Contents 

• Part I: Introduction
• Chapter1: Introduction; History of Evolutionary Thought
• Chapter 2: Mendelian and Molecular Genetics
• Chapter 3: The Evidence for Evolution
• Chapter 4: Natural Selection and Variation
• Part II: Evolutionary Genetics
• Chapter 5: The Theory of Natural Selection 
• Chapter 6: Random Events in Population Genetics
• Chapter 7: Molecular Evolution and the Neutral Theory
• Chapter 8: Multilocus Models
• Chapter 9: Quantitative Genetics
• Part III: Adaptation and Natural Selection
• Chapter 11: The Analysis of Adaptation
• Chapter 12: The Units of Selection
• Chapter 13: Adaptive Explanation
• Part IV: Evolution and Diversity
• Chapter 14: Evolution and Classification
• Chapter 15: The Idea of a Species (Kilburn)
• Chapter 15: Species concepts (Koenemann)
• Chapter 16: Speciation
• Chapter 16: Speciation (Koenemann)
• Chapter 17: Phylogeny reconstruction (Koenemann)
• Chapter 18: Evolutionary biogeography (Koenemann)
• Comprehensive questions for final exam

Introduction 
1. Briefly state the different meanings of the term "evolution." 

2. Briefly describe some of the ways evolutionary thought has been misapplied to political, social, and/or economic thought. 

Chapter 1: History of Evolutionary Thought 
1. Who was Plato? Describe his Theory of Forms (essentialism/idealism) and explain, using examples, how this idea affected biological thought. How is it manifested today? 

2. Who was Aristotle? Describe his scala naturae, including its important implications.  

3. How did Aristotle's view of the ideal differ from Plato's? What were the consequences of this for later biologists? 

4. Describe Aristotle's four causes. What is teleology? 

5. Were the Dark Ages "dark" everywhere in the world? Why or why not? 

6. Describe the major changes in scientific thought that characterized the early Renaissance. 

7. Describe the major changes in scientific thought that characterized the late Renaissance. Why did a strong vitalist teleology begin to permeate the natural sciences? What were its primary characteristics? 

8. Discuss the role of the Industrial Revolution in "driving" the Enlightenment. What specific contributions did the development of geology make to the growth and change in biological thought? 

9. What were the common beliefs/approaches shared by the comparative anatomists, embryologists, and other biologists of England, France, and Germany during the late 1700's - early 1800's? 

10. Describe the specific contributions and ideas of Linnaeus, Lamarck, and Cuvier. Compare and contrast Lamarck's, Cuvier's, and Aristotle's views about the cause and pattern of biological diversity (e.g., their views on change and the organization of living things into recognizable categories). 

11. Briefly outline the key elements of Darwin's intellectual context (i.e., what ideas were common, which ideas were changing?). 

12. Describe Darwin's early history, through the voyage of the Beagle, with attention to the key events that later helped him develop his ideas about descent with modification. 

13. Describe Darwin's later life, including the roles of Lyell, Hooker, and Wallace. Why is Darwin, rather than Wallace, generally credited with "the theory of evolution"? 

14. Discuss the key elements of Darwin's ideas about descent with modification. In what ways were these ideas new and/or radical? 

15. Why was Darwin largely successful in convincing the scientific community of the historical fact of descent? Why was he largely unsuccessful in convincing the scientific community of the importance of natural selection? 

16. What was the Modern Synthesis? Describe the important events that took place during this time, using examples of specific individuals to illustrate your points. 

17. Give an overall summary of the key changes in how we view and study the natural world from the time of the Greeks to the present. 

2. Describe the function of DNA and RNA (including the differences between them) from the level of the components of nucleotides to the level of the functional polymer. 

3. What feature(s) of DNA allow self-replication? What kind of information does DNA store? How? 

4. Briefly describe the processes by which DNA is replicated and by which the information from DNA is used to synthesize proteins. 

5. Why is the genetic code a triplet code? What does it mean to say that the genetic code is redundant? 

6. Describe the organization of DNA into chromosomes in eukaryotes. Include a description of introns/exons and how they are processed during transcription and translation. 

7. Described the major types of point mutation as classified according to (a) the kind of change taking place and (b) the effect of the change on amino acid sequences. 

8. Describe the major types of chromosomal mutations. In what general way can these mutations affect genetic information? 

9. Define the terms gene, locus, allele, haploid, diploid, homozygous, heterozygous, genotype, phenotype. 

10. Be able to "work" simple Mendelian patterns of inheritance in one and two-gene systems given simple and incomplete dominance. 

11. Briefly describe the phenomena of linkage, recombination, co-dominance, pleiotropy, and polygenic inheritance. 

2. List and briefly describe the three "levels" of scientific explanation, from the most tentative to the least tentative (most certain). 

3. Describe the evidence, from studies of both natural and laboratory systems that a) species exhibit small scale variation and/or change over time; and b) the amount of variation seen in nature and in laboratory systems is sufficient to "cross species boundaries" (i.e., is sufficient to give rise to reproductively isolated groups). c) What basic principles of scientific thought allow us to generalize from small scale patterns and processes to large-scale patterns and processes? 

4. Describe the evidence from homology, vestigial structures, the fossil record, and biogeography that living species are related by descent? Be sure to define all relevant terms. 

2. Compare and contrast directional, stabilizing, and disruptive selection using both graphical models and actual examples. 

3. Briefly describe the methods used to assess variation at the level of proteins and DNA. In general, how does the amount of variation change as we move from the level of morphology to proteins to DNA? 

4. What are the sources of genetic variation? Is genetic variation random with respect to the environment? Explain why or why not, and discuss the consequences of this for our view of evolution. 

2. Give the "population genetics" definitions of genotype frequency, gene frequency. How are each of those calculated? Define P, Q, R, p and q. Can gene frequencies be calculated from genotype frequencies? If so, how? If not, why not? Can genotype frequencies be calculated from gene frequencies? If so, how? If not, why not? 

3. Outline the general steps used to answer the question "given gene or genotype frequencies in generation n, what will be the gene or gentoype frequencies in generation n+1." 

4. Explain/describe the Hardy-Weinberg equilibrium in both words and mathematical symbols. Be sure to include the conditions under which this equilibrium will exist. 

5. Describe how to determine gene frequencies from genotype frequencies in a population. Be able to perform that calculation. 

6. Describe how to test the hypothesis that a populatin is in Hardy-Weinberg equilibrium given its genotype frequencies. Be able to perform such a test. 

7. Define, both verbally and mathematically, the terms selection coefficient and fitness. How are they abbreviated? 

8. Describe how to determine the change in gene frequency in a population given its genotype frequencies and selection coefficients. Be able to perform this operation. 

9. Describe, verbally, graphically and mathematically, the general outcome of selection against a recessive trait. 

10. Describe, verbally and mathematically, how deleterious dominant mutations may be maintained in populations over time. 

11. Verbally define/describe heterozygote advantage, using sickle-cell anemia as an example. What is the effect of this phenomenon on genetic variability? Define the term balanced polymorphism. 

12. What will be the outcome for gene frequencies if selection coefficients vary (1) with the frequency of genotypes in the population or (2) among habitats within an environment? Give examples and define all relevant terms as appropriate. 

13. What are the potential consequences of population subdivision and migration on gene frequencies? Give examples and define all relevanat terms as appropriate. 

2. Explain the probabilistic nature of the Hardy-Weinberg equilibrium. 

3. Define the terms "genetic drift", "random drift", "neutral drift". 

4. Explain the relationship between the rate of change due to drift and population size. In what two specific ways will this relationship be manifested (i.e., exactly what will change as population size decreases?). 

5. Explain figures 6.1 and 6.4 in the text. 

6. Describe the processes referred to as "founder effect" and "bottleneck effect". In what specific ways will populations experiencing these effects differ from their parent populations? What are the consequences of these effects for conservation? Use examples as appropriate. 

7. Describe the relationship between genetic drift and levels of homozygosity in populations. How is that relationship affected by population size? Explain in both mathematical and biological (verbal) terms. 

8. Explain, mathematically and biologically/verbally, how the "march to homozygosity" might be balanced in natural populations. Define all relevant terms and explain how the process you've identified is mediated by population size. 

9. What are the "general" and "population genetics" definitions of N (population size)? Define Ne (effective population size), explain its relationship to drift, and describe four ways in which Ne may be decreased. Use examples as appropriate. 

2. Explain how rates of change in DNA and proteins are calculated, including what kinds of measurements are used. 

3. Name, define, and be able to calculate (given a simple example) the two measures of protein polymorphism used to describe levels of protein variation in populations. 

4. Define the term "genetic load" and explain why selectionists predict that it limits the rate of evolutionary change and the amount of polymorphism that ought to occur in natural populations. 

5. Describe the predictions made by the "neutral" hypothesis about rates of evolutionary change and levels of heterozygosity in natural populations. Which predictions are met by the available empricial evidence? Explain. 

6. Describe the phenomenon referred to as the "molecular clock." Which of the two hypotheses predicts its existence, and why? Which of the two hypotheses is best supported by the available evidence? Explain. 

7. Describe the difference in rates of evolution between functionally constrained and unconstrained regions of DNA and proteins. Which of the two hypotheses do these patterns support? Explain. 

2. Define the term "haplotype" and "haplotype frequency". To what element of single-locus models are these terms analogous? 

3. Describe, in general terms, the relationship between haplotype frequency and the degree of linkage between loci. What structural feature of chromosomes determines the degree of linkage between loci? Define "linkage disequilibrium" conceptually and discuss the range of values it can have. What do D values of 0 and 1 mean biologically? 

4. Explain the change in linkage disequilibrium that would occur if two tightly linked genes had no selection pressure acting on them (be sure to explain why this happens). Would this result be obtained as quickly as Hardy-Weinberg equilibrium would be? Why or why not? 

5. Other than selection, what natural processes can cause linkage disequilibrium? 

6. Describe the effects of selection on linkage disequilibrium on genes with independent fitness effects and those with epistatic fitness effects. 

2. Describe the patterns of beak size observed in Galapagos finches before and after the drought of 1976-77. Be sure to address the pattern of variation in beak sizes between and within species, the relationship of beak size to food size, the genetic basis for beak size, and how changes in selection pressures changed beak size. Also be sure to include evidence as appropriate. 

3. Describe the way in which the basic population genetics model "dissects" phenotypic variation among individuals. Be sure to define P, G, and E and the relationship between them. Then compare and contrast additive and dominance genetic effects -- what are they, and which is more important for natural selection? 

4. Describe how the basic model in #3 is extended to whole populations. Under what conditions might populations exhibit large responses to selection? Under what conditions will resonses to selection be limited? 

5. Define the term "heritabiliy" and give its mathematical formula. Under what conditions might h2=0? Under what conditions might h2=1? What are the consequences of those values of h2 for selection? 

6. Describe how selection differentials and responses to selection are measured. Discuss the the corn-oil directional selection experiments at the State Agricultural Laboratory in Illinois, with special attention to the effects of continued selection on the response to selection and on heritability. What implications do these results have for the long-term consequences of directional selection in nature? 

7. Using pink salmon and Galapagos finches as examples, explain how the basic quantitative genetics model may be used to study the strength of and response to selection in natural populations. 

8. Describe the "reduced variation problem" of population genetics. What is it, and what solutions have been proposed for it? 

2. Describe the general approach used to test adaptive hypotheses. Explain, as appropriate, why each step is necessary and relate this approach to the major steps of the "scientific method." Be sure to mention what the alternative(s) to adaptive hypotheses is/are. 

3. Define "sexual selection" and discuss the observations that led Darwin to propose it as an important mechanism of evolution. What two general mechanisms drive the evolution of male ornamentation? Explain how Darwin tested this model (be sure to include the reasoning behind the test; don't forget the relationship between the strength of selection and the mating system). 

4. Compare and contrast the general "good genes" and "runaway" models for sexual selection via female choice. Be sure to address the assumptions and "requirements" of each. 

5. Explain the basic "runaway" process as described in class. Describe Ryan's sensory exploitation model, explain how it's been tested, and discuss its relationship to runaway models in general. 

6. Explain Zahavi's "handicapped male" and Hamilton and Zuk's "parasite-load" hypotheses. How has the latter hypothesis been tested, with what results? 

7. Is male ornamentation adaptive? Describe the state of our understanding of this phenomenon in terms of analyzing adaptation. 

Chapter 13: Adaptive Explanation 
1. Describe the relationship between natural selection, adaptation, and other evolutionary processes. 

2. Describe the general properties an adaptive explanation must have in order to explain the evolution of complex structures. Explain the "argument from design" in this context. 

3. In The Origin, Darwin wrote: "To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree." Of course, he then made a good argument in favor of selection as the mechanism responsible for the evolution of the eye. Set Mr. Darwin's mind at rest by discussing the current evidence in favor of the evolution of the eye by natural selection. 

4. Can natural selection explain the evolution of complex traits? Explain. 

5. What major components must be included in a good evolutionary history of a given trait? Within that context, compare and contrast the "historical" and "current function" definitions of adaptation. Which is right? Justify your answer. 

6. What is "naive adaptationism"? Are all traits adaptations? Are all beneficial traits adaptations? Justify your answers. 

7. Can natural selection produce "perfect adaptation"? Discuss the constraints on selection, using examples to illustrate as appropriate. 

2. Outline the major areas of controversy about biological classification. What, if any, areas of agreement exist? Be specific. 

3. Compare and contrast phenetics, cladistics, and evolutionary systematics in terms of (1) the kind(s) of information on which each bases its classifications, (2) the special procedures (if any) used to construct classifications based on that information, and (3) the current status of each in current practice. Be sure to include the relative practical advantages and disadvantages of each, as well as any specific analytical techniques each may have developed. 

4. Define the terms monophyletic, paraphyletic, and polyphyletic. Which kinds of lineages are recognized by each of the three major schools of classification? 

5. Defend the statement (contrary to the author of your text) that all biological classification systems are arbitrary and subjective. 

2. Who developed the biological and evolutionary species concepts? When? In general terms, what prompted each author to develop his species concept? 

3. Compare and contrast morphological, biological, and evolutionary species concepts. What are the relative strengths and weaknesses of each? 

4. Explain "logical connection" among the three species concepts. Are these concepts mutually exclusive (i.e., is one "right" and the others "wrong"?). 

5. Briefly discuss key "problem areas" for current species concepts (i.e., for what kinds of groups is identifying species "boundaries" difficult, and why?). Do these problem areas represent difficulties for the validity of evolutionary theory in general? Why or why not? 

6. Describe the difference between "defining" and "recognizing" species. 

2. What general process must be involved in any speciation process? Why is this process necessary (explain in terms of population genetics). 

3. Define the terms allopatric, parapatric, and sympatric. 

4. Why is allopatric speciation generally considered the most "important" mode of speciation? 

5. Describe the process of allopatric speciation, including examples of barriers to gene flow and the processes responsible for genetic divergence. What are the three basic possible outcomes? Include a definition and brief discussion of reinforcement. 

6. Describe and give an example of each of the major prezygotic reproductive isolating mechanisms. Define the forms of postzygotic isolation and briefly describe their underlying mechanisms. 

7. What is speciation by peripheral isolation? Summarize Mayr's arguments for believing that this form of allopatric speciation has been both common and powerful. Describe the evidence for and against this view. 

8. Describe the process of parapatric speciation. Compare the role of hybrid zones in this model with that played in allopatric speciation. Summarize the evidence for and against this general model. 

9. Describe the "special case" of parapatric speciation via chromosomal mutation. What specific role to chromosomal mutations play in this model? In what kind(s) of organisms might we expect to see this process? 

10. Describe the conditions generally necessary for sympatric speciation to take place. Describe the models proposed for sympatric speciation in green lacewings and in phytophagous insects. 

11. Describe, in general terms, the processes involved in sympatric speciation in plants. 

12. Define the term adaptive radiation. Does this process involve speciation mechanisms other than the ones discussed above? 

13. Discuss the general conditions thought to be required for an adaptive radiation to take place. Why are these thought to be necessary? 

14. Describe the general process of adaptive radiation using Hawaiian honeycreepers and African cichlids as examples. 

Part I: Introduction  
1. Describe Platonic idealism and Aristotelean teleology (final cause). In what ways do those ideas linger in our popular (non-scientific) culture? What ideas in modern evolutionary biology have replaced them? 

2. Describe the evidence from studies of natural and laboratory systems that speciation is possible. Describe the evidence that living things are related by descent.  

3. Under what conditions will natural selection occur? Compare and contrast directional, stabilizing, and disruptive selection; give at least one example of each and be able to recognize which is operating from written or graphical information. 

4. What are the sources of genetic variation? Describe what is meant by the statement that "genetic variation is random with respect to the environment". 

Part II: Population genetics 
1. Describe, in general terms, what mathematical models are and how they are used. Illustrate this by describing the general framework and uses of single-locus, multi-locus, and quantitative genetics models. 

2. List the conditions under which the Hardy-Weinberg equilibrium will occur; identify and briefly describe the general processes that might be expected if each of the conditions were violated. 

3. Explain the relationship between epistasis, coadapted genes, and supergenes.  

4. Describe the relationship between supergenes, natural selection, and linkage disequilibrium. 

5. Describe Sewall-Wright's adaptive landscape model. Explain the relationship between this model and Gaylord Simpson's evolutionary species concept. 

6. Defend the statement that quantitative genetics is the most useful population genetics model for studying natural populations. Use examples as appropriate. 

Part III. Adaptation 
1. Describe the general approach used to test adaptive hypotheses and compare this to the general scientific method for hypothesis testing. 

2. Compare and contrast sexual and natural selection. Do these processes always work in "opposite" directions? Justify your answer. 

3. What are the units of selection? Justify your answer. 

4. Describe the relationship between natural selection, evolution, and adaptation. 

5. Describe the characteristics an adaptive hypothesis must have in order to explain the evolution of complex traits. 

2. Describe the major steps in the process by which a new species is introduced to the scientific community. What is the "Red Book"?   Explain the difference between a description and a diagnosis. 

3. Based on the description in #2 above, what problems can you identify that might arise in the case of species described on the basis of a single specimen? 

4. Compare and contrast the morphological (typological), biological, ecological, cladistic, and  phenetic species concepts. Be sure to include a brief definition of each, its major proponents (if any), and its advantages and disadvantages. 

5. What is the pluralistic species concept? Illustrate its potential advantages using polytypic species, syngameons, and character displacement (it would probably be a very good idea to describe those phenomena!). 

6. Are species real units in nature? Are higher taxonomic categories real units in nature? Defend your answer (note that it may vary with species concepts – so you should probably address that). 

1. What essential process must occur for speciation to take place? 

2. What is clinal variation? 

3. Outline the major reproductive isolating mechanisms and give at least one example of each. Under what condition(s) will these mechanisms evolve? Define and briefly explain the process of reinforcement. Is this a well-established process, or is it more hypothetical? 

4. Describe the general process of allopatric speciation, being sure to address both"dumb-bell". What process(es) produce(s) barriers to gene flow? What are the possible outcomes when formerly isolated populations come back into contact? Compare and contrast the "dumb-bell" and peripheral isolates models of allopatric speciation. Why does Mayr believe that peripheral isolation is more likely to result in speciation than the "dumb-bell" model? What key prediction can be used to test this hypothesis? 

5. Describe the parapatric model of speciation. What essential characteristic must a species exhibit if parapatric speciation is going to be possible? Compare and contrast the hybrid zones produced by this mechanism with those produced by allopatric speciation. Which of the two processes is considered to be more common? 

6. Define "sympatric speciation". Under what conditions is it thought to be possible in animals (give examples)? In plants? In which of the two groups is it more common? 

7. Define "adaptive radiation" (include a definition of "adaptive zone"). Under what conditions might adaptive radiation take place? Give examples. 

1. Define "phylogeny". Explain why our ability to reconstruct phylogeny is important. 

2. Describe the general steps used in cladistic analysis to determine common ancestry. What does it mean when we say that character states are polarized? How do we determine ancestral states? 

3. Compare and contrast homologous and analagous characters. For each type of characteristic, outline the major forms they may take. Which forms are used in cladistic analysis and why? 

4. What is a cladogram? What does it represent? 

5. Discuss the major types of molecules that are used to reconstruct phylogeny. What are the relative advantages and disadvantages of using these types of data? Are the methods or principles of analysis different for biochemical than for morphological data? Are all molecular data equally valuable for all types of studies? Explain. 

6. What is the "total evidence" approach to phylogeny reconstruction? 

7. Define "parsimony" as it applies to phylogenetic inference and describe how it is applied. 

8. Briefly explain likelihood and distance methods of analysis. Which is more commonly used and for what kind(s) of data? 

1. How is "biogeography" generally defined? 

2. Given a map with faunal regions delineated, be able to correctly identify Nearctic, Palearctic, Neotropical, Ethiopian, Oriental, and Australian faunal regions. 

3. Compare and contrast endemic, disjunct, and global distributions. Are these types of distribution mutually exclusive? Explain. 

4. Define "dispersal" and discuss the general processes that this may involve (or the various forms it may take). 

5. Discuss the way(s) in which ecological factors may limit species distributions. Define fundamental and realized niches, being sure to clearly state the relationship between them. Are species always distributed in places where conditions are appropriate to their fundamental niches? If not, why not? 

6. Define "center of origin", "refuge" and "dispersal corridor" and give an example of each. 

7. Describe how historical factors may affect species distributions, using the Pleistocene "ice ages" to illustrate. Use the model of glacial forest refuges to link concepts of biogeography with allopatric speciation. 

8. Define "vicariance" and "vicariant event." 

9. Name the scientist generally credited with "discovering" continental drift. Why wasn't his model accepted at the time it was developed? When did it become widely accepted? 

10. Explain the relationship between continental drift and vicariance. Before continental drift became widely established, what was the major hypothesis used to explain patterns of species distribution? 

11. Describe how dispersal and vicariance hypotheses can be tested. Use examples to illustrate your answer.