Source: UNIVERSITY OF ILLINOIS submitted to
ADVANCING ENVIRONMENTAL DNA [EDNA] TOOLS FOR MONITORING INVASIVE AND IMPERILED FRESHWATER SPECIES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
Reporting Frequency
Annual
Accession No.
1008988
Grant No.
(N/A)
Project No.
ILLU-875-926
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Jan 12, 2016
Project End Date
Sep 30, 2020
Grant Year
(N/A)
Project Director
Larson, ER.
Recipient Organization
UNIVERSITY OF ILLINOIS
2001 S. Lincoln Ave.
URBANA,IL 61801
Performing Department
Natural Resources & Environmental Sciences
Non Technical Summary
We believe that eDNA has enormous potential to transform the routine monitoring of organisms at low population abundances, whether for the early detection of invasive species or the management and conservation of imperiled species. However, to date, statistical and modeling interpretation of eDNA data has not necessarily kept pace with rapid laboratory advancements that are moving this approach from single species to whole community metabarcoding approaches. My laboratory is well positioned in both spatial modeling (Larson and Olden 2012, Larson et al. 2014) and field and laboratory eDNA techniques (Dougherty et al. in press) to build bridges between these methodologies. Importantly, better statistical and spatial modeling of eDNA data has high capacity to both test and improve upon the credibility of this emerging technique, and further demonstrate its viability to the broader community of field biologists and conservation scientists.
Animal Health Component
0%
Research Effort Categories
Basic
40%
Applied
40%
Developmental
20%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1350399107050%
1350399119050%
Goals / Objectives
Objectives: The overall project objective is to develop capacity for applied uses of eDNA in freshwater ecology and management, while advancing statistical modeling frameworks for the better interpretation of this new type of biodiversity data. Specifically, we will:1) Advance applications of occupancy estimation with detection probability modeling to eDNA data and questions.2) Demonstrate uses of "riverscape" concepts like empirical semivariogram analysis to quantify and explore spatial dependencies between eDNA results in directionally flowing, dendritic stream and river networks.3) Build capacity and technical expertise in field, laboratory, and modeling applications of eDNA for use in applied conservation and management of freshwaters in Illinois and adjacent states.
Project Methods
Field sampling for eDNA of target species will use well-established water sample collection, filtering, and preservation techniques previously used by the PI. Owing to the nature of eDNA sampling, vertebrate animals will not be directly handled in this study. However, if this changes, IACUC approval will be sought through the University of Illinois. Laboratory methods will use single-species PCR or qPCR assays previously applied by the PI lab in studies like Dougherty et al. in press. Statistical modeling of eDNA data will include existing and potentially newly developed tools like occupancy estimation with detection probably, and riverscape "semivariogram" analyses. Novelty of the project is related to combining eDNA with statistical tools that can better handle sources of error and uncertainty from this sampling method, as well as non-independence between some sample locations in river networks owing to eDNA transport.

Progress 01/12/16 to 09/30/20

Outputs
Target Audience:Federal, state, and tribal natural resource managers working on the management of invasive species and the conservation of native species, as well as academic research scientists developing environmental DNA surveillance tools and guidelines for their use. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?This project funded several postdoc, graduate, and undergraduate students working in my laboratory, who developed expertise in field and laboratory methods in eDNA and statistical analysis of this data, many of whom have gone on to careers using these approaches. How have the results been disseminated to communities of interest?We have published eightpeer reviewed journal articles related to this Hatch project, which have together (cumulatively) been cited over 200 times (per Google Scholar) since the first paper in 2016. Several of these are among the most influential papers (per citations) in eDNA research relative to the age of the paper (de Souza et al. 2016, Larson et al. 2017, Rice et al. 2018). Five of the eight papers have been published open access, facilitating their availability to a broad community of managers, scientists, and policy makers. We have directly communicated these results to managers and other researchers using eDNA methodologies. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? We advanced applications of occupancy estimation with detection probeling modeling to eDNA data and questions through the publications de Souza et al. 2016, Rice et al. 2018, and Kessler et al. 2018. We demonstrated uses of "riverscape" concepts for eDNA data in directionally flowing, dendritic stream and river networks in Rice et al. 2018 and Kessler et al. 2018. We built substantial capacity and technical expertisein eDNA applications for a number of postdoctoral, graduate, and undergraduate students over the life of the project.

Publications

  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Kessler, E.J., K.T. Ash, S. Barratt, E.R. Larson and M.A. Davis. 2020. Radio telemetry reveals effects of upstream biomass and UV exposure on environmental DNA occupancy and detection for a large freshwater turtle. Environmental DNA. 2(1):13-23.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Curtis, A.N. and E.R. Larson. 2020. No evidence that crayfish carcasses produce detectable environmental DNA (eDNA) in a stream enclosure experiment. PeerJ e9333.
  • Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Curtis, A.N., E.R. Larson and M.A. Davis. 2021. Field storage of water samples affects measured environmental DNA concentration and detection. Limnology. (In Press).


Progress 10/01/18 to 09/30/19

Outputs
Target Audience:Target audiences were government agencies including the Alabama Natural Heritage Program, the U.S. Fish and Wildlife Service, the California Department of Fish and Wildlife, the Idaho Department of Fish and Game, the Illinois Department of Natural Resources, and non-profits like the Nature Conservancy. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?One PhD student (Amanda Curtis) and one undergraduate reseaercher (George Balto) have been trained under the project in 2019. A departed postdoc (Kurt Ash) worked on this project in late 2018 and early 2019, before starting a new postdoc on related topics at the University of Tennessee. How have the results been disseminated to communities of interest?We have published seven total papers (past progress reports) related to this Hatch Project, and had a high volume of presentations at scientific conferences to stakeholders in this past year (2019). What do you plan to do during the next reporting period to accomplish the goals?I anticipate that two eDNA papers will be published from my lab group in 2020. Specifically, one onthe the persistence of eDNA from animal carcasses in streams, and one on the role of stream flow or discharge on diluting eDNA concentrations. I anticipate two or three conference presentations on eDNA methodologies at conferences like the Midwest Fish and Wildlife Conference and Society for Freshwater Science.

Impacts
What was accomplished under these goals? We published one paper (in press) and gave a large number of conference presentations on in-progress work, that we anticipate will be published in summer 2020. We completed field research on a Hatch-related proejct, and leveraged our eDNA research expertise into a new project on Department of Defense lands at Ft. Polk, Louisiana.

Publications

  • Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Curtis, A.N., J.S. Tiemann, S.A. Douglas, M.A. Davis and E.R. Larson. 2019. Should I stay or should I flow? The clash between Corbicula eDNA and stream flow. Ecological Society of America Meeting, Louisville, KY.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Tiemann, J.S., A.N. Curtis, S.A. Douglass, M.A. Davis and E.R. Larson. 2019. Should I say or should I flow? The clash between Corbicula e-DNA and stream flow. Freshwater Mollusk Conservation Society Symposium, San Antonio, TX.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Curtis, A.N., M.A. Davis, J. Tiemann, S. Douglass and E.R. Larson. 2019. Should I stay or should I flow? The clash between Corbicula fluminea eDNA and stream flow. Illinois American Fisheries Society Meeting, Champaign, IL.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Larson, E.R., J.A. Drummond, Y. Li, D.M. Lodge, C.A. Gantz, M. Pfrender, M.A. Renshaw and S.P. Egan. 2019. Effect of sample depth and location on environmental DNA performance for fish, zooplankton, and zoobenthos in temperate lakes. Illinois American Fisheries Society Meeting, Champaign, IL.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Balto, G.C., A.N. Curtis and E.R. Larson. 2019. Do stream flow extremes predict abundance of the invasive clam Corbicula fluminea? Illinois American Fisheries Society Meeting, Champaign, IL.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Kessler, E.J., K.T. Ash, S.N. Barratt, E.R. Larson and M.A. Davis. 2019. Can we use environmental DNA to detect alligator snapping turtles (Macrochelys temminckii) at the edge of their range? Midwest Fish and Wildlife Conference, Cleveland, OH.
  • Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Kessler, E.J., K.T. Ash, S. Barratt, E.R. Larson and M.A. Davis. 2019. Radio telemetry reveals effects of upstream biomass and UV exposure on environmental DNA occupancy and detection for a large freshwater turtle. Environmental DNA. (In Press).


Progress 10/01/17 to 09/30/18

Outputs
Target Audience:Target audiences weregovernment agencies including the Alabama Natural Heritage Program, the U.S. Fish and Wildlife Service, the California Department of Fish and Wildlife, the Idaho Department of Fish and Game, the Illinois Department of Natural Resources, and non-profits like the Nature Conservancy. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?One postdoc (Kurt Ash), one PhD student (Amanda Curtis), and one undergraduate researcher (Nicole Principe) have been trained on eDNA laboratory and field methodology during this project in 2018. How have the results been disseminated to communities of interest?Three papers related to the project objectives were published in 2018, and three conference presentations were given on in-progress research. A state wildlife grant from Alabama was awarded to continue some of this work on hellbender and a collaboration with a Department of Defense installation (Ft. Polk, Louisiana) was initiated using eDNA to monitor for five at-risk taxa. What do you plan to do during the next reporting period to accomplish the goals?I anticipate that three papers on environmental DNA methodolgy will be published from my lab group in 2019, specifically on a new eDNA assay for alligator snapping turtle, on the the persistence of eDNA from animal carcasses in streams, and on the role of stream flow or discharge on diluting eDNA concentrations. I anticipate that four conference presentations on eDNA methodology will be made at meetings including the Illinois Chapter of the American Fisheries Society, the Midwest Fish & Wildlife Conference, and the Ecological Society of America.

Impacts
What was accomplished under these goals? Three papers related to the project objectives were published in 2018, and three conference presentations were given on in-progress research. A state wildlife grant from Alabama was awarded to continue some of this work on hellbender, anda collaboration with a Department of Defense installation (Ft. Polk, Louisiana) was initiated using eDNA to monitor for five at-risk taxa.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Rice, C.J., Larson, E.R. and Taylor, C.A. 2018. Environmental DNA detects a rare large river crayfish but with little relation to local abundance. Freshwater Biology, 63(5), pp.443-455.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Cowart, D.A., Breedveld, K.G., Ellis, M.J., Hull, J.M. and Larson, E.R. 2018. Environmental DNA (eDNA) applications for the conservation of imperiled crayfish (Decapoda: Astacidea) through monitoring of invasive species barriers and relocated populations. Journal of Crustacean Biology, 38(3), pp.257-266.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Cowart, D.A., Renshaw, M.A., Gantz, C.A., Umek, J., Chandra, S., Egan, S.P., Lodge, D.M. and Larson, E.R. 2018. Development and field validation of an environmental DNA (eDNA) assay for invasive clams of the genus Corbicula. Management of Biological Invasions.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Godwin, J., L. de Souza, M. Renshaw and E. Larson. 2018. Environmental DNA (eDNA) in the detection and monitoring of aquatic species. Southeast Biodiversity Conservation Forum, Chapel Hill, NC.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Kessler, E.J., K.T. Ash, S.N. Barratt, E.R. Larson and M.A. Davis. 2018. Assessing the efficacy of environmental DNA to detect alligator snapping turtles (Macrochelys temminckii) at the edge of their range. Turtle Survival Alliance Annual Symposium, Ft. Worth, TX.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Larson, E., J. Drummond, Y. Li, D. Lodge, C. Gantz, M. Pfrender, M. Renshaw and S. Egan. 2018. Effects of field sampling design on environmental DNA performance for fish, zooplankton, and zoobenthos in temperate lakes. Society for Freshwater Science Meeting, Detroit, MI.


Progress 10/01/16 to 09/30/17

Outputs
Target Audience:State and federal fish and wildlife management or natural resource conservation agencies, including the Illinois Department of Natural Resources, the U.S. Forest Service (Shawnee National Forest), and the U.S. Fish and Wildlife Service. This work is also relevant to academic researchersat institutions similar to the Universityof Illinois. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Six months of postdoc (Lesley S. de Souza) advised, eight months of postdoc (Kurt Ash) advised. First postdoc hired to permanent job at Field Museum in Chicago. Co-advising MS student on eDNA applications for stream crayfish (Chris Rice) who will defend November 2017. Recruiting PhD student (Amanda Curtis) who began Fall 2017, working on eDNA projects related to and supported by Hatch project. How have the results been disseminated to communities of interest?For the first year of this project, one peer-reviewed eDNA manuscript published, two in review, and several conference presentations on eDNA project given. What do you plan to do during the next reporting period to accomplish the goals?Revise two in-review eDNA papers through to publication, submit November or December 2017 new eDNA paper on USFWS endangered crayfish, write 1-2 new eDNA papers based on Hatch-funded projects during Spring and Summer 2018. Mentor PhD student working on eDNA applications, help mentor postdoc to employment following funding termination in Winter 2018.

Impacts
What was accomplished under these goals? Objective One and Objective Two: Rice et al. in review manuscript used detection porbability modeling for eDNA data and questions, and specifically addresses "riverscape" concepts around eDNA transport in streams and rivers. Additional accomplishments include publication of eDNA paper Larson et al. (2017) and Cowart et al. (2017) manuscript in review. Objective Three: Have trained two postdocs in eDNA modeling applications (first postdoc now permanently employed at Field Museum of Natural History), co-advising Masters student (Rice) on eDNA project that will be defended in November 2017; PhD student started Fall 2017 for dissertation focused on eDNA applications.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Larson, E.R., M.A. Renshaw, C.A. Gantz, J. Umek, S. Chandra, D.M. Lodge and S.P. Egan. 2017. Environmental DNA (eDNA) detects the invasive crayfishes Orconectes rusticus and Pacifastacus leniusculus in large lakes of North America. Hydrobiologia. 800:173-185.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2017 Citation: Larson, E. 2017. An overview of environmental DNA (eDNA) applications to conservation and management of freshwater species. North American Native Fishes Association Convention, Meramec State Park, MO.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2017 Citation: Rice, C., E. Larson and C. Taylor. 2017. The use of environmental DNA for the detection of a narrowly endemic crayfish in a high-discharge, lotic ecosystem. Society for Freshwater Science Meeting, Raleigh, NC.
  • Type: Journal Articles Status: Under Review Year Published: 2017 Citation: Cowart, D.A., M.A. Renshaw, C.A. Gantz, J. Umek, S. Chandra, S.P. Egan, D.M. Lodge and E.R. Larson. 2017. Development and field validation of an environmental DNA (eDNA) assay for the invasive Asian clam, Corbicula fluminea (M�ller, 1774). Management of Biological Invasions.
  • Type: Journal Articles Status: Under Review Year Published: 2017 Citation: Rice, C.A., E.R. Larson and C.A. Taylor. 2017. Downstream transport overwhelms local abundance in explaining environmental DNA detection probability for a rare crayfish. Freshwater Biology.


Progress 01/12/16 to 09/30/16

Outputs
Target Audience:State and federal fish and wildlife management or natural resource conservation agencies, including Illinois Department of Natural Resources, U.S. Forest Service (Shawnee National Forest), and U.S. Fish and Wildlife Service. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Six months of postdoc (Lesley S. de Souza) advised, resulting in published eDNA manuscript in Plos One. Postdoc washired to permanent job conducting natural history surveys at the Field Museum in Chicago. Co-advising MS student on eDNA applications to stream crayfish populations on related project. Hiring undergrad technician on this project in Spring 2017 and recruiting for eDNA Masters student to begin full-time in Fall 2017. How have the results been disseminated to communities of interest?Beyond the published manuscript, public presentations on eDNA to research scientists and agency managers have included: Larson, E.R. 2016. Environmental DNA at the University of Illinois: A new resource for freshwater conservation and management of invasive species. Illinois Water Conference, Champaign, IL. Davis, M.A., E.R. Larson and M.L. Niemiller. 2016. Perceiving the imperceptible: Harnessing environmental DNA as a tool for measuring and monitoring biodiversity in Illinois and beyond. Illinois Department of Natural Resources Seminar Series, Springfield, IL. Larson, E.R., M.A. Renshaw, C.A. Gantz, J. Umek, S. Chandra, S.P. Egan and D.M. Lodge. 2016. A test of environmental DNA for benthic arthropods using the reciprocal invasive ranges of the rusty (Great Lakes) and signal crayfishes (California, Nevada). Society for Freshwater Science Meeting, Sacramento, CA. Larson, E.R., M.M. Dougherty, M.A. Renshaw, C.G. Gantz, J. Umek, S. Chandra, S.P. Egan, D.M. Erickson and D.M. Lodge. 2016. Applying environmental DNA (eDNA) to monitor crayfish populations. Southern Division American Fisheries Society Meeting, Wheeling, WV. de Souza, L.S., J. Godwin, M.A. Renshaw and E.R. Larson. 2016. Applying occupancy estimation with detection probability models to environmental DNA (eDNA) survey data for the flattened musk turtle (Sternotherus depressus) and Black Warrior waterdog (Necturus alabamensis). Southeast Partners in Amphibian and Reptile Conservation Meeting, Camp McDowell, AL. de Souza, L.S., M.A. Davis, M.L. Niemiller and E.R. Larson. 2016. Environmental DNA (eDNA) at the University of Illinois: A new tool for freshwater conservation and management with demonstration to the Eastern Hellbender. Illinois Water Day, Urbana, IL. What do you plan to do during the next reporting period to accomplish the goals?Will submit 2-3 eDNA manuscripts for publication in journals including Hydrobiologia, Conservation Genetics Research, Journal of Fish and Wildlife Management or Knowledge and Management of Aquatic Ecosystems. All will receive NIFA acknowledgment. One manuscript is already drafted, one is in prep, one has lab work underway. Field season collecting eDNA water samples for Endangered Species Act candidate salamanders in Illinois and Alabama. Mentor MS student preparing results of crayfish field surveys toward manuscript preparation and submission. Recruit MS student to begin salamander eDNA project in Alabama.

Impacts
What was accomplished under these goals? 1) First manuscript (de Souza et al. 2016 Plos One) used occupancy estimation with detection probability modeling for novel application to eDNA data and questions. 2) Project in progress with Masters student will apply "riverscape" statistics to data collected during Summer 2016. 3) Have trained one postdoc in eDNA modeling applications, and am presently co-advising a Masters student on field, lab, and statistical applications of eDNA. Undergraduate technician hire anticipated for same in Spring 2017; currently recruiting for Masters student to start on eDNA projects in Fall 2017.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: de Souza, L.S., J.C. Godwin, M.A. Renshaw and E. Larson. 2016. Environmental DNA (eDNA) detection probability is influenced by seasonal activity of organisms. Plos One 11(100:e0165273).