Name:
BIOL 464/GEN 535 Population Genetics
Fall 2011
Test # 2, 11/2/2011
Please answer all questions unless otherwise specified. Show as much of your work as you can, including which
formulas you use (even if actual calculations are done with software). Use the back of the page and additional
sheets as necessary.
1. Indicate the correct relationship between the terms or parameters in the table, all else being equal. (15 points)
Term 1
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
Genetic drift in large populations
HT
Census population size
Number of alleles prior to bottleneck
FST with high gene flow between populations
Variance in allele frequencies among
completely isolated populations undergoing
genetic drift
FST among populations with very small
effective population sizes
Average allele frequency among many isolated
subpopulations before genetic drift
Genetic match probability with genotyping
error included
Genetic match probability with population
structure included
FRT
Match probability for 10 loci with 2 alleles
with equal population frequencies
Time to coalescence for first coalescent event
for a locus with six alleles
Average time to fixation of a favored allele in a
large population
Number of possible rooted trees for a group of
taxa
≤ or ≥
or =
Term 2
Genetic drift in small populations
Average HS
Effective population size
Number of alleles after bottleneck
FST with low gene flow between populations
Variance in allele frequencies within
completely isolated populations undergoing
genetic drift
FST among populations with very large
effective population sizes
Average allele frequency among many isolated
subpopulations after genetic drift
Genetic match probability without considering
genotyping error
Genetic match probability without considering
population structure
FST
Match probability for 2 loci with 10 alleles
with equal population frequencies
Time to coalescence for fifth coalescent event
for a locus with six alleles
Average time to fixation of a favored allele in a
small population
Number of possible unrooted trees for a group
of taxa
2. 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 (5 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 circle). (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)
3. A Fish and Game warden detains a fisherman suspected of catching trout illegally in Blackwater Creek,
where fishing is prohibited. The fisherman claims to have caught the fish legally in a recreational lake that is
routinely stocked. The warden, having taken BIOL 464, decides to resolve the issue with microsatellites.
Based on the following profile, calculate an appropriate likelihood ratio. Be sure to state the two hypotheses
that you are comparing, and present a proper interpretation of the results. (15 points)
Locus
1
2
3
Fish Genotype
121
135
148
121
139
154
Blackwater Creek (native)
Allele Frequencies
0.68
0.68
0.59
0.32
0.69
0.31
Tygart Lake (stocked) Allele
Frequencies
0.24
0.24
0.07
0.09
0.21
0.06
4. Blackwater Creek in problem 3 has a highly degraded trout population due to historical overfishing and
habitat degradation. The current population size is estimated to be 50. Only two alleles are detected for
Locus 3, as shown in the table.
a. What is the probability that allele 148 will eventually become fixed in this population due to
genetic drift? (5 points)
b. What is the mean expected time to fixation for allele 148 in the Blackwater Creek
population? (10 points)
c. What are the key assumptions of this calculation? What would cause underestimation of the
time to fixation? What could cause overestimation? (5 points)
5. The following table contains data from locus 3 for 7 trout populations.
a. Assuming equal population sizes, estimate the proportion of genetic variation that is due to
differentiation among populations. (10 points)
Population
Blackwater Creek
Poplar Creek
Cheat River
Monongahela River
New River
HSi
0.47
0.29
0.40
0.48
0.45
Gauley River
Shavers Fork
0.47
0.31
HT = 0.42
b. What can you infer about the degree of connectedness and genetic exchange among these
populations? (5 points)
c. Based on this calculation, would you revise your conclusions in problem 4? Why? (5 points)
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)
6. Explain how genetic drift plays a central role in Wright’s Shifting Balance theory.
7. A. How does genetic drift affect the efficiency of selection in small populations?
B. How does the level of dominance affect this relationship?
8. What is the difference between cladistic and phenetic approaches to phylogenetic analysis? What are the
advantages and disadvantages of each?
9. Compare and contrast coalescent and phylogenetic approaches to the study of evolution. How does one
depend on the other?
10. List at least three possible types of errors in paternity analysis, and explain how each of these can these
be overcome.
11. What does the following equation mean, what are its underlying assumptions, and what are some
alternatives to this approach?
Nm 
1 FST
4 FST