Here are the answers to exam 1. For some of the questions, I have provided explanatory material in regular type, and the answer in bold; all you need to write down is the answer. If you don't understand why your answer was wrong, you may e-mail me, talk to me before or after class, or set up a time to talk to me in my office. The exam was worth 15 points, so each question was worth one point.
1. Use a topic search to find one or more papers about insects that walk on snow.
2. Look in the reference list of those papers to find older papers.
3. Use the "Times Cited" feature in Web of Sciene to find more recent papers that have cited the papers from the first two steps.
4. Keep looking in the reference list and "Times Cited" of relevant papers until I'm not seeing anything new.
You got points off if you said you'd start with a focal paper, but didn't say how you would find it.
2. Even though the new alleles increase fitness, they are lost due to random genetic drift most of the time. The graph shows what happens to the "r" allele, which increases fitness; the rr genotype has a fitness of 1.0, rb is 0.95, and bb is 0.90. If there was no random drift, the r allele would rapidly increase in frequency (the thick, smooth line). The graph shows 10 replicates, but only two of the ten increase in frequency and get fixed by directional selection (the jaggedy lines); the other eight are lost. Sad!
3. Knowing the heritability will help predict the response to selection; if heritability is high, the urchins may be able to adapt to lower pH, while if heritability is low, they might go extinct..
4. They found that flies in northern North America also had larger wings that flies in southern North America. You could have also said that they found that the flies in northern North America evolved larger wings over a period of a few decades, although I don't think anyone mentioned that. You got points off if you said that Gilchrist et al. (2001) looked at flies in Asia, or Australia, or "around the world"; they just looked at North America.
5. The number of rats that survived the poisoning on Poirier Island must have been fairly large; if the number was very small, random drift would have caused a substantial change in allele frequencies. You got points off if you just said that the results showed that some rats survived; the question asked for your conclusion about the number of rats that survived.
6. Gray is recessive and black is dominant, so you would take the square root of the frequency of the gray phenotype to get the frequency of the gray allele. You would then subtract that from one to get the frequency of the black allele. You got points off for saying that black was recessive. (The allele that causes black fur in squirrels really is dominant, and some idiot really did introduce Sciurus carolinensis to Ireland in 1911, but I have no idea what the frequency of black squirrels is in Ireland.)
7. The frequency will stay about the same, with some small change due to drift. You got points off for saying that the frequency would stay exactly the same (there's always drift!) or for saying the frequency would definitely go up, or definitely go down, or that one allele would definitely get fixed. (In reality, there probably is selection on this polymorphism; black squirrels stay warmer longer when it's cold, but they're more visible to predators.)
8. The rate of mutations will stay the same; new mutations are random, they do not occur because they would be favorable.. You got points off if you interpreted "mutation rate" to mean "allele frequency." The mutation rate is how often new mutations appear; it is measured in mutations per generation (or mutations per year). A mutation is an event, the changing of one DNA sequence to another; a mutation creates a new allele. An allele is one variant of a gene. Allele frequency is the proportion of genes in a population that have a particular allele.
9. Much less DNA sequence polymorphism near the FOX2P gene than in regions further away from it would be evidence of a selective sweep caused by recent, strong directional selection. You got points off if you just said "Evidence of a selective sweep" or "Evidence of hitchhiking," you had to say what the evidence is for a sweep (reduced polymorphism). Another kind of evidence would be a higher ratio of amino acid replacement/synonymous fixed differences, compared to the ratio of amino acid replacement/synonymous polymorphisms (the McDonald-Kreitman test). If that was your answer, you couldn't just say that there were a lot of amino acid fixed differences; you had to say that it was more than expected, based on comparing the ratios of replacement to synonymous.
10. Collect data on EPAS1 allele frequencies in different parts of the world; if EPAS1-D is at higher frequency in high-altitude areas than low-altitude in other parts of the world, it's evidence for selection by increased altitude. (There's been some interesting research on this gene in humans, you'll hear more about it later in the semester.)
11. Allele frequencies for the 99 genes would be kept similar by migration; the difference in allele frequency at the MCR1 gene would be due to selection favoring different alleles in Oregon and Delaware. If you said the 99 polymorphisms were kept similar by balancing selection, and MCR1 was different due to drift, I accepted it; that's possible, although not very likely compared to the first answer. Northern flickers really do show differences in genes controlling pigment patterns betweeen the east and west coast, while being similar in other respects, but I have no idea if anyone has looked at the genetics.
12. They found evidence for sexual selection; their evidence was that individuals with smaller eyes were more likely to be in amplexus (mated pairs) than individuals with larger eyes. If you answered the first part by saying "directional selection," I accepted it, although I was looking for the more specific sexual selection. If you said the evidence was that amphipods in caves had smaller eyes than those outside caves, you got points off; that's true, but the question asked about the experiments in the Jones and Culver (1989) paper, which were about evidence for sexual selection from mated pairs. They just referred to other papers about the difference between cave and non-cave populations.
13. Boag (1983) looked at beak size in relatives, such as parents and offspring; because the beak sizes of offspring were similar to the beak size of their parents, he could tell that heritability was high. If you said the evidence for high heritability was that the beak size changed over time as the environment changed, you got points off; that evidence came in later papers by other authors.
14. Recombination increases the rate of adaptation by bringing together favorable alleles at different genes on the same chromosome. For example, if one parent has an allele to resist disease A, and the other parent has an allele at a different gene to resist disease B, some of their offspring will produce gametes containing the resistance alleles for both diseases. Without recombination, the only way to get a chromosome with both resistance alleles is to have the mutation for resistance to B occur on a chromosome that already has resistance to A, or vice versa. Some of you said that recombination can lead to gene duplications that may increase fitness; I wasn't thinking of that when I wrote the question, but it's a good answer and you got full credit. If you said something vague about "increasing variation," you probably got full credit or close to it, even though I wanted something a little more specific. If you said that recombination is good because it causes hitchhiking, you got a lot of points off; for one thing, recombination is what breaks up hitchhiking, and for another, through a process we didn't talk about in class, hitchhiking can actually reduce the rate of adaptation.
15. They found evidence for balancing selection; their evidence was that were several amino acid polymorphisms in humans, which is more than would be expected when looking at the ratio of replacement to synonymous fixed differences between humans and chimps. You got points off for saying that they found evidence that heterozygotes could see more colors; Verrelli and Tishkoff (2004) speculated that this might be the reason for the selection, but they didn't measure color vision in anyone (and as mentioned in class, there still doesn't seem to be good evidence that heterozygotes see more colors).
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