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Fish and Aquatic Ecology

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By Alaska Science Center September 30, 2025

Fish and aquatic habitats in Alaska support important commercial, sport, and subsistence fisheries and provide forage fish that support wildlife populations.  The USGS Alaska Science Center conducts interdisciplinary research to inform local, state, federal, and international policy makers regarding conservation of fish, aquatic species, and their habitats.  We work collaboratively with hydrologists, geologists and other biologists to study fish and aquatic systems in an ecosystem based framework.  The goal of our current research effort is to improve our understanding of the biocomplexity, resilience, and function of aquatic ecosystems to better inform future predictions of fish and aquatic ecosystems as they respond to a changing environment.

Return to Ecosystems

Media
Two people pulling a beach seine net in Salmon Lake.
Sources/Usage: Public Domain. View Media Details
Beach seining on the spawing grounds of sockeye salmon in Salmon Lake. This is the headwater of the Pilgrim River which is the northern edge of the sockeye salmon distribution.(Credit: Mike Carey, USGS. Public domain.)

Below are other science projects associated with this project.

Filter Total Items: 16

Below are data or web applications associated with this project.

Filter Total Items: 44
No Result Found

Below are multimedia items associated with this project.

Filter Total Items: 100
No results found.

Below are publications associated with this project.

Filter Total Items: 73

Long-term increases in young-of-the-year growth of Arctic cisco Coregonus autumnalis and environmental influences Long-term increases in young-of-the-year growth of Arctic cisco Coregonus autumnalis and environmental influences

Arctic cisco Coregonus autumnalis young-of-year (YOY) growth was used as a proxy to examine the long-term response of a high-latitude fish population to changing climate from 1978 to 2004. YOY growth increased over time (r2 = 0·29) and was correlated with monthly averages of the Arctic oscillation index, air temperature, east wind speed, sea-ice concentration and river discharge with and...
Authors
Vanessa R. von Biela, Christian E. Zimmerman, L. L. Moulton
By
Ecosystems Mission Area, Alaska Science Center

Electronic tags and genetics explore variation in migrating steelhead kelts (oncorhynchus mykiss), Ninilchik river, Alaska Electronic tags and genetics explore variation in migrating steelhead kelts (oncorhynchus mykiss), Ninilchik river, Alaska

Acoustic and archival tags examined freshwater and marine migrations of postspawn steelhead kelts (Oncorhynchus mykiss) in the Ninilchik River, Alaska, USA. Postspawn steelhead were captured at a weir in 2002-2005. Scale analysis indicated multiple migratory life histories and spawning behaviors. Acoustic tags were implanted in 99 kelts (2002-2003), and an array of acoustic receivers...
Authors
J.L. Nielsen, S.M. Turner, Christian E. Zimmerman
By
Ecosystems Mission Area, Alaska Science Center

Status and distribution of the Kittlitz's Murrelet Brachyramphus brevirostris along the Alaska Peninsula and Kodiak and Aleutian Islands, Alaska Status and distribution of the Kittlitz's Murrelet Brachyramphus brevirostris along the Alaska Peninsula and Kodiak and Aleutian Islands, Alaska

The Kittlitz's Murrelet Brachyramphus brevirostris is adapted for life in glacial-marine ecosystems, being concentrated in the belt of glaciated fjords in the northern Gulf of Alaska from Glacier Bay to Cook Inlet. Most of the remaining birds are scattered along coasts of the Alaska Peninsula and Aleutian Islands, where they reside in protected bays and inlets, often in proximity to...
Authors
Erica N. Madison, John F. Piatt, Mayumi L. Arimitsu, Marc D. Romano, Thomas I. van Pelt, S. Kim Nelson, Jeffrey C. Williams, Anthony R. DeGange
By
Ecosystems Mission Area, Alaska Science Center

Kittlitz’s and Marbled Murrelets in Kenai Fjords National Park, south-central Alaska: At-sea distribution, abundance, and foraging habitat, 2006–08 Kittlitz’s and Marbled Murrelets in Kenai Fjords National Park, south-central Alaska: At-sea distribution, abundance, and foraging habitat, 2006–08

Kittlitz’s murrelets (Brachyramphus brevirostris) and marbled murrelets (B. marmoratus) are small diving seabirds and are of management concern because of population declines in coastal Alaska. In 2006–08, we conducted a study in Kenai Fjords National Park, south-central Alaska, to estimate the recent population size of Brachyramphus murrelets, to evaluate productivity based on juvenile...
Authors
Mayumi L. Arimitsu, John F. Piatt, Marc D. Romano, E.N. Madison, Jeffrey S. Conaway
By
Ecosystems Mission Area, Alaska Science Center

Characteristics of fall chum salmon spawning habitat on a mainstem river in Interior Alaska Characteristics of fall chum salmon spawning habitat on a mainstem river in Interior Alaska

Chum salmon (Oncorhynchus keta) are the most abundant species of salmon spawning in the Yukon River drainage system, and they support important personal use, subsistence, and commercial fisheries. Chum salmon returning to the Tanana River in Interior Alaska are a significant contribution to the overall abundance of Yukon River chum salmon and an improved understanding of habitat use is...
Authors
Sean E. Burril, Christian E. Zimmerman, James E. Finn
By
Ecosystems Mission Area, Alaska Science Center

Abundance, Timing of Migration, and Egg-to-Smolt Survival of Juvenile Chum Salmon, Kwethluk River, Alaska, 2007 and 2008 Abundance, Timing of Migration, and Egg-to-Smolt Survival of Juvenile Chum Salmon, Kwethluk River, Alaska, 2007 and 2008

To better understand and partition mortality among life stages of chum salmon (Oncorhynchus keta), we used inclined-plane traps to monitor the migration of juveniles in the Kwethluk River, Alaska in 2007 and 2008. The migration of juvenile chum salmon peaked in mid-May and catch rates were greatest when water levels were rising. Movement of chum salmon was diurnal with highest catch...
Authors
Sean E. Burril, Christian E. Zimmerman, James E. Finn, Daniel Gillikin
By
Ecosystems Mission Area, Alaska Science Center

A likelihood framework for joint estimation of salmon abundance and migratory timing using telemetric mark-recapture A likelihood framework for joint estimation of salmon abundance and migratory timing using telemetric mark-recapture

Many fisheries for Pacific salmon Oncorhynchus spp. are actively managed to meet escapement goal objectives. In fisheries where the demand for surplus production is high, an extensive assessment program is needed to achieve the opposing objectives of allowing adequate escapement and fully exploiting the available surplus. Knowledge of abundance is a critical element of such assessment...
Authors
Jeffrey F. Bromaghin, Kenneth S. Gates, Douglas E. Palmer
By
Ecosystems Mission Area, Alaska Science Center

Recent ecological divergence despite migration in sockeye salmon (Oncorhynchus nerka) Recent ecological divergence despite migration in sockeye salmon (Oncorhynchus nerka)

Ecological divergence may result when populations experience different selection regimes, but there is considerable discussion about the role of migration at the beginning stages of divergence before reproductive isolating mechanisms have evolved. However, detection of past migration is difficult in current populations and tools to differentiate genetic similarities due to migration...
Authors
Scott A. Pavey, Jennifer L. Nielsen, Troy R. Hamon
By
Ecosystems Mission Area, Alaska Science Center

Perspectives: Gene Expression in Fisheries Management Perspectives: Gene Expression in Fisheries Management

Functional genes and gene expression have been connected to physiological traits linked to effective production and broodstock selection in aquaculture, selective implications of commercial fish harvest, and adaptive changes reflected in non-commercial fish populations subject to human disturbance and climate change. Gene mapping using single nucleotide polymorphisms (SNPs) to identify...
Authors
Jennifer L. Nielsen, Scott A. Pavey
By
Ecosystems Mission Area, Alaska Science Center

Fine-scale population genetic structure in Alaskan Pacific halibut (Hippoglossus stenolepis) Fine-scale population genetic structure in Alaskan Pacific halibut (Hippoglossus stenolepis)

Pacific halibut collected in the Aleutian Islands, Bering Sea and Gulf of Alaska were used to test the hypothesis of genetic panmixia for this species in Alaskan marine waters. Nine microsatellite loci and sequence data from the mitochondrial (mtDNA) control region were analyzed. Eighteen unique mtDNA haplotypes were found with no evidence of geographic population structure. Using nine
Authors
Jennifer L. Nielsen, Sara L. Graziano, Andrew C. Seitz
By
Ecosystems Mission Area, Alaska Science Center

A method of mounting multiple otoliths for beam-based microchemical analyses A method of mounting multiple otoliths for beam-based microchemical analyses

Beam-based analytical methods are widely used to measure the concentrations of elements and isotopes in otoliths. These methods usually require that otoliths be individually mounted and prepared to properly expose the desired growth region to the analytical beam. Most analytical instruments, such as LA-ICPMS and ion and electron microprobes, have sample holders that will accept only one...
Authors
C.J. Donohoe, Christian E. Zimmerman
By
Ecosystems Mission Area

Estuarine Ecology of Juvenile Salmon in Western Alaska: a Review Estuarine Ecology of Juvenile Salmon in Western Alaska: a Review

In the late 1990s and early 2000s, large declines in numbers of chum salmon Oncorhynchus keta and Chinook salmon O. tshawytscha returning to the Arctic-YukonKuskokwim (AYK) region (Alaska, USA) illuminated the need for an improved understanding of the variables controlling salmon abundance at all life stages. In addressing questions about salmon abundance, large gaps in our knowledge of...
Authors
Christian E. Zimmerman, Nicola Hillgruber
By
Ecosystems Mission Area, Alaska Science Center

Fish and aquatic habitats in Alaska support important commercial, sport, and subsistence fisheries and provide forage fish that support wildlife populations.  The USGS Alaska Science Center conducts interdisciplinary research to inform local, state, federal, and international policy makers regarding conservation of fish, aquatic species, and their habitats.  We work collaboratively with hydrologists, geologists and other biologists to study fish and aquatic systems in an ecosystem based framework.  The goal of our current research effort is to improve our understanding of the biocomplexity, resilience, and function of aquatic ecosystems to better inform future predictions of fish and aquatic ecosystems as they respond to a changing environment.

Return to Ecosystems

Media
Two people pulling a beach seine net in Salmon Lake.
Sources/Usage: Public Domain. View Media Details
Beach seining on the spawing grounds of sockeye salmon in Salmon Lake. This is the headwater of the Pilgrim River which is the northern edge of the sockeye salmon distribution.(Credit: Mike Carey, USGS. Public domain.)

Below are other science projects associated with this project.

Filter Total Items: 16

Below are data or web applications associated with this project.

Filter Total Items: 44
No Result Found

Below are multimedia items associated with this project.

Filter Total Items: 100
No results found.

Below are publications associated with this project.

Filter Total Items: 73

Long-term increases in young-of-the-year growth of Arctic cisco Coregonus autumnalis and environmental influences Long-term increases in young-of-the-year growth of Arctic cisco Coregonus autumnalis and environmental influences

Arctic cisco Coregonus autumnalis young-of-year (YOY) growth was used as a proxy to examine the long-term response of a high-latitude fish population to changing climate from 1978 to 2004. YOY growth increased over time (r2 = 0·29) and was correlated with monthly averages of the Arctic oscillation index, air temperature, east wind speed, sea-ice concentration and river discharge with and...
Authors
Vanessa R. von Biela, Christian E. Zimmerman, L. L. Moulton
By
Ecosystems Mission Area, Alaska Science Center

Electronic tags and genetics explore variation in migrating steelhead kelts (oncorhynchus mykiss), Ninilchik river, Alaska Electronic tags and genetics explore variation in migrating steelhead kelts (oncorhynchus mykiss), Ninilchik river, Alaska

Acoustic and archival tags examined freshwater and marine migrations of postspawn steelhead kelts (Oncorhynchus mykiss) in the Ninilchik River, Alaska, USA. Postspawn steelhead were captured at a weir in 2002-2005. Scale analysis indicated multiple migratory life histories and spawning behaviors. Acoustic tags were implanted in 99 kelts (2002-2003), and an array of acoustic receivers...
Authors
J.L. Nielsen, S.M. Turner, Christian E. Zimmerman
By
Ecosystems Mission Area, Alaska Science Center

Status and distribution of the Kittlitz's Murrelet Brachyramphus brevirostris along the Alaska Peninsula and Kodiak and Aleutian Islands, Alaska Status and distribution of the Kittlitz's Murrelet Brachyramphus brevirostris along the Alaska Peninsula and Kodiak and Aleutian Islands, Alaska

The Kittlitz's Murrelet Brachyramphus brevirostris is adapted for life in glacial-marine ecosystems, being concentrated in the belt of glaciated fjords in the northern Gulf of Alaska from Glacier Bay to Cook Inlet. Most of the remaining birds are scattered along coasts of the Alaska Peninsula and Aleutian Islands, where they reside in protected bays and inlets, often in proximity to...
Authors
Erica N. Madison, John F. Piatt, Mayumi L. Arimitsu, Marc D. Romano, Thomas I. van Pelt, S. Kim Nelson, Jeffrey C. Williams, Anthony R. DeGange
By
Ecosystems Mission Area, Alaska Science Center

Kittlitz’s and Marbled Murrelets in Kenai Fjords National Park, south-central Alaska: At-sea distribution, abundance, and foraging habitat, 2006–08 Kittlitz’s and Marbled Murrelets in Kenai Fjords National Park, south-central Alaska: At-sea distribution, abundance, and foraging habitat, 2006–08

Kittlitz’s murrelets (Brachyramphus brevirostris) and marbled murrelets (B. marmoratus) are small diving seabirds and are of management concern because of population declines in coastal Alaska. In 2006–08, we conducted a study in Kenai Fjords National Park, south-central Alaska, to estimate the recent population size of Brachyramphus murrelets, to evaluate productivity based on juvenile...
Authors
Mayumi L. Arimitsu, John F. Piatt, Marc D. Romano, E.N. Madison, Jeffrey S. Conaway
By
Ecosystems Mission Area, Alaska Science Center

Characteristics of fall chum salmon spawning habitat on a mainstem river in Interior Alaska Characteristics of fall chum salmon spawning habitat on a mainstem river in Interior Alaska

Chum salmon (Oncorhynchus keta) are the most abundant species of salmon spawning in the Yukon River drainage system, and they support important personal use, subsistence, and commercial fisheries. Chum salmon returning to the Tanana River in Interior Alaska are a significant contribution to the overall abundance of Yukon River chum salmon and an improved understanding of habitat use is...
Authors
Sean E. Burril, Christian E. Zimmerman, James E. Finn
By
Ecosystems Mission Area, Alaska Science Center

Abundance, Timing of Migration, and Egg-to-Smolt Survival of Juvenile Chum Salmon, Kwethluk River, Alaska, 2007 and 2008 Abundance, Timing of Migration, and Egg-to-Smolt Survival of Juvenile Chum Salmon, Kwethluk River, Alaska, 2007 and 2008

To better understand and partition mortality among life stages of chum salmon (Oncorhynchus keta), we used inclined-plane traps to monitor the migration of juveniles in the Kwethluk River, Alaska in 2007 and 2008. The migration of juvenile chum salmon peaked in mid-May and catch rates were greatest when water levels were rising. Movement of chum salmon was diurnal with highest catch...
Authors
Sean E. Burril, Christian E. Zimmerman, James E. Finn, Daniel Gillikin
By
Ecosystems Mission Area, Alaska Science Center

A likelihood framework for joint estimation of salmon abundance and migratory timing using telemetric mark-recapture A likelihood framework for joint estimation of salmon abundance and migratory timing using telemetric mark-recapture

Many fisheries for Pacific salmon Oncorhynchus spp. are actively managed to meet escapement goal objectives. In fisheries where the demand for surplus production is high, an extensive assessment program is needed to achieve the opposing objectives of allowing adequate escapement and fully exploiting the available surplus. Knowledge of abundance is a critical element of such assessment...
Authors
Jeffrey F. Bromaghin, Kenneth S. Gates, Douglas E. Palmer
By
Ecosystems Mission Area, Alaska Science Center

Recent ecological divergence despite migration in sockeye salmon (Oncorhynchus nerka) Recent ecological divergence despite migration in sockeye salmon (Oncorhynchus nerka)

Ecological divergence may result when populations experience different selection regimes, but there is considerable discussion about the role of migration at the beginning stages of divergence before reproductive isolating mechanisms have evolved. However, detection of past migration is difficult in current populations and tools to differentiate genetic similarities due to migration...
Authors
Scott A. Pavey, Jennifer L. Nielsen, Troy R. Hamon
By
Ecosystems Mission Area, Alaska Science Center

Perspectives: Gene Expression in Fisheries Management Perspectives: Gene Expression in Fisheries Management

Functional genes and gene expression have been connected to physiological traits linked to effective production and broodstock selection in aquaculture, selective implications of commercial fish harvest, and adaptive changes reflected in non-commercial fish populations subject to human disturbance and climate change. Gene mapping using single nucleotide polymorphisms (SNPs) to identify...
Authors
Jennifer L. Nielsen, Scott A. Pavey
By
Ecosystems Mission Area, Alaska Science Center

Fine-scale population genetic structure in Alaskan Pacific halibut (Hippoglossus stenolepis) Fine-scale population genetic structure in Alaskan Pacific halibut (Hippoglossus stenolepis)

Pacific halibut collected in the Aleutian Islands, Bering Sea and Gulf of Alaska were used to test the hypothesis of genetic panmixia for this species in Alaskan marine waters. Nine microsatellite loci and sequence data from the mitochondrial (mtDNA) control region were analyzed. Eighteen unique mtDNA haplotypes were found with no evidence of geographic population structure. Using nine
Authors
Jennifer L. Nielsen, Sara L. Graziano, Andrew C. Seitz
By
Ecosystems Mission Area, Alaska Science Center

A method of mounting multiple otoliths for beam-based microchemical analyses A method of mounting multiple otoliths for beam-based microchemical analyses

Beam-based analytical methods are widely used to measure the concentrations of elements and isotopes in otoliths. These methods usually require that otoliths be individually mounted and prepared to properly expose the desired growth region to the analytical beam. Most analytical instruments, such as LA-ICPMS and ion and electron microprobes, have sample holders that will accept only one...
Authors
C.J. Donohoe, Christian E. Zimmerman
By
Ecosystems Mission Area

Estuarine Ecology of Juvenile Salmon in Western Alaska: a Review Estuarine Ecology of Juvenile Salmon in Western Alaska: a Review

In the late 1990s and early 2000s, large declines in numbers of chum salmon Oncorhynchus keta and Chinook salmon O. tshawytscha returning to the Arctic-YukonKuskokwim (AYK) region (Alaska, USA) illuminated the need for an improved understanding of the variables controlling salmon abundance at all life stages. In addressing questions about salmon abundance, large gaps in our knowledge of...
Authors
Christian E. Zimmerman, Nicola Hillgruber
By
Ecosystems Mission Area, Alaska Science Center
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