Biology 206. Midterm Test 1. Multiple Choice Questions (1 pt each) YOUR NAME:

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1 Biology 206 MT of 11 Biology 206 Multiple Choice Questions (1 pt each) 1) Even though HAART can eliminate detectable HIV viral-load, why is a patient still likely to die of AIDS? a) HIV sufferers rarely give up lifestyles that place them at risk of the disease. b) With massive population sizes and rapid generation time, HIV will inevitably acquire the mutations necessary to thwart HAART c) HAART has toxic side-effects that most cannot tolerate indefinitely. d) The body contains a bank of dormant cells, some of which will harbour the virus. e) Both (c) and (d). 2) The shift from the CCR5 to CXCR4 coreceptor was cited as an example of shortsighted evolution because X4 strains tend to infect naïve T-cells and Midterm Test 1 February 11 th, 2011 Prof. a.k. chippindale YOUR NAME: Instructions: This exam is out of 40 points. There are 19 multiple choice (1 point), 6 T/F (1/2 point) and 6 short answer (3 point) questions. The exam duration is approximately 55 minutes so budget time accordingly. In each case, choose the best answer, whether or not you feel another answer might be correct under limited or unusual circumstances. Use a pencil to blacken answers on the Scantron answer sheet; for regrading purposes, pen is recommended for written answer questions. If you are unsure about a question then guess. There is no penalty for wrong answers. No electronic devices are permitted. No actual individuals, extinct or living, are depicted above. a) uninfected hosts have low CXCR4 T-cell counts, reducing transmission probability. b) CXCR4 T-cells are naturally resistant to HIV, causing a decline in the within-host replication rate of the virion. c) X4 involves a mutation in the Nef gene of the virus, which lowers viral titre and transmission rate. d) this form of the virus evades antiretroviral drug therapy, but resistant forms of the virion copy more slowly, ultimately reducing virion fitness. 3) Bacteria that evolve antibiotic resistance are often competitively inferior to susceptible strains, in the absence of antibiotics, but this disadvantage is reduced by continued exposure to the drug. This change is referred to as a) genetic assimilation. b) directed mutation. c) compensatory evolution. d) phyletic transformation. 4) Which of the following characters is expected to show the lowest heritability estimate in a medium ground finch population? a) beak pointedness. b) female egg number. c) male courtship behaviour. d) metabolic rate.

2 Biology 206 MT of 11 Biology 206 MT of 11 5) In Reznick et al. s experiments with guppies in Trinidad, adding the pike cichlid Crenicichla alta to locations above waterfalls was predicted to: a) promote rapid changes in coloration (less) and maturation time (earlier). b) promote rapid changes in coloration (more) and maturation time (earlier). c) promote rapid changes in coloration (more) and maturation time (later). d) promote rapid changes in coloration (less) and maturation time (later). e) promote retention of established characters via stabilizing selection. 6) Domestic dogs and Brassica oleracea were used to highlight which model of change 9) The 1977, 1980, and 1982 drought years on Daphne Major caused changes in the morphology of the resident medium ground finch population. However, in 2002 the finches beak size was the same as it had been in the early 1970s. Why? a) After the droughts, the birds had consumed all of the Tribulus seeds and had to specialize on a new plant. b) Moister years in the late 80s and 90s selected for smaller body and beak size. c) The trait had low heritability and was mainly determined by environmental factors. d) Immigration from neighbouring islands drove down gene frequencies for big beaks. sp1 sp2 sp3 sp4 sp5 sp6 a) jello against the wall. b) sliding jello. c) evolutionary conservatism. d) punctuated equilibrium. DATA FOR Q 7 & 8 Position A A T C C C T T G T A A T C T C C T G A A A T C T C C T G A G A T C C C C T G A A G T C C C T T G T A A T C C C T T G T 9) When natural selection acts to modify an existing trait for a new function, like the lobe-fins of fishes as legs for walking, we call this. a) preadaptation. b) a polytomy. c) homoplasy. d) convergence. 10) Two major problems in understanding the nature of inheritance and variation in the early 20 th century were a) convergence and mutation. b) parsimony and taxonomy. c) heritability and taxidermy. d) dominance and blending. 7) The data shown above support which tree for the 6 species? a) Tree A. b) Tree B. c) Tree C. d) None of the above. 8) If you used a maximum likelihood model to make the tree, which substitution(s) would it treat as the most reliable (improbable due to chance) substitutions? a) the substitutions at positions 1 & 2. b) the substitution at position 5. c) the substitution at position 7. d) the substitution at position ) Why is the fossil shown above, Tiktaalik, deemed important? a) It is believed an early proto-whale with numerous features reflecting adaptation from land to water. b) It is believed to be a transitional form between lobe-finned fishes and tetrapods. c) It is believed to be a key node linking crocodiles, reptiles, and dinosaurs. d) It is the first fossil showing evidence of an amniotic egg and lungs; keys to life on land.

3 Biology 206 MT of 11 Biology 206 MT of 11 12) The WHIPPO hypothesis is supported by most molecular phylogenetic approaches as well as what other recent evidence? a) Phylogenetic analysis shows that manatees and dugongs are a missing link. b) Early whale-like fossils with hindlimbs have a pulley-like astralagus bone. c) Early whale-like fossils have an even number of toes, like pigs do. d) The finding that hippos and seals are close relatives; whales have features of both, uniting this clade. e) The Green Bay Packers winning the Super Bowl despite a hobbled defensive backfield. 13) Biologists concerned with the evolution of sexual reproduction have been especially concerned with the non-additivity in mutational effect known as synergistic epistasis. This would be recognized by a) a steady decline in fitness over time in mutation accumulation experiments. b) a decreasing rate of decline in fitness over time in mutation accumulation experiments c) an increasing rate of decline in fitness over time in mutation accumulation experiments. c) an increase in fitness over time in mutation accumulation experiments. e) The Green Bay Packers winning the Super Bowl despite a hobbled defensive backfield. 14) A principle of phylogenetics stating that the shortest tree is the best is: a) Homoplasy. b) Convergence. c) Homogamy. d) Parsimony. 15) Genes are duplicated through at least two distinct mechanisms: retrotransposition and unequal cross-over. Can we tell the difference? How? a) Retro = far from original, lacking introns; Unequal = close to original, with introns. b) Unequal = far from original, lacking introns; Retro = close to original, with introns. c) Retro = nested within original, with introns; unequal = next to original, lacking introns. d) Retro = far from original, lacking introns; Unequal = nested within original, with introns. 16) In Richard Lenski s long term E. coli experiment, adaptation can best be characterized as a) the product of new spontaneous mutations periodically arising from an initially invariant population of cells. b) the product of selection operating on an initially variable population of cells but bounded by that variation like the jello against the wall. c) the product of selection operating on an initially variable population of cells but unbounded that initial variation like the sliding jello. d) primarily the product of drift in small populations. 17) The capacity to aerobically metabolize citrate appeared suddenly in line Ara - 3 after 33, 000ish generations of selection. The authors attributed the remarkable adaptation to historical contingency, meaning a) the cit + mutation arose purely by chance in the population, and Lenski and students were extraordinarily lucky to witness it. b) earlier chance mutations in the population played a role in creating conditions that would favour a cit + mutation later on. c) the founding cells for the Ara -3 population happened to carry variation that would, through recombination, eventually come together and allow cit + metabolism. d) Ara -3 became a mutator strain, making this (still amazing) event more likely. 18) Chameleons are found on African continent, on Madagascar, the Seychelle Islands, and in India, leading to questions about their origin and spread around the Indian Ocean. Which of the following models was supported by phylogeographic analysis by Raxworthy et al.? a) Chameleons originated before the supercontinent, Gondwana, split apart forming the Indian Ocean; they traveled with the new continents. b) Chameleons have only recently dispersed (est d years) with humans with the advent of boat travel and migration from Africa. c) Chameleons in India and the Seychelles are not closely related to those in Africa (the true chameleons). They are convergent and their classification is being revised. d) Chameleons arose in Madagascar and have migrated to Africa and the Seychelles, and from Africa to India, on vegetation rafts.

4 Biology 206 MT of 11 Biology 206 MT of 11 19) It is generally assumed that mutant plants that produce diploid gametes create a barrier to future survival. Why did Brian Husband question the barrier concept and call it a bridge? a) Polyploid plants are hardy and robust, often surviving better than diploids. b) Triploid plants shed balanced diploid gametes at a rate of about 1/200, which is non-trivial in evolutionary terms. c) In isolated populations, the advantages of polyploidy may help establishment of breeding populations. d) All of the above. True / False Questions (0.5 pt each) 21) T / F. Based upon data from yeast and E. coli, most mutations are mildly deleterious (s < 0.02). a) True b) False 22) T / F. The LINES and SINES used in phylogenetic analysis represent long and short running protein fragments on an electrophoretic gel, respectively. a) True b) False 23) T / F. Although some trees based on morphology map the whales outside of Artiodactyla, molecular data suggest that modern whales evolved from hippo ancestors. a) True. b) False 24) T / F. All synapomorphies are homologies, but not all homologies are synapomorphies. a) True b) False 25) T / F. In a mutation accumulation experiment covering the entire fly genome, fitness declined an average of 30% over 60 generations in 10 lines. Researchers assumed that s=0.01. If so, the mutation rate was 2/genome/generation. a) True. b) False 26) T / F. The eyes of Octopus and vertebrates are convergent structures. a) True. b) False WRITTEN ANSWER QUESTIONS 1) Myxoma virus from South America was used in Australia to control rabbit populations, where it successfully wiped out most bunnies soon after introduction in the 1950s. Today, myxomatosis is much less likely to kill an Australian rabbit, or a European rabbit experimentally infected with Aussie myxoma. What do these observations suggest about the evolution of the virus, and what factors may have driven the change? (3pt) 2) What is meant by the statement evolution is short-sighted. Explain using an example from HIV. (3pt)

5 Biology 206 MT of 11 Biology 206 MT of 11 3) What is heritability? Explain how Peter Boag estimated it in Darwin s finches on Galapagos. Then explain how heritability estimates might be improved in an organism like the zebra finch, which is easy to keep in an aviary. Be specific. Use words, equations, or diagrams. (3pt) 5) According to the International Code of Zoological Nomenclature, Reptilia (shown in shaded area) and Aves (birds) are both vertebrate classes. Is this a cladistic classification? Why or why not? What is a bird to a cladist? (3pt) [Testudines = turtles and relatives; Lepidosauria = lizards and snakes] 4) Soapberry bugs in Florida have made a host shift from balloon vine fruit (L) to the introduced relative: the flat-podded rain tree fruit (shown on R). Scott Carroll s measured beaks of bugs grown on both kinds of fruit. Why was it important to measure both populations on both hosts, and what did they find? (3pt) 6) Explain the creationist argument for irreducible complexity in one or two sentences, and no more. Point to a putative biological example. (3pt)

6 Biology 206 MT of 11 Bonus! (0.25pt ea snapper round) In which I wrote several bonus questions based upon trivia in the course. 202 years old on Saturday.