Chapter 5

1. Know end of chapter questions 1, 4, 5, 8, 10, 11, 12, 13
2. I will emphasize section 5.2 and gene duplication portions from lecture.
3. What are the different types of mutations?
4. What are the following types of substitutions/mutations? replacement, silent, synonymous, non-synonymous, neutral, deleterious, advantageous.
5. Calculate allele frequencies from genotype counts or frequencies.
6. Do most populations harbor large or small amounts of genetic variation at most genes? What is the evidence?
7. Interpret maps showing geographic variation in ABO allele frequencies, CCR5 allele frequncies, ADH frequencies in flies, LDH frequency in fish, etc.
8. What is the evidence that gene duplication is common?
9. Explain the evolution of hemoglobin genes in terms of gene duplication and divergence in function after duplication.
   
   

Chapter 6

1. End of chapter questions 1, 3, 5, 6, 7, 8
2. Know Quiz questions 1, 3-6, 8-15, 17, 21, 22.
3. Know homework results! I will emphasize these.
4. I am very likely to ask you to provide an evolutionary explanation for an empirical pattern. You need to explain in terms of the evolutionary forces described in chapters 5-7.
5. Given genotype frequencies at time 1, be able to predict the genotype and allele frequencies at time 2, given that all the assumptions of the Hardy-Weinberg model occur. What are the assumptions of the Hardy-Weinberg model?
6. Assuming Hardy-Weinberg conditions, calculate the frequency of a rare, recessive allele given the frequency of recessive homozygotes.
7. If you are given the equation for our general model of selection, be able to use it to predict change in allele frequency, given starting frequencies and relative fitness of each genotype.
   
   
8. What is the relationship of the rate of evolution to a) the strength of selection and b) amount of genetic variation?
   
   
9. What are directional selection, overdominance, and underdominance? What are the equilibrium allele frequencies for each? Which one can maintain a stable polymorphism?
   
   
10. What is frequency dependent selection? Can it maintain a stable polymorpism? Give at least two examples.
    
    
11. What is balancing selection? What pattern of DNA sequence variation is associated with balancing selection? Given an example.
12. What phylogenetic patterns are caused by balancing selection? (examples: MHC genes, self-incompatibility genes)
    
    
13. Why is it difficult for selection to completely eliminate a deleterious recessive allele from a population? How is this observation relevant to the U.S. government’s efforts to eliminate undesirable traits by sterilizing people with those traits in the first half of this century?
    
    
14. In a large population (no drift) why is it difficult for a new mutation that is recessive but advantageous to rise to high frequency in a population? (for example, set allele A1 initial frequency=.001, fitnesses=(2, 1, 1), and population size=infinite. A1 barely begins to rise by 1000 generations).
    
    
15. What is mutation-selection balance? How is it related to q_equilibr.= squareroot(m/s)? Why does it seem unlikely that the frequency of Hb^s or the CFTR loci are maintained by mutation-selection balance? What hypothesis seems more plausible?
    
    
16. How can selection result in evolutionary divergence of two populations?
17. Why is the CFTR allele thought to be maintained by overdominance (describe how different CFTR genotypes affect fitness).
18. What is the evidence for overdominance at the CFTR locus?
19. Examples to know: MHC loci; Elderflower flower color; Selection on the CCR5 D32 allele. Is HIV likely to cause a rapid increase in the D32 allele in Africa?
20. Pier and his colleagues have found, in 11 European countries, an association between the severity of typhoid outbreaks and the frequency of the delta-F508 allele of CFTR (the most common loss-of-function mutation) a generation later. What hypothesis is this a test of? Is it a fair test? Explain.

Chapter 7.

21. Know quiz questions 1-13, 15-19, 21, 22.
22. End of chapter questions 1, 3, 4, 5, 8, 9, 13, 14
23. What is gene flow. Does it always involve migration of individuals? What determines the rate of evolution by gene flow?
24. How does gene flow between two populations affect the allele frequencies in them (in the absence of other evolutionary forces)?
25. How does gene flow affect the divergence of populations?
26. What is a cline? Give a real example. What forces interact to maintain a cline, and how do they do it? What would be the result of either force acting in the absence of the other? How does this all relate to Lake Erie water snakes?
27. What is genetic drift? What are its main effects? How are bottlenecks and founder events related to genetic drift?
28. Why does genetic drift predict a relationship between population size and genetic diversity? Why is this prediction important for conservation biology?
29. What determines the rate of evolution by genetic drift?
30. How does the genetically effective population size (N_e) differ from the actual population size? How does unequal sex ratio affect N_e?
31. If I give you the formula for calculating N_e when there are unequal sex ratios or variation in population size over time, be able to use it.
32. How can genetic drift result in evolutionary divergence of two populations? In what major way would this divergence differ from divergence due to selection?
33. Describe two measures of genetic diversity?
34. How fast is the rate of loss of heterozygosity due to genetic drift?
35. What is a founder effect? How does it relate to genetic drift?
36. What happened to silvereyes as a result of founder effects?
37. Are founder effects known in human populations? Describe recent evidence of founder effects in humans.
38. What is Fst? Why did red bladder campion on Swedish islands exhibit high Fst? What force caused Fst to decline over time? What about in lupin at mount st. helens?
    
    
39. What is inbreeding?
    
    
40. What is the inbreeding coefficient (F) and what are its properties? What is the relationship between F and heterozygosity in a population?
    
    
41. Does inbreeding change allele or genotype frequencies?
    
    
42. What is inbreeding depression? How can we measure it? Give examples.
43. Is there evidence of inbreeding depression in humans? What's weird in the data from Iceland?
44. What is the evidence that inbreeding depression is more severe under harsher conditions?
    
    
45. What is an inbreeding avoidance mechanism? Give examples from plants, and relate to female philopatry vs. male emigration in mammals.
    
    
46. Why is inbreeding often expected to select for inbreeding avoidance mechanisms?
    
    
47. Why do inbreeding and drift in small populations potentially lead to extinction of the population? Why would introducing outside migrants potentially rescue the population? Describe what happened with the Illinois prairie chicken and the Florida panther. Your discussion should include a) why the population of prairie chickens was declining even though habitat was increasing, and why introducing outside prairie chickens helped.
48. Population genetics in conservation biology: What is the "one migrant per generation rule"? What is the "50/500 rule"
49. What is the neutral theory of molecular evolution? That is, what does it claim about the evolutionary forces that cause most of the fixed substitutions between species, and most of the polymorphisms within species? What are some of the patterns that are predicted by it?
50. Why does comparing non-synonymous and synonymous substitution rates provide a test for selection on coding sequences?