Project

The Aquatic eDNAtlas Project

Goal: Aquatic environmental DNA (eDNA) sampling is rapidly transforming our ability to describe and monitor biological communities. Adoption of this sampling technology is occurring broadly across many natural resource organizations and now results in thousands of new samples being collected each year in rivers, streams, lakes, ponds, springs, and wetlands. To reduce redundancy and maximize data sharing among organizations, the National Fish & Wildlife Foundation commissioned the Aquatic eDNAtlas project to develop a comprehensive interagency database, sampling template maps, and a website to ensure standardization of data collections while providing access to results from samples collected in association with the National Genomics Center for Wildlife and Fisheries Conservation (https://www.fs.fed.us/rmrs/groups/national-genomics-center-wildlife-and-fish-conservation). Results describing species occurrence are posted to the website after meeting stringent field and laboratory QA/QC procedures and can be downloaded using dynamic ArcGIS Online mapping tools in geospatial database formats with accompanying metadata. The eDNAtlas website and database were launched in August 2018 (https://www.fs.fed.us/rm/boise/AWAE/projects/the-aquatic-eDNAtlas-project.html) with approximately 8,000 samples collected by dozens of agencies for a variety of purposes across the western U.S. The database contains information for ~30 species although many samples are currently being processed. Species assays and results for an additional 50 species are under development and new data will be regularly added to the website as results become available and the project expands to include partner agencies in the eastern U.S. Precise species occurrence data from the eDNAtlas website has many uses, including species status assessments, trend monitoring, distribution modeling, detection and tracking of nonnative species invasions or removal efforts, and assessments of habitat restoration efforts. For more information please visit the eDNAtlas website which contains detailed documentation regarding protocols, supporting science, and contact information for scientists that can assist those interesting in conducting new eDNA surveys and contributing to the eDNAtlas.

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Daniel J Isaak
Daniel J Isaak
added an update
The 2021 eDNAtlas database update was published on June 30 with thousands of new samples results for the U.S.
Just sending word regarding the 2021 update of species occurrence results to the Aquatic eDNAtlas, which is an open-access, crowd-sourced database being jointly developed by dozens of natural resource agencies across the eastern and western U.S. The database at the eDNAtlas Project website (https://www.fs.fed.us/rm/boise/AWAE/projects/the-aquatic-eDNAtlas-project.html) now hosts results for 17,246 eDNA samples at stream, river, lake, pond, and wetland sites, with thousands of additional samples currently being processed at the lab for future database updates. The database is updated annually and currently contains occurrence records for 72 species of fish, mussels, amphibians, reptiles, and even a few mammals, with eDNA markers under development for another 101 species to facilitate future survey efforts.
Species occurrence results in the eDNAtlas are processed through the National Genomics Center for Wildlife and Fish Conservation (NGC), which is a science collaborative within the Rocky Mountain Research Station of the U.S. Forest Service. All field samples were collected using the same standardized field protocol (https://www.fs.usda.gov/treesearch/pubs/52466), are properly georeferenced to reaches in the National Hydrology Dataset (https://www.usgs.gov/core-science-systems/ngp/national-hydrography), are accompanied by comprehensive metadata, and are easily downloadable as shapefile geodatabases using this nifty ArcGIS dynamic mapping tool (https://usfs.maps.arcgis.com/apps/webappviewer/index.html?id=b496812d1a8847038687ff1328c481fa). The website also contains information about the peer-reviewed publications supporting aquatic eDNA science and species-specific markers, a predefined national sampling grid at 1-km resolution for rivers and streams to facilitate planning new eDNA surveys, and contact information for project staff to assist those interesting in collecting samples to contribute to the eDNAtlas effort. Brief and easily readable descriptions of the Atlas project and example basin inventory efforts are contained in the attached summary papers.
The original funding to develop the eDNAtlas database was provided by the National Fish and Wildlife Foundation Bring Back the Natives Program. The database was developed to increase the efficiency & cost-effectiveness of collecting & sharing data among agencies as eDNA sampling becomes widespread and because concrete and precise information about species distributions is fundamental to addressing many questions about the status and trends of popular sport-fishes, sensitive species, and invasive species. If you have additional questions, please contact any of us & forward this email to others that may be interested in eDNA sampling of aquatic environments.
Best regards, Dan Isaak, Mike Young, Mike Schwartz, Taylor Wilcox, Kevin McKelvey, Jennifer Hernandez, Tommy Franklin, Joe Dysthe, Kristine Pilgrim, Gwynne Chandler, Dave Nagel, Sherry Wollrab, Kellie Carim, Sharon Parkes-Payne, Dona Horan
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  • 28 Reads
Daniel J Isaak
Daniel J Isaak
added an update
7/31/2020 Update. The Aquatic eDNAtlas Project: Database update published online with thousands of additional species occurrence results
Hi Everyone, Just sending word regarding the latest update of species occurrence results to the eDNAtlas, which is an open-access, crowd-sourced database being jointly developed by dozens of natural resource agencies across the U.S. The database at the eDNAtlas Project website (https://www.fs.fed.us/rm/boise/AWAE/projects/the-aquatic-eDNAtlas-project.html) now hosts results for 12,753 species determinations at more than 14,000 unique stream & river sites, with thousands of additional samples currently being processed at the lab for posting to the website in future updates. The database is updated biannually and currently contains occurrence records for 53 species with eDNA markers under development for another 50 species to facilitate future survey efforts.
Species occurrence results in the eDNAtlas are processed through the National Genomics Center for Wildlife and Fish Conservation (NGC), which is a science collaborative within the Rocky Mountain Research Station of the U.S. Forest Service. All field samples were collected using the same standardized field protocol (https://www.fs.usda.gov/treesearch/pubs/52466), are properly georeferenced to reaches in the National Hydrology Dataset (https://www.usgs.gov/core-science-systems/ngp/national-hydrography), are accompanied by comprehensive metadata, and are easily downloadable as shapefile geodatabases using this nifty ArcGIS dynamic mapping tool (https://usfs.maps.arcgis.com/apps/webappviewer/index.html?id=b496812d1a8847038687ff1328c481fa). The website also contains information about the peer-reviewed publications supporting aquatic eDNA science and species-specific markers, a predefined national sampling grid at 1-km resolution for rivers and streams to facilitate planning new eDNA surveys, and contact information for project staff to assist those interesting in collecting samples to contribute to the eDNAtlas effort.
Brief and easily readable descriptions of the Atlas project and several example basin inventory efforts are contained in the attached briefing papers. Also attached is a recent paper by Wilcox describing a new high-throughput qPCR technique that enables multiple species occurrence determinations (10, 20, or more species) to be obtained simultaneously from an eDNA sample, while maintaining the specificity and sensitivity that single species qPCR is known for. The new high-throughput qPCR technique also doesn’t cost a lot more than single-species qPCR, so on a per species basis is actually cheaper.
The other noteworthy item embedded in this release of the eDNAtlas database is the huge number of Pacific lamprey results that are now available across a significant portion of the species range in OR/WA/ID. Kellie Carim (kellie.carim@usda.gov) at the NGC has done a great job of organizing and promulgating the regional eBLIMP (https://www.researchgate.net/project/eBLIMP-The-eDNA-Basinwide-Lamprey-Inventory-Monitoring-Project) lamprey project the last few years, & hundreds of additional sites are scheduled to be sampled for lamprey again this summer to provide an up-to-date status assessment for this species of concern. If you are interested in surveying for lamprey in your streams, please contact Kellie.
Funding to develop the eDNAtlas database was provided by the National Fish and Wildlife Foundation Bring Back the Natives Program. The database was developed to increase the efficiency & cost-effectiveness of collecting & sharing data among agencies as eDNA sampling becomes widespread and because concrete and precise information about species distributions is fundamental to addressing many questions about the status and trends of popular sport-fishes, sensitive species, and invasive species. If you have additional questions, please contact any of us & forward this email to others that may be interested in eDNA sampling of aquatic environments.
Best regards, Dan Isaak, Mike Young, Mike Schwartz, Taylor Wilcox, Kevin McKelvey, Jennifer Hernandez, Tommy Franklin, Joe Dysthe, Kristine Pilgrim, Gwynne Chandler, Dave Nagel, Sherry Wollrab, Kellie Carim, Sharon Parkes-Payne, Dona Horan
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  • 54 Reads
Daniel J Isaak
Daniel J Isaak
added an update
new multispecies assay technique for qPCR samples
Significant new paper describing cost effective, multi-species qPCR technique by several of the eDNAtlas project collaborators. this will significantly drive down per-species costs for results and help leverage new information from the eDNAtlas database archive, which now houses 17,000+ samples.
Wilcox, T.M., McKelvey, K.S., Young, M.K., Engkjer, C., Lance, R.F., Lahr, A., Eby, L.A. and Schwartz, M.K., Parallel, targeted analysis of environmental samples via high‐throughput quantitative PCR. Environmental DNA. DOI: 10.1002/edn3.80
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  • 45 Reads
Daniel J Isaak
Daniel J Isaak
added an update
2019 eDNAtlas database update & expansion to cover eastern and western U.S.
Hi Everyone, Just sending a heads up regarding the late 2019 eDNAtlas database update, which now hosts results for 16,708 species determinations at 11,018 unique stream & river sites (ponds, lakes & spring results coming this winter) for dozens of species and is updated biannually with additional results for a growing list of species (29 species at present with another ~50 species in the future). Most samples hosted at the website were collected in the western U.S in the last few years but the geospatial database framework has now been developed & expanded to the eastern U.S. to encompass the rest of the country. eDNA species occurrence results were processed through the National Genomics Center for Wildlife and Fish Conservation (NGC), which is a science collaborative within the Rocky Mountain Research Station of the U.S. Forest Service. All field samples were collected using the same standardized field protocol (https://www.fs.usda.gov/treesearch/pubs/52466), are properly georeferenced to reaches in the National Hydrology Dataset (https://www.usgs.gov/core-science-systems/ngp/national-hydrography), are accompanied by comprehensive metadata, and are easily downloadable as geodatabases using these nifty ArcGIS dynamic mapping tools (https://www.fs.fed.us/rm/boise/AWAE/projects/eDNAtlas/the-edna-atlas-results.html). The website also contains information about the peer-reviewed publications supporting aquatic eDNA science and the design of species-specific markers, a predefined national sampling grid at 1-km resolution to facilitate planning of new eDNA surveys, and contact information for project staff that are willing and able to assist partners in designing new eDNA sample surveys. Additional details about the eDNAtlas are available at the project website, are summarized in the attached briefing paper, and this slide presentation (https://www.fs.fed.us/rm/boise/AWAE/projects/stream_temp/downloads/18eDNAtlas-for-North-America_AtlanticCity_AFS.pdf).
Funding to develop the eDNAtlas database was provided by the National Fish and Wildlife Foundation Bring Back the Natives Program. The database was developed to increase the efficiency & cost-effectiveness of collecting & sharing data among agencies as eDNA sampling becomes widespread and because concrete and precise information about species distributions is fundamental to addressing many questions about the status and trends of popular sport-fishes, sensitive species, and invasive species. If you have additional questions, please contact any of us & forward this email to others that may be interested in eDNA sampling of aquatic environments.
Best regards, Dan Isaak, Mike Young, Mike Schwartz, Taylor Wilcox, Kevin McKelvey, Dave Nagel, Tommy Franklin, Joe Dysthe, Kristine Pilgrim, Gwynne Chandler, Sherry Wollrab, Kellie Carim, Sharon Parkes-Payne, Dona Horan, Jennifer Hernandez
p.s., Below are a few initial examples demonstrating how data from the eDNAtlas database can be used (accompanying datasets are permanently archived & downloadable from the database) but for a comprehensive list of the rapidly expanding literature on aquatic eDNA science and applications, see this bibliography maintained by Washington State University (https://labs.wsu.edu/edna/references/).
eDNAtlas Data Applications:
1. Dysthe JC, Rodgers T, Franklin TW, Carim KJ, Young MK, McKelvey KS, Mock KE, Schwartz MK. 2018. Repurposing environmental DNA samples—detecting the western pearlshell (Margaritifera falcata) as a proof of concept. Ecology and Evolution, 8:2659–2670.
2. Franklin, T.W., Dysthe, J.C., Golden, M., McKelvey, K.S., Hossack, B.R., Carim, K.J., Tait, C., Young, M.K., and Schwartz, M.K. 2018. Inferring habitat occupancy of the western toad (Anaxyrus boreas) species complex using environmental DNA. Global Ecology and Conservation, Doi: 10.1016/j.gecco.2018.e00438.
3. Isaak, D.J., Young, M.K., McConnell, C., Roper, B.B., Archer, E.K., Staab, B., Hirsch, C., Nagel, D.E., Schwartz, M.K. and Chandler, G.L., 2018. Crowd-sourced databases as essential elements for Forest Service partnerships and aquatic resource conservation. Fisheries, 43: 423-430.
4. McKelvey KS, Young MK, Knotek WL, Carim KJ, Wilcox TM, Padgett-Stewart TM, Schwartz MK. 2016. Sampling large geographic areas for rare species using environmental DNA: a study of bull trout Salvelinus confluentus occupancy in western Montana. Journal of Fish Biology, 88:1215-1222.
5. Rubenson, E.S., and J.D. Olden 2019. An invader in salmonid rearing habitat: current and future distributions of smallmouth bass (Micropterus dolomieu) in the Columbia River Basin. Canadian Journal of Fisheries and Aquatic Sciences, Doi: 10.1139/cjfas-2018-0357.
6. Wilcox, T.M., Young, M.K., McKelvey, K.S., Isaak, D.J., Horan, D.L. and Schwartz, M.K., 2018. Fine-scale environmental DNA sampling reveals climate-mediated interactions between native and invasive trout species. Ecosphere 9: e02500.
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  • 75 Reads
Daniel J Isaak
Daniel J Isaak
added a research item
Daniel J Isaak
Daniel J Isaak
added a research item
Fine-scale environmental DNA sampling reveals climate-mediated interactions between native and invasive trout species
Article
  • Nov 2018
It is widely recognized that biotic interactions may act as important mediators of species responses to climate change. However, collecting the abiotic and biotic covariates at the resolution and extent needed to reveal these interactions from species distribution models is often prohibitively expensive and labor-intensive. Here we used crowd-sourced environmental DNA sampling-the inference of species presence from genetic material in the environment-and high-resolution habitat covariates across 630 sites over an area of nearly 10,000 km 2 to build an accurate species distribution model (AUC = 0.96; prediction accuracy = 0.90) for bull trout in cold-water habitats that incorporates fine-scale, context-dependent interactions with invasive brook trout. We then used this model to project possible climate change and brook trout invasion scenarios for bull trout forward in time. Our environmental DNA sampling results were concordant with traditional electrofishing samples in the basin and revealed species patterns that were consistent with previous studies: Bull trout were positively associated with larger stream sizes and negatively associated with high brook trout abundances. However, our modeling also revealed an important nuance: At high abundance, brook trout appear to exclude bull trout from small streams, even those below the thermal optima for brook trout. Climate projections suggest a loss of suitable bull trout habitat as streams warm and summer flows decrease, which could make deleterious interactions with brook trout more common in the future. Where brook trout are invading bull trout habitats, streams that are both large and cold are most likely to provide native bull trout with long-term refuges.
Daniel J Isaak
Daniel J Isaak
added an update
eDNAtlas website is live as of 8/9/18
The eDNAtlas website is live and contains a plethora of information pertaining to aquatic eDNA sampling as well as results for species presence/absence at thousands of sites. New results will be added regularly as they become available. here is the website link https://www.fs.fed.us/rm/boise/AWAE/projects/the-aquatic-eDNAtlas-project.html
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  • 194 Reads
Daniel J Isaak
Daniel J Isaak
added a research item
Crowd‐Sourced Databases as Essential Elements for Forest Service Partnerships and Aquatic Resource Conservation
Article
  • Sep 2018
High‐quality information is needed for conservation and management of aquatic resources on lands administered by the Forest Service. Information is ultimately derived from data so the Forest Service maintains a series of databases that are used to describe the status and trends of aquatic habitats and biota. Those databases are spatially explicit and are crowd‐sourced, meaning that distributed networks of professionals and technicians operating throughout the National Forest System collect stream and biological measurements which are stored in central repositories. How those databases are developed is evolving and ranges from agency‐specific endeavors to collaborative projects that involve dozens of natural resource organizations and extensive user‐communities throughout the U.S. The rate of data collection is accelerating and databases now often encompass millions of records, so proper archiving and maintenance by information technology specialists is necessary to maximize the utility of data for natural resource planning. Here, we describe several of the aquatic databases maintained by the Forest Service, applications arising from novel syntheses of databases, and the increasingly important roles databases play in collaborative partnerships and cost‐effective stewardship of aquatic resources. This article is protected by copyright. All rights reserved.
Daniel J Isaak
Daniel J Isaak
added an update
Rangewide Bull Trout eDNA project update: New results posted to online database for distribution
Hi Bull-trout-ologists,
Just sending word that the latest results from the Rangewide Bull Trout eDNA project have been posted online at the project website (https://www.fs.fed.us/rm/boise/AWAE/projects/BullTrout_eDNA.html). To view or download the data in a nifty ArcGIS Online mapper, just scroll to the bottom of the webpage and click on the map icon where it says, “Completed bull trout eDNA Survey Results.” There are now results from ~3,000 sites in 5 different states online for your perusal & use as you see fit. The sites were sampled last summer by an army of volunteers from resource agencies and private groups interested in better resolving bull trout distributions. Highlights associated with this database update include finding a few new bull trout populations along the west side of the Bitterroot Basin in Montana and a few new ones in some Wenatchee River tributaries. As I type, things are revving up for this summer’s field sampling blitz that will be at least as large as last year and probably larger by the time the final eDNA is amplified at the lab next winter. On a related matter, our science team is currently in the midst of the geotechnical & database design work needed to implement the much larger Aquatic eDNAtlas & Archive project that will expand online access to crowd-sourced eDNA datasets to encompass all aquatic species throughout the western U.S. & Alaska. When that website & database goes live next winter we anticipate having >10,000 samples online for use by the aquatic community and we will simply update the database annually with new data like we’re now doing for the bull trout project. More details about the eDNAtlas project are in this recent LCC webinar (http://greatnorthernlcc.org/event/941). Please forward this email to those who might be interested &/or drop one of the fine people at the National Genomics Center for Wildlife & Fish Conservation (https://www.fs.fed.us/research/genomics-center/) a line if interested in eDNA sampling aquatic environments near you and being a part of this crowd-sourcing adventure for the western U.S. Best regards, Dan, Mike^2 (NGC), Kevin (NGC), Tommy (NGC), Taylor (NGC), Kristy (NGC), Kellie (NGC), Dave, Dona, Sherry, and Sharon
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  • 364 Reads
Daniel J Isaak
Daniel J Isaak
added an update
Interview with Mike Schwartz at NGC in Yale360 "A Splash of River Water Now Reveals the DNA of All Its Creatures"
http://e360.yale.edu/features/edna-rivers-fish-bull-trout-forest-service
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  • 248 Reads
Daniel J Isaak
Daniel J Isaak
added an update
Recent interview by Oregon Public Radio with Mike Young & other scientists studying aquatic eDNA is available here http://www.opb.org/news/article/edna-stream-science/
"Is 'eDNA' The Next Big Thing For Wildlife Science?"
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  • 223 Reads
Daniel J Isaak
Daniel J Isaak
added an update
This link goes to a recording of a webinar presentation Mike Young & I gave recently for the Conservation Biology Institute...
Building a Climate Shield and Aquatic eDNAtlas to protect biodiversity in the American West
https://consbio.org/products/webinars/building-climate-shield-and-aquatic-ednatlas-protect-biodiversity-american-west
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  • 206 Reads
Daniel J Isaak
Daniel J Isaak
added 9 project references
Daniel J Isaak
Daniel J Isaak
added an update
Here's a 1-page briefing paper that describes the Aquatic eDNAtlas & provides contact information for project scientists if you are interested in learning more...
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  • 198 Reads
Daniel J Isaak
Daniel J Isaak
added a project reference
Daniel J Isaak
Daniel J Isaak
added a project goal
Aquatic environmental DNA (eDNA) sampling is rapidly transforming our ability to describe and monitor biological communities. Adoption of this sampling technology is occurring broadly across many natural resource organizations and now results in thousands of new samples being collected each year in rivers, streams, lakes, ponds, springs, and wetlands. To reduce redundancy and maximize data sharing among organizations, the National Fish & Wildlife Foundation commissioned the Aquatic eDNAtlas project to develop a comprehensive interagency database, sampling template maps, and a website to ensure standardization of data collections while providing access to results from samples collected in association with the National Genomics Center for Wildlife and Fisheries Conservation (https://www.fs.fed.us/rmrs/groups/national-genomics-center-wildlife-and-fish-conservation). Results describing species occurrence are posted to the website after meeting stringent field and laboratory QA/QC procedures and can be downloaded using dynamic ArcGIS Online mapping tools in geospatial database formats with accompanying metadata. The eDNAtlas website and database were launched in August 2018 (https://www.fs.fed.us/rm/boise/AWAE/projects/the-aquatic-eDNAtlas-project.html) with approximately 8,000 samples collected by dozens of agencies for a variety of purposes across the western U.S. The database contains information for ~30 species although many samples are currently being processed. Species assays and results for an additional 50 species are under development and new data will be regularly added to the website as results become available and the project expands to include partner agencies in the eastern U.S. Precise species occurrence data from the eDNAtlas website has many uses, including species status assessments, trend monitoring, distribution modeling, detection and tracking of nonnative species invasions or removal efforts, and assessments of habitat restoration efforts. For more information please visit the eDNAtlas website which contains detailed documentation regarding protocols, supporting science, and contact information for scientists that can assist those interesting in conducting new eDNA surveys and contributing to the eDNAtlas.
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  • 115 Reads
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