Environmental Genetics

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, TIn 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. 2019Environmental 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. 2019Biotic factors influencing the unexpected distribution of a Humboldt marten population in forested sand dunes. PLoS ONE

Harrer, L.E.F.Levi, T. 2018The 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. 2016Environmental DNA from residual saliva for efficient noninvasive genetic monitoring of brown bears (Ursus arctos). PLoS ONE