My research program focuses on aquatic invasive species risk assessment, early detection, and management in the West. I coordinate the Rapid Environmental DNA Assessment and Deployment Initiative & Network (READI-Net) project associated with the U.S. Department of the Interior National Early Detection Rapid Response program.
Research Interests
Adam Sepulveda’s research program provides science to inform aquatic invasive species management. Focal elements of his research program include:
- Research to operations of autonomous environmental (e)DNA samplers to improve detection rates
- Development of standardized procedures and statistical approaches to ensure confidence in eDNA results
- Decision support and communication tools to facilitate the uptake of eDNA results by decision-makers
Professional Experience
Research Zoologist, USGS Northern Rocky Mountain Science Center, Bozeman, MT, 2014 – Present
Aquatic Biologist, USGS Northern Rocky Mountain Science Center, Bozeman, MT, October 2010 – 2014
Education and Certifications
Ph.D. Ecology. 2010. University of Montana, Missoula, MT
B.A. Environmental Biology and English. 2002. Dartmouth College, Hanover, NH
Science and Products
READI-Net: Transitioning eDNA aquatic invasive species surveillance from research to actionable science
Environmental DNA (eDNA): Combining Technology and Biology to Detect Aquatic Invasive Species and Pathogens
Using Robots in the River: Biosurveillance at USGS streamgages
High-Resolution, Interagency Biosurveillance of Threatened Surface Waters in the United States
Predicting Climate-Induced Expansions of Invasive Fish in the Pacific Northwest: Implications for Climate Adaptation of Native Salmon and Trout
Western Waters Invasive Species and Disease Research Program
Developing a mechanistic understanding between recent climate patterns and Aquatic Vital Signs in the Greater Yellowstone Network
American bullfrog suppression in the Yellowstone River floodplain
Conservation of native salmonids in South-Central Alaska
An investigation of aquatic invasive species in pristine sites in the Greater Yellowstone Area
Columbia River Basin calcium and pH data accessed on 2022 March 31 for dreissenid mussel risk assessments
Environmental DNA results from dreissenid mussel early detection surveys in Montana, Minnesota, and Wisconsin 2017-2018
Data describing vulnerability of Pacific salmon to invasion of northern pike (Esox lucius) in southcentral Alaska, 2017-2019
Predicted consequences of detecting dreissenid mussel eDNA in Jordanelle Reservoir Utah, 2021
Environmental DNA water sample analyses for smallmouth bass surveillance, Gardner River, Montana, March 2022
Juvenile Smallmouth Bass Sampling from the Yellowstone River, Montana 2016-2019
Environmental DNA data, fish abundance data, and stream habitat data from northwest Montana and northeast Washington and southern British Columbia, Canada
T. bryosalmonae detection in fish and water, DNA sequence, and simple sequence repeat data collected in the Inter-Mountain West from 2011 to 2019
Environmental DNA surveillance data for USGS streamgage sampling in the Columbia River Basin, 2018
Environmental DNA robotic and manual sampling data, Yellowstone and Snake Rivers, 2017-2019
PCR results from dreissenid mussel round robin assay analyses, 2018-2019
Microsatellite data for American bullfrogs in the Yellowstone River Montana, 2013-2017
Critical considerations for communicating environmental DNA science
When are environmental DNA early detections of invasive species actionable?
Toward a national eDNA strategy for the United States
Can big data inform invasive dreissenid mussel risk assessments of habitat suitability?
Invasion risk assessments of habitat suitability provide insight on early detection effort allocation; however, sufficient data are rarely available to inform assessments. We explored tradeoffs of leveraging big data from the National Water Quality Portal (WQP), a standardized water quality database in the United States, to inform calcium- and pH-based risk assessments of invasive mussel (Dreissen
Gaining decision-maker confidence through community consensus: Developing environmental DNA standards for data display on the USGS Nonindigenous Aquatic Species database
An initial assessment of plankton tow detection probabilities for dreissenid mussels in the western United States
The importance of phenology and thermal exposure to early life history success of nonnative Smallmouth Bass in the Yellowstone River
Using structured decision making to evaluate potential management responses to detection of dreissenid mussel (Dreissena spp.) environmental DNA
A framework to integrate innovations in invasion science for proactive management
Time to get real with qPCR controls: The frequency of sample contamination and the informative power of negative controls in environmental DNA studies
Strategic considerations for invasive species managers in the utilization of environmental DNA (eDNA): Steps for incorporating this powerful surveillance tool
Science and Products
- Science
READI-Net: Transitioning eDNA aquatic invasive species surveillance from research to actionable science
USGS researchers are working with the Monterey Bay Aquarium Research Institute to optimize autonomous, robotic samplers for detection of DNA fragments shed by biological threats (BT; invasive species, parasites, pathogens) in our nation’s waters. Finding DNA fragments (a method known as environmental DNA sampling) produced by an emerging BT in water is akin to finding a needle in a haystack—many...ByEcosystems Mission Area, Biological Threats and Invasive Species Research Program, Columbia Environmental Research Center, Eastern Ecological Science Center, Forest and Rangeland Ecosystem Science Center, New York Water Science Center, Northern Rocky Mountain Science Center, Upper Midwest Environmental Sciences Center, Wetland and Aquatic Research Center , Wyoming-Montana Water Science Center, Pacific Northwest Environmental DNA LaboratoryEnvironmental DNA (eDNA): Combining Technology and Biology to Detect Aquatic Invasive Species and Pathogens
Using DNA, USGS researchers are able to detect the presence of invasive species in aquatic ecosystems. The DNA they use is literally floating around in the environment and is called environmental DNA (eDNA) and is a powerful tool for the early detection of invasive species and pathogens, which can cause serious ecological and economic damage. USGS researchers are also combining the use of eDNA...Using Robots in the River: Biosurveillance at USGS streamgages
For more than a decade, researchers around the world have shown that sampling a water body and analyzing for DNA (a method known as eDNA) is an effective method to detect an organism in the water. The challenge is that finding organisms that are not very abundant requires a lot of samples to locate this needle in a haystack. Enter the "lab in a can", the water quality sampling and processing robot...High-Resolution, Interagency Biosurveillance of Threatened Surface Waters in the United States
Advances in information technology now provide large volume, high-frequency data collection which may improve real-time biosurveillance and forecasting. But, big data streams present challenges for data management and timely analysis. As a first step in creating a data science pipeline for translating large datasets into meaningful interpretations, we created a cloud-hosted PostgreSQL database thaPredicting Climate-Induced Expansions of Invasive Fish in the Pacific Northwest: Implications for Climate Adaptation of Native Salmon and Trout
The headwaters of the Columbia River Basin in the Northern Rocky Mountains region is widely recognized as a stronghold for native fish, containing some of the last remaining connected cold-water habitats for species such as the threatened bull trout and native westslope cutthroat trout. However, as temperatures rise, non-native invasive fish species could be poised to prosper in the region as condWestern Waters Invasive Species and Disease Research Program
Researchers at the Northern Rocky Mountain Science Center's Western Waters Invasive Species and Disease Research Program work extensively with federal, state, tribal, regional, and local partners to deliver science to improve early detection and prevention of invasive species and disease; understand complex interactions that promote invasive species and disease, and their impacts (and associated...Developing a mechanistic understanding between recent climate patterns and Aquatic Vital Signs in the Greater Yellowstone Network
The National Park Service Inventory and Monitoring program was established to provide park managers with a broad understanding of the status of park resources using the best available science. This program acknowledges that NPS managers are confronted with complex challenges associated with the management of dynamic landscapes responding to multiple, interacting drivers of change. To provide tools...American bullfrog suppression in the Yellowstone River floodplain
The American bullfrog (Rana catesbeiana) has recently invaded backwater and side-channel habitats of the Yellowstone River, near Billings, Montana. In other regions, bullfrog invasions have been linked to numerous amphibian declines (e.g., Adams and Pearl 2007). Immediate management actions may be able to suppress or eradicate localized populations of bullfrogs because they are present at low...Conservation of native salmonids in South-Central Alaska
The proliferation of introduced northern pike in Southcentral Alaska is an urgent fishery management concern because pike are voracious predators that prey heavily on juvenile salmonids. Eradication of pike is not possible in connected freshwater networks, so managers must develop control methods that reduce pike populations to less destructive numbers. We are using field and bioenergetics...An investigation of aquatic invasive species in pristine sites in the Greater Yellowstone Area
Aquatic invasive species (AIS) are aquatic organisms that move into ecosystems beyond their natural, historic range and cause severe and irreversible damage to the habitats they invade. Most AIS arrive as a direct result of human activity, such as boating and angling. The threat of AIS introduction is especially high in the Greater Yellowstone Area, as humans from all over the world come to see... - Data
Filter Total Items: 16
Columbia River Basin calcium and pH data accessed on 2022 March 31 for dreissenid mussel risk assessments
Calcium and pH data collected at lake, reservoir, impoundment and stream site types in the Columbia River Basin. These data were downloaded from the National Water Quality Portal on 03/31/2022 and cleaned and filtered. We limited calcium data to just those values that described dissolved calcium and total calcium concentrations. We included total calcium to maximize the amount of data available foEnvironmental DNA results from dreissenid mussel early detection surveys in Montana, Minnesota, and Wisconsin 2017-2018
Positive and negative dreissenid mussel DNA quantitiative PCR results from environmental DNA water samples collected in Montana, Wisconsin and Minnesota to assess if environmental DNA can extend the seasonal window for dreissenid mussel early detection.Data describing vulnerability of Pacific salmon to invasion of northern pike (Esox lucius) in southcentral Alaska, 2017-2019
The shapefile contains the data necessary to recreate the analyses used in Jalbert et al., in review, Vulnerability of Pacific salmon to invasion of northern pike (Esox lucius) in southcentral Alaska. Specifically, users will be able to view 1) intrinsic potential model calculations for 5 Pacific salmonids (Chinook, chum, pink, sockeye, and coho salmon) and northern pike and 2) all parent nodes ofPredicted consequences of detecting dreissenid mussel eDNA in Jordanelle Reservoir Utah, 2021
U.S. Geological Survey decision analysts and technical experts worked with representatives from the U.S. Bureau of Reclamation, Utah Division of Wildlife Resources, and Central Utah Water Conservancy District to predict the consequences of alternative actions following environmental DNA detections of dreissenid mussel eDNA in Jordanelle Reservor, Utah. This dataset provides the consequence and modEnvironmental DNA water sample analyses for smallmouth bass surveillance, Gardner River, Montana, March 2022
Environmental DNA results for March 2022 smallmouth bass surveillance in the Gardner River, MontanaJuvenile Smallmouth Bass Sampling from the Yellowstone River, Montana 2016-2019
Field data of age-0 smallmouth bass (Micropterus dolomieu) estimated age, lengths and weights, distribution from field sampling, and results from environmental DNA surveys from the Yellowstone River in Montana. Data were used in conjunction with existing stream temperature data from USGS gages to evaluate if temperature is related to age-0 size at the onset of winter.Environmental DNA data, fish abundance data, and stream habitat data from northwest Montana and northeast Washington and southern British Columbia, Canada
Field estimates of the abundance of two trout species (bull trout and westslope cutthroat trout) in Montana and rainbow trout in Washington and British Columbia were collected in concert with environmental DNA samples (eDNA) to evaluate if eDNA copy numbers correlated with abundance of trout. In addition, stream habitat data including channel units (pools, riffles), substrate, large woody debris,T. bryosalmonae detection in fish and water, DNA sequence, and simple sequence repeat data collected in the Inter-Mountain West from 2011 to 2019
This data release contains molecular diagnostic results and molecular detection of the myxozoan parasite Tetracapsuloides byrosalmonae in fish tissue and environmental DNA samples collected from the inter-mountain West, USA.Environmental DNA surveillance data for USGS streamgage sampling in the Columbia River Basin, 2018
Environmental DNA quantitative PCR results for water samples collected in 2018 at USGS streamgages downstream of Columbia River Basin reservoirs that are considered to have moderate to high suitability for invasive dreissenid mussels. Water samples were tested for DNA of dreissenid mussels, kokanee salmon, and yellow perch. This is version 1.1 of this data release. The Kokanee_Perch_eDNA data anEnvironmental DNA robotic and manual sampling data, Yellowstone and Snake Rivers, 2017-2019
Environmental DNA detection results from samples collected using autonomous water sampling robots and manual approaches. Samples were collected in the Upper Yellowstone River (Montana) and Upper Snake River (Idaho/Wyoming) in 2018 and 2019. Samples were tested for the DNA of the following species: the waterborne protozoa Naegleria spp., the fish pathogen Tetracapsuloides bryosalmonae, Scomber japoPCR results from dreissenid mussel round robin assay analyses, 2018-2019
Real-time PCR results of a round robin evaluation of 5 assays that target dreissenid mussel DNA. Water samples collected from waters with and without dreissenid mussels were analyzed using these five assays in four USGS laboratories. Samples from waters without dreissenid mussels were spiked with known amounts of dreissend DNA.Microsatellite data for American bullfrogs in the Yellowstone River Montana, 2013-2017
We used 7 microsatellites to characterize the invasion genetics of 528 American bullfrogs sampled from the Yellowstone River floodplain (Montana). American bullfrog samples were collected from a 140 km section of the Yellowstone River near Billings, MT in 2013 - 2017. - Multimedia
- Publications
Filter Total Items: 69
Critical considerations for communicating environmental DNA science
The economic and methodological efficiencies of environmental DNA (eDNA) based survey approaches provide an unprecedented opportunity to assess and monitor aquatic environments. However, instances of inadequate communication from the scientific community about confidence levels, knowledge gaps, reliability, and appropriate parameters of eDNA-based methods have hindered their uptake in environmentaAuthorsEric D. Stein, Christopher L. Jerde, Elizabeth Allan, Adam J. Sepulveda, Cathryn Abbott, Melinda R. Baerwald, John Darling, Kelly D Goodwin, Rachel Meyer, Molly Timmers, Peter ThielenWhen are environmental DNA early detections of invasive species actionable?
Environmental DNA (eDNA) sampling provides sensitive early detection capabilities for recently introduced taxa. However, natural resource managers struggle with how to integrate eDNA results into an early detection rapid response program because positive eDNA detections are not always indicative of an eventual infestation. We used a structured decision making (SDM) framework to evaluate appropriatAuthorsAdam J. Sepulveda, Christine E. Dumoulin, Denise L. Blanchette, John Mcphedran, Colin Holme, Nathan Whalen, Margaret Hunter, Christopher M. Merkes, Catherine A. Richter, Matthew Neilson, Wesley Daniel, Devin Nicole Jones, David R. SmithToward a national eDNA strategy for the United States
Environmental DNA (eDNA) data make it possible to measure and monitor biodiversity at unprecedented resolution and scale. As use-cases multiply and scientific consensus grows regarding the value of eDNA analysis, public agencies have an opportunity to decide how and where eDNA data fit into their mandates. Within the United States, many federal and state agencies are individually using eDNA data iAuthorsRyan Kelly, David M. Lodge, Kai Lee, Susanna Theroux, Adam J. Sepulveda, Chris Scholin, Joseph M. Craine, Elizabeth Allan, Krista M. Nichols, Kim M. Parsons, Kelly D Goodwin, Zachary Gold, Francisco P. Chavez, Rachel T. Noble, Cathryn Abbott, Melinda R. Baerwald, Amanda Naaum, Peter Thielen, Ariel Simons, Christopher L. Jerde, Jeffrey J. Duda, Margaret Hunter, John Hagan, Rachel Meyer, Joshua Steele, Mark Stoeckle, Holly Bik, Christopher Meyer, Eric D. Stein, Karen James, Austen Thomas, Elif Demir-Hilton, Molly Timmers, John Griffith, Michael J Weise, Steve WeisbergCan big data inform invasive dreissenid mussel risk assessments of habitat suitability?
Invasion risk assessments of habitat suitability provide insight on early detection effort allocation; however, sufficient data are rarely available to inform assessments. We explored tradeoffs of leveraging big data from the National Water Quality Portal (WQP), a standardized water quality database in the United States, to inform calcium- and pH-based risk assessments of invasive mussel (Dreissen
AuthorsAdam J. Sepulveda, Joshua A. Gage, Timothy Counihan, Anthony F. PrisciandaroGaining decision-maker confidence through community consensus: Developing environmental DNA standards for data display on the USGS Nonindigenous Aquatic Species database
To advance national efforts for the detection and biosurveillance of aquatic invasive species (AIS), we employed a community consensus process to enable the incorporation of environmental DNA (eDNA) detection data into the U.S. Geological Survey’s (USGS) Nonindigenous Aquatic Species (NAS) database (https://nas.er.usgs.gov/eDNA/). Our goal was to identify minimum standards and best practices for tAuthorsJason Ferrante, Wesley Daniel, Jonathan (Contractor) Adam Freedman, Katy E. Klymus, Matthew Neilson, Yale Passamaneck, Christopher B. Rees, Adam J. Sepulveda, Margaret HunterAn initial assessment of plankton tow detection probabilities for dreissenid mussels in the western United States
Early detection of dreissenid mussels (Dreissena polymorpha and D. rostriformis bugensis) is crucial to mitigating the economic and environmental impacts of an infestation. Plankton tow sampling is a common method used for early detection of dreissenid mussels, but little is known about the sampling intensity required for a high probability of early detection using the method. We used implicit dynAuthorsMeaghan Winder, Adam J. Sepulveda, Andrew HoeghThe importance of phenology and thermal exposure to early life history success of nonnative Smallmouth Bass in the Yellowstone River
Knowledge of potential spread by introduced species is critical to effective management and conservation. The Smallmouth Bass Micropterus dolomieu is an example of a fish that has been introduced globally, often spreads after introduction, and has substantial predatory impacts on fish assemblages. Nonnative Smallmouth Bass in the free-flowing Yellowstone River, Montana, have expanded from warmer,AuthorsNicholas S. Voss, Robert K. Al-Chokhachy, Adam J. Sepulveda, Christine E. Verhille, Michael P. Ruggles, Alexander V. ZaleUsing structured decision making to evaluate potential management responses to detection of dreissenid mussel (Dreissena spp.) environmental DNA
Environmental (e)DNA tools are sensitive and cost-effective for early detection of invasive species. However, the uncertainty associated with the interpretation of positive eDNA detections makes it challenging to determine appropriate natural resource management responses. Multiple sources of error can give rise to positive detections of eDNA in a sample when individuals of that species are not prAuthorsAdam J. Sepulveda, David R. Smith, Katherine M O'Donnell, Nathan Owens, Brittany White, Catherine A. Richter, Christopher M. Merkes, Skylar Wolf, Mike Rau, Matthew Neilson, Wesley Daniel, Christine E. Dumoulin, Margaret HunterA framework to integrate innovations in invasion science for proactive management
Invasive alien species (IAS) are a rising threat to biodiversity, national security, and regional economies, with impacts in the hundreds of billions of U.S. dollars annually. Proactive or predictive approaches guided by scientific knowledge are essential to keeping pace with growing impacts of invasions under climate change. Although the rapid development of diverse technologies and approaches haAuthorsCharles B. van Rees, Brian K. Hand, Sean C. Carter, Charles Bargeron, Timothy Joseph Cline, Wesley Daniel, Jason A. Ferrante, Keith Gaddis, Margaret E. Hunter, Catherine S. Jarnevich, Melodie A. McGeoch, Jeffrey T. Morisette, Matthew E. Neilson, Helen E. Roy, Mary Ann Rozance, Adam J. Sepulveda, Rebekah D. Wallace, Diane Whited, Taylor Wilcox, John S. Kimball, Gordon LuikartTime to get real with qPCR controls: The frequency of sample contamination and the informative power of negative controls in environmental DNA studies
Environmental (e)DNA methods have enabled rapid, sensitive and specific inferences of taxa presence throughout diverse fields of ecological study. However, use of eDNA results for decision-making has been impeded by uncertainties associated with false positive tests putatively caused by sporadic or systemic contamination. Sporadic contamination is a process that is inconsistent across samples andAuthorsPatrick Ross Hutchins, Leah Nicole Simantel, Adam J. SepulvedaStrategic considerations for invasive species managers in the utilization of environmental DNA (eDNA): Steps for incorporating this powerful surveillance tool
Invasive species surveillance programs can utilize environmental DNA sampling and analysis to provide information on the presence of invasive species. Wider utilization of eDNA techniques for invasive species surveillance may be warranted. This paper covers topics directed towards invasive species managers and eDNA practitioners working at the intersection of eDNA techniques and invasive species sAuthorsJeffrey Morisette, Stanley Burgiel, Kelsey Brantley, Wesley M. Daniel, John Darling, Jeanette Davis, Thomas W. Franklin, Keith Gaddis, Margaret Hunter, Richard Lance, Tracy Leskey, Yale Passamaneck, Antoinette J. Piaggio, Brian Rector, Adam J. Sepulveda, Melissa Smith, Carol A Stepien, Taylor Wilcox - News