Download Biology 4154/5154

Biology 4974/5974
D. F. Tomback
Fall 2013
Name____Key______________100 points
Evolution: Exam #2
You have the lecture period to complete the exam and may leave the class after turning it in.
Please answer questions in pen. Make sure that you read all questions carefully before answering
them. Make sure that answers are written in complete sentences on short essays. Points will be
taken off for misspelling terminology or names discussed in lecture. More than one answer is
possible for multiple choice questions. Please keep your eyes on your own paper.
Part I. Synthesis questions
1. (4 pts) Name the fundamental genetic mechanisms that result in evolution (changes
in allele frequencies) within a population over time. 1 pt each
a. natural selection
b. mutation
c. gene flow (migration)
d. genetic drift
2. (5 pts) Compare and contrast the effects of inbreeding vs. genetic drift over time
within a population on the following:
a. Allele and genotype frequencies (3 pts)
In inbreeding, allele frequencies stay the same, but there is a loss of
heterozygotes and a gain of homozygotes in proportion as determined by F.
In genetic drift, allele frequencies change over time, leading to a change as well in
genotype frequencies.
b. Maintaining heterozygosity and genetic diversity over time (2 pts)
Both result in a loss in heterozygosity over time: In inbreeding, there is a loss of
heterozygosity as populations becomes more inbred over time. This can lead to
expression of deleterious alleles.
In genetic drift, by chance an allele may become lost or fixed, resulting in a
decline in genetic diversity and a loss of heterozygosity as well.
3. (6 pts) a) Explain the steps in the process of sympatric speciation also known as
ecological speciation. Start with one large population. (3 pts)
 At the beginning there is one population with free interbreeding.
 There may be more than once condition within the population, and different
phenotypes may be adapted to different conditions (e.g., host plant or
environment).
 Increasing genetic divergence occurs through reduced gene flow, and
hybrids become disadvantaged.
 Assortative mating and selection against hybrids starts further reducing
gene flow.
 Speciation is complete when reproductive isolation is achieved.
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b. Use the events described for sockeye salmon in the Hendry et al. paper, “Rapid
evolution of reproductive isolation in the wild: evidence from introduced salmon” to
provide examples of steps in this process. (3 pts)
 Salmon introduced to Lake Washington (1937 to 1945), which resulted in a
breeding population in Cedar River.
 New population breeding along a beach in Lake Washington in 1957.
 Different phenotypes selected by the river vs. beach environment.
 Hybrids selected against because of reproductive disadvantage (females
more successful if longer if breeding in river, and shorter at beach), males
more successful if more slender in river but if greater body depth along
beach).
 Reproductive isolation occurring (with reduced gene flow) with assortative
mating. This has happened in about 13 generations.
 Salmon not distinct species yet, because the two populations are not
completely reproductively isolated.
4. (5 pts) a) Homeobox gene 1 (Prox 1) controls sensory organ development in animals.
Explain how the upstream regulatory gene Sonic hedgehog (Shh) can produce two
morphs of the Mexican tetra fish, a cave and a surface form, as a result of differing
response from two organ systems. (3 pts)
 If the Shh gene is expressed, it creates the cave morph with suppressed
eye development but greater olfactory ability and more sensitive lateral line
organ development.
 If the Shh is knocked out, it creates a surface morph with good eye
development but less olfaction and less lateral line development.
b) What if Shh expression in this fish were environmentally-triggered? Does this
provide a mechanism of phenotypic plasticity? Explain (hint: example of the North
American Emerald Moth caterpillar with two morphs). (2 pts)
 True phenotypic plasticity would mean that in cave environments, cave
morphs developed and outside of caves, surface morphs developed.
 This would mean that Shh would be expressed in caves but not strongly
expressed outside of caves.
Part II. Lecture concepts
1. (3 pts) a) In general, why do many scientists think that RNA was the first major
molecule involved in the origin of life, as opposed to proteins? What can RNA do?
Some general statement about RNA is helpful here, such as it can act both as a
template and also as a catalyst (1 pt). Some scientists think that the first molecule
had to be self-replicating.
Provide at least two of the following examples, which are the best arguments,
although RNA does more.
 RNA can catalyze its own replication without protein enzymes
 RNA can bind ATP for energy.
 RNA can form peptide bonds.
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


Introns in m-RNA and nuclear RNA are self-splicing.
“Ribozymes” cleave phosphoester bonds of RNA.
RNA can catalyze the cleavage of an amide bond.
2. (2 pts) Which of the following provides evidence for the endosymbiosis hypothesis
explaining the origin of mitochondria? 3 answers for 2 pts.
a. Mitochondria have their own DNA and ribosomes like prokaryotes.
b. Mitochondrial DNA in eukaryotes generally includes all genes found in most
prokaryotes.
c. The primitive amoeba Pelomyxa and other protozoan species have
prokaryote symbionts.
d. The mitochondrial genome of the freshwater protozoan Reclinomonas
americana resembles the genome of a rickettsia-like bacterium.
e. Mitochondria are capable of living independently of eukaryotic cells.
3. (3 pts) Briefly explain the evolutionary significance, if any, of
a. gene duplications: At the minimum, more product may be produced, or
isozymes may evolve, or it frees one copy of a gene to evolve to have a different
function (neofunctionalization).
b. chromosomal inversions and translocations: Can be a step in reproductive
isolation between populations in the speciation process.
c. missense point mutations: Results in a new amino acid in a polypeptide
sequence. Can result in altered protein function or new function.
4. (2pts) Which gene regulation mechanisms are “pre-transcriptional”?
a. RNA editing
b. cis regulation
b. trans regulation
c. prokaryote operons d. RNA degradation e. none of the above
Fig. 17-11
5. (4 pts) What is the relationship between Homeobox gene number and developmental
complexity and specialization along the anterior-posterior body axis that can be
deduced from this figure?
There are two trends in changes in Homeobox genes with complexity: a single
set with increasing number caused by gene duplications, and multiple sets of the
same Homeobox genes. A basic set of Homeobox genes has been reconstructed
for the hypothetical ancestor. The more complex the body form along the a-p
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axis, the greater the number of the basic single set of Homeobox genes.
Amphioxus has more genes than Drosophila. In contrast, the mouse, the most
complex animal here, shows multiple sets of the basic Homeobox genes.
6. (3 pts) Calculate gene frequencies of the following:
98AA + 84Aa + 18aa = 200 individuals. (Hint: you need to know the number of total
genes. You can do these calculations without a calculator.)
Total genes = 200 x 2 = 400.
A: [(98 x 2) + 84]/400 = 280/400 = 0.7
a: [(18 x 2) + 84]/400 = 120/400 = 0.3
7. (4 pts) Explain the adverse effects of inbreeding, as demonstrated by the following
examples:
a) Song sparrow survival vs. death on Mandarte Island during a severe winter. (2 pts)
The less inbred Song sparrows survived whereas the more inbred individuals
died. This suggests that the more inbred birds were not as well adapted.
b) Declining hatching success and low genetic variation in isolated populations of the
Greater Prairie Chicken in Illinois. Why? How were the populations “rescued”? (2 pts)
These populations were suffering from inbreeding, which affects reproduction
because of widespread expression of deleterious alleles. Introducing new nonrelatives increased heterozygosity in one generation.
8. (4 pts) a) Draw a graph and illustrate what happens to the normal curve for a trait
over time under stabilizing (normalizing selection). (2 pts.)
b) Briefly describe one example from lecture illustrating stabilizing selection. (2 pts)
Three examples were given:
 House sparrows that survived a severe storm had measurements around
the mean.
 Human birth weights showed selection for around 8 lbs.
 Larvae in gall-making flies induce galls of an intermediate size to avoid bird
predation at the large extreme and parasitoid wasps at the small extreme.
9. (3 pts) a) What are the two mechanisms that result in sexual selection?
The two mechanisms are female choice of male and also male-male competition.
Sometimes males also select certain females as well. (2 pts)
b) How does kin selection work from the genetic perspective?
An altruistic behavior by one individual saves multiple individuals with the same
genes as the altruist, resulting in these individuals reproducing and contributing
shared genes to the next generation. This is another way an individual can make
a genetic contribution.(1 pt)
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10. (2 pts) If the fitness W of the AA genotype is 0.8, what is the selection value s?
The s value is 0.2.
11. (2 pts) For which of the following allele types can allele frequency go to zero (p = 0)
in one generation?
a. recessive lethal allele
b. dominant lethal allele
c. dominant lethal allele at high frequency d. neutral allele
e. all of the above
12. (3 pts) a) What is the Red Queen hypothesis?
The Red Queen had to keep in moving to stay in place. This is used as a
metaphor to suggest that species must evolve constantly to maintain the status
quo. In other words, they must evolve to stay up with the coevolutionary “arms
race” in ecological interactions and adaptation to a changing environment. (2 pts)
b) What are the implications of the Red Queen hypothesis for all species?
All species are constantly evolving to maintain their place in the biotic and abiotic
environment. (1 pt)
13. (2 pts) ^q = u/(u + v) ^p = v/(u + v) Which best describes these equations?
a. frequencies of alleles A and a based on relative gene migration.
b. equilibrium frequencies of alleles A and a due to genetic drift
c. relative frequencies of alleles A and a dependent on their respective fitness
values W
d. equilibrium value of two alleles maintained by heterozygote advantage
e. equilibrium frequencies of two neutral alleles of a gene based on relative
mutation rates.
14. (2 pts)
a) What process is illustrated here?
The process is genetic drift.
b) For the curve representing populations of
1000 individuals, why is the curve shaped
so it goes up at the extreme ends? What is
happening in these populations?
This population size has a high probability
of either losing the allele as q approaches
0 at the left end, or of fixation of the allele
as q approaches 1.0 at the other end.
(This is not disruptive selection. That is a
very different process dealing with
phenotypic differences and not allelic
differences. In genetic drift, NO selection
is involved.)
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15. (3 pts) These questions refer to Wright’s Adaptive Landscape Theory and Shifting
Balance Theory: a) What genetic mechanism moves a deme off an adaptive peak?
Genetic drift is the major mechanism that moves a population off an adaptive
peak. (1 pt).
b) What kinds of genetic changes can move a deme further down a peak, across a
valley, and then up a new adaptive peak?
Genetic drift, migration in of new allelic variation, and mutation can further alter
gene frequencies leading a deme down a peak and across the valley of
“nonadaptation”. Natural selection moves the deme up a new adaptive peak. (2
pts)
16. (3 pts) What are the three types of ecological interactions that result in
coevolution?
a. competition
b. mutualism
c. predator-prey interaction
17. (2 pts) The figure below depicts an example of
a. competitive exclusion
b. resource partitioning
c. character displacement
d. mutualism
e. none of the above
18. (3 pts) a) What is the key difference between the
initiation of allopatric speciation and sympatric
speciation?
In allopatric speciation, there is a geographic
barrier that immediately prevents gene flow. In
sympatric speciation, another mechanism, such as
hybrid inferiority or assortative mating, leads to
reduced gene flow. (1 pt)
b) Why are populations with phenotypic plasticity good
candidates for sympatric speciation?
When a population has phenotypic plasticity or
more than one reaction norm, different phenotypes
may be selected in different biotic or abiotic
environments. This can lead to sympatric
speciation. (2 pts)
19. (4 pts) Identify the significance of the following as it pertains to class material:
a. hawthorn fruits vs. apples: These were the two foods of the North
American fly (apple maggot) that is undergoing sympatric speciation, producing a
phenotype that specializes on hawthorn fruits and one that specializes on apples.
( 2pts)
b. Pharyngeal jaws: This was the morphological adaption in cichlids that led
to rapid adaptive radiation since the Pleistocene in Lake Victoria and elsewhere.
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This is a second set of jaws that varies with diet, resulting in many feeding
niches. (2 pts)
20. (2 pts) Speciation between contiguous but non-overlapping populations.
a. peripatric speciation
b. allopolyploidy
c. parapatric speciation
d. sympatric speciation
e. none of the above
21. (3 pts) What is the main difference between prezygotic and postzygotic isolating
mechanisms?
Prezygotic prevents mating with the wrong species (1 pt) whereas postzygotic
isolation is in effect after mating has occurred. (2 pts)
Prezygotic isolating mechanisms, such as courtship behavior, season, or habitat,
prevents interbreeding between two species, so mistakes are not made.
Postzygotic isolation comes from genetic incompatibility, which arises after
mating has occurred and a mistaken choice has been made.
22. (2 pts) In peripatric speciation, what processes change the genetic make-up of the
small, founding population?
A variety of genetic mechanisms can work in these small populations to alter the
genetic make-up. These include genetic drift, mutation, chromosomal
rearrangements, inbreeding, but also natural selection in a different environment.
Part III. Concepts from supplemental reading
1. (3 pts) K. Willmore, “Development influences evolution.”
Explain the developmental changes implied by the processes of a) heterochrony and b)
heterotopy.
Heterochrony refers to a change in the timeframe of a developmental event,
whereas heterotopy refers to a change in the location in the embryo of a
developmental event.
2. (6 pts.) F. Gould, “The evolutionary potential of crop pests.”
a) Was rotating crops between corn and soybeans a success in defeating the
northern corn rootworm in Illinois? Why or why not?
No, this was not successful, because a proportion of the corn rootworm
population evolved extended diapause, remaining dormant for another year. (4
pts)
b) According to mathematically modeling, under which of the following conditions did
the multi-toxin approach most successfully slow the evolution of genetic resistance:
1. Genetic inheritance pattern of resistance?
Recessive inheritance of resistance slowed the evolution of toxin resistance (1
pt).
2. Percent of susceptible plants?
A 30% mixture of susceptible plants among the plants with toxin-producing
plants delayed the evolution of resistance the most (1 pt).
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3. (6 pts) S. Carroll, Endless forms most beautiful, chapters 2 and 3.
a) How did the discovery that the same genes controlled development in flies, worms,
and humans (and all other animals) shake up evolutionary thinking?
This ran counter to the prevailing view of the modern evolutionary synthesis. It
was thought that different animal groups had entirely different gene complexes
guiding development and coming up with the same solutions. (3 pts)
(Please note that the discovery of Homeobox genes is another and a major form
of evidence for descent with modification and unification by common ancestor of
ALL animals! Talk about a major find for evolution! Just like “frozen accident” of
the genetic code, the homeobox genes are a highly conserved set of genes that
shape but also limit the forms of animal life. )
b) How did the discovery of Drosophila homeotic mutants (“Frankenflies”) lead to a
revolution in embryology?
Homeotic mutants in Drosophila caused the wrong structure to develop in a
particular location. Each was the result of a single mutation. By finding the genes
involved, scientists started piecing together the developmental toolkit, and
understanding the gene regulation role of the homeodomain. (3 pts).
4. (4 pts) The preceding table is from the Hendry et al. paper. D in the table is Nei’s
genetic distance and GD is based on a statistical test, with the P value shown.
a. Based on this table, is there genetic evidence for genetic differentiation between
salmon groups? If so, which groups? Justify your statement with the appropriate
numbers.
Yes, river residents are genetically differentiated from beach residents, and beach
residents are genetically differentiated from beach immigrants. (2 pts)
b. What possible role did fish morphology play in reducing gene flow?
Beach residents apparently discriminated against beach immigrants as mates.
Beach females preferred the deeper body shape of beach males, and beach males
may have preferred the shorter body length of beach females. ( 2 pts)
Regardless, there were differences in morphology between river residents and
beach residents; the immigrants were in between. These differences may have
reduced gene flow, which was demonstrated by recursive models.