Flow is a critical variable in streams since it affects aquatic and riparian biological communities and human uses of water (i.e., recreation, public water supply, etc.). Flow regimes are changing due to anthropogenic (e.g., water withdrawals) and natural impacts (e.g., extreme weather events).
Benjamin H Letcher
Ben Letcher is an Ecologist at the USGS Eastern Ecological Science Center in Turners Falls, Massachusetts.
Ben is a population ecologist focusing on stream habitats, science communication and the development of data systems. A collection of data systems and interactive data visualization tools can be found in our EcoSHEDS environment.
Professional Experience
1995-now USGS, Ecology section leader, Anadromous Fish Research Center, Turners, Falls, MA, and adjunct professor Department of Natural Resources
Conservation, University of Massachusetts - Amherst1994-1995 Oak Ridge Postdoctoral Fellow (with Dr. David Conover) State University of New York, Stony Brook, NY
1992-1994 Electric Power Research Institute Fellow, North Carolina State University, Raleigh, NC
1990-1992 Wisconsin Sea Grant Fellow, North Carolina State University, Raleigh, NC
1987-1990 URI-USEPA Cooperative Research Fellow, University of Rhode Island, Kingston, RI
1986-1987 Research Assistant, Center for Coastal Studies, Provincetown, MA.
1985-1986 Research Assistant, University of Massachusetts, Amherst, MA.
Education and Certifications
PhD, 1994, NC State, Zoology with statistics and modeling minor
M.S. 1990, URI School of Oceanography, biological option
B.S. 1985, Trinity College, Biology
Science and Products
Strong variation in Brook Trout trends across geology, elevation, and stream size in Shenandoah National Park
Aging contrast: A contrastive learning framework for fish re-identification across seasons and years.
Spatial asynchrony and cross-scale climate interactions in populations of a coldwater stream fish
CGS: Coupled growth and survival model with cohort fairness
A new genomic resource to enable standardized surveys of SNPs across the native range of brook trout (Salvelinus fontinalis)
Closing the gap between science and management of cold-water refuges in rivers and streams
Community for data integration 2019 project report
Identifying mechanisms underlying individual body size increases in a changing, highly seasonal environment: The growing trout of West Brook
Towards continuous streamflow monitoring with time-lapse cameras and deep learning
Stream size, temperature, and density explain body sizes of freshwater salmonids across a range of climate conditions
VIMTS: Variational-based Imputation for Multi-modal Time Series
Cohort strength and body size in co-occurring salmonids in a small stream network: Variation in space and time
Brook trout vulnerability to drought: eastern component of USGS national integrated ecohydrological research
Integrating Streamflow and Temperature to Identify Streams with Coldwater Refugia in the Northeast
Enabling AI for citizen science in fish biology
Enhancing Water Temperature Monitoring Efforts across Alaska through Collaborative Leveraging of a Statewide Database
North Atlantic-Appalachian AI/ML Capabilities
Enabling AI for citizen science in fish ecology
Understanding Brook Trout Persistence in Warming Streams
Scoping the Feasibility of Incorporating Climate Change into Risk Assessments of Aquatic Invasive Species in the Upper Midwest
Brook Trout Population Responses to Climate Variation Across the Southeast USA
A generic web application to visualize and understand movements of tagged animals
Climate change forecasts for eastern salmonids
The West Brook Story
Brook trout abundance in streams across southern Appalachia from 1958-2021
West Brook Trout Data, Whatley, Massachusetts.
Brook trout imagery data for individual recognition with deep learning
USGS EcoDrought Stream Discharge, Gage Height, and Water Temperature in Shenandoah National Park, Virginia
USGS EcoDrought Stream Discharge, Gage Height, and Water Temperature Data in Massachusetts
Annotated fish imagery data for individual and species recognition with deep learning
Flow is a critical variable in streams since it affects aquatic and riparian biological communities and human uses of water (i.e., recreation, public water supply, etc.). Flow regimes are changing due to anthropogenic (e.g., water withdrawals) and natural impacts (e.g., extreme weather events).
Flow is a critical variable in streams since it affects aquatic and riparian biological communities and human uses of water (i.e., recreation, public water supply, etc.). Flow regimes are changing due to anthropogenic (e.g., water withdrawals) and natural impacts (e.g., extreme weather events).
Flow is a critical variable in streams since it affects aquatic and riparian biological communities and human uses of water (i.e., recreation, public water supply, etc.). Flow regimes are changing due to anthropogenic (e.g., water withdrawals) and natural impacts (e.g., extreme weather events).
Flow is a critical variable in streams since it affects aquatic and riparian biological communities and human uses of water (i.e., recreation, public water supply, etc.). Flow regimes are changing due to anthropogenic (e.g., water withdrawals) and natural impacts (e.g., extreme weather events).
Flow is a critical variable in streams since it affects aquatic and riparian biological communities and human uses of water (i.e., recreation, public water supply, etc.). Flow regimes are changing due to anthropogenic (e.g., water withdrawals) and natural impacts (e.g., extreme weather events).
Flow is a critical variable in streams since it affects aquatic and riparian biological communities and human uses of water (i.e., recreation, public water supply, etc.). Flow regimes are changing due to anthropogenic (e.g., water withdrawals) and natural impacts (e.g., extreme weather events).
Flow is a critical variable in streams since it affects aquatic and riparian biological communities and human uses of water (i.e., recreation, public water supply, etc.). Flow regimes are changing due to anthropogenic (e.g., water withdrawals) and natural impacts (e.g., extreme weather events).
Interactive Catchment Explorer (ICE)
Interactive Catchment Explorer (ICE) is a web-based data visualization tool for exploring complex, multivariate environmental datasets and model results. It is designed to help researchers and resource managers identify spatial patterns in hydro-ecological conditions and to prioritize locations for restoration or further study.
Flow Photo Explorer
The Flow Photo Explorer is an integrated database, machine learning, and data visualization platform for monitoring streamflow and other hydrologic conditions using timelapse images.
EcoSHEDS
EcoSHEDS is a collection of Spatial Hydro-Ecological Data Systems (SHEDS) designed to improve our understanding of stream ecosystems. The goal of EcoSHEDS is to provide a series of user-friendly tools for gaining insight and supporting transparent research, management, and decision-making of hydro-ecological resources.
Ecosheds.org
LSC Conte Anadrmous Fish Laboratory is currently involved in https://ecosheds.org.
Science and Products
- Publications
Filter Total Items: 92
Strong variation in Brook Trout trends across geology, elevation, and stream size in Shenandoah National Park
ObjectiveLandscape context structures fish abundance and dynamics, and understanding trends in fish abundance across the landscape is often prerequisite for effective conservation. In this study, we evaluated the status and trends of Brook Trout Salvelinus fontinalis in Shenandoah National Park to understand how these are structured across bedrock geology, elevation, and stream size.MethodsWe usedAuthorsEvan S. Childress, David E Demarest, John E.B. Wofford, Nathaniel P. Hitt, Benjamin LetcherAging contrast: A contrastive learning framework for fish re-identification across seasons and years.
The fields of biology, ecology, and fisheries management are witnessing a growing demand for distinguishing individual fish. In recent years, deep learning methods have emerged as a promising tool for image-based fish recognition. Our study is focused on the re-identification of masu salmon from Japan, wherein fish were individually marked and photographed to evaluate discriminative body characterAuthorsWeili Shi, Z. Zhou, Benjamin Letcher, Nathaniel P. Hitt, Yoichiro Kanno, R. Futamura, O. Kishida, K. Morita, Sheng LiSpatial asynchrony and cross-scale climate interactions in populations of a coldwater stream fish
Climate change affects populations over broad geographic ranges due to spatially autocorrelated abiotic conditions known as the Moran effect. However, populations do not always respond to broad-scale environmental changes synchronously across a landscape. We combined multiple datasets for a retrospective analysis of time-series count data (5–28 annual samples per segment) at 144 stream segments diAuthorsGeorge Valentine, Xinyi Lu, Evan S. Childress, C. Andrew Dolloff, Nathaniel P. Hitt, Matthew Kulp, Benjamin Letcher, Kasey C. Pregler, Jacob Rash, Mevin B. Hooten, Yoichiro KannoCGS: Coupled growth and survival model with cohort fairness
Fish modeling in complex environments is critical for understanding drivers of population dynamics in aquatic systems. This paper proposes a Bayesian network method for modeling fish survival and growth over multiple connected rivers. Traditional fish survival models capture the effect of multiple environmental drivers (e.g., stream temperature, stream flow) by adding different variables, which inAuthorsErhu He, Yue Wan, Benjamin Letcher, Jennifer Burlingame Hoyle Fair, Yiquin Xie, Xiaowei JiaA new genomic resource to enable standardized surveys of SNPs across the native range of brook trout (Salvelinus fontinalis)
Understanding how genetic diversity is distributed across spatiotemporal scales in species of conservation or management concern is critical for identifying large-scale mechanisms affecting local conservation status and implementing large-scale biodiversity monitoring programmes. However, cross-scale surveys of genetic diversity are often impractical within single studies, and combining datasets tAuthorsNadya Mamoozadeh, Andrew R. Whiteley, Benjamin Letcher, David C. Kazyak, Charlene Tarsa, Mariah H. MeekClosing the gap between science and management of cold-water refuges in rivers and streams
Human activities and climate change threaten coldwater organisms in freshwater ecosystems by causing rivers and streams to warm, increasing the intensity and frequency of warm temperature events, and reducing thermal heterogeneity. Cold-water refuges are discrete patches of relatively cool water that are used by coldwater organisms for thermal relief and short-term survival. Globally, cohesive manAuthorsFrancine H. Mejia, Valerie Ouellet, Martin Briggs, Stephanie M. Carlson, Rose Casas-Mulet, Mollie Chapman, Matthias J. Collins, Stephen J. Dugdale, Joseph L. Ebersole, Danielle M. Frechette, Aimee H. Fullerton, Carol-Anne Gillis, Zachary Johnson, Christa Kelleher, Barret L. Kurylyk, Rebecca Lave, Benjamin Letcher, Knut M. Myrvold, Tracie-Lynn Nadeau, Helen Neville, Herve Piégay, Kathryn E. Smith, Diego Tonolla, Christian E. TorgersenCommunity for data integration 2019 project report
The U.S. Geological Survey Community for Data Integration annually supports small projects focusing on data integration for interdisciplinary research, innovative data management, and demonstration of new technologies. This report provides a summary of the 14 projects supported in fiscal year 2019 and outlines their goals, activities, and accomplishments. Proposals in 2019 were encouraged to addreAuthorsAmanda N. Liford, Caitlin M. Andrews, Aparna Bamzai, Joseph A. Bard, David S. Blehert, John B. Bradford, Wesley M. Daniel, Sara L. Caldwell Eldridge, Frank Engel, Jason A. Ferrante, Amy K. Gilmer, Margaret E. Hunter, Jeanne M. Jones, Benjamin Letcher, Frances L. Lightsom, Richard R. McDonald, Leah E. Morgan, Sasha C. Reed, Leslie HsuByEcosystems Mission Area, Water Resources Mission Area, Science Synthesis, Analysis and Research Program, Science Analytics and Synthesis (SAS) Program, Volcano Hazards Program, Community for Data Integration (CDI), Geology, Geophysics, and Geochemistry Science Center, Geosciences and Environmental Change Science Center, National Wildlife Health Center, Oklahoma-Texas Water Science Center, Southwest Biological Science Center, Volcano Science Center, Western Geographic Science Center, Wetland and Aquatic Research Center , Woods Hole Coastal and Marine Science Center, Science Data ManagementIdentifying mechanisms underlying individual body size increases in a changing, highly seasonal environment: The growing trout of West Brook
As air temperature increases, it has been suggested that smaller individual body size may be a general response to climate warming. However, for ectotherms inhabiting cold, highly seasonal environments, warming temperatures may increase the scope for growth and result in larger body size.In a long-term study of individual brook trout Salvelinus fontinalis and brown trout Salmo trutta inhabiting aAuthorsBenjamin Letcher, Keith Nislow, Matthew J. O'Donnell, Andrew R. Whiteley, Jason Coombs, Todd L. Dubreuil, Daniel TurekTowards continuous streamflow monitoring with time-lapse cameras and deep learning
Effective water resources management depends on monitoring the volume of water flowing through streams and rivers, but collecting continuous discharge measurements using traditional streamflow gauges is prohibitively expensive. Time-lapse cameras offer a lowcost option for streamflow monitoring, but training models for predicting streamflow directly from images requires streamflow data to use as lAuthorsAmrita Gupta, Tony Chang, Jeffrey Walker, Benjamin LetcherStream size, temperature, and density explain body sizes of freshwater salmonids across a range of climate conditions
Climate change and anthropogenic activities are altering the body sizes of fishes, yet our understanding of factors influencing body size for many taxa remains incomplete. We evaluated the relationships between climate, environmental, and landscape attributes and the body size of different taxa of freshwater trout (Salmonidae) in the USA. Hierarchical spatial modeling across a gradient of habitatsAuthorsRobert K. Al-Chokhachy, Benjamin Letcher, Clint C. Muhlfeld, Jason B. Dunham, Timothy Joseph Cline, Nathaniel P. Hitt, James Roberts, David SchmetterlingVIMTS: Variational-based Imputation for Multi-modal Time Series
Multi-modal time series data in real applications often contain data of different dimensionalities, e.g., high-dimensional modality such as image data series, and low-dimensional univariate time series. Multi-modal time series data with missing high-dimensional modal values are ubiquitous in real-world classification and regression applications. To accurately predict the target labels, it is imporAuthorsXiaowei Jia, Jennifer Burlingame Hoyle Fair, Benjamin LetcherCohort strength and body size in co-occurring salmonids in a small stream network: Variation in space and time
Trout and salmon commonly coexist in stream networks. Exploring similarities and differences among species can help explain coexistence and invasive ability. Here, we describe spatial distribution, cohort strengths and size-at-age of three co-occurring species in a small stream network. Spatial distributions varied dramatically among species; native brook trout occupied all stream reaches, naturalAuthorsBenjamin Letcher, Keith H. Nislow, Matthew O'Donnell, Andrew R. Whiteley, Jason A. Coombs, Todd L. Dubreuil - Science
Filter Total Items: 17
Brook trout vulnerability to drought: eastern component of USGS national integrated ecohydrological research
There is a growing and urgent need to develop and implement innovative strategies to research, monitor, and manage freshwater resources as societal demands escalate simultaneously with climate-driven changes in water availability.Integrating Streamflow and Temperature to Identify Streams with Coldwater Refugia in the Northeast
The amount of water flowing through a stream is an important driver of aquatic habitat, but scientists don’t often measure streamflow in the small stream networks that feed larger rivers. Monitoring smaller streams is especially important as climate change is causing them to (a) flood more often and more intensely, and (b) lose habitat as drought events and water temperatures increase. A better unEnabling AI for citizen science in fish biology
Artificial Intelligence (AI) is revolutionizing ecology and conservation by enabling species recognition from photos and videos. Our project evaluates the capacity to expand AI for individual fish recognition for population assessment. The success of this effort would facilitate fisheries analysis at an unprecedented scale by engaging anglers and citizen scientists in imagery collection. This...Enhancing Water Temperature Monitoring Efforts across Alaska through Collaborative Leveraging of a Statewide Database
Water temperatures affect the distribution, growth potential, and productivity of stream fishes that are targeted in subsistence, sport, and commercial fisheries across Alaska, making stream and lake temperature data critical for managing freshwater resources. Evaluating the variation in temperatures across Alaska will improve understanding of impacts of both climate change and development on fresNorth Atlantic-Appalachian AI/ML Capabilities
Artificial Intelligence (AI) and Machine Learning (ML) includes a broad suite of flexible data-driven empirical approaches to perform tasks that are difficult to implement using conventional methods. AI and ML harness the power of computing resources to evaluate the underlying patterns and relationships within a dataset without explicit instructions. The North Atlantic-Appalachian AI/ML Capability...Enabling AI for citizen science in fish ecology
Artificial Intelligence (AI) is revolutionizing ecology and conservation by enabling species recognition from photos and videos. Our project evaluates the capacity to expand AI for individual fish recognition for population assessment. The success of this effort would facilitate fisheries analysis at an unprecedented scale by engaging anglers and citizen scientists in imagery collection.This projeUnderstanding Brook Trout Persistence in Warming Streams
Cold-water adapted Brook Trout were historically widely distributed – ranging from northern Quebec to Georgia, and from the Atlantic Ocean to Manitoba in the north, and along the Appalachian ridge in the south. However, studies show that due to factors associated with climate change, such as increased stream temperature and changing water flow, the number of streams containing Brook Trout is decliScoping the Feasibility of Incorporating Climate Change into Risk Assessments of Aquatic Invasive Species in the Upper Midwest
Aquatic invasive species threaten our lakes, streams, and wetlands. These species not only change the biology within the waterbody, but they can change the way we use those waterbodies and the resources they produce. Those changes may have large economic impacts, such as direct management costs and indirect costs to fisheries, tourism and commerce. These species can be small like zebra mussels orBrook Trout Population Responses to Climate Variation Across the Southeast USA
Brook trout are the only native fish from the salmon family in the southeastern United States. Despite their recreational and cultural significance, human activities, such as habitat degradation and introduction of non-native species, have led to serious declines of brook trout populations in the region. Stream temperature and flow alterations from climate change are projected to impact this cold-A generic web application to visualize and understand movements of tagged animals
The goal of this project was to maximize the value of expensive animal tagging data. We developed an interactive web application to help scientists understand patterns in their own tagging datasets and to help scientists, funders and agencies communicate tagging data to decision-makers and to the general public. Interactive visualizations have emerged recently as a valuable tool for identifying paClimate change forecasts for eastern salmonids
Small streams in forests are likely to see dramatic shifts as global climate change influences air temperature and rain patterns. We have already seen warmer stream temperatures as air temperatures increase in summer in the Northeastern US. The intensity and duration of floods and droughts are also expected to magnify as future rain patterns shift. This project will evaluate how stream temperature...The West Brook Story
Natural systems, like rivers and streams, are remarkably complex, with many interacting parts. Data visualization tools make understanding and communicating complex ecological processes easier. Effective visualizations help users learn about patterns in data and how models work. Interactive visualizations are particularly useful, as they let users explore data and develop a personal understanding... - Data
Brook trout abundance in streams across southern Appalachia from 1958-2021
This Data Release compiles records of brook trout abundance from 745 unique sites across the southern Appalachian mountains from 1958-2021. Records were compiled from 10 institutions, primarily state natural resource agencies. Data were collected from wadeable stream environments with standard backpack electrofishing methods, and observed abundances of adult and juvenile brook trout are reported fWest Brook Trout Data, Whatley, Massachusetts.
The Ecology Section at the USGS Conte Laboratory has studied fish in the West Brook since 1997. The goal is to understand the strength and direction of drivers on fish growth, movement, reproduction and survival in the wild. We hope to provide a comprehensive understanding of fish population dynamics and ultimately individual fitness (natural selection and evolution) in the study area.Brook trout imagery data for individual recognition with deep learning
This Data Release provides imagery data for the development of deep-learning models to recognize individual brook trout (n=435). Images were collected at the Paint Bank State Fish Hatchery (Paint Bank, VA) on August 9, 2021 using a GoPro Hero 9 camera mounted approximately 50 cm above a fish board. The Paint Bank State Fish Hatchery is operated by the Virginia Department of Wildlife Resources.USGS EcoDrought Stream Discharge, Gage Height, and Water Temperature in Shenandoah National Park, Virginia
The U.S. Geological Survey (USGS) Water Mission Area (WMA) - Ecosystems Mission Area (EMA) EcoDrought project is comprised of interdisciplinary teams in five pilot regions across the country. The over-arching project goal is to measure streamflow in headwater streams and to relate flow variation to stream fish population dynamics. For the catchments located in Shenandoah National Park, Virginia,USGS EcoDrought Stream Discharge, Gage Height, and Water Temperature Data in Massachusetts
The USGS Water Mission Area (WMA) - Ecosystems Mission Area (EMA) EcoDrought project is comprised of interdisciplinary teams in five pilot regions across the country. The over-arching project goal is to measure streamflow in headwater streams and to relate flow variation to stream fish population dynamics. In the northeast, the New England Water Science Center (NewEngWSC) partnered with the fishAnnotated fish imagery data for individual and species recognition with deep learning
We provide annotated fish imagery data for use in deep learning models (e.g., convolutional neural networks) for individual and species recognition. For individual recognition models, the dataset consists of annotated .json files of individual brook trout imagery collected at the Eastern Ecological Science Center's Experimental Stream Laboratory. For species recognition models, the dataset consist - Multimedia
Eyes On Streams - The Short Story
Flow is a critical variable in streams since it affects aquatic and riparian biological communities and human uses of water (i.e., recreation, public water supply, etc.). Flow regimes are changing due to anthropogenic (e.g., water withdrawals) and natural impacts (e.g., extreme weather events).
Flow is a critical variable in streams since it affects aquatic and riparian biological communities and human uses of water (i.e., recreation, public water supply, etc.). Flow regimes are changing due to anthropogenic (e.g., water withdrawals) and natural impacts (e.g., extreme weather events).
Eyes On Streams - The Short Story (AD)Flow is a critical variable in streams since it affects aquatic and riparian biological communities and human uses of water (i.e., recreation, public water supply, etc.). Flow regimes are changing due to anthropogenic (e.g., water withdrawals) and natural impacts (e.g., extreme weather events).
Flow is a critical variable in streams since it affects aquatic and riparian biological communities and human uses of water (i.e., recreation, public water supply, etc.). Flow regimes are changing due to anthropogenic (e.g., water withdrawals) and natural impacts (e.g., extreme weather events).
Imagery as Streamflow Data: Introducing the USGS Flow Photo ExplorerImagery as Streamflow Data: Introducing the USGS Flow Photo ExplorerImagery as Streamflow Data: Introducing the USGS Flow Photo ExplorerFlow is a critical variable in streams since it affects aquatic and riparian biological communities and human uses of water (i.e., recreation, public water supply, etc.). Flow regimes are changing due to anthropogenic (e.g., water withdrawals) and natural impacts (e.g., extreme weather events).
Flow is a critical variable in streams since it affects aquatic and riparian biological communities and human uses of water (i.e., recreation, public water supply, etc.). Flow regimes are changing due to anthropogenic (e.g., water withdrawals) and natural impacts (e.g., extreme weather events).
Imagery as Streamflow Data: Introducing the USGS Flow Photo Explorer (AD)Imagery as Streamflow Data: Introducing the USGS Flow Photo Explorer (AD)Imagery as Streamflow Data: Introducing the USGS Flow Photo Explorer (AD)Flow is a critical variable in streams since it affects aquatic and riparian biological communities and human uses of water (i.e., recreation, public water supply, etc.). Flow regimes are changing due to anthropogenic (e.g., water withdrawals) and natural impacts (e.g., extreme weather events).
Flow is a critical variable in streams since it affects aquatic and riparian biological communities and human uses of water (i.e., recreation, public water supply, etc.). Flow regimes are changing due to anthropogenic (e.g., water withdrawals) and natural impacts (e.g., extreme weather events).
- Web Tools
Interactive Catchment Explorer (ICE)
Interactive Catchment Explorer (ICE) is a web-based data visualization tool for exploring complex, multivariate environmental datasets and model results. It is designed to help researchers and resource managers identify spatial patterns in hydro-ecological conditions and to prioritize locations for restoration or further study.
Flow Photo Explorer
The Flow Photo Explorer is an integrated database, machine learning, and data visualization platform for monitoring streamflow and other hydrologic conditions using timelapse images.
EcoSHEDS
EcoSHEDS is a collection of Spatial Hydro-Ecological Data Systems (SHEDS) designed to improve our understanding of stream ecosystems. The goal of EcoSHEDS is to provide a series of user-friendly tools for gaining insight and supporting transparent research, management, and decision-making of hydro-ecological resources.
- Software
Ecosheds.org
LSC Conte Anadrmous Fish Laboratory is currently involved in https://ecosheds.org.