University of Michigan
Department of Ecology and Evolutionary Biology

Tropical forest ecosystems, previously thought to be in a state of dynamic equilibrium, have been found to be undergoing widespread changes. Of particular concern is the increasing dominance of lianas (woody climbing vines). Changing concentrations of atmospheric carbon dioxide have been implicated as a driver of these recently observed changes. Using a combination of elevated CO2 experiments, field surveys, and remote sensing imagery analysis I seek to understand and quantify any impact increasing liana dominance has on the capacity of tropical forest ecosystems to store carbon. REU students will have the opportunity to develop a complimentary project of their own that includes field-based work in Panama, Costa Rica, or other tropical countries.

This project's goals are to broadly census the climbing plant (vines and lianas) community in the Eastern United States, from the Mississippi River to the Atlantic Ocean in moist to wet habitats, largely forests. At each half hectare site censused, we identify and measure all climbing plants and census the tree dominants of the site. We determine the age of the older trees using tree coring techniques, or land use history records. For each forest censused, we investigate the site history and prior research using published and grey literature, natural resource departments of adjacent universities, and the state's department of natural resources. Each student involved will be responsible for at least one of the site backgrounds, anticipated species list, data compilation, and write-up. That student will also participate in compiling species accounts for climbing plants that occur in the local region but that have not been encountered in prior studies. The lab group will meet at least once every two months for a general summary of accomplishments. Research will be carried out both in the Ann Arbor laboratory of Burnham and in the field throughout the eastern United States.

Feeding habits are one of the fundamental ecological properties of individuals and species. For many modern mammals, feeding habits are poorly known because it is difficult to monitor feeding behavior for hours, days, or months in the wild. Two methods of inferring diet are stable-isotope analysis (for isotopes of carbon, oxygen, and nitrogen) and dental microwear analysis. For mammalian herbivores, stable isotopes in tooth enamel provide information about vegetation and seasonality during the period of tooth formation. Microscopic pits and scratches record properties of chewed food during the last week of an animal's life. I use both of these methods to characterize dietary attributes of living and fossil mammals. Ongoing work in my research group includes documenting stable isotope composition and dental microwear of mammals from Amboseli National Park in Kenya and from fossil mammals from Pakistan. The outcome of this research on dietary habits contributes to evaluating the environmental processes that cause changes in mammalian faunas across continents and over deep time. This research will involve lab work on the Ann Arbor campus.

Students will be closely integrated into an ongoing project to study how climate change is increasing fire and thermokarst failure in arctic tundra, and what impacts these disturbances have on aquatic ecosystems. Within this study there are several individual projects that could be developed, including: (1) experimentally testing the effects of burning on the character of soil waters drained from burned tundra (e.g., changes in biochemistry), (2) determining the quantity and impacts of nutrients that are flushed from thermokarst sediments into lakes, or (3) investigating how the sediment inputs from a thermokarst failure impact the benthic ecology of a lake, such as changes in the concentration and distribution of chlorophyll or nutrient release from lake sediments. This work will be done onsite at the Toolik Lake Field Station in Alaska, which is the premiere U.S. research facility in the Arctic and where students will be exposed to a world-class group of international scientists.

Biological invasions ranging from infectious diseases to newly introduced species constitute one of the major ecological challenges of our time. While numerous theoretical and empirical investigations have assessed the potential consequences of biological invasions on ecological communities, we continue to lack a unifying framework that provides us with an understanding as to why and how some communities are invaded. Our research focuses on the tropical little fire ant Wasmannia auropunctata which is considered to be a major agricultural pest on tropical islands where it is not native and as a consequence negatively impacts the invertebrate community. W. auropunctata is commonly found throughout the Neotropics where its impact on the native ant fauna varies widely. The main goal of our research program is to discover why W. auropunctata acts as an agricultural pest on shaded coffee farms of Puerto Rico while the same species does not appear to severely impact the native ant fauna of shaded coffee farms in Mexico. Our approach seeks to integrate evolutionary game-theory in combinations with network theory and dynamical systems in order to discover the underlying rules that give rise to biological invasions. An REU student would seek to answer these and other questions using computational modeling of spatial interactions, experimental testing of spatial games, collective exploration of ants, and development of game-theoretic approaches to biological questions. This work would be done on coffee farms in Mexico and Puerto Rico.

The control of infectious diseases through improved sanitation and vaccination is one of the great success stories of modern medicine and science. However, in recent years it has become increasingly clear that the great successes achieved against diseases such as smallpox and polio may be exceptions, rather than the rule. With the failure to eradicate or even control a large number of infectious diseases (e.g., influenza, malaria) and the emergence of new diseases (e.g., HIV/AIDS) has come a recognition that the ecology and evolution of diseases are as important as their clinical characteristics. In this project, the REU student will contribute to solving the mysteries of whooping cough, a potentially fatal disease caused by the highly-contagious bacterium Bordetella pertussis. Using a computer-modeling approach informed by the epidemiological details of specific countries, they will help to explore the influence on disease dynamics of vaccination programs; contact rates within and between age groups; and the spatial distribution of humans and the bacterium. This project is an excellent opportunity to learn how an ecological perspective is essential to the control and prediction of infectious diseases, to explore the intersection of biology, policy, and social factors, and to learn new skills, such as computer programming and analysis of large data sets.

The cognitive abilities of animals vary widely across species and there is much interest in what accounts for this variation. Two potential factors may influence cognitive abilities: 1) the natural history and behavior of a species or 2) the evolutionary history of a species. The REU student will be involved in testing the cognitive abilities of paper wasps through training. The student will answer specific questions about the capabilities of wasps. In addition, by comparing cognition across different wasp species, the student will be able to test why species differ in their abilities. The work will involve some field work in Michigan as well as laboratory work on the Ann Arbor campus.

A complete life cycle of sexually reproducing eukaryotes consists of a diploid phase and a haploid phase. The relative length of either phase varies greatly among different lineages of eukaryotes. Under a recently reconstructed molecular phylogeny of streptophytes (charophyte algae and land plants), we examined the pattern of life cycle change in Characeae, liverworts, mosses, hornworts, lycophytes, monilophytes, and seed plants, and found that the life cycle of land plants had evolved in a direction of continuously expanding the diploid phase while reducing the haploid phase. In other words, evolution of land plants can be viewed as a series of events of delaying meiosis after fertilization and reducing mitosis after meiosis. In this project, we investigate evolution of genes that are involved in the timing of meiosis initiation in a diverse set of land plants. Basic techniques include DNA extraction, gene amplification, cloning, sequencing, bioinformatic and evolutionary analyses. This work would be done on the Ann Arbor campus in the Qiu Laboratory.

The formation of a complex, multi-cellular organism from a single cell is a remarkable biological process. Every cell within an individual contains the same DNA, yet hundreds of distinct cell types are produced. At a molecular level, this cellular diversity is created by differences in gene expression as well as interactions among the RNA and protein products of expressed genes. Genetic mutations that alter the expression and/or activity of a gene provide raw material for evolution. A subset of these mutations persists within populations, contributing to intraspecific variation, and even fewer ultimately become fixed between species, contributing to interspecific divergence. Research in my laboratory investigates the evolution of a specific trait (i.e., pigmentation in fruit flies) as well as gene expression in general. Specific projects will be developed in consultation with individual students, taking into consideration both the student's interests and the current needs of the lab. This work would be done on the Ann Arbor campus in the Wittkopp Laboratory.

Rates of parasitism and species invasions are both increasing, making it so that there are increasing numbers of outbreaks of disease that result from novel host-parasite pairings. How does parasitism influence population dynamics of native and invasive hosts? One possibility is that native parasites can provide a form of biotic resistance, slowing the spread of the invasive species. Another possibility, however, is that, if the invasive host is very tolerant of disease, it might increase disease burden, allowing infections to “spill back” into the native host. If parasite spillback occurs, population densities of the native host would be further reduced. This project will involve carrying out small- (beaker) and medium- (large bucket) scale experiments testing for parasite spillback, and quantifying the tolerance of the native and invasive host to the parasite. Other projects are also available and could be developed in consultation with individual students, based on mutual interest of the student and the lab. This work would be done on the Ann Arbor campus in the Duffy Laboratory.

Forest structure and function changes as the forests develop following catastrophic disturbance. Many forests in the Midwest were cut and then burned from the 1880s to the 1920s. The forests at the University of Michigan Biological Station (UMBS) were cut and burned in 1911. Since then UMBS has conducted a series of cuts and burns to produce an experimental chronosequence: the Burn Plots. We measure the regrowth of the trees in the Burn Plots to learn about how forest structure and function recover from disturbance. One way to measure forest structure is by building a stem map. The species, their size, and exact position are recorded in a stem map. I will work with ED-QUEST students to produce stem maps of some of the Burn Plots or other stands of trees at UMBS. I am also willing to work with ED-QUEST students develop a complementary study in the experimental forest at UMBS. Work will likely include both field and lab work and will be conducted at UMBS. See the links below for more information

http://umbs.lsa.umich.edu/research/researchsite/umbs-burn-plots.htm
http://umbs.lsa.umich.edu/research/projects/mechanisms-maintaining-productivity-in-chronosequence-of-northern-forests.htm
http://www.lsa.umich.edu/umbs/students/guidetolivingatthestation

The rapid ecological divergence of populations can drive speciation and promote diversification. Members of the predatory marine gastropod genus Conus show dramatic differences in feeding specializations at inter- and intraspecific levels. Conus utilize a venom comprised of numerous peptide neurotoxins to capture prey and venom composition too exhibits tremendous differences both within and between species. This project seeks to understand the evolution of dietary specializations and origins of adaptations related to feeding ecology in Conus through coupled investigations of diets and venom composition. This work would be done on the Ann Arbor campus in the Duda Laboratory, although opportunities may exist for field studies in the tropical Pacific.

Recent studies have shown that old forests are net absorbers of atmospheric carbon dioxide (CO2).  By absorbing more CO2 than they are emitting to the atmosphere, these forests are helping to mitigate the climate changing effects that come from burning fossil fuels.   I study the mechanisms responsible for the persistence of carbon uptake by old forests.  I also study how nitrogen cycling interacts with and constrains carbon absorption.  In my studies, I use a combination of experimental and observational approaches that employ both meteorological and ecological techniques.  I will work with ED-QUEST students to design and implement a study in the experimental forest at the University of Michigan Biological Station (UMBS).  Work will include both field sampling and lab work and will be conducted at UMBS.  See the links below for more information about my research and about UMBS. 
 
http://umbs.lsa.umich.edu/research/projects/forest-accelerated-succession-experiment-faset.htm
http://umbs.lsa.umich.edu/research/projects/forests-in-transition.htm
http://www.lsa.umich.edu/umbs/students/guidetolivingatthestation

Genetic approaches can not only provide great insights into the processes generating patterns of diversity, but also have immediate consequences for preserving that diversity, including biological systems that capture our imaginations and are often at the greatest risk of loss – recently originated species and evolutionary radiations. Yet, these are also the very situations where a disconnect between the way in which genetic data are interpreted and the actual underlying evolutionary processes can result in (i) a distorted picture of the history of speciation, and (ii) mis-specified targets of conservation concern. This project addresses two areas in which this gap between the inferences we make with our genetic analyses and the biological realities we aim to capture may be bridged by recent advances – the identification of species boundaries and the direct estimation of species trees. This project involves both theoretical work with the construction of species trees and laboratory work in genetics. This work would be done on the Ann Arbor campus in the Knowles Laboratory.

Phytoplankton communities (algae, diatoms and other aquatic photosynthetic organisms living in the water column) are responsible for half of Earth’s net primary productivity. Because species differ in their requirements and uptake of essential elements (e.g, C, N, P), phytoplankton community composition affects biogeochemical cycles. Therefore, it is important to understand which factors control phytoplankton composition. We plan to use an existing collection of the 60 most common species of North American planktonic freshwater green algae to: (i)  determine how associated bacterial communities alter algal growth dynamics, algal-algal competitive interactions, and species coexistence; and (ii)  determine whether phycosphere bacterial community similarity and the bacterial impact on algal-algal competition are evolutionarily conserved. The student will be involved in laboratory experiments focused on characterizing the bacteria associated with algae using microscopy and molecular methods (DNA sequencing), as well as in performing competition experiments.

This project seeks to understand how a complex ecosystem provides ecosystem services to organic coffee production. Based on several years research, a complex system involving an ant, a fly parasitoid, a scale insect, an entomopathogenic fungus, a plant pathogenic fungus, and a predacious beetle has been studied from a spatial dynamics point of view. An REU student could become engaged in this research in a variety of ways (as have undergraduate students in the past). The project involves activities that range from computer modeling of spatial processes to surveying organisms in Mexico, to experiments involving insects or fungi. Behavioral observations can be used to instantiate many of the parameters in already existing models of the system, or new models can be envisioned associated with the many subcomponents of the system. This work would be done onsite in Chiapas, Mexico.

What if two species of tropical trees looked almost the same in a forest of over a thousand? How many “cryptic” species are unknown to science, and how many species should be "lumped" together? If two tree species are so similar-looking, what makes them ecologically different? This project uses genetics to investigate the number and evolutionary relationships of over 30 species in Pouteria, a genus of tropical trees that is ecologically important but particularly prone to mis-identification. We collect leaf tissue samples in Yasuni National Park, Ecuador, for DNA extraction and sequencing in the lab of Christopher Dick. After processing the genetic data to delineate species, we test for evolutionary and trait-based patterns in the Pouteria community to address another enigma of tropical diversity: how so many tree species can seemingly coexist in the same square mile of forest.

The emergence of urban agriculture in cities around the world provides a convenient landscape to test questions of spatially-explicit ecological dynamics.  Can wildlife successfully travel between patchworks of habitat in otherwise inhospitable urban environments? To answer this question, we can look to pests, nature’s best migrants, for an answer. In agriculture, one pest may have several natural enemies, which together prevent crop devastation. But this observation conflicts with the traditional ecological theory that two organisms cannot coexist on the same, limited resource. Biocomplexity may provide a loophole to this conundrum in the form of non-linear relationships between competitors, where competitors having negative effects on one another limit exploitation of shared resources and thus help maintain diversity in the system. Crop diversity in urban gardens provides another layer of complication to the relationship between natural enemies. If pests are kept under damaging levels by complex interaction networks of organisms, how well do these systems remain intact across diversity gradients and the urban landscape as a whole? We will apply field, theoretical, and lab work towards understanding the patterns and mechanisms of pest and natural enemy dispersal through urban areas. We will concentrate our work in Ann Arbor, but there may be opportunities to explore similar questions in Detroit, or even Puerto Rico. Students interested in any or a combination of field identification of insects, dynamic host/pathogen/predator population modeling, GIS, and possible genetic analyses of aphid populations to track field dispersal are encouraged to apply.

 I am looking for a summer student to work on an independent project I am developing specifically for Ed-Quest. The goal of this project will be to test the hypothesis that during particular times of year (i.e. during a particular season) the human nervous system is acutely susceptible to neuronal damage by neurodegenerative diseases. The student will analyze multiple (novel and very exciting) data sets containing case and mortality data for infectious and non-infectious neurodegenerative diseases. Specifically, they will focus on Alzheimer’s disease, Parkinson’s disease, viral meningitis, and viral encephalitis. I am looking for a student with an interest in disease, population ecology, and physiology. Throughout the summer I will work one-on-one with the student and I will be teaching them the computer programing and statistical skills needed to tackle this project. I am part of a large research group here at Michigan that studies infectious diseases with the aim of informing public health policy and improving human health. My student will be immersed in a very rich academic environment where they will engage with myself and other scientists during lab meetings and informal discussions to learn about disease ecology. 

Galeommatoidea is a superfamily of hyper-diverse marine clams. Those animals often exhibit exotic morphological features and reproductive behaviors. In addition, many species in this group have commensal life styles with other marine invertebrates (i.e. they live on or inside other marine animals but do not harm them). In this project, we will investigate speciation processes within this group and test various hypotheses regarding mechanisms that may lead to their unusual diversity. We will especially look at how commensalism may affect their speciation rate and diversification patterns. We will mainly use molecular phylogenetic approaches to address above questions; however morphological studies are also used to accompany the analysis.

A typical workflow will include: field trips to various coastal sites or marine stations for collecting specimens; lab work for extracting DNA from the specimens and obtaining sequence data; and computer work for analyzing the data. Dissecting and anatomical studies might also be included. An REU student is welcome to join any part of the process, but it is preferred that the student participate in the project from its beginning. This will enable the student to generate his or her own data for analysis and eventually carry on certain sub-projects independently. Field sites vary based on the progress of the project and lab work would be done on the Ann Arbor campus in the Ó Foighil Lab.