Phylogenetics Exam Solutions
Course Introduction
Phylogenetics is the study of evolutionary relationships among biological entities, often species, individuals, or genes. This course covers the principles and methods used to infer these relationships, including the construction and interpretation of phylogenetic trees, molecular sequence analysis, and the use of computational tools. Students will explore models of DNA and protein evolution, methods for tree building (such as maximum parsimony, maximum likelihood, and Bayesian inference), and practical applications in comparative biology, systematics, and epidemiology. Emphasis is placed on both theoretical foundations and hands-on analysis using real biological data sets.
Recommended Textbook
Evolutionary Analysis 5th Edition by Jon C. Herron
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Chapter 1: A Case for Evolutionary Thinking: Understanding HIV
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Q1) What is the molecular mechanism by which reverse transcriptase inhibitors,such as AZT,prevent viral replication?
Answer: These molecules are analogues of the nucleotide building blocks of DNA,and typically prevent binding or elongation of the of the transcribed DNA molecule.
Q2) The proteins that enable the HIV virus to bind to cells are typically CD4 and CCR5.On what type of cells are these proteins typically observed?
A) plasma cells
B) dendritic cells
C) effector helper T cells
D) memory helper T cells
E) both C and D
Answer: E
Q3) In what host cell protein is the 32 mutation found,and what type of mutation is this?
Answer: The 32 mutation is found in the CCR5 coreceptor on CD4 helper T cells,and is a 32-base pair deletion.
Q4) What does the acronym AIDS stand for?
Answer: Acquired Immune Deficiency Syndrome
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Chapter 2: The Pattern of Evolution
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Q1) The age of the Earth is estimated at 4.6 billion years.When are the first unicellular organisms thought to have evolved on Earth?
Answer: 3.2 to 3.4 billion years ago
Q2) On what basic physical principle does radiometric dating rely?
Answer: Unstable isotopes decay into either other elements or different isotopes of the same element.Each isotope decays at a constant rate,and the resultant half-life can be used to estimate the age of rocks and once-living materials.
Q3) After several generations of selectively breeding mice in a laboratory,Ted Garland and his colleagues established populations of mice that voluntarily chose to run great distances on exercise wheels.The process of establishing these populations of mice is termed ________.
A) natural selection
B) artificial selection
C) population selection
D) experimental selection
E) random selection
Answer: B
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Chapter 3: Evolution by Natural Selection
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Q1) Beginning around 1930,the ________ [two words] developed as a reformulation of Darwinian natural selection based on the ways in which knowledge in genetics has informed us about heredity.
Answer: modern synthesis
Q2) Before Mendel's work was rediscovered,some argued that natural selection would not work because favorable traits would merge into existing traits over time and become lost.This hypothesis is known as ________.[two words]
Answer: blending inheritance
Q3) ________,in general terms,is an individual's ability to survive and reproduce. Answer: Fitness
Q4) Which of the following U.S.Supreme Court decisions struck down laws prohibiting the teaching of evolution?
A) The State of Tennessee v. John Thomas Scopes, 1925
B) Epperson v. Arkansas, 1968
C) Edwards v. Aguillard, 1987
D) Tammy Kitzmiller, et al. v. Dover Area School District, et al., 2005
Answer: B
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Chapter 4: Estimating Evolutionary Trees
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Q1) The wings of bats and birds and the streamlined body form of sharks and whales represent examples of ________.
A) convergence
B) reversal
C) outgroups
D) a clade
Q2) A(n)________ [two words] is a novel feature that evolved in a lineage and may be unique to a species or shared among species.
Q3) An ancestor and all of its descendants are known as a monophyletic group or a(n)________.
A) apomorphy
B) plesiomorphy
C) synapomorphy
D) clade
Q4) A preexisting,ancestral character is also known as a(n)________.
A) apomorphy
B) plesiomorphy
C) synapomorphy
D) clade
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Chapter 5: Variation Among Individuals
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Q1) What does one call a mutation that occurs in a DNA sequence that changes the amino acid specified by that sequence?
Q2) An organism that develops different phenotypes in different environments is said to exhibit what trait?
Q3) Which of the following is NOT one of the types of variation that occurs within individuals?
A) genetic variation
B) environmental variation
C) normalizing variation
D) genotype-by-environment variation
Q4) Explain the function of retroposition (retroduplication)in gene duplication.Describe the cellular mechanism used for this method of gene duplication,and the manner in which these typically nonfunctional pseudogenes can become active,functional genes.
Q5) Organisms that exhibit different phenotypes in different environments are said to exhibit phenotypic plasticity.Using the tobacco hornworm,Manduca sexta,studied by Suzuki and Nijhout,describe the experiments done to illustrate the dependence of color on temperature.Be sure to explain the importance of using reaction norms in this type of study.
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Chapter 6: Mendelian Genetics in Populations I: Selection and Mutation
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Q1) The Hardy-Weinberg equilibrium principle is known as the null hypothesis.List the five assumptions that are required for a population to be in Hardy-Weinberg equilibrium.
Q2) The point at which the rate that a deleterious allele is being eliminated from a population by natural selection is in equilibrium with the rate at which the deleterious allele is being replaced by a new mutation is termed ________.
A) mutation-dependent selection
B) frequency-dependent selection
C) mutation-dependent equilibrium
D) mutation-selection balance
Q3) Cystic fibrosis in humans is caused by a recessive loss-of-function mutation in a locus on chromosome 7 that encodes for a protein called ________.[five words]
Q4) Chun-Hong Chen and colleagues (2007)designed a new gene that would carry a strong selective advantage and confer the resistance to malaria on free-living mosquitoes.What was the acronym given this gene,and what does the acronym stand for?
Q5) Two processes that can maintain rare or deleterious alleles in populations are ________ [four words] and ________.[two words]
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Chapter 7: Mendelian Genetics in Populations II: Migration, Drift,
& Nonrandom Mating
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Q1) Although most of the mechanisms of evolution are nonrandom,the one that is absolutely random is ________.
A) sexual selection
B) natural selection
C) artificial selection
D) genetic drift
Q2) The survival and fertility rates of the offspring of related individuals are commonly reduced.This is known as ________.[two words]
Q3) Compare and contrast natural selection with genetic drift as mechanisms of evolution.
Q4) Suppose a large population exists on a continent,and a new population is formed by the migration of a few individuals to an island some distance away.The fact that the alleles being carried to this island are not going to be a complete and representative set,as compared to the continental population,is a case of genetic drift known as the ________.[two words]
Q5) ________,the most common type of nonrandom mating,will not change allelic frequencies,but it will change genotypic frequencies toward homozygosity.
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Chapter 8: Evolution at Multiple Loci: Linkage and Sex
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Q1) When genotypes at one locus of a chromosome are nonrandomly associated with the genotypes at another locus of the same chromosome,the two loci are ________.
A) in linkage equilibrium
B) in linkage disequilibrium
C) nonrandomly associated
D) None of the above.
Q2) Besides selection on multilocus genotypes,there are two other mechanisms that can create linkage disequilibrium.What are they?
Q3) Which of the following conditions accurately represent Muller's ratchet,in terms of the selective advantage of sexual reproduction?
A) Deleterious mutations accumulate in asexual populations, resulting in a significant genetic load.
B) Sexual reproduction is selected because it reintroduces no-mutation genotypes that have been lost from the population.
C) Linkage disequilibrium increases in populations by genetic drift because no-mutation multilocus genotypes are lost by chance.
D) All of the above accurately represent the conditions of Muller's ratchet.
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Chapter 9: Evolution at Multiple Loci: Quantitative Genetics
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Q1) It becomes possible to predict evolutionary changes in a population after we have measured two attributes affecting the population in question.What two measures allow us to make such predictions?
Q2) In populations where individuals with extreme values of a trait have the highest fitness,the average value of the trait may not change,but the amount of variance in the trait does increase over time.This set of circumstances is known as ________.[two words]
Q3) Variation among individuals that is due to factors other than genetic factors is called ________.
A) phenotypic variation
B) environmental variation
C) broad-sense heritability
D) narrow-sense heritability
Q4) Explain,using examples/equations,the similarities and differences between broad-sense and narrow-sense heritability estimates.
Q5) ________ refers to the fraction of the total variation in a trait that is due to variation in genes.
Q6) Compare and contrast qualitative traits/genetics with quantitative traits/genetics.
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Chapter 10: Studying Adaptation: Evolutionary Analysis of
Form and Function
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Q1) What is the purpose of the null hypothesis in experimental design?
Q2) Futuyma and colleagues (1995)demonstrated that host shifts by the herbivorous leaf beetles of the genus Ophraella in feeding on members of the sunflower family are due to the ________.
A) frequency-dependent selection properties among beetle populations
B) low mutation rate observed in beetle populations
C) need for populations to maintain sufficiently large sizes on a small number of hosts
D) availability of genetic variation sufficient for evolutionary change
Q3) Douglas Taylor and colleagues (2002)used yeast (Saccaromyces cerevisiae)to examine selection.Yeast can harvest energy by either fermentation or respiration.Explain how this characteristic enabled the researchers to utilize parasitic mitochondria to examine selection across varying population sizes.
Q4) To determine the role of mimicry in the behavior of the tephritid fly Zonosemata vittigera and the jumping spider Phidippus apacheanus,Greene and colleagues (1987)conducted carefully controlled experiments to correlate appearance and behaviors with the deterrence of predation.What two factors were found important in preventing predation of the tephritid fly by the jumping spiders?
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Chapter 11: Sexual Selection
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Q1) Pawlowski and colleagues (2000)gathered data from over 3,000 Polish men,and investigated the hypothesis that sexual dimorphism in humans is the result of female choice.They found that there was a slight but significant level of sexual selection on
A) the body mass index (BMI) of men in their twenties, thirties, and forties for both marriage and producing offspring
B) the weight of men in their twenties, thirties, and forties for both marriage and producing offspring
C) the height of men in their twenties, thirties, and forties for both marriage and producing offspring
D) the intelligence quotient (IQ) of men in their twenties, thirties, and forties for both marriage and producing offspring
Q2) Provide an example from the text illustrating the following: If one parent invests in his or her offspring more than the other parent,the heavily investing parent is often limited by resources and time.Also,the lightly investing parent is limited by its access to mates.
Q3) In general,mothers typically make a larger parental investment in each offspring than males do.What is meant by the term parental investment?
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Page 13
Chapter 12: The Evolution of Social Behavior
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Q1) Explain Hamilton's Rule in the context of altruistic behavior.
Q2) Social behavior in which the "actor" benefits at the expense of the "recipient" is termed ________.
Q3) Social behavior between animals where the actor benefits at the expense of the recipient is called ________.
A) mutual benefit
B) selfishness
C) altruism
D) spite
Q4) The sum total of an individual's direct and indirect fitness is known as ________.[two words]
Q5) Compare and contrast,in general terms,cooperative breeding in birds,as described in your text with the case study on the white-fronted bee-eaters,also described in your text.
Q6) Multilevel selection/cooperation has been documented in ________.
A) bacteria
B) plants
C) humans
D) All of the above.
Page 14
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Chapter 13: Aging and Other Life-History Characters
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Q1) The hypothesis that predicts that parents will attempt to rear the number of offspring that maximizes the survival rates of offspring is known as ________.[two words]
Q2) Life-history analysis may provide us with clues to human female menopause more specifically,the way in which your text describes it,"Why should women's reproductive systems shut down by age 50,while the rest of their organs and tissues are still in good repair?" Two hypotheses were discussed; describe,compare,and contrast them.Which one do you think is more likely,and why?
Q3) Living things show a wide range of diversity where reproductive strategies are concerned.The branch of evolution devoted to the analysis of this diversity is known as ________ analysis.
Q4) In an "ideal" world,organisms that are fine-tuned for reproduction would ________.
A) mature at birth
B) produce high-quality offspring continuously and in high numbers
C) live forever
D) All of the above, taken together.
Q5) Tandem repeat sequences found at the ends of chromosomes,such as TTAGGG as found in vertebrates,are known as ________.
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Page 15
Chapter 14: Evolution and Human Health
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Q1) The idea that fundamental aspects of human behavior are "hardwired" or "programmed" by human genes is sometimes called ________.[two words]
Q2) A group of lineages such as viral strains that all descend from a common ancestor makes up a ________.
Q3) Your text discusses one of the most well-known examples in which human populations have evolved in response to selection imposed by changes in lifestyle.Specifically,this example has to do with a change toward the life-long production of an enzyme that allows humans to digest something our ancestors normally would have ingested only as infants.What is the name of this enzyme?
Q4) Strokes,cancer,and heart disease are sometimes called ________ [three words] because they are/were rare in hunter-gatherer populations.
Q5) The statement "The virulence of many pathogens in humans may not be a target of selection itself,but rather an accidental by-product of selection on other traits" describes
A) the coincidental evolution hypothesis
B) the shortsighted evolution hypothesis
C) the trade-off hypothesis
D) the energy-balance hypothesis
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Chapter 15: Phylogenomics and the Molecular Basis of Adaptation
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Q1) Why have gene families evolved? Choose the most accurate answer for gene families in general.
A) Although in some cases researchers have inferred that gene families are adaptive, gene families may also evolve due to genetic drift.
B) Having multiple copies of a gene can increase transcription and translation of the gene, so when increased transcription is adaptive, then natural selection favors genes duplicating into gene families.
C) Gene families are adaptive because each gene can produce a slightly different protein, which allows for diverse functions that are favored by natural selection.
D) Gene families evolve because of the activity of mobile genetic elements, which cause repeated gene duplication events.
Q2) Which statement accurately describes a relationship between mutation rate and genome size?
A) Larger genomes have higher mutation rates across all domains of life.
B) Larger genomes have lower mutation rates across all domains of life.
C) Mutation rate increases with genome size in multicellular organisms.
D) Mutation rate increases with genome size in unicellular organisms.
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Chapter 16: Mechanisms of Speciation
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Q1) Speciation events that occur when the geographic ranges of the populations involved overlap are termed ________.
Q2) Each of the species concepts (morphospecies,biological,and phylogenetic)have strengths and weaknesses.Compare and contrast all three,and evaluate them for their relative usefulness.
Q3) Relative to chromosome numbers,hybridization can produce speciation in two ways.What are they?
Q4) Which of the following models of speciation hinges on a physical barrier which prevents gene flow between populations?
A) dispersive allopatric
B) dispersive sympatric
C) vicariant allopatric
D) vicariant sympatric
E) Both A and C.
Q5) The model of speciation that hinges on a physical barrier preventing gene flow is ________ speciation.
Q6) The classical hypothesis of speciation is comprised of a three-step process.What are the three steps?
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Chapter 17: The Origins of Life and Precambrian Evolution
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Q1) The earliest fossil records of bacteria-like organisms,dated at over 3 billion years,________.
A) are too spotty to allow us to trace lines of descent to present-day organisms
B) unquestionably belong to cyanobacteria
C) show that early cells had membranes made of short amino acid chains
D) used only RNA molecules for both information storage and chemical catalysis
E) already contained endosymbiotic organelles
Q2) Proteins carry out much of the biochemistry of life,including DNA replication,but DNA stores the information needed to build correct proteins.Early life forms would have needed both proteins and DNA,but neither can exist without the other.The RNA world hypothesis is an appealing solution to this problem,because it states that ________.
A) RNA can evolve into DNA by natural selection
B) proteins can store the information needed for their own synthesis
C) RNA is more chemically stable than DNA
D) nucleotides of RNA are chemically similar to amino acids
E) some RNA molecules both store information and catalyze chemical reactions
Q3) Fossil evidence suggests that the latest possible date for root of the universal phylogeny predates the ________ billion-year mark.
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Chapter 18: Evolution and the Fossil Record
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Q1) Rock layers right at the K-Pg boundary have enriched concentrations of the element iridium.This is significant for understanding the mass extinction that happened at the time,because ________.
A) iridium is toxic to life and could have killed off many species
B) iridium is very rare in the Earth's crust but relatively common in meteorites
C) iridium forms under conditions of extreme shock and heat
D) iridium would have caused an episode of severe acid rain
E) iridium-rich dust is particularly effective at blocking incoming solar radiation
Q2) Which of the following is NOT key evidence for a large meteorite impact striking the Earth approximately 65 million years ago?
A) tiny particles of glass called microtektites
B) "shocked quartz" grains, with fine parallel planes caused by a burst of intense pressure
C) the disappearance of many taxa of large reptiles beginning about 70 million years ago
D) a worldwide layer of sediments highly enriched in the element iridium
E) gravity anomalies that allow us to map the now-buried meteorite crater
Q3) An exceptionally rich fossil deposit is known as a(n)________.
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Page 20
Chapter 19: Development and Evolution
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Q1) The most significant conclusion of the experiments on Heliconius butterfly mimics is that ________.
A) evolution can sometimes happen by sudden jumps
B) genes can occasionally be transferred between completely unrelated organisms
C) natural selection is the only mechanism for evolutionary diversification
D) the same developmental genetic mechanisms underlie a great range of variants
E) development must be studied separately from evolutionary genetics
Q2) The eighteenth-century French scientist Étienne Geoffroy Saint-Hilaire argued for a far-reaching concept of what we would now call homology.For example,he argued that the vertebrae and ribs of vertebrates are fundamentally the same structures,built on the same plan,as the segmented exoskeleton and legs of insects and other arthropods.Insects,according to Geoffroy Saint-Hilaire,quite literally live inside their vertebrae and walk on their ribs.His idea is not really true in the sense that he conceived it and yet,in the light of discoveries about Hox genes and developmental regulation,some modern evolutionary biologists have had good things to say about Geoffroy Saint-Hilaire's work.(See "Brotherhood by Inversion" in Stephen Jay Gould's book Leonardo's Mountain of Clams and the Diet of Worms,for example.)Explain why a modern "evo-devo" specialist might find Geoffroy Saint-Hilaire's ideas worth revisiting in the light of current knowledge.
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Chapter 20: Human Evolution
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Q1) In humans and possibly even in chimpanzees,there seems to be a neurological correlation between ________ and ________.
Q2) Green and colleagues assessed the degree of past interbreeding between modern Homo sapiens populations and extinct premodern populations by looking at an aspect of genetic diversity known as ________.[three words]
Q3) All of the following traits are shared by all great apes,except ________.
A) increased flexibility of the wrist and thumb
B) spoken language
C) absence of a tail
D) increased flexibility of hips and ankles
E) relatively large brains
Q4) "Robust australopithecines," now classified in the genus Paranthropus,are distinctive as compared to other hominins because of their ________.
A) great height
B) unusually large brains
C) knuckle-walking ability
D) cave paintings and other artwork
E) huge teeth, faces, jaws, and jaw muscles
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