Collecting a 1-liter water sample in the Boise River for eDNA analysis (Boise, ID)"
Matthew B Laramie (Former Employee)
Science and Products
If you are unable to access or download a product, email fresc_outreach@usgs.gov a request, including the full citation, or call (541) 750-1030.
Comparison of environmental DNA sampling protocols for detection of stream fishes in the Pacific Northwest, 2019 (ver. 2.0, November 2025) Comparison of environmental DNA sampling protocols for detection of stream fishes in the Pacific Northwest, 2019 (ver. 2.0, November 2025)
This dataset contains environmental DNA (eDNA) data (field, extraction, and qPCR) for rainbow trout sampling efforts conducted in the Pacific Northwest in 2019. Samples were collected using three eDNA sampling methods. Also included are qPCR data for extraction negatives, no-template controls (NTC), and standard dilutions of rainbow trout gBlock. NTC and gBlock qPCR data were used to...
Fishes of the Harney Basin revisited: A contemporary assessment of the distribution of fish fauna throughout the Harney Basin from 1990 to 2019 (ver. 2.0, April 2022) Fishes of the Harney Basin revisited: A contemporary assessment of the distribution of fish fauna throughout the Harney Basin from 1990 to 2019 (ver. 2.0, April 2022)
We compiled electrofishing and habitat data sampled from 1990 to 2019 in the Harney Basin by the US Geological Survey (USGS), Oregon Department of Fish and Wildlife (ODFW) and the High Desert Partnership (HDP) to describe native and non-native fish distributions and their habitat associations. USGS collected eDNA data in 2019 to refine the known distributions of common carp (Cyprinus...
Okanogan Basin Pacific lamprey eDNA detections and translocations for 2012-2020 (ver. 1.1, April 2022) Okanogan Basin Pacific lamprey eDNA detections and translocations for 2012-2020 (ver. 1.1, April 2022)
Prior to the initiation of translocation efforts in 2017, Pacific lamprey (Entosphenus tridentatus) were last documented in the Okanogan river subbasin in 2010. It appears as if lamprey were extirpated in the Okanogan subbasin some time shortly after that. However, until 2017, monitoring and management actions for lamprey were minimal in the Okanogan subbasin. This lack of monitoring has...
Environmental DNA data, fish abundance data, and stream habitat data from northwest Montana and northeast Washington and southern British Columbia, Canada 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...
Occupancy data for spatiotemporal distribution assessments of bull trout (Salvelinus confluentus) and rainbow trout (Oncorhynchus mykiss) in the Bruneau and Jarbidge River Basins, Idaho and Nevada, USA, in water year 2016 Occupancy data for spatiotemporal distribution assessments of bull trout (Salvelinus confluentus) and rainbow trout (Oncorhynchus mykiss) in the Bruneau and Jarbidge River Basins, Idaho and Nevada, USA, in water year 2016
eDNA-based spatiotemporal distribution data (occupancy model format) for rainbow trout (Oncorhynchus mykiss) and bull trout (Salvelinus confluentus) within the Bruneau-Jarbidge Rivers Wilderness in southern Idaho and northern Nevada, USA. Data also include stream discharge and stream temperature data for each site. All data were collected between October 2015 and September 2016.
Collecting DNA in the Boise River (Boise, ID)
Collecting a 1-liter water sample in the Boise River for eDNA analysis (Boise, ID)"
If you are unable to access or download a product, email fresc_outreach@usgs.gov a request, including the full citation, or call (541) 750-1030.
Filter Total Items: 16
Amphibian diversity of the western Colorado canyonlands including potential threats from nonnative bullfrogs and disease Amphibian diversity of the western Colorado canyonlands including potential threats from nonnative bullfrogs and disease
Throughout the canyons of the Colorado and Uncompahgre Plateaus, water is a limited resource for wildlife, with patchy distribution and seasonal availability. Tributary creeks within these canyons drain into mainstem rivers, providing habitat and breeding sites for native amphibians. Yet, little is known about the diversity and distribution of amphibians that live in these harsh, dynamic
Authors
Denita M Weeks, David Pilliod, Madeline (Nikki) Grant-Hoffman, Anjelica F Quintana Spencer, Daniel Neubaum, Paul Hampton, Michaela Grossklaus, Matthew B Laramie, Erin L. Muths
Fishes of Harney Basin revisited: An assessment of the distribution of native and nonnative fishes over a half century Fishes of Harney Basin revisited: An assessment of the distribution of native and nonnative fishes over a half century
The Harney Basin is Oregon's largest internally draining basin and contains a unique native fish assemblage. The first and only comprehensive study of the origin and distribution of Harney Basin fishes occurred in 1971. Here, we update this study and identify potential threats to the basin's native fishes a half century later. Our assessment documents that all species of native fishes...
Authors
Matthew Laramie, Jason B. Dunham, Francine Mejia, Emily Heaston, Peter A Bisson
It’s complicated…environmental DNA as a predictor of trout and char abundance in streams 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 dynamics. We therefore evaluated the...
Authors
Adam Sepulveda, Robert Al-Chokhachy, Matthew Laramie, Kyle Crapster, Ladd Knotek, Brian Miller, Alexander Zale, David Pilliod
A round-robin evaluation of the repeatability and reproducibility of environmental DNA assays for dreissenid mussels 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...
Authors
Adam Sepulveda, Patrick Hutchins, Craig Jackson, Carl Ostberg, Matthew Laramie, Jon Amberg, Timothy D. Counihan, Andrew Hoegh, David Pilliod
2016 Chief Joseph hatchery annual report 2016 Chief Joseph hatchery annual report
The Colville Confederated Tribes (CCT) Chief Joseph Hatchery (CJH) is the fourth hatchery obligated under the Grand Coulee Dam/Dry Falls project, originating in the 1940s. Leavenworth, Entiat, and Winthrop National Fish Hatcheries were built and operated as mitigation for salmon blockage at Grand Coulee Dam, but the fourth hatchery was not built, and the obligation was nearly forgotten...
Authors
Andrea Pearl, Matthew Laramie, Casey Baldwin, John Rohrback, Brian Dietz, Pat Phillips, Taylor Scott
Integration of eDNA-based biological monitoring within the US Geological Survey’s national streamgage network Integration of eDNA-based biological monitoring within the US Geological Survey’s national streamgage network
This study explores the feasibility and utility of integrating environmental DNA (eDNA) assessments of species occurrences into the United States (U.S.) Geological Survey’s national streamgage network. We used an existing network of five gages in southwest Idaho to explore the type of information that could be gained as well as the associated costs and limitations. Hydrologic technicians...
Authors
David Pilliod, Matthew Laramie, Dorene McCoy, Scott Maclean
Adding invasive species bio-surveillance to the U.S. Geological Survey streamgage network 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...
Authors
Adam Sepulveda, Christian Schmidt, Jon Amberg, Patrick Hutchins, Christian Stratton, Christopher Mebane, Matthew Laramie, David Pilliod
The Chief Joseph Hatchery Program spring Chinook 2018 annual report The Chief Joseph Hatchery Program spring Chinook 2018 annual report
No abstract available.
Authors
Andrea Pearl, Matthew Laramie, Casey Baldwin, John Rohrback, Brian Dietz, Matt McDaniel
Exploring the use of environmental DNA to determine the species of salmon redds Exploring the use of environmental DNA to determine the species of salmon redds
Annual redd counts are used to monitor the status and trends of salmonid populations, but methods to easily and reliably determine which of sympatric species made specific redds are lacking. We explored whether environmental DNA (eDNA) analysis might prove useful for determining the species of salmon redds. We collected eDNA samples from the interstitial spaces of redds of Chinook Salmon
Authors
Burke Strobel, Matthew Laramie, David Pilliod
The Chief Joseph Hatchery Program 2014 Annual Report The Chief Joseph Hatchery Program 2014 Annual Report
The Chief Joseph Hatchery Program is comprised of both operations and maintenance of the Chief Joseph Hatchery, located near Bridgeport, Washington and the monitoring and evaluation of natural- and hatchery-origin Chinook salmon in the Okanogan Subbasin. In 2014, the Chief Joseph Hatchery released 44,267 yearling and 186,050 subyearling integrated Chinook from the Omak acclimation pond...
Authors
Andrea Pearl, Matthew Laramie, Casey Baldwin, John Rohrback, Pat Phillips
Critical considerations for the application of environmental DNA methods to detect aquatic species Critical considerations for the application of environmental DNA methods to detect aquatic species
Species detection using environmental DNA (eDNA) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods...
Authors
Caren Goldberg, Cameron Turner, Kristy Deiner, Katy Klymus, Philip Thomsen, Melanie Murphy, Stephen Spear, Anna McKee, Sara Oyler-McCance, Robert Cornman, Matthew Laramie, Andrew R. Mahon, Richard Lance, David S. Pilliod, Katherine Strickler, Lisette Waits, Alexander K. Fremier, Teruhiko Takahara, Jelger Herder, Pierre Taberlet
Salmon redd identification using environmental DNA (eDNA) Salmon redd identification using environmental DNA (eDNA)
Introduction The purpose of this project was to develop a technique to use environmental DNA (eDNA) to distinguish between redds made by Chinook salmon (Oncorhynchus tshawytscha) and redds made by Coho salmon (O. kisutch) and to distinguish utilized redds from test/abandoned redds or scours that have the appearance of redds. The project had two phases: Phase 1. Develop, test, and...
Authors
David S. Pilliod, Matthew Laramie
Science and Products
If you are unable to access or download a product, email fresc_outreach@usgs.gov a request, including the full citation, or call (541) 750-1030.
Comparison of environmental DNA sampling protocols for detection of stream fishes in the Pacific Northwest, 2019 (ver. 2.0, November 2025) Comparison of environmental DNA sampling protocols for detection of stream fishes in the Pacific Northwest, 2019 (ver. 2.0, November 2025)
This dataset contains environmental DNA (eDNA) data (field, extraction, and qPCR) for rainbow trout sampling efforts conducted in the Pacific Northwest in 2019. Samples were collected using three eDNA sampling methods. Also included are qPCR data for extraction negatives, no-template controls (NTC), and standard dilutions of rainbow trout gBlock. NTC and gBlock qPCR data were used to...
Fishes of the Harney Basin revisited: A contemporary assessment of the distribution of fish fauna throughout the Harney Basin from 1990 to 2019 (ver. 2.0, April 2022) Fishes of the Harney Basin revisited: A contemporary assessment of the distribution of fish fauna throughout the Harney Basin from 1990 to 2019 (ver. 2.0, April 2022)
We compiled electrofishing and habitat data sampled from 1990 to 2019 in the Harney Basin by the US Geological Survey (USGS), Oregon Department of Fish and Wildlife (ODFW) and the High Desert Partnership (HDP) to describe native and non-native fish distributions and their habitat associations. USGS collected eDNA data in 2019 to refine the known distributions of common carp (Cyprinus...
Okanogan Basin Pacific lamprey eDNA detections and translocations for 2012-2020 (ver. 1.1, April 2022) Okanogan Basin Pacific lamprey eDNA detections and translocations for 2012-2020 (ver. 1.1, April 2022)
Prior to the initiation of translocation efforts in 2017, Pacific lamprey (Entosphenus tridentatus) were last documented in the Okanogan river subbasin in 2010. It appears as if lamprey were extirpated in the Okanogan subbasin some time shortly after that. However, until 2017, monitoring and management actions for lamprey were minimal in the Okanogan subbasin. This lack of monitoring has...
Environmental DNA data, fish abundance data, and stream habitat data from northwest Montana and northeast Washington and southern British Columbia, Canada 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...
Occupancy data for spatiotemporal distribution assessments of bull trout (Salvelinus confluentus) and rainbow trout (Oncorhynchus mykiss) in the Bruneau and Jarbidge River Basins, Idaho and Nevada, USA, in water year 2016 Occupancy data for spatiotemporal distribution assessments of bull trout (Salvelinus confluentus) and rainbow trout (Oncorhynchus mykiss) in the Bruneau and Jarbidge River Basins, Idaho and Nevada, USA, in water year 2016
eDNA-based spatiotemporal distribution data (occupancy model format) for rainbow trout (Oncorhynchus mykiss) and bull trout (Salvelinus confluentus) within the Bruneau-Jarbidge Rivers Wilderness in southern Idaho and northern Nevada, USA. Data also include stream discharge and stream temperature data for each site. All data were collected between October 2015 and September 2016.
Collecting DNA in the Boise River (Boise, ID)
Collecting a 1-liter water sample in the Boise River for eDNA analysis (Boise, ID)"
Collecting a 1-liter water sample in the Boise River for eDNA analysis (Boise, ID)"
If you are unable to access or download a product, email fresc_outreach@usgs.gov a request, including the full citation, or call (541) 750-1030.
Filter Total Items: 16
Amphibian diversity of the western Colorado canyonlands including potential threats from nonnative bullfrogs and disease Amphibian diversity of the western Colorado canyonlands including potential threats from nonnative bullfrogs and disease
Throughout the canyons of the Colorado and Uncompahgre Plateaus, water is a limited resource for wildlife, with patchy distribution and seasonal availability. Tributary creeks within these canyons drain into mainstem rivers, providing habitat and breeding sites for native amphibians. Yet, little is known about the diversity and distribution of amphibians that live in these harsh, dynamic
Authors
Denita M Weeks, David Pilliod, Madeline (Nikki) Grant-Hoffman, Anjelica F Quintana Spencer, Daniel Neubaum, Paul Hampton, Michaela Grossklaus, Matthew B Laramie, Erin L. Muths
Fishes of Harney Basin revisited: An assessment of the distribution of native and nonnative fishes over a half century Fishes of Harney Basin revisited: An assessment of the distribution of native and nonnative fishes over a half century
The Harney Basin is Oregon's largest internally draining basin and contains a unique native fish assemblage. The first and only comprehensive study of the origin and distribution of Harney Basin fishes occurred in 1971. Here, we update this study and identify potential threats to the basin's native fishes a half century later. Our assessment documents that all species of native fishes...
Authors
Matthew Laramie, Jason B. Dunham, Francine Mejia, Emily Heaston, Peter A Bisson
It’s complicated…environmental DNA as a predictor of trout and char abundance in streams 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 dynamics. We therefore evaluated the...
Authors
Adam Sepulveda, Robert Al-Chokhachy, Matthew Laramie, Kyle Crapster, Ladd Knotek, Brian Miller, Alexander Zale, David Pilliod
A round-robin evaluation of the repeatability and reproducibility of environmental DNA assays for dreissenid mussels 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...
Authors
Adam Sepulveda, Patrick Hutchins, Craig Jackson, Carl Ostberg, Matthew Laramie, Jon Amberg, Timothy D. Counihan, Andrew Hoegh, David Pilliod
2016 Chief Joseph hatchery annual report 2016 Chief Joseph hatchery annual report
The Colville Confederated Tribes (CCT) Chief Joseph Hatchery (CJH) is the fourth hatchery obligated under the Grand Coulee Dam/Dry Falls project, originating in the 1940s. Leavenworth, Entiat, and Winthrop National Fish Hatcheries were built and operated as mitigation for salmon blockage at Grand Coulee Dam, but the fourth hatchery was not built, and the obligation was nearly forgotten...
Authors
Andrea Pearl, Matthew Laramie, Casey Baldwin, John Rohrback, Brian Dietz, Pat Phillips, Taylor Scott
Integration of eDNA-based biological monitoring within the US Geological Survey’s national streamgage network Integration of eDNA-based biological monitoring within the US Geological Survey’s national streamgage network
This study explores the feasibility and utility of integrating environmental DNA (eDNA) assessments of species occurrences into the United States (U.S.) Geological Survey’s national streamgage network. We used an existing network of five gages in southwest Idaho to explore the type of information that could be gained as well as the associated costs and limitations. Hydrologic technicians...
Authors
David Pilliod, Matthew Laramie, Dorene McCoy, Scott Maclean
Adding invasive species bio-surveillance to the U.S. Geological Survey streamgage network 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...
Authors
Adam Sepulveda, Christian Schmidt, Jon Amberg, Patrick Hutchins, Christian Stratton, Christopher Mebane, Matthew Laramie, David Pilliod
The Chief Joseph Hatchery Program spring Chinook 2018 annual report The Chief Joseph Hatchery Program spring Chinook 2018 annual report
No abstract available.
Authors
Andrea Pearl, Matthew Laramie, Casey Baldwin, John Rohrback, Brian Dietz, Matt McDaniel
Exploring the use of environmental DNA to determine the species of salmon redds Exploring the use of environmental DNA to determine the species of salmon redds
Annual redd counts are used to monitor the status and trends of salmonid populations, but methods to easily and reliably determine which of sympatric species made specific redds are lacking. We explored whether environmental DNA (eDNA) analysis might prove useful for determining the species of salmon redds. We collected eDNA samples from the interstitial spaces of redds of Chinook Salmon
Authors
Burke Strobel, Matthew Laramie, David Pilliod
The Chief Joseph Hatchery Program 2014 Annual Report The Chief Joseph Hatchery Program 2014 Annual Report
The Chief Joseph Hatchery Program is comprised of both operations and maintenance of the Chief Joseph Hatchery, located near Bridgeport, Washington and the monitoring and evaluation of natural- and hatchery-origin Chinook salmon in the Okanogan Subbasin. In 2014, the Chief Joseph Hatchery released 44,267 yearling and 186,050 subyearling integrated Chinook from the Omak acclimation pond...
Authors
Andrea Pearl, Matthew Laramie, Casey Baldwin, John Rohrback, Pat Phillips
Critical considerations for the application of environmental DNA methods to detect aquatic species Critical considerations for the application of environmental DNA methods to detect aquatic species
Species detection using environmental DNA (eDNA) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods...
Authors
Caren Goldberg, Cameron Turner, Kristy Deiner, Katy Klymus, Philip Thomsen, Melanie Murphy, Stephen Spear, Anna McKee, Sara Oyler-McCance, Robert Cornman, Matthew Laramie, Andrew R. Mahon, Richard Lance, David S. Pilliod, Katherine Strickler, Lisette Waits, Alexander K. Fremier, Teruhiko Takahara, Jelger Herder, Pierre Taberlet
Salmon redd identification using environmental DNA (eDNA) Salmon redd identification using environmental DNA (eDNA)
Introduction The purpose of this project was to develop a technique to use environmental DNA (eDNA) to distinguish between redds made by Chinook salmon (Oncorhynchus tshawytscha) and redds made by Coho salmon (O. kisutch) and to distinguish utilized redds from test/abandoned redds or scours that have the appearance of redds. The project had two phases: Phase 1. Develop, test, and...
Authors
David S. Pilliod, Matthew Laramie