NAME:
BIOL 464/GEN 535 Population Genetics
Spring 2014
1. Match each term to the description that fits best. (10 points)
Term
Description
Genetic Drift
A
Acts to reduce linkage disequilibrium among loci.
Gene Flow
B
The difference between observed and expected gamete
frequencies
AMOVA
C
Genetic differentiation among regions.
D
D
Cryptic gene flow must be taken into account.
FRT
E
It is X times more likely that the suspect is the murderer
than that any other person in the world could be the
murder.
Recombination
F
Genetic differentiation among subpopulations.
FST
G
Partitioning of genetic variation into hierarchical levels of
organization.
Paternity Exclusion
H
Prediction of the generation at which alleles become fixed
due to drift.
Prosecutor’s Fallacy
I
Tends to reduce differentiation of finite subpopulations.
Diffusion approximation
J
Tends to reduce heterozygosity and variance within finite
subpopulations.
2. The following table contains data from a single microsatellite locus from an endangered fish
species for 7 populations divided among three regions. Assuming equal population sizes,
calculate the overall FRT and FST for this locus, and provide a brief biological interpretation of
your results. (10 points)
a.
Region
Population
HSi
HRk
HT = 0.647
Bylas Springs
0.109
Bylas Spring 1
0
Bylas Spring 2
0.204
Sonoita Creek Springs
0.469
Cottonwood Spring
0.401
Monkey Spring
0.024
Sonoita Creek
0.411
Coalmine Canyon
0.411
Sonoita Creek
Red Rock Falls
0.366
0.434
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3. Assume that trout from each of the Bylas Springs and Sonoita Creek populations have been
completely isolated from one another, and randomly mating within each population for
many years. An MS student in the WVU Fisheries program sampled fish from each portion of
the creek above and below a culvert that effectively prevented mixing of the populations. He
determined the following SNP allele counts for two loci for each population:
Locus
MYB1-150
NAC1-239
Allele
A
G
C
T
Above Culvert
10
90
10
90
Below Culvert
80
20
80
20
a. What are the expected gamete frequencies in these two populations for these two loci?
(10 pts)
b. The severe winter of 2014 caused destruction of the culvert that previously prevented
mixing between the populations. The populations have now mixed and undergone
completely random mating in 2014. Calculate the following for the mixed population,
assuming the loci are completely physically unlinked.
i. D (10 points)
ii. r (5 points)
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4.The cast of The Simpsons are blown wildly off course while partying on a yacht in the Pacific
Ocean. After a horrendous shipwreck, Marge, Crazy Cat Lady, Brandine, Helen Lovejoy, and
Professor Frink wash up on an uncharted island, never to be found again. They go on to found a
new colony that remains isolated for 2 generations. The effective number of males and females in
each generation is as follows:
Generation
NM
NF
1
1
4
2
5
20
NE
a. What is the effective population size after 2 generations? (10 pts)
b. Assuming the average expected heterozygosity of the five castaways was H0=0.3, what
will be the expected heterozygosity after 2 generations? (10 pts)
c. What are the main assumptions of the calculation in part b? How would you predict that
the actual result would differ from the theoretical result, and why? (5 pts)
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5. The figures on the next page are from a manuscript by Kanno et al. (2011) describing
population structure in the brook trout (Salvelinus fontinalis) in a stream system in
Connecticut (map) with seasonal barriers in the form of summer waterfalls. Fish were
collected throughout the system and genotyped with 8 microsatellite markers. The authors
used the Structure program to identify homogeneous groups.
a. What was the best-supported number of groups in the river system as a whole
(Jefferson Hill-Spruce Brook)? (5 points)
b. What was the best-supported number of groups in the Jefferson-Hill Brook when
considered alone? Why did this change? (5 points)
c. Propose a reasonable biological hypothesis to explain the patterns observed. Be sure to
discuss the differences between Spruce Brook and Jefferson Hill Brook, and the possible
determinants of genetic differentiation within this system. Are there alternative
hypotheses as well? (5 points)
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Kanno, Y., J. C. Vokoun, et al. (2011). "Fine-scale population structure and riverscape genetics
of brook trout (Salvelinus fontinalis) distributed continuously along headwater channel
networks."Molecular Ecology 20(18): 3711-3729.
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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. The “Out of Africa” hypothesis posits that European populations were derived from one or a few
migration events from Africa. Given what you know about demographic effects on linkage
disequilibrium, which group would tend to have higher Linkage Disequilibrium (larger
haplotypic linkage blocks), Europeans or Africans? Explain your answer.
7. The Fisher-Wright model of genetic drift is based on a large number of independent
subpopulations containing finite numbers of individuals. Fill out the following table, predicting
the effects of drift over a large number of generations for the individual subpopulations versus
the entire, merged population.
Within Subpopulations
Overall Population
Allele Frequency
Variance in Allele Frequencies
Expected Heterozygosity
Observed Heterozygosity
Hardy-Weinberg Equilibrium
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8. Explain how selection, drift, and dispersal interact to maintain variation within species according
to Wright’s Shifting Balance Theory.
9. State and defend one hypothesis to explain the relationship between genome size and effective
population size.
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10. Explain how loci on different chromosomes can be in significant linkage disequilibrium in a
diploid, outcrossing organism in a randomly-mating population.
11. Explain the following equation and clearly indicate how it is intended to be used. Why does FST
only appear in one part of the equation?
P'   [ pi2  pi (1  pi ) FST ] 2 pi p j
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