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BIOL404/504 MOLECULAR EVOLUTION: MIDTERM I SEPTEMBER 26, 2008 Please answer the following succinctly; multiple choice questions may have >1 answer. Number of points for each question in parenthesis after the question (60 points total). NAME:__________________________ 1. Define molecular evolution (do not use the words “molecular” or “evolution” in your answer). (2) Change over time at the DNA, RNA, and protein levels. 2. List 4 (of 6) of Darwin’s postulates (i.e., necessary conditions for evolution). (4) Any of the following: 1. there is individual variation 2. there is a mechanism for heredity 3. there is overproduction of offspring 4. there is a struggle for existence 5. only the fittest survive 6. there is change over time 3. Circle one of the following that was NOT a tenet of the modern synthesis? (2) a) Evolutionary phenomena can be explained by existing genetic knowledge b) Evolution generally relies on mutations with large effects c) Selection is the primary process driving evolution d) The population level is the primary level for understanding evolution e) Micro and macro evolutionary explanations are fundamentally compatible 4. What does the term “ring of life” refer to? (2) Eukaryotic genomes appear to be an Archaea-Bacteria chimera – so the early “branches” on the tree of life may be more “ring-like” than “tree-like” 5. People generally simplify one of the principles of molecular evolution to “mutations are random”. Please give 3 examples of why this is not strictly true. (3) Mutations are not truly randomly distributed across: 1. species 2. organelles 3. genomes 4. environmental conditions 6. Please write the reverse complement of the following sequence: GTAAACCGTA (2) TACGGTTTAC 7. What are 3 reasons that a population’s effective population size might be lower than its census population size? (3) Any of the following: 1. Generational overlap 2. Unequal sex ratios 3. Polygamous matings 4. Historical bottleneck 8. What is the difference between a synonymous and a non-synonymous substitution? (5) Synonymous substitutions do not cause an amino acid change (only a nucleotide change) while nonsynonymous substitutions cause an amino acid replacement. Which do you expect to see more of in a genome? Synonymous substitutions Why? Synonymous substitutions are under less functional constraint than non-synonymous substitutions. Mutations that cause amino acid replacements are more likely to have a (negative) functional consequence and thus be weeded out by selection. At which codon position do you expect to see the most synonymous substitutions? 3rd 9. You come across two populations of whoositwhats when searching for a study system. The populations appear to be fairly distinct genetically. You decide to monitor these populations for the next 1000 generations. Please circle the correct choices below. (4) How would you expect drift to affect the genetic variation within each local population? a) increase variation b) decrease variation c) no change How would you expect drift to affect the genetic variation between the two populations? a) increase variation b) decrease variation c) no change After the first 500 generations a new migration route is established between the populations. How would you expect migration to affect genetic variation within each population? a) increase variation b) decrease variation c) no change How would you expect migration to affect the genetic variation between the two populations? a) increase variation b) decrease variation c) no change 10. Why is selection considered “inefficient” at removing a recessive deleterious allele in a population? (3) Because they are “hidden” from selection when heterozygous. 11. For a new neutral mutation which of the following are dependent on population size? (2) a) Probability of fixation = 1/N b) Rate of fixation = u c) Interval between fixation events = 1/u d) Average time to fixation = 4N (in a diploid) 12. Identify the following types of selection. The dotted line indicates the trait distribution before selection and the solid line indicates the trait distribution after selection. (3) Directional Stabilizing Disruptive or Diversifying frequency trait 13. Identify one major idea or advance associated with each of the following (3) Motoo Kimura: neutral theory Rosalind Franklin: DNA x-ray crystallography Charles Lyell: geological uniformitarianism 14. Is there better evidence for the “RNA first” or the “RNA early” hypothesis? (3) RNA early What is the difference between the two ideas? The RNA early hypothesis suggests that RNA preceded DNA and proteins in evolutionary history but does not claim that RNA was necessarily the first complex organic compound. 15. What is the difference between overdominant and underdominant allelic interactions? (3) In overdominance heterozygotes are more fit than either homozygote. In underdominance heterozygotes are less fit than either homozygote. Which is more likely to maintain multiple alleles in a population? Overdominance (remember the graphs with stable vs unstable polymorphism) 16. You receive a phone call from a very detail oriented colleague who has been evolving bacteria for many generations and sequencing the full genome of every individual. She started with a genetically homogenous population but she has just discovered the first mutation in her population. She wants you to predict for her what the fate of the mutation will be (i.e., whether it will ultimately be lost, fixed, or maintained as a polymorphism). (6) If you were a strict neutralist, what two pieces of information would you ask her for about the mutation/population? 1. Population size 2. Initial mutation frequency If you were a pan-selectionist what two pieces of information would you ask her for about the mutation/population? 1. Strength of selection 2. Mode of allelic interaction 17. The neutral theory is easily misinterpreted. Which of the following IS a tenet (or ARE tenets) of the neutral theory? (2) a) organisms are not adapted to their environments b) all morphological variation is neutral c) all genetic variation is neutral d) deleterious mutations are more common than advantageous mutations 18. The Hardy-Weinberg equation is useful for predicting the percent of a human population that may be heterozygous carriers of recessive alleles for certain genetic diseases. Phenylketonuria (PKU) is a human metabolic disorder that results in mental retardation if it is untreated in infancy. In the United States, one out of approximately 10,000 babies is born with the disorder. Approximately what percent of the population are heterozygous carriers of the recessive PKU allele? (6) q2 = 1/10,000 so q = 0.1 so p = 0.99 so 2pq = 0.0198 so 1.98% of population are carriers What are 4 assumptions of HWE equation? Any of the following: 1. infinite population size 2. random mating 3. no mutation 4. no selection 5. no gene flow 19. So far how is the level and pacing of this course for you (i.e., too easy/hard, fast/slow)? (1) What suggestions do you have for improving the course for the rest of the semester? (1)