NAME:
BIOL 464/GEN 535 Population Genetics Spring 2014
Final Exam, 4/29/2014
1. Indicate whether Term 1 would usually be greater than, less than, or approximately equal to Term 2,
with all else being equal. (1 pt each)
a
Term 1
Tajima’s D following a bottleneck
b
c
d
e
f
g
h
i
Broad Sense Heritability
dN/dS with purifying selection
θ with stepwise mutation model
Number of possible unrooted trees
Coalescence time with high gene flow
π in the vicinity of a selective sweep
Forward mutation rate
Number of markers required for genome-wide QTL
analysis using a single human family
j
Diversity of African human populations
<,>,=
Term 2
Tajima’s D with purifying selection
Narrow Sense Heritability
dN/dS under neutrality
θ with infinite alleles model
Number of possible rooted trees
Coalescence time with low gene flow
π in vicinity of a neutral locus
Reverse mutation rate
Number of markers required for genome-wide
association analysis using a population of
unrelated individuals
Diversity of European human populations
2.
a. Calculate π for the following nucleotide sequence alignment, assuming the haplotypes
occur at equal frequency (10 points):
ATG AAT AGC AGA GAT GAC TGT TGG TTT TGT
ATG AAT AGT CGA GAT GAC TGC TCG TTT TGC
b. Estimate θπ and θS for the above sequences (15 pts).
c. Calculate the ω = dN/dS ratio, assuming these are protein-coding loci with the coding
frame indicated by separation of codons. (15 points)
d. Does this locus appear to be under selection? If so, what type of selection is acting? (5
points)
3. The following phylogeny and Structure bar plot was derived from 96 microsatellite genotypes
for 69 dog breeds (Parker et al. 2004)
Parker et al. 2004. Genetic Structure of the Purebred Domestic Dog. Science 304: 1160-1164.
A. Based on the phylogenetic tree above, mark the following statements True or False (10 points)
1.
2.
3.
4.
5.
The Akita is more closely related to the Siberian Husky than to the Afghan Hound. T F
The Akita is more closely related to the Chow Chow than to the Shiba Inu. T F
The Akita is more closely related to the Shiba Inu than to the Chinese Shar-Pei. T F
The Basenji is more closely related to the Siberian Husky than to the Saluki. T F
The Basenji is more closely related to the Saluki than to the Akita. T F
B. Based on the figures on the previous page, propose a reasonable hypothesis for the origin and
evolution of the Alaskan Malamute (marked with star). (5 points)
C. Why do you think the phylogenetic analysis failed to resolve the relationships among most of the
highly domesticated breeds? (5 points)
D. What additional analyses would you perform with this same set of genetic data to evaluate
substructure and relationships among the breeds? (5 points)
4. In the Common Mormon butterfly (Papilio polytes) wing pattern is controlled primarily by a
single locus. The dominant wild-type allele at this locus causes a wing pattern that looks similar
to that of a toxic species, the Common Rose butterfly (Pachliopta aristolochiae). Mutations from
this allele to a recessive version that encodes a plain wing pattern occur at a rate of 4x10-4.
Reversions to the mimicry allele occur at a rate of approximately 1x10-6.
a. Assuming that this locus is neutral, what is the expected equilibrium allele frequency of the wildtype allele? (10 pts)
b. Assuming that the mutant alleles cause a fitness disadvantage of 0.2 relative to the dominant,
wild-type allele, what is the expected equilibrium frequency of the wild-type allele? You can
safely ignore reverse mutations in this scenario. (10 pts)
c. Assuming that the mutant allele is codominant with the wild-type allele (h=0.5), and all other
conditions are the same as in part b, what is the expected equilibrium allele frequency of the
wild-type allele? (10 pts)
Short Answer. Graduate students answer any 3. Undergraduates answer any 2. Please aim for no more
than a paragraph (less than 150 words) per answer. (Grads: 10 points each; Undergrads: 15 points
each)
5. Describe the similarities and differences between QTL Mapping and Genetic Association Studies.
List at least two major advantages and disadvantages of each approach.
6. Whole genome duplication is a common occurrence in some evolutionary lineages, most
notably plants and bony fishes. Based on the principles that you have learned in this class,
describe some possible fates of duplicated genes, assuming that the duplicates have fully
redundant functions shortly after duplication occurs.
7. Compare and contrast coalescent and phylogenetic approaches to the study of evolution. How
does one depend on the other?
8. Coding regions often show negative Tajima’s D values in human populations in Europe, but
noncoding sequences typically show a positive Tajima’s D in these same populations. How do
you reconcile these observations?
9. How do linkage disequilibrium and population structure affect the confidence in statistical
associations between molecular polymorphisms and quantitative traits like disease
susceptibility?
10. Are Neanderthals and Denisovans ancestors of modern humans? Explain the hypothesized
relationships among these groups.