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Name (2 points if printed in pencil)____________________________Biology 425 Exam 1A Please answer the following multiple choice questions (2 pts each). Note: there are numerous extra points built into this exam, so you can miss quite a few questions and still score 100% (in other words, you probably will end up doing better than you think you are doing!). 1. From a population standpoint, what are distinctions between the AIDS pandemic in Africa and the rest of the world? a) the incidence of AIDS in Africa is higher b) more men than women are afflicted in Africa c) a+b d) neither a nor b 2. Which cells in the human immune system have the shortest lifespan? a) naïve T cells b) memory T cells c) effector cells 3. Do individuals evolve? a) yes b) no 4. For the Eda rescue experiment that created transgenic sticklebacks, what was the phenotype of the parents? a) both complete b) both low c) one complete, one low 5. Bell’s experiments on sticklebacks in Loberg Lake showed a) a rapid increase in the frequency of the complete-plated morph b) evidence for a two-year lifecycle c) a+b d) neither a nor b 6. Circle the graph that best shows the molecular clock assumption? Number of Base pair substitutions (Y axis for all four graphs) Amount of time elapsed since genetic divergence 7. According to Gould, what do orchids have in common with the Panda’s thumb? a) adaptation usual leads to perfect solutions to problems b) natural selection operates on existing variation c) natural selection can operate on structures that originally served very different functions d) a+b e) a+c f) b+c g) all are true 8. Which of the following is true about bootstrapping a sequence of DNA that is 500 bases long? a) Each position (or site) is randomly chosen for each data set b) it is unlikely that the actual DNA sequence will be one of the data sets used in the bootstrap analysis c) bootstrapping is used to determine which tree is most parsimonious d) a+b e) a+c f) b+c g) all are true 9. A purine replaces a pyrimidine in a a) deletion e) duplication 1 b) indel c) transition d) transversion 10. What did Ellegren’s analysis of microsatellite mutations show? a) dinucleotide repeats tended to get longer, while tetranecleotide repeats tended to get shorter b) dinucleotide repeats tended to get longer, while tetranecleotide repeats had no trend c) dinucleotide repeats and tetranecleotide repeats tended to get longer d) dinucleotide repeats tended to get shorter, while tetranecleotide repeats tended to get longer e) dinucleotide repeats tended to get shorter, while tetranecleotide repeats had no trend f) dinucleotide repeats and tetranecleotide repeats tended to get shorter 11. Humans have a DNA sequence that looks like the chimp gene for the CMAH enzyme, except that humans have a 92 base pair deletion that makess it nonfunctional. This is an example of a a) homoplasy b) vestigial trait c) reversal d) none of these 12. In the greenish warbler ring series a) the northwestern and northeastern forms will readily mate in their contact zone b) the southwestern and southeastern forms will readily mate in their contact zones c) a+b d) neither a nor b 13. The principle that geological processes taking place now operated similarly in the past is a) ontological naturalism b) homology c) homplasy d) catastrophism e) uniformitarianism 14. Large fruit in domestic tomatoes is due to a) high expression of a repressor protein b) low expression of a repressor protein c) high expression of auxins d) low expression of auxins 15. Research by Jones and Reithel on snapdragons showed that visits by bees b) yellow flowers had higher seed set a) yellow flowers had more c) a+b d) neither a nor b 16. The droughts of 1977 and 2003 affected medium ground finches by selecting for a) increased beak depth in both cases b) decreased beak depth in both cases c) increased beak depth in 1977, but decreased in 2003 d) decreased beak depth in 1977, but increased in 2003 17. How does the eel sperm flagellum differ from the more typical eukaryotic flagellum? a) it lacks the central pair complex b) it lacks the A tubule c) it lacks the B tubule 18. Why are short and long interspersed elements so useful in reconstructing phylogeny? a) because homoplasy is very common b) because their loss is associated with loss of a part of the host genome c) a+b d) neither a nor b 19. How did Chameleons get from Africa to India a) they didn’t b) they floated on rafts c) they road chunks of Gondwana as it broke up 20. Most of the mutations isolated by Denver and colleagues from C. elegans nuclear DNA were a) transitions b) transversions c) indels 21. Which is the more common cause of gene duplication? a) retrotransposition b) unequal cross-over 2 22. Est inversions in Drosophila are a) more common in higher latitudes in North America b) more common in higher latitudes in south America c) a+b d) neither a nor b 23. Individuals of genotype CCR5-∆32/ CCR5-∆32 are b) more common in northern Europe c) a+b a) more susceptible to HIV infection d) neither a nor b Short answers 1. (4 pts) At time 0, patients were switched from AZT to another anti-HIV treatment (DDI). Draw the curves representing the sensitivity of the HIV virus to each of the two drugs after the switch. sensitivity 0 2 4 6 time (months) 8 2. (3 pts) After 8 years of chronic HIV infection, the HIV RNA stops diverging (as measured in genetic distance) from the initial RNA of the infecting HIV. Why? 3. (3 pts) If you find a stickleback fish with four dermal plates, what is most likely its genetic constitution (hint: remember to consider all of the genes influencing the phenotype)? 4. (4 pts) Research on the beak of the finch yielded the following graph. Give two plausible interpretations of why this relationship could exist in finches. Offspring Beak depth parent beak depth 3 5. (6 pts) Please answer the questions based on the tree below. A B C D E F G a) Which species (may be more than one) is/are most closely related to E. b) Which species (may be more than one) is/are most closely related to A c) The area surrounded by the circle forms a ___________________ group. 6. (6 pts) When MutS+/MutS+ E. coli were competed against MutS-/MutS- E.coli in a novel environment (with equal initial population size) there were some interesting dynamics. a) Draw a graph that shows the results of this experiment b) provide an explanation for this result. 4 7. (3 pts) Please explain why the bones in the forelimb bones in bats and birds are homologous, but the use of forelimbs for powered flight is homoplastic in these two groups. 8. (3 pts) Give a plausible explanation for why humans, chimps and orangatans share the 16 MYA processed pseudogene (AS7), while it is missing in gorillas. 9. (6 pts) a) Build a tree using the following DNA base sequence information Species A Species B Species C Species D Species E ATTGCAGCA CTTGTAGGC CATGTAGGC ATTGCAGCC CGAGTATTA b) Identify one location on your tree where a reversal occurred (and what was that reversal)? Name _______________________ (10 pts) There is lots of extra credit embedded in this exam. Ace it! (2 pts) The following statements pertain to questions 1-9. Fill in the letter that describes the process that best explains each statement. A) frequency dependent selection B) directional selection C) underdominance D) heterozygote superiority (heterosis) E) not an evolutionary process _____1. explains the world-wide distribution of sickle-cell anemia _____2. Explains fruit set in two color morphs of elderflower orchids 5 _____3. the very flat insect on a branch probably resulted from this type of selection _____4. Susceptibility to kuru _____5. Fitness of individuals with a trait is variable _____6. Mosquitoes evolve resistance to DDT _____7. Foster’s research on selection on Drosophila with compound chromosomes _____8. Decrease in lactose intolerance in Euro/American humans _____9. Change in human cranial shape from American Colonial period to present Multiple choice (2 pts each) 10. Genetic drift leads to evolutionary change more rapidly in which size populations? a) small b) medium c) large d) infinite 11. Genetic drift is more likely to lead to fixation of an allele more rapidly in which size population? a) small b) medium c) large d) infinite 12. Collared lizards in the Ozark Mountains have heterozygosity b) fixation of different alleles in different small populations nor b a) a high degree of c) a+b d) neither a 13. Referring to question 12, what is an expected result of controlled burns conducted by the Missouri Department of Conservation? a) more gene flow b) more genetic drift c) larger populations d) a+b e) a+c f) b+c g) all of the above 14. Why does Kimura argue that natural selection’s effect on allele frequencies is relatively small? a) beneficial mutations are rare b) deleterious mutations are selected out of the population before they get established c) a+b d) neither a nor b 15. Gojobori’s study of the RNA sequence in influenza showed a) support for the neutral theory b) a much higher rate of replacement mutations than synonymous mutations c) a+b d) neither a nor b 16. Andrew Young’s study of population size, allele richness and polymorphism showed a) a higher allele richness in Eucalyptus than the other species b) polymorphism increased with population size, but allele richness did not c) good evidence for genetic drift being a more potent force in large populations d) a+b e) a+c f) b+c g) all of the above 6 17. What is the inbreeding depression if the fitness of a selfed plant is 75% that of the fitness of an outbred plant a) .25 b) .5 c) .75 d) none of these 18. What type of mating system do prairie chicens have polygyny d) none of these a) monogamy b) polyandry c) lek 19. Which is true of the prairie chicken population in Illinois? a) hatching success has increased since 1990 b) individuals were imported from other states to increase gene flow c) a+b d) neither a nor b 20. Experiments by Paul Weeks provide evidence that the interaction between oxpeckers and cows is best described as a) mutualism b) competition c) parasitism d) none of these 21. Which of the following treatments did Erick Greene use for his exeriments on spider mimicry by tephritid fllies a) Zonosemata with own wings cut and reglued b) Zonosemata with housefly wings c) Housefly with Zonosemata wings d) a+b e) a+c f) b+c g) all of the above 22. Which groups show large testes in species with low levels of sperm competition? primates b) bats c) a+b d) neither a nor b a) 23. Which is not part of Felsenstein’s comparative method for evaluating phylogenetically independent contrasts? a) figure out the phylogeny of the species b) plot all sister species on a scatterplot c) move the lines connecting the contrasts, so that the species with the lower x-value is at the origin d) erase the point at the origin e) convert all continuous variables to nominal variables 24. Bat species with high relative testes size will usually have b) moderate relative brain size d) low relative brain size a) high relative brain size 25. According to research by Schenske and Agren, female flower size in Begonia involuctra has been determined by a) directional selection for smaller female flowers b) tradeoff between flower color and floral retention c) a+b d) neither a nor b 26.Which of the following is an assumption of the Hardy-Weinberg equilibrium? a) no natural selection b) no gene flow c) no random mating d) no genetic drift e) all are assumptions of the Hardy-Weinberg equilibrium 27. Why have body feather lice switched hosts less frequently than wing feather lice? a) because they are more firmly attached to the body feathers than the wing feather lice are to the wing feathers b) they don’t hitchhike very often on parasitic flies c) a+b d) neither a nor b 7 28. According to Gould and Lewontin, arguing that the spandrels of San Marcos were built as spaces to house mosaics is analogous to a) arguing that noses are adaptations for supporting eyeglasses b) arguing that all adaptations evolved to serve their current function c) a+b d) neither a nor b 29. (3 pts). DD and Dd individuals have 25% survival rates and dd individuals have a 20% survival rate. They all produce the same number offspring on average. Calculate the fitnesses and selections coefficients. 30. (9 pts) a). In a population of elk 10 males with the largest antlers fathered 200 fawns while the 100 smaller antlered males fathered 220 fawns. What are the reproductive fitnesses and selection coefficients of the 2 types of males? b) Of the 10 large antlered elk that mated in the spring, five survived through the following winter to mate again. Of the 100 smaller antlered males, 70 were still alive the following spring. What are the survival fitnesses and selection coefficients of the 2 types of males? c) What are the overall fitnesses of the large and small antlered males in question 30 if you consider their abilities to survive and reproduce? 31. (4 pts) A population of reindeer is in Hardy-Weinberg equilibrium for a gene for nose color, in which having a red nose is determined by a recessive allele. A population geneticist named Sandy Claws finds 64 red-nosed reindeer in his flock of 100. What is the frequency of the recessive allele. 8 32. (6 pts) What did Gerald Pier and colleagues hypothesize regarding why cystic fibrosis is so prevalent in the human population, despite having a negative influence on fitness of affected individuals? b) Describe two research findings that support their hypothesis? 33. (5 pts) The following population of individuals is not in hardy Weinberg Equilibrium. numbers of individuals AA Aa aa 10 140 50 a) What is the allele frequency? b) What will be the genotype frequencies the next generation if it returns to Hardy-Weinberg equilibrium? 34 (6 pts). a) What are two alternatives discussed by Gould and Lewontin to the adaptationist programme. 9 b) Give an example of each alternative that you’ve learned about in this class. 34. (14 pts) Alarm calls are common in ground squirrels of several species. When a squirrel squeals the equivalent of "heads up", all the squirrels are supposed to scurry into their little holes and hide. If they do, they avoid getting eaten by predators. In a really silly population of 100 squirrels, only 19 respond to the "heads up" squeal by scurrying into a hole and hiding, while the remaining 81 respond by "sticking their heads out the hole", and thus suffer a mortality (death) rate of 70% before reaching reproductive age. Assume that squirrels who stick their heads out of a hole (instead of hiding) are homozygous for a recessive allele. Assume that our population initially was in Hardy-Weinberg equilibrium. a) What are the allele frequencies? b) What are the genotype frequencies c) What is the selection coefficient operating against the "sticking their head out the hole" phenotype? d) Given your answer to C, if there are also 100 squirrels next generation, what number (you will have to round off to the nearest squirrel) will stick their heads out of the hole in response to "heads up"? 10 e) What will be the allele frequency of the "sticking their head out of the hole" allele next generation (no longer in HW equilibrium)? 36. (4 pts) If A population of 10 individuals has 20% heterozygosity, what is the expected % heterozygosity in the next generation as a result of genetic drift? Name (10 pts if printed) __________________________________ Biology 425 Exam Final 1. Which of the following are predictions of the rate of living theory for the evolution of aging? a) aging rate is negatively correlated with metabolic rate b) species can be selected to evolve longer life-spans c) a+b d) neither a nor b 2. Which group had the highest lifetime energy expenditure in Austad and Fisher’s study? a) bats b) carnivores c) artiodactyls (deer) d) lagomorphs (rabbits) 3. Which influenza virus is most dangerous to humans a) A b) B c) C 4. How did the flue pandemic of 1918 differ from the flu outbreaks in the previous years? a) it inflicted high mortality on people in their 20s and 30s. b) it was an RNA virus c) a+b d) neither a nor b 5. Which of the following is true about the distribution of breast cancer? a) breast cancer incidence is higher in Eastern Europe than Western Europe b) breast cancer incidence is highest in areas with Mus musculus c) a+b d) neither a nor b 6. Strassmann’s results on Dogon women, and on women in other West African communities, suggest that a) breast cancer is caused by high levels of childbirth b) breast cancer is caused by a virus c) a+b d) neither a nor b 7. In what ways are the Africanized honeybees less desirable than their European counterparts? a) more susceptible to disease b) more likely to swarm c) lower pollination rates d) a+b e) a+c f) b+c g) all of the above 11 8. The evolutionary psychology principle that different neural circuits are specialized for solving different adaptive problems is exemplified by a) our ability to learn to solve complex problems b) our tendency to make simplifications of our experiences c) the brain functions as a computer d) instincts 9. Which species has the fewest chromosomes? gorilla a) humans b) chimpanzees c) 10. In which tissue is the FOXP2 gene product much more highly expressed in humans in comparison to other primates? a) brain b) blood c) liver d) heart 11. Current evidence supports the hypothesis that chimps and bonobos shared a common ancestor most recently with a) humans b) gorillas c) orangatans d) gibbon 12. Comparisons of Neanderthal to modern humans indicate that a) there was no evidence of culture in Neanderthals b) Neanderthals had smaller cranial capacity c) neanderthals have identical hyoid bones d) a+b e) a+c f) b+c g) all of the above 13. Blasting the mitochondrial D-loop hypervariable region 1 DNA of modern humans vs. Neanderthals and comparing % similarity against comparisons with other species that hybridize and produce non-viable offaspring indicates a) modern human and Neanderthal % similarity is greater than the other pairs b) modern human and Neanderthal % similarity is equivalent to the other pairs c) modern human and Neanderthal % similarity is less than the other pairs 14. Which species concepts defines a species on the basis of whether individuals are able to successfully reproduce? a) biological species concept b) morphospecies concept c) phylogenetic concept 15. Which speciation model has no physical barriers? peripatric d) sympatric a) allopatric b) parapatric c) 161. F2 hybrids of Pundamilia pundamilia and P. nyerei showed a) preference index of -.25 and low variance in mate choice b) preference index of -.25 and high variance in mate choice c) preference index of 0 and low variance in mate choice d) preference index of 0 and high variance in mate choice e) preference index of +.25 and low variance in mate choice f) preference index of +.25 and high variance in mate choice 17. Which continents have had avian flu outbreaks that affected humans? a) North America b) Africa c) Asia d) a+b e) a+c f) b+c g) all of the above 18. Which virus is more lethal in mice? a) DK/12 b) DK/27 19. Which taxonomic group goes against the trend that diversification and speciation is correlated with the number of Hox genes? a) mammals b) sea urchins c) fruit flies molluscs 12 d) 20. Which of the following is true? a) Closely related species will tend to have a greater number of similar Hox genes than distantly related species b) Closely related species will tend to have Hox genes that are expressed in similar locations of the body than more distantly related species c) a+b d) neither a nor b 21. Which of the following are selected for by intersexual selection? a) copulatory plugs b) sperm removal function of damselfly penis c) a+b d) neither a nor b 22. How do Hawaiian drosopholids support the dispersal mechanism of speciation? a) flies on more recently formed islands are more similar genetically b) because lava flows within the islands created two distinct populations of flies c) a+b d) neither a nor b 23. Analysis of snapping shrimp sister pairs on either side of the isthmus of Panama support which speciation hypothesis? a) dispersal b) parapatric c) peripatric d) sympatric e) vicariance 24. In female Gunnison’s prairie dogs a) fertility rates were higher if the female had multiple mates b) surviving litter size was higher if the female had multiple mates c) a+b d) neither a nor b 25. In the pipefish Sygnathus typhle, males prefer females with many spots c) a+b d) neither a nor b a) large skin folds b) 26. Delph’s study showed that when animal pollinated plants have flowers that are sexually dimorphic for investment in pollinator attraction, investment by males tends to be larger in a) number of flowers per inflorescence b) strength of floral odor c) nectar quantity d) a+b e) a+c f) b+c g) all of the above 27. In the Yanomamo a) 40% of the men commit homicide b) homicidal men have more children than non-homicidal men c) a+b d) neither a nor b 28. At the U.S. Military academy at West Point, taller men had, over the course of a lifetime a) more wives b) younger second wives c) more children d) a+b e) a+c f) b+c g) all of the above h) none of the above 29. Pryke and Anderson’s study on red-collared widowbirds showed that a) long tails caused health to decline b) long tails caused reproductive success to decline c) a+b d) neither a nor b 30. What is r between full cousins? a) .5 b) .25 c) .125 13 d) <.05 31. Quellar and colleagues showed that in slime molds a) in the lab, wild-type cells have high reproductive success b) in the soil, wild-type cells are geenbeard altruists c) a+b d) neither a nor b 32. Bell’s experiments on sticklebacks in Loberg Lake showed a) a rapid increase in the frequency of the complete-plated morph b) evidence for a two-year lifecycle c) a+b d) neither a nor b 33. Which graph that best shows the molecular clock assumption? A B C D Number of Base pair substitutions (Y axis for all four graphs) Amount of time elapsed since genetic divergence a) A b) B c) C d) D 34. Which of the following is true about bootstrapping a sequence of DNA that is 500 bases long? a) Each position (or site) is randomly chosen for each data set b) it is unlikely that the actual DNA sequence will be one of the data sets used in the bootstrap analysis c) bootstrapping is used to determine which tree is most parsimonious d) a+b e) a+c f) b+c g) all are true 35. What did Ellegren’s analysis of microsatellite mutations show? a) dinucleotide repeats tended to get longer, while tetranecleotide repeats had no trend b) dinucleotide repeats tended to get longer, while tetranecleotide repeats tended to get shorter c) dinucleotide repeats and tetranecleotide repeats tended to get longer d) dinucleotide repeats tended to get shorter, while tetranecleotide repeats had no trend e) dinucleotide repeats tended to get shorter, while tetranecleotide repeats tended to get longer f) dinucleotide repeats and tetranecleotide repeats tended to get shorter 36. How did Chameleons get from Africa to India a) they didn’t b) they floated on rafts c) they road chunks of Gondwana as it broke up 37. Bat species with high relative testes size will usually have b) moderate relative brain size d) low relative brain size a) high relative brain size 38. According to research by Schenske and Agren, female flower size in Begonia involuctra has been determined by a) directional selection for smaller female flowers b) tradeoff between flower color and floral retention c) a+b d) neither a nor b 39. Experiments by Paul Weeks provide evidence that the interaction between oxpeckers and cows is best described as a) mutualism b) competition c) parasitism d) none of these 14 40. Which of the following treatments did Erick Greene use for his exeriments on spider mimicry by tephritid fllies a) Zonosemata with own wings cut and reglued b) Zonosemata with housefly wings c) Housefly with Zonosemata wings d) a+b e) a+c f) b+c g) all of the above 41. Andrew Young’s study of population size, allele richness and polymorphism showed a) a higher allele richness in Eucalyptus than the other species b) polymorphism increased with population size, but allele richness did not c) good evidence for genetic drift being a more potent force in large populations d) a+b e) a+c f) b+c g) all of the above 42. Why does Kimura argue that natural selection’s effect on allele frequencies is relatively small? a) beneficial mutations are rare b) deleterious mutations are selected out of the population before they get established c) a+b d) neither a nor b Short answers 1 (6 pts). Briefly describe three studies (including the results) that provide evidence that fever is an adaptive response by the body? 2. (4 pts) What did the 16S rRNA analysis reveal about the evolution of botulism? 3. (4 pts) What are four morphological or physiological adaptations favoring bipedalism in modern humans? 15 4 (5 pts). Briefly describe 5 hypotheses for the adaptive significance of bipedalism in humans? 5 (4 pts). Here are two graphs. For each graph, draw in one curve for SCID newborns, and a second curve for control. Percentile Percentile Total lymphocytes/mm3 Total T-cells/mm3 6 (4 pts). Describe the sequence of events that occurred when researchers induced a DK/27 DK/12 mutation in a virus after the mouse was inoculated with DK/27? 16 7 (7 pts). a) Discuss Andrade’s two hypotheses for why redback widow males threw themselves into the jaws of their mates. b) What evidence did she use to decide which hypothesis was likely to be correct? 8 (5 pts). Discuss the likely reproductive behavior of males and females based on the graph below. Make sure you justify your argument. females Number of Offspring males Number of Mates 17 9 (6 pts). a) What is Hamilton’s rule, and how does it relate to the evolution of altruism? b) Discuss one study that demonstrates how Hamilton’s rule can help us understand the evolution of altruistic behavior. Make sure your discussion includes a description of the question or hypothesis addressed by the researchers, the experiments or observations, the results of the study, and the conclusions. 10. (3 pts) Please explain why the bones in the forelimb bones in bats and birds are homologous, but the use of forelimbs for powered flight is homoplastic in these two groups. 11. (4 pts) Research on the beak of the finch yielded the following graph. Give two plausible interpretations of why this relationship could exist in finches. Offspring Beak depth parent beak depth 18 12. (9 pts) a). In a population of elk 20 males with the largest antlers fathered 100 fawns while the 100 smaller antlered males fathered 150 fawns. What are the reproductive fitnesses and selection coefficients of the 2 types of males? b) Of the 20 large antlered elk that mated in the spring, five survived through the following winter to mate again. Of the 100 smaller antlered males, 80 were still alive the following spring. What are the survival fitnesses and selection coefficients of the 2 types of males? c) What are the overall fitnesses of the large and small antlered males in question 30 if you consider their abilities to survive and reproduce? 13. (14 pts) Alarm calls are common in ground squirrels of several species. When a squirrel squeals the equivalent of "heads up", all the squirrels are supposed to scurry into their little holes and hide. If they do, they avoid getting eaten by predators. In a really silly population of 100 squirrels, only 36 respond to the "heads up" squeal by scurrying into a hole and hiding, while the remaining 64 respond by "sticking their heads out the hole", and thus suffer a mortality (death) rate of 60% before reaching reproductive age. Assume that squirrels who stick their heads out of a hole (instead of hiding) are homozygous for a recessive allele. Assume that our population initially was in Hardy-Weinberg equilibrium. 19 a) What are the allele frequencies? b) What are the genotype frequencies c) What is the selection coefficient operating against the "sticking their head out the hole" phenotype? d) Given your answer to C, if there are also 100 squirrels next generation, what number (you will have to round off to the nearest squirrel) will stick their heads out of the hole in response to "heads up"? e) What will be the allele frequency of the "sticking their head out of the hole" allele next generation (no longer in HW equilibrium)? 20