BISC 656, Evolutionary Genetics, Spring 2013
Study guide for the exam
The exam will be Thursday, March 21. If you will be absent that day, e-mail me as soon as possible 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 about 10 to 15 questions. Some of the questions may be answered with one or two sentences, while other questions may require longer, essay-type answers (and would therefore be worth more). I haven't yet decided on the balance of short and long-answer questions to use.
Here is a list of basic concepts that I've covered in lecture. The questions will not ask you to recite definitions for these; instead, they will ask you to apply your knowledge and understanding of these concepts to new situations.
- replacement (non-synonymous) variation
- synonymous variation
- linkage equilibrium and disequilibrium
- random drift
- neutral model
- molecular clock
- relative fitness
- directional selection
- purifying selection
- balancing selection
- viability or survival selection
- sexual selection
- codon bias
- nearly neutral model
- dN/dS tests
- MK test
- HKA test
- Tajima-type tests
Here are some practice questions. We'll go over the answers in class on Tuesday, March 19.
- A population of 20,000 garter snakes lives on an island in Lake Erie. The mother of Sammy the Snake ate a pesticide-laden grasshopper, and the pesticide caused a mutation in the gamete that became Sammy. So Sammy is heterozygous for a brand new allele. What is most likely to happen to that allele over the next generations? Why?
- Drosophila sechellia is a species of fruit fly that lives only in the Seychelles Islands, a group of islands in the Indian Ocean, where it lays its eggs only in the fruit of the Morinda citrifolia tree. D. simulans is closely related to D. sechellia, but it is found all over the world, living on a wide variety of fruit. Which species would you expect to have a higher level of codon bias? Why?
- You are studying a species of frog that mates on one night of the year. You've found that a simple one-gene, two-allele polymorphism controls croaking volume in males: LL croak very loudly, Ll croak moderately, and ll croak rather softly. You've captured all of the mating pairs and frogs that couldn't find a mate in a pond and have measured the croaking volume of each male. You find that the frequency of the LL genotype is higher in mating frogs than in frogs that aren't mating. The frequency of Ll is about the same in mating and non-mating frogs, while ll is less common in mating frogs than in non-mating frogs. What kind of selection is this? Which genotype has the highest relative fitness, and which has the lowest? If this continued for many more generations, what would you expect to see? If you follow this population for 10 more years, and the allele frequency doesn't do what you expected, what might be causing a result different from what you predicted?
- You have sequenced the ATPase-6 gene in polar bears and brown bears, and 0.4 percent of the synonymous sites are different between the species. You want use this data to estimate the time of the most recent common ancestor of these two species. What further information do you need? How would you obtain it?
- Lewontin and Hubby (1966) used allozyme electrophoresis to estimate the amount of polymorphism in several enzymes in the fly Drosophila pseudoobscura. How were their results a surprise to the people at that time? What hypothesis to explain Lewontin and Hubby's results gained new prominence in the years after 1966?
- There are four possible codons for glycine: GGA, GGC, GGG, and GGT. You examine a large number of genes in the bacterium Clostridium botulinum and find that over half of the glycine codons are GGC. What is this kind of pattern called, and what's one possible explanation for it?
- You set up a laboratory colony of ten thousand nematodes. Every generation, you measure the allele frequency at a polymorphism in the Gpi gene in a sample of 500 nematodes. You plot the allele frequencies over time and get the following graph:
Make up some numbers for relative fitnesses for the three genotypes that are consistent with this graph:
What evolutionary process or processes are affecting the allele frequencies?
- According to the neutral model, which species will show a higher rate of evolution at synonymous sites: the fruit fly Drosophila simulans, with a population size in the hundreds of millions, or the fruit fly Drosophila sechellia, with a population size in the hundreds of thousands? Why?
- According to the nearly neutral model, which species will show a higher rate of evolution at synonymous sites: the fruit fly Drosophila simulans, with a population size in the hundreds of millions, or the fruit fly Drosophila sechellia, with a population size in the hundreds of thousands? Why?
- You use the Hudson-Kreitman-Aguade test to compare the polymorphism to divergence ratio of two genes in the tungara frog (using another species of frog as the comparison for divergence). Both genes have about the same amount of divergence between species, but the Apk gene has much more silent polymorphism than the Pac-6 gene. The difference in polymorphism-to-divergence ratios is statistically significant. What are two completely different possible explanations for this difference between the genes?
- You are trying to estimate the phylogeny of 12 species of pine trees. You sequence the RBCL gene in each species of pine. You also sequence RBCL in a redwood tree, which you're confident is distantly related to the pines. If you're only interested in the phylogeny of pines, what's the point of sequencing the gene in a redwood tree? Don't just give a name for the concept, say what the purpose of sequencing it is.
- You get your RBCL data and sit down to estimate the phylogeny. You've been reading the literature on phylogeny estimation, and you like the maximum likelihood technique the best--you think it makes the most sensible, rigorous and epistomologically justifiable assumptions. Should you use any other phylogenetic estimation techniques? Why or why not?
- You collect data on a polymorphism in the Mpi gene in snails from several locations in on the shore of Delaware Bay. Snails near the mouth of the bay have a high frequency of the Mpi100 allele, while the frequency of Mpi100 goes down (and Mpi90 goes up) as you go up the bay. This could be natural selection by the different environmental conditions in the lower and upper bay, or it could be random drift. How could you test these hypotheses using additional data on geographic variation in allele frequencies?
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