Bio 312, Exam 3 ( 1 ) Name:

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1 Bio 312, Exam 3 ( 1 ) Name: Please write the first letter of your last name in the box; 5 points will be deducted if your name is hard to read or the box does not contain the correct letter. Written answers should be concise and precise; answers typically have short correct answers. The exam is 100 POINTS Do not write below the dark horizontal line at the bottom of the first four pages, nothing below will be graded. (1) HARDY-WEINBERG EQUILIBRIUM. Hardy and Weinberg did the math to demonstrate what alleles frequencies woould be under certain assumptions. I described this scenario as a Hardy-Weinberg equilibrium and described two major purposes for studying it. (a, 4 pts) What is the main thing that is or is not happening at Hardy-Weinberg equilibrium? (b, 10 pts) List the 5 assumptions that the Hardy-Weinberg equilibrium process requires (c, 3 pts) One of the reasons we focus on the Hardy-Wieinberg process is conceptual, it helps us in a way more than just by providing equations. What is the main conceptual benefit that understanding these assumptions provides us? (d, 3 pts) If a population is at Hardy-Weinberg equilibrium the equations allow us to do something practical if we know how common each allele is; what is the main thing that the Hardy-Weinberg equilibrium equations provide us when we know the allele frequencies?

2 Bio 312, Exam 3 ( 2 ) Name: (2) EQUILIBRIUM FREQUENCY CALCULATIONS. In class we saw the derivation of equations for the equilbrium frequency of an allele when the heterozgotes have a higher fitness than either homozygote. (a, 3 pts) Derive an equation for the equilibrium frequency of the "A" allele given fitnesses W 11, W 12, and W 22. Assume that W 12 > W 22 > W 11. Present the equilibrium value in terms of these 3 fitness values in the box. (b, 3 pts) Using your equation, what would the equilbrium frequency of the "A" allele be if W 11 = 0.80, W 12 = 1.11, W 22 = 0.90? (provide your answer to the nearest 0.001) (c, 2 pts) When fitness are like this we can describe the "A" allele with two adjectives; the "A" allele is best described as and. (d, 2 pts) We then need to test the stability of the equilbrium derived in (b) using a certain type of analysis. Name and verbally describe the method we would then use. Do not just name it, describe the idea and concept behind the method (you don't have to do the calculations).

3 Bio 312, Exam 3 ( 3 ) Name: (3) EQUILIBRIUM FREQUENCY CALCULATIONS. In class we derived the equation for the equilbrium frequency of a deleterious allele when the fitnesses were given as: W 11 = 1 W 12 = 1 W 22 = 1-s (a, 6 pts) The first step of that derivation was to use the equation below. In the three boxes given, verbally describe what each of the 3 indicated pieces represent. ( ) ( ) (b, 4 pts) Now, using the same process as was done in class, derive an equation for the equilibrium frequency of a recessive deleterious allele. Instead of using the fitnesses above, use the fitnesses W 11, W 12, and W 22. Assume that W 11 =1, W 12 =1, and W 22 <1 (i.e, do not use the value 1-s for the fitness of the inferior genotype, keep the W 22 value in your equation). Also, model the mutational process in each generation by p'= p instead of the way it was done in class. Derive the equilibrium frequency of deleterious alleles and write the final equation you obtain in the box below. Your answer might have W 11, W 12, W 22 and terms, but maybe not all if things cancel out. ( Note that X(Y) = X(1-(1-Y)) )

4 Bio 312, Exam 3 ( 4 ) Name: (4) EQUILIBRIUM REQUENCY OF A DELETERIOUS ALLELE. Imagine a scenario in which there are two alleles at a locus that controls the color of a bird species. The "G" allele is dominant and results in green coloration that provides beneficial camoflague against predators whereas the "O" allele results in an orange color that is obvious to predators. The fitnesses of each phenotype are shown to the right and you may assume that the mutation rate that knocks out the "G" allele and results in an "O" allele is (provide all answers to 3 sig. figs) W Green Orange (a, 3 pts) What is the expected eqiuilbrium frequency of the "O" allele? (b, 3 pts) What percentage of green individuals are heterozygous at equilibrium? (c, 3 pts) If the orange allele were dominant instead, what would the equilibrium frequency be in that scenario? f(o) = f(ao) = % f(o) = (d, 3 pts) If the predators in this region were to suddenly go extinct, what would you expect to happen to the frequency of each allele on the short to medium term?

5 Bio 312, Exam 3 ( 5 ) Name: FOR THE REMAINING QUESTIONS USE YOUR SCANTRON FORM, 3 pts each (1) We examined a particular situation in which the genotype frequencies changed consistently yet the allele frequencies did not. Although the population was clearly changing over time, by our restrictive definition of evolution, the population was not "evolving". What caused this interesting situation? (A) Assortative mating (C) Stochasticity (E) Epistasis (B) Genetic drift (D) Perturbations (2) The surprising result that the genetic load depends on the deleterious mutation rate rather than the fitness effects of the deleterious mutations was termed. (A) Fisher's fundamental theorem (D) The neutral theory (B) The Haldane-Muller principle (E) The nearly-neutral theory (C) The hitchiking effect (3) The effective population size of a population with 300 males and 600 females is? (A) 650 (B) 700 (C) 750 (D) 800 (E) 850 (4) Consider a population of 800 individuals with genotypes that have fitnesses: W 11 = 1.10, W 12 = 1.04, and W 22 = What is the fixation probability of a novel "A" mutation in a population of individuals with only "a" alleles at all other loci? (A) 1.25% (B) 4% (C) 8% (D) 10% (E) 20% (5) Additive genetic variance divided by phenotypic variance is called. (A) The broad sense heritability (D) The selection differential (B) The narrow sense heritability (E) The selection gradient (C) The realized heritability (6) When we identify a specific genetic location in a genome as varying between different individuals we term a. (A) Linkage equilibrium (C) Transition (E) Polymorphism (B) Linkage disequilibrium (D) Transversion (7) The molecular clock relies on which of the following? (A) The rate of mutation is constant per generation. (B) The rate of mutation is constant per year. (C) The rate of substitution is constant per generation. (D) The rate of substitution is constant per year. (E) The mutation rate is the same as the substitution rate. (8) When a novel nucleotide changes the amino acid to one with a similar charge and size we would say which of the following? (A) The nonsynonymous nucleotide change caused a conservative amino acid change. (B) The synonymous nucleotide change caused a conservative amino acid change. (C) The nonsynonymous nucleotide change caused a radical amino acid change. (D) The synonymous nucleotide change caused a radical amino acid change. (E) The mutation caused a substitution. (9) A mutation which creates a novel stop codon is best termed a(n) mutation. (A) Frameshift (C) Nonsense (E) Silent (B) Indel (D) Replacement

6 Bio 312, Exam 3 ( 6 ) Name: (10) Which of the following types of genetic changes would you predict to occur the most quickly? (A) Substitutions in introns. (B) Substitutions in the first position of codons. (C) Substitutions in the second position of codons. (D) Substitutions in the third position of codons. (E) Substitutions in synonymous codons. (11) A population is one in which any individual can mate with any other easily. (A) Polymorphic (C) Heterozygous (E) Panmictic (B) Stochastic (D) Quantitative For the last questions on this page consider the diagram of migration patterns between a mainland and an island shown below. The number of individuals in each location and the frequencies of the allele "A" are indicated as well as the migration rate to and from the mainland/island mainland N=1000 p=0.2 m 1 =0.03 m 2 =0.01 p=0.6 island N=200 (12) If the population on the main land were to increase to N=2000 and all other factors stay pretty much the same (i.e., behaviors, weather, etc.), what would you expect the values of m 1 and m 2 to then be? (A) m 1 = 0.03, m 2 = (C) m 1 = 0.06, m 2 = (E) m 1 = 0.01, m 2 = 0.03 (B) m 1 = 0.03, m 2 = 0.01 (D) m 1 = 0.06, m 2 = 0.01 (13) Which of the following is the best description of what the value m 1 = 0.03 represents? (A) On average, one migrant arrives on the island from the mainland every 3 generations. (B) On average, 3 migrants arrive on the island from the mainland every generation. (C) Three times as many individuals go to the island every generation as go to the mainland. (D) 3% of the individuals in the mainland emmigrate to the island each generation. (E) 3% of the individuals in the island originate from the mainland each generation. (14) Which of the following values is closest to the frequency of the allele "A" in the island after one generation? (A) 0.54 (B) 0.56 (C) 0.58 (D) 0.6 (E) 0.62 (15) Which of the following values is closest to the frequency of the allele "A" in the mainland after one generation? (A) 0.26 (B) 0.24 (C) 0.22 (D) 0.20 (E) 0.18 (16) Which of the following values is closest to the long-term equilibrium frequency of the allele "A" in the mainland and island populations? (A) 0.2 (B) 0.3 (C) 0.4 (D) 0.5 (E) 0.6