1.
Briefly describe (verbally and graphically) the phenomenon of genetic linkage. Define the term "haplotype." Use a numerical/graphical example to illustrate why, when we consider multiple loci, we can't necessarily accurately describe the genetic structure of populations by knowing only allele frequencies.
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2.
Describe the phenomena of linkage equilibrium and linkage disequilibrium (being sure to accurately define each term). What conditions are true of loci if and only if they are in linkage equilibrium? When Hardy-Weinberg conditions are met and two loci are in linkage equilibrium, how will chromosome frequencies change over time? What if the loci are in linkage disequilibrium?
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3.
Describe the mechanisms that create linkage disequilibrium in random-mating populations. What, fundamentally, do they have in common? What eliminates linkage disequilibrium from a population? Illustrate your answer using Clegg et al.'s work on fruit flies.
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4.
Can selection at one locus cause a change in allele frequency at another locus? Illustrate your answer using Betancourt and Pesgraves study of Drosophila coding sequences. Under what condition(s) can this occur? Are these conditions likely to be met frequently in nature? Defend your answer using Dawson et al's work on human chromosome 22, Huttley et al.'s work on the human genome and Miyashita et al.'s work on Arabidopsis.
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5.
Using the CCR5 locus as your example, explain how patterns of linkage disequilibrium can help investigators reconstruct the evolutionary history of genes and populations.
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6.
What feature of G6PD deficiency initially suggested that it confers resistance to malaria? Describe the genetic signature Sabeti and colleagues used to determine whether the G6PD-202A allele was under recent positive selection, including the reasoning behind their determination. Refer to Figure 7.14 on page 273 for help. Is the allele under positive selection? Justify your answer by explaining their findings.
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7.
Define the term parthenogenesis and give examples of organisms capable of both sexual and asexual reproduction. Describe the paradox for evolutionary theory presented by Maynard Smith's null model for the relative advantages of sexual and asexual reproduction. Be sure to explain the null model itself, including its assumptions.
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8.
Describe Dunbrack et al.'s tests of Maynard Smith's model, with careful attention to how they simulated the conditions of asexual reproduction. What outcome(s) did the null model predict? What did they find, and what general conclusions can be drawn from this work?
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9.
What is the consequence of sex at the level of population genetics? Explain how this fact relates to Otto and Lenormand's findings about the relationship between artificial selection and recombination (of course, you should explain what those findings were -- a graph of their results is presented below). Based on these principles, what essential "ingredients" must any population-genetic model for the evolution of sex include?
[Hint ]
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10.
Describe Muller's ratchet (see figure below), with special attention to (1) how drift creates linkage disequilibrium, (2) how genetic load increases over time, and (3) and how sexual reproduction "breaks" the ratchet. According to Haigh's mathematical model, under what conditions of population size, mutation rate, and impact of deleterious mutations does the ratchet operate the most quickly?
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11.
Describe Andersson and Hughes' and Lambert and Moran's experimental studies of Muller's ratchet, with special attention to the mechanism(s) permitting drift to operate. What is the problem with models that explain sex by positing drift as the source of linkage disequilibrium, and how do Dunbrack et al.'s experimental results support that reasoning?
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12.
Describe the basic reasoning behind "changing environment" models for the benefit of sexual reproduction, with special attention to how selection on multilocus genotypes creates linkage disequilibrium and why selection would favor mechanisms to reduce linkage disequilibrium. Describe the specific "Red Queen" hypothesis and discuss Lively's test of the hypothesis.
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