Adam Sepulveda, Ph.D.
Biography
Education
Ph.D. Ecology. 2010. University of Montana, Missoula, MT
M.S. Science Education. 2004. Teton Science School, Kelly, WY
B.A. Environmental Biology and English. 2002. Dartmouth College, Hanover, NH
Research Interests
I am an aquatic ecologist with the U.S. Geological Survey’s Northern Rocky Mountain Science Center in Bozeman, MT. My specific research focuses on understanding the ecosystem and community-level consequences of aquatic invasive species and testing new tools for the early detection of aquatic invasive species. My research program consists of a combination of field and laboratory studies.
Science and Products
Environmental 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...
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...
Predicting 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...
Western 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...
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...
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...
Effects 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...
Couch, Claire E; Wise, Benjamin; Scurlock, Brandon M.; Rogerson, Jared D.; Fuda, Rebecca K.; Cole, Eric K; Szcodronski, Kimberly E; Sepulveda, Adam J.; Hutchins, Patrick R.; Cross, Paul Exploration 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....
Hutchins, Patrick Ross; Sepulveda, Adam J.; Hartikainen, Hanna; Staigmiller, Ken D.; Opitz, Scott T.; Yamamoto, Renee M.; Huttinger, Amberly; Cordes, Rick J.; Weiss, Tammy; Hopper, Lacey R.; Purcell, Maureen K.; Okamura, Beth Integrating 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...
Sepulveda, Adam J.; Hoegh, Andrew B.; Gage, Joshua A.; Caldwell Eldridge, Sara L.; Birch, James M.; Stratton, Christian; Hutchins, Patrick R.; Barnhart, Elliott It’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...
Sepulveda, Adam J.; Al-Chokhachy, Robert; Laramie, Matthew; Crapster, Kyle; Knotek, Ladd; Miller, Brian T.; Zale, Alexander V.; Pilliod, David The 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...
Sepulveda, Adam J.; Hutchins, Patrick R.; Forstchen, Meghan; Mckeefry, Madeline; Swigris, Anna M Robotic environmental DNA bio-surveillance of freshwater health
Autonomous water sampling technologies may help to overcome the human resource challenges of monitoring biological threats to rivers over long time periods and large geographic areas. The Monterey Bay Aquarium Research Institute has pioneered a robotic Environmental Sample Processor (ESP) that overcomes some of the constraints associated with...
Sepulveda, Adam J.; Birch, Jim M.; Barnhart, Elliott; Merkes, Christopher M.; Yamahara, Kevan; Marin, Roman III; Kinsey, Stacy; Wright, Peter R.; Schmidt, Christian msocc: Fit and analyse computationally efficient multi‐scale occupancy models in R
Environmental DNA (eDNA) sampling is a promising tool for the detection of rare and cryptic taxa, such as aquatic pathogens, parasites and invasive species. Environmental DNA sampling workflows commonly rely on multi‐stage hierarchical sampling designs that induce complicated dependencies within the data. This complex dependence structure can be...
Stratton, Christian; Sepulveda, Adam J.; Hoegh, Andrew B. Are environmental DNA methods ready for aquatic invasive species management?
Multiple studies have demonstrated environmental (e)DNA detections of rare, invasive species. However, invasive species managers struggle with using eDNA results because detections might not indicate species presence. We evaluated if eDNA methods have matured to a point where they can be widely applied to aquatic invasive species management. We...
Sepulveda, Adam J.; Nelson, Nanette M; Jerde, Christopher L.; Luikart, Gordon Climate-induced expansions of invasive species in the Pacific Northwest, North America: A synthesis of observations and projections
Climate change may facilitate the expansion of non-native invasive species (NIS) in aquatic and terrestrial systems. However, empirical evidence remains scarce and poorly synthesized at scales necessary for effective management. We conducted a literature synthesis to assess the state of research on the observed and predicted effects of climate...
Gervais, Jennifer; Kovach, Ryan P.; Sepulveda, Adam J.; Al-Chokhachy, Robert K.; Giersch, J. Joseph; Muhlfeld, Clint C. A round-robin evaluation of the repeatability and reproducibility of environmental DNA assays for dreissenid mussels
Resource managers may be hesitant to make decisions based on environmental (e)DNA results alone since eDNA is an indirect method of species detection. One way to reduce the uncertainty of eDNA is to identify laboratory‐based protocols that ensure repeatable and reproducible results. We conducted a double‐blind round‐robin analysis of probe‐based...
Sepulveda, Adam J.; Hutchins, Patrick R.; Jackson, Craig; Ostberg, Carl; Laramie, Matthew; Amberg, Jon J.; Counihan, Timothy; Hoegh, Andrew B.; Pilliod, David The Yellowstone River fish-kill: Fish health informs and is informed by vital signs monitoring
Trout are socioeconomically and ecologically important in the Greater Yellowstone Area (GYA); yet these fish face numerous threats. Disease may begin to play a larger role in reducing fish populations, partly because many existing threats may interact to exacerbate the frequency, extent, and severity of fish diseases (Lafferty 2009). For example,...
Hutchins, Patrick R.; Sepulveda, Adam J.; Hopper, Lacey R.; Staigmiller, Ken Consistent compensatory growth offsets poor condition in trout populations
1. Compensatory growth – when individuals in poor condition grow rapidly to “catch up” to conspecifics – may be a mechanism that allows individuals to tolerate stressful environmental conditions, both abiotic and biotic. This phenomenon has been documented fairly widely in laboratory and field experiments, but evidence for compensatory growth in...
Al-Chokhachy, Robert; Kovach, Ryan; Sepulveda, Adam J.; Strait, Jeff; Shepard, Bradley B.; Muhlfeld, Clint C.
Use of Robotic DNA Samplers That Can Rapidly Detect Invasive Aquatic Species
USGS researchers and their collaborators demonstrated the efficacy of using robotic environmental DNA samplers for bio surveillance in freshwater systems, showing that samples collected, processed, and preserved by robotic sampler detect organism DNA in the environment at rates comparable to those collected traditionally by human technicians.
Detecting Invasive and Rare Species with the National Streamflow Network
Two recently published papers suggest the integration of environmental DNA, or eDNA, sampling at select National Streamflow Network streamgages in the U.S. Northwest is feasible.
Innovation in Addressing Invasive Species and Disease in Montana Waters
Western waters support some of the most intact aquatic ecosystems in North America, yet invasive species and emerging infectious diseases pose significant and immediate threats to these ecosystems.
Bullfrog Genetics Confirm Source and Degree of Spread in Montana
Bozeman - A new U.S. Geological Survey study illustrates the usefulness of genetic approaches to track invasive bullfrog introductions. Results will inform management actions for identifying and controlling importation and secondary spread of invasive bullfrogs in Montana.
Bullfrog Invasion of the Yellowstone River
The American bullfrog has expanded its invasion of the Yellowstone River floodplain in Montana, according to a new study released in “Aquatic Invasions.”
Invasive Pike Persist When Preferred Prey Decline
Invasive northern pike in southcentral Alaska are opportunistic and adaptable predators that feed on multiple native fish species when their preferred prey, native salmonids, are no longer abundant, according to a new study released in Ecology of Freshwater Fish.