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Ecology 

1. A fundamental goal in physiological ecology has been to establish mechanistic connections between physiological traits and fitness. In your opinion, have we already established these connections (such that the field can move on), or should establishing such connections remain an important goal moving forward? Include at least one example of a specific system where we clearly understand how variation in physiological traits connects to fitness in your answer.
2. Life-history strategies (e.g., patterns of growth and reproduction) are thought to evolve in response to environmental conditions. What are some of the classic ecological models that describe expected evolutionary responses of life-history strategies to different environments? Describe some of the hypothesized life-history traits of organisms at different environmental extremes , as well as the assumptions implicit in these models. What empirical evidence is there to support these ideas?
3. Many factors affect habitat or resource selection by animals. Describe how animals’ requirements affect their selection of resources, especially in the context of ecological tradeoffs between risks and benefits. Define the term ecological niche and discuss how resource selection at the population level is affected by heterogeneity among individuals. How do predator-avoidance behaviors affect habitat selection?
4. Explain Tinbergen's four questions and their utility for studying behavior. Should they always be addressed separately? If so, why? If not, why not?
5. Does metabolic theory provide a conceptual foundation for much of ecology, just as genetic theory provides a foundation for much of evolutionary biology?
6. How can physiology help us understand the distributions of species, and how might it help us understand how those distributions might change as climate changes?
7. Discuss the principle of allocation and describe circumstances when it must apply as well as reasons it may not apply.
8. What is meant by the idea of population regulation, and what is the difference between density-dependent and density-independent regulation? With reference to a particular study system or taxonomic group, discuss how population regulation has been measured and the factors that appear to be most important.
9. Define the term metapopulation. (a) What are the factors that characterize metapopulations, and what conditions need to be satisfied in order for metapopulations to persist? (b) Describe what data you would collect to test whether populations in a fragmented habitat were behaving as a metapopulation.
10. What are the Lotka-Volterra equations and how have they been used to advance ecological theory? As part of your answer, address assumptions and limitations of this approach to population ecology.
11. What factors limit the geographic ranges of species? Your answer should include a definition of geographic range, and a discussion of the extent to which a “range” is a constant (or variable) thing. Finally, do you expect that the same factors will limit a species’ range across its entire distribution (for example, for a wide-ranging species, will the same limiting factors be important at high and low latitudes)?
12. Interactions among organisms in nature range from mutualistic to antagonistic. Give examples of mutualistic and antagonistic interactions and discuss some ecological and evolutionary consequences of these interactions. Also, which types of interactions are more important for network structure in communities, and why do you think that is the case?
13. Direct and indirect interactions among species strongly influence the dynamics of populations and the structure of communities. Describe two to three different kinds of indirect interactions, giving examples from nature. Discuss the relative importance of indirect interactions, relative to direct interactions, in mediating population and community processes.
14. Because plants are the foundation of terrestrial food webs, resource allocation in plants has implications for countless interspecific interactions. Discuss models or hypotheses that address the differential allocation of resources by plants to (a) growth vs defense, and (b) to different types of defense.
15. Predation influences demography and individual fitness in some ecological settings. Discuss scenarios where predation plays an important ecological role and others where it appears to be less important. In cases where predation has a lower impact on population processes, discuss potential mechanisms for this lack of effect.
16. What mechanisms are postulated to explain species coexistence, and hence underlie the maintenance of species diversity? Which mechanisms have the strongest theoretical support? Which has the strongest empirical support? Part of your answer should include a definition of diversity.
17. Briefly describe the unified neutral theory of biodiversity and biogeography in terms of its major postulates and related evidence. Discuss, in particular, the issue of ecological equivalence, both the role it plays in the theory and some of the ways that it has been interpreted and misinterpreted by the wider ecological community.
18. There has been a long-standing discussion about the relative importance of top-down versus bottom-up processes in structuring communities. Discuss the concepts of top-down and bottom-up processes, giving examples of each. Explain your position on the relative importance of these processes for both terrestrial and aquatic communities.
19. Compare the biogeochemical cycles of N, P, and C. Specifically concerning plant growth, discuss how these nutrients might be limiting in some contexts and not in others.
20. How does landscape heterogeneity influence the distribution of resources, and the fluxes of essential resources (water, nutrients, energy) within and among landscapes? Describe how these patterns of heterogeneity can benefit or constrain any aspect of biological occurrence, persistence, interactions, or behavior with reference to specific regions or landscapes.
21. What is the stress gradient hypothesis? What research approaches have been used to test it against empirical data, and what are the strengths and weaknesses of these approaches? What are some implications of the stress gradient hypothesis for how species respond to environmental change (e.g., global warming)?
22. What is the definition of ecosystem function, and what are some examples of different categories of ecosystem function? Thinking of your study system, are there ways you could quantify changes in function in response to environmental fluctuations or other perturbations?
23. The “problem of scale” is often mentioned as the central problem of ecology, and much of the discipline of landscape ecology is concerned with translating information across spatial scales and levels of ecological complexity. First, explain what is meant by the “problem of scale,” and your answer should include specific examples of ecological phenomena for which inferences are different depending on the scale of study. Second, discuss some fundamental approaches to scaling that have emerged within the field of landscape ecology.

Conservation Biology

1. Describe the concept of the extinction vortex and its underlying mechanisms. How might you use this concept to help a management agency set research priorities?
2. With the hope of conserving genetic diversity and evolutionary potential, there is much discussion of the notion of “genetic rescue”. What types of activities fall under this general idea? What are the population genetic underpinnings of this conservation strategy—that is, why does it work (if and when it does)? What are the challenges and opportunities of such an approach?
3. How is propagule pressure related to the success and impact of invasive species or species with extremely broad geographic ranges? Discuss both evolutionary and ecological hypotheses that can explain the link between propagule pressure and invasion.
4. The accelerating spread of non-native species is a major component of anthropogenic global change. a) What characteristics of communities influence their susceptibility to invasion by non-native species? b) What characteristics of non-native species facilitate their ability to become established in novel environments and become invasive? and c) How is climate change affecting the invasion process?
5. What is diversity? What is the importance of diversity – at the population, species, and genotype level? Make an argument for which metric of diversity is the most important to conserve.
6. Describe the Equilibrium Theory of Biogeography. How does this theory apply to the design of protected areas and our expectations of species dynamics within and among these areas? 
7. What is the relationship between biodiversity and ecosystem services? How does the nature of this relationship apply to conservation?
8. As species’ distributions shift, they may come in contact with species they are not reproductively isolated from. What might be the consequences?
9. Species and ecosystem management is rapidly changing to incorporate “climate-aware” management approaches. Describe at least three climate-aware approaches that might be applied in particular scenarios.
10. Explain what is meant by the concept of novel ecosystems, explain how it potentially poses a challenge to traditional conservation and restoration, and discuss your position on the issue.
11. What is the evidence that we are living through a mass extinction event? How do current rates of extinction compare to other periods in Earth’s history? Which species are most threatened with contemporary extinction, and why? (i.e., do some traits predispose species to extinction risk)?
12. Give at least two examples of organismal translocations that have been performed and the ecological and evolutionary outcomes of those efforts. How can these results help inform the design of assisted migration efforts?
13. Describe the adaptive management framework. How might the “resist, accept, direct” framework be integrated into the traditional adaptive management framework? What research priorities do you suggest to augment the effectiveness of these conservation planning approaches?
14. Describe the importance of identifying a reference community in restoration ecology and the multiple ways in which such a community might be identified.
15. The concepts of “land sparing” and “land sharing” provide a framework for identifying conservation value in all landscapes. Describe these concepts and provide examples of their effective implementation in support of conservation.
16. Global and national priorities have set a “30 x 30” goal for establishing protected areas. How well do existing protected areas protect the world’s biodiversity? Where are the shortfalls? Which areas should be prioritized and based on what metric(s)?
17. There is growing recognition that synergies between different stressors may have profound impacts on loss of biodiversity. Describe advances in our understanding of these synergies and how this knowledge may be translated into effective conservation management.
18. In the literature on disease ecology, there is an ongoing debate about the validity of the so-called “dilution effect”. The premise is that sites with higher species diversity have a lower risk of infectious disease relative to sites with lower species diversity. On the other hand, some researchers have found that an increase in species diversity may be associated with an increased risk of infectious disease (i.e., an amplification effect). What are some possible mechanisms that could lead to a dilution or an amplification effect for an infectious disease? What are some of the conservation/management implications for each of these scenarios?
19. Describe two ways that species might respond to climate change. What conservation actions might facilitate these responses?
20. How might regulatory tools like the Endangered Species Act be integrated with incentive-based resource economic tools to build partnerships and augment conservation effectiveness?
21. What is meant by the effective population size (Ne)? What does the ratio Ne/N tell you about population processes and how might this apply to population management?
22. Wright’s F-statistics have long been the standard approach to assessing population genetic structure. What can be inferred from these measures and how might these data inform land use planning?

Evolution

1. What are some of the constraints that may limit the responses of wild populations to natural selection?
2. What are some of the ways that we can measure or infer natural selection in populations? Discuss at least one method that is based on molecular data and at least one that is based on measuring phenotypes.
3. Compare the effects of selection, genetic drift, and gene flow on genetic diversity in and among populations.
4. What are stabilizing, directional, and disruptive selection, and in what contexts would you expect to see each occur (and why)?
5. What is phenotypic plasticity? Under what conditions would you expect increased versus decreased phenotypic plasticity to evolve?
6. The adaptive landscape concept was developed by Sewall Wright in 1932 to convey the core ideas in his shifting balance theory of evolution. The adaptive landscape has since been adopted more broadly by evolutionary biologists to conceptualize adaptation. What is an adaptive landscape as Sewall Wright first imagined it, and how has the idea changed over time?
7. Contrast the “adaptationist” versus “neutralist” views of evolutionary biology. What is the evidence in support of the assertion that most variation at the level of genomes has arisen from neutral processes (i.e., drift)? What is the evidence in support of the argument that natural selection has played an important role in shaping sequence variation?
8. Contrast sexual and asexual reproduction. What are the advantages and disadvantages of each? In your answer discuss why, theoretically, sexual reproduction may have evolved.
9. Some authors have argued that there is a need for an Extended Evolutionary Synthesis. What are some recently studied phenomena that have challenged some basic tenets of the Modern Synthesis? Do you agree that an Extended Evolutionary Synthesis is needed? Explain why or why not.
10. From an evolutionary perspective, what are some of the features of populations that might be crucial for predicting their ability to persist in the face of rapid environmental change?
11. What are the Spandrels of San Marco, and what role did they play in how we think about traits or study adaptations?
12. How can cooperation among unrelated individuals evolve? What are the underlying mechanisms?
13. What are eco-evolutionary feedbacks, and how can eco-evolutionary feedbacks influence the dynamics and structure of biological communities?
14. Compare three prominent species concepts. How might an evolutionary biologist, ecologist, and conservation biologist differ in the species concept that they prefer or are more likely to employ?
15. What is ecological speciation? Compare this model with other proposed drivers of speciation. Do you think it is the dominant mode of speciation? Support your argument with evidence from the literature.
16. What kinds of data are used to build phylogenies, and do certain data types have strengths over others? What types of assumptions are made when constructing trees?
17. What role(s) does sexual selection play in species diversification? Compare sexual selection and natural selection as mechanisms of evolutionary change in populations.
18. Coevolutionary processes have been major drivers in speciation and diversification. Compare different types of coevolutionary relationships and their potential to drive rapid adaptation and speciation.
19. Why would we need to take into account evolutionary relationships when studying trait differences between a group of closely related organisms?
20.  What is the Hardy-Weinberg principle? Discuss its assumptions and the role it has played in the field of population genetics.
21. Briefly explain how advances in DNA sequencing have improved our ability to investigate evolutionary questions. What are some key questions that these advances have enabled us to address?
22. Why is it important to understand the genetic architecture underlying adaptive traits? How will a response to selection differ if traits are controlled by loci with additive effects, pleiotropy, or epistasis? As part of your answer, be sure to discuss the evolution of correlated characters.
23. Discuss the relative importance of genes and environment in determining trait values. How useful is the concept of heritability in natural environments?

Quantitative methods

1. Define pseudo-replication in general terms and with reference to common pseudo-replicated designs in Ecology. Then discuss the alternative position, namely that "pseudo-replication is a pseudo-issue.”
2. A manipulative experiment is among the most powerful tools for scientific inference. In your opinion, what are the most important elements of a well-designed experiment? Starting with a real or hypothetical research question related to ecology or evolution, describe how you would design an experiment to address that question, taking into consideration common challenges such as limited resources (time and/or money) and non-independent samples (related individuals, limited collection sites, etc.)? As part of your answer, please define how negative and positive controls can be combined to inform scientific inference.
3. Ecologists use varying levels of control of nature ranging from experiments with controls and replication, through “natural experiments” to observational studies, in which correlation is used as the basis for inference. Discuss the pros and cons of each of these approaches and how they can be combined in the scientific learning process.
4. Explain mixed models/hierarchical models and the use of random effects, especially with reference to common uses in Ecology and Evolutionary Biology. How might the definition of a random effect depend on your statistical approach (e.g. frequentist vs. Bayesian)? In your response, please describe at least one example of an appropriate use of mixed/hierarchical models in Ecology and Evolutionary Biology and your interpretation of parameters.
5. What assumptions must be met to justify the use of linear regression? How would you determine if a data set meets those assumptions? What options are available to deal with data that do not? As part of your answer, please provide an explanation of how the generalized linear model is useful in these situations. Include an example in which you would utilize a generalized linear model and why.
6. What is multicollinearity in the context of linear models and how can we measure it? Why is it an issue in statistical analysis? What are some of the strategies for analyzing data with multicollinearity issues?
7. Discuss differences between Bayesian methods and frequentist approaches for both model building and inference. For what purposes are each well suited?
8. What are some ways in which multivariate statistical methods are commonly used in ecology and evolution? Describe the goals of ordination vs. classification analysis – do these two types of analysis represent non-overlapping paradigms, or are they complementary? Can these methods be used only for description, or are there situations (if so, provide one or more examples) in which they can be used for inferential purposes?
9. Machine-learning algorithms (e.g., gradient boosting, random forest, neural networks) have been gaining traction in Ecology. Describe how machine-learning methods differ from classical statistical approaches and discuss the advantages and disadvantages of both analytical paradigms. Are there situations where these methods can be complementary?
10. Data simulation is useful at multiple stages of research. Describe how data simulation can contribute important insights in both design-based and model-based inference.
11. Discuss the importance of bootstrapping in the fields of ecology, evolution, and conservation biology, providing examples of how it contributes to statistical inference in these fields.
12. Discuss the concepts of sampling distribution, sample distribution, and population distribution in the context of statistical inference. Be sure to mention the Central Limit Theorem in your discussion.
13. Define and discuss the relationship between sensitivity, specificity, and power, as well as Type I and Type II errors. How are these concepts relevant to statistical inference in EECB beyond the traditional null hypothesis testing framework? Describe some of the potential consequences of committing each type of error. Please provide one or more examples (real-world or hypothetical) of a power analysis that goes beyond simply computing sample size requirements for a comparison of two means under a specified alpha level.
14. Define a null model and explain how null models are important for ecology and evolutionary biology.
15. There are a variety of methods for model and variable selection including information-theoretic approaches and null hypothesis testing. Describe the philosophical and theoretical underpinnings of these 2 approaches, their proper use, and the advantages and disadvantages of each. In your answer, please discuss p-values and their proper use and interpretation.
16. Prediction is often a goal of an analysis; however accurate prediction can come at the expense of generalizability. What does it mean for a statistical model to be generalizable? What are the trade-offs between generalizability and prediction? Describe an instance where prediction is the primary goal of the study and an instance where generalizability is favored. What tools/analyses are well suited to each? Consider approaches that relate to study design in addition to model fitting and validation. Provide specific examples wherever possible.
17. Fitting statistical models is usually followed by several model evaluation steps. Please describe how researchers can assess (1) model adequacy (goodness-of-fit) and (2) model performance. In your answer, describe how an inadequate model can exhibit strong performance, and vice versa.
18. Some claim that causality can only be achieved through experimental manipulations, while others think that such questions can be addressed with statistical models. Explain both sides of this debate. Can causality be addressed with observational data?
19. How have changing paradigms concerning scientific epistemology (how knowledge is acquired) influenced the way ecologists design studies and analyze data, for inferring truths concerning the natural world?
20. A famous quote often attributed to British statistician George Box states that, “All models are wrong, some are useful”. Assuming you agree that all models are wrong, what does it mean for a model to be useful or not useful? How can we determine whether or not a model is useful? In your answer, provide at least one real or hypothetical example of a “wrong” model from ecology or evolution that is not useful, and another example of a “wrong” model that is useful.
21. What is Popperian falsification? What do you make of the fact that many modern philosophers of science dismiss falsification, or at least suggest that scientists rely too heavily on it? On the other hand, many practitioners of science (at least in our field) often discuss the falsifiability of an idea. Do you think falsification is important in ecology and evolution?