- (15 pts) The coalescent method that was developed in the 1980s provides a way of inferring population history, such as demographic changes and timing of divergence among lineages. What is meant by coalescence? Would you expect large populations to have a common ancestor deeper in the past, more recent in the past, or no difference from small populations? What difference does it make to time of coalescence if you used mitochondrial or chloroplast DNA as opposed to nuclear DNA?
- (15 pts) Directional selection and population bottlenecks may show similar signals of FST and heterozygosity in the genetic structure of contemporary populations. What are these signals? How do we distinguish between these two evolutionary forces if their signals are similar? In your answer define directional selection and population bottlenecks.
- (10 pts) Selection and migration may be opposing forces for genetic change. Explain what this means. How do selection and migration interact to determine the shape of a cline across a zone where two lineages (could be two interfertile species) meet?
- (15 pts) Epigenetic change may provide a route of rapid adaptation to environmental change. Explain. Include in your answer what distinguishes epigenetic change from genetic adaptation and plasticity. Discuss the mechanisms of epigenetic change and why DNA methylation is the preferred method to study epigenetic change in ecology and evolutionary biology. Choose one of the recent studies presented in lecture, slides 20-25, and summarize the utility of the author’s approach for answering the question at the top of the slide: 1) How much epigenetic variation is environmentally induced? 2) How does epigenetic variation shape phenotype? 3) To what extent does the genotype control the epigenetic state? 4) Does epigenetic inheritance affect adaptation?
- (10 pts) Rare alleles can become common in newly colonized populations. How does this happen? Explain how disadvantageous alleles could increase in frequency at the colonizing front.
- (15 pts) Estimating recent historic abundance from contemporary levels of genetic diversity can be a misleading process. Referring to the review by Palsbøll et al. (2013), explain some sources of error for estimating Nc. Be sure to refer to equations 1 and 2 in your answer. Discuss the issues estimating mutation rate. Discuss the difficulty of inferring an estimate of theta, be sure to include at least one complication that is temporal and one that is spatial. Finally, explain the significance of an underestimation of Ne for population management practices.
- (20 pts) How do you think an understanding of genetics of populations can help in predicting effects of environmental change on populations? In your response discuss what both climatic change and fragmentation do to the demographics and genetics of populations. You should compare and contrast species with different life histories (this could include, but is not limited to, population densities, distributions, mating systems, and vagility). You should develop arguments for at least three life history traits and how these might affect (positively or negatively) a species’ ability to compensate for shifting climatic conditions or habitat fragmentation.
