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Bioinformatics Take Home Test #5
(This is an open book exam based on the honors system -- you can use notes, lecture notes, online manuals,
and text books.
Teamwork is not allowed on the exams, write down your own answers, do not cut and paste from webpages.
If your answer uses a citation, give the source of the quoted text.)
1. 1pt Which of the following pairs is an example of orthologs?
a. The ATPsynthase and the RHO termination factor
b. The ATPsynthase and the Flagellar ATPase
c. The catalytic and noncatalytic subunits of the ATPsynthase
d. The Bacterial F-type ATPsynthase and the Vacuolar-type ATPase
e. Alpha and Beta hemoglobin
2. 1pt True/False Paralogs are NOT a type of homolog.
3. 1pt True/False Orthologs ARE a type of homolog.
4. 1pt True/False Xenologs are homologs that have been horizontally transferred.
5. 1pt According to Hennig a natural taxonomy should be based on (circle all that apply, more
than one might be correct)
- clades,
- clanns
- monophyletic groups,
- paraphyletic groups,
- shared derived characters,
- shared primitive characters,
- synapomorphies,
- sympleisiomorphies,
- autapomorphies,
- a Hennigian comb
6. 1pt True/False Go plots are conclusive proof of the intron early hypothesis, because an
intron was found separating two Go domains, exactly where it was predicted to be.
7. 1pt What is the introns early hypothesis?
a. Introns are relicts of the RNA world and so arose early, spreading throughout the
primordial genomes.
b. Primordial proteins were created, using introns, in a process similar to present day
exon shuffling.
c. Introns invaded the ancestral Eukaryote with the origin of the mitochondria. Introns
are early with respect to Eukaryote evolution.
d. Introns are left over bits of ancient viruses that invaded the primordial genomes,
early on in the evolution of life, but after the RNA world.
e. None of the above.
8. 1pt What is the introns late hypothesis?
a. Introns, as parasites, invaded proteins that were already fully functional. In general
they play no role in evolution of prokaryotic proteins, but they may have been useful,
through exon shuffling, in Eukaryogenesis.
b. Introns are selfish sequences that evolved in the middle of the genes they intervene.
They have been in these same genes for their entire life-histories, but since they
evolved later than the protein coding sequence, they are termed late.
c. Introns invaded the ancestral Eukaryote with the origin of the endoplasmic reticulum,
which happened relatively late with comparison to the origin of life.
d. Introns are left-over bits of modern viruses that invaded genomes, relatively late in
the evolution of life, and much after the RNA world.
e. None of the above.
9. 1pt Which came first, self-splicing introns or spliceosomal introns (circle one)?
10. 1pt What is the definition of phylogeny?
11. 1pt Why are phylogenies and phylogenetics in general important in bioinformatics?
12. 2pt Which of the following groups represent proper taxonomic groups (i.e., they form a clade
in the "traditional" version of tree of life):
- Bacteria
- Prokaryotes
- Protists
- Green Algae
- Eukaryotes
- Reptiles
- Mammals
- Birds
- Eukaryotes + Archaea
13. 1pt True/False If the alignment is improperly calculated and non-homologous positions are
aligned, all down-stream reconstruction efforts will be unable to rectify this problem and will
simply regurgitate the same error.
14. 1pt True/False Phylogenetic trees of flu virus strains are used every year in the decision
making process with regards to which strain to immunize for, because phylogenetic
information is used in identifying which strain will spread.
15. 2pt Please draw the following for five taxa A, B, C, and D, where A is sister to B and C is sister
to D and E is equil distance between A, B, C, and D:
a. A rooted tree (the root is on the branch leading to E)
b. An unrooted tree
16. 1pt True/False The term branch in phylogenetics refers to the same thing as the term branch
does in botany, i.e. an internal node and all of the twigs that descend from it.
17. 1pt How many rooted and unrooted trees with different topology are possible for 4 OTUs?
18. 1pt How many rooted and unrooted trees with different topology are possible for 10 OTUs?
19. 1pt The place of the root in the tree of life was first determined
A) using a random sequence as outgroup
B) using an ancient gene duplication
C) finding the group of organisms that had most primitive characters
20. 1pt Which of the following terms is NOT a synonym for the leaves in a phylogenetic tree?
a. Terminal Node
b. Taxa
c. OTU
d. Species
e. None of the above
21. 1pt Which of the follow terms is a synonym for the branches of a tree?
a. Split
b. Bifurcation
c. Interior Node
d. All of the above
e. None of the above
22. 1pt What are the reason why a gene tree could be different from the species tree?
a. Lack of resolution
b. Lineage sorting
c. Gene duplication or loss
d. Horizontal gene transfer
e. All of the above
23. 1pt Phylogenetic reconstruction based on the maximum likelihood principle aims to find the
phylogenetic tree
A) that explains the evolutionary history that gave rise to the aligned sequences with the least
number of substitution events.
B) that is most probable given the data.
C) under which the data set (e.g., aligned sequences) is most probable.
D) that is in the best possible agreement with the observed number of substitutions observed
between the sequences.
24. 1pt Phylogenetic reconstruction based on the parsimony principle aims to find the
phylogenetic tree
A) that explains the evolutionary history that gave rise to the aligned sequences with the least
number of substitution events.
B) that is most probable given the data.
C) under which the data set (e.g., aligned sequences) is most probable.
D) that is in the best possible agreement with the observed number of substitutions observed
between the sequences.
25. 1pt Phylogenetic reconstruction using Markov chain Monte Carlo sampling aims to find the
phylogenetic tree
A) that explains the evolutionary history that gave rise to the aligned sequences with the least
number of substitution events.
B) that is most probable given the data.
C) under which the data set (e.g., aligned sequences) are most probably.
D) that is in the best possible agreement with the observed number of substitutions observed
between the sequences.
Extra credit:
26. 1pt Please draw the following tree (((A, B) , (C, D)), E)
27. 1pt How many trees are possible given three taxa?
28. 2.5 pt There are five different ways to turn this unrooted tree into a rooted tree. Draw all five:
For Graduate Students: Short essays please.
29. 3pt Who was Willig Hennig? What contribution did he make to phylogenetics? Why is that contribution so
important? And is his system of classification, or is the one that came after him, superior and why?
30. 3pt Who was Walter Fitch? What contributions did he make to phylogentics and bioinformatics
(at least one for each)? Why were his contributions important? What is remarkable about his role
in the design of a vaccine (hint, one of his contributions should involve vaccine development)?