Midterm Exam #1
MB 451
Microbial Diversity
Honor pledge: “I have neither given nor received unauthorized aid on this test.”
Signed : ____________________________________________________________
Date : __Feb 5, 2007__________________
Name : ___KEY__________________________________________________________
1. What are the three primary evolutionary branches of life? (5 points)
Archaea, Bacteria, and Eukarya
Multiple choice (2 points each)
2. __D__ Which of the following is not an aspect of a taxonomy?
5. _ D__ Which of these evolutionary representations is
both objective and quantitative?
A. the 5-Kingdom tree
B. the Evolutionary Ladder
A. Grouping
C. the Prokaryote/Eukaryote dichotomy
B. Naming
D. the 3-Domain molecular phylogenetic tree
C. Identifying
E. None of the above
D. Isolating
E. None of the above
3. __ E__ Which describes a phylogeny?
A. a genealogy
B. a tree
C. evolutionary pathways
D. natural relationships between organisms
E. All of the above
4. __ A__ Species evolve by ...
6. __ D__ Which if the following is not an algorithm for
generating phylogenetic trees from molecular
data?
A. Neighbor-joining
B. Parsimony
C. Maximum likelihood
D. Jukes & Cantor
E. all of the above
7. __ B__ A photoheterotroph gets its energy from X and
its carbon from Y.
A. diversification
A. X= light ; Y= carbon dioxide
B. progression
B. X= light ; Y= organic compounds
C. linear advancement
C. X= inorganic compounds ; Y= carbon dioxide
D. magic
D. X and Y both = organic compounds
E. none of the above
E. none of the above
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Short answer & fill in the blank (points as indicated)
8. Usually the best single molecular sequence for phylogenetic analysis is __ ssu-rRNA_______________________. (2 points)
9. A 2-dimensional matrix of molecular sequences is called a(n) ___sequence alignment______________________. (2 points)
10. Molecular sequences may be alignable using _______structural superimposition_____________________________ even
if they are so different from one another that they cannot be reliably aligned based on the sequence alone. (2 points)
11. ___bootstrapping_____________________________ is a way to judge the reliability of the branches in a tree. (2 points)
12. Why is an understanding of phylogeny important? (4 points)
Both to make predictions about the properties of an organism, and to prevent inappropriate comparisons between unrelated organisms.
13. What are the main steps of a molecular phylogenetic analysis? (4 points)
1. Decide on organisms and sequences
2. Obtain this data
3. Identify homologous residues
4. perform phylogenetic analysis
14. Why is raw sequence similarity an underestimate of evolutionary distance? (5 points)
Because of the occurrence of multiple substitutions at a single site that are only counted as a single difference, or in the
case of reversion, as no difference at all.
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Tree interpretation : answer the following questions based on this ssu-rRNA-based phylogenetic tree. The scale bar (0.10)
represents evolutionary distance. Sequences/organisms without names (i.e.pBB, Nak_9, SRI-240, and VC2.1bac27) are
D. Go! tz and others
from uncultivated species. (2 points each)
............................................
Fig. 3. Effect of tem
of strain EX-H1T (s
presence of 3 % (w/
.................................................................................................................................................
15. Is this a dendrogram
a phenogram?
__________phenogram___________________________________________________
Fig.or 2.
Maximum-likelihood
phylogenetic tree showing the
positions of strain EX-H1T and strain EX-H2T. The scale bar
represents the number of fixed mutations per nucleotide
16. Which sequence(s) is/are presumably the outgroup? __Methanococcus jannashii___________________________________
DNA base compo
position. The numbers at the branch nodes are bootstrap values
based on 100 bootstrap resamplings.
The G!C conte
strain EX-H1T
This is consisten
18. What is the evolutionary distance between Persephonella marina and Hydrogenobacter thermophilus? _0.2__________
Aquificales, whos
initially formed from pre-existing plasma membrane
for Hydrogenob
and were excised once elongated. Although internal
19. Circle (on the tree above) the last common ancestor of Bacillus subtilis and Thermus thermophilus.
Aquifex pyrophil
membranes are often used to align enzymes for
ditionally, EX-H
complex metabolic reactions, the function of these
20. Except for the outgroup, which two sequences in this tree are the most distantly related?
membranous structures is not yet known. Similar
genetically distin
membranous structures have not previously been
similar to A. pyr
______Flexibacter flexilis_______________________ and ________pBB_________________________________________
reported in the Aquificales. Negative stains of cells
genobacter therm
revealed that thin, flexible, pili-like filaments extended
other, and 92–94
21. Which branch(es) would you have the least confidence in?
from the cell surface of many of the cells (Fig. 1,
that fall within th
The one between the 2 Persephonella species, and the one between E.coli and B.subtilis (the one between pBB and NAK_9
bottom).
the recently de
is also right up there).
17. Which sequence is most closely related to Bacillus subtilis? _____Escherichia coli__________________________________
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Table 2. Electron donors and acceptors utilized by strain EX-H1T, strain EX-H2T a
chemolithoautotrophic members of the order Aquificales
............................................................................................................................................................................................................
Strains (reference) : 1, Strain EX-H1T ; 2, Strain EX-H2T ; 3, Aquifex pyrophilus (Huber
Problem-solving (points as indicated)
22. Align the following sequences: (8 points)
Sequence 1
G G G G U U C G C U C A
- G G G G U U C G C U C A
Sequence 2
A G A G G U U G C U C U
A G A G G U U - G C U C U
Sequence 3
C G A G G C U G C U C
C G A G G C U - G C U C -
Sequence 4
U G A G G C U C G C U C A
U G A G G C U C G C U C A
23. Generate a similarity matrix from the following alignment: (10 points)
Seq1
Seq2
Seq3
Seq4
Sequence 1
G A U C G A U C G A
Seq1
XX
XX
XX
XX
Sequence 2
G A U A G A U C G A
Seq2
0.9
XX
XX
XX
Sequence
3
G A similarity
C C G A Cmatrix
C G A to a distance
Seq3 matrix
_0.8_ _0.7_
XX Jukes
XX& Cantor curve.
10) (10 points)
Convert
the
using the
Sequence 4
G A G U G A C C G A
Similarity matrix
Seq4 _0.7_ _0.7_ _0.8_
XX
Distance matrix
24. Convert the following similarity matrix into a distance matrix using the Jukes & Cantor curve: (10 points)
A
A
X
B
C
D
Similarity matrix
X
A
Distance matrix
D
X
X
X
X
X XX
X
Seq1
XXB
XX0.05
XX
XXX
X
X
0.90 0.80
XX
XX X XX
C Seq20.75
X
Seq2
0.12
C
XX0.30
XX
XX
0.25
X
X
Seq3
0.55 0.30
Seq4
0.77 0.90 1.30
0.90
X
B Seq10.95XX
D
X
XX
XX
Seq3
0.60 0.75
Seq4
0.50 0.45 0.35
0.50
1.0
0.60
XX
XX
0.45
XX
X
X
C
X
Seq1 Seq2 Seq3 Seq4
A
B
Seq1 Seq2 Seq3 Seq4
D
XX
0.75
XX
0.55
XX
JUKES & CANTOR CURVE
0.9
Similarity
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0.0
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 2.0
Evolutionary distance
11) (10 points) Redraw the dendrogram below, to the same approximate scale, as a phylogram.
C
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25. Convert the following phenogram into a dendrogram. (10 points)
A
B
A
D
B
C
C
D
26. Generate a tree using the neighbor-joining method from the following distance matrix. SHOW YOUR WORK! You need
only solve the structure of the tree; you do not need to solve the branch lengths. (10 points)
A
B
C
D
E
A
X
X
X
X
X
B
0.3
X
X
X
X
C
0.6 0.5
X
X
D
1.7 1.6 1.7
X
E
1.0 0.9 1.0 1.7
reduced matrix
A/B
C
D
E
A/B
X
X
X
X
X
C
0.55
X
X
X
X
D
1.65
1.7
X
X
X
E
0.95
1.0
1.7
X
A
B
E
The nearest neighbors are
A and B, so these are joined:
C
D
A
E
B
C
D
Average distances in the matrix
to A/B; the nearest neighbors
are then between A/B and C, so
these are joined:
A
E
B
D
The nodes are completely
resolved - you’re done!
C
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