BIS181_MT2_2023_FORM_A_KEY
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Information Systems
Date
Dec 6, 2023
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Copyright 2023 Julin Maloof and The Regents of the University of California. May not be
reproduced without permission.
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__________________, _____________________
_______________
last name
first name
Student ID #
BIS181 Midterm 2
Fall, 2023
This exam consists of 21 questions worth a total of 100 points.
There is a blank page at the end that you can use as scratch space.
This is exam form
A
Do not open the exam until instructed to do so.
Copyright 2023 Julin Maloof and The Regents of the University of California. May not be
reproduced without permission.
2
BIS181 Midterm 2
Fall, 2023
PART I:
Multiple choice. There are 15 questions in this section, each worth 3 points.
Choose the
ONE
best answer for each question. Write your selection in the box using
CAPITAL LETTERS
.
1)
Leaves evolved in seed plants. The spines of the cactus plant, the snapping jaws of the
Venus fly trap, and the insect capturing pitcher of the carnivorous pitcher plant are all
modified leaves. The different structures in these three seed plant species are an
example of
A)
Plant defense
B)
Homology
C)
Analogy
D)
Differential rates of evolution
Answer:
2)
Which of the following can contribute to quantitative rather than qualitative trait
segregation?
A)
Large allelic effect sizes relative to environmental or “error” variance
B)
Alleles having a dominant/recessive instead of additive relationship
C)
Alleles segregating at multiple genes that affect the trait
D)
All of the above
E)
None of the above
Answer:
B
C
Copyright 2023 Julin Maloof and The Regents of the University of California. May not be
reproduced without permission.
3
3)
A patient with a genetic ataxia disorder is suspected to have a mutation in a gene called
ATX.
The patient’s gene is sequenced and compared against the normal
ATX
gene using
a Dot Plot.
What type of mutation is consistent with the dot plot analysis?
A)
A deletion in the patient’s
ATX
gene
B)
An insertion in the patient’s
ATX
gene
C)
A point mutation in the patient’s
ATX
gene
D)
A duplication within the patient’s
ATX
gene
E)
An inversion within the patient’s
ATX
gene
Answer:
4)
Which QTL mapping “problem” is solved by the interval mapping technique?
A)
Multiple segregating loci that effect the trait can increase “noise” when not
accounted for?
B)
Recombination between the causative loci and the marker SNP can increase “noise”
C)
Poor mapping resolution due to low recombination
D)
“Noise” caused by environmental variation
E)
All of the above
Answer:
D
B
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5)
In the Gaucher_2003 paper, an ancestral EF-Tu protein was re-constructed using EF-Tu
sequences from modern bacteria to estimate the temperature at the origin of bacterial
life . The justification for selecting EF-Tu was based on (select best answer):
A)
EF-Tu sequences show extensive divergence making changes easy to identify
B)
EF-Tu sequences show high conservation which facilitates meaningful alignments
C)
EF-Tu is important for protein synthesis but not for transcription
D)
B and C
Answer:
6)
You are mapping nostril diameter in a mapping population of dairy cows. You are
focused on one interval between two markers X and Y. Let the two alleles of X be X1 and
X2 and the two alleles of Y be Y1 and Y2. One parent of your cross is genotype X1 Y1
and the other is X2 Y2.
You find the following average diameters (in centimeters (cm)) for the different
progeny classes in the mapping population:
X1 Y1: 4.0 cm
X2 Y2: 2.0 cm
X1 Y2: 3.0 cm
X2 Y1: 3.0 cm
Where is the QTL?
A)
Closer to X
B)
Closer to Y
C)
About equidistant between X and Y
D)
Not enough information to determine
Answer:
B
C
Copyright 2023 Julin Maloof and The Regents of the University of California. May not be
reproduced without permission.
5
7)
The figure shows an analysis of dN and dS across part of the genome of the Covid-19
(SARS Cov-2) virus. The spike protein used for vaccine design is encoded by the region
of the genome designated by S on the X-axis (from approx. 7000 to 8300). The lines
along the Y-axis show the values of
w
for all codons in this region for which
w
is
significantly different from 1.
You plan to use a peptide to make a vaccine from a short region of the S-protein. You
are given a choice of regions x, y, and z, indicated in the figure. You decide to select
the peptide that will protect against the most number of SARS Cov-2 strains
circulating in the population. Select the peptide that will work best for the purpose.
A)
Peptide x
B)
Peptide y
C)
Peptide z
D)
Any of the peptides should work equally well.
Answer:
C
Copyright 2023 Julin Maloof and The Regents of the University of California. May not be
reproduced without permission.
6
8)
You are doing an experiment to look for evidence of positive selection acting on gene
expression in humans. Which of the scenarios below would provide the best evidence of
positive selection acting on gene expression of a given gene?
A)
The gene shows significantly different mRNA abundance in different humans and
had a dN/dS > 1
B)
SNPs in the gene promoter are significant for GWAS for controlling
cis
gene
expression and have a |iHS| score near 0
C)
SNPs in the gene promoter are significant for GWAS for controlling cis gene
expression and have dN/dS >1
D)
SNPs in the gene promoter are significant for GWAS for controlling cis gene
expression and have a |iHS| score > 6
E)
SNPs in the gene promoter have a |iHS| score > 6 and are in linkage disequilibrium
with SNPs in the coding region.
Answer:
9)
You are studying the evolution of human myoglobin. Myoglobin is present in all
vertebrates. You generate an unrooted phylogeny tree shown below using sequences of
myoglobin proteins from 4 different species:
A = human, B = mouse, C = shark and D = frog
Which protein sequence can be used to root the tree?
A)
Human
B)
Mouse
C)
Shark
D)
Dog
Answer:
C
D
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10)
You are performing a QTL mapping experiment in rice and find a QTL peak associated
with grain length. The LOD score is 4. This LOD scores tells you that:
A)
The likelihood of there being a QTL location is 10,000 times greater than the
likelihood of there not being a QTL at this location
B)
The QTL increases grain length 4-fold
C)
The p-value for this QTL is 0.0001 The p-value for this QTL is 0.04
D)
The likelihood of there being a QTL location is 4 times greater than the likelihood of
there not being a QTL at this location
Answer:
11)
The
FOXP2
gene from two echolocating bat species contains the following nucleotide
sequences at the same position (amino acid 699) in the coding region of the gene.
Species X:
TTG
Species Y:
TTC
The codon table tells you that the amino acid Leucine has the following codons:
CUU, CUC, CUA, CUG, UUA, UUG
What can you conclude about this nucleotide substitution between species X and Y?
A)
Synonymous
B)
Non-synonymous
C)
Neither Synonymous nor Non-synonymous
D)
Insufficient information
Answer:
12)
Which of the following could be taken as evidence of positive selection on a
Neanderthal allele at gene X in modern humans?
A)
Neanderthal allele frequency at gene X is lower than genome-wide Neanderthal
allele frequency
B)
Neanderthal allele frequency at gene X is higher than genome-wide Neanderthal
allele frequency
C)
Cis
eGWAS peak at gene X
D)
High |iHS|at gene X
E)
B and D
Answer:
B
A
E
Copyright 2023 Julin Maloof and The Regents of the University of California. May not be
reproduced without permission.
8
13)
The tree below shows the nucleotide at a SNP within a gene in 5 different taxa.
Using the maximum parsimony method, which nucleotide should be at position X in the
tree?
A)
A
B)
G
C)
C
D)
T
Answer:
14)
Select the correct statement regarding the use of haplotype block size and determining
the date of mating between different species (e.g. Neandertals and Anatomically
Modern Humans)
A)
Relatively smaller introgressed haplotype blocks are indicative of a larger number
of generations after the inter-species mating.
B)
Relatively smaller introgressed haplotype blocks are indicative of a smaller number
of generations after the inter-species mating.
C)
Relatively smaller introgressed haplotype blocks are indicative of positive selection
on the introgressed region.
D)
Haplotype block size is not useful for determining mating date.
Answer:
C
A
Copyright 2023 Julin Maloof and The Regents of the University of California. May not be
reproduced without permission.
9
15)
In which ways has modern genomics technology improved QTL mapping and follow-up
experiments?
A)
Ease of obtaining markers increases resolution and makes the experiments less
labor intensive
B)
The likely availability of a sequenced genomes for the organism being studied
makes defining candidate genes easy and cloning the QTL causative gene possible.
C)
High throughput “Omics” techniques enable QTL analysis of expression (eQTL) and
metabolite (mQTL) traits
D)
All of the above
E)
None of the above
Answer:
D
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PART II:
Short Answer.
16)
A)
You would like to find loci that determine redwood tree height at maturity. (It takes
around 500 years for a redwood tree to reach full height). Would you choose QTL or
GWAS for this study?
One word:
B)
Explain your choice (1 – 2 sentences)
GWAS
I would choose GWAS because for QTL I would need to mate trees and wait for new
populations to grow and I have not yet found the fountain of youth.
Copyright 2023 Julin Maloof and The Regents of the University of California. May not be
reproduced without permission.
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17)
(8 points) The protein SOD1 (Superoxide Dismutase1) has been implicated in ALS (Lou
Gehrig’s disease).
You plan to use the worm
C. elegans
SOD1 as a model for human
SOD1. Below is a short stretch of human and worm SOD1 sequences with very low
identity that you want to align:
Human: KGDGP
Worm: LRGET
Using the PAM250 substitution matrix, which of the two possible alignments (1 or 2) is
better? Show your work.
Alignment 1
Alignment 2
Answer (“1” or “2”):
Human K G D G P Human K G D G P | | | | | | | | Worm L R G E T Worm L R G E T Calculations:
Alignment 1 scores: -4 (G/L), -1 (D/R), +5 (G/G), -1 (P/E). Sum = -1
Alignment 2 scores: +3 (K/R), +5 (G/G), +3 (D/E), 0 (G/T). Sum = +11
2
Copyright 2023 Julin Maloof and The Regents of the University of California. May not be
reproduced without permission.
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18)
(7 pts) The following tree shows a SNP across two different taxa, with branches
proportional to the rates of nucleotide substitutions leading to each one.
You calculate the probabilities for all four nucleotides (A, C, G or T) nucleotide at
position X leading to G (top) and A (bottom), and obtain the following values.
A: 0.10
C: 0.05
G: 0.20
T: 0.15
A)
3 pts) Which is the most likely ancestral nucleotide for that position in the gene?
Explain (1 line).
B)
(4 pts) Compute the posterior probability that
A
is the ancestral nucleotide. Show
your work.
Posterior probability:
G = Highest probability
Calculations:
P(A)= 0.1
Sum of probabilities (A +G + C + T) = 0.5
Posterior probability of A = 0.1/0.5 = 0.2
0.2
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19)
(12 pts) You have two short peptides A and B that you would like to compare with a dot
plot.
The amino acid sequences of the peptides are as follows:
Peptide A:
VNCTCT
Peptide B:
VACTTL
You are asked to make a dot plot comparison of the two peptides using a sliding window
size of 3 and a stringency of 2. (See below).
A)
(4 points) Write the amino acids that correspond to each window of
peptide A (X
axis)
in the spaces provided below.
Window 1: ____________
Window 2: ____________
Window 3: ____________
Window 4: ____________
B)
(8 points) Use the stringency threshold to place dots in the spaces of dot plot below.
(Note: Incorrectly placed dots will earn negative points, so please don’t mark dots in
every square!)
VGC
GCT
CTC
TCT
reproduced without permission.
20)
Woolly mammoths are an extinct species of elephants that lived in the artic and were
adapted to extreme cold temperatures (average winter temperatures -30˚ to -50˚ C.).
Krause and colleagues (Nature, 2006) sequenced the mitochondrial genome of a
12,000-year-old woolly mammoth fossil and compared it to the mitochondrial genomes
of existing African and Asian elephants. They reconstructed the phylogenetic tree
below and determined SNP counts similar to what is shown in the table:
Woolly
Mammoth
Asian Elephant
African
Elephant
SNP Count
B
A
A
348
A
A
B
403
Asian and African elephants diverged about 6 million years ago. Using the information
above, when did woolly mammoth and Asian elephants diverge? (Round to the nearest
1,000):
5,562,000 years ago
Calculations:
Nmammoth: 348
Nafrica: 403
Nmammoth / ((Nmammoth +Nafrica)/2)
348 / ((348+403)/2)
348 / 375.5 = 0.927
0.927 * 6,000,000 = 5,562,000 years ago
Copyright 2023 Julin Maloof and The Regents of the University of California. May not be
reproduced without permission.
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21)
(12 points) Researchers used the following tree to look for ancient mating between
Denisovans and either Papuans (people from Papua New Guinea) or people from
France. The proportion of SNPs with different patterns are shown below.
Papuans
French
Denisovan
Chimpanzee
A
A
B
A
0.205
A
B
A
B
0.195
A
B
B
A
0.095
B
B
B
A
0.32
B
B
A
A
0.08
B
A
B
A
0.105
A)
(6 pts) Calculate Patterson’s D.
Answer
:
B)
(6 pts) Interpret the value you calculated in part A in regards to Denisovan
introgressions into French and Papuans.
ABBA: 0.095
BABA: 0.105
(Pr(ABBA) – Pr(BABA))
(Pr(ABBA) + Pr(BABA))
(0.095 – 0.105)
(0.095 + 0.105)
-0.01 / 0.2 = -0.05
Patterson’s D is negative meaning more BABA than ABBA and an excess of “B” alleles in Papuans.
This indicates that there was mating between Denisovans and Papuans but not French.
-0.05
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