1. BASICS OF POPULATION GENETICS.

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1 Bio 312, Fall 2016 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. Regrade requests cannot be made for exams completed in pencil for any reason. * Note: provide all decimal answers to 3 significant figures * 1. BASICS OF POPULATION GENETICS. The exam has 100 points total Consider a population of 1800 Drosophila individuals at Hardy-Weinberg equilibrium with two alleles in the population, "Wt" and "Mu", which cause only two distinct phenotypes. Individuals who are "Wt/Wt" or "Wt/Mu" have normal body coloration whereas individuals who are "Mu/Mu" are pale. If we determine that there are 1152 pale individuals, answer the following questions. (a, 1pt ea) If the pale coloration is better at blending in against the natural background and reduces predation, what two adjectives are best used to describe the "Wt" allele? "The Wt allele is a(n) dominant deleterious allele. (b, 2pts ea) What are the values of p and q? Round to nearest p = _0.20_ q = _0.80_ (c, 2pts ea) How many "Wt/Wt", "Wt/Mu", and "Mu/Mu" individuals will there be? Round to closest integer. # Wt/Wt = _72_ # Wt/Mu = _576_ # Mu/Mu = _1152_ (d, 2pts) What percentage of all of the individuals are heterozygous? Round to nearest 0.01% (e, 2pts) What percentage of the normal colored individuals are heterozygous? Round to nearest 0.01% % Het. = _32.00%_ % Het. = _88.89%_

2 Bio 312, Fall 2016 Exam 3 ( 2 ) Name: 2. MIGRATION DYNAMICS. Consider the migration situation shown below. Two islands are between two mainlands and they receive immigrants as depicted in the figure - island A receives migrants from both mainlands and island B receives migrants from only the Eastern mainland. (provide answers to nearest 0.001) p=0.7 q=0.3 m=0.02 Island A p=0.4 q=0.6 Island B m=0.03 (a, 3 pts) What is the value of p on island A after one generation of these processes? p = _0.403 (b, 3 pts) What is the value of p on island B after one generation of these processes? p = _0.396_ W N S E p=0.5 q=0.5 m=0.04 p=0.3 q=0.7 (c, 3 pts) What is the value of p on island B after eight generations of these processes? p = _0.399_ (d, 3 pts) What is the value of p on island A after a very large number of generations of these processes? (i.e., the equilibrium frequency) p = _0.460_ (e, 3 pts) What is the value of p on island B after a very large number of generations of these processes? (i.e., the equilibrium frequency) p = _0.300_

3 Bio 312, Fall 2016 Exam 3 ( 3 ) Name: 3. MUTATION:SELECTION BALANCE. Genetic diseases arise from the segregation of deleterious alleles. These are usually recessive, but in rare cases they are co-dominant or dominant. Consider a hypothetical genetic variant, "a", which researchers find is associated with reduced rates of infant survival compared to individuals with the wildtype "A" allele. Studies show that individuals that are homozygous for this allele have only 40% the normal chance of surviving until adulthood. Heterozygotes are unaffected. (a, 3 pts) Assuming a mutation rate of 10-8 for this genetic disorder (approximately correct for single nucleotide mutation rates), what is the predicted frequency of this allele in the population? (Provide answer to the 3 significant figures) (b, 3 pts) The population of the US is approximately 350,000,000. Assuming this, what is the expected number of afflicted individuals in the US? (round to the nearest integer) (c, 3 pts) The population of the world is approximately 6,000,000,000. Assuming this, what is the expected number of carriers (i.e., heterozygotes) in the world? (round to the nearest integer) f(a) = _1.29 x 10-4 _ # sick = _6_ # carriers = _1,548,993_ Now consider the situation in which this deleterious allele were dominant instead. (d, 3 pts) The population of the world is approximately 6,000,000,000. Assuming this, what is the expected number of afflicted individuals in the world? (round to the nearest integer) # carriers = _200_ (A) q eq = (10-8 /0.6) 1/2 = = 1.29 x 10-4 (B) 3.5 x 10 8 x q eq 2 = 3.5 x 10 8 x ( x 10-4 ) 2 = 5.83 (C) 2 ( x 10-4 )( x 10-4 ) 6,000,000,000 = 1,548,993 (D) q eq = (10-8 /0.6) = x 10-8, 2 ( x 10-8 )( x 10-8 ) 6,000,000,000 = 200.0

4 Bio 312, Fall 2016 Exam 3 ( 4 ) Name: 4. Effective population size. (provide answers to nearest 0.01) (a, 2pts) What is the effective population size of a population that cycles between 950 and 1050 members on alternate years? (b, 2pts) What is the effective population size of a population that has 450 males and 550 females? Ne= _997.50_ Ne= _990.00_ (c, 2pts) Which population will maintain genetic diversity for longer and why? The first population will because it has the higher effective population size. 5. Evolutionary rates. (provide answers to nearest ) Consider a situation in which the homozygote for an advantageous allele (AA) experiences a 8% fitness advantage over the other homozygote (aa) and the frequency of the advantageous allele is p=0.2. (a, 2pts) If the "A" allele is dominant, what is the frequency of the allele in the next generation? (b, 2pts) If the "A" allele is co-dominant (h=1/2), what is the frequency of the allele in the next generation? (c, 2pts) If the "A" allele is recessive, what is the frequency of the allele in the next generation? p' = _0.2100_ p' = _0.2063_ p' = _0.2026_ 6. Equilibrium frequencies. (provide answers to nearest 0.001) For the three sets of overdominant fitness values below, provide the equilibrium frequency of the "A" allele. (You may find it fastest to solve for the general case using algebra and then plug in the appropriate values into your derived equation) Genotype: AA Aa aa (a, 2pts) Fitness: p eq = _0.200 (b, 2pts) Fitness: p eq = _0.333 (c, 2pts) Fitness: p eq = _0.555

5 Bio 312, Fall 2016 Exam 3 ( 5 ) Name: FOR THE REMAINING QUESTIONS USE YOUR SCANTRON FORM, MULTIPLE CHOICE: (3 pts each). (1) What explanation arising from our analysis of allele frequencies and selection was provided for the observation that almost all genetic disorders are recessive? (A) Advantageous alleles are dominant and selected so the deleterious ones must therefore be recessive. (B) Because biochemical pathways have rate-limiting steps, deleterious mutations are always selected to become recessive. (C) In diploid individuals a functioning allele can always make up for the deficiencies of the other allele. (D) Mutations from dominant alleles to recessive ones are more likely to be selected than the converse. (E) Selection to remove recessive alleles from populations is much less effective than it is for removing dominant ones. (2) One of the processes we examined causes genotype frequencies to change consistently while allele frequencies do not. Although the population therefore changes over time, by our restrictive definition of evolution as allele frequency change the population does not "evolve". What process was this? (A) Epistasis (C) Inbreeding (E) Stochasticity (B) Genetic drift (D) Perturbations (3) The technical term for a population in which any individual can mate with any other, without geographic factors or distance being important, is which of the following (A) Epistatic (C) Overdominant (E) Perturbed (B) Normal (D) Panmictic (4) Fisher's fundamental theorem is best paraphrased by which of the following? (A) Higher immigration rates lead to faster rates of evolution. (B) Higher levels of environmental variation lead to faster rates of evolution. (C) Higher levels of genetic variation lead to faster rates of evolution. (D) Higher mutation rates lead to faster rates of evolution. (E) Larger population sizes lead to faster rates of evolution. (5) The Haldane-Muller principle is best paraphrased by which of the following? (A) The rate of mutation is constant over time (B) The rate of substitution, per year, is constant (C) The rate of substitution, per generation, is constant (D) The effects of deleterious mutations on individuals depend only on their rate, not on the fitness effect. (E) The effects of deleterious mutations on population mean fitness depend only on their rate, not on the fitness effect. (6) Which of the following pairs of nucleotide substitutions describe both a transition and a transversion? (A) Adenine to guanine and cytosine to thiamine. (B) Adenine to cytosine and guanine to adenine. (C) Cytosine to guanine and guanine to thiamine. (D) Cytosine to thiamine and guanine to adenine. (E) Guanine to thiamine and thiamine to adenine.

6 Bio 312, Fall 2016 Exam 3 ( 6 ) Name: For the next two questions consider a cross between an AABbccDD and an aabbccdd individual where the alleles at the four loci influence a quantitative trait. (7) How many different genotypes can result from the cross? (A) 2 (B) 3 (C) 4 (D) 5 (E) 6 (8) Assume that the effects of the different alleles at each locus are identical with regard to increasing or decreasing the trait and that all the alleles are perfectly co-dominant. How many different phenotypes can result from the cross? (A) 1 (B) 2 (C) 3 (D) 4 (E) 5 For the next two questions consider a cross between an AaBbCCDd and an AaBbccDd individual where the alleles at the four loci influence a quantitative trait. (9) How many different genotypes can result from the cross? (A) 4 (B) 16 (C) 27 (D) 48 (E) 64 (10) Assume that the effects of the different alleles at each locus are identical with regard to increasing or decreasing the trait and that capital letters indicate alleles dominant to lower case ones. How many different phenotypes can result from the cross? (A) 1 (B) 2 (C) 3 (D) 4 (E) 5 The following 3 questions are based upon the videos you watched in preparation for this exam. (11) What general morphological pattern was seen in the different islands. (A) Closer to the water, the body sizes got smaller. (B) Closer to the water, the toe pads got larger. (C) Higher up in the trees, the legs got shorter. (D) Higher up in the trees, the skin got lighter. (E) Higher up in the trees, the tails got longer. (12) What experiment did the scientists do? (A) They brought lizards into the lab and saw reproductive isolation evolve in only 4 years when they were physically separated. (B) They isolated DNA from the different species and identified which genes were responsible for the morphological differences seen. (C) They put lizards from one species onto empty islands and saw changes that matched the pattern seen on larger islands with multiple species. (D) They showed females the dewlaps of different males on a computer screen to see which colors they responded to. (E) They used high speed cameras to measure the running, swimming, and climbing speeds of different species of lizards. (13) Which evolutionary concept from this semester did the video focus the most on? (A) Convergent evolution (D) Sexual selection (B) Life history theory (E) Stabilizing selection (C) Perturbation analyses