Skip to main content
U.S. flag

An official website of the United States government

Species We Study: Fish Active

By Species Management Research Program September 27, 2022

We are a scientific leader in aquatic species biology, genetics, toxicological and pathogenic disease, ecology, and population tracking and dynamics for at-risk aquatic species including native fish and their ecosystems.

Fish Research

link
Brook trout image

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.
By
Ecosystems Mission Area, Species Management Research Program, Eastern Ecological Science Center
link

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.
Learn More
link
brook trout

Enabling 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...
By
Core Science Systems Mission Area, Ecosystems Mission Area, Species Management Research Program, Eastern Ecological Science Center
link

Enabling 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...
Learn More
link
Water flowing in the Wailuku River in Hawai'i

Webinar: Assessing the Impact of Future Climate and Introduced Species on Hawaiʻi's Aquatic Ecosystems

View this webinar to learn how a warming climate will have fundamental impacts on freshwater, a critical driver of tropical island ecosystems.
By
Ecosystems Mission Area, Climate Adaptation Science Centers
link

Webinar: Assessing the Impact of Future Climate and Introduced Species on Hawaiʻi's Aquatic Ecosystems

View this webinar to learn how a warming climate will have fundamental impacts on freshwater, a critical driver of tropical island ecosystems.
Learn More
link
Adult Chinook salmon

Chinook Salmon (Oncorhynchus tshawytscha) - KFFS

Species Studied - Chinook Salmon (Oncorhynchus tshawytscha)
By
Ecosystems Mission Area, Western Fisheries Research Center, Klamath Falls Field Station (KFFS)
link

Chinook Salmon (Oncorhynchus tshawytscha) - KFFS

Species Studied - Chinook Salmon (Oncorhynchus tshawytscha)
Learn More
link
Beach seining Nisqually River

Puget Sound Fall Chinook Estuarine Utilization

The WFRC has partnered separately with both the Skagit River System Tribal Cooperative and the Nisqually Tribe to research the use of otoliths (calcium carbonate deposits beneath the brain used in hearing and balance that grow in proportion to the overall growth of the fish) as a tool in examination of Puget Sound Fall Chinook salmon life history.
By
Ecosystems Mission Area, Species Management Research Program, Western Fisheries Research Center
link

Puget Sound Fall Chinook Estuarine Utilization

The WFRC has partnered separately with both the Skagit River System Tribal Cooperative and the Nisqually Tribe to research the use of otoliths (calcium carbonate deposits beneath the brain used in hearing and balance that grow in proportion to the overall growth of the fish) as a tool in examination of Puget Sound Fall Chinook salmon life history.
Learn More
link
Chinook salmon (Oncorhynchus tshawytscha)

Chinook Salmon (Oncorhynchus tshawytscha)

Species Studied - Chinook Salmon (Oncorhynchus tshawytscha)
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Species Management Research Program, Western Fisheries Research Center
link

Chinook Salmon (Oncorhynchus tshawytscha)

Species Studied - Chinook Salmon (Oncorhynchus tshawytscha)
Learn More
link
Anadromous Bull trout (Salvelinus confluentus)

Bull Trout (Salvelinus confluentus)

Species Studied - Bull Trout (Salvelinus confluentus)
By
Ecosystems Mission Area, Species Management Research Program, Western Fisheries Research Center
link

Bull Trout (Salvelinus confluentus)

Species Studied - Bull Trout (Salvelinus confluentus)
Learn More
link
fish passage hydraulic flume

Fish Passage Hydraulic Flume

Many existing upstream and downstream fish passage structure designs (fishways, culverts, screens, downstream bypasses, etc.) function poorly or only for a narrow range of species or environmental conditions. Resource agencies consistently seek new or improved designs that pass a broader range of species with high efficiency and reliability, under a wider range of hydraulic operating conditions...
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Species Management Research Program, Eastern Ecological Science Center
link

Fish Passage Hydraulic Flume

Many existing upstream and downstream fish passage structure designs (fishways, culverts, screens, downstream bypasses, etc.) function poorly or only for a narrow range of species or environmental conditions. Resource agencies consistently seek new or improved designs that pass a broader range of species with high efficiency and reliability, under a wider range of hydraulic operating conditions...
Learn More
link
Scientist Holding an Adult Pacific Lamprey

Pesticides, Flame Retardants, and Mercury in Tissues from Columbia Basin Pacific Lamprey

Pesticides, flame retardants, and mercury were present in Pacific lampreys (Entosphenus tridentatus) at levels that may be contributing to their overall decline in the Columbia River Basin.These findings are based on the largest available dataset of contaminants measured in lamprey tissues and lamprey habitats by the U.S. Geological Survey (USGS) and the Columbia River Inter-Tribal Fish Commission...
By
Ecosystems Mission Area, Contaminant Biology, Environmental Health Program
link

Pesticides, Flame Retardants, and Mercury in Tissues from Columbia Basin Pacific Lamprey

Pesticides, flame retardants, and mercury were present in Pacific lampreys (Entosphenus tridentatus) at levels that may be contributing to their overall decline in the Columbia River Basin.These findings are based on the largest available dataset of contaminants measured in lamprey tissues and lamprey habitats by the U.S. Geological Survey (USGS) and the Columbia River Inter-Tribal Fish Commission...
Learn More
link
Image: Beach of the Great Lakes

Webinar: Predicted Climate Change Effects on Fisheries Habitat and Production in the Great Lakes

View this webinar to learn more about fisheries management in the Great Lakes.
By
Ecosystems Mission Area, Climate Adaptation Science Centers, Climate Adaptation Science Centers
link

Webinar: Predicted Climate Change Effects on Fisheries Habitat and Production in the Great Lakes

View this webinar to learn more about fisheries management in the Great Lakes.
Learn More

Explore our science using the data below.

The North American Freshwater Migratory Fish Database (NAFMFD): Characterizing the migratory life histories of freshwater fishes of Canada, the United States, and Mexico

We developed the North American Freshwater Migratory Fish Database (NAFMFD) that synthesizes current knowledge of migratory status, pattern, and behavior for native and non-native freshwater fish species throughout North America, including 1,241 species representing 79 families and 322 genera.
By
Wetland and Aquatic Research Center

Aquatic Prey Resources in Response to Estuary Restoration in Willapa Bay, Washington (2014-2015)

The ongoing restoration of more than 200 hectares of estuarine habitat at Willapa National Wildlife Refuge, southwestern Washington, is expected to benefit a variety of species, including salmonids that use estuarine and tidal marshes as rearing and feeding areas as well as migratory waterbirds. During March through June 2014 and 2015, this study was initiated to assess aquatic prey resources. We
By
Western Ecological Research Center (WERC)

Age, Trace Metal, Stable Isotope, and Fatty Acid Data Collected from Sturgeon Captured in the Mississippi and St. Croix Rivers, Minnesota and Wisconsin, 2015-2016.

Proposed invasive carp barriers may threaten populations of migratory fishes in the St. Croix National Scenic Riverway and the Mississippi National River and Recreation Area by preventing movements between rivers needed to fulfill life history requirements. Moreover, reproducing populations of invasive carp could alter aquatic food webs and negatively affect mussels and migratory fishes. In this s
By
Upper Midwest Environmental Sciences Center

Image and biometric data for fish from Great Lakes tributaries collected during spring 2019

Image and biometric data were collected for 22 species of fish from Great Lakes Tributaries in Michigan and Ohio, and the Illinois River for the purpose of developing a fish identification classifier. Data consists of a comma delimited spreadsheet that identifies image file names and associated fish identification number, common name, species code, family name, genus, and species, date collected,
By
Great Lakes Science Center

Water Temperature and Dissolved Oxygen Measured During a Manipulative Thermal Challenge Experiment for Adult Salmonids, Yukon River, Alaska, 2018

This data set documents the temperature and dissolved oxygen of water during the implementation of a new experimental thermal challenge protocol for migrating adult Pacific salmon in remote settings. This experiment was conducted with migrating adult Chinook salmon near Pilot Station, Alaska, along the Yukon River in a location without access to utilities. The analysis of this data was published i
By
Alaska Science Center

Gene Transcription and Heat Shock Protein 70 Abundance Results from Migrating Adult Chinook Salmon, Yukon Watershed, 2016-2017

This data set documents the gene transcription levels for a panel of 12 selected genes and the heat shock protein 70 (HSP70) protein abundance measured in the muscle tissue of individual wild Chinook salmon captured from locations within the U.S. portion of the Yukon River watershed. Chinook salmon were primarily captured in 2016 and 2017 from existing field efforts (n = 477). A small number of ad
By
Alaska Science Center

Environmental DNA (eDNA) is an Effective Tool to Track Recolonizing Migratory Fish Following Large-Scale Dam Removal, field data

We collected environmental DNA (eDNA) data from the Elwha River, home to the world?s largest dam removal project, to track the spatial and temporal patterns of species responses following dam removal. In total, we collected data for 11 different fish taxa, sampled at 25 sites ranging across 56 river kilometers in a wilderness river for 4 years following dam removal. We show that eDNA can effective
By
Ecosystems Mission Area, Species Management Research Program, Western Fisheries Research Center

Recent publications (2020-2022) related to USGS migratory fish research are listed below. A complete listing of USGS migratory fish publications is available from the button below.

Complete List of Publications
Filter Total Items: 22

Brief oil exposure reduces fitness in wild Gulf of Mexico mahi-mahi (Coryphaena hippurus)

The Deepwater Horizon (DWH) disaster released 3.19 million barrels of crude oil into the Gulf of Mexico (GOM) in 2010, overlapping the habitat of pelagic fish populations. Using mahi-mahi (Coryphaena hippurus)─a highly migratory marine teleost present in the GOM during the spill─as a model species, laboratory experiments demonstrate injuries to physiology and behavior following oil exposure. Howev
Authors
Lela S. Schlenker, John D. Stieglitz, Justin Blaine Greer, Robin Faillettaz, Chi Hin Lam, Ronald H. Hoenig, Rachael M. Heuer, Charles J. McGuigan, Christina Pasparakis, Emma B. Esch, Gabrielle M. Ménard, Alexandra L. Jaroszewski, Claire B. Paris, Daniel Schlenk, Daniel D. Benetti, Martin Grosell
By
Ecosystems Mission Area, Western Fisheries Research Center, Fish Health Program (FHP)

One shell of a problem: Cumulative threat analysis of male sea turtles indicates high anthropogenic threat for migratory individuals and Gulf of Mexico residents

Human use of oceans has dramatically increased in the 21st century. Sea turtles are vulnerable to anthropogenic stressors in the marine environment because of lengthy migrations between foraging and breeding sites, often along coastal migration corridors. Little is known about how movement and threat interact specifically for male sea turtles. To better understand male sea turtle movement and the
Authors
Micah Ashford, James I. Watling, Kristen Hart
By
Ecosystems Mission Area, Land Management Research Program, Wetland and Aquatic Research Center , Gulf of Mexico

The North American Freshwater Migratory Fish Database (NAFMFD): Characterizing the migratory life histories of freshwater fishes of Canada, the United States and Mexico

AimMigratory freshwater fishes are those that must access discrete habitats to complete their life cycles. Freshwater fish migrations occur around the world and provide numerous ecosystem services for humans and natural systems; however, many migratory species are in decline globally. A limiting factor to successfully conserve freshwater migratory fishes is that the migratory life histories of man
Authors
Emily M. Dean, Arthur R. Cooper, Lizhu Wang, Wesley Daniel, Solomon David, Clayton Ernzen, Keith B. Gido, Edward Hale, Tim J. Haxton, William Kelso, Nancy J. Leonard, Chris Lido, Joseph Margraf, Michael D. Porter, Casey A. Pennock, David L. Propst, Jared Ross, Michelle Staudinger, Dana M. Infante, Gary Whelan
By
Ecosystems Mission Area, Wetland and Aquatic Research Center

A climate-mediated shift in the estuarine habitat mosaic limits prey availability and reduces nursery quality for juvenile salmon

The estuarine habitat mosaic supports the reproduction, growth, and survival of resident and migratory fish species by providing a diverse portfolio of unique habitats with varying physical and biological features. Global climate change is expected to result in increasing temperatures, rising sea levels, and changes in riverine hydrology, which will have profound effects on the extent and composit
Authors
Melanie J. Davis, Isa Woo, Christopher S. Ellings, Sayre Hodgson, David Beauchamp, Glynnis Nakai, Susan E. W. De La Cruz
By
Ecosystems Mission Area, Cooperative Research Units, Species Management Research Program, Western Ecological Research Center (WERC), Western Fisheries Research Center

Factors affecting spatiotemporal variation in survival of endangered winter-run Chinook Salmon outmigrating from the Sacramento River

Among four extant and declining Chinook salmon (Oncorhynchus tshawytscha) runs in California’s Central Valley, none have declined as precipitously as Sacramento River winter-run Chinook Salmon. In addition to habitat loss, migratory winter-run employ a life history strategy to reside and feed in stopover habitats on their way from freshwaters to the ocean. This life history strategy is widely cons
Authors
Jason L. Hassrick, Arnold J. Ammann, Russell Perry, Sara N. John, Miles E. Daniels
By
Ecosystems Mission Area, Species Management Research Program, Western Fisheries Research Center, Columbia River Research Laboratory (CRRL)

Reconnecting the Elwha River: Spatial patterns of fish response to dam removal

The removal of two large dams on the Elwha River was completed in 2014 with a goal of restoring anadromous salmonid populations. Using observations from ongoing field studies, we compiled a timeline of migratory fish passage upstream of each dam. We also used spatially continuous snorkeling surveys in consecutive years before (2007, 2008) and after (2018, 2019) dam removal during summer baseflow t
Authors
Jeffrey J. Duda, Christian E. Torgersen, Samuel J. Brenkman, Roger J. Peters, Kathryn T. Sutton, Heidi A. Connor, Philip R. Kennedy, Stephen C. Corbett, Ethan Z. Welty, Anna Geffre, Josh Geffre, Patrick Crain, Dave Shreffler, John R. McMillan, Mike McHenry, George R. Pess
By
Ecosystems Mission Area, Species Management Research Program, Forest and Rangeland Ecosystem Science Center, Western Fisheries Research Center

Culverts delay upstream and downstream migrations of river herring (Alosa spp.)

Alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis) are iteroparous anadromous fish found throughout the East Coast of North America. The phenology of anadromous fish migrations is important for fitness, and the duration of spawning migrations has been compressed in recent years in response to climate change. Anthropogenic barriers to movement, such as dams and culverts at road-
Authors
Derrick Alcott, Elsa Goerig, Theodore R. Castro-Santos
By
Ecosystems Mission Area, Eastern Ecological Science Center

Survival and spawning success of American shad (Alosa sapidissima) in varying temperatures and levels of glochidia infection

Temperature fluctuations and climate change impacts may substantially affect spawning success of fish, especially migratory species with a limited spawning window. Factors affecting American shad (Alosa sapidissima) spawning success and survival were investigated at different temperatures and periods (peak- and late-spawning periods) during the Connecticut River, USA, spawning migration in 2017. W
Authors
Shannon M Bayse, Amy M. Regish, Stephen D. McCormick
By
Ecosystems Mission Area, Eastern Ecological Science Center

From drought to deluge: Spatiotemporal variation in migration routing, survival, travel time and floodplain use of an endangered migratory fish

We developed a novel statistical model to relate the daily survival and migration dynamics of an endangered anadromous fish to river flow and water temperature during both extreme drought and severe flooding in an intensively managed river system. Our Bayesian temporally stratified multistate mark recapture model integrates over unobserved travel times and route transitions to efficiently estimate
Authors
Dalton Hance, Russell Perry, Adam Pope, Arnold J. Ammann, Jason L. Hassrick, Gabriel S. Hansen
By
Ecosystems Mission Area, Species Management Research Program, Western Fisheries Research Center, Columbia River Research Laboratory (CRRL)

Spatial and temporal distribution of radio-tagged Lost River (Deltistes luxatus) and shortnose (Chasmistes brevirostris) suckers in Clear Lake Reservoir and associated spawning tributaries, Northern California, 2015–17

Executive SummaryData from a multi-year radio telemetry study were used to assess seasonal distribution patterns for two long-lived, federally endangered catostomids across substantially different water conditions in Clear Lake Reservoir, northern California. Lost River (Deltistes luxatus) and shortnose (Chasmistes brevirostris) suckers, two species endemic to the Klamath Basin, were implanted wit
Authors
Nathan Banet, David A. Hewitt, Amari Dolan-Caret, Alta C. Harris
By
Ecosystems Mission Area, Western Fisheries Research Center, Klamath Falls Field Station (KFFS)

Environmental factors influencing annual sucker (Catostomus sp.) migration into a Great Lakes tributary

Fish migration in rivers is a growing area of concern as mounting anthropogenic influences, particularly fragmentation from dams and barriers, constitute major threats to global river species diversity. Barriers can impede the movement of fishes between areas critical to the completion of their lifecycle, affecting both population and ecosystem viability. In response, fish passage solutions have b
Authors
Reid G Swanson, Erin L. McCann, Nicholas S. Johnson, Daniel P. Zielinski
By
Ecosystems Mission Area, Great Lakes Science Center

Partial migration and spawning movements of humpback chub in the Little Colorado River are better understood using data from autonomous PIT tag antennas

Choosing whether or not to migrate is an important life history decision for many fishes. Here we combine data from physical captures and detections on autonomous passive integrated transponder (PIT) tag antennas to study migration in an endangered fish, the humpback chub (Gila cypha). We develop hidden Markov mark-recapture models with and without antenna detections and find that the model fit wi
Authors
Maria C. Dzul, William Louis Kendall, Charles Yackulic, Dana L. Winkelman, David Randall Van Haverbeke, Mike Yard
By
Ecosystems Mission Area, Southwest Biological Science Center

Explore our science through the interactive tools below.

Arctic Rivers Project: Connecting Indigenous knowledge and western science to strengthen collective understanding of the changing Arctic

The Arctic Rivers Project will weave together Indigenous knowledges, monitoring, and the modeling of climate, rivers (flows, temperature, ice), and fish to improve understanding of how Arctic rivers, ice transportation corridors, fish, and communities might be impacted by and adapt to climate change.

By
Ecosystems Mission Area, Water Resources Mission Area, Land Management Research Program, Alaska Science Center

Mercury in Freshwater Fish of the Chesapeake Bay Watershed—Story Map

The US Geological Survey (USGS), working with the partners in the watershed, compiled mercury data for freshwater fishes to understand how mercury concentrations, and risk to consumers, varies across the watershed.

By
Ecosystems Mission Area, Environmental Health Program, Land Management Research Program, Chesapeake Bay Activities, Forest and Rangeland Ecosystem Science Center

BEST Large Rivers Monitoring Network (LRMN)

The Biomonitoring of Environmental Status and Trends (BEST) Program's Large River Monitoring Network (LRMN) has examined fish health in multiple river basins by using a suite of organismal and suborganismal endpoints, which monitor and assess the effects of environmental contaminants in fish.

By
Columbia Environmental Research Center

Chinook Salmon Use of Eelgrass Habitats Skagit River Delta Washington

The degree to which eelgrass on river deltas provides critical habitat for estuarine fishes, especially out‐migrating juvenile salmon, is an important scientific and management issue that bears on efforts to conserve and restore both eelgrass and fish.

By
Ecosystems Mission Area, Species Management Research Program, Pacific Coastal and Marine Science Center, Western Fisheries Research Center

LTRM Spatial Data Query Tool

The Upper Mississippi River Restoration (UMRR) Program Long Term Resource Monitoring (LTRM) element has collected millions of records of information over 20+ years. Fisheries, water quality, vegetation, and invertebrates have all been sampled. Geographic locations were collected for all sampling points. 

By
Land Management Research Program, Upper Midwest Environmental Sciences Center

Explore our science using the software below.

Mercury Condition Index Tool

The Mercury Condition Index Tool uses existing data of mercury concentrations in invertebrates, fish, and birds within national parks to estimate a park level Condition Index (and associated uncertainty) for mercury, based on its potential risk to fish and wildlife health. The tool employs a series of logic steps to convert provided data into standardized units, based upon both basic stoichiometr
By
Ecosystems Mission Area, Species Management Research Program, Forest and Rangeland Ecosystem Science Center

Data Retrieval and Graphing Using the LTRM Fish Catch GeoJSON Data Service

UMESC hosts a web service for the retrieval of LTRM fish catch data using the GeoJSON data format. By using this data service, the public can automate data access to LTRM fisheries data. UMESC has written a series of example Python scripts that illustrate data retrieval and plotting. These example scripts focus on plotting fish catch, but there are limitless geo-spatial, tabular, and plotting pr
By
Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Upper Midwest Environmental Sciences Center

SPECRICH2

Estimates the total number of species from species presence-absence data on multiple sample sites or occasions using model M(h) from program CAPTURE.

By
Eastern Ecological Science Center

See what's in the news!

link

Engaging Stakeholders for Prioritizing Investments in Recovery of Threatened Bull Trout

The natural resource agencies involved in conservation of the threatened Bull Trout have a shared goal of recovering the species. However, this goal...

Read Article
link

Stream Food Web Responses to Riparian Forest Thinning

Resource managers may decide to thin riparian forests to increase the amount of light that streams receive and enhance aquatic productivity. However...

Read Article
link

New Map Identifies Optimal Stream Reaches for Endangered Atlantic Salmon

The new web application uses certain environmental parameters to show which stream reaches in Maine may have deeper, colder waters that are ideal...

Read Article
link

In Blue Water: Tracking Animals in the Open Ocean

Scientists are attaching tracking tags to marine animals at Palmyra Atoll to learn how marine protected areas can best serve diverse species. 

Read Article
link

USGS Study Suggests Atlantic Sturgeon Spawning Population Declined by More Than 99% in the Delaware River Since the Late 1800s

The population of adult Atlantic sturgeon that migrate to the Delaware River each year was once comprised of hundreds of thousands of individual fish...

Read Article
link

Unraveling the Mysteries of Wild Fish Populations – Deducing Marine Disease Impacts in Fisheries Stocks

Determining the causes of natural mortality in wild marine fish populations is extremely challenging. Scientists at WFRC and University of Washington...

Read Article
link

Exploring the Feasibility of Reintroducing Salmon to the Upper Columbia River

Reintroducing anadromous fish upstream of Grand Coulee and Chief Joseph dams has the potential to substantially contribute to the recovery of salmon...

Read Article
link

Riverscapes, Dam Removal and River Restoration—Exploring how River Ecosystems Respond to Dam Removals

Rivers around the world provide valuable ecosystem services like food, drinking water, and recreational opportunity, as well as important...

Read Article
link

Wanted: Information about capelin spawning on beaches in Alaska

Capelin, a small forage fish, are spawning on beaches around Alaska and your observations can contribute to our understanding of beach spawning...

Read Article
link

Science Supporting Water Management Decisions and Pacific Salmon Enhancement in the Willamette River Basin

Science supporting water management decisions and Pacific salmon enhancement in the Willamette River Basin

Read Article
link

Translating the Relevance of USGS Science to Trout Unlimited’s Conservation and Engagement Work

Scientists with the USGS and Trout Unlimited (TU) recently hosted an event to facilitate cross-organizational learning and collaborative...

Read Article