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
