Molecular Evolution Practice Exam
Course Introduction
Molecular Evolution explores the mechanisms and patterns underlying genetic change at the molecular level across organisms. This course covers foundational concepts such as mutation, selection, genetic drift, recombination, and gene flow, examining how these processes drive the diversification of DNA and protein sequences. Students will analyze molecular phylogenies to trace evolutionary relationships, study the evolution of genomes and gene families, and learn about the molecular basis of adaptation and speciation. The course combines theoretical frameworks with current research, emphasizing methods for reconstructing evolutionary histories and interpreting molecular data in the context of evolutionary biology.
Recommended Textbook
Evolution 1st Edition by Carl T. Bergstrom
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Page 2
Chapter 1: An Overview of Evolutionary Biology
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Sample Questions
Q1) More than 100 years ago,Charles Darwin and his colleague Thomas Huxley hypothesized that humans share a common ancestor based on A)anatomical evidence.
B)fossil evidence gathered during Darwin's voyage on the HMS Beagle.
C)manipulative experiments.
D)All of the above
Answer: A
Q2) Which source(s)of data do evolutionary biologists use to test their hypotheses?
A)Molecular data
B)Morphological and behavioral data
C)Data from the fossil record
D)All of the above
Answer: D
Q3) How has artificial selection been used to shape the characteristics of food producing plants?
Answer: Answers will vary but should include increasing harvest yields and may include characteristics such as increased palatability or nutritional value.
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3
Chapter 2: Early Evolutionary Ideas and Darwins Insight
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Q1) While various religious leaders challenged almost all of Darwin's major conclusions, A)all early experimental evolutionists agreed with Darwin.
B)many British scientists embraced Darwin's ideas on evolution.
C)many British scientists rejected Darwin's proposed mechanism of natural selection.
D)B and C
Answer: D
Q2) To explain how varieties were on the path to becoming new species,Darwin introduced the concept of A)descent and modification.
B)variational change.
C)transformational change.
D)All of the above
Answer: A
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4
Chapter 3: Natural Selection
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Sample Questions
Q1) The 2000-2004 drought in California
A)shortened the growing season of the mustard plant.
B)led to earlier flowering in the mustard plant.
C)created selective forces that changed the characteristics of the mustard plant.
D)A and C
E)All of the above
Answer: E
Q2) Researchers studying variations in oldfield mouse coat color found that the light coat color of many beach populations was due to a
A)mutation in the Mc1R protein, which reduces the ability of a-MSH to bind.
B)mutation in the regulatory region of the Agouti gene, which increases ASP expression.
C)reduction in eumelanin production.
D)All of the above
Answer: D
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Chapter 4: Phylogeny and Evolutionary History
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Q1) Which of the following pairs correctly matches the phylogenetic tree type (1,2,or 3)with the information it represents (i,ii,or iii).
1)Cladograms
2)Phylograms
3)Chronograms
i.A tree with aligned branch tips that indicates only the evolutionary relationships among the taxa shown
ii.A tree in which branch lengths represent actual time rather than the amount of evolutionary change
iii.A tree in which branch lengths represent the relative amount of evolutionary change
A)(1-i),(2-ii),and (3-iii)
B)(1-i),(2-iii),and (3-ii)
C) 1-ii),(2-i),and (3-iii)
D)(1-ii),(2-iii),and (3-i)
Q2) In what ways do the processes of reconstructing phylogenetic trees and mapping evolutionary events onto trees generate hypotheses?
Q3) What are the differences between rooted and unrooted phylogenetic trees?
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Chapter 5: Inferring Phylogeny
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Q1) Why is phylogenetic inference a difficult and computationally intensive problem? What solution do evolutionary biologists use to address this problem?
Q2) How many unrooted trees are possible for five species?
A)15
B)25
C)5
D)105
Q3) Why do some evolutionary biologists have philosophical concerns about using distance methods to construct evolutionary trees?
Q4) Long-branch attraction is
A)the inferring of too close a relationship between rapidly evolving species or populations.
B)the inferring of too close a relationship between slowly evolving species or populations.
C)a method for inferring phylogentic ancestry of rapidly evolving clades.
D)a method for inferring phylogenetic ancestry of slowly evolving clades.
Q5) Does the Fitch algorithm indicate the most likely character states for the ancestral node?
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Chapter 6: Transmission Genetics and the Sources of
Genetic Variation
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Q1) In a _________ mutation,part of a chromosome is transferred to a nonhomologous chromosome.
A)deletion
B)inversion
C)translocation
D)fission
E)fusion
Q2) RNA that directs protein synthesis is called
A)ribosomal RNA.
B)microRNA.
C)messenger RNA.
D)transfer RNA.
E)translation RNA.
Q3) Which of the following statements regarding the difference between RNA and DNA is true?
A)Only RNA uses guanine.
B)Only RNA uses cytosine.
C)Only RNA uses adenine.
D)Only RNA uses uracil.
E)Only RNA uses thymine.
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Chapter 7: The Genetics of Populations
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Q1) What is the frequency of homozygous individuals in a Hardy-Weinberg population that experiences inbreeding expressed in terms of the frequencies of alleles (p,q)and the value of F.
Q2) In pocket mice,possession of the D allele at the Mc1R locus confers dark coloration and homozygous d individuals are light in color.Why would one expect to see more D alleles in a population living on lava?
Q3) List five assumptions of the Hardy-Weinberg equilibrium.
Q4) Mating preferences drive assortative mating
A)all of the time.
B)none of the time.
C)some of the time.
D)every other time.
E)in selfing plants.
Q5) Pacific salmon hatch in streams and grow up out in the Pacific Ocean.At the end of their life,they mate once then die.Assuming that not all salmon survive life in the ocean and that those who do survive produce equal numbers of offspring,this would be an example of _________ selection.
Q6) Lifetime fitness,as demonstrated by Cummings et al.'s work on sunflowers,is dependent on what two components?
Page 9
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Chapter 8: Evolution in Finite Populations
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Sample Questions
Q1) Please describe the allele substitution rate in terms of the effective population size (N ),the number of neutral loci in the population (k)and mutation rate (n).Please show all of your work.
Q2) One consequence of genetic drift is
A)increasing heterozygosity in the population.
B)the maintenance of multiple alleles across long periods of time.
C)that populations diverge in terms of their allele frequencies.
D)that populations maintain the same set of alleles through time.
E)All of the above
Q3) Population bottlenecks can lead to the fixation or loss of alleles in otherwise large populations because the bottleneck
A)selectively eliminates or fixes alleles.
B)reduces the effective population size to close to the size of the bottleneck.
C)allows migrant alleles to overwhelm native alleles.
D)A and B
E)All of the above
Q4) What are the observed and expected heterozygosities in a population that has three genotypes with the following occurrences: f(A A )= 100,f(A A )= 25,f(A A )= 100.
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Chapter 9: Evolution at Multiple Loci
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Q1) If recombination between locus A and locus B is 0.15,and the initial value of linkage disequilibrium is 0.20,what will the value of linkage disequilibrium be after one generation of recombination? Show your work.
Q2) Explain why a population may never reach its most fit phenotype.
Q3) In Lake Malawi cichlid fish,one can observe two color variants,Black Barred (BB)and Orange Blotch (OB).Sex in these fish is not determined by a sex chromosome but by a gene on an autosome,which produces either males or females.Both of these phenotypes are controlled by one biallelic locus each.OB females have a selective advantage in terms of their survivability: The OB phenotype allows females to blend into their background.OB males have a selective disadvantage because their reproductive coloration is disrupted and they have little mating success.How would this process influence the association of alleles at the color locus and sex determining locus?
Q4) In a population of dragonflies,wing structure is determined by two loci (A,B),each with two alleles (Aa,Bb).Abnormal wings are produced in aa individuals unless they possess at least one B allele.This is an example of
Q5) Why would we expect genotypic adaptive landscapes to have rugged contours?
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Chapter 10: Genome Evolution
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Q1) A bacteriophage was the first organism to have its genome sequenced.Sequencing of this genome was facilitated by
A)its complex genome.
B)its short genome.
C)previous studies of bacterial genomes.
D)A and C
E)All of the above
Q2) A limitation of examining Ka/Ks ratios is that they
A)are sensitive to demographic changes.
B)cannot be used in introns.
C)can only detect positive selection.
D)cannot detect drift.
E)None of the above
Q3) Syntenic dot plots are useful when
A)comparing gene orders in prokaryotes.
B)identifying inversions.
C)examining genomic evolution.
D)A and B
E)All of the above
Q4) Explain how horizontal gene transfer is different than sexual reproduction.
Page 12
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Chapter 11: The Origin and Evolution of Early Life
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Q1) How does comparative data on genes of extant species help us to make estimates of what happened before the phylogenetic event horizon?
A)Common genes must have existed for a long time.
B)If the first life-forms consisted of RNA, then current RNA-coding genes must be the ancestral genes.
C)Common functional genes imply the minimal characteristics of early cells.
D)Because so many small genome bacteria are endosymbionts, the earliest cells must have been endosymbionts.
Q2) Ribozymes are
A)capable of replicating RNA.
B)capable of copying RNA into DNA.
C)proteins.
D)RNA enzymes.
Q3) Encapsulation of a hypercycle would not be favored when A)the costs of a membrane exceed the benefits of the cycle.
B)the membrane provides a defensive mechanism.
C)natural selection favors mutations in component members.
D)RNA components act through molecular mutualism.
Q4) What does the abbreviation LUCA stand for and what is it?
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Chapter 12: Major Transitions
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Sample Questions
Q1) The chemical signal for slime mold amoebas to aggregate is A)cAMP.
B)cGMP.
C)cCMP.
D)cTMP.
Q2) What are apicoplasts,and what is the advantage of using them as a drug target for the treatment of malaria?
Q3) Which of the following is not a reason that volvocine algae are ideal for studying the evolution of individuality?
A)They transitioned to multicellularity relatively recently.
B)Within the group, there are multiple, separate transitions to germ and soma lines.
C)The group exhibits extensive variation in their degree of multicellularity.
D)They readily form aggregate slugs.
Q4) Why does genetic imprinting inhibit parthenogenesis?
Q5) Why do the benefits of group living focus on foraging and predation?
A)Reproduction is irrelevant for the fitness of individuals in a group.
B)Individuals in groups always forage and are vigilant together.
C)Groups only exist for foraging and anti-predator behavior.
D)Much of an organism's time is spent foraging and avoiding predators.
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Chapter 13: Evolution and Development
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Q1) How can changes in genetic enhancers affect morphology?
Q2) How does facultative neoteny in other species support the paedomorph advantage hypothesis for axolotls?
Q3) The idea that life evolves from simple to complex began with A)Darwin.
B)William Bateson.
C)the ancient Greeks.
D)J. F. Meckel.
E)Etienne Serres.
Q4) A totipotent cell
A)is fixed into a single developmental pathway.
B)has homeotic transformation.
C)can differentiate into any adult cell.
D)will become a stem cell.
Q5) What is meant by the colinearity of Hox genes?
Q6) How can natural selection lead to the loss of a gene duplication?
Q7) If paedomorphosis via neoteny involves the retention of juvenile traits in adults,what is responsible for paedomorphosis via progenesis?
Q9) Does all life evolve from simple to complex? Explain. Page 15
Q8) What evidence suggests that MADS-box genes are older than flowers?
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Chapter 14: Species and Speciation
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Q1) Suppose that we find an example of the peripheral isolate model of allopatric speciation in which a species pair results.One species is the progenitor,and one is the derivative species.How will these two species differ in geographical distribution,genetic diversity,and allele sharing?
Q2) In the past,many hominins coexisted,such as Paranthropus robustus and Paranthropus boisei.Imagine that these species were not prezygotically isolated and occasionally formed hybrids.Why might sterility or inviability of hybrids be limited to one sex? In which sex would this occur,and what pattern does this represent?
Q3) How might secondary contact result in a cline?
A)Reproductive character displacement completes the speciation process.
B)Hybrid matings may have low fitness.
C)Reproductive isolation is partially complete and a spatial gradient of hybrids forms.
D)Reproductive isolation is incomplete and the two populations form a single species without spatial variation.
Q4) What is the advantage of using DNA sequences from many genes to reconstruct the evolutionary history of humans?
Q5) How can reproductive isolation in plants be mediated through pollinators?
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Page 17
Chapter 15: Extinction and Evolutionary Trends
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Q1) What effect of mass extinctions is described by the expression "dead clade walking"?
Q2) The earliest Homo sapiens fossils are about 200,000 years old.Could you use radiocarbon dating to determine the age of fossils from that period? Briefly justify your answer.
Q3) Which mass extinction led to the disappearance of the dinosaurs?
A)K-T mass extinction
B)Triassic mass extinction
C)Permian mass extinction
D)Devonian mass extinction
Q4) What is the hallmark trait of aquatic organisms that survived the Permian extinction?
A)They lived in shallow seas.
B)They were exceptionally small.
C)None of them inhabited reefs.
D)They were able to withstand anoxic conditions.
E)All of the above
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18
Chapter 16: The Evolution of Sex
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Q1) Are there any costs when asexual organisms reproduce automictically as opposed to apomictically?
A)Yes, recombination may disrupt coadapted gene complexes.
B)Yes, recombination is the cause of the twofold cost of sex.
C)No, both are forms of asexual reproduction.
D)No, recombination will produce better adapted individuals.
E)C and D
Q2) The Amazon molly,Poecillia formosa,is a freshwater fish that is gynogenetic.In order to reproduce,individuals of this all-female species must mate with a male from a closely related species to initiate the development of their offspring.The male's genetic material does not,however,enter the Amazon molly's egg.What costs of sexual reproduction does the Amazon molly potentially experience?
A)None. It reproduces asexually.
B)The costs associated with finding a mate.
C)The fish may spend energy competing with other females for mates.
D)It has no means of turning back Muller's ratchet.
E)B and C
Q3) What are the two immediate benefits to sexual reproduction in unpredictable environments,according to Kondrashov?
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Page 19
Chapter 17: Sexual Selection
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Q1) To study sperm competition in beetles,you sample a population that is effectively monogamous,as chances of meeting more than one mating partner in nature are extremely low.In the lab,you pair multiple individuals to create a polygamous mating system,but you also maintain a monogamous control line.Would you expect sperm competition in the polygamous line to increase,decrease,or remain the same relative to the monogamous control line (assuming there was heritable variance for this trait in the population)?
Q2) _________ first proposed sexual selection as an evolutionary mechanism.
A)Maynard-Smith
B)Darwin
C)Aristotle
D)Fisher, Haldane, and Wright
Q3) Must sexually selected traits be "honest indicators" under the runaway sexual selection model?
A)Yes, traits under sexual selection always must be costly.
B)No, female preference alone is sufficient under runaway selection.
C)Yes, otherwise genetic linkage could not be established.
D)No, the model only requires female preference and male traits are coded on the same chromosome.
E)B and C
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Chapter 18: The Evolution of Sociality
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Q1) In an analysis of independent contrast,researchers found that fetuses in polyandrous species of primates had faster growth rates than those in monogamous species.What did the researchers conclude from these results?
A)Fetuses develop faster to "make room" for offspring from a different male.
B)Extracting more resources from the mother maximizes offsprings' inclusive fitness in polyandrous species.
C)Fast fetal growth rates are always optimal.
D)Fetal growth rates represent phylogenetic constraints and are unrelated to mating systems.
Q2) Why does conflict arise between different alleles at the same locus even though they are part of a single individual's genome?
Q3) Allele X codes for a cooperative behavior among full siblings.Recipients of this behavior receive a benefit of 7 fitness units,and the behavior costs the donor 3 fitness units.Use Hamilton's rule to determine whether allele X will spread in the population.
Q4) Name the three familial conflicts.
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21
Chapter 19: Coevolution
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Q1) Is any form of adaptation coevolution?
A)Yes, evolution always happens in response to environmental change.
B)Yes, other species are always part of an organism's environment.
C)No, only evolution as an action-reaction response to a selection pressure imposed by interacting organisms on each other qualifies as coevolution.
D)No, coevolution is by definition limited to mutualistic interactions.
Q2) Which of the following differs between intra- and interspecific interactions when it comes to the evolution and maintenance of cooperation?
A)Interacting partners from different species are not linked by inclusive fitness.
B)We cannot apply game theory to interspecific systems.
C)Cooperative interactions cannot shift into antagonistic ones in intraspecific systems.
D)All of the above
Q3) How can cultural transmission of male songs facilitate the early stages of species formation in Darwin's finches?
Q4) Name two forms of antagonistic coevolution.
Q5) Define "obligate mutualism" in one sentence.
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Chapter 20: Evolution and Medicine
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Q1) Under which hypothesis may pathogens ultimately be responsible for the evolution of sexual reproduction in multicellular organisms?
A)Good genes hypothesis
B)Red Queen hypothesis
C)Mutation accumulation hypothesis
D)Rate-of-living hypothesis
Q2) Which part of the immune system's "learning system" is responsible for maintaining life-long immunity against measles after a measles infection?
A)Somatic recombination
B)Affinity maturation
C)Clonal expansion
D)Retention of responding cells
Q3) Why is there no lifelong vaccine protection against flu as there is by a measles vaccine?
A)The variety of flu strains is too great to be captured by a single vaccine.
B)Flu can escape host immunity by evolving new variants that re-infect hosts.
C)The flu is too virulent to effectively vaccinate against.
D)The antigenic memory against flu has a short half-life.
Q4) Name three methods that pathogens use to subvert their host's immune system.
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