Adam Sepulveda, Ph.D.
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
PCR results from dreissenid mussel round robin assay analyses, 2018-2019
Microsatellite data for American bullfrogs in the Yellowstone River Montana, 2013-2017
Environmental DNA results for large and small volume water samples in mesocosm experiments at Creston Fish Hatchery and field surveys in the Flathead River Basin, MT in 2016
Yellowstone Cutthroat Trout and Brown Trout capture-recapture and diet data from Duck Creek, MT in summer and fall (2013-2016)
Environmental DNA detection data of Northern pike (Esox lucius) using a portable, field-based platform and a lab-based platform
Conventional and quantitative PCR assays for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples
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
What do you mean by false positive?
Strategic considerations for invasive species managers in the utilization ofenvironmental DNA (eDNA): Steps for incorporating this powerful surveillance tool
Vulnerability of Pacific salmon to invasion of northern pike (Esox lucius) in Southcentral Alaska
A small proportion of breeders drive American bullfrog invasion of the Yellowstone River floodplain, Montana
Effects of supplemental feeding on the fecal bacterial communities of Rocky Mountain elk in the Greater Yellowstone Ecosystem
Exploration of the 2016 Yellowstone River fish kill and proliferative kidney disease in wild fish populations
Integrating environmental DNA results with diverse data sets to improve biosurveillance of river health
The elephant in the lab (and field): Contamination in aquatic environmental DNA studies
It’s complicated…environmental DNA as a predictor of trout and char abundance in streams
Science and Products
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PCR 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.Environmental DNA results for large and small volume water samples in mesocosm experiments at Creston Fish Hatchery and field surveys in the Flathead River Basin, MT in 2016
Quantitative PCR data from mesocosm experiments and field evaluations comparing coarse filter-large water volume environmental DNA samples vs. fine filter-small water volume environmental DNA samples for detection and quantification of rainbow trout (Oncorhynchus mykiss) and bull trout (Salvelinus confluentus) DNA. Mesocosm experiments took place at the US Fish & Wildlife Service's Creston Fish HaYellowstone Cutthroat Trout and Brown Trout capture-recapture and diet data from Duck Creek, MT in summer and fall (2013-2016)
We collected lengths and weights and diets of Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and brown trout (Salmo trutta) above (Yellowstone cutthroat trout allopatry) and below (Yellowstone cutthroat trout sympatry with brown trout) a natural barrier in Duck Creek, Montana.Environmental DNA detection data of Northern pike (Esox lucius) using a portable, field-based platform and a lab-based platform
We used a portable, field-based approach (hereafter referred to as Biomeme approach) and a standard lab-based approach (hereafter referred to as lab approach) to analyze field water samples for northern pike ((Esox lucius) DNA. The Biomeme approach included a field-capable DNA extraction, a shelf-stable assay, and a portable real-time PCR thermocycler. The lab approach included lab-based DNA extraConventional and quantitative PCR assays for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples
We developed and validated conventional and quantitative real-time PCR assays for the detection of DNA from the myxozoan parasite Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease in fish. Assays were tested on fish tissue and on field-collected water samples to assess diagnostic and environmental DNA capabilities. The specificity, sensitivity, and broad applicabil - Multimedia
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A 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 WilcoxWhat do you mean by false positive?
Misunderstandings regarding the term “false positive” present a significant hurdle to broad adoption of eDNA monitoring methods. Here, we identify three challenges to clear communication of false-positive error between scientists, managers, and the public. The first arises from a failure to distinguish between false-positive eDNA detection at the sample level and false-positive inference of taxa pAuthorsJohn A. Darling, Christopher L. Jerde, Adam J. SepulvedaStrategic considerations for invasive species managers in the utilization ofenvironmental 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 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 WilcoxVulnerability of Pacific salmon to invasion of northern pike (Esox lucius) in Southcentral Alaska
The relentless role of invasive species in the extinction of native biota requires predictions of ecosystem vulnerability to inform proactive management strategies. The worldwide invasion and range expansion of predatory northern pike (Esox lucius) has been linked to the decline of native fishes and tools are needed to predict the vulnerability of habitats to invasion over broad geographic scales.AuthorsChase S. Jalbert, Jeffrey A. Falke, Andrés López, Kristine J. Dunker, Adam J. Sepulveda, Peter A. H. WestleyA small proportion of breeders drive American bullfrog invasion of the Yellowstone River floodplain, Montana
The American bullfrog (Lithobates catesbeianus) is a non-native invader of aquatic habitats across the northwestern United States. It recently invaded the Yellowstone River, Montana, and has spread to over 140 km of floodplain habitat. We analyzed seven microsatellites in 528 tadpoles sampled across nearly the entire Yellowstone River invasion (about 140 river km) to characterize invasion geneticsAuthorsDaniel M. Bingham, Adam J. Sepulveda, Sally PainterEffects of supplemental feeding on the fecal bacterial communities of Rocky Mountain elk in the Greater Yellowstone Ecosystem
Supplemental feeding of wildlife is a common practice often undertaken for recreational or management purposes, but it may have unintended consequences for animal health. Understanding cryptic effects of diet supplementation on the gut microbiomes of wild mammals is important to inform conservation and management strategies. Multiple laboratory studies have demonstrated the importance of the gut mAuthorsClaire E Couch, Benjamin Wise, Brandon Scurlock, Jared D. Rogerson, Rebecca K. Fuda, Eric K Cole, Kimberly E Szcodronski, Adam J. Sepulveda, Patrick R. Hutchins, Paul C. CrossExploration of the 2016 Yellowstone River fish kill and proliferative kidney disease in wild fish populations
Proliferative kidney disease (PKD) is an emerging disease that recently resulted in a large mortality event of salmonids in the Yellowstone River (Montana, USA). Total PKD fish mortalities in the Yellowstone River were estimated in the tens of thousands, which resulted in a multi‐week river closure and an estimated economic loss of US$500,000. This event shocked scientists, managers, and the publiAuthorsPatrick Ross Hutchins, Adam J. Sepulveda, Hanna Hartikainen, Ken D. Staigmiller, Scott T. Opitz, Renee M. Yamamoto, Amberly Huttinger, Rick J. Cordes, Tammy Weiss, Lacey R. Hopper, Maureen K. Purcell, Beth OkamuraIntegrating environmental DNA results with diverse data sets to improve biosurveillance of river health
Autonomous, robotic environmental (e)DNA samplers now make it possible for biological observations to match the scale and quality of abiotic measurements collected by automated sensor networks. Merging these automated data streams may allow for improved insight into biotic responses to environmental change and stressors. Here, we merged eDNA data collected by robotic samplers installed at three U.AuthorsAdam J. Sepulveda, Andrew B. Hoegh, Joshua A. Gage, Sara L. Caldwell Eldridge, James M. Birch, Christian Stratton, Patrick R. Hutchins, Elliott BarnhartThe elephant in the lab (and field): Contamination in aquatic environmental DNA studies
The rapid evolution of environmental (e)DNA methods has resulted in knowledge gaps in smaller, yet critical details like proper use of negative controls to detect contamination. Detecting contamination is vital for confident use of eDNA results in decision-making. We conducted two literature reviews to summarize (a) the types of quality assurance measures taken to detect contamination of eDNA sampAuthorsAdam J. Sepulveda, Patrick R. Hutchins, Meghan Forstchen, Madeline Mckeefry, Anna M SwigrisIt’s complicated…environmental DNA as a predictor of trout and char abundance in streams
The potential to provide inferences about fish abundance from environmental (e)DNA samples has generated great interest. However, the accuracy of these abundance estimates is often low and variable across species and space. A plausible refinement is the use of common aquatic habitat monitoring data to account for attributes that influence eDNA dynamics. We therefore evaluated the relationships betAuthorsAdam J. Sepulveda, Robert Al-Chokhachy, Matthew Laramie, Kyle Crapster, Ladd Knotek, Brian T. Miller, Alexander V. Zale, David Pilliod - News