Comprehensive exam study questions
The following questions on the standardized exam will be similar, but not necessarily identical, to the questions listed below.
- A fundamental goal in physiological ecology has been to establish mechanistic connections between physiological traits and fitness. In your opinion, have we already learned what we need to know (more or less), or should that remain an important goal moving forward? Be specific with respect to areas of ecology and evolutionary biology for which that physiology and fitness connection is (or has been) most important.
- What are the fundamental physiological challenges associated with living in terrestrial versus aquatic environments? How have organisms overcome these challenges?
- Life history strategies (patterns of growth and reproduction) are thought to evolve, at least in part, in response to environmental conditions. What are some of the classic ecological models that describe expected evolutionary responses in different environments? Describe some of the life history features of organisms at different ends of these spectra, as well as the assumptions implicit in these models. What evidence is there to support these ideas?
- Many factors affect habitat or resource selection by animals. Describe how the different requirements of animals affect selection of resources, especially in the context of ecological tradeoffs between risks and benefits. Discuss how resource selection at the level of the population is affected by heterogeneity among individuals. How do anti-predator or ‘risky’ behaviors affect habitat selection?
- Explain Tinbergen's four questions, and their utility for studying behavior. Should they always be addressed separately? If so, why? If not, why not?
- The question of what keeps signals honest has been a subject of much historical and current debate in the field of animal behavior/communication. Explain "the problem of reliability", and describe a few selected examples (both theoretical and empirical) that you would use in teaching a section of an undergraduate course on the evolution of reliable signaling.
- How is population regulation measured? What are the factors that appear to be most important in regulating wild populations? You may restrict your answer to a particular taxonomic group. Is density-dependent population regulation a “law” of ecology?
- Why are small populations more likely to go extinct?
- 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.
- 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.
- What factors limit the geographic range of species? Are the borders constant? Do you expect the same factors to operate along the different margins of a species’ distribution?
- What are the Lotka-Volterra equations and how have they been used to advance ecological theory? When do they work well as predictive models and when do they help provide insight into mechanisms of population changes?
- Interactions between organisms in nature may range from mutualistic to antagonistic. Give examples of mutualistic versus antagonistic interactions and discuss some ecological and evolutionary consequences of these interactions. Some models conclude that mutualisms should be less common in nature; critique that position, either for or against.
- Direct and indirect interactions between species strongly influence the dynamics of populations and the structure of communities. Describe the nature of indirect interactions, giving examples that illustrate the different kinds of indirect interactions. Explain the relative importance of indirect interactions, relative to direct interactions, in mediating population and community processes.
- Discuss and explore models and hypotheses (e.g., the carbon-nutrient balance hypothesis) that make predictions about how and when plants should allocate resources to chemical or morphological defenses. Which models or hypotheses currently have the most support?
- 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.
- Plants defend themselves against herbivores using a variety of mechanisms, including constitutive and induced defenses. Describe these two major categories of defenses, with examples. What evidence is there for costs and benefits associated with these strategies? Do the same concepts (of constitutive and induced defenses) have any utility outside of plants?
- To what extent are the outcomes of species interactions context-dependent? Does the amount of variation differ among the types of species interactions that exist in nature? What factors drive the variable outcomes of interactions? What are the broader consequences or implications of context-dependent outcomes in species interactions?
Community Ecology & Biogeography
- What is diversity? What are the drivers of diversity? And what is the importance of diversity – at the population, species, and genotype level – for ecosystem function?
- Considering any particular lineage or group of organisms, discuss factors involved in the origin, maintenance and distribution of species-level diversity.
- What mechanisms are postulated to explain coexistence of species, and hence underlie the maintenance of species diversity? Which mechanisms have the strongest theoretical support? Which have the strongest empirical support?
- The theory of island biogeography predicts species richness based upon the distance of the island from the mainland and the size of the island. Describe how these two factors interact with colonization and extinction rates to predict species richness. Under what conditions (i.e. island size and distance from mainland) would species richness peak?
- Briefly describe the unified neutral theory of biodiversity and biogeography in terms of its major postulates, and evidence for these. In particular, discuss 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.
- What is the current state of understanding with respect to the global latitudinal gradient in diversity?
- In early 1970, Dan Janzen and Joe Connell independently postulated a mechanism that sustains tropical rainforest biodiversity. The Janzen-Connell hypothesis suggests that diversity is maintained by host-specific “enemies” that cause offspring to perform poorly underneath the parent plant. This results in negative density dependence of individual species. Summarize evidence for or against the hypothesis, with reference to specific systems where possible, that need not be restricted to the tropical biome.
- In general, how is predator (or consumer) diversity related to prey (or resource) diversity? What alternative hypotheses might lead to the expectations of positive, negative, complex, or no relationship between diversity at these trophic levels?
- In the literature, there has been continuing discussion of the relative importance of top-down versus bottom-up processes in structuring systems and in determining their resulting complexity and function. Start by discussing the concepts of top-down and bottom-up processes giving examples of these processes, then discuss the role that bottom-up versus top-down processes play in structuring communities. Include in your answer your position on the relative importance of these two types of processes in structuring systems. Also, the vast majority of studies investigating relationships between organismal diversity and community processes involve tens of species. What do you think you might learn if you could do the same community experiments using thousands of species?
- In a given area, the number of species interactions is hypothesized to asymptote more quickly than the diversity of unique species. Explain why this pattern may happen. Would you expect this pattern to hold for both tropical and temperate communities? Why or why not?
- Under what circumstances would you expect change in a plant or animal community aboveground to be reflected in change in the biotic community belowground?
- What is the stress gradient hypothesis? What research approaches have been used to test it against empirical data, and what are strengths and weaknesses of these approaches? What are implications of the stress gradient hypothesis for how species respond to environmental change (e.g., global warming)?
- What is a niche? Describe how the niche concept serves to bridge the fields of ecology and evolutionary biology. How do niches evolve?
- All ecosystems are controlled by a combination of physical and biological processes. Present arguments and examples for both physical and biological processes structuring an ecosystem of your choice.
- Compare and contrast the biogeochemical cycles of N, P, and C. Include the origins and importance of gaseous, liquid, and solid phases in soils (organic, primary mineral, extractable). Discuss the occurrence of limitations of these nutrients to plant growth – specifically, which of these nutrients is most often growth limiting and why?
- Discuss approaches that you might use for taking an inventory of the carbon and nutrients in a grassland or forest ecosystem. What are some pros and cons of different methods?
- What is the definition of an ecosystem service, and what are some examples of different categories of ecosystem services? Thinking of your study system, are there ways you could quantify changes in different types of services in response to alternate management actions?
- How do common tools used to assess net primary productivity generate similar or dissimilar estimates of NPP at different spatial and temporal scales? In the process of answering the question, please describe the different methods, their strengths and weaknesses, and where and when they provide similar and dissimilar estimates of NPP?
- What are the consequences of the different chemical bond structures of carbon, nitrogen, and phosphorus for ecosystem processes? How would the availability of these resources alter the abundance or function of microbial communities? What are the mechanisms for evolution within the microbial community given an increase in the relative availability of nitrogen relative to phosphorus?
- How does landscape heterogeneity influence the distribution of resources, and the fluxes of essential resources (water, nutrients, energy) within and among landscapes?
- The problem of scale” was identified as the central problem of ecology by Simon Levin, and much of the discipline of landscape ecology is concerned with translating information across spatial scales and levels of ecological complexity. First, discuss some fundamental approaches to scaling that have emerged within the field of landscape ecology. Second, relate these approaches to the problem of scaling up trophic interactions across ecological hierarchies, and to broad geographic extents.
- Many studies in landscape ecology make use of species distribution models; how is habitat generally represented in habitat-based species distribution models? What are some strengths and limitations to these commonly applied methods, and what criticisms have been levied against them? What would be your ideal method to model habitat, and what are some limitations to achieving this goal?
Global Change Ecology
- What is the evidence that climate change is occurring, and what is the evidence that it is human caused? Describe some of the effects of climate change on species distributions, community composition, and ecosystem function.
- How is climate change influencing evolutionary processes? As part of your answer, include both a contemporary and a paleontological example.
- How do the characteristics of species affect their ability to thrive versus decline in the face of anthropogenic change?
- 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 range affecting the invasion process? In answering these questions, summarize empirical evidence and discuss and evaluate the conceptual frameworks that have been proposed to address these topics.
- A number of ideas have been developed to understand the process of invasion and why non-native species often behave differently in systems that they have invaded as compared to their native systems. Describe 2-3 of the most influential of these ideas and provide examples that illustrate them.
- How do individual organisms and populations of organisms respond to environmental change, such as shifts in temperature, rainfall, and competitive interactions at different time scales, from seconds through years and generations? Can the magnitude of a response at one time scale (e.g., days) affect the magnitude of the response at another time scale?
Natural Selection & Adaptation
- What is adaptive evolution and what is required for it to occur? What are some of the constraints that limit the responses of wild populations to natural selection?
- What is the evidence for natural selection in the wild, and how variable is it in terms of direction and intensity? How do we measure natural selection in wild populations? How would you do this in your study system? In answering this question, include techniques that have been used for decades as well as more recent molecular approaches.
- Compare and contrast the effects of selection, random genetic drift and gene flow on genetic diversity within and among populations.
- What is the relative importance of random genetic drift and directional natural selection as causes of population differentiation in quantitative traits, and should the degree of divergence in neutral marker loci predict the degree of divergence in genes coding quantitative traits?
- Compare and contrast stabilizing, directional and disruptive selection. Use graphs and give examples of each.
- What are five of the most important discoveries in evolutionary biology since Darwin? Write a paragraph on each justifying your choice.
- What are some notable mechanisms of evolution that Darwin had wrong or was not aware of and how has modern biology corrected these mistakes?
- Why don’t all species evolve a specialist strategy? What evolutionary pressures create generalists? You may discuss specialists and generalists with respect to any niche axis you choose (resources, habitats, etc.).
- What is local adaptation? How is local adaptation measured?
- What is adaptive phenotypic plasticity? Include in your answer to this question an explanation as to why, since adaptations are traditionally thought of as genetically fixed traits, an adaptation can be plastic. Provide ecological examples of adaptive phenotypic plasticity. Be sure to explain in these examples why the plasticity you describe is adaptive.
- Discuss Sewall Wright’s Shifting Balance Theory. As a part of your answer, comment on the current utility of this theory in evolutionary biology.
- Some evolutionary biologists have argued that the neutral theory should be taken as the null hypothesis to explain genetic variation within species or populations and genetic differences among them. In this view, adaptation and natural selection should be the preferred explanation only if genetic drift cannot explain the data. Others might argue that since there is so much evidence that natural selection has shaped species’ characteristics, selection should be the explanation of choice, and that the burden of proof should fall on advocates of the neutral theory. Why might one of these points of view be more convincing than the other?
- Heterogeneity in individual quality is increasingly recognized as a key component of the structure of populations and an important influence on response to natural selection. Briefly discuss how such heterogeneity influences response to selection. How do we reconcile apparently constant levels of such heterogeneity with steady directional selection for specific trait values?
- What is Fisher's fundamental theorem of natural selection?
- What are the Spandrels of San Marco, and what role did they play in evolutionary biology research?
- What types of reproductive systems are found in animals, plants, or microbes, and how did they evolve?
- What is an evolutionary tradeoff? Why do they occur? How does the occurrence of trade-offs illuminate the general question of whether all traits are adaptive? Illustrate with at least one example.
- Who was involved in the modern synthesis and what ideas did they pioneer?
Species & Speciation
- Name and describe three prominent species concepts, and compare and contrast their utility. How might an evolutionary biologist, ecologist, and conservation biologist differ in their use of the species concept? Which perspective do you find most valuable, and why?
- What are the most common modes of speciation? What are the most interesting current questions in the area of speciation research?
- The study of speciation has been a unifying theme for decades in the science of evolutionary biology, and research in speciation has very often involved the study of reproductive isolation or “barriers” to gene flow in the context of speciation. Address two issues: (a) what are some of the most important things that have been learned from research in this area? and (b) what are the most pressing issues moving forward? Note: if you take a position critical to this area of research, be sure to outline the traditional as well as critical points of view.
- Focusing on a group or lineage that you are familiar with, discuss mechanisms likely to be important in diversification. As a part of your answer, describe how you would evaluate the importance of different proposed mechanisms.
- Much research in evolutionary biology has recently focused on possible connections between ecological adaptations and the evolution of reproductive isolation (ecological speciation). What have we learned in this field, and what are the most interesting (in your opinion) questions that are being addressed now or which should be addressed in the future?
- When closely-related species come into secondary contact, hybridization can occur. In some cases, hybrid zones can form that are relatively stable over hundreds of years. Why do these zones persist even when hybrids have relatively lower fitness compared to members of either source population? What ecological conditions contribute to the stability of hybrid zones?
Macroevolution & Phylogenetics
- How are phylogenies constructed and why are they useful or necessary? How do we use them to avoid problems of pseudoreplication?
- Discuss multiple sequence alignment methods and how they are important for modern phylogenetics.
- What is phylogenetic signal, why is it important, and how do we test for it? Provide some examples from the literature and some hypothetical examples using a taxon of your choice.
- Discuss coevolution in the context of competition, predators and prey, and mutualisms. Which of these would be easier to study, and why?
- How might habitat fragmentation disrupt a co-evolutionary dynamic among parasites and their hosts? Begin by defining co-evolution and discuss what data would be required to establish that a co-evolutionary relationship exists.
- Could natural selection, at any level of organization, ever cause the extinction of a population or species?
- Why is genetic variation important? What form of genetic diversity is most important for retaining evolutionary potential and why? What factors influence the spatial distribution of genetic variation?
- Define genetic effective population size (Ne). What does the ratio Ne/N tell you about population processes?
- Consider the number of traits a gene pleiotropically affects, and the magnitude of the effect of different alleles on each of these characteristics. How would these variables affect the rate of adaptation to a novel environment?
- What is the Hardy-Weinberg principle? Discuss its assumptions and the role it has played in the field of population genetics.
- Next generation DNA sequencing technologies have rapidly changed our ability to collect genomic scale data at a minute fraction of the time and cost previously required. Discuss examples of these new technologies, what type of data they produce, and the type of major questions in Biology they stand to help us answer. Second, discuss how this sequencing technology might be applied to answer questions in ecology and evolutionary biology, and the expected difficulties or limitations of working with such data.
- With an emphasis on recent discoveries using genomic technologies, what has been learned about the genetic architecture of traits in wild populations? As a part of your answer, consider the extent to which phenotypic plasticity contributes to natural variation.
- Wright’s F statistics have long been the standard approach to assess population genetic structure, but newer methods include assignment tests and Bayesian clustering analyses. Discuss each of these approaches including what type of data is used in each, the underlying assumptions and the potential limitations.
- Define epigenetics, including real examples of experiential effects on phenotypes, and discuss evidence for and against the proposition that epigenetics is a serious challenge to traditional ecological and evolutionary theory.
- Compare and contrast the roles played by Ronald Fisher and Sewall Wright in the formation of the field of Population Genetics.
- How should scientific research influence endangered species listing decisions and management?
- In your opinion what are the greatest threats to wildlife and habitats and conservation of wildlife? What are the biggest obstacles to the conservation of wildlife at the level of the landscape? Suggest at least 2 solutions to the obstacles that you have identified. How can those solutions be implemented? Explain how you reached this conclusion.
- The conservation community is struggling to develop climate-sensitive management approaches. What might some of these approaches be and where do you see particular knowledge gaps that research could address?
- Assuming that we never know everything about any particular species, how much do we need to know about a species to manage it effectively? What is the most critical information to have about a species and its relationship to other species in order to manage for biodiversity or conservation? What information is secondary or possibly non-essential? With a limited budget and resources what are the most important things to know?
- Conservation scientists can find themselves conflicted between objective science and advocacy for conservation. How should a conservation biologist aim to balance these factors when they come into conflict? In your answer, please address the general question of whether there is a role for advocacy of political action within the sciences, including the understanding and respect given to scientists by the public at large.
- The setting of conservation priorities within species requires explicit goals and identification of the appropriate targets for conservation. Moritz (1999) has suggested that the goal of conservation should be to conserve ecological and evolutionary processes, rather than preservation of specific phenotypic variants (the products of those processes). Do you agree with this statement, or not, and why?
- The maintenance of biodiversity is a core issue touted by most conservation biologists, yet much research in conservation biology focuses on the viability of single populations or suites of populations. Do you think conservation biology should be more concerned with biodiversity without regard to the fates of particular species, or with persistence of particular species without regard to overall biodiversity? If your view lies between these extremes, how would you balance these perspectives?
- What is the S.L.O.S.S. debate and how has this discussion shifted over time?
- In recent decades, extensive acreage of tropical rainforests has been deforested and burned, often to create grazing lands. Temperate ecologists, environmentalists and governments (among others) have been critical of these land use practices. Tropical ranchers, businessmen and governments (among others) have declared their temperate zone critics to be hypocrites because northern countries continue to clearcut their own forests. The reason for the apparent hypocrisy of northerners is that clear cutting a tropical rainforest has a much greater impact on the environment than clear cutting a temperate forest. Why? Consider all important ecological aspects of the problem in your response.
- Russ Lande wrote an influential paper in 1988 on genetics and demography in biological conservation. What was the debate surrounding genetic and demographic data to determine extinction risk?
- Discuss what you consider to be some of the most important climate-aware or climate-sensitive conservation planning approaches. How can we prepare our ecosystems (or even just the biotic component of these systems) for such change?
- Discuss the pros and cons of species translocations for conservation purposes. Provide examples of translocations that have been performed and the outcomes of those efforts. Also, compare the evidence on translocations with the evidence from ecological invasions in terms of ecological impacts.
- With the hope of conserving genetic diversity and evolutionary potential, there is much discussion of the notion of “genetic rescue”. What types of activities (realized or only potential) 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?
- 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 (which is another way of asking which traits predispose species to extinction)?
- What traits of species predispose them to survive mass extinction events? Are these the same traits associated with survival under normal or background levels of extinctions?
- It seems to be the case that not all species or lineages are equally prone to extinction. Certain prominent evolutionary biologists have maintained that extinction (especially during mass extinction events) is essentially a lottery (i.e. random). Address the following two issues: (a) what does the paleontological and neontological evidence say with respect to the randomness of extinction? and (b) what are the consequences of stochasticity (or a lack thereof) in extinction for our understanding of ecological communities?
- 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.
- Explain mixed models and the use of random effects, especially with reference to common uses in Ecology and Evolutionary Biology. Discuss how analyses from your own research might incorporate mixed models.
- Define pseudoreplication in general terms and with reference to common pseudo-replicated designs in Ecology. Discuss the alternative position that has been promoted by a few authors for some research questions or issues, namely that "pseudoreplication is a pseudo-issue.”
- What are the ways in which multivariate statistical methods are commonly used in ecology and evolution? Describe the goals of ordination vs. classification analysis – do the two types of analysis represent non-overlapping paradigms, or are they complementary? Can these methods be used only for description, or are there situations (please give examples) in which they can be used for inferential purposes?
- Analysis of variance (ANOVA) is a common statistical procedure. For the general linear model, what assumptions must be met to justify the use of frequentist ANOVA? How would you determine if a data set meets those assumptions? What options are available to deal with data that do not meet those assumptions?
- At a conference poster session, a crusty old professor looks at your path analysis results and snarls, “correlation is not causation!” How would you respond? Explain how structural equation modeling (SEM) differs from simple correlations and regular generalized linear models.
- How would you design an experiment to test for a relationship between ecosystem function and diversity? What are some of the pitfalls that researches have stumbled into in the past?
- What are the pros and cons of observational vs experimental studies? Are the data treated in the same way for the two different approaches (i.e. will the same statistical analyses be applied)?
- 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. Include the objective of making inferences across a range of temporal and spatial scales in your evaluation of the importance of various levels of control.
- There has been recent controversy over p-values, including a rare statement by the American Statistical Association on their proper (and improper) use. Please summarize the proper use of p-values within a broader summary discussion of other methods for model and variable selection. Include in that discussion the proper ways of using those methods, their biases, and any common misapplications.
- Experimental manipulations often try to isolate an individual behavioral activity, but by their very nature likely affect other behaviors. Observation tries to understand behavior by watching repeated activities without influence. What is the balance between these two approaches and under what conditions does it become essential to design an experiment to manipulate behavior? Assuming one begins with observational studies, how does the researcher know when to switch to experimentation?
- Experimentalists take great care in designing studies to address particular scientific questions. For example, they often utilize negative or positive controls to inform the inferences they draw from the experimental results. Discuss the strengths and weaknesses of research using historical evidence or survey data from the field, which was not designed or controlled, relative to an experimental approach. Compare the inferential confidence that can be obtained from these approaches.
Modern Statistical Paradigms
- Discuss differences between Bayesian methods and frequentist approaches to statistical analysis. For what purposes are each well suited?
- Explain Approximate Bayesian Computation so that someone with a reasonable background in statistics (i.e. at least a couple of undergrad courses) could understand it. Include at least one example of how ABC might be used in a field other than population genetics.
- Provide an overview of how Monte Carlo methods are used in applied statistics. How have these methods enhanced Bayesian, frequentist, and information theory approaches to parameter estimation and hypothesis tests?
- Information theoretic approaches have increased dramatically in use over the past decade. Describe the philosophical and theoretical underpinnings of these approaches and their advantages over traditional hypothesis testing. Are there any disadvantages of information theoretic approaches or situations for which hypothesis testing might be superior? As a part of your answer, address the controversy over the use of P-values in ecological and evolutionary research.
- 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?
- What is the role of simulation modeling in ecological research? Provide examples of different types of simulation models and discuss the benefits and limitations of these approaches in depth.
- How can generalizability be achieved in statistical modeling? In other words, what are the general approaches whereby researchers in EECB-related disciplines can avoid over-fitting their data? Consider approaches that relate to the following stages of conducting an analysis: sampling design, model development, model inference, and model validation. Provide specific examples wherever possible. Are there situations in which prediction might be favored over generalization?
- Define the term “random” and explain how it is an important component of statistical, analytical, and simulation models in ecology and evolutionary biology.
- Define a null model and explain how null models are important for ecology and evolutionary biology.
- What is the role of analytical as opposed to statistical models in Ecology and Evolutionary Biology? Give an example of an analytical model in a subfield related to your interests.
Philosophy of Science
- 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?
- What is Popperian falsification? What do you make of the fact that many modern philosophers of science seem to dismiss falsification, while many practitioners of science (at least in our field) often discuss the falsifiability or not of an idea?
- Oftentimes, there can be a philosophical debate between scientists who do mostly experimental or field-based research versus those who primarily do modeling. How would you explain the value of modeling to someone who argues that experimental and field-based research provides real data whereas you can design a model to give you any result you want?