BISC 656, Evolutionary Genetics, Spring 2016

Study guide for the exam

The exam will be Thursday, March 24. and will be worth 30 percent of your grade for the course. If you will be absent that day, e-mail me by the end of the day on Friday, March 18, so that we can schedule your makeup exam.

You may not use your notes during the exam. You will not need a calculator.

The exam will consist of 20 questions. Each of your answers should consist of one to a few sentences. You may include drawings in your answers if they help you make your point. While there is no strict length limit, you may get points off for writing long, rambling answers that say the same thing over and over.

Here are some practice questions. Try answering them, then highlight the invisible text inside the red box (drag your cursor across it) to see my answer.

1. Based on their similar size, short tails, and cute noses, you think that guinea pigs and rabbits are more closely related to each other than they are to rats and mice. How would you test this hypothesis? What result would be consistent with your hypothesis?

Answer: I would collect DNA sequence data from one or more genes in the four species. If my hypothesis were correct, I would expect the difference in the DNA sequences between guinea pigs and rabbits to be smaller than the difference between them and rats or mice.
--->[If a question asks for one answer, and you can think of more than one possible answer, just put down the one that you think is most likely to be correct. You won't get extra credit for having both correct answers if only one was asked for, and if one of your answers is right and one is wrong, you'll get graded based on the wrong answer. For example, if you wrote: "I would collect DNA sequence data from one or more genes in the four species. If my hypothesis were correct, I would expect the difference in the DNA sequences between guinea pigs and rabbits to be smaller than the difference between them and rats or mice. I would also look for rabbit-guinea pig hybrids in the Precambrian fossil record; if my hypothesis were correct, I would find them", you would get zero points, because the second half of your answer is very wrong.]

2. Rodents make the enzyme L-gulonolactone oxidase, which they use to synthesize vitamin C; primates do not make this protein, and therefore have to get vitamin C from their diet rather than synthesizing it. How would you determine whether the common ancestor of rodents and primates was able to synthesize vitamin C? Give all the possible results of your experiment and how you would interpret each one.

Answer: I would use DNA sequence data to estimate the evolutionary tree of rodents, primates, and other mammals. If the closest outgroup to rodents and primates could synthesize vitamin C, I would conclude that the common ancestor of rodents and primates could synthesize it; if the closest outgroup could not synthesize vitamin C, I would conclude that this ability evolved in the rodent lineage.
--->[Diagrams of evolutionary trees could be a useful part of this answer.]

3. You've decided to write your term paper about ammonites. What are the three most important things you would do to find scientific literature about ammonites?

Answer: 1. Do a topic search for ammonites in the Web of Science.
2. Pick some of the articles from the topic search and look at their reference lists for good older papers.
3. Pick some of the best papers from steps 1 and 2 and use the Web of Science to find more recent papers that cite them.
--->[Note that if a question asks for more than one answer, be sure to give the correct number of answers. Numbering the answers, as I've done here, may help you keep track of this.]

4. The spadefoot toad, Scaphiopus couchii, lives in southern New Mexico. Some toads live on dark rock and are dark colored; some live on white sand and are light colored. You want to know whether this difference in color is genetic. You don’t know whether any genes are involved, much less which genes. What experiment could you do to tell whether the difference in color between populations of toads from dark rock vs. white sand is genetic? What would the result be if the difference is not genetic?

Answer: In a lab, raise some offspring of dark-colored toads in a dark-colored environment and some in a light-colored environment. Do the same for the offspring of light-colored toads. If the trait is not genetic, toads will match the color of their environment, not their parents.

5. Berry et al. (1991) measured DNA sequence polymorphism on the fourth chromosome of two species of Drosophila and found that the fourth chromosome had much less polymorphism than other chromosomes. What is this evidence of? Why?

Answer: This is evidence for recent positive selection; because there is no recombination on the fourth chromosome, any positively selected mutation will "sweep" through the population, and all of the fourth chromosomes will be identical until new mutations occur.

6. Some people have wet, sticky earwax; other people have dry, crumbly earwax. This is caused by variation at a single gene with two alleles; the allele for wet earwax (W) is dominant over the dry allele (d). Right now, the frequency of W is about 90% in the United States. What do you expect to happen to the frequency of W in the United States over the next 100 years? Why?

Answer: I would expect the frequency of W to stay about the same, because even if there is selection on the earwax gene, I don't think it would be very strong. (If you say the frequency will stay exactly the same, you get a little off, because there's always random drift. If you say W will go up because it's dominant, you get 0 points and I will throw an eraser at you.)

7. Flies in the species Drosophila heteroneura have their eyes on the end of long stalks. Some individuals have longer stalks than others. Without using any kind of DNA data, what kind of experiments would you do to tell whether this variation in stalk length within a population is genetic? What result would you get if the variation is mostly genetic?

Answer: See how much variation there is among relatives (siblings, parents/offspring, etc.) compared to the variation among the total population. If the trait is mostly genetic, flies will be very similar to their relatives in stalk length.
Or rear the flies for several generations in the lab, impose strong selection (such as only let the flies with the longest stalks survive), and see how fast the average stalk length changes. If the trait is mostly genetic, the average length will change quickly.

8. You've convinced yourself that the variation in stalk length in question 7 is mostly genetic. You've done careful observations and shown that there's no difference in survival between long and short-stalked flies. Since you're interested in finding out whether there's selection on stalk length, what other kind of experiment should you do? Why?

Answer: You should observe mating success of flies with different stalk lengths, to see if there's any sexual selection on stalk length.

9. Janet Weiss of Denton University is studying a genetic polymorphism in cats, the long hair locus. Cats with the dominant L allele have short hair, while cats that are homozygous for the recessive l allele have long hair. She observes the hair length (long or short) on 100 cats from Hockessin, Delaware and estimates the allele frequency of l is 0.60. How did she do that? (You don’t have to do the calculations, just describe how the basic principle she used works.)

Answer: She used the Hardy-Weinberg principle: the allele frequency of the recessive l allele is the square root of the frequency of the recessive homozygote phenotype (long haired cats).

10. Kärkkäinen et al (2004) found that plants in one area of Finland had a high frequency of trichomes, while plants in other areas had a low frequency of trichomes. What additional evidence did they collect and how did it show evidence that natural selection affected the trichome gene?

Answer: They looked at several protein polymorphisms, and they showed much less geographic variation than trichomes. If proteins and trichomes were only affected by random drift and migration, with no selection, they would all show about the same amount of geographic variation.

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