Patrick Hutchins
Patrick Hutchins manages the laboratory spaces at NOROCK and conducts research in detection of rare/cryptic species using molecular tools. His investigations range from threatened/endangered species to invasives to parasites. He has extensive experience in designing/validating molecular markers for eDNA and population genetics studies and has designed programming tools for qPCR curve analysis.
My laboratory experience ranges from fish dissection and histological, microscopy, and molecular sample preparation and preservation to next generation high throughput sequencing library preparation. I have extensive experience with methods pertaining to environmental DNA (eDNA) sample collection, processing, and analysis. My analytical skills span advanced curve analysis and transformation methods, linear and non-linear modeling, and both frequentist and Bayesian statistical methods. I am proficient with the R programming language and am familiar with Python. Regarding field-base skills, I am comfortable with coastal marine and inland waters motorized and non-motorized boat operation, multi-day backcountry operations under adverse conditions, being in the presence of large carnivores, and electrofishing with backpack, barge, and boat shocking equipment. I also have extensive experience operating handheld, electric, and heavy equipment for construction and carpentry tasks.
Professional Experience
Biologist, USGS Northern Rocky Mountain Science Center, Bozeman, MT, June 2022 - Present
Education and Certifications
M.S. Cellular, Molecular, and Microbiology, University of Montana
M.S. Coastal Marine and Wetland Studies, Coastal Carolina University
B.S. Marine Science, Coastal Carolina University
Science and Products
qPCR detection and quantitative results for Northern Pike (Esox lucius) from environmental (e)DNA samples collected along Miller Creek, Kenai Peninsula, Alaska in February and March of 2024
The dataset contains qualitative detection and quantitative results of Esox Lucius DNA in environmental (e)DNA water samples collected from Miller Creek, Alaska and analyzed with quantitative PCR.
qpcr amplification data for tissue and water samples collected from glacier national park in 2020 amplified with a lednia tumana specific assay
Tabular amplification data for individual technical replicates of tissue and water samples collected from Glacier National Park in 2020 and amplified with a Lednia tumana species-specific qPCR assay. Reported results include fractional detection rates, mean quantification cycles, and estimated gene copies per reaction.
Quantitative polymerase chain reaction detection data for controlled DNA contamination experiments
This data shows the quantification cycle at which fluorescence signals crossed a threshold fluorescence for samples analyzed as part of controlled experiments to determine whether contaminating DNA is present in samples under varying experimental conditions.
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.
Validation of a species-specific probe-based qPCR assay for the threatened meltwater stonefly, Lednia tumana, in environmental samples
A probe-based quantitative real-time PCR assay was developed to detect meltwater stonefly (Lednia tumana) environmental (e)DNA in water samples. The limits of detection and quantification, respectively, were 12.1 and 58.4 gene copies for calibration standards and these values were similarly low in a relevant environmental sample matrix (8.6 and 174.2, respectively). The assay’s utility was demonst
Authors
Patrick Ross Hutchins, Jonathan Giersch, Adam J. Sepulveda, Clint C. Muhlfeld
Time 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 and
Authors
Patrick Ross Hutchins, Leah Nicole Simantel, Adam J. Sepulveda
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 studies have demonstrated the importance of the gut m
Authors
Claire 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. Cross
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. This event shocked scientists, managers, and the publi
Authors
Patrick 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 Okamura
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 collected by robotic samplers installed at three U.
Authors
Adam J. Sepulveda, Andrew B. Hoegh, Joshua A. Gage, Sara L. Caldwell Eldridge, James M. Birch, Christian Stratton, Patrick R. Hutchins, Elliott Barnhart
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 measures taken to detect contamination of eDNA samp
Authors
Adam J. Sepulveda, Patrick R. Hutchins, Meghan Forstchen, Madeline Mckeefry, Anna M Swigris
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 assays for DNA of dreissenid (Dreissena spp.) mussel
Authors
Adam J. Sepulveda, Patrick R. Hutchins, Craig Jackson, Carl Ostberg, Matthew Laramie, Jon Amberg, Timothy Counihan, Andrew B. Hoegh, David Pilliod
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, habitat loss and low summer flows might interact to
Authors
Patrick R. Hutchins, Adam J. Sepulveda, Lacey R. Hopper, Ken Staigmiller
Adding invasive species bio-surveillance to the U.S. Geological Survey streamgage network
The costs of invasive species in the United States alone are estimated to exceed US$100 billion per year so a critical tactic in minimizing the costs of invasive species is the development of effective, early-detection systems. To this end, we evaluated the efficacy of adding environmental (e)DNA surveillance to the U.S. Geological Survey (USGS) streamgage network, which consists of > 8,200 stream
Authors
Adam J. Sepulveda, Christian Schmidt, Jon Amberg, Patrick R. Hutchins, Christian Stratton, Christopher A. Mebane, Matthew Laramie, David Pilliod
Tradeoffs of a portable, field-based environmental DNA platform for detecting invasive northern pike (Esox lucius) in Alaska
Environmental DNA (eDNA) has improved detection probabilities of aquatic invasive species but lab-based analyticalplatforms for eDNA analyses slow opportunities for rapid response. Effective approaches that address this analyticalbottleneck and improve capacity for rapid response are urgently needed. We tested the sensitivity of a portable, field-basedeDNA platform relative to widely used lab-base
Authors
Adam J. Sepulveda, Patrick R. Hutchins, Robert L. Massengill, Kristine J. Dunker
Improved conventional PCR assay for detecting Tetracapsuloides bryosalmonae DNA in fish tissues
Conventional PCR is an established method to detect Tetracapsuloides bryosalmonaeDNA in fish tissues and to confirm diagnosis of proliferative kidney disease (PKD) caused by T. bryosalmonae. However, the commonly used PKX5f‐6r primers were designed with the intention of obtaining sequence information and are suboptimal for determining parasite DNA presence. A new PCR assay to detect T. bryosalmona
Authors
Patrick R. Hutchins, Adam J. Sepulveda, Renee M. Martin, Lacey R. Hopper
A probe-based quantitative PCR assay for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples
A probe-based quantitative real-time PCR assay was developed to detect Tetracapsuloides bryosalmonae, which causes proliferative kidney disease in salmonid fish, in kidney tissue and environmental DNA (eDNA) water samples. The limits of detection and quantification were 7 and 100 DNA copies for calibration standards and T. bryosalmonae was reliably detected down to 100 copies in tissue and eDNA sa
Authors
Patrick R. Hutchins, Adam J. Sepulveda, Renee Martin, Lacey Hopper
Non-USGS Publications**
Brusa, J.L., Rotella, J.J., Banner, K.M., Hutchins, P.R., 2021, Challenges and opportunities for comparative studies of survival rates: An example with male pinnipeds: Ecology and Evolution, v. 11(12), p. 7980-7999.
Miller, S.R., Longley, R., Hutchins, P.R., Bauersachs, T., 2020, Cellular innovation of the cyanobacterial heterocyst by the adaptive loss of plasticity: Current Biology, v. 30(2), p. 344-350. e4
Sano, E.B., Wall, C.A., Hutchins, P.R., Miller, S.R., 2018, Ancient balancing selection on heterocyst function in a cosmopolitan cyanobacterium: Nature Ecology & Evolution, v. 2(3), p. 510-519.
Hutchins, P.R.; Miller, S.R., 2017, Genomics of variation in nitrogen fixation activity in a population of the thermophilic cyanobacterium Mastigocladus laminosus: The ISME Journal, v. 11(1), p. 78-86.
Hutchins, P.R., Smith, E.M., Koepfler, E.T., Viso, R.F., Peterson, R.N., 2014, Metabolic responses of estuarine microbial communities to discharge of surface runoff and groundwater from contrasting landscapes: Estuaries and coasts, v. 37, p. 736-750.
Peterson, R.N., Breier, J.A., Harmon, L.R., Brusa, J.L., Hutchins, P.R., 2013, Development of a sparging chamber for field radon analysis: Journal of Radioanalytical and Nuclear Chemistry, v. 298, p. 1347-1357.
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
Science and Products
qPCR detection and quantitative results for Northern Pike (Esox lucius) from environmental (e)DNA samples collected along Miller Creek, Kenai Peninsula, Alaska in February and March of 2024
The dataset contains qualitative detection and quantitative results of Esox Lucius DNA in environmental (e)DNA water samples collected from Miller Creek, Alaska and analyzed with quantitative PCR.
qpcr amplification data for tissue and water samples collected from glacier national park in 2020 amplified with a lednia tumana specific assay
Tabular amplification data for individual technical replicates of tissue and water samples collected from Glacier National Park in 2020 and amplified with a Lednia tumana species-specific qPCR assay. Reported results include fractional detection rates, mean quantification cycles, and estimated gene copies per reaction.
Quantitative polymerase chain reaction detection data for controlled DNA contamination experiments
This data shows the quantification cycle at which fluorescence signals crossed a threshold fluorescence for samples analyzed as part of controlled experiments to determine whether contaminating DNA is present in samples under varying experimental conditions.
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.
Validation of a species-specific probe-based qPCR assay for the threatened meltwater stonefly, Lednia tumana, in environmental samples
A probe-based quantitative real-time PCR assay was developed to detect meltwater stonefly (Lednia tumana) environmental (e)DNA in water samples. The limits of detection and quantification, respectively, were 12.1 and 58.4 gene copies for calibration standards and these values were similarly low in a relevant environmental sample matrix (8.6 and 174.2, respectively). The assay’s utility was demonst
Authors
Patrick Ross Hutchins, Jonathan Giersch, Adam J. Sepulveda, Clint C. Muhlfeld
Time 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 and
Authors
Patrick Ross Hutchins, Leah Nicole Simantel, Adam J. Sepulveda
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 studies have demonstrated the importance of the gut m
Authors
Claire 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. Cross
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. This event shocked scientists, managers, and the publi
Authors
Patrick 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 Okamura
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 collected by robotic samplers installed at three U.
Authors
Adam J. Sepulveda, Andrew B. Hoegh, Joshua A. Gage, Sara L. Caldwell Eldridge, James M. Birch, Christian Stratton, Patrick R. Hutchins, Elliott Barnhart
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 measures taken to detect contamination of eDNA samp
Authors
Adam J. Sepulveda, Patrick R. Hutchins, Meghan Forstchen, Madeline Mckeefry, Anna M Swigris
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 assays for DNA of dreissenid (Dreissena spp.) mussel
Authors
Adam J. Sepulveda, Patrick R. Hutchins, Craig Jackson, Carl Ostberg, Matthew Laramie, Jon Amberg, Timothy Counihan, Andrew B. Hoegh, David Pilliod
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, habitat loss and low summer flows might interact to
Authors
Patrick R. Hutchins, Adam J. Sepulveda, Lacey R. Hopper, Ken Staigmiller
Adding invasive species bio-surveillance to the U.S. Geological Survey streamgage network
The costs of invasive species in the United States alone are estimated to exceed US$100 billion per year so a critical tactic in minimizing the costs of invasive species is the development of effective, early-detection systems. To this end, we evaluated the efficacy of adding environmental (e)DNA surveillance to the U.S. Geological Survey (USGS) streamgage network, which consists of > 8,200 stream
Authors
Adam J. Sepulveda, Christian Schmidt, Jon Amberg, Patrick R. Hutchins, Christian Stratton, Christopher A. Mebane, Matthew Laramie, David Pilliod
Tradeoffs of a portable, field-based environmental DNA platform for detecting invasive northern pike (Esox lucius) in Alaska
Environmental DNA (eDNA) has improved detection probabilities of aquatic invasive species but lab-based analyticalplatforms for eDNA analyses slow opportunities for rapid response. Effective approaches that address this analyticalbottleneck and improve capacity for rapid response are urgently needed. We tested the sensitivity of a portable, field-basedeDNA platform relative to widely used lab-base
Authors
Adam J. Sepulveda, Patrick R. Hutchins, Robert L. Massengill, Kristine J. Dunker
Improved conventional PCR assay for detecting Tetracapsuloides bryosalmonae DNA in fish tissues
Conventional PCR is an established method to detect Tetracapsuloides bryosalmonaeDNA in fish tissues and to confirm diagnosis of proliferative kidney disease (PKD) caused by T. bryosalmonae. However, the commonly used PKX5f‐6r primers were designed with the intention of obtaining sequence information and are suboptimal for determining parasite DNA presence. A new PCR assay to detect T. bryosalmona
Authors
Patrick R. Hutchins, Adam J. Sepulveda, Renee M. Martin, Lacey R. Hopper
A probe-based quantitative PCR assay for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples
A probe-based quantitative real-time PCR assay was developed to detect Tetracapsuloides bryosalmonae, which causes proliferative kidney disease in salmonid fish, in kidney tissue and environmental DNA (eDNA) water samples. The limits of detection and quantification were 7 and 100 DNA copies for calibration standards and T. bryosalmonae was reliably detected down to 100 copies in tissue and eDNA sa
Authors
Patrick R. Hutchins, Adam J. Sepulveda, Renee Martin, Lacey Hopper
Non-USGS Publications**
Brusa, J.L., Rotella, J.J., Banner, K.M., Hutchins, P.R., 2021, Challenges and opportunities for comparative studies of survival rates: An example with male pinnipeds: Ecology and Evolution, v. 11(12), p. 7980-7999.
Miller, S.R., Longley, R., Hutchins, P.R., Bauersachs, T., 2020, Cellular innovation of the cyanobacterial heterocyst by the adaptive loss of plasticity: Current Biology, v. 30(2), p. 344-350. e4
Sano, E.B., Wall, C.A., Hutchins, P.R., Miller, S.R., 2018, Ancient balancing selection on heterocyst function in a cosmopolitan cyanobacterium: Nature Ecology & Evolution, v. 2(3), p. 510-519.
Hutchins, P.R.; Miller, S.R., 2017, Genomics of variation in nitrogen fixation activity in a population of the thermophilic cyanobacterium Mastigocladus laminosus: The ISME Journal, v. 11(1), p. 78-86.
Hutchins, P.R., Smith, E.M., Koepfler, E.T., Viso, R.F., Peterson, R.N., 2014, Metabolic responses of estuarine microbial communities to discharge of surface runoff and groundwater from contrasting landscapes: Estuaries and coasts, v. 37, p. 736-750.
Peterson, R.N., Breier, J.A., Harmon, L.R., Brusa, J.L., Hutchins, P.R., 2013, Development of a sparging chamber for field radon analysis: Journal of Radioanalytical and Nuclear Chemistry, v. 298, p. 1347-1357.
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.