Author Archives: Sara Monk

Taal Levi

Taal Levi

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.

Jennifer Allen

Jennifer Allen

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.

Jenny Urbina

Jenny Urbina

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!

Marie Tosa

Marie Tosa

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.

Joel Ruprecht

Joel Ruprecht

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?
Joel Ruprecht
Aimee Massey

Aimee Massey

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.

Charlotte Eriksson

Charlotte Eriksson

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.

Kenneth Loonam

Kenneth Loonam

PhD Student

I am a PhD student in the Levi Lab. For my dissertation, I will be looking at the community effects of an elk reduction experiment in Starkey Experimental Forest and Range in eastern Oregon.  The elk reduction is part of a long-term research project at Starkey run by the US Forest Service and Oregon Department of Fish and Wildlife. Thanks to the long term nature of the project and the phenomenal efforts of our collaborators, data abounds in the forms of capture histories, collars, cameras, flights, and scats, which will provide ample opportunity for us to look at some fascinating ecology in an experimental setting.

Prior to beginning my PhD, I completed an MS in wildlife biology at the University of Montana. For my masters I tested the robustness of the time- and space-to-event models for estimating abundance of unmarked populations with remote cameras. I looked at both the response to assumption violations and how well they perform in real-world settings when densities and detection rates are low. I also spent about five years working on various field projects between my undergraduate degree at Texas A&M and my masters. The allure of wildlife work was strong, but it needed more math. Now, in my free time, I enjoy long walks through other people’s buggy code, cold beers while I cook, and short runs in the mountains.

Cara Appel

Cara Appel

PhD Student

I grew up here in the Pacific Northwest and have a B.A. in Environmental Studies from the University of Washington and an M.S. in Wildlife from Humboldt State University. For my master’s research, I studied habitat ecology of North American porcupines in the Tolowa Dunes of northern California. I have also been working on distribution modeling and optimizing monitoring methods for porcupines in light of their apparent declines in western North America.

For my Ph.D. research, I am using passive monitoring and deep learning methods to study wildlife community ecology in forests of the Pacific Northwest. I am co-advised by Dr. Damon Lesmeister with the U.S. Forest Service PNW Research Station, where an ongoing bioacoustics project is being developed to monitor northern spotted owls and other species. We are using convolutional neural networks to automate the identification of a host of different bird and mammal species from acoustic recordings and camera trap images, which allows us to explore dynamics within and between wildlife communities.

Ellen Dymit

Ellen Dymit

MS Student

Growing up in Minnesota, my love of wilderness was born when I first heard wild wolves howl. By a delightful twist of fate, my Master’s research in the Levi lab now centers on the foraging ecology of coastal wolves on the Alaskan peninsula in Katmai National Park. Using noninvasive DNA sampling and other monitoring techniques, our project will illuminate the fascinating lives of wolves throughout Katmai’s uniquely pristine, bear-dense, and salmon-rich maritime environment.

Although I am principally interested in carnivore behavioral ecology, the eclectic nature of my past research reflects my broad curiosity about wildlife science. As an undergrad at Emory University, I worked on projects concerning the phenology of plant-pollinator interactions, the movement of urban coyotes, bumblebee social learning, Amazonian bat species richness, and salamander population dynamics. Prior to beginning at OSU, I completed a year-long Fulbright research project on arctic fox conservation and interactions among tundra carnivores in northern Norway. I remain excited about many different things within and beyond ecology, including Buddhist philosophy, Cenozoic Era paleontology, and the fantastic world of fungi.