PhD Student

I am a conservation social science PhD student masquerading as a wildlife ecologist. For my dissertation, I will be looking at the social-ecological system of wolves, ranchers, and drought in eastern Oregon and the Pacific Northwest, more broadly. Our work will explore how wolves, wild and domestic ungulates, and drought affect the relationships between people and wildlife on Western rangelands. We hope to understand how humans make decisions regarding drought, wolves, and other rangeland conditions, and how large ungulates respond to drought and wolf activity. When not working, I enjoy hiking, reading, and trying to get my cat to hang out with me.

I earned my B.S. in Ecology from the University of Georgia and my M.S. in Fisheries and Wildlife Sciences from Virginia Tech. My master’s research focused on human disturbance of fall migrating shorebirds in the Northeastern U.S. I have been fortunate to be involved in a variety of research efforts across the U.S. and internationally, and these experiences and my broad interest in wildlife ecology has shown me the importance of understanding the intersection between human and natural systems. I believe that understanding people’s relationships with nature is essential to the future of conservation and human communities.

MS Student

I am interested in wildlife population dynamics. Specifically, building methods, techniques and models to estimate population abundance, distribution and habitat use. I have spent four years working in the field in an on-going wildlife and habitat monitoring program in Malawi. In my Masters dissertation I will work on modelling abundance and distribution of key species in Nkhotakota Wildlife Reserve using data collected with camera traps. I will be co-advised by Dr. Damon Lesmeister, U.S. Forest Service PNW Research Station

In an effort to repopulate Nkhotakota Wildlife Reserve, the African Elephant and other animals were translocated to the Reserve from other protected areas in Malawi. This work is particularly relevant because it is essential in long term monitoring of the animal populations that were translocated. I obtained my undergraduate degree in natural resources management from the University of Malawi, Bunda College. In my undergraduate thesis, I assessed how institutions support protected area management. Over the years, I have worked across various fields of wildlife conservation relating to conservation education; promoting knowledge and skills transfer

Postdoctoral Research Associate

I am passionate about combining applied aquatic research with ecologically broad theory to inform conservation and management. My research has focused on the intersection of predation and migration in aquatic environments and how humans modify these interactions. I use diverse approaches including experiments, observational data, models, and syntheses to scale from individual predator-prey interactions to population and ecosystem consequences. I have examined patterns of juvenile salmon mortality and behavior as influenced by habitat and hatchery practices, and how seascape features influence salmon foraging, growth, survival, and bycatch in the ocean. I value thinking big picture and have created new conceptual theory and a review of predator effects on migratory prey relevant across taxa.

I obtained my undergraduate degree in Environmental Science from Miami University of Ohio and Masters and PhD degrees in Ecology and Evolutionary Biology from the University of California Santa Cruz. I am currently a postdoc in the Levi lab studying Chinook salmon bycatch in the Pacific hake fishery. In my free time, I enjoy biking, baking, and cheering on my hometown Chicago sports teams.

Associate Professor

Hello, and welcome to my lab at Oregon State University. I combine empirical data, fieldwork, and quantitative methods to address applied problems. My focus is broad, extending from understanding how to assess the spatial extent and ecological consequences of wildlife overexploitation, to fisheries management, the ecology and conservation of predators, disease ecology, and population dynamics in a changing climate. In each case, anthropogenic impacts have altered biotic interactions, and these alterations have consequences for things that humans care about, which is where management options need to be considered. Although my work is rooted in ecology and applied mathematics, I like to cross discipline boundaries to explore implications for human livelihoods and health.

Environmental Genetics Lab Manager

I run the environmental genetics program in the Levi Lab at Oregon State University. We use separate facilities for pre-PCR and post-PCR genetics work and multiple UV-irradiated laminar-flow PCR cabinets to reduce the risk that environmental samples are contaminated. In our lab we primarily work with fecal DNA, environmental DNA (eDNA) from water filters, and DNA in residual saliva.

Ongoing eDNA projects are focused on testing and calibrating DNA in water as a tool to quantify fish abundance and phenology. These include two projects in Southeast Alaska where for three years we have compared weir counts of salmon passage with the DNA concentrations of each salmon species, and three years of eulachon population monitoring with mark-recapture paired with synchronous eDNA samples. We are also using eDNA to monitor eulachon run timing and relative abundance on the Columbia River.

We have several projects that use DNA from residual saliva. We have recently used eDNA from residual saliva on Devil’s Club berry stalks to determine the degree to which brown bears and black bears consume this fruit, and eDNA from saliva on partially consumed salmon carcasses as a source of high-quality DNA for genotyping bears in order to estimate population density and identify the bears that use salmon streams.

Recent work with fecal DNA includes genotyping of brown bears for population density estimation in the Chilkoot River Valley, Southeast Alaska, and an array of diet analyses using DNA metabarcoding

We are using DNA metabarcoding, a method that amplifies barcode genes from bulk DNA samples to identify the species within the sample using high-performance computing, to conduct diet analyses for bats, coastal martens, and Alexander Archipelago wolves.

Publications

Wheat, R.E., Allen, J.M., Miller, S.D.L, Wilmers, C.C., Levi, T. In review. Environmental DNA from residual saliva for efficient noninvasive genetic monitoring of brown bears (Ursus arctos). Molecular Ecology Resources

Levi, T., Wheat, R., Allen, J.M., Wilmers, C.C. 2015. Differential use of salmon by vertebrate consumers: implications for conservation. PeerJ. 3:E1157

Kuo, D.S., Labelle-Dumais, C., Mao, M., Jeanne, M., Kauffman, W.B., Allen, J., Favor, J. and Gould, D.B., 2014. Allelic heterogeneity contributes to variability in ocular dysgenesis, myopathy and brain malformations caused by Col4a1 and Col4a2 mutations. Human molecular genetics, 23(7), pp.1709-1722.

Million-Weaver, S., Alexander, D.L., Allen, J.M. and Camps, M., 2012. Quantifying plasmid copy number to investigate plasmid dosage effects associated with directed protein evolution. Microbial Metabolic Engineering: Methods and Protocols, pp.33-48.

Guthrie, V.B., Allen, J., Camps, M. and Karchin, R., 2011. Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories. PLoS Comput Biol,7(9), p.e1002184.

Allen, J.M., Simcha, D.M., Ericson, N.G., Alexander, D.L., Marquette, J.T., Van Biber, B.P., Troll, C.J., Karchin, R., Bielas, J.H., Loeb, L.A. and Camps, M., 2011. Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication. Nucleic acids research, 39(16), pp.7020-7033.

Troll, C., Alexander, D., Allen, J., Marquette, J. and Camps, M., 2011. Mutagenesis and functional selection protocols for directed evolution of proteins in E. coli. JoVE (Journal of Visualized Experiments), (49), pp.e2505-e2505.

Postdoctoral Research Associate

I am an ecologist and I am interested on understanding the effects of habitat disturbance, invasive species and emerging infectious diseases (EID’s). During my PhD, I was trained in experimental biology using the system chytrid-amphibians to evaluate impacts of the chytrid through the life history of native and invasive amphibian species. I also studied changes in reproductive size in bullfrogs in invaded areas, and the effects of different chytrid strains on bullfrog survival.

I joined the Levi lab in 2017 to continue my path working and learning about disease ecology while incorporating new tools and skills. Currently, I am working on a collaborative project with the National Park service at Mount Rainier (MORA), studying a psychrophilic (cold-loving) fungus that causes the white-nose syndrome (WNS), an emerging infectious disease-causing unprecedented declines of bats populations.

Using guano and swab samples, I am evaluating and quantifying the presence of the fungus, and we are planning to incorporate the use of new molecular tools to increase the likelihood of detection of this fungus. Additionally, I will work on the identification of bat species from guano with molecular tools.

In my free time, I do Zumba, travel around and enjoy sharing time with friends!

PhD student

I grew up in the suburbs of Boston, but became interested in the natural world working on a bat physiology project in high school. I went on to earn a BA in Biology and Environmental Studies from New York University and MS in Zoology from the Cooperative Wildlife Research Laboratory at Southern Illinois University Carbondale. My master’s thesis was on the ecology and behavior of white-tailed deer in southern Illinois. It focused on survival, contact rates, and the impact of localized removal. I am broadly interested in ecological theory and applying ecological theory to management and conservation. When not working, I enjoy cooking, hiking, archery, and playing soccer.

For my dissertation, I will be exploring the terrestrial food web of the Pacific Northwest Forests. Specifically, I will be investigating the interactions between and survival of small carnivores and their prey at the HJ Andrews Experimental Forest, a National Science Foundation (NSF) Long Term Ecological Research (LTER) site. I hope to contribute to the impressive existing body of knowledge and to integrate the long-term data on small mammals, songbirds, and weather with carnivore data. A better understanding of this terrestrial food web will be important for conservation and basic ecology.

Postdoctoral Research Associate (previously PhD Student)

I am extremely grateful to be studying the spatial ecology of carnivores for my dissertation in the Levi Lab. The research is conducted at Starkey Experimental Forest and Range in the Blue Mountains of northeastern Oregon and focuses on interactions between cougars, coyotes, bobcats and bears, as well as their influences on prey populations. We have collected a unique dataset of GPS collar data from over 60 individuals, over 2,000 carnivore scats (for diet and genotypes), and millions of trail camera photos from a grid of 100 cameras over 4 years. The carnivore dataset is being leveraged against existing ungulate datasets maintained by researchers at the Starkey Experimental Forest. The study is part of a larger research project studying the demographic, nutritional and spatial ecology of mule deer. We collaborate closely with Oregon Department of Fish and Wildlife, the US Forest Service PNW Research Station, and researchers at University of Idaho and University of Nevada-Reno.

My dissertation has 3 components:

• Use spatial density estimation models (e.g. spatial mark-resight, spatial capture-recapture) to make inferences about the abundance of each of the 4 carnivore species. Evaluate bias and precision between methods and data sources (camera vs scat), and determine the value of ancillary information (e.g. GPS collar data) in estimating population sizes
• Use contemporaneous GPS collar data and movement models to study the interactions between members of the carnivore guild. Determine the degree to which the space use of carnivores is influenced by the proximity to other carnivore species after controlling for habitat and landscape variables
• Study the behavior of predators in response to the ungulate birth pulse. Are carnivores actively seeking out the seasonal pulse of immobile neonates, or simply opportunistically encountering them?

NSF Postdoctoral Research Fellow (previously PhD student)

I am broadly interested in applying ecological methods and theory to conservation problems. My training and continued interests focus on combining methods in disease ecology, quantitative ecology, and mammalian ecology to address issues of human-wildlife conflict and the impacts of environmental disturbance on species interactions, populations, and communities. As an undergraduate, I worked in a variety of field and lab settings investigating animal health and behavior including a field course in the Panamanian rainforest and a biomedical research institute (MMCRI). Most recently, I completed my master’s at the University of Michigan where I was involved in two projects in central Kenya investigating the impacts of land-use change on the interplay between zoonotic disease, wildlife, and human-wildlife conflict.

As a graduate student in the Levi lab, I will be addressing the role of land-use change and biodiversity loss as drivers of infectious disease dynamics across a gradient of deforestation and forest fragmentation in the Brazilian Amazon. This work is particularly exciting because it has implications for both bettering our understanding of basic ecology as well as for guiding conservation efforts.

Postdoctoral Research Associate (previously PhD Student)

I am broadly interested in using noninvasive techniques to study different aspects of carnivore ecology. I obtained my undergraduate degree in Biology and Environmental Science from University of Sydney, Australia, and my Master’s degree in Conservation Biology from Lund University, Sweden. I first found my way to the Levi lab as a visiting scholar during my master’s where I studied the diet, prey availability, distribution of predators and competitors of coastal martens in Oregon¹. Now as a PhD student I am balancing a multitude of very exciting projects including the density and diet of jaguars in Brazil, developing a new noninvasive genotyping method using SNPs and next-generation sequencing² and a multi-species diet study of carnivores in northeastern Oregon using DNA metabarcoding.

1 Eriksson, CE., Moriarty, KM., Linnell, MA., Levi, T. 2019. Biotic factors influencing the unexpected distribution of a Humboldt marten (Martes caurina humboldtensis) population in a young coastal forest. PloS one 14 (5), e0214653

2 Eriksson, C.E., Ruprecht, J., Levi, T. In revision. More affordable and effective noninvasive SNP genotyping using high-throughput amplicon sequencing.