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National Genomics Center for Wildlife and Fish Conservation

A scientist crouches near a stream, holding a funnel in the water that is connected to a pump and bucket with tubing.

We need your help! Samples needed for validation of an aquatic invasive species biochip

To validate a biochip panel that will test for 50 of the worst aquatic invaders, we need to test for specificity against closely related, non-target species. We are looking for partners who can contribute tissue samples for this effort. Please see our Sample Wishlist for current needs.

A protocol for collecting environmental DNA samples from streams

eDNA needs to be sampled in a manner that has been tested and found effective and rigorous procedures must be designed to avoid sample contamination. This GTR describes a sampling protocol designed for detecting fish that has been shown to be exceedingly sensitive; no case of field contamination has been detected.
A screenshot of the eDNAtlas map for the Pacific Northwest.

eDNA Story Maps

These story maps include the results map for the eDNAtlas project, which provides spatial information on aquatic species across the United States based on standardized eDNA field sampling.
A researcher in a stream with eDNA sampling equipment.

Black and White and Shed All Over: How eDNA Analysis Can Help to Answer Your Species Questions

Keeping tabs on the whereabouts of invasive or endangered species in the landscape is an important job for managers. Traditionally, species monitoring has often relied on physical observations of organisms in the field, which requires expertise in species identification and can be labor-intensive.
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A scientist leaning over a stream holding a collection funnel in the water.
Katie Zarn collects an eDNA sample from Fossil Creek in Arizona. Photo by Matthew R. Jones.

eDNA

Keeping tabs on the whereabouts of invasive or endangered species is an important job for managers, but it can be a nearly impossible task to accomplish across a vast landscape. Traditionally, species monitoring has relied on physical observations of organisms in the field. These surveys can be labor-intensive, particularly when surveying in remote areas or for organisms that are rare or difficult to find. Today, there is a powerful new approach that can determine the presence of a species simply by sampling a cup of water: environmental DNA (eDNA).

Organisms continually shed cells containing their DNA into their surroundings. For example, DNA in skin cells sloughed from a fish can be found in water, or DNA in plant pollen can be found in the air. That DNA persists in the environment, where it can be collected in an air, soil, or water sample and analyzed for species of interest.

Environmental DNA is major breakthrough in wildlife and fish monitoring. It ties traditional field-based ecology to advanced computational tools and exacting molecular methods, such as quantitative polymerase chain reaction (qPCR), which is able to detect DNA from just a couple cells in an environmental sample. It can reveal important information about species presence or absence more quickly and cost-effectively than traditional sampling techniques. It is particularly useful for detecting organisms in low abundance, like threatened and endangered species or individuals at the leading edge of an invasion. For example, scientists used filtered water samples to detect the spread of invasive feral pigs in the Southwestern United States and Burmese python in Florida. Scientists are using similar techniques in the Rocky Mountains to determine the distribution of endangered bull trout, invasive brook trout, Canada lynx, and wolverine.

This technology has been used primarily to survey for fishes and amphibians. However, samples collected from water, air, and soil all contain DNA of many species, and applications are expanding to other aquatic taxa, such as mollusks and insects, as well as semi-aquatic mammals like river otter and beaver. Environmental DNA is also found in snow tracks allowing reliable species identification of carnivores such as wolverine, fisher, and Canada lynx.

Lab techniques for eDNA analysis vary depending on the specific research question. For example, targeted analysis designed to detect a particular species may be used to detect the presence or absence of a rare species. Nontargeted approaches are less sensitive for individual species, but can be used to answer questions about community diversity or reveal previously unknown members of ecological communities. The National Genomics center is also pioneering a third option, high-throughput qPCR, which completes multiple targeted analyses simultaneously. For example, identifying which species is responsible for a track in snow is one of the many potential application for high-throughput qPCR.

eDNAtlas

A screenshot of the eDNAtlas map for the Pacific Northwest.The eDNAtlas is an open-access database developed through crowd-sourced field surveys that provides precise spatial information on the occurrence locations of aquatic species in the United States. The eDNA samples constituting the database are collected using a standardized field sampling protocol by numerous natural resource agencies and non-governmental organizations partnered with the National Genomics Center for Wildlife and Fish Conservation. The eDNAtlas database contains results from thousands of sites and dozens of species and is updated annually with additional results for a growing list of species. Funding to develop the eDNAtlas database was provided by the National Fish and Wildlife Foundation Bring Back the Natives Program. Additional information can be found here: project background, eDNA sampling grid map, & eDNAtlas interactive results map.

eDNA Assay Development

We have designed and validated over 75 qPCR assays for eDNA applications including both aquatic and terrestrial species. Assays are typically designed on a project-need basis then published in a peer-reviewed journal. We are continually designing and validating new assays and would love to work with you on your species of interest. If you do not see the species you are interested in listed on the Assay List, please contact Tommy Franklin (thomas.franklin@usda.gov) or Mike Young (michael.k.young@usda.gov). 

Assay List

If you do not see the species listed below that you are interested in working with, please do not hesitate to contact Tommy Franklin (thomas.franklin@usda.gov) or Jennifer Hernandez (jennifer.hernandez@usda.gov).

American bullfrog*
American dipper
American eel*
Any salmonid DNA
Any sculpin DNA
Bluehead sucker
Bobcat
Burbot
California/Winged floater
Channel catfish
Chihuahua chub
Chinook salmon
Chum salmon
Chytrid fungus*
Coastal cutthroat trout
Coastal tailed frog
Coho salmon
Columbia slimy sculpin
Common carp*
Coyote
Dolly Varden
Dreissenid mussels*
Fisher
Green sunfish
Grizzly bear
Harlequin duck
Lahontan cutthroat trout
Lake trout
Lampetra spp.
Marten
Mountain lion
Mountain sucker
New Zealand mud snail*
Olympic mudminnow
Oregon chub
Oregon floater
Paiute cutthroat trout
Plains killifish
Plains topminnow
Polar bear
Ranavirus*
Red fox
Rio Grande chub
Rio Grande sucker
Rocky Mountain sculpin
Roundtail chub
Sacramento pikeminnow*
Sauger
Slimy sculpin (Rocky Mountain variant)
Snake River Physa snail
Umpqua chub
Umpqua pikeminnow
Western pond turtle*
Western ridged mussel
Western spadefoot toad
Wood frog*
Yaqui catfish
 
*Validated or modified from a previously published assay
Updated June 2020

Someone off camera holds a bull trout just above water. The trout has a temporary tag attached under its dorsal fin.

The Range-Wide Bull Trout eDNA Project

The bull trout is an Endangerd Species Act-listed species with a historical range that encompasses many waters across the Northwest. Though once abundant, bull trout have declined in many locations and are at risk from a changing climate, nonnative species, and habitat degradation. Informed conservation planning relies on sound and precise information about the distribution of bull trout in thousands of streams, but gathering this information is a daunting and expensive task. To overcome this problem, we coupled 1) predictions from the range-wide, spatially precise Climate Shield model on the location of natal habitats of bull trout with 2) a sampling template for every 8-digit hydrologic unit in the historical range of bull trout, based on the probability of detecting bull trout presence using environmental DNA (eDNA) sampling (McKelvey et al. 2016). The template consists of a master set of geospatially referenced sampling locations at 1-km intervals within each cold-water habitat. We also identified sampling locations at this same interval based on the U.S. Fish and Wildlife Service's designation of critical spawning and rearing habitat. Based on field tests of eDNA detection probabilities conducted by the National Genomics Center for Wildlife and Fish Conservation, this sampling approach will reliably determine the presence of populations of bull trout, as well as provide insights on non-spawning habitats used by adult and subadult fish. The result will be a rapid, robust, and repeatable range-wide assessment of natal habitats of this species. Additional information can be found here: project background & interactive map of bull trout eDNA survey results

eDNA from Snow-tracks

The management of rare species is a conservation priority worldwide, but this task is made difficult by detection errors in population surveys. Both false positive (misidentification) and false negative (missed detection) errors are prevalent in surveys for rare species and can affect resulting inferences about their population status or distribution. In 2018, we developed qPCR assays for Canada lynx, fisher, and wolverine and validated eDNA sampling techniques for identifying DNA from these rare carnivore species in snow-tracks (see Franklin et al. 2019). We are currently expanding this research to include additional species such as bobcats, coyotes, grizzly bears, martens, mountain lions, and red foxes. Further, we are finalizing a snow track collection and filtering protocol and continuing to investigate detection probabilities. These methods have the potential to revolutionize winter surveys for rare species in terrestrial settings by reducing or eliminating misidentifications and missed detections due to the sensitivity of well designed qPCR assays. Partners include: Idaho Department of Fish and Game, MPG Ranch, Woodland Park Zoo, USFS Regions 1 & 4, and USFS Pacific Northwest Research Station. 

A flow chart showing the steps for using eDNA in eradication from the featured publication.
A guide for using eDNA methods to assist invasive fish eradication in streams. From Carim et al, 2020.

 

Sampling Protocols and Forms

The documents listed here provide necessary information for collecting environmental DNA samples from streams and snow tracks while avoiding sample contamination.

Selected Publications

A full list of searchable NGC publications can be found here.

  1. Carim, K. J.; Bean, N. J.; Connor, J. M.; Baker, W. P.; Jaeger, M.; Ruggles, M. P.; McKelvey, K. S.; Franklin, T. W.; Young, M. K.; Schwartz, M. K. 2020. Environmental DNA sampling informs fish eradication efforts: Case studies and lessons learned. North American Journal of Fisheries Management. 40: 488-508.
  2. Franklin, Thomas W.; McKelvey, Kevin S.; Golding, Jessie D.; Mason, Daniel H.; Dysthe, Joseph C.; Pilgrim, Kristine L.; Squires, John R.; Aubry, Keith B.; Long, Robert A.; Greaves, Samuel E.; Raley, Catherine M.; Jackson, Scott; MacKay, Paula; Lisbon, Joshua; Sauder, Joel D.; Pruss, Michael T.; Heffington, Don; Schwartz, Michael K. 2019. Using environmental DNA methods to improve winter surveys for rare carnivores: DNA from snow and improved noninvasive techniques. Biological Conservation. 229: 50-58.
  3. Dysthe, Joseph C.; Rodgers, Torrey; Franklin, Thomas W.; Carim, Kellie J.; Young, Michael K.; McKelvey, Kevin S.; Mock, Karen E.; Schwartz, Michael K. 2018. Repurposing environmental DNA samples - detecting the western pearlshell (Margaritifera falcata) as a proof of concept. Ecology and Evolution. 8: 2659-2670.
  4. Wilcox, Taylor M.; Zarn, Katherine E.; Piggott, Maxine P.; Young, Michael K.; McKelvey, Kevin S.; Schwartz, Michael K. 2018. Capture enrichment of aquatic environmental DNA: A first proof of concept. Molecular Ecology Resources. 18: 1392-1401.
  5. McKelvey, K. S.; Young, M. K.; Knotek, W. L.; Carim, K. J.; Wilcox, T. M.; Padgett-Stewart, T. M.; Schwartz, M. K. 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.

eDNA Services

The NGC provides a variety of services to facilitate eDNA sampling. These include:

Sample analysis. Samples that have been collected using established protocols may be processed at the NGC for species that have quantitative PCR (qPCR) assays developed at the NGC or that have been developed elsewhere and used by the NGC previously. For aquatic species, our standard service includes assistance in determining an appropriate sampling design to meet your information needs, providing sampling materials (e. g. “kits”, pumps, and batteries) sufficient to complete the design, qPCR based species analysis for one or more species, uploading of results to the eDNAtlas, and sample archiving. We offer similar services for collection of carnivore DNA from snow tracks.

Assay development. Assay development is often required prior to qPCR-based eDNA analysis because species of interest are often local endemic species for which no assays have previously been developed. While fairly standard, assay development is a collaborative process between the investigator and the NGC: tissue samples must be obtained for the target species to facilitate in vitro testing, and environmental samples must be taken in both known positive and known negative locations to test field efficacy. 

Training. We will travel to locations to provide hands-on training for field crews on how to use specific field protocols.

If you are interested in eDNA services through the NGC and pricing estimates please contact ngc@usda.gov.

Working with Us

If you would like to propose a project using eDNA, please contact Tommy Franklin (thomas.franklin@usda.gov) or Mike Young (michael.k.young@usda.gov). 

If you would like to borrow equipment for eDNA sampling, please contact Jennifer Hernandez (jennifer.hernandez@usda.gov).