For all of your answers EXPLAIN fully with examples as needed. 

REVIEW QUESTIONS - - CHAPTER 1

  1. What did Dobzhansky mean by the statement "Nothing in Biology Makes Sense Except in the Light of Evolution"?
  2. Why is understanding evolution important?
  3. In one sentence, what did Darwin's mean by evolution?
  4. Evolution is better defined as any change in ___________ traits of a ________ that occurs from one _________ to the ______
  5. Using Recent and fossil whales as examples, define and explain the significance to evolutionary biology of the following
    1. Population
    2. Lineage
    3. Character
    4. Convergent evolution
    5. Homology
    6. Synapomorphy
    7. Phylogeny
    8. Vestigial structure
    9. Natural selection
  6. How do we know whales are mammals?
  7. What does DNA indicate about the relationships of whales?
  8. How does the fossil record show that whales are artiodactyls? (Figs. 1.7, 1.8 and more)
  9. What is the significance of the astragalus and involucrum to the study of whale evolution?
  10. How has the fossil record of the origin of whales provided evidence for evolution?
  11. What is the involcrum? What is significant about its presence in Pakicetus? (Fig. 1.4)
  12. What do oxygen isotopes tell us about whale ecology? Explain how oxygen isotopes provide this information. (Figure 1.9)
  13. What do oxygen isotopes tell us about the early evolution of the whales, paricularly the following genera
    1. Pakicetus
    2. Ambulocetus
    3. Georgiacetus
  14. For the following fossil whales, explain their significance to whale phylogeny, behavior, and ecology.
    1. Pakicetus
    2. Ambulocetus
    3. Georgiacetus
  15. For the following fossil whales, discuss what the changes to the limbs and skull indicate about whale evolution.
    1. Pakicetus
    2. Ambulocetus
    3. Georgiacetus
  16. How has locomotion changed from the earliest whales such as Pakicetus through Ambulocetus to modern whales?
  17. What information does embryology and molecular genetics provide about whale evolution, particularly the reduction of the hind limb? (Fig. 1.10) How is this information useful in understanding what the fossil record  shows concerning the evolution of the hind limb in whales? (Fig.1.11)
  18. What is the evidence (from fossils, embryology,  and genetics) that living baleen whales are derived from toothed ancestors
  19. Why did whales and humans evolve large brains?  How does this demonstrate that evolution does not occur because of future needs?
  20. What is genetic drift?

The Following questions are not covered in the 2nd edition and will not be asked.

  1.  What is the evidence that antigenic sites evolve more rapidly in vaccinated mice than non-vaccinated mice (Fig. 1.20).  What causes this to happen in the virus?
  2. Why does the flu virus evolve so rapidly in the 9 passages through vaccinated mice?
  3. Why does the flu virus evolve so slowly in the 9 passages through non-vaccinated mice?
  4. What is evolution a fact?
  5. Why is evolution a theory?
  6. Why are the following misconceptions about what evolution really is (i.e., why are they wrong?)?
    1. Evolution is 'just' a theory
    2. Evolutionary biologists understand everything about the history of life 
    3. Evolutionary biologists search for missing links
    4. Evolution violates the second law of thermodynamics (entropy)
    5.  Evolution is natural selection
    6. Evolution is entirely random
    7. Organisms evolve adaptations  they 'need'
    8.  Evolution is a march of progress
    9. Evolution always moves from simple to complex
    10. Evolution results from individuals adapting to environment (Be sure to include a discussion of populations versus individuals)
    11. Organisms are perfectly adapted to their environment
    12. Evolution happens for the good of the species
    13.  Evolution promotes selfishness and cruelty
    14. Evolution seeks peaceful harmony in nature
    15. Life can be divided into higher and lower forms
    16.  Evolution has produced a stable diversity of life
  7. Why can't evolution purposely produce adaptations that will be needed for future conditions?
  8. What is random about evolution? What is non-random?

 

REVIEW QUESTIONS - CHAPTER 2

  1. Key Terms from Chapter 2 to define
    1.  Adaptations
    2. Extinction
    3. Genetic drift
    4. Homologous traits
    5. Hypothesis
    6. Natural selection
    7. Paleontology
    8. Stratigraphy
    9. Theory
    10. Taxa (singular, taxon)
    11. Taxonomy
    12. Uniformitarianism
  2. Although Darwin (and Wallace) was the first to propose a succesful mechanism (natural selection) to explain the history of life, he had many intellectual predecessors.  What contributions did each of the following make towards development of Darwin's grand theory?
    1. Aristotle
    2. Steno
    3. Buffon
    4. Linnaeus
    5. Cuvier
    6. Hutton
    7. Smith
    8. Lyell
    9. Malthus
    10. Wallace
  3. Define the following and explain their significance to the History of Evolutionary Biology
    1. Scala Naturae
    2. uniformitarianism
    3. Principle of faunal succession.
    4. Inheritence of aquired characteristics
    5. Natural theology
    6. Excess reproductive capacity
    7. Voyage of the Beagle
    8. Principle of succession
    9. Galapagos Islands
  4. How did Cuvier demonstrate the fact of extinction?  Why was this important in challenging the dominant European worldview of the time?
  5. What is biological plenitude and how did Cuvier demonstrate it was false?
  6. What is the Scala Naturae and why does it present an incorrect picture of the history of life?
  7. How did Charles Lyell influence Darwin's ideas?
  8. How did Thomas Malthus influence Darwin's ideas?
  9. What is uniformitarianism?  Why did Darwin incorporate it into his theory of evolution?
  10. What are phylogenetic trees?  Why did Darwin consider them so important?
  11. Define the following terms. Explain how each provides evidence for evolution. Discuss examples for each illustrating the process of evolution.
    1. Artificial selection
    2. Structural homology
    3. Embryological or Developmental homology
    4. Genetic homology 
  12. Explain the significance to evolutionary biology of Figure 2.18 (2.14? in the 1st edition) from your homework shows the arrangement of branching blood vessels in adult sharks and human embryos at various stages of development.
    1. At which of the stage of human development pictured does the pattern of blood vessels look most similar to the pattern found in sharks?
    2. If scientists were only to examine human embryos at 56 days, would the homologies be apparent?
    3. Explain how this homology indicate about the relationship between fishes and humans?
  13. Fig. 2.19 (2.15 in the 1st edition) is a flow chart showing Darwin's logic in developing the theory of natural selection 
    1. As presented in the Z&E textbook, the theory of natural selection started with three facts.  What are they? (Fig. 2.15)
    2. From these three facts, he drew two inferences. What are they? (Fig. 2.15)
    3. To develop the theory he used two more facts.  What are they? (Fig. 2.15)
    4. This led to his conclusion (Inference 3). What is it.
  14. What components to natural selection have been added since Darwin's death?

REVIEW QUESTIONS - CHAPTERS 3 and 4

  1. People, fossils, and terms to know
    1. James Ussher
    2. Radiometric dating
    3. Stromatolite
    4. Pelycosaur
    5. Phylogeny
    6. Coelocanth
    7. Tiktaalik
    8. Archaeopterix
  2. What is a scientific theory?
  3. How did Kelvin determine the age of the earth?
  4. Why did Kelvin's research pose a major problem for Darwin?
  5. How did Darwin solve the problem posed by Kelvin?
  6. Why was Kelvin wrong?
  7. How is radioactive decay used to age-date rocks?
  8. How was the geologic time scale (Cambrian, Ordovician, etc.) based on relative time established?
  9. Why is the study of stratigraphy and paleontology important to understanding evolutionary theory?
  10. How old is the earth?
  11. What are the ealiest forms of life on earth?  Approximately when did life first appear?
  12. What is a stomatolite?  Why are stomatolites important for the evolution of more complex cells and organisms?
  13. What is the Ediacaran fauna?  What does it show about the evolution of life?
  14. How is the Cambrian recognized in the fossil record?
  15. What is the Burgess Shale fauna?  What does it show about the evolution of life?
  16. What is the "big picture" in the fossil record concerning the evolution of vertebrates?
  17. How does homology relate to the theory of evolution?
  18. What is a phylogenetic tree (i.e., what does it represent)?  What is the significance of using synapomorphies to construct these trees?
  19. How does horizontal gene transfer complicate the tree of life? In which organisms is horizontal gene transfer most important? What was its major effect on the history of life?
  20. What is homoplasy? Why does it pose problems in constructing phylogenies?
  21. Why are lungfish  and coelocanths more closely related to birds and mammals than they are to tuna fish and goldfish?
  22. Why is Tiktaalik one of the most important fossils discovered in the last 50 years.  How(and why) did paleontologists decide to look for this fossil?
  23. What are the features present in Tiktaalik that make it such an important discovery?
  24.  Why are feathers an excellent example of exaption?
  25. Define and give examples of preadaptation and exaption. What do they indicate about the nature of the evolutionary process.
  26. Why is the importance of Ardipithicus to human evolution?

REVIEW QUESTIONS - CHAPTER 5

  1. Define and discuss the importance to Evolutionary Biology  of the following terms.
    1. Semiconsevative replication
    2. Mutation
    3. Gene
    4. Plasmids
    5. Horizonatal gene transfer
    6. Vertical gene transfer
    7. Ploidy
    8. polyploidy
    9. Autosomes and sex chromosomes
    10. Allele
    11. Universal genetic Code
    12. Gene Expression
    13. Epigenetics
    14. RNA splicing and alternative splicing
    15. point mutation
    16. synonymous substitution
    17. non-synonymous substitution
    18. loss-of-function mutation
    19. frameshift mutation
    20. jumping gene ("transposon") insertion (Mobile genetic elements)
    21. gene duplication.
    22. pseudogenes
    23. inversion
    24. Somatic mutation
    25. Germ-line mutation
    26. Independent assortment
    27. genetic recombination
    28. Crossing over
    29.  Dominant and recessive alleles
    30. Qualitative trait
    31. Polyphenic trait
    32. Quantitative trait
    33. Phenotype and Phenotypic plasticity
    34. Quantitative trait
    35. Genome
    36. Genotype
  2. What two products does DNA code for? What is the other important function of DNA?
  3. How does the DNA of a prokaryote differ from that of a eukaryote?
  4. What is the Central Dogma?  Is it a dogma?  To what is it central?
  5. How can many different proteins be made from a single gene?
  6. What is a point mutation?  Do all point mutations results in changes in protein function? Explain.
  7. What is the difference between a somatic and gene-line mutation?
  8. What is the difference between genotype and phenotype?
  9. Describe the basic structure of DNA, and briefly summarize the processes of replication, DNA repair, transcription, and translation.
  10. Explain why the genetic code is called a triplet code. What is a codon?
  11. In what way is the code redundant?
  12. Is all of the DNA in eukaryotic genomes used to build proteins? Explain.
  13. Briefly describe the structure of eukaryotic mRNA, being sure to define the terms intron and exon. What is mRNA processing?
  14. Is all of the DNA in eukaryotic genomes used to build proteins? Explain. Briefly describe the structure of eukaryotic genes, being sure to define the terms intron and exon. What is mRNA processing?
  15. What are point mutations?  What causes them, and what are the different kinds?
  16. What is a point mutation?  Do all point mutations results in changes in protein function? Explain.
  17. How does sexual reproduction increase variability? Define and discuss the roles of independent assortment, genetic recombination (crossing over) and fusion of gametes.
  18. What is the difference between a synonymous and non-synonymous point mutation?
  19. Discuss the development of horns in dung beetles as an example of a polyphenic trait. (Figure 5.19).
  20. Figure 5.21A graphs the heights of monozygotic (identical) twins; 5.21B, dizygotic (fraternal) twins. Which graph enables you to better predict the height of an unknown twin from that of a known twin? Is there a correlation in the height of fraternal twins? Explain why the two graphs differ for both sets of twins.

REVIEW QUESTIONS - CHAPTER 6

  1. Try solving these problems from Kansas State, Principles of Biology, Biology 108 
  2. set 1
  3. set 2

More Problems

  1. If the dominant trait for being able to taste the chemical PTC (phenylthiocarbamide) is present in 60% of the population, what is the frequency of the recessive ALLELE (nontaster) in the population. What percent of the population are nontasters.
  2. Consider a stable population in which the recessive allele has a frequency of 0.8.  What percent of the population would be heterozygous?
  3. In a stable population, 91% of the individuals express the dominant phenotype.  What are the allele frequencies for the dominant and recessive alleles?  What percent of individuals expressing the dominant phenotype are homozygous?  (read this question carefully)
  4. In a population of 500 individuals, 200 are genotype AA, 125 are genotype Aa, and 175 are genotype aa.  What is the frequency of the dominant allele A?  What is the frequency of the recessive allele a?  Given these allele frequencies, what does Hardy-Weinberg predict will be the frequencies of each of the three genotypes?  Is the population in Hardy-Weinberg equilibrium?  Fully explain your answer.
  5. In a population of plants, there are white (A1A1), pink (A1A2), and red (A2A2) flowers. The genotype frequencies of these flowers are 0.16 white, 0.48 pink, and 0.36 red.  
    1. What are the allele frequencies for A1 and A2?
    2. Due to a decrease in the bee population the white flowers have lower relative fitness. w11 = 0.5 (only 50% of the white flowers produce offspring as opposed to 100% of the pink or red). What are the new genotype frequencies?
  6. A certain population has p = 0.6 and q = 0.4 for the dominant and recessive alleles of a certain gene.  Assuming a stable population, what is the percentage of each genotype in the following generation?  If the fitness of the homozygous recessive phenotype = 0, what is the value of p and q and the percentage of each genotype in the following generation?
  7. For recessive alleles, the equilibrium frequency of that allele = q = (μ / s)1/2, where μ is the mutation rate and s is the selection coefficient against the recessive allele.
    1. 1/2000 of the people of northern Europe have cystic fibrosis (CF can be considered a recessive lethal allele).  If the population is in Hardy-Weinberg equilibrium, what is the frequency of the CF allele.  If this is the equilibrium frequency, what is the expected mutation rate.  If the actual mutation rate is 0.0000067, what conclusions can be drawn.  Why?
    2. If the mutation rate for the recessive sickle cell allele (lethal if homozygous) is 10-4, what is the expected percent of in individuals who are homozygous for this trait if it is established by mutation alone.  The actual frequency for individuals with this trait is 0.16. What is the most likely explanation for this?  Correctly use this formula [q = s1/(s1+s2)] to find the fitness of the homozygous dominant to support your answer. [s1 is the selection coefficient for the homozygous dominant and s2 is the selection coefficient for the homozygous recessive]
  8. In regions with malaria, individuals heterozygous for the recessive sickle cell allele have the highest fitness (w = 1), versus homozygous normals (w = 0.5), or homozygous recessives (w = 0).   Calculate the equilibrium frequencies expected for the three genotypes.  [q = s1/(s1+s2) ] 
  9. Scale- eating fish a dominant "right-handed" allele frequency of  about 0.3.  Use Hardy-Weinberg to explain why this this is necessary if the left handed and right  phenotypes are both 50% .

Review questions -- CHAPTER 6

  1. Define, discuss the importance to Evolutionary Biology, and give examples of the following terms.
    1. Genetic locus
    2. Null hypothesis
    3. Population genetics
    4. Fixed allele
    5. Fitness
    6. Genetic bottleneck
    7. Founder Effect
    8. Relative fitness
    9. Pleiotropy
    10. Antagonistic Pleiotropy
    11. Positive selection.
    12. Negative selection
    13. Epistasis
    14. Additive allele
    15. Balancing selection
    16. Negative frequency dependent selection
    17. Heterozygote advantage
    18. Inbreeding coefficient
    19. Inbreeding depression
    20. Genetic distance
    21. Landscape genetics
    22. Population structure
    23. Gene flow
  2. What conditions must be satisfied to achieve Hardy-Weinberg equilibrium?
  3. Why is the Hardy Weinberg model used a null model in research in evolutionary biology
  4. Discuss the interaction between selection, genetic drift, and mutation in small and large populations.
  5. In Figure 6.4 showing Buri's experiment, why is fruit fly heterozygosity declining over 20 generations?
  6. Discuss and explain what Figure 6.6 shows about the effects of drift in small, medium, and large populations.
  7. Discuss and explain what Figure 6.7 (6.8 in 2nd) shows about the effects of drift and selection in small, medium, and large populations.
  8. Define and give examples of each of the following. Discuss the effect of each on Hardy-Weinberg equilibrium, genetic diversity, allele frequency, and evolution.  How does population size affect each?
    1. migration (Fig. 6.11)
    2. genetic drift
    3. genetic bottleneck (Fig. 6.8)  (6.9 in 2nd)
    4. founder effect
    5. inbreeding depression
  9. Discuss Fig. 6.9.  What does it show about the probability of losing an allele?  Why?
  10. Discuss the effectiveness of genetic drift and natural selection in small and large populations.  Explain why each process is stronger/weaker depending on the population size (Fig. 6.12) (6.13 in 2nd).
  11. What is antagonistic pleiotropy?  How does it affect evolution?  Use the example of the Ester1 allele in mosquitoes as shown in figure 6.2.  Why is this allele common on the coast, but rare inland?
  12. Why was the Ester1 allele replaced by the  the Ester4 allele after 1986 (Fig. 6.13) (6.14 in 2nd)?
  13. Describe Lenski's 20 year experiment with bacteria (Fig. 6.14).  What was being selected for?  How was this done?
  14. How did Lenski determine that bacteria increased in fitness after 20,000 generations (Fig. 6.15) (6.16 in 2nd)? 
  15. How did Lenski demonstrate that the BoxG1 allele was involved in increasing fitness?
  16. Why are rare alleles mostly in the heterozygous condition, and not the homozygous condition.  Use the equation for the Hardy Weinberg equilibrium to justify your answer.
  17. Discuss (and give examples of) the effects of selection of on allele frequencies when (see Fig.6.16)
  18. (6.17 in 2nd)
    1. the phenotype with greater fitness is determined by additive alleles
    2. the dominant phenotype has a greater fitness than the recessive phenotype.
    3. the recessive phenotype has a greater fitness than the dominant phenotype.
    4. the heterozygotes have greater fitness than either of the homozygotes
  19. What is mutation-selection balance?  Why can the frequency of Spinal muscular atrophy be explained by mutation-selection balance?
  20. What is frequency-dependent selection?  How does it maintain the two color morphs of the Elderflower orchid?
  21. Discuss how Gigord's experiment with Elderberry orchids demonstrated negative frequency dependent selection in both male and female flowers (Fig. 6.17) (6.18 in 2nd).
  22. Discuss the role of selection for the A and S alleles in regions with and without malaria (Fig. 6.18) (6.19 in 2nd).  Which is an example of heterozygote superiority? Why?
  23. Non-random mating can affect evolution (Fig. 6.20) (6.22 in 2nd).
    1. Define the coefficient of inbreeding using the Habsburg dynasty as an example. (Fig. 6.21) (6.22 in 2nd)
    2. Define the term "inbreeding depression using the Habsburg dynasty as an example (Fig. 6.22) (6.23 in 2nd)
  24. How does inbreeding affect the genetic structure of a population?
  25. What is the probability that the offspring of the half siblings below will inherit two copies of the same allele. What about the offspring of full siblings?
  26. Discuss the effects of nonrandom mating genotype frequency and on allele frequency? Specifically demonstrate changing genotype frequencies over five generations of selfing. Give several actual examples of the evolutionary consequences of non-random mating.
  27. Why does the genotype distribution for the PAP allele of 33 sea otters (SS =16, SF = 7, FF = 10) indicate they are inbred?  Show your calculations that demonstrate this
  28. How does gene flow affect the genetic diversity of a species? If there is little gene flow between populations, how will this affect the genetic distance of the populations? What is the role of genetic drift in this process?
  29. Under what conditions of landscape genetics are conservation biologists most concerned about inbreeding depression? Discuss and give examples.

Chapter 6 Zimmer and Emlen end of chapter questions

  1.  A survey through 23andMe.com found that of 4737 individuals of European ancestry, 3002 said they could smell asparagus in their urine and 1735 said they could not. The A allele for odor detection is dominant over the G allele for lack of odor detection, and 1027 individuals are heterozygotes.
    1.  What are the genotype frequencies?
    2. What are the allele frequencies for this locus, assuming random mating?
    3. Is the population in Hardy-Weinberg equilibrium?
  2. Why did the genetic variation of elephant seal populations remain low for thousands of generations after the bottleneck event? How could genetic drift have played a role in slowing the recovery of genetic diversity?
  3. What would happen to the frequency of heterozygous carriers of sickle-cell anemia (with an AS genotype) if mosquitoes were completely wiped out in a large region? Explain.
  4. How can a drastic reduction in population size lead to inbreeding depression?  

 Freeman and Herron end of chapter questions that apply to lecture

  1. In humans the COLA1A1 locus codes for a certain collagen protein found in bone. The normal allele at this locus is denoted with S. A recessive allele s is associated with reduced bone mineral density and increased fractures inn Ss and ss women. A recent study showed of 1778 women showed that 1194 were SS, 526 were Ss, and 58 were ss.
    1. What are the genotype frequencies?
    2. What are the allele frequencies?
    3. Are these two alleles in Hardy-Weinberg equilibrium? How do you know? 
    4. What information do you need to determine whether the alleles will be in equilibrium in the next generation?
    5.  Redo A-C with the following data: of 1278 women, 1194 were SS, 26 were Ss, and 58 were ss.

 Freeman and Herron web site questions that apply to lecture

  1. Explain what is meant by the statement that the Hardy-Weinberg equilibrium equations are a null model.
  2. What, specifically, do the Hardy-Weinberg equations describe (be sure to explain any conditions that are assumed by the model)?
  3. Clearly explain what p and q represent in the Hardy-Weinberg equations. Write the equations and verbally describe the mathematical relationships among those variables and the conditions under which those relationships hold.
  4. Given genotype frequencies, be able to calculate allele frequencies. Given allele frequencies and assuming the conditions of Hardy-Weinberg are met, be able to calculate genotype frequencies.
  5. When the conditions of the Hardy-Weinberg equations are met, what happens to allele frequencies in populations over time? What happens to genotype frequencies?
  6. How can you test whether or not a population is in Hardy-Weinberg equilibrium? Given data in the form of genotype frequencies, be able to perform this test.
  7. Briefly discuss the differences between selection acting on recessive alleles and selection acting on dominant alleles.
  8. Define heterozygote superiority and explain its effects on allele frequencies over time. Use sickle-cell anemia as an example in your explanation.
  9. What is frequency-dependent selection?  What are the general effects of this form of selection?
  10.  By itself, does mutation cause substantial evolutionary change?
  11. Describe the mutation-selection balance model for the maintenance of deleterious alleles in populations. How can a mutation-selection balance hypothesis be tested? Use spinal muscular atrophy to illustrate.
  12. Petal color in a hypothetical population of flowering plants is determined by a single gene with two co-dominant alleles. RR plants have red flowers, WW plants have white flowers, and RW plants have flowers with red and white striped petals. In a random sample of plants from this population you find 50 plants with red flowers, 20 with striped flowers, and 30 with white flowers. Calculate the frequency of each genotype and of each allele. Is the population in Hardy-Weinberg equilibrium? Why or why not?

Review questions -- CHAPTER 7  For all of your answers EXPLAIN fully with examples as needed. 

  1. Define and discuss the importance to Evolutionary Biology  of the following terms.  Give examples
    1. qualitative trait
    2. quantitative trait
    3. Broad sense heritability
    4. narrow-sense heritability
    5. additive, dominance, and epistatic effects on heritability
    6. response to selection
    7. phenotypic plasticity
    8. reaction norm
    9. stabilizing selection
    10. directional selection
    11. disruptive selection
  2. What are quantitative traits?  What is distinct about their phenotypic expression?  Why?
  3. What causes continuous variation in phenotype?
  4. How can Mendelian genetics explain quantitative traits (Fig. 7.2)?
  5. If a trait is controlled by one locus with two aleles per locus, how many genotypes and phenotypes can their be?  two loci?  three loci?
  6. How is narrow-sense heritability measured? What is its importance in evolutionary biology?
  7. What is additive genetic variation?  Why is it important in determining narrow sense heritability?
  8. What do different values of h2 indicate as determined from the regression of offspring versus parental characteristics (e.g., Fig. 7.5) indicate about a trait?  Discuss what a high value indicates versus a low value.
  9. What are the three modes of selection? How does each affect the average value and variation of the character being studied?
  10. How does directional selection differ from stabilizing selection?  from disruptive selection? How does disruptive differ from stabilizing?
  11. Give examples of each of the three modes of selection.
  12. Why is it expected that most of the time stabilizing selection should be the most common?
  13. Why has there been stabilizing selection on human birth weight?
  14. Discuss and explain the selection factors at work and their results on the gall-making fly.
  15. Discuss the significance of Fig 7.7 showing selection for either high oil or low oil content in corn.
  16. Discuss the Thoday and Gibson experiment (Fig. 7.8) demonstrating disruptive selection on flies with different numbers of bristles starting with populations with similar numbers.
  17. What is phenotypic plasticity?
  18. Why are some snowshoe hares becoming maladapted to their environments (Fig. 7.23) (7.24 in 2nd)? What is the expected evolutionary response
  19. How might selection drive the evolutionary response of snowshoe hare populations experiencing warming in the far North due to climate change?

Questions from Freeman and Herron and Zimmer and Emlen

  1. Define "heritability," clearly explaining what this quantity does and does not measure.
  2. Describe the relationship among heritability, phenotypic variation, genetic variation, and environmental variation.
  3. How might selection drive the evolutionary response of snowshoe hare populations experiencing warming in the far North due to climate change?

Review questions -- CHAPTER 8  For all of your answers EXPLAIN fully with examples as needed. 

  1. Define and discuss the importance to Evolutionary Biology  of the following terms.  Give examples from chapter 8
    1. heritability
    2. artificial selection
    3. gene flow
    4. Batesian mimicry
    5. aposemetism
    6. extended phenotypes
    7. stabilizing selection
    8. genetic linkage
    9. selective sweep
    10. lactase persistence
  2. Why is beak shape an important attribute for an evolutionary biologist to study?
  3. Why are the Galapagos Islands such an excellent laboratory for evolution?
  4. Be sure to explain the figure completely. Thinking about how the Finch bill demonstrates Darwin's critical ingredients for natural selection (the facts and inferences in Fig. 2.15),
    1. What does the top figure 8.4 demonstrate?
    2. What does the middle figure 8.4 demonstrate?
    3. What does the bottom figure 8.4 demonstrate?
    4. What does Figure 8.5 demonstrate?
  5. Of the three figures in Fig. 8.4, which shows natural selection.  Explain why.
  6. Of the three figures in Fig. 8.4, which shows evolution.  Explain why.
  7. Why was it important for the Grants to show that beak depth is heritable.  How did they do this?
  8. Concerning the research done by Hoekstra and colleagues on beach mice (Fig. 8.6)
    1. Why was it necessary to perform an experiment to show the effects of crypsis?
    2. How did they do this?
    3. What were the experimental and control mice for their experiment?
    4. What were the results?
    5. How did the experimentors demonstrate stabilizing selection?
  9. Concerning the research done by Hoekstra and colleagues on the phylogeny of beach mice (Fig. 8.7)
    1. What two hypotheses were they testing?
    2. What did they determine?
    3. What is the evolutionary significance of this research?
  10. In scarlet kingsnakes, discuss the roles of gene flow and selection (predation) to the color pattern of kinsnakes  (Fig. 8.8)
    1. where kingsnakes and coral snakes co-occur (sympatry)
    2. where kingsnakes and coral snakes do not co-occur (allopatry)
    3. Why don't all kingsnakes look like coral snakes?
  11. How was it demonstated that gall size is an extended phenotype of the gallfly? (Fig. 8.10)
  12. Discuss and explain the selection factors at work and their results on the gall size and the gall-making fly (Fig. 8.11)
  13. Why are there two stickleback phenotypes (Fig. 8.12)?
  14. What is the genetic basis (Eda) for stickleback morphology?  What alleles are being selected for in marine and freshwater environments?
  15. Why have sticklebacks evolved different morphologies as they moved from marine to freshwater environments? (Fig. 8.12).
  16. What does the fossil record show when marine sticklebacks invade a freshwater lake (Fig. 8.13)?
  17. Why are most adult mammals "lactose intolerant"?
  18. What caused the lactase persistant allele to be selected for in human populations?
  19. What is the relationship between lactose tolerance and the geography of domestication (Fig. 8.14)  (8.16 in 2nd)?
  20. What is positive selection? Why does selective sweep demonstrate positive selection (Fig. 8.15)  (8.17 in 2nd)?
  21. What is the evidence for positive selection for the lactase tolerance allele (Fig. 8.16)  (8.18 in 2nd)?
  22. The domestication of corn is a well documented example of artificial selection.
    1. What is the archeological evidence or this (Figs. 8.18, 8.19)  (8.20, 8.21 in 2nd)?
    2. What alleles have been selected for in this process?
  23. Regarding the herbicide herbicide Roundup
    1. Why is Roundup an efficient herbicide?
    2. How have plants been genetically engineered to be Roundup resistant?
    3. What happens to weed species exposed to Roundup?
  24. Regarding Bt-toxin
    1. What is its source and what does it do?
    2. How have plants been genetically engineered to produce it?
    3. What happens to insects exposed to Bt-toxin?  What does this result in?  What are the benefits to insects?  the costs?
    4. Why is it required that Bt-free refuges be placed around genetically modified crops?
  25. Why is the evolution of resistance to pesticides so rapid? How do scientists, farmers, and public health officials try to slow this resistance to pesticides?
  26.  Regarding introduced cane toads in Australia (Fig. 8.24) (8.27 in 2nd)  
    1. How has natural selection affected the toads?
    2. How has natural selection affected snake predators?
  27. What type of selection has hunting imposed on horn length in bighorn sheep populations? (Fig. 8.25) (8.28 in 2nd)
  28. How has overfishing afffected the life history of Atlantic cod? (Fig. 8.26) (8.29 in 2nd)

Questions from Zimmer and Emlen

  1. What things did Peter and Rosemary Grant's team need to measure or record in order to demonstrate the effect of natural selection on the beak size of finches in the Galapagos?
  2. Describe how Peter and Rosemary Grant demonstrated the following components necessary to demonstrate evolution by natural selection:
    1. Variation in the population:
    2. Heritability
    3. Differential reproductive success
  3. What are the differences and similarities between directional and stabilizing selection?
  4. In the gall fly example, why did Abrahamson and Weis examine gall size of related flies on plant clones?
  5. Hopi Hoekstra and colleagues were interested in whether lighter coat coloration arose in Gulf and Atlantic coast populations through convergent evolution.  How did they test this and what did they find?
  6. Describe how natural selection and gene flow combine to produce the geographical pattern of coloration in scarlet kingsnakes.
  7. For evolution by natural selection to occur, why is it important for the coat color of oldfield mice to be variable and at least partly heritable? What would happen if the variation or heritability were reduced?
  8. What general kinds of data have been used to understand the evolution of sticklebacks? What does each kind of evidence tell researchers about their evolution?
  9. Is domesticated corn (maize) better adapted to its environment than teosinte, the wild plant it evolved from? Why or why not?
  10. Why is the evolution of resistance so rapid? How do farmers and scientists attempt to slow the evolution of resistance in pest populations?
  11. What were the steps involved for snakes to evolve a smaller gape width in Australia after the introduction of cane toads?
  12. How does the 'refuge' strategy proposed by Tabashnik to slow the evolution of Bt resistance.

 

Review questions -- CHAPTER 9  For all of your answers EXPLAIN fully with examples as needed. 

  1. Define and discuss the importance to Evolutionary Biology  of the following terms.  Give examples from chapter 9
    1. Phylogeny
    2. Homoplasy
    3. Purifying selection
    4. replacement (or nonsynonymous) mutations
    5. silent (or synonymous) mutations
    6. neutral theory of evolution
    7. molecular clocks
  2. How did Hillis et al. test whether DNA phylogenies of viruses follow their actual lineages? (Fig. 9.7)
  3. What do DNA and the fossil record show about the origin of the tetrapoods? (Fig. 9.9)
  4. Concerning the evolution of modern humans
    1. What is the multiregional model?
    2. What is the out-of-Africa model?
    3. What does mitochondrial DNA indicate about the relationships of modern humans? (Fig. 9.11).
    4. In particular, what does mtDNA indicate about human populations in Africa today? (Fig. 9.11)
  5. What are the two main hypotheses about the origins of the Darwin's finches on the Galapagos and Cocos?
  6. What does DNA indicate about the origins of the Darwin's finches on the Galapagos and Cocos? (Fig. 9.10)
  7. What does the evolultionary tree of the HIV-1 virus indicate about its origins and how it infected humans (Fig. 9.12)
  8. What observations led Motoo Kimura to develop the neutral model of evolution?
  9. What evidence supports a constant (clock-like) rate of nucleotide substitution in genes (Fig. 9.13).
  10. In figure 9.13, how is the time (X) axis determined?
  11. Is the rate of substitution the same for all types of DNA (Fig. 9.14). 
  12. What type of DNA has the highest rate of evolution? Why?
  13. How does neutral drift explain the molecular clock?
  14. Figure 9.15 illustrates how the nucleotide sequences of HIV-1 samples collected in the 1980's and 1990's were used to construct a molecular clock. 
    1. The earliest known sample of HIV-1 (DRC 1959) was used to test the clock.  How was this done
    2. The clock was used to estimate when HIV-1 first infected humans.  How was this done?
  15. Figures 9.15 and 9.16 show the results of a 2011 study using a molecular clock to determine the timing of major mammalian events.
    1. When and what occurred during the first major diversification event?
    2. When and what occurred during the second major diversification event?
    3. Your beloved perfesser, although pleased that this study is an improvement over previous studies, is still not happy with the results.  He is much more impressed with a more recent study (previewed in this article).  Why?
  16. Why do synonymous substitutions evolve more rapidly than non-synonymous substitutions undergoing purifying (negative) selection?
  17. Why do synonymous substitutions evolve more slowly than non-synonymous substitutions undergoing positive selection?
  18. What is the ratio of nonsynonymous substitutions per site (kn) to synonymous substitutions per site (ks) when replacements 
    1. decrease fitness
    2. are neutral
    3. increase fitness
  19. How has FOXP2 influenced human evolution?
  20. What is the evidence that there has been positive selection on FOXP2 in humans, but not in other mammals (Fig. 9.18)?

Questions from Zimmer and Emlen

  1. How is the theory of neutral evolution different from the theory of evolution by natural selection? How is it the same?
  2. Chris Stringer proposed the hypothesis that all major ethnic groups of humans, Africans, Europeans, and Asians, were derived from recent African ancestry. How did Sarah Tishkoff and her colleagues test this hypothesis?

 

Review questions -- CHAPTER 10  For all of your answers EXPLAIN fully with examples as needed. 

  1. Define and discuss the importance to Evolutionary Biology  of the following terms.  Give examples from chapter 10
    1. Homology
    2. Complex adaptations
    3. Regulatory networks
    4. Hox genes
    5. Novel traits
    6. Promiscuous proteins
    7. Horizontal gene transfer
    8. Paralogs
    9. unequal crossing over
    10. Gene duplication
    11. Gene recruitment
    12. Gene co-option
    13.  evo-devo
    14. regulatory genes
    15. cis-regulatory element
    16. Paralogs
    17. orthologs
    18. beta-defensins
    19. Sonic hedgehog
    20. Crystallin proteins
    21. Opsin
    22. G-Protein Coupled receptors
    23. Evolutionary constraints
    24. antagonistic pleiotropy
    25. Convergent evolution
    26. Australian mammals
    27. saber-toothed carnivores
    28. deep homology

  2. Discuss the evidence that Lenski et al used to show the evolution of a novel trait in E. coli (Fig. 10.6).
  3. How do Hox genes produce the different regions of the fruit fly body (Figs. 10.3, 10.12)?
  4. Describe how the gene duplication can lead to the formation of a gene with a different function (Fig. 10.5).
  5. What is the significance of Dr. Copley's research on PCP eating bacteria?
  6. What is the evolutionary relationship between beta-defensins and crotamine?  How was this transformation accomplished (Fig. 10.8)?
  7. Why are components of snake venom excellent examples of gene recruitment (Fig. 10.9 10.10)?
  8. What is the evidence that snake venoms evolved in one lineage of lizards before one part of that lineage gave rise to snakes (Fig. 10.11)
  9. Compare and contrast the formation of the gut and nervous system in vertebrates and invertebrates (Fig. 10.14).
  10. What is the evidence that limb formation in insects and mammals is controlled by orthologous genes (Fig. 10.15)?
  11. What happens to mammal limbs when Sonic Hedghog is disrupted? Why? (Fig. 10.15, 10.16)
  12. What genetic changes occured to cause snakes to have such elongate bodies and no limbs (Fig. 10.17)?
  13. Even though the common ancestor of all animals with eyes lacked eyes, and that complex eyes evolved at least three times, in what ways are these complex eyes homologous rather than convergent (Figs 10.21, 10.22)
  14. What is the evidence that crystallins evolved through gene recruitment (Fig. 10.23)?
  15. Discuss the hypothesis for evolution of the vertebrate eye (Fig. 10.24)
  16. Why is sickle cell disease an example of antagonistic pleiotropy?
  17. Why do almost all mammals have only seven cervical vertebrae, when the number can vary in other vertebrates?
  18. The recurrent laryngeal nerve in giraffes is an excellent example of why evolution is not perfect (Fig. 10.27).  Why is it poorly designed and why did it evolve his way?
  19. Why is convergence (for examples see figs 10.27) better explained by evolution instead of divine creation?

END OF CHAPTER QUESTIONS

  1. How can horizontal gene transfer give rise to a new adaptation?
  2. What are the differences and similarities between gene duplication and gene recruitment?
  3. Why do mice and flies have the same genetic toolkit of patterning genes? Explain in general terms how these patterning genes guide the development of a fly’s limb.
  4. . Describe how a defensin gene was co-opted for predation in snakes
  5. Describe the role of opsins and crystallins in the evolution of the vertebrate eye.

 

 

Review questions -- CHAPTER 11  For all of your answers EXPLAIN fully with examples as needed. 

  1. What are the advantages of asexual reproduction.  Explain the significance of Figure 11.4 in terms of this..
  2. Why does asexual reproduction give a reproductive advantage?  Give a numerical example to illustrate the reproductive advantage.
  3. Discuss the Difficulties and Costs Associated with Sexual Reproduction listed in Table 11.1
    1. Search Cost
    2. Reduced Relatedness
    3. Risk of Sexually Transmitted Diseases
  4. Why is sexual reproduction so widespread when the costs of reproducing sexually are so high?
  5. Explain how differential investment by males and females in sexual reproduction can lead to sexual selection
  6.  Muller's ratchet
    1. Describe how Muller's ratchet increases the number of deleterious mutations
    2. What are the roles of mutation and drift in Muller's ratchet
    3. Explain why drift tends to eliminate the classes with the fewest numbers of deleterious mutations, but not the classes with the highest How do drift and mutation increase genetic load?
    4. How does sex stop Muller's ratchet?
    5. In light of the Muller's ratchet model, what is the selective advantage of sexual reproduction?
    6. Explain how Muller's ratchet affects sexual populations differently from asexual populations
    7.  Why are the shortcomings of Mueller's ratchet as an explanation for the evolution of sexual reproduction.
  7. What is the Red Queen hypothesis?
  8. How does the Red Queen hypothesis explain the evolution of sexual reproduction? What is the evidence that sex is an adaptation to short-term change?
  9. How does the study on New Zealand snails (Fig. 11.6) support the host parasite arms race hypothesis for the evolution and maintenance of sexual reproduction?
    1. Explain how the Red Queen hypothesis explains why sex is advantageous in the face of parasites or disease .
    2. In Lively's study of New Zealand snail populations (Fig. 11.6), why are males less common in populations with low parasite infection rates?
    3. In Lively's study of New Zealand snail populations (Fig. 11.6), why are males more common in populations with high parasite infection rates?
  10. Discuss the persistence of asexual reproduction in Bdelloid rotifers (Box 11.1)
    1. How do they deal with parasites in the absence of sexual reproduction?
    2. Discuss the unusual mechanism present in these rotifers to produce new genes.
  11. Using information from chapter 11, define, give examples of, and explain the evolutionary significance of
    1. sexual dimorphism
    2. sexual selection
    3. two-fold cost of sex
    4. anisogamy
    5. uncertain paternity
    6. relative parental investment
    7. intersexual competition
    8. male-male competition
    9. intrasexual competition
    10. operational sex ratio
    11. female choice
    12. reverse sexual dimorphism
    13. direct benefits
    14. nuptial gifts
    15. indirect benefits
    16. good genes hyppothesis
    17. sensory bias hypothesis
    18. Fisher's Runaway selection.
    19. Sexy son hypothesis
    20. sperm competition
    21. monogamy
    22. polyandry
    23. polygyny
    24. Sperm competion
    25. altruistic sperm
    26. antagonistic sexual co-evolution
  12. Why can't sexual dimorphism be explained by natural selection?
  13. Why is sexual dimorphism a puzzle for evolutionary biologists?  Give examples.
  14. How do selection pressures on females usually differ from those on males?  What fundamental asymmetry does this lead to? 
  15. What is uncertain paternity? How may it explain why male parental care is rare?
  16. How does the operational sex ratio of some animals explain male-male competition?
  17. Discuss what limits reproductive success in male and female reed warblers (Fig. 11.8).    Explain how male reproductive output differs from female reproductive output.
  18. Discuss what limits reproductive success in male and female elephant seals (Fig. 11.12).  Explain how male reproductive output differs from female reproductive output.
  19. How do survivorship and lifespan (Fig 11.13A) and reproductive success (Fig. 11.13B) differ in female and male red deer? Explain why they differ. (Fig. 11.13).
  20. Discuss male-male competition in harlequin beetles (figs. 11.14A, 11.15).  What has been selected for in males?  Why does this give them a reproductive advantage?
  21. In female choice, what is the difference between direct and indirect benefits?
  22. Reverse sexual dimorphism occurs in birds such as the phalerope, sea horses, and pipefish. Discuss why they are considered "exceptions that prove the rule."  Explain the factors that have led to the males' appearance and reproductive strategies.
  23. Table 11.2 lists 5 direct benefits females may receive as a result of female choice.  Know and be able to give examples of all five (food, protection, territories/nests, help raising young, reduced risk)
  24. How do female katydids benefit from nuptial gifts (Fig. 11.16)?
  25. What is the evolutionary advantage of voluntary self-sacrifice in male redback spiders.  What life history conditions have led to this being selected for?
  26. Why are elaborate or bright male ornaments considered evidence of the good genes process?  How does it benefit the female? Table 11.3
  27. Female guppies prefer to mate with male guppies with bright orange spots (Fig. 11.22).  Why is this used as an example of pre-existing sensory bias for sexual dimorphism?  What else can explain theis?
  28. Discuss why sexual dimorphism in stalk flies is used as an example Fisher's Runaway selection.
  29. Discuss how female choice can explain sexual dimorphism in in red-collared widowbirds (Fig. 11.23).
  30. Why are ornaments costly in males such as the widowbird?  What is the evidence for this?
  31.  How was female choice in widowbirds tested experimentally?
  32. What is the evidence that polyandry selects for male traits that increase paternity in seed beetles?  what is the advantage of having long genital spines  (Fig. 11.26)
  33. What is the evidence that sperm competition drives evolution of larger testes in mammals such as primates (Fig. 11.27)?
  34. Why are sperm in some mice considered altruistic (Fig. 11.28)?  What factors caused the evolution of this behavior?
  35. Discuss how females benefit from polyandrous mating systems.
  36. Why are pipefish used as exception that proves the rule regarding sexual selection (Fig. 12.8)?
  37. Discuss how antagonistic co-evolution caused certain ducks to evolve bizarre reproductive structures in both males and females.
  38. Explain how Fig. 11.31 supports sexual conflict as an explanation for the reproductive tract morphology in female ducks .
  39. What is the evidence for antagonistic coevolution in Drosophila exposed to sexual conflict (Fig. 11.32)
  40. Why might male Drosophila benefit from seminal fluid containing chemicals that are harmful to a female?

Chapter 11: Short Answer Questions

  1. Why is sexual reproduction so widespread when the costs of reproducing sexually are so high?
  2. Would sexual cannibalism be more likely in a species with a mating system of polygyny or polyandry? Why? Upon what would the likelihood of sexual cannibalism depend ?
  3. House finch males differ in their expression of a sexually selected ornament, a patch of red feathers on the face and breast. Why might selection favor females who choose the male with brightest and most extensive red color, over others, as a mate?
  4. What is polyandry? Describe some of the advantages of polyandry to a female. How could this system of mating increase the chances of survival of her offspring?
  5. Why might male Drosophila benefit from seminal fluid containing chemicals that are harmful to a female

 

Review questions -- CHAPTER 13  For all of your answers EXPLAIN fully with examples as needed. 

  1. Define, give examples of, and explain the evolutionary significance with regard to speciation of
    1. biological species concept
    2. phylogenetic or evolutionary species concept
    3. metapopulation
    4. anagenesis
    5. cladogenesis
    6. isolating barriers
    7. extrinsic barriers to gene flow
    8. geographic barriers
    9. intrinsic barriers to gene flow
    10. reproductive barriers
    11. allopatry
    12. sympatry
    13. prezygotic reproductive barriers
    14. pollinator isolation
    15. habitat isolation
    16. gametic isolation
    17. gametic incompatibility
    18. postzygotic reproductive barriers
    19. Bateson-Dobzhansky-Muller Incompatibilities
    20. hybridization
    21. reinforcement
    22. geographic isolation
    23. allopatric speciation
    24. dispersal
    25. vicariance
    26. ring species
    27. sympatric speciation
    28. assortative mating
    29. sibling or cryptic species
    30. polyploidy
    31. horizontal gene transfer
  2. What are the advantages of the biological species concept?  The disadvantages?  What does it have in common with other widely used species definitions?
  3. What are the advantages of the  phylogenetic (evolutionary) species concept?  The disadvantages?
  4. Why are premating barriers important for speciation?
  5. Give examples of the following premating barriers and explain how they work
    1. Behavioral isolation
    2. Mechanical isolation
    3. Ecological isolation
  6. How do corals maintain reproductive isolation  (Fig. 13.4)?
  7. How do monkeyflowers maintain reproductive isolation  (Fig. 13.5)?
  8. How do carabus beetles maintain reproductive isolation (p. 420)?
  9. How do postmating but prezygotic reproductive barriers work (Fig. 13.7)
  10. What are the two intrinsic causes of lower hybrid fitness?
  11. What are the two extrinsic causes of lower hybrid fitness?
  12. Why is reinforcement important to speciation when two allopatric populations come back into contact?
  13. Divergent populations come can back into secondary contact 
    1. What are the two major possible outcomes of this process? 
    2. What are the three possible outcomes of hybridization?
    3. What favors and promotes reinforcement? 
    4. How can genetic engineering cause potential problems? 
    5. What is the significance of hybridization to plant evolution? 
    6. What factors promote genetic isolation even if there is no immediate contact between isolated populations?
  14. Define the two major classes of reproductive barriers (hint: = prezygotic and postzygotic) between closely related species?  Discuss the major examples of each of the two.
  15. What conditions are needed for hybridization to create a new species?  Give an example.
  16. Explain and compare and contrast isolation by dispersal and isolation by vicariance.
  17. What is the difference between allopatric and sympatric speciation?   How are allopatric and sympatric speciation similar?
  18. Is isolation essential for speciation?  Discuss its role in allopatric and sympatric speciation.  How do vicariance and dispersal differ as mechanisms promoting isolation?
  19. Explain the history o f Caribbean and Pacific snapping shrimp shown in Fig. 13.9.  What is the significance of the branching pattern .   How can this pattern be explained by geologic history.
  20. Discuss the stages and mechanisms involved in the evolution of Caribbean and Pacific snapping shrimp. What is the evidence that supports this hypothesis.
  21. How does Figure 13.13 suggest that speciation in Hawaiian crickets the result of dispersal events?  Include a discussion of the geologic history of these islands as it relates to speciation .
  22. Why is the Siberian greenish warbler important to our understanding of the speciation process?  Discuss how the genotype and gene flow of the Siberian greenish warbler varies across its range. Include a discussion of “speciation by force of distance” in the face of ongoing gene flow. What is required for speciation to occur?
  23.  Regarding Rhagoletis, the maggot fly.
    1. Are the flies that parasitize apples and hawthorns distinct races /species ? Why is this an unexpected conclusion? 
    2. What has led to the divergence of the apple and hawthorn races? Be specific about the processes involved.   Explain the role of natural selection in these processes.
    3. What are the three factors that led to the switch to apples? (i.e., the three factors that increase fitness by laying eggs on apples rather than on hawthorn fruit) 
    4. What alleles had to be modified for the switch from hawthornes to apples?  Why are hybrids between the apple/hawthorne races less fit than their parents?
    5. What conclusions about evolutionary processes can be drawn from this?
  24. Discuss the reinforcement processes at work promoting the genetic divergence of maggot flies.
  25. How can allopolyploidy lead to extremely rapid speciation (Figs. 13.15, 13.16)
  26. *******Dr. Bohm presented a guest lecture on Rice and Salt's laboratory experiment on Drosophila showing how selection could drive sympatric speciation. What was being selected for in the experimental groups? Why was this result a significant step in developing reproductive isolation?*******
  27. How has the use of the phylogenetic species concept when applied to giraffes modified our understanding of giraffe diversity?  Why is this important for conservation biology? 
  28. Discuss cryptic diversity in skipper butterflies in Costa Rica (Fig. 13.17).  Why were they regarded as a single species?  What DNA and morphological evidence suggests they are not?   Why is this important for conservation biology? 
  29. What is horizontal gene transfer and how does it create difficulties when trying to delineate bacterial species? 
  30. What is horizontal gene transfer?  What problems does this pose for the biological species concept?  the phylogenetic (evolutionary) species concept?
  31. Discuss the challenges of applying species concepts to bacteria and archaea.

 

End of Chapter Questions

  1. Predict what would happen if you took a female greenish warbler from the oldest, extreme southern end of its distribution and transplanted her to the most northern end of the warbler’s range in Siberia, where the two extremes of the ring species overlap. Would she be able to successfully mate with either an east or west Siberian warbler? Both? Neither? In your explanation, refer to both behavior and genetics.
  2. What are the similarities and differences between allopatric and sympatric speciation?
  3. . Why is allopatric speciation “easier” to achieve than sympatric speciation?

Freman and HeronWeb Site Questions 

  1. Describe the role of natural selection as a mechanism of genetic divergence using apple and hawthorn maggot flies to illustrate your answer. What mechanism is thought to have isolated these populations? What evidence suggests that genetic divergence has occurred and that natural selection is the mechanism responsible? Is divergence due to host and/or habitat switching rare or common? Defend your answer.
  2. Do hybrid offspring between genetically divergent parents always have reduced fitness?

Questions from Dr. Kilburn's webpage

  1. Compare and contrast anagenesis (phyletic change) with cladogenesis. Which represents "true" speciation (i.e., produces an increase in the number of species)
  2. Outline the three basic steps of cladogenesis. Compare and contrast allopatric speciation with sympatric speciation in terms of the geographic distribution of diverging species proposed by each. What kinds of barriers to gene flow do allopatric speciation models propose? Define and give examples of both dispersal and vicariant events and explain how each can be tested using the examples in the text to illustrate. What kinds of barriers to gene flow do sympatric speciation models propose? Outline the basic process by which each can produce a barrier to gene flow, using relevant examples to illustrate your answer.
  3. Explain the role played by genetic drift and natural selection in causing the genetic divergence of isolated populations. Discuss Mayr's model of allopatric speciation by peripheral isolation. Does the current evidence support as important a role for genetic drift as he proposed? Explain. Using the example of Rhagoletis pomella to illustrate, describe how selection can promote genetic divergence of isolated populations. Be sure to include the experimental tests of the relevant hypotheses in your answer.
  4. Describe Dobzhansky's reinforcement hypothesis for the evolution of reproductive isolating mechanisms. What is the current evidence for the importance (or non-importance) of reinforcement? Outline the major reproductive isolating mechanisms as classified by Dobzhansky, being sure to define and give an example of each.

 

 

Review questions -- CHAPTER 14  For all of your answers EXPLAIN fully with examples as needed. 

 

  1. Discuss how the relationship beteen origination rates and extinction rates determine biological diversity.

  2. How do vicariant events affect biogeography?  How does this affect biodiversity?

  3. Regarding marsupial mammals (Fig. 14.6)

    1. How has plate tectonics resulted in the present distribution of marupial mammals? 

    2. Where did marsupials originate? 

    3. How did they get to Australia? 

    4. What is the significance of the fossil marsupials in Anartica? What is their relationship to living marsupials in South America? In Australia?

    5. Why are marsupials more diverse in Australia than elsewhere in the world?

  4. How do vicariance and dispersal account for the present distribution and diversity of marsupials?

  5. The living South American marsupials form a paraphyletic group.  Explain why this is significant.

  6. How is the fossil record of biological diversity biased so that it may not accurately reflect past biological diversity (Fig.14.9).  What does an unadjusted fossil record show about the diversification of marine invertebrates? What is the evidence that Raup and colleagues used to show was the actual pattern?

  7. Characterize the three "evolutionary faunas" (Fig. 14.8).

  8. Discuss the factors that may led to the adaptive radiation of the Hawaiian honeycreepers (Fig. 14.11).

  9. Why are the Hawaiian silverswords are considered “the best example of adaptive radiation in plants” (Fig. 14.12)? What geographic, environmental, and genetic factors led to this diversity? How does this phenotypic and genetic diversity compare to their mainland relations? What does their genetic diversity indicate about the causes for their diversification?

  10. How does the genetic diversity of the Hawaiian silverswords compare to the genetic diversity of their closest mainland relatives, the tarweeds?  (Fig. 14.15)?  What does this show about the evolution of the silverswords?

  11. Why are cichlids in African lakes excellent examples of adaptive radiations? of convergent evolution (Fig. 14.13)?  What is it that makes the Lake Victoria cichlids the most impressive example?

  12. What is the Cambrian "explosion"?  Was it really an explosion?  What is the evidence for it being or not being an explosive event?   What is the evidence for increased complexity of biological interactions during this event? 

  13. What are the two most important environmental causes for the Cambrian explosion? Explain how each affected life on earth.

  14. What genetic changes may have led to this event? Explain how this led to animal diversification.

  15. What does the fossil record show about the diversity of multicellular life in the 100 million years before the start of the Cambrian?

  16. How did the evolution of predators affect the diversification of life in the Cambrian (Fig. 14.17)?

  17. What do the Burgess Shale fossils indicate about the evolution of the phylum Arthropoda  (Fig. 14.16)?

  18. How are the five largest mass extinction events recognized in the fossil record?

  19. What may have caused the end Permian mass extinction? How did it affect life on earth during and after the extinction?

  20. What may have caused the end Cretaceous mass extinction? How did it affect life on earth during and after the extinction?

  21. What is the evidence that humans may be driving a sixth mass extinction?  How does habitat loss contribute to extinction today?

  22. How do current extinction rates compare to background extinction rates?  If threatened and endangered organisms are included, what does this indicate about a likely mass extinction?

  23. How do todays carbon dioxide levels compare to those of the past one million years?  How will future carbon dioxide levels affect biodiversity?

  24. Using information from chapter 14, define, give examples of, and explain the evolutionary significance of
    1. microevolution
    2. macroevolution
    3. biogeography
    4. evolutionary fauna
    5. adaptive radiation
    6. background extinction
    7. mass extinction
    8. Ediacaran biota
    9. Burgess Shale Fauna

End of Chapter Questions

  1. What are the differences between microevolution and macroevolution? What are the similarities?

  2. Should humans be concerned about the pace of extinctions of organisms that are not directly related to our survival?

  3. What lines of evidence have macroevolutionary biologists used to determine the origin of marsupials? How are these lines distinct?

  4. How did an increased understanding of plate tectonics help biogeographers better understand the distribution of species.? 

  5. Why did David Raup feel that the amount of amount of physical area and volume of preserved rock was important to examine when calculating changes in biodiversity through time?

  6. Discuss two abiotic factors that may have contributed to the profusion of animal diversity during the Cambrian.

  7. Describe lines of evidence suggesting an asteroid impact may have contributed to the end-Cretaceous extinction.          

 

 

 

Review questions -- CHAPTER 1.2 and CHAPTER 18  For all of your answers EXPLAIN fully with examples as needed. 

 

  1. What is a retrovirus?  How are retroviruses similar to other kinds of viruses?  How do retroviruses differ from other kinds of viruses?
  2. How do retroviruses reproduce? Include all the steps in the life history of the flu virus. (Figs. 1.18, 1.19)
  3. During which of these stage of the flu life cycle is new variation produced? Explain how. (Figs. 1.18, 1.19)
  4. What are the three factors that enable flu viruses to evolve so rapidly?
  5. How do viruses recognize which cells they have evolved to infect? How do they attach to the host cell?
  6. Why do flu viruses have such a high mutation rate?
  7. What are the molecular and evolutionary significances of replication using reverse transcriptase rather than DNA polymerase? Explain why there are these differing results.
  8. Describe the Influenza A genome (Fig. 1.17).  Why is this interesting?
  9. What is the difference between a drug and a vaccine?  How are each used in treating and/or combating infectious diseases?   
  10. What is an epitope (antigenic site)?  What is the advantage of having a high mutation rate in the genes that code for them?
  11. What is a vaccine? Explain the molecular basis of how they work. Include a discussion of epitopes
  12. What are the two most important mechanisms for the flu virus to change genetically?
  13. What is function of hemagglutinin in the flu virus?  What is the significance of its antigenic sites?
  14. Outline the structure of the influenza A virus and briefly relate that structure to human immune response to the virus.
  15. How are viruses able to shuffle genes? (Fig.1.22)
  16. Why are new flu vaccines needed yearly?
  17. What do the H and N stand for in a flu virus identied as the HxNy strain?  What to the numbers x and y indicate (Fig. 1.23)?
  18. What is viral reassortment? What was its role in the production of the 2013 H7N9 flu strain (Figs. 1.23)
  19. Discuss the reasoning behind, and evidence for, the hypothesis that flu pandemics such as the 2009 H1N1 pandemic begin when human and bird strains of influenza A simultaneously infect a pig, swap genes, then infect people.

Chapter 18

  1. Why is important for health professionals to understand Evolutionary Medicine?
  2. What enables pathogens to evolve so rapidly?
  3. What is the evidence that the human herpesvirus 5 has had a long co-evolutionary history with other species of mammals? Discuss and explain figure 18.9.
  4. What does a comparison of the evolutionary history of parasites (such as herpeviruses) with the evolutionary history of their hosts (such as primates including humans) usually demonstrate (such as in Fig. 18.9)? How does this provide additional support that humans and chimps share a common ancestor?
  5. What is the evidence that MERS in an emergent disease, new to our species?  Where did it come from? What is the evidence for this (Explain figure 18.11)?
  6. Alhough palm civets carry a SARS-like virus, the evidence shows that civets are not the source of human infections. How did humans and civets both get infected? What is the evidence? (Fig. 18.4)
  7. How was a polio vaccine made from live polio viruses, so that they rarely cause health problems for humans? (Fig. 18.12)Include a discussion of natural selection on the virus.
  8. How have virologists used natural selection to make a polio virus that rarely caused human illness? Why could this virus still be used to make a vaccine?
  9. For a pathogen, what is host shifting?  What conditions are needed for it to occur?
  10. For a pathogen, what is vertical transmission? What will be selected for in pathogens for this process?
  11. For a pathogen, what is horizontal transmission? What will be selected for in pathogens for this process?
  12. Discuss how the transmission rate hypothesis explains whether pathogens will have high or low virulence.
  13. What is the source reservoir of the Ebola virus? Why hasn't Ebola become epidemic in human populations?
  14. What are the two most important mechanisms for the flu virus to change genetically?  Why are new flu vaccines needed every year?
  15. Why are viruses that have more opportunities for horizontal transmission more virulent than those that have fewer?
  16. Why are vectorborne pathogens more virulent than those that are transmitted directly?   Explain the role of natural selection in this process
  17. What human conditions made the 1918 flu so virulent? Explain in terms of the transmission rate hypothesis.
  18. What was learned about the 1918 flu when it was recreated by Tumpey et al?
  19. What is meant by host/pathogen coevolution?  Explain the role of natural selection in this process.
  20. Why is host-pathogen coevolution referred to as an 'evolutionary arms race'?
  21. In what sense(s) are pathogens and hosts in conflict?
  22. Do antibiotics directly cause the mutations that confer resistance in bacteria such as Staphlococcus aureus.  Explain and justify your answer.
  23. Why did diseases such as smallpox and measles have such a devastating impact on populations native to the Americas, while the Europeans who transmitted them were much less seriously affected by them?
  24. Discuss the role of mutation and selection in generating the evolutionary advantages and disadvantages that made the sickle-cell anemia allele (HbS) common in Africa. Why is this allele so rare in the United States and northern Europe. How does selection act on the three genotypes in both locations.
  25. Discuss the evolution of antibiotic resistance? Explain the role of natural selection in this process.
  26. What is Achromatopsia? Discuss and explain the evolutionary processes that caused it to become so common among the Pingalapese.
  27. What evolutionary processes have caused Ellis-van Creveld syndrome to be so common among the Amish?
  28. Discuss the statement "Aging can be explained by evolutionary trade-offs" in relation to antagonistic pleiotropy. Why does natural selection act on individuals differently in youth and in old age.
  29. Why does natural selection act on individuals differently in youth and in old age?
  30. Huntington's disease is a homozygous dominant lethal allele.  Why is it unusually common, since natural selection should eliminate it?
  31. What is the function of the p53 tumor-supressor protein?  At what life stage is it beneficial? Harmful? Explain the reasons for this difference?

End of Chapter Questions

  1. Why are outbreaks of the Ebola virus so localized?
  2. Would you consider the HbS allele to be an adaptation to malaria? Why or why not?