylogenetic
analysis. Illustrate with a suitable example.
14. Explain delayed and accelerated transformation
approaches for tree reconstruction.
Or
How to evaluate the reliability of phylogenetic
trees?
15. Describe steps involved in phylogenetic tree
construction using Phylip.
Or
Discuss the process of bootstrapping during
phylogenetic analysis.
RW-10869
3
Ws8
Part C 10 30)
Answer any three questions.
16. Recount how taxonomy led to phylogeny and discuss the
reason why molecular markers are important in
phylogeny?
17. Explain how phylogenetic trees are reconstructed,
including a description of DNA sequence alignment and
how the accuracy of tree is assessed.
18. Describe in detail any two distance based methods that
could be used for phylogenetic analysis.
19. What are the applications of phylogenetic tree? Compare
the phylogenetic tree obtained using DNA and protein
sequence.
20. Describe the clustal W tool used for Multiple Sequence
Alignment (MSA). What are the considerations we take
while choosing a MSA software for analysis?