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.
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.
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!
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.
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.
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.
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.
Originally from Michigan, I have spent the last ten years working for various wildlife research projects that have largely focused on mammalian population dynamics. From studying spotted hyenas in Kenya to cougars and mule deer in northern California, I have spent a lot of time in the field collecting data, sleeping in a tent, and getting to know wonderful people who have inspired my curiosities of wildlife. Most recently I have been working for the Yellowstone Cougar Project which focuses on understanding the role of this solitary carnivore living amongst a diverse predator and prey community.
I am stoked to be joining the Levi Lab to continue working with data from Yellowstone, develop quantitative skills, and learn from lab members who are conducting all sorts of cool science. Specifically, I hope my research improves our understanding of how intact predator guilds can exhibit positive effects on prey communities, and how such interactions are influenced by seasonal weather patterns. Besides wildlife, my other interests involve reading fantasy books, dreaming of snowy mountains with skis on my feet, throwing frisbees, and providing my dog with all the support she needs to fulfill her endless quest of finding the best place to hide bones, sticks, and other valuables found while walking through the woods.
The route I took to become a Master’s student in the Levi Lab was fairly circuitous. A large swath of conservation land was my playground growing up and I was academically inclined toward quantitative pursuits but I took a detour through the art world before coming back to computer programming as a webmaster at a software development firm. After a time I decided to pursue something more meaningful so I returned to school and volunteered at the Eagle Creek Fish Hatchery and the Julia Butler Hansen Wildlife Refuge with their Columbian White- Tailed Deer Project. Everything came into place when I realized that I could use my computer programming and quantitative abilities to help protect and preserve the natural world.
That we can use code to develop methods to analyze genetic code is fascinating to me. Continued advancements in sequencing technologies have made complex genetic analyses accessible to resource-deprived wildlife organizations and it is my goal to facilitate wildlife management and conservation efforts by developing novel molecular methods to monitor wildlife.
MS Winter 2019 (Now Executive Director of Takshanuk Watershed Council)
Growing up in upstate New York and spending lots of time tromping through streams and fields instilled a wonder about ecology. This continued through my undergraduate studies at the State University of New York College of Environmental Science and Forestry (SUNY-ESF, “stumpies”) where I majored in Environmental Science with a focus on watershed science and engineering. I then found my way to Alaska and have spent the past 7 years working for a small non-profit watershed council in Haines. My Masters research takes place in the large glacier fed rivers near Haines, AK. The focus is a small anadromous smelt species called eulachon or hooligan (Thaleichthys pacificus). Eulachon are a very important subsistence species for the Alaskan natives and vital forage fish for marine mammals and sea birds, however there is relatively little ecological knowledge about the species – limited population data, poor understanding of marine habitat, and unknown fidelity to natal streams, etc. My research will calibrate the concentration of environmental DNA (eDNA) against estimates of eulachon biomass from mark-recapture and catch-per-unit-effort methods. This relationship will provide insight into population monitoring techniques that can be implemented regionally.
Former Postdoctoral Research Associate, now postdoc at UC Santa Cruz
For many species, fitness is a function of an individual’s ability to match his or her behavior to available conditions. Thus in making decisions that affect their fitness, animals translate the conditions they experience into demographic consequences at the individual and population levels. I’m interested in: 1) exploring the causes and consequences of animal behavior, particularly with regards to movement; 2) using an understanding of the attendant cues, costs and incentives to enhance approaches to studying species distribution and abundance; and 3) applying 1&2 to inform management and conservation actions. These questions surrounding the extent of a species ability to adapt behaviorally to changing conditions are at the heart of understanding population-level vulnerability to anthropogenic change. In the service of these goals I’ve also taken an interest in developing platforms that improve the dissemination and application of important quantitative tools.
My PhD research focused on understanding how partial migration is maintained in federally-endangered Sierra Nevada Bighorn Sheep, but also included quantifying migratory behavior is several other ungulate systems. As part of this research I wrote the R package “migrateR”, which improves and automates model-driven methods for movement classification (available online at: https://github.com/dbspitz/migrateR). As the Jack Ward Thomas Postdoctoral Fellow, I now contribute as a member of the Starkey Project. This collaboration extends my interest in ungulate movement ecology to a broader range of spatial and temporal scales, from quantifying the long-term effects of fire history on ungulates to evaluating the fitness consequences of fine-scale strategies for predator avoidance.
MS Spring 2018 (Now Wildlife Biologist with Confederated Tribes of the Grande Ronde)
I grew up outside of Chicago and spent my youth wandering the forests and lakes of the upper Midwest. After receiving my undergraduate degree from the University of Vermont I moved west and have worked in many different places. Most of my work has been focused on mustelids, and spotted owls in northern California and Oregon. In my spare time I enjoy hiking, fly fishing, and spending time with my dog, Finn.
My master’s thesis in the Levi lab focuses on the distribution of fisher (Pekania pennanti) in southwestern Oregon and is nested in a multi-species monitoring framework. Fisher are rare forest carnivores with relatively unknown distributions in Oregon. I use remote cameras and genetic sampling to survey landscapes for these animals and ask additional questions about the ecology of carnivore guilds in the area.
MS Fall 2017 (now instructor at Oregon State University – Cascades)
I have worked in various fish and wildlife positions across the Western United States. I worked for the Birds and Burns project at Montana State University where I earned my B.S. in Fish and Wildlife Science. After graduating, I interned at an environmental consulting company in Tucson, AZ, where I participated in a wide variety of avian, reptilian and plant surveys. Over the last couple of years I have been working at a pharmaceutical research and development company in Bend, Oregon, but I am very excited to get back into wildlife at OSU.
My Master’s project in the Levi lab focuses on bears’ roles as seed dispersers in the Southeastern Alaskan ecosystem. Specifically, I am using qualitative and quantitative methods to determine which species consumes the largest proportion of berries from the widely dispersed shrub, Oplopanax horridus (Devil’s club). Due to the nature in which bears consume O. horridus, I am also researching this shrub’s potential to noninvasively monitor bear movement and density in this habitat.
MS Winter 2017 (now Wildlife Biologist with Alaska Department of Fish and Game)
Over the past five years I have been involved in various wildlife projects throughout the Western United States. I began working with small mammals and pumas while pursuing my Bachelor’s degree in Environmental Studies at the University of California Santa Cruz. After completing my degree, I spent the next three years deploying GPS collars to track the survival, feeding behavior and reproductive success of pumas in central California. I have also worked with wolves, golden eagles, black swifts and other wildlife throughout Montana, Wyoming and Colorado. I am broadly interested in carnivore ecology, behavioral ecology and conservation efforts.
As a Masters student in the Levi lab, I will be investigating the ecological role of bears in the dispersal of a variety of fruiting plant species in Southeast Alaska. The tremendous amounts of fruit consumed by bears results in seed filled scats throughout the landscape, which may provide a feasible foraging resource for small mammals during times of food scarcity and an important form of seed dispersal. Understanding the interspecific interactions between bears and small mammals will aid in a better understanding of the potential cascading effects of bears on small mammal populations and how it may impact avian predators and mesopredators.
There is no place in the world humankind has not put its footprint. Few remote places on earth are still primeval and healthy, but most of them have suffered habitat loss, defaunation, introduction of alien species, and many are degraded ecosystems. The role of the ecologist in the 21st century should be to deepen knowledge of the ecological consequences of the Anthropocene and addressing conservation policy, ecological restoration, and human wellbeing for future generations.
I am from Brazil and currently doing my PhD at São Paulo State University – Rio Claro, Brazil (2014-) at Mauro Galetti’s lab (labic.eco.br and facebook.com/labicunesp/). I came to Oregon State University for a one-year internship at Taal Levi’s lab (2017), with the support of FAPESP. In my thesis, I have been investigating the ecological and human dimension of feral hog Sus scrofa invasion. In the Neotropics, feral hogs are now a key ecological element of the landscape. On the one hand, we have a large-bodied vertebrate fulfilling interactions interrupted by fragmentation and defaunation processes, and on the other we have the need to control feral hog populations so they do not compromise human wellbeing. This work led me to participate in the formulation of the Federal Control Plan for feral hogs in Brazil. This is a permanent and continuous effort led by a diversity of stakeholders interested in adopting improved strategies for feral hog control nationwide.
My current passion is Alaskan rainforest ecosystems, where I have been investigating the ecological interactions of salmon, bears and zoochoric plants. My permanent passions are being outdoors – hiking, biking, camping, traveling and experiencing new cultures.
I was born and raised in Borneo, Malaysia and doing a 5-months internship with the Fisheries and Wildlife Department, under the supervision of Nicole Duplaix and Taal Levi. I have finished my Bachelor degree in Conservation Biology in 2015 and currently pursuing my MSc in Universiti Malaysia Sabah (UMS). My MSc project is on the ecology of otter in the Lower Kinabatangan Wildlife Sanctuary in Sabah, which focuses on their distribution, presence and absence across different habitat types in Kinabatangan river as well as investigating their activity pattern using camera trapping. I am very passionate about learning about the ecology of wildlife as I think it is important to know their ecology in order to establish an effective conservation plan for the wildlife. Besides wildlife, I also enjoy hiking, traveling and reading. I am hoping to gain more experiences and knowledge during my internship period and apply what I have learned in conservation management in my own country.
We work on a variety of disease systems. In the past, the community ecology of Lyme disease and tick-borne pathogens was a major focus. Currently we work on how deforestation in the southern Amazon interacts with biodiversity (hosts), vectors, and pathogens to influence disease risk to humans. Our primary focus is Leishmaniasis, which is transmitted by sand flies, but we also work with other pathogens. In addition, we work on developing and testing genetic tools to detect the fungal pathogen that causes white-nose syndrome in bats. We have recently started a project geared toward the treatment of infected bats in the field.
Relevant Publications
Sabino-Santos Jr., G., Fernandes, F.F, da Silva, D.J.F., Melo, D.M., da Silva, S.G., São Bernardo, C.S., Filho, M.D.S., Levi, T., Figueiredo, L.T.M., Peres, C.A., Bronzoni, R.V.M, Canale, G.R. 2019. Othohantavirus antibodies among phyllostomid bats from the arc of deforestation in Southern Amazonia, Brazil
Vieira C.J.S.P., Andrade, C.D, Kubiszeski, J.R., Silva D.J.F., Barreto, E.S., Massey, A.L., Canale, G.R., Bernardo, C.S.S., Levi, T., Peres, C.A., Bronzoni, R.V.M. 2019. Detection of Ilheus virus in mosquitoes from Southern Amazon, Brazil. Transactions of the Royal Society of Tropical Medicine and Hygiene
Urbina, J., Chestnut, T., Schwalm, D., Allen, J., Levi, T. 2019. Experimental evaluation of degradation rates of genomic DNA of the pathogen Pseudogymnoascus destructans (Pd) in bat guano. PeerJ
Ostfeld, R.S.*, Levi, T.*, Keesing, F., Oggenfuss, K. Canham, C.D. 2018. Tick-borne disease risk in a forest food web. Ecology*authors contributed equally
Kilpatrick, M., Dobson, A.D.M., Levi, T., Salkeld, D.J., Swei, A., Ginsberg, H.S., Kjemtrup, A., Padgett, K.A., Jensen, P.M., Fish, D., Ogden, N.H., Diuk-Wasser, M. 2017. Lyme disease ecology in a changing world: consensus, uncertainty, and critical gaps for improving control. Philosophical Transactions of the Royal Society B
Burtis, J.C., Sullivan, P., Ostfeld R.S., Levi, T., Yavitt, J.B., Fahey, T.J. 2016. The impact of temperature and precipitation during Ixodes scapularis questing periods on human Lyme disease incidence and natural tick densities in long-term endemic and emerging regions. Parasites and Vectors
Levi, T., Keesing, F., Holt, R.D., Barfield, M., Ostfeld, R.S. 2016. Quantifying dilution and amplification in a community of hosts for tick-borne pathogens. Ecological Applications
Ostfeld, R.S., Levi, T., Jolles, A., Martin, L.B., Hosseini, P.R., Keesing, F. 2014. Life history and demographic drivers of reservoir competence for three tick-borne zoonotic pathogens. Plos ONE. 9(9) e107387
Pacific salmon are fantastic (and tasty) animals. They are born in freshwater, migrate to sea, and return to their natal stream where they spawn and die. They provide an enormous pulse of marine derived nutrients to terrestrial systems. Predators, and particularly bears, rely heavily on salmon. Humans also rely on salmon for livelihoods and food. My research evaluates salmon management goals and their impact on wildlife by quantifying the level of competition between salmon fisheries and wildlife users of salmon. Fishery certifiers such as the Marine Stewardship Council state that fisheries must have acceptable impacts on the ecosystem, but quantitative methods to determine whether these goals are being met are still lacking. I am working to develop these goals for Pacific salmon fisheries.
In addition to quantitative research, our fieldwork near Haines, Alaska quantifies the importance of salmon carcasses to terrestrial wildlife, and the ecosystem effects of abundant salmon-supported bears. (Original artwork by Yiwei Wang)
Relevant Publications
Levi. T., Allen, J. M., Bell, D., Joyce, J. Russel, J. R., Tallmon, D. A., Vulstek, S. C., Yahan, Y., Yu, D. W. 2019. Environmental DNA for the enumeration and management of Pacific salmon. Molecular Ecology Resources
Shakeri, Y., White, K.W., Levi, T. 2018. Seed dispersal and resource subsidies from salmon-supported bears to granivores. Ecosphere
Harrer, L.E.F., Levi, T. 2018. The primacy of bears as seed dispersers in salmon-bearing ecosystems. Ecosphere
Adams, M.S., Service, C., Bateman, A., Bourbonnais, M., Artelle, K., Nelson, T., Paquet, P., Levi, T., Darimont, C.T. 2017. Intrapopulation isotopic niche diversity over landscapes; spatial patterns inform conservation of bear-salmon systems. Ecosphere
Wheat, R.E., Lewis, S.B., Wang, Y., Levi, T., Wilmers, C.C. 2017. Intraspecific variation in movement strategies among bald eagles (Haliaeetus leucocephalus) in an anadromous fish system.Movement Ecology
Wheat, R.E., Allen, J.M., Miller, S.D.L, Wilmers, C.C., Levi, T. 2016. Environmental DNA from residual saliva for efficient noninvasive genetic monitoring of brown bears (Ursus arctos). PLoS ONE
Levi, T., Wheat, R., Allen, J.M., Wilmers, C.C. 2015. Differential use of salmon by vertebrate consumers: implications for conservation. PeerJ. 3:E1157
Subsistence hunting provides a crucial food source for rural populations in tropical forests but is often said to be unsustainable. However, previous methods treat sustainability as a binary ‘yes’ or ‘no’ question, which is particularly problematic because the answer to that question depends entirely on the spatial scale being considered. To remedy this, my research treats sustainability as an inherently spatial problem. Rather than label hunting as sustainable or not sustainable, I quantify the spatial area where hunting will cause local extirpation, and assess how this area depends on the adoption of firearms, human population growth, the creation of new settlements, hunter effort, and the speed at which animals recolonize hunted areas. Previous methods were also limited to assessing sustainability in a single settlement, but the models that I have developed predict wildlife population densities in space even when hunted by multiple settlements with overlapping hunting ranges and different human population sizes. My models also predict how human harvest rates change as wildlife are depleted, which has implications for the livelihoods of subsistence hunters. To make these methods accessible, I provide software-based tools, including a toolbox for ArcGIS, to assist in managing and mapping the spatial extent of hunting.
I have worked primarily with two large projects. The first is the People vs. Parks project in Manu National Park, Peru where I lived and worked with Matsigenka hunters to monitor hunting behavior and harvest. I recently joined Project Fauna in the Rupununni region of Guyana. Project fauna conducted ambitious wildlife sampling with the help of Macuxi and Wapishana Indians on a massive spatial scale. I use distance sampling and statistical models to assess how wildlife population densities relate to anthropogenic disturbance, such as hunting, versus natural variation in habitat and fruit availability.
Relevant Publications
Sabino-Santos Jr., G., Fernandes, F.F, da Silva, D.J.F., Melo, D.M., da Silva, S.G., São Bernardo, C.S., Filho, M.D.S., Levi, T., Figueiredo, L.T.M., Peres, C.A., Bronzoni, R.V.M, Canale, G.R. In review. Othohantavirus antibodies among phyllostomid bats from the arc of deforestation in Southern Amazonia, Brazil
Wolf, C., Levi, T., Ripple, W.J., Zárrate-Charry, D.A., Betts, M.G. In review. Forest loss within the world’s protected areas
Pedrosa, F., Bercê, W., Levi, T. Pires, M., Galetti, M. In revision. Invasive species promote critical seed dispersal services in defaunated landscapes
Pedrosa, F., Bercê, W., Costa, V.D., Levi, T., Galetti, M. In revision. Large scale agriculture is subsidizing the invasion of wild pigs in Brazil
Betts, M.G., Wolf, C., Ripple, B., Phalan, B., Millers, K., Duarte, A., Butchart, S., Levi, T. 2017. Global forest loss disproportionately erodes biodiversity in intact landscapes. Nature
Ripple, W.J., Chapron, G., Lopez-Bao, J.V., Durant, S.M., Macdonald, D.W., Lindsey, P.A., Bennett, E.L., Beschta, R.L., Bruskotter, J.T., Campos-Arceiz, A., Corlett, R.T., Darimont, C.T., Dickman, A.J., Dirzo, R., Dublin, H.T., Estes, J.A., Everatt, K.T., Galetti, M., Goswami,V.R., Hayward, M.W., Hedges, S., Hoffman, M., Hunter, L.T.B., Kerley, G.I.H., Letnic, M., Levi, T., Maisels, F., Morrison, J.C., Nelson, M.P., Newsome, T.M., Painter, L., Pringle, R.M., Sandom, C.J., Terborgh, J., Treves, A., Valkenburgh, B.V., Vucetich, J.A., Wirsing, A.J., Wallach, A.D., Wolf, C., Woodroffe, R., Young, H., Zhang, Li. 2016. Conserving the World’s Megafauna and Biodiversity: The Fierce Urgency of Now. Bioscience.
Ripple W.J., Abernethy, K., Chapron, G., Levi, T., Lindsey, P.A., Newsome, T.M., Peres, C.A., Wallach, A.D., Wolf, C. 2016. Are we eating the world’s mammals to extinction. Royal Society Open Science
Antunes, A.P., Fewster, R., Venticinque, E.M., Peres, C.A., Levi, T., Rohe, F., Shepard-Jr, G.H. 2016. Empty rivers rather than empty forests: a century of commercial hunting in Amazonia. Science Advances
Yu, D.W., Shepard, G.H., Ohl-Schacherer, J., Levi, T., 2013. Resolviendo el conflicto “parque-personas” en el Manu, con la estrategia “Ocupar la Amazonía”. Groenendijk, J., and A. Tovar editors. Reporte Manu: Pasión por la Investigación en la Amazonía Peruana. San Diego Zoo Global Peru y SERNANP. 466pp
I am interested in the interactions of predator species and the causes and consequences of coexistence versus competitive exclusion. For example, my research explores the possiblity that wolves suppress coyotes, which allows fox populations to increase. This has implications for our understanding of how strongly top predators structure ecosysems. Our current research explores the role of bears in ecosystems, and how the widespread extirpation of brown bears has impacted ecosystems. We have particularly focused on the seed-dispersal services provided by brown bears and are increasingly interested in brown bears as predators.
We participate in a large collaborative project at Starkey Experimental Forest with GPS-collared bears, coyotes, bobcats, cougars, as well as cattle, deer, and elk. This intensive project allows for detailed understanding for how species interact.
Another major focus in recent years has been the ecology and conservation of small forest carnivores in the Pacific Northwest. Pacific fisher, Humboldt marten, and western spotted skunks have been our primary study systems.
Relevant Publications
Pedrosa, F., Bercê, W., Levi, T. Pires, M., Galetti, M. In revision. Invasive species promote critical seed dispersal services in defaunated landscapes
Pedrosa, F., Bercê, W., Costa, V.D., Levi, T., Galetti, M. In revision. Large scale agriculture is subsidizing the invasion of wild pigs in Brazil
Spitz, D.B., Rowland, M., Clark, D.A., Wisdom, M.J., Smith, J.B., Brown, C.L., Levi, T. In press. Non-consumptive behavioral responses and nutritional consequences of elk when avoiding human hunters. Ecosphere
Eriksson, C.E., Moriarty, K.M., Linnell, M.A., Levi, T. 2019. Biotic factors influencing the unexpected distribution of a Humboldt marten population in forested sand dunes. PLoS ONE
Spitz, D., Clark, D., Wisdom, M.J., Rowland, M., Johnson, B., Long, R.A. Levi, T. 2018. Fire history influences large-herbivore behavior at circadian, seasonal, and successional scales. Ecological Applications
Wolf, C., Betts, M. G., Levi. T., Newsome, T. M., Ripple, W. J. 2018. Large species within Carnivora are large carnivores. Royal Society Open Science
Shakeri, Y., White, K.W., Levi, T. 2018. Seed dispersal and resource subsidies from salmon-supported bears to granivores. Ecosphere
Linnell, M.A., Moriarty, K.M., Green, D.S., Levi, T. 2018. Density and population trajectories of coastal marten: a rare and geographically isolated small carnivore. PeerJ
Ostfeld, R.S.*, Levi, T.*, Keesing, F., Oggenfuss, K. Canham, C.D. 2018. Tick-borne disease risk in a forest food web. Ecology*authors contributed equally
Smith, J.A., Thomas, A.C. , Levi, T., Wang, Y., Wilmers, C.C. 2018. DNA metabarcoding reveals human-induced shifts in dietary niche partitioning in a carnivore guild. Oikos
Harrer, L.E.F., Levi, T. 2018. The primacy of bears as seed dispersers in salmon-bearing ecosystems. Ecosphere
White, K.S., Gregovic, D., Levi, T. 2017. Projecting the future of an alpine ungulate under climate change scenarios. Global Change Biology
Adams, M.S., Service, C., Bateman, A., Bourbonnais, M., Artelle, K., Nelson, T., Paquet, P., Levi, T., Darimont, C.T. 2017. Intrapopulation isotopic niche diversity over landscapes; spatial patterns inform conservation of bear-salmon systems. Ecosphere
Ripple, W.J., Chapron, G., Lopez-Bao, J.V., Durant, S.M., Macdonald, D.W., Lindsey, P.A., Bennett, E.L., Beschta, R.L., Bruskotter, J.T., Campos-Arceiz, A., Corlett, R.T., Darimont, C.T., Dickman, A.J., Dirzo, R., Dublin, H.T., Estes, J.A., Everatt, K.T., Galetti, M., Goswami,V.R., Hayward, M.W., Hedges, S., Hoffman, M., Hunter, L.T.B., Kerley, G.I.H., Letnic, M., Levi, T., Maisels, F., Morrison, J.C., Nelson, M.P., Newsome, T.M., Painter, L., Pringle, R.M., Sandom, C.J., Terborgh, J., Treves, A., Valkenburgh, B.V., Vucetich, J.A., Wirsing, A.J., Wallach, A.D., Wolf, C., Woodroffe, R., Young, H., Zhang, Li. 2016. Conserving the World’s Megafauna and Biodiversity: The Fierce Urgency of Now. Bioscience.
Wheat, R.E., Allen, J.M., Miller, S.D.L, Wilmers, C.C., Levi, T. 2016. Environmental DNA from residual saliva for efficient noninvasive genetic monitoring of brown bears (Ursus arctos). PLoS ONE
Ripple W.J., Abernethy, K., Chapron, G., Levi, T., Lindsey, P.A., Newsome, T.M., Peres, C.A., Wallach, A.D., Wolf, C. 2016. Are we eating the world’s mammals to extinction. Royal Society Open Science
Antunes, A.P., Fewster, R., Venticinque, E.M., Peres, C.A., Levi, T., Rohe, F., Shepard-Jr, G.H. 2016. Empty rivers rather than empty forests: a century of commercial hunting in Amazonia. Science Advances
Fragoso, J.M.V., Levi, T., Oliveira, L.F.B., Luzar, J.B., Overman, H., Read, J.M., Silvius, K.M. 2016. Line transect surveys under detect terrestrial mammals: implications for the sustainability of subsistence hunting. PLoS ONE
Peres, C.A., Emilio, T., Schietti, T., Desmoulière, S.J.M, Levi, T. 2016. Dispersal limitation induces long-term biomass collapse in overhunted Amazonian forests. Proceedings of the National Academy of Sciences. 113: 892-897
Beschta, R.L., Painter, L.E., Levi, T., Ripple, W.J. 2016. Long-term aspen dynamics and trophic cascades in Northern Yellowstone. Canadian Journal of Forest Research. 46: 548-556
Ripple, W.J., Newsome, T.M., Wolf, C., Dirzo, R., Everatt, K.T., Galetti, M., Hayward, M.W., Kerley, G.I.H., Levi, T., Lindsey, P.A., Macdonald, D.W., Malhi, Y., Painter, L.E., Sandom, C.J., Terborgh, J., Van Valkenburgh, B. 2015. Collapse of the World’s Largest Herbivores. Science Advances. 1(4): e1400103
Wilmers, C.C., Ram, K., Watson, F.G.R, White, P.J., Smith, D.W., Levi, T. 2013. Climate and vegetation phenology – Predicting the effects of warming temperatures. inWhite, P.J., editor. Yellowstone’s Wildlife in Transition. Harvard University Press
We operate an environmental genetics lab with separate spaces (on distinct floors) for high-DNA and low-DNA applications as well as a biosafety lab for working with pathogens. Major projects include DNA metabarcoding for animal diet analysis and food webs. We have now processed well over 10,000 carnivore scats from across the Pacific Northwest and Alaska.
Environmental DNA in aquatic systems has also been a major focus with a long-term collaborative project with the Chilkoot Indian Association in Alaska to monitor eulachon using eDNA. We are now in our 7th year of monitoring and have demonstrated that eDNA produces a faithful quantitative signature to allow the tribe to affordably monitor rivers for the presence and abundance of eulachon. Also in Alaska, we compared daily weir counts of salmon to daily (or near-daily) eDNA samples and demonstrated a substantial quantitative signal, making rough counts of salmon using eDNA plausible. In this same region, we’ve used traces of DNA from bear saliva to identify individual bears that have fed on salmon carcasses and bear species/sex that consume berries to quantify seed dispersal services.
A major focus of the lab is now the Oregon Biodiversity Genome Project, lead by current student Emily Dziedzic in collaboration with state and federal agencies. Emily is sequencing and assembling the full mitogenome of all aquatic vertebrates and will be developing ‘optimal’ eDNA metabarcoding assays now armed with full information of the genomic library of our species.
Most recently, we have developed a highly sensitive, accurate, and affordable genotyping method adapted from GT-seq for noninvasive genetic samples. We hope that this will help increase the use of noninvasive wildlife research.
Relevant Publications
Eriksson, C.E., Ruprecht, J., Levi, T. In revision. More affordable and effective noninvasive SNP genotyping using high-throughput amplicon sequencing
Ruprecht, J.S., Eriksson, C.E., Forrester, T.D., Clark, D.A., Wisdom, M.J., Rowland, M.M., Johnson, B.K., Levi, T. In review. Integrating spatial capture-recapture models with variable individual identification
Penaluna, B.E., Allen, J.M., Arismendi, I., Levi, T., Garcia, T.S., Walter, J. In review. Better Boundaries: Environmental DNA improves detection of the upper limit of fish distribution in forested streams compared to electrofishing
White, K.W., Breen, J., Britt, M., Levi, T., Merondun, J.B., Martchenko, D., Shakeri, Y., Porter, B., Shafer, A. In review.Extensive field-sampling reveals the uniqueness of a trophy mountain goat population
Roeffler, G.H., Allen, J.M., Massey A.L., Levi, T. In review.Regional metabarcoding of fecal DNA shows that dietary diversification in wolves substitutes for ungulates in an island archipelago
Massey, A.L., Roeffler, G., Vermeul, T., Allen, J.M., Levi, T. In review. Comparison of mechanical sorting and DNA metabarcoding for diet analysis with degraded wolf scats
Pochardt, M., Allen, J.M., Hart, T., Miller, S.D., Yu, D.W., Levi, T. 2020. Environmental DNA facilitates accurate, inexpensive, and multi-year population estimates of millions of anadromous fish. Molecular Ecology Resources
Levi. T., Allen, J. M., Bell, D., Joyce, J. Russel, J. R., Tallmon, D. A., Vulstek, S. C., Yahan, Y., Yu, D. W. 2019. Environmental DNA for the enumeration and management of Pacific salmon. Molecular Ecology Resources
Urbina, J., Chestnut, T., Schwalm, D., Allen, J., Levi, T. 2019. Experimental evaluation of degradation rates of genomic DNA of the pathogen Pseudogymnoascus destructans (Pd) in bat guano. PeerJ
Eriksson, C.E., Moriarty, K.M., Linnell, M.A., Levi, T. 2019. Biotic factors influencing the unexpected distribution of a Humboldt marten population in forested sand dunes. PLoS ONE
Harrer, L.E.F., Levi, T. 2018. The primacy of bears as seed dispersers in salmon-bearing ecosystems. Ecosphere
Wheat, R.E., Allen, J.M., Miller, S.D.L, Wilmers, C.C., Levi, T. 2016. Environmental DNA from residual saliva for efficient noninvasive genetic monitoring of brown bears (Ursus arctos). PLoS ONE
It turns out that bears disperse a LOT of seeds. It’s not just black bears. Brown bears disperse even more seeds at our field site than do black bears! Here is a video for you to enjoy. Each devil’s club berry cluster contains hundreds of berries.
Scientists studying brown bears in Southeast Alaska have been using saliva left behind in half-eaten salmon carcasses to identify individual bears faster and with improved efficiency. Did I mention that nearly 300 fecal samples were also taken for a comparative analysis? Yum! “We found that using bear saliva is not only easier and cheaper as … Continue reading
