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REU Faculty Mentors

Disease Ecology, Ecological Immunology & Physiology, Animal Behavior

Invasive pathogens pose existential threats to biodiversity worldwide, with critical consequences for human and domestic animal health. The Adelman lab seeks to understand how native wildlife can fight these invasive pathogens, primarily using house finches (Haemorhous mexicanus) and their recently emerged bacterial pathogen, Mycoplasma gallisepticum. Currently, the lab focuses on a little-understood means by which animals combat pathogens: tolerance of infection, or the ability to maintain fitness despite high pathogen loads. Because such studies involve diverse skill sets, theoretical underpinnings, and research contexts, myriad possibilities exist for students to discover how to design experiments, conduct research, and disseminate their findings. Potential projects include: (1) Using the Mycoplasma system to address issues of invasive species and biodiversity to evaluate potential tolerance genes across a range of host species. The Adelman lab is currently identifying differentially expressed genes that may underlie tolerance in house finches and an REU student could ask if other, more tolerant species show homology in these genomic regions; and (2) Revisiting the potential for cross-species transmission in an emerging infectious disease. Here an REU student could conduct captive experiments on multi-species-flocks to determine how likely other species are to harbor M. gallisepticum when sharing food resources with house finches.

Jim Adelman

Assistant Professor
Ph.D. Princeton University

E. Keith Bowers
Assistant Professor

Director, Meeman Field Station
Ph.D. Illinois State University

Evolutionary, Physiological & Behavioral Ecology, Evolution of Life Histories, Ecoimmunology, Climate Change

The disruption of basic evolutionary processes is both a cause and consequence of the current Biodiversity Crisis, and no system is better-suited to investigate this than wild populations of readily tractable individuals. Conducting long-term research on wild birds, Dr. Bowers’s research foci span multiple levels, from individual physiology and behavior to interspecific interactions, such as host-parasite dynamics, and induced immune responses that affect the fitness of individuals and populations. His research sheds light on the strength and shape of selection acting on avian breeding phenology under global environmental change, and he is now studying interactions between prothonotary warblers (Protonotaria citrea) and multiple parasite guilds, including brood-parasitic cowbirds (Molothrus ater) and hematophagous blowflies (genus Protocalliphora), an ecto-parasite with devastating effects on host fitness. Watch-listed as a Partners-in-Flight Species of Continental Concern, the prothonotary warbler is rapidly declining, with multiple threats throughout their North American breeding range and their South American winter range. A major priority of the Bowers Lab is to understand the ever-evolving life history of this species of special concern. Potential projects include a range of topics suited to a diverse population of students, including those attracted to biomedical sciences (e.g., measuring immune responses or hormone production). Such projects may include: (1) determining how parents choose who among their young to keep alive in the presence of multiple parasite guilds, (2) studying transgenerational effects of maternal immune activation on offspring parasite defense and survival, or (3) studying pressures on breeding phenology and the timing of seasonal events.

Shawn Brown
Assistant Professor
Ph.D. Kansas State University

Microbial Ecology, Mycology, Community Ecology, Snow Microbiology, Endophytes

Fungi are one of the most biodiverse groups of organisms, yet one of the most understudied. They are inextricably likened to, and associated with, every organism and ecosystem on earth and the Biodiversity Crisis that is threatening organismal diversity is also impacting fungal diversity in currently undefined ways. Research in the Brown lab connects fungal biodiversity with environmental disturbances and understudied ecosystems to define drivers of, and threats to, fungal biodiversity. REU students will develop independent inquiry-driven projects that align with current research foci in the Brown Lab. REU students working in the Brown lab will have the opportunity to help design manipulative field and laboratory experiments, and natural field experiments. Brown lab members will train students in culture techniques, library preparation for next-generation DNA sequencing, and bioinformatic tools. Potential projects include: 1) culture-based competition assays to test hypotheses on differential nutrient utilization, 2) test hypotheses on, and quantify population structure of, psychrotolerant snow fungi (extremophilic species capable of growth and reproduction in low temperatures) using NGS sequencing; and (3) studying how fungal communities respond to environmental perturbations.

Bernie J. Daigle Jr.
Assistant Professor
Ph.D. Stanford University

Human activities such as deforestation and poaching pose a significant threat to global biodiversity, in part by exposing impacted species to traumatic experiences that cause lasting psychological effects. To better understand the causes of these effects and potential treatments to prevent or reverse them, the Daigle lab works to identify diagnostic and prognostic biomarkers for post-traumatic stress disorder (PTSD) in humans and model organisms. One of the main categories of PTSD symptomatology is changes in physical emotions and reactions, which include always being on guard for danger, self-destructive behavior, difficulty sleeping or concentrating, and aggression. The biological foundation of this stress response is explained by the hypothalamic-pituitary-adrenal (HPA) axis, where an organism’s ability to survive terrifying events relates to the fight-or-flight response orchestrated by its sympathetic nervous system. Given the evolutionary conservation of the fight-or-flight response across vertebrate species, comparative studies of PTSD in humans and closely related species may shed light on shared causes of, and responses to, the disorder. This would be particularly helpful in understanding the effects of trauma to animals resulting from ongoing threats to biodiversity such as deforestation and poaching. For example, early traumatic experiences in baboons can shorten longevity, lower fitness, and spur comorbid disorders such as cardiovascular disease [12]. In addition, symptoms of PTSD and depression have been observed in chimpanzees that experienced histories of experimentation, illegal seizure, or maternal separation [13]. REU participants in the Daigle lab will learn biomarker identification techniques (along with learning practical computing skills, exploratory data analysis, descriptive statistics, and basic machine learning) and apply them to human and chimpanzee data to identify cross-species PTSD biomarkers. The Daigle lab, in collaboration with members of the DoD-funded Systems Biology of PTSD Consortium (SBPC), is currently working to identify PTSD biomarkers in clinical and molecular data collected from veteran soldiers with and without PTSD. A potential project includes: Applying these bioinformatics techniques to human SBPC data to identify clinical measurements predictive of PTSD. Given these candidate biomarkers, students will query chimpanzee clinical data derived from published case reports of 20 traumatized chimpanzees [13] to find cross-species as well as unique PTSD biomarkers.

Genomic Data Integration, Single-cell Gene Expression, Computational Systems Biology, Software Development, Bioinformatics

Mike Ferkin
Jack H. Morris Professor
Ph.D. Boston University

Animal Behavior, Animal Cognition, Behavioral Ecology, Sperm Competition

Species-centric conservation and management practices are essential to protecting biodiversity, and fundamental to such developments is enhancing our understanding of animal physiology and behavior and their role in sensory ecology. The Ferkin lab primarily studies how mammals use social cues to obtain information about others in their own species. In particular, the lab focuses on understanding how individuals acquire and use information about their surroundings in decision-making, particularly in the context of mate choice and condition-dependent signaling. Individuals often obtain information about the phenotype of signalers, including their interactions with the environment or other individuals. In terrestrial mammals, this information is often encoded in scents from biological exudates and specialized sebaceous glands. Dr. Ferkin’s group studies these processes primarily in meadow voles (Microtus pennsylvanicus), which are promiscuous, seasonally-breeding rodents with a highly localized pattern of scent sources on their bodies that are used to attract mates and deter same-sex rivals. Recent findings suggest that (i) secretions from different glands and parts of the body encode different information, and (ii) individuals often mark a given location using a variety of scents. These findings raise several new questions that are readily testable in this system. REU students will gain hands-on experience and training, including meadow vole behavioral observations, hormone treatments, and ELISA hormone assays. Potential projects include: (1) investigating whether scent marks from the same anatomical source, but different individuals, convey similar or dissimilar information to conspecifics; and (2) determining whether scent marks from multiple sources on the same individual provide unique or overlapping information about the signaler.

Dave Freeman
Associate Professor
Ph.D. University of Connecticut

Biological Rhythms, Eusociality (Mammals), Neuroendocrinology, Reproductive Strategies, Aging, Animal Behavior, Animal Physiology

Understanding the ecology, evolution, and physiology of seasonal rhythms in stress and immunity allows for the creation of models regarding how climate change may impact organisms with seasonal components to their life history. The Freeman lab conducts research focused on hormones, brains and behavior with special interest in biological timing and mammalian mating strategies. Climate change has already resulted in a mismatch between day lengths and the ultimate factors that they historically predicted. For example, migratory birds are arriving to their breeding grounds based on the photoperiodic information that accurately predicted insect hatches in the past. However, due to climate change, they arrive to find the insect hatches have already occurred. Events like this will likely be further impacted by eliciting stress responses and altering the seasonal rhythm in immune function. This mismatch between ancient photoperiodic systems and the rapid changes in current climate is likely to negatively impact biodiversity in temperate areas of the planet. The Freeman lab’s second area of research includes identifying the neuroendocrine and behavioral mechanisms that establish and maintain eusociality in mammals. Though relatively common among insects, eusociality is a rare mating system in mammals, and has so far been documented in only two species of African mole-rat. Understanding eusocial mating systems may allow us to better understand the selective pressures that shape the diverse array of mammalian mating systems and behavior. REU students will develop question-driven independent projects around one of the following topics of current research in the Freeman lab, and students will be involved in all aspects of these projects, from experimental design to learning and performing neuroendocrine techniques and surgeries, to data analysis and manuscript preparation. Potential projects include: (1) The neuroendocrine mechanisms mediating seasonal changes in energetics, stress physiology and immune function in Siberian hamsters, and (2) The mechanisms underlying the evolution of eusociality in the Damaraland mole rat.

Plant Population Genetics & Phylogenetics

Understanding and exploring the world’s past and present biodiversity is critical to creating and maintaining healthy and sustainable natural and human environments. Research in the Mandel lab centers on understanding how genetic and genomic variation generate present patterns of plant biodiversity. A driving force of their work is to understand how changes in the environment, including the landscape and climate, affect species abundance and geographic distribution. Their research draws upon the disciplines of ecological genomics, quantitative and population genetics, phylogenetics, and conservation biology and focuses on flowering plants in the species-rich family Asteraceae (the sunflower family). Research in the Mandel lab has been focused on understanding both the evolutionary relationships among members of the sunflower family, and the causes and consequences of evolutionary processes that generate plant biodiversity. Potential projects include: (1) Conservation and population genetics of local flora, especially those that could be sampled from the Meeman Biological Station; (2) A phylogenomic study in the sunflower family comprising wet lab methods and data analyses; and (3) Mitochondrial and plastid genome evolution and causes of discordance in sunflower relatives.

Jennifer Mandel

Associate Professor

Assistant Director, Center for Biodiversity Research

Ph.D. Vanderbilt University

Insect Systematics, Genomics, Evolution, & Diversity

Duane McKenna

William Hill Professor

Director, Center for Biodiversity Research

Director, Agriculture & Food Technologies Research Cluster, FedEx Institute of Technology

Ph.D. Harvard University

Insect-plant interactions are fundamental to terrestrial biodiversity [14], but threatened by climate change, habitat loss, and other drivers of biodiversity decline. The McKenna lab seeks to better understand insect biodiversity and facilitate its conservation through studying beetle (Coleoptera) phylogeny and evolution, the genomic basis of specialized phytophagy in beetles and other insects, and geographic patterns of insect diversity and endemism. REU students will develop projects that involve generating new molecular data (transcriptomes, phylogenomic data obtained via target enrichment, or gene family annotations), and utilize unpublished lab data, and/or publicly available data. These data will be used to study the evolution of beetle genes known to support phytophagy, and to address questions about beetle phylogeny, evolution, and feeding interactions with plants. Students will be mentored on all aspects of project design, data generation and mining from databases, and data analysis (using the UofM high performance computing cluster). Potential projects include: (1) Reconstructing the evolutionary origins of beetle genes supporting phytophagy: Where in the phylogeny of phytophagous beetles (the Phytophaga) were different beetle-encoded plant cell wall degrading enzymes (PCWDEs) acquired via horizontal gene transfer from microbes?; and (2) The evolutionary origins of specialized phytophagy in beetles: Do the genomes of phytophagous beetles with similar modes of plant feeding, such as wood-borers or leaf-miners, encode similar repertoires of PCWDEs, regardless of the degree of phylogenetic relatedness?

Cassandra Nuñez
Research Assistant Professor
Ph.D. Princeton University

Behavioral Ecology, Reproductive & Stress Physiology, Wildlife Ecology & Management

Providing for species’ behavioral, physiological, and ecological needs is paramount if we are to effectively conserve animal biodiversity. The Nuñez lab investigates the important linkages among these factors using feral horses as a model system. Feral horses organize themselves into stable social groups, consisting of the male, his females, and their offspring. The stability of these groups is critical for animal health and has even been shown to affect offspring survival, making feral horses an excellent model to investigate the potential effects of human perturbation to animal social structure and functioning. Nuñez’s work with the feral horses living on Shackleford Banks, NC, has demonstrated how contraception management increases females’ propensity to leave their current group to join new ones, thereby decreasing group stability. These changes affect female stress physiology and alter the subsequent behavior and stress physiology of their male associates. These human “perturbations” provide a rare, experimental manipulation of female behavior in the wild which can help us better understand the importance of social organization to population health. Moreover, Shackleford horses live across three distinct ecological regions varying in visibility and resource distribution, enabling rigorous tests of how habitat features can either exacerbate or mitigate these effects. Potential projects include: (1) Assessing whether increased group changing behavior by females affects their propensity for aggression and their subsequent ability to form strong social bonds with group associates a) for contracepted vs. uncontracepted females and b) before and after contraception management; and (2) Assessing the effects of increased group changing behavior by females on resident offspring. Within these behavioral-oriented projects students could also (1) examine the parasite loads, and/or cortisol levels of adult females and/or foals to determine whether increases in female group changing behavior affect individual- and/or population-level health and (2) compare results across island region to determine the effects of ecology on the animals’ responses.

Matthew Parris
Associate Professor
Ph.D. University of Missouri

Amphibian Disease Ecology, Population Ecology, Herpetology, Ecotoxicology

Global amphibian biodiversity is severely impacted by emergent infectious diseases. Of the nearly 4000 extant species of amphibians, more than one-third are facing unprecedented population declines. Worldwide patterns of population decline and species extinction are associated with infection by fungal pathogens. The Parris lab examines how ecological, behavioral, and immunological factors impact amphibian host-pathogen dynamics. Topics studied in the lab include amphibian response to the fungal pathogen Batrachochytrium dendrobatidis (Bd) and the evolutionary ecology of host-pathogen dynamics. REU students will perform laboratory and field experiments in mesocosms at the Meeman Biological Station. These projects will provide novel data about the evolutionary ecology of an emergent infectious disease threatening an imperiled vertebrate taxon. Potential projects include: (1) Studying the relative importance of abiotic and biotic environmental cofactors on susceptibility and pathogen impact, including whether xenobiotic pollutants (e.g., pesticides, herbicides, and fungicides) alter host-pathogen dynamics; and (2) Host behavioral influences on disease transmission, including how amphibian community structures influence disease transmission; and (3) Whether tolerant host species can serve as super-spreaders for disease and whether host shifts in behavior (e.g., behavioral fever) alter epidemiological predictions of disease spread.

Emily Puckett
Assistant Professor
Ph.D. University of Missouri

Phylogeography, Population Genomics, Bears, Conservation Genetics

Species conservation is greatly informed through identifying intraspecific genetic diversity across its geographic range, particularly for decisions related to populations to conserve, allow extirpation, or use for translocation. The Puckett lab studies spatial genomic diversity in North American mammals of conservation concern. Specifically, the lab uses phylogeographic and population genomic approaches to elucidate patterns of genetic diversity and differentiation through space and time. Current work is focused on American black bears (Ursus americanus) and grizzly bears (U. arctos). Their research aims to understand the demographic history of these species and to characterize patterns of intraspecific genomic variation, including variants that underlie coat-color phenotypes of interest. The lab has ongoing collaborations with numerous state and federal agencies responsible for the management of bear populations; thus, analyses of these populations will be reported to the agency and may directly inform management decisions. Moreover, the Puckett lab has over 650 samples of bears from across the range and continues to collect; thus, the potential for regional or range-wide projects could be quickly implemented within the timeframe of an REU student. Summer projects will focus on questions relevant to the conservation and management of bear populations. Potential projects include: (1) Using and/or generating population genomic data to answer questions related to population structure, sex-biased dispersal, landscape genetics, (2) Analyzing effective population size change through time, demographic history, and Y-chromosome phylogeography, and (3) Estimating the timing of derived variants in candidate genes.

Jaime Sabel
Assistant Professor
Ph.D. University of Nebraska

Classroom Scaffolds, Tools & Environments, Formative Assessment, Self-regulated Learning, Metacognition

Dr. Sabel is a biology education researcher and studies the effective use of various classroom scaffolds, i.e., learning tools meant specifically to support undergraduate students in learning biology. This work informs the design of undergraduate and graduate biology courses by integrating learning scaffolds that will best support students to reach complex biological understanding. In addition to understanding the scope of the biodiversity crisis through research, we will need to educate other scientists and the public about the current status of biodiversity science and conservation, including ways they can contribute to addressing the crisis. Projects in the Sabel lab focus on developing educational interventions, implementing them in classrooms, and examining their effects on undergraduate student understanding. Potential projects include: (1) Majors Metacognition - a student could examine how students are thinking and learning biodiversity concepts and could be involved in developing and testing new scaffolds to support students in that endeavor. (2) Nonmajors Reflection – a student could be involved in analyzing students’ ideas regarding biodiversity-related topics discussed in the course and could work to develop and test a biodiversity-themed Real-World Scenario for the classroom. (3) Plant Awareness Disparity (PAD, formerly plant blindness) – a student could be involved in analyzing aspects of an instrument designed to test PAD or in developing and testing new scaffolds related to PAD and biodiversity.

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