Hardy-Weinberg Equilibrium in Population Genetics
Hardy-Weinberg Equilibrium in Population Genetics
1. Which of the following options factually completes the statement, "If a population is in Hardy-
Weinberg equilibrium..."?
c. Allele frequencies will not change from one generation to the next.
C, Allele frequencies will not change from one generation to the next.
Correct Answer:
2. If allele frequencies do not change from one generation to the next, is the population definitely in
Hardy-Weinberg equilibrium? Why or why not?
No, it might not be in Hardy-Weinberg equilibrium. Any process that selectively targets
heterozygotes can affect genotype frequencies without necessarily changing allele frequencies in the
next generation. Examples are nonrandom mating, overdominance, and underdominance.
a. If the allele frequencies in a population are given by p and q, the genotype frequencies are given by
p2, 2 pq and q2.
c. If the allele frequencies in a population are given by p and q, the genotype frequencies are given by
p2 and q2. d. The first and third answers are correct.
4.
The processes are mutation, which introduces new alleles into the population; selection, which occurs
when genotypes have different reproductive success; migration, the movement of new individuals into
or out of the population; and genetic drift, the random change in allele frequencies due to chance. (A
fifth process, nonrandom mating, can affect genotype frequencies but will not affect allele frequencies
unless it is accompanied by selection, e.g. nonrandom mating that results in certain individuals
attracting more mates.)
5. Match the key terms in this chapter listed below with the phrase that is the best match for it.
6. The HIV epidemic is unlikely to lead to an increase in the CCR5 delta-32 allele over the short term
because ___________________.
e. in populations with a high frequency of the allele, selection pressure is relatively low.
D, The first and second choices are correct.
Correct Answer:
Selection will eventually cause an advantageous allele to become more common, but it's a slow
process. For selection to cause a rapid increase in an allele's frequency, the selection must be strong
and the allele must already be somewhat common. The delta-32 allele of CCR5 is most common in
European populations, but HIV infection is low there. Selection due to HIV is strongest in Africa, but
the delta-32 allele is very rare there.
7. Eastern grey squirrels (the common urban squirrel of most of the United States) sometimes can be
completely black. Black squirrels usually are seen in certain isolated squirrel populations in city parks
of the northeastern U.S., and are particularly common around the campus of Princeton University, in
New Jersey. Black color appears to be caused by a single dominent allele, and squirrel litters can
include both black and grey pups.
In 1986, 1987, and 1994, three different Princeton biology classes walked the campus and counted the
number of black and grey squirrels. Here are their results. (Data from Ken Nicholson, Woodrow
Wilson Biology Institute, 1994).
Part I: Referring to the information about Eastern grey squirrels, calculate the percentage of black
squirrels in each year. Have phenotype frequencies changed over time in this population, and if so, can
you tell why? Can you determine if the population is in, or close to, Hardy-Weinberg equilibrium?
Part II: Referring again to the information about Eastern grey squirrels, assuming the population is in
Hardy-Weinberg equilibrium, calculate the frequencies of the black and grey alleles in each year.
Part I: The observed frequency of black squirrels was 16% in 1986, 26% in 1987, and 17% in 1994.
The data show fluctuation in black squirrel frequency, but it is unclear whether this fluctuation is
"real" - it may be due to small sample size or observational technique, and if real, there is not enough
information to tell whether drift, selection, or migration, or nonrandom mating are the causes.
(Mutation is unlikely to produce allele frequency changes this rapidly.) Since black squirrels may be
homozygotes or heterozygotes, we cannot determine actual genotype frequencies, and thus we cannot
determine if the population is in Hardy-Weinberg equilibrium.
Part II: If the population is in Hardy-Weinberg equilibrium, genotype frequencies can be calculated
by knowing that the frequency of grey squirrels will equal q2, solving for q, and then calculating p = 1-
q. Frequencies for the grey allele and black allele were:
Black coat color in squirrels is theorized to be advantageous in cold climates due to greater absorption
of solar radiation, but disadvantageous where natural predators are numerous due to the
conspicuousness of black squirrels. This may explain the greater frequency of the black color morph in
northeastern city parks, which have cold winters but few natural predators.
8. Over the long term, selection favoring the rare phenotype in a polymorphic population (i.e.,
negative frequency dependent selection), will __________ genetic diversity in the population.
a. decrease
b. increase
c. maintain
C, maintain
Correct Answer:
Negative frequency-dependent selection maintains rare alleles in the gene pool. It can even keep
alleles that are slightly deleterious in the population, if the alleles gain a strong advantage when their
phenotype becomes rare. (Remember that another process that can maintain rare or deleterious alleles
is heterozygote superiority.)
c. Allele frequencies may initially hover at an unstable equilibrium, but will eventually change.
10. When selection acts against a recessive allele that is initially at high frequency in a population,
____________________.
a. the frequency of the allele will stay high for a long time, then decline slowly.
b. the population will remain in Hardy-Weinberg equilibrium. the frequency of the allele will decline
rapidly, and then stabilize at very low frequency.
the frequency of the allele will decline rapidly, and then stabilize at very low
Correct Answer: frequency.
a. both alleles are maintained at a frequency different from that predicted by Hardy-Weinberg
principles based on the strength of selection against the recessive allele.
b. the selective advantage enjoyed by the deleterious allele in the heterozygote exactly
c. genetic diversity in the population can be maintained indefinitely, in spite of selection acting against
the allele. balances the selective disadvantage suffered by homozygous recessive individuals.
b. the most common outcome will be that the most common allele will become fixed (will increase to
a frequency of 1) in the population.
c. both alleles are maintained in the population at frequencies different from those predicted by Hardy-
Weinberg principles.
the most common outcome will be that the most common allele will become
Correct Answer: fixed (will increase to a frequency of 1) in the population.
This is a case of underdominance. Allele frequencies may initially hover at an unstable equillibrium,
but inevitably, sooner or later, it will drift from that equilibrium. As soon as it starts to drift, the rarer
allele will be found more frequently in heterozygotes, where it will be selected against, and it will
quickly be lost.
13. Pier and his colleagues have suggested that cystic fibrosis is maintained at relatively high levels in
people of European ancestry because of heterozygote superiority; specifically, he proposposes that
heterozygotes are more resistant to typhoid fever than are the dominant homozygotes. Evidence in
favor of this hypothesis includes which of the following findings?
a. The mutation rate for new loss-of-function mutations in the CFTR gene is too low for the
prevalence of the disease to be explained by mutation/selection balance.
b. Pier and his colleagues have found, in 11 European countries, an association between the severity of
typhoid fever outbreaks and the frequency of the delta-F508 allele (the most common loss-of-function
mutation) a generation later.
c. Pier et al. engineered cells homozygous for functional CFTR alleles, homozygous for a common
loss-of-function allele, and heterozygous for the two. The loss-of-function homozygotes were virtually
impervious to invasion by typhoid fever-causing bacteria; heterozygotes were more vulnerable, but
accumulated 86% fewer bacteria than did the dominant homozygotes.
e. Salmonella typhi bacteria manipulate their host cells, causing them to express more CFTR protein
on their membranes.
14. According to the basic model of mutation/selection balance, if selection is strong and mutation rate
is low, the equilibrium frequency of a deleterious allele will be __________; when selection is weak
and the mutation rate is high, the frequency of the allele will be relatively __________.
low/high
Correct Answer:
A model that predicts an equilibrium frequency that is equal to the square root of selection strength
over mutation rate.
The process that currently maintains the high frequency of the cystic fibrosis phenotype.
16. What are compound chromosomes, and how do they affect fertility? Why are they uniquely suited
for studies of underdominance?
Compound chromosomes are chromosomes that have swapped entire arms. Animals with compound
chromosomes can produce fertile offspring only if they mate with other individuals carrying the same
compound chromosome (and even then, 3/4 of zygotes are inviable). Therefore, a population in which
some individuals have one kind of compound chromosome, and some have a different compound
chromosome, will be analogous to a case of underdominance, because some purebred zygotes
(analogous to homozygotes) will survive, but all hybrid zygotes (analogous to heterozygotes) will die.
17. Three of the following conditions are necessary for selection of one phenotype over another to lead
to evolutionary change. Which statement is not?
18. Describe at least two major biological flaws in logic of the forced sterilization program for
eliminating feeblemindedness.
Two of the biggest flaws were, first, "feeblemindedness" had a very strong environmental component
and was not clearly related to heritable genetic variation as had been proposed; the estimates of
heritability were biased due to circular reasoning in data collection. Second, even if
"feeblemindedness" were mostly due to a rare recessive allele, even strong selection would not
appreciably reduce the frequency of the allele.
19. There are two common alleles for the human muscle enzyme ACE (angiotensin-converting
enzyme)-a shorter D allele, and a longer I allele that has an insertion of 287 base [Link] ACE coded
by the I allele has lower activity, but it is also associated with superior muscular performance after
physical training. One study (Williams et al. 2000) of 35 II and 23 DD men found that though they
didn't differ in muscular efficiency before training, after 11 weeks of aerobic training, the II
homozygotes had 8% greater muscular [Link] I allele is also associated with greater endurance
and greater muscular growth after strength training.
Speculate on why the D allele still remains at relatively high frequency in the human population. How
could you test your ideas?
There are many possible answers. The I allele might have some costs, such as (say) lowered speed of
muscle contraction; the D allele might have unknown benefits; there might be heterozygote
superiority. Also, genetic drift, mutation or migration might have caused the D allele to be at higher
frequency than would be predicted by selection alone, particularly since the strength advantage for II
homozygotes appears relatively minor. Some obvious research paths are: testing other measures of
fitness; testing heterozygotes; investigating mutation rate; examining allele frequencies in various
different human populations.
20. Consider what makes a new mutant allele dominant or recessive. To guide your thinking, imagine
an enzyme that changes substance A to substance B. If B is a nutrient that is needed only in minimal
amounts, will a loss-of-function mutation be dominant or recessive? If A is an abundant toxin that
must be entirely broken down, will a loss-of-function mutation be dominant or recessive? How about a
new mutant allele that results in a form of the protein that can catalyze an entirely new reaction (say,
from A to new substance C?) Can you think of other examples of protein function that will affect
whether a new allele is dominant or recessive?
Whether an allele is dominant or recessive depends on what happens in heterozygotes, which in turn
often depends on whether the dose of normal gene product is more important than its mere presence.
Consider a heterozygote with one normal allele and one loss-of-function allele. The heterozygote's
cells will only produce half of the normal amount of gene product. If the only thing that matters for the
trait is whether the gene product is produced at all, then the heterozygote will appear normal - the
normal allele will be dominant over loss-of-function allele. But if the amount of the gene product is
very important, then the heterozygote will have an altered phenotype, because it is only making half
the gene product. in this case, loss-of-function alleles will be either dominant or codominant. In the
examples given, a loss-of-function allele will usually be recessive for production of a minimally
needed nutrient; dominant for breaking down an abundant toxin; and dominant for catalyzing a new
reaction.
21. West Nile virus is an emerging disease that has rapidly spread across North America in recent
years, infecting birds, humans and horses. It can cause severe flu-like symptoms and fatal encephalitis
in humans. Glass and colleageus recently sequenced CCR5 genotypes in several hundred West Nile
virus patients in Arizona and Colorado, and compared them to another group of patients that also had
flu-like illnesses, but did not have West Nile. Here are the distributions of genotypes in patients with
and without West Nile:
Part I: Referring to the West Nile virus information given above, what was the frequency of the
CCR5-delta32 allele in both of these patient cohorts? The CCR5-delta32 allele is at Hardy-Weinberg
equilibrium in the North American population at large. Does either patient population appear to be in
Hardy-Weinberg equilibrium? (You may assess your data "by eye," without statistical tests, if you
wish.)
Part II: The percentage of CCR5-delta homozygotes in North America is usually 1%. How does this
compare to both populations?
Part III: Propose an explanation for the data. How does this compare with the situation of CCR5-delta
in HIV susceptibility? What are the selective forces of the two diseases on this locus?
Part I: Genotype frequencies in the West Nile population were 0.88 for the normal CCR5 allele, and
0.12 for the delta-32 allele. For the control population, frequencies were 0.93 for the normal CCR5
allele, and 0.07 for the delta-32 allele. The West Nile patients appear to not be in Hardy-Weinberg
equilibrium (actual percentages 0.80, 0.16, 0.04; compared to expected Hardy-Weinberg genotype
frequencies of 0.77, 0.21, and 0.01. (The deviation from Hardy-Weinberg equilibrium is statistically
significant.) The control patients are in virtually perfect Hardy-Weinberg equilibrium (frequencies of
0.86, 0.13, and 0.01).
Reference: Glass, W.G., D.H. McDermott, J.K. Lim, S. Lekhong, S.F. Yu, W.A. Frank, J. Pape, R.C.
Cheshier, and P.M. Murphy. 2006. CCR5 deficiency increases risk of symptomatic West Nile virus
infection. J. Exp. Med. 203(1):35-40.
Part II: CCR5-delta32 homozygotes are present at the normal frequency in the control patients, but
are nearly four times more common than usual in the West Nile patients.
Reference: Glass, W.G., D.H. McDermott, J.K. Lim, S. Lekhong, S.F. Yu, W.A. Frank, J. Pape, R.C.
Cheshier, and P.M. Murphy. 2006. CCR5 deficiency increases risk of symptomatic West Nile virus
infection. J. Exp. Med. 203(1):35-40.
Part III: Several explanations are possible. CCR5-delta32 is suspected to increase susceptibility to
West Nile virus infection, and/or increase risk of progression to the severe form of the disease. (It also
increased risk of mortality in this study.) This is in sharp contrast to the situation in HIV, in which
CCR5-delta32 confers protection against infection by HThe two diseases are exerting opposing
selection on the CCR5 locus, West Nile selecting against the delta32 allele, and HIV selecting for it.
The opposing effects of these two diseases make more sense if we consider West Nile's type of viral
attack is quite typical for viruses, while HIV is very unusual in its specific targeting of immune cells.
In other words, West Nile is the kind of virus that the immune system probably evolved to defend
against, but HIV is not.
Alert readers will also have noticed a deficit of heterozygotes in the West Nile group. It is possible that
there might be a heterozygote advantage.
Reference: Glass, W.G., D.H. McDermott, J.K. Lim, S. Lekhong, S.F. Yu, W.A. Frank, J. Pape, R.C.
Cheshier, and P.M. Murphy. 2006. CCR5 deficiency increases risk of symptomatic West Nile virus
infection. J. Exp. Med. 203(1):35-40.
22. Left-handedness in humans is associated with a variety of subtle health and fitness costs, yet
remains at high frequency in some human populations. Left-handers often have an advantage in
baseball, tennis, fencing and other sports in which pairs of individuals face off against each other.
Since most players train against right-handers, they are less able to defend themselves against a left-
handed opponent. Based on this phenomenon in sports, it has been proposed that left-handedness may
be maintained in human populations due to an advantage in hand-to-hand combat.
Part II: Geneticists Charlotte Faurie and Michel Raymond recently studied the frequency of left-
handers in traditional societies, compared to the level of "violence" in those societies. They used
homicide rate as an index of violence. The figure below shows their data. Are the data consistent with
the hypothesis that left-handedness gives an advantage in combat?
Part III: Suppose the combat hypothesis is true. In extremely violent societies, would you predict that
left-handedness would increase to fixation?
Part IV: If left-handedness had no costs, would you expect left-handedness to change over time in any
of these societies? Explain.
Your Answer:
v
Part I: frequency-dependent selection
Part II: The data are consistent with the combat hypothesis.
Part III: No. First, left-handers would lose their combat advantage if the frequency of left-handedness
rose above 0.50. In addition, recall that left-handedness also carries several costs that right-handedness
does not carry. This should keep left-handedness below 0.50, even in a population with a large amount
of hand-to-hand combat. (The Yanomamo may represent the maximum frequency for left-
handedness.)
Part IV: If left-handedness carried no costs, we would expect left-handedness to increase to 0.50 (half
the population) in all societies. This should occur more quickly in the more violent societies. Once at
0.50, left-handedness and right-handedness should remain at equal frequency. (Any time that one
phenotype declined below 0.50, it would begin to enjoy a selective advantage in combat, and should
come back up to 0.50 again.)
CHAPTER SEVEN: MIGRATION AND DRIFT
a. gene flow
b. evolution
c. selection
d. mutation
A gene flow
Correct Answer:
2. Banded water snakes migrate from the mainland of Lake Eerie to various islands. Unbanded water
snakes persist at relatively high frequency on the islands in spite of migration because
_____________.
a. as juveniles, unbanded morphs have higher survivorship on the islands than do banded morphs
b. heterosis
3. If migration proceeds unopposed by any other evolutionary process, the result will be
_____________.
a. intermediate aged
b. older
c. younger
A intermediate-aged
Correct Answer:
The intermediate-aged populations have had enough time for migration to homogenize allele
frequencies across populations. Younger and older populations had fewer individuals, and were
dominated by genetic drift.
a. Explains the low frequency of genetic diseases in some island populations of humans. b. Tends to
reduce genetic variability in the founder population compared to the source population.
c. Tends to lead to lowered heterozygosity. d. Is a process that randomly affects allele frequencies.
Tends to reduce genetic variability in the founder population compared to the source
Correct Answer: population.
The smaller the population, the stronger and faster the effects of genetic drift.
6. Each of the figures (A, B, and C) illustrates the results of a series of computer simulations of
changes in allele frequency in a group of populations due to chance alone. Figure _____ most likely
represents the simulations performed on the smallest populations; Figure _____ most likely represents
the simulations performed on the largest populations.
a. B; C
b. A; B
c. B; C
d. A; C
A; C
Correct Answer:
The smaller the population, the faster drift will act, and the faster alleles will move to fixation or loss.
7. The computer models of genetic drift shown in Figure 7.15 demonstrate that three of the statements
below are true. Which statement is false?
a. genetic drift causes allele frequencies to wander between 0 and 1.
b. Genetic drift strongly affects only populations that are very small.
c. Genetic drift tends to eventually lead to fixation or loss of any given allele.
8. In Buri's classic experiment on genetic drift in flies, what was surprising about the change in
average heterozygosity over time? What is a likely explanation?
Average heterozygosity declined faster than predicted. In Figure 7.17, the predicted result is shown
by the dashed grey line (for populations of 16 individuals); but the experimental data match the solid
grey line, which is the expected result for populations of 9 individuals. This indicates that not all
individuals reproduced. Some flies may have died before mating; others may have been rejected as
mates. Another way to state this is that though the actual population size was 16, the effective
population size was 9.
9. Consider a population of 100 mice on an island, with allele frequencies B = 0.20 for black coat
color, and b = 0.80 for white coat color, Black, B, is dominant to white, b, and the population is in
Hardy-Weinberg equilibrium. Twenty-five homozygous black mice from the mainland float to the
island on an uprooted tree after a storm. What are the allele frequencies now? What were the genotype
frequencies before and after the migration event? Is the population in Hardy-Weinberg equilibrium?
How long will it take it to get back into Hardy-Weinberg equilibrium if no more mice arrive, and if
there are no other forces affecting allele frequencies?
Originally there were 100 mice, and the gene pool contained100 copies of the black allele and 100
copies of the white allele. The Hardy-Weinberg genotype frequencies were BB= 0.25, Bb = 0.50, and
bb = 0.25; that is, there were 25 homozygous black mice, 50 heterozygous black mice, and 25 white
mice. After the storm, there are now 125 mice, and the gene pool contains 150 copies of the black
allele (the 100 old copies plus 50 new ones) and 100 copies of the white allele. These are distributed in
50 homozygous black mice (25 old + 25 new), 50 heterozygous black mice, and 25 white mice. The
new allele frequencies are B= 0.60 (150/250) and b = 0.40 (100/250), and the genotype frequencies are
BB = 0.40 (50/125), Bb = 0.40 (50/125), and bb = 0.20 (25/125). These genotype frequencies do not
match Hardy-Weinberg equilibrium frequencies (0.36, 0.48, and 0.16, respectively). The population is
not in Hardy-Weinberg equilibrium. In theory, a single bout of random mating will put the population
back in Hardy-Weinberg equilibrium in the next mouse generation. (Note, though, that in reality,
parental mice do not disappear instantly. Until the first-generation mice have all died, the population
will not be in Hardy-Weinberg equilibrium. In mice, this will take about a year and a half.)
10. Refer to the information presented in the previous question. Now, suppose the twenty-five black
mice float away again on another tree without breeding, and the island is back to its original state.
Allele frequencies on the island are back to B=0.20, b=0.80. On the continent, there is a large
population of many thousands of mice, with allele frequencies B=0.80, b=0.20. One year, human ships
begin moving back and forth between the island and the continent, and occasionally a mouse comes
along for the ride, and stays and breeds. Equal numbers of mice ride in each direction. The shipping
trade continues indefinitely. Where will the allele frequencies ultimately stabilize? (Assume that no
other forces are affecting allele frequencies.)
b. The island and continent populations will both end up at a stable equilibrium of B=0.50, b=0.50.
11. Small relictual populations of collared lizards remain in glades of desert-like habitat scattered
throughout the oak-hickory forests in parts of the Ozark Mountains. Templeton and colleagues
supported the hypothesis that drift had been acting in these populations by documenting that
_____________.
a. most populations were fixed for a single genotype, but genotypes varied among populations
b. all populations were fixed for the same allele at each locus studied.
d. individual populations were polymorphic for several loci and most populations were genetically
similar to one another.
most populations were fixed for a single genotype, but genotypes varied among
Correct Answer: populations
This is not what we would predict if selection had been acting, but is exactly what we would predict
if drift were the major evolutionary force. Random fixation of alleles due to genetic drift has caused
different genotypes to become fixed in different populations, even though they all live in very similar
environments.
12. Briefly describe the fundamental tenets of Kimura's neutral theory, and its two surprising
implications. What data was this theory based on? Is the theory supported by recent data?
Kimura's neutral theory holds that virtually all mutations are selectively neutral, that the substitution
rate is equal to the mutation rate, and that the evolution of DNA sequences is dominated by genetic
drift. The two surprising implications were that neither population size nor natural selection have an
effect on the rate of DNA sequence change. The theory was based on amino acid substitutions in a
fairly small number of genes that had been studied at the time. Recent data shows that though the
neutral theory is applicable to noncoding regions and some coding regions, a large fraction of coding
regions have been affected by selection.
13. What were the two early observations about amino acid substitutions that led to development of
the neutral theory?
The first was Zuckerkandl and Pauling's discovery that amino acid substitutions in vertebrates
appeared to occur at a steady, clock-like rate. The second was Kimura's calculations showing that
amino acid substitutions occur every two years on average in the vertebrates (when substitution rates
for well-studied genes are extrapolated to the whole genome). These substitution rates seemed too fast
and too steady to be explainable by selection.
14. What was the key finding of McDonald and Kreitman's comparison of the Adh gene in three
different fly species? What is the interpretation of the finding? What is the logic of comparing
sequences both between and within species?
McDonald and Kreitman found that 29% of fixed differences between their fly species were
synonymous substitutions, but that only 5% of polymorphic differences within species were
synonymous. They reasoned that if there were no selection (i.e. if the neutral theory were true), then
the ratio of synonymous to nonsynonymous substitutions should be constant both within and between
species. However, if there are differences in this ratio between vs. within species, the within-species
ratio should represent the neutral replacement rate, and the higher between-species ratio is thought to
be evidence of selection.
15. Genes associated with which of these traits have shown evidence of recent positive selection?
a. Parasite-host interactions
b. Symbiont interactions
Symbiont interactions
16.
Match the key terms in this chapter listed below with the phrase that is the best match for it.
Your
Option Phrase answer
gene flow, or A. The apparent number of breeding
16.1 migration individuals in a population, as
reflected in the genetic and
evolutionary trends of a population;
usually lower than the actual number
of individuals
inbreeding B. A change in allele frequencies of a
16.2 depression new population due to its being started
by a small random sample from a large
population
sampling C. Random discrepancy between
16.3 error, or observations and expected results, due
sampling to selection of just a small part of the
bias population (not the whole population)
18. According to Westemeier et al., the "extiction vortex" in Illinois greater prairie chickens was due,
in effect, to a positive feedback loop between ____________.
19. Westemeier and others supported their hypothesis for the decline of the Illinois greater prairie
chicken by demonstrating which of the following?
a. A comparison of DNA collected from prairie chickens in the 1990's with DNA from museum
specimens collected in the 1930's and 1960's showed a loss of genetic diversity over time.
b. Hatching rates increased when prairie chickens from other, more genetically diverse, populations
were transplanted to the Jasper County populations.
c. Illinois prairie chickens had less diversity at six selectively neutral loci than did prairie chickens
from populations in other states.
20. Sunflowers were domesticated fairly recently from a wild sunflower native to North America, and
have been under intense artificial selection for increased number of seeds, size of seeds, and
sunflower-oil content. Domestic sunflower strains have lower genetic diversity at most loci than do the
wild populations. On one chromosome, there is a cluster of loci called LG06 that all show signs of
recent positive selection in domestic sunflowers. Some of the common alleles at certain of these loci
increase seed size and oil content. However, at other loci in this cluster, the most common allele (in
domestic sunflowers) is associated with maladaptive traits.
Why do domestic sunflowers have lower genetic diversity than wild sunflowers? Why did the LG06
maladaptive alleles become more widespread during the domestication of sunflowers?
Domestic sunflowers probably have lower genetic diversity due both to a founder effect and probably
to strong selection that has eliminated undesirable alleles. (It appears that sunflowers passed through
several "genetic bottlenecks" during domestication.) There are several reasons that maladaptive traits
could have become common, including inbreeding depression, genetic drift, etc., but in this case, they
seem to have hitchhiked to fixation in a selective sweep, due to being physically linked to desirable
alleles that increase seed size and oil content. (The LG in LG06 stands for "linkage group.")
Reference: J.M. Burke, S.J. Knapp, and L.H. Rieseberg. 2005. Genetic consequences of selection
during the evolution of cultivated sunflower. Genetics 171:1933-1940.
21. A recent study of 170 threatened species found that 77% of the threatened taxa have lower
heterozygosity (measured at many loci) than closely related taxa that are not threatened. What does
this imply for the long-term future of these threatened taxa?
Many answers are possible. Low heterozygosity, in and of itself, indicates that the populations
probably have low allelic diversity, which will make them less able to evolve in response to changing
environmental conditions. In addition, the lowered heterozygosity is likely to have resulted from small
population size and associated genetic drift (including founder effects) and/or inbreeding. Small
population size is always cause for concern, and inbreeding can lower fitness via inbreeding
depression. In either case the prognosis for long-term survival is not good.
Reference for this data: D. Spielman, B.W. Brook, and R. Frankham. 2004. Most species are not
driven to extinction before genetic factors impact them. Proc. Natl. Acad. ScUSA 101(42):15261-
15264.
22. An important tool for testing whether selection or drift is acting on a particular gene is to calculate
the ratio of nonsynonymous substitutions per site (dN) to synonymous substitutions per site (dS).
Correctly match each of the following ratios to its correct interpretation.
Your Correct
Option Interpretation answer answer Comments
dN/dS A. replacements C If the rate of nonsynonymous
22.1 < 1 are neutral replacements is less than the rate
of of synonymous replacements,
the implication is that selection is
eliminating the nonsynonymous
mutations.
dN/dS B. replacements A Correct!
22.2 = 1 are
advantageous
dN/dS C. replacements B If nonsynonymous replacements
22.3 > 1 are deleterious exceed silent replacements, it
must be because they're favored
by selection.
CHAPTER EIGHT: EVOLUTION AT MULTIPLE LOCI
c. Is increased by any random sampling error that happens to create or destroy certain chromosome
genotypes but not others
e. Exists when D is less than zero, but not when it is greater than zero.
[Link] two loci are in linkage equilibrium, the allele carried on a chromosome at one locus is
independent of the allele carried on the chromosome at another locus. When this is the case,
a. the frequency of each haplotype can be calculated by multiplying the frequency of its two alleles
allele frequencies will not change over time
b. all possible haplotypes occur at equal frequency
c. the two loci (or, more specifically, their protein products) do not interact.
the frequency of each haplotype can be calculated by multiplying the frequency of its
Correct Answer: two alleles
5. In Clegg et al.'s experiment on linkage disequilibrium in freely mating fruit flies, why did linkage
disequilibrium decline faster than expected? Why did the blue line overshoot the zero-disequilibrium
point on the graph shown in Figure 8.7?
The most likely explanation is that linkage disequilibrium declined faster than expected because of
heterozygote superiority. This would have resulted in selection for heterozygotes, causing an
overrepresenation of flies that were heterozygous for both loci, and fewer flies that were homozygous
for both locCrossing-over in heterozygous flies creates new chromosome genotypes (reducing linkage
disequilibrium); crossing-over in homozygous flies does not. If this was the case, more genetic
recombination would have occurred, per generation, than was expected.
The blue line overshot the zero point simply due to sampling error in a finite population of flies.
Notice that this is an example of how genetic drift can create linkage disequilibrium in a population
that was in linkage equilibrium.
a. genetic recombination
b. crossing over
c. sexual reproduction
d. all of these
D all of these
Correct Answer:
Crossing-over during meiosis breaks up "old" combinations; because the diploid genotype consists of
haplotypes from two different parents, crossing-over will create new allelic combinations (or
haplotypes).
7. Match the key terms in this chapter listed below with the phrase that is the best match for it.
Correct
Option Your Prase
Answer
A Haplotype A. All of the alleles present on a single
7.1 chromosome or in a single haploid
gamete.
B Linkage equilibrium B. A state in which the probability of an
7.2 allele being present at one locus is
independent of the allele present at
another locus on the same chromosome.
E Genetic load C. The blending of gene pools that occurs
7.3 when two different populations meet.
D Genetic recombination D. Creation of new combinations of
7.4 (crossing-over can also be alleles during sexual reproduction.
accepted as an answer)
C Population admixture E. The fitness burden caused by the
7.5 accumulation of deleterious mutations in
a population.
8. Summarize the logic behind Diaz et al.'s effort to establish the age of the 84GG allele in the
Ashkenazim. What are the three possible causes of linkage disequilibrium, and how did Diaz et al. rule
out two of them in this case? Could either of those two actually be a factor? What information did
Diaz et al. have to know to calculate the age of the 84GG allele?
The logic is that if linkage disequilibrium is introduced by genetic drift, the two loci should gradually
come back into equilibrium at a rate determined by the amount of crossing-over between the two
locThe three possible causes of linkage disequilibrium are selection on multilocus genotypes,
population admixture, and genetic drift. Selection was ruled out because one of the loci is selectively
neutral, and population admixture was ruled out because the 84GG allele is not known to occur in
other populations. However, it is possible that one of these two causes might be a factor - there might
be a third linked locus, as yet unidentified that selection is acting on, or a now-vanished population
might have contributed the 84GG allele. However, if selection is not a factor, the origin of 84GG can
be calculated using the known rate of crossing-over to estimate the rate of decay of linkage
disequilibrium.
9. Which of the following statements regarding linkage disequilibrium between Ashkenazi disease
alleles and nearby marker loci are true?
a. Appears due to genetic drift, associated with three periods of founder effects
c. Can be used to estimate the age of the most recent common ancestor of each allele.
Appears due to genetic drift, associated with three periods of founder effects
Correct Answers:
Decays at a rate determined by crossing-over between the two loci.
Can be used to estimate the age of the most recent common ancestor of each allele.
Recall that selection on multilocus was ruled out because the marker loci are selectively neutral.
Population admixture was ruled out because, in the cases discussed, the Ashkenazi are already the
population with the highest known frequency of these alleles; i.e. there is no known source population
with a higher frequency.
10. The genetic signature of recent positive selection on a locus is _______________.
e. Has been recovered from Stone Age skeletons that are approximately 20,000 years old.
12. Why did Maynard-Smith's model of sex present a paradox for evolutionary biology? Why does his
model not work in real life?
Correct answer: Maynard-Smith's model showed that if sexual and asexual reproduction result in
equal numbers of equally fit young for each female, then asexual reproduction has a large fitness
advantage because it results in twice as many grand-offspring. Therefore, most populations should end
up composed entirely of asexual reproducers. The paradox is that this has not happened - most
populations in the wild reproduce sexually. The solution lies in the fact that the assumptions of his
model must be wrong, particularly, the assumption that the offspring of sexual reproduction have the
same fitness as the offspring of asexual reproduction.
13. Which of the following accurately characterize(s) Muller's ratchet model for the selective
advantage of sexual reproduction?
Drift establishes linkage disequilibrium because multilocus genotypes with few mutations are
eliminated by chance events. All of the above correctly characterize Muller's ratchet model for
the evolution of sexual reproduction. Sex is favored selectively because it recreates the zero-
mutation genotypes lost due to drift. In populations without sexual reproduction, deleterious
mutations accumulate, eventually imposing such a burden that the population goes extinct.
All of the above correctly characterize Muller's ratchet model for the evolution of
Correct Answer: sexual reproduction.
Muller's ratchet is one of the ways in which sexual reproduction can gain an advantage over asexual
reproduciton. But notice that because of its reliance on drift and mutation, Muller's ratchet is a very
slow process.
14. Which of the following statements regarding sexual reproduction are true?
a. Is probably maintained in natural populations mostly because of its effect of breaking Muller's
ratchet.
c. Produces only half as many offspring per female, compared to asexual reproduction.
e. Causes genetic recombination via crossing-over, which combines genotypes from different parents.
f. Produces only half as many grand-offspring per female, compared to asexual reproduction.
15. Describe Andersson and Hughes' study of Muller's ratchet in bacteria. What features of their
populations might have increased the effect of Muller's ratchet? Approximately how many generations
reproduced during the experiment, and how many bottlenecks occurred? Were the results consistent
with the Muller's ratchet theory? Did Muller's ratchet affect most populations, and is it thought to be
the major reason for the dominance of sexual reproduction.
Correct Answer:
C
Andersson and Miller allowed 444 cultures of bacteria to grow for two months, with one bottleneck
every day during which each culture was reduced to a single individual. The combination of asexual
reproduction with frequent population bottlenecks was expected to cause Muller's ratchet to operate,
i.e., accumulation of deleterious mutations and consequently reduced fitness. At the end of the two
months, representing roughly 1700 generations and roughly 60 bottlenecks, all cultures were
compared to the wild-type strain. 5% of the experimental cultures had reduced fitness (reduced growth
rate) and none had increased fitness, so the result was consistent with Muller's ratchet. But since,
Muller's ratchet takes a very large number of generations to have an appreciable effect - and even then
the effect is small - it is not thought to be the major process favoring sexual reproduction.
16. Which of the following correctly characterize(s) the "changing environment" hypothesis for the
selective advantage of sexual reproduction?
a. Linkage disequilibrium is created because different multilocus genotypes are favored in under
different conditions.
b. Sexual reproduction is favored because it can create the new mutlilocus genotypes favored under
new environmental conditions.
c. Changing environments will favor asexually reproducing females because of their higher
reproductive rate.
17. From the end of this chapter: "There are two classes of models for sex. In the first class, genetic
drift creates linkage disequilibrium. Sex is then favored because it helps to re-create high-fitness
genotypes lost by drift. In the second class, natural selection creates linkage disequilibrium. Then the
pattern of selection changes, and sex is favored because it helps to re-create the now-favorable
genotypes recently selected against."
Refer to the paragraph above. Which of the following models or experimental results is an example of
the first class?
a. Muller's ratchet
18. From the end of this chapter: "There are two classes of models for sex. In the first class, genetic
drift creates linkage disequilibrium. Sex is then favored because it helps to re-create high-fitness
genotypes lost by drift. In the second class, natural selection creates linkage disequilibrium. Then the
pattern of selection changes, and sex is favored because it helps to re-create the now-favorable
genotypes recently selected against."
Reference the paragraph above in answering this question: By wyat class is sexual reproduction
thought to be maintained?
c. both
Both
Correct Answer:
The second class is suspected to act more quickly and have greater effects, but both are important.
19. Cancer is thought to arise when a cell accumulates an unlucky set of deleterious mutations, by
chance, that switches the cell from being a harmonious part of a multicellular body to being a
"parasite." Like true parasites, a dividing population of cancer cells uses materials and resources
entirely for their own advantage, disrupting the health and integrity of the rest of the body. In addition,
cancer cells have high mutation rates, and face a problem of a steady accumulation of deleterious
mutations. This can become so severe that some cancer populations die out simply due to their own
mutations - a Muller's ratchet effect.
Part I: Refer to the paragraph above in answering this question. In general, do parasites tend to
reproduce sexually or asexually? Why?
Part II: Refer to the paragraph above in answering this question. Do cancer cells reproduce sexually
or asexually? Would they gain any advantages if they switched from one mode of reproduction to the
either?
Part III: Refer to the paragraph above in answering this question. The most dangerous development in
a cancer is metastasis - formation of new cancer tumors in other organs. Metastasis requires
coordination of many genes involving cell-cell adhesion and cell movement. Recently it has become
clear that metastasis is associated with a peculiar tendency of cancer cells to fuse with nearby normal
cells, combining its genes with the genes of the other cell. Why does it make sense, evolutionarily, that
cancer cells do this?
Part I: Parasites tend to use sexual reproduction. Parasites live in the environment of their hosts'
bodies, which are constantly evolving to counteract the parasite. Since sexual reproduction gives an
advantage in changing environments, the speedily and constantly changing environment of a parasite-
host evolutionary arms race gives sexual reproduction a large advantage over asexual reproduction.
(This is the "Red Queen hypothesis" of parasite-host coevolution.)
Part II: Cancer cells generally reproduce asexually, by cell division. However, they should gain
advantages if they could switch to sexual reproduction. The genetic recombination could allow the
cancer cells to act as more successful parasites and evade the host's cancer-killing abilities. In addition,
genetic recombination would allow cancer cells to escape the Muller's ratchet caused by their tendency
to rapidly accumulate deleterious mutations.
Part III: Cell-cell fusion is analogous to sexual reproduction because it results in genetic
recombination. This is particularly useful for cancer cells, which often have such high mutation rates
that many of their genes are disabled. Fusion with a normal cell allows a cancer cell to regain
functional versions of many of these genes, and to combine them with certain unusual mutations, such
as those that allow evasion of cancer-killing processes. Note that cell-cell fusion allows cancer cells
both to avoid Muller's ratchet and also to survive as parasites in a changing environment. Hence, both
advantages of sexual reproduction are at work.
Interestingly, some work indicates that a fused cancer cell will metastasize not to any organ, but
specifically to the "home organ" of the cell that it fused with. This may be because the cancer acquires
actively transcribed genes that gave the normal cell the ability to recognize and adhere with other cells
of that organ.
20. Each graph represents one of Dunbrack et al's experimental populations of Tribolium beetles.
Correctly match each graph with the description of its experimental treatment.
Both A. C. Which
20 popula populatio
.4 tions n, red or
are black,
asexua has the
l; red advantag
beetles e in this
have a graph?
three- Which
fold should
reprod have the
uctive advantag
advant e in the
age. treatment
specified
by the
question?
Incorrect.