Midterm Exam #1
MB 451
Microbial Diversity
Honor pledge: “I have neither given nor received unauthorized aid on this test.”
Signed : ___KEY_______________________________________________________Date : __________________________
Name : ___________________________________________________________
PIN* : ___________________________
* Please give me a “PIN” (a string of numbers, letters, &c, that are not personally identifiable) of no more than 6 characters that I
can use to anonymously post your scores. Try to choose a PIN unlikely to be chosen by another student (e.g. “666” or “123456”)
or rejected by me (I’ll leave this to your imagination). If you do not wish your scores to be posted, leave this blank.
1. What are the 3 primary evolutionary branches of life? (5 points)
Archaea, Bacteria & Eukarya
2. __B__ An organism that gets energy from a chemical
reaction and carbon by fixing CO2 is a ... (2 points)
5. __A__ The identification of homologous residues in a
collection of sequences is called... (2 points)
A. chemoheterotroph
A. aligning the sequences
B. chemoautotroph
B. calculating the similarity matrix
C. photochemotroph
C. calculating the distance matrix
D. photoheterotroph
D. the substitution model
E. photoautotroph
E. the Jukes & Cantor method
3. __E__ If an organism is labeled a “prokaryote”, this
means it is .... (2 points)
A. an organism without a nucleus
B. a particular kind of organism
C. a bacterium
D. primitive
E. not a eukaryote
4. __E__ Which of the following is a valid distinction
between eukaryotes and prokaryotes? (2 points)
A. size (small verses large cells)
B. the presence (or not) of mitochondria
C. the presence (or not) of histones
D. chromosome structure
E. none of the above
6. __B__ An outgroup is used to ... (2 points)
A. determine the reliability of the tree
B. locate the root of the tree
C. counteract long-branch attraction in a tree
D. to create a “Universal” tree
E. none of the above
7. __E__ Which of the following is not a tree construction algorithm? (2 points)
A. neighbor-joining
B. maximum likelihood
C. parsimony
D. Fitch
E. Jukes & Cantor
Page 1 of 6
8. Describe in one sentence the purpose of “bootstrapping”. (3 points)
The purpose of bootstrapping is to assess the reliability of the each branch in the tree structure.
9. Describe in one sentence how we know that all known organisms share a common ancestry. (3 points)
We know all know living things share a common ancestry because their biochemistry and structure are so much
alike in even the smallest detail.
10. A good molecule for phylogenetic analysis should exhibit “clock-like behavior”. Describe in one sentence what
“clock-like behavior” is. (3 points)
A molecule exhibits clock-like behavior if the extent of divergence between different versions of the sequence is a
reliable measure of the evolutionary distance between them.
11. Describe in one sentence why the number of differences between two sequences an underestimate of the evolutionary distance between them. (3 points)
The number of differences between two sequences underestimates the evolutionary distance between them because the occurrence of multiple changes at single position causes us to undercount the number actual changes
between two sequences.
Page 2 of 6
12. Briefly describe one method other than rRNA molecular phylogenetic analysis that can be used to examine relationships between microorganisms. (5 points)
e.g....
Serology is used primarily to identify very closely-related clinical isolates, usually different strains of a single species. This method uses antisera developed from various strains of Bacteria to identify which strain a new isolate is.
For example, when Salmonella is isolated from a patient, a bank of antisera is used to determine which of the hundreds of serotypes that particular isolate is. This is an old but still widely used method, since the antisera are easy
to make and the assay is very quick, easily automated, & reliable. The commonly-used ELISA is a serological
method.
(many other answers are possible)
13. Align the following sequences: (10 points)
Sequence 1 : U G A C C U U C G A A A C U
Sequence 2 : G A C C A U U U G C A A C C
Sequence 3 : C G A C C C U U C G U A A C C
Sequence 4 : C G A C C U U C G A A C
Sequence 1 : U G A C C - U U C G A A A C U
Sequence 2 : - G A C C A U U U G C A A C C
Sequence 3 : C G A C C C U U C G U A A C C
Sequence 4 : C G A C C - U U C G - A A C -
14. Convert the following alignment to a similarity matrix: (10 points)
1
2
3
4
Sequence 1 : U A A C G U G C G C
1
X
X
X
X
Sequence 2 : U A G C G C G C G C
2
0.8
X
X
X
Sequence 3 : U G A C G G G C G U
3
0.7
0.6
X
X
Sequence 4 : U A C C G U G C G U
4
0.8
0.7
0.7
X
Page 3 of 6
10) (10 points) Convert the similarity matrix to a distance matrix using the Jukes & Cantor curve.
Similarity
matrix matrix to a distance matrix using the Distance
matrix
15. Convert
the following similarity
Jukes & Cantor
curve. (10 points)
A
Seq1
A Seq1 X
B
Similarity matrix
Seq2
C
D
Seq3
A
Seq4
Distance matrix
B
C
D
Seq1
Seq2
Seq3
Seq4
XX X
XX X
XX X
XX
A
X
Seq1
X
XX
X
XX
XXX
XX
B Seq2
0.950.90 X
XX X
XX X
XX
B
Seq2
0.05
0.12
X
XX
X
XXX
XX
XX
XX
C
Seq3
0.30
0.31
0.20
X
XXX
XX
D
0.75
Seq4
0.77
1.00
1.63
XX
C Seq3
0.750.750.80 0.82 X
D
Seq4
0.50
0.50
0.60
0.42
0.45
X
0.30
X
XX
0.25
0.55
0.90
1.4
1.6
X
JUKES & CANTOR CURVE
1.0
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
1.5
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.
16. Convert this dendrogram into a phenogram. Be sure to keep the branch lengths approximately correct. (5 points)
C
C
B
D
B
A
D
E
B
E
D
C
A
A
Page 4 of 6
Page 4 of 5
17. Generate a tree from the following distance matrix, using either the neighbor-joining or Fitch methods. SHOW
YOUR WORK! You need to solve both the structure of the tree and the lengths of the branches. (15 points)
A
B
C
D
E
A
X
X
X
X
X
B
0.3
X
X
X
X
C
0.8
0.9
X
X
X
D
0.6
0.7
0.8
X
X
E
0.4
0.5
0.8
0.6
X
A
A
B
E
B
E
C
D
D
C
A
A/B
A/B
C
D
E
X
X
X
X
C
0.85
X
X
X
D
0.65
0.8
X
X
E
0.45
0.8
0.6
X
B
E
C
D
A
0.1
0.2
E
0.2
B
0.1
0.1
0.5
0.3
C
D
The real reason dinosaurs became extinct
Page 5 of 6
This tree is based on the an alignment of telomerase RNAs. Answer the questions below about this tree.
24
23
18. Is this a dendrogram or a phenogram? (circle one) (2 points)
19. Which sequence(s) is/are the closest relative(s) of B. taurus (European domestic cattle)? (2 points)
H. sapiens & P. pygmaeus (H. sapiens alone is acceptable)
20. Which sequence(s) is/are presumably the outgroup? (2 points)
S. cerevisiae (bakers yeast) and S. pombe)
21. Which sequence is most distantly related to that of S. pombe? (fission yeast) (2 points)
M, musculus
22. What is the approximate evolutionary distance between M. musculus (house mouse) and P. pygmaeus (orangutan)?
(2 points)
0.1
23. Where is the last common ancestor of D. rerio (zebrafish) and the X. tropicalis (Western clawed frog) (circle it and
label it “23”). (2 points)
24. Which is the least reliable branch in the tree (circle it above and label it “24”). (2 points)
25. What do you think of this branch, based on your knowledge of basic biology? Why? (2 points)
It’s wrong - the branching arrangement here should be the other way around so that the frog branches off of a
common ancestor shared with the mammals AFTER the common ancestor of all of these with the fish.
Page 6 of 6