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At least 361 records · Page 20Linked to original sources
USGS2010

Mechanical suppression of northern pike (Esox lucius) populations in small Arizona reservoirs

Introduced populations of northern pike Esox lucius have provided angling opportunities in the western United States (McMahon and Bennett 1996). However, the northern pike is a voracious piscivore and its large size, high fecundity, and broad physiological tolerance make it capable of drastically altering ecosystems it invades (Marchetti et al. 2004). Indeed, predation by northern pike has been shown to significantly alter fish community structure and put native fishes at a higher extinction risk (He and Kitchell 1990, Findlay et al. 2000). Predation by northern pike is viewed as a significant threat to native stocks of salmonids in Washington, British Columbia, and California (McMahon and Bennett 1996, California Department of Fish and Game [CDFG] 2003).

Arizona↗
USGS2005

Co-occurrence of Pacific sleeper sharks Somniosus pacificus and harbor seals Phoca vitulina in Glacier Bay

We present evidence that Pacific sleeper sharks Somniosus pacificus co-occur with harbor seals Phoca vitulina in Glacier Bay, Alaska, and that these sharks scavenge or prey on marine mammals. In 2002, 415 stations were fished throughout Glacier Bay on a systematic sampling grid. Pacific sleeper sharks were caught at 3 of the 415 stations, and at one station a Pacific halibut Hippoglossus stenolepis was caught with a fresh bite, identified as the bite of a sleeper shark. All 3 sharks and the shark-bitten halibut were caught at stations near the mouth of Johns Hopkins Inlet, a glacial fjord with the highest concentration of seals in Glacier Bay. Using a bootstrap technique, we estimated the probability of sampling the sharks (and the shark-bitten halibut) in the vicinity of Johns Hopkins Inlet. If sharks were randomly distributed in Glacier Bay, the probability of sampling all 4 pots at the mouth of Johns Hopkins Inlet was very low (P = 0.00002). The highly non-random distribution of the sleeper sharks located near the largest harbor seal pupping and breeding colony in Glacier Bay suggests that these 2 species co-occur and may interact ecologically in or near Johns Hopkins Inlet.

Alaska Fishery Research Bulletin↗
USGS2003

Pop-up archival transmitting (PAT) tags: A method to investigate the migration and behavior of Pacific halibut ( Hippoglossus stenolepis ) in the Gulf of Alaska

Pop-up archival transmitting (PAT) tags provide a fisheries-independent method of collecting environmental preference data (depth and ambient water temperature) and migration distance. In this study, we evaluate the use of pop-up archival transmitting tags as a method to investigate demersal fish. We report the results from eight pop-up archival transmitting tagged Pacific halibut Hippoglossus stenolepis (from 107 to 165 cm FL) that were released in and around Resurrection Bay, Alaska. Commercial fishermen recovered three tags, while five tags transmitted data to Argos satellites. Horizontal migration was not consistent among fish as four Pacific halibut remained in the vicinity of release while the other four traveled up to 358 km from the release site. Vertical movement was not consistent among fish or over time; however, they spent most of their time at depths of 150 to 350 m. The minimum and maximum depths reached by any of the Pacific halibut were 2 m and 502 m, respectively. The fish preferred water temperatures of approximately 6°C, but experienced temperatures between 4.3 and 12.2°C. Light attenuation with depth prevented geolocation software and light sensing hardware from accurately estimating geoposition for the majority of days. The methods, adapted from investigations on large pelagic fish, proved to be effective for studying Pacific halibut in the northern Gulf of Alaska. PAT tags allowed us to obtain high accuracy locations of the fish at the end of the tag deployments as well as preliminary data to identify approximate seasonal locations and to characterize their depth and temperature characteristics. By using PAT tags, we will be able to ensure tag returns during the winter season (which is closed to fishing) and gain valuable biological information even if fish migrate large distances or to unexpected locations.

Alaska Fishery Research Bulletin↗
USGS2024

Assessing habitat use and population dynamics of fisheries resources at Kaloko Fishpond

Throughout Hawai'i, fishponds are considered by their local communities as important cultural touchstones, a source of local, sustainably produced food, and an important component to the development of community-based management for nearshore fisheries. Within Kaloko-Honokōhau National Historical Park, the restoration of Kaloko Fishpond for traditional aquaculture management is a goal of both the National Park Service (NPS) and Hui Kaloko-Honokōhau, a community-based group of kia'i, i.e., caretakers and native Hawaiian cultural practitioners. However, existing data on the demographics and condition of the fish populations within the pond, and the fish-habitat quality are poor to non-existent. Therefore, the objectives of this study were to: catalog fish species composition and distribution in the pond; estimate the abundance of focal species/taxonomic groups; and evaluate the occupancy patterns of the invasive algae Acanthophora spicifera and Upside-down Jellyfish Cassiopea andromeda. As part of these objectives, a survey protocol and analysis framework were designed and evaluated to ensure that the NPS and community group would be able to refine and implement them to continue their monitoring efforts. We conducted dual-observer shore-based visual surveys multiple times per week during September-October 2020 and April-September 2022. A total of 41 species/taxonomic groups were recorded over the course of the surveys. The largest number of species/taxonomic groups were observed at survey stations located on or near the kuapā, or wall separating the fishpond from the ocean. N-mixture models fitted to the data estimated a total population of 353 – 392 mullets, 134 – 192 flagtails (āholehole), and 189 – 277 Milkfish (Awa) Chanos chanos occurring within the 1.2-ha portion of Kaloko Fishpond that could be surveyed visually from the shoreline. Multi-season occupancy models fitted to the surveyed presence of A. spicifera and Upside-down Jellyfish indicted sites throughout most of the pond exhibited moderate and consistent occupancy (ψ = 0.30 – 0.40) throughout much of the pond, except for the northeast corner of the pond (Kaloko Iki) where colonization rates were lower and extinction rates higher than other areas within Kaloko. The visual survey method developed for this study provides a low-cost and effective starting point for the development of methodology that can be used both by NPS personnel and volunteers from the community group. However, we were only able to estimate fish populations for approximately 24% of the area of Kaloko Fishpond with this method. Given that the deeper areas of Kaloko Fishpond are completely inaccessible to the visual survey method used, generating population estimates for the entire pond based on the parameters estimated in the current study is not recommended without further investigation into fish movement and habitat use. Various means to refine this protocol to better meet the needs and abilities of the NPS and community group are proposed.

Hawaii↗
USGS2025

Introducing disciplinary perspectives and interdisciplinary possibilities for studying recreational fishers and fisheries

Individuals from many disciplines conduct research to understand the social dimension of recreational fisheries. This diverse inquiry has produced a comprehensive understanding of the behaviours of recreational fishers, the outcomes from fishing, and the relationships among fishers, others, and the natural and human environment. The associated body of research, however, is largely disconnected across disciplines. Our goals here are to help readers understand the similarities and differences among disciplines and to identify opportunities for interdisciplinary-based research on recreational fishers. Before addressing these goals, we begin by answering basic questions: What is a discipline? What are the primary disciplines used to study recreational fishers? And what is the genealogy of research on recreational fishers? Seven key disciplines are then classified by multi-criteria related to both focus and epistemological and methodological approaches. This classification reveals clear connections among: (i) ecological science and resource economics, and to a lesser extent historical ecology; (ii) environmental history and political ecology; and (iii) behavioural economics and social psychology. We next describe and provide possible remedies for barriers that inhibit interdisciplinary research, including different epistemologies, nomenclature, and reward bias. Finally, we highlight opportunities to conduct interdisciplinary research by describing the types of benefits that each discipline can provide when conducting interdisciplinary research on recreational fisheries.

Book chapter↗
USGS2014

Guidelines for use of fishes in research: Revised and expanded

The Guidelines for the Use of Fishes in Research (2014; 2014 Guidelines ), now available through the American fisheries Society (AFS) website and in print from the AFS bookstore, is a resource to aid researchers and regulatory authorities regarding responsible, scientifically valid research on fish and aquatic wildlife. The Guidelines for the Use of Fishes in Field Research (American Society of Ichthyologists and Herpetologists [ASIH] et al. 1987, 1988) emphasized field research and was followed by the 2004 Guidelines including laboratory research topics. Each version of the Guidelines has been jointly endorsed and/or published by the ASIH, the American Institute of Fishery Research Biologists (AIFRB), and AFS--each focusing on the scientific understanding, global conservation, and sustainability of aquatic animals, fisheries, and ecosystems. Changes with time necessitate revisions to make the Guidelines consistent with contemporary practices and scientific literature so to remain relevant as a technical resource. This document provides not only general principles relevant for field and laboratory research endeavors but includes specific requirements for researchers working within the United States and outside of the country. Within the scope of their expertise, the 2014 Uses of Fishers in Research (UFR) Committee members updated and revised sections, resulting in a 90-page 2014 Guidelines having undergone through peer review. As before, topical areas were addressed (see Table of Contents on page 416). Expanded coverage was provided on U.S. and international agencies and programs relevant to research with fishes. The Surgical Procedures and the Marking and Tagging section received special focus by a UFR Subcommittee. Feeds and Feeding and the Administration of Drugs, Biologics and Other Chemicals are just some of the newly added topics. The 2014 Guidelines is user-friendly by way of hyperlinks to external Internet sites, intradocument sections, and tables of acronyms with corresponding terms, low regulatory priority drugs, and Office of International des Epizooties notifiable disease agents. Again, the Institutional Animal Care and Use Committee (IACUC) role is explained, expectations for research are provided, and a brief checklist for IACUC readiness is included. Overall, the ,i>2014 Guidelines is the taxon-specific resource for our professional societies and is a principal document for standards on the care and use of fish and aquatic vertebrates in research.

Fisheries↗
USGS2019

The future of recreational fisheries: Advances in science, monitoring, management, and practice

Recreational fisheries (RF) are complex social-ecological systems that play an important role in aquatic environments while generating significant social and economic benefits around the world. The nature of RF is diverse and rapidly evolving, including the participants, their priorities and behaviors, and the related ecological impacts and social and economic benefits. RF can lead to negative ecological impacts, particularly through overexploitation of fish populations and spread of non-native species and genotypes through stocking. Hence, careful management and monitoring of RF is essential to sustain these ecologically and socioeconomically important resources. This special issue on recreational fisheries contains diverse research, syntheses, and perspectives that highlight the advances being made in RF research, monitoring, management, and practice, which we summarize here. Co-management actions are rising, often involving diverse interest groups including government and non-government organizations; applying collaborative management practices can help balance social and economic benefits with conservation targets. Technological and methodological advances are improving the ability to monitor biological, social, and economic dynamics of RF, which underpin the ability to maximize RF benefits through management actions. To ensure RF sustainability, much research focuses on the ecological aspects of RF, as well as the development of management and angling practices that reduce negative impacts on fish populations. For example, angler behavior can be influenced to conform to conservation-minded angling practices through regulations, but is often best accomplished through growing bottom-up social change movements. Anglers can also play an important role in fisheries monitoring and conservation, including providing data on fish abundance and assemblages (i.e., citizen science). The increasing impacts that growing human populations are having on the global environment are threatening many of the natural resources and ecosystem services they provide, including valuable RF. However, with careful development of research initiatives, monitoring and management, sustainable RF can generate positive outcomes for both society and natural ecosystems and help solve allocation conflicts with commercial fisheries and conservation.

Fisheries Research↗
USGS2021

Consequences of changing water clarity on the fish and fisheries of the Laurentian Great Lakes

Human-driven environmental change underlies recent changes in water clarity in many of the world’s great lakes, yet our understanding of the consequences of these changes on the fish and fisheries they support remains incomplete. Herein, we offer a framework to organize current knowledge, guide future research, and help fisheries managers understand how water clarity can affect their valued populations. Emphasizing Laurentian Great Lakes findings where possible, we describe how changing water clarity can directly affect fish populations and communities by altering exposure to ultraviolet radiation, foraging success, predation risk, reproductive behavior, or territoriality. We also discuss how changing water clarity can affect fisheries harvest and assessment through effects on fisher behavior and sampling efficiency (i.e., catchability). Finally, we discuss whether changing water clarity can affect understudied aspects of fishery performance, including economic and community benefits. We conclude by identifying generalized predictions and discuss their implications for priority research questions for the Laurentian Great Lakes. Even though the motivation for this work was regional, the breadth of the review and generality of the framework are readily transferable to other freshwater and marine habitats.

Great Lakes↗
USGS2016

To manage inland fisheries is to manage at the social-ecological watershed scale

Approaches to managing inland fisheries vary between systems and regions but are often based on large-scale marine fisheries principles and thus limited and outdated. Rarely do they adopt holistic approaches that consider the complex interplay among humans, fish, and the environment. We argue that there is an urgent need for a shift in inland fisheries management towards holistic and transdisciplinary approaches that embrace the principles of social-ecological systems at the watershed scale. The interconnectedness of inland fisheries with their associated watershed (biotic, abiotic, and humans) make them extremely complex and challenging to manage and protect. For this reason, the watershed is a logical management unit. To assist management at this scale, we propose a framework that integrates disparate concepts and management paradigms to facilitate inland fisheries management and sustainability. We contend that inland fisheries need to be managed as social-ecological watershed system (SEWS). The framework supports watershed-scale and transboundary governance to manage inland fisheries, and transdisciplinary projects and teams to ensure relevant and applicable monitoring and research. We discuss concepts of social-ecological feedback and interactions of multiple stressors and factors within/between the social-ecological systems. Moreover, we emphasize that management, monitoring, and research on inland fisheries at the watershed scale are needed to ensure long-term sustainable and resilient fisheries.

Journal of Environmental Management↗
USGS2025

An analytical approach to explore prospects and limits of nutrition-sensitive fisheries governance under climate change

Researchers and policymakers increasingly recognize the contribution of aquatic food systems, such as fisheries, to food security and nutrition. Yet governing fisheries for nutrition objectives is complicated by the multiple overlapping processes that shape availability and access to nutrients over time, including fishing sustainability, climate change, trade dynamics, and consumer preferences. Anticipating the effect of governance interventions to sustain or enhance nutritional benefits from fisheries entails accounting for these multiple interacting influences. We develop an analytical approach to link available data on aquatic foods production, nutrition, distribution, and potential climate impacts to evaluate the nutrition implications of fishery management and post-harvest allocation interventions. We demonstrate this approach using national and publicly available datasets for five case study countries: Peru, Chile, Indonesia, Sierra Leone, and Malawi. As examples, we evaluate the potential to enhance domestic supply of key nutrients to nutritionally-vulnerable populations by (a) dynamically adjusting fishing effort in response to climate impacts on fish stocks, and (b) retaining aquatic foods currently diverted via trade or foreign fishing. The results indicate substantial differences across countries in terms of anticipated climate change effects, with potential for substantially increased nutrition yield in Chile and Peru under adaptive management, vs more modest yield increases in Indonesia. The impacts of post-harvest allocation policies related to foreign fishing, exports, fishing sector, and subnational trade also vary, with exports weighing heavily on nutrient availability in Sierra Leone. This methodological approach represents a step toward operationalizing calls to manage fisheries as part of national food and nutrient supplies, in light of climate change risks.

Environmental Research: Food Systems↗
USGS2008

Rivers and streams: Physical setting and adapted biota

Streams and rivers are enormously important, with their ecological, and economic value, greatly outweighing their significance on the landscape. Lotic ecology began in Europe with a focus on the distribution, abundance, and taxonomic composition of aquatic organisms and in North American with a focus on fishery biology. Since 1980, stream/river research has been highly interdisciplinary, involving fishery biologists, aquatic entomologists, algologists, hydrologists, geomorphologists, microbiologists, and terrestrial plant ecologists. Stream and river biota evolved in response to, and in concert with, the physical and chemical setting. Streams/rivers transport water and move sediments to the sea as part of the hydrologic cycle that involves evaporation, plant evapotranspiration, and precipitation. Ephemeral streams flow only in the wettest year, intermittent streams flow predictably every year during capture of surface runoff, and perennial streams flow continuously during wet and dry periods, receiving both stormflow and groundwater baseflow. The lotic biota, for example, algae, macrophytes, benthic invertebrates, and fishes, have evolved adaptations to their running-water setting. Dominant physical features of this setting are current, substrate, and temperature. Key chemical constituents are dissolved gases, dissolved inorganic ions and compounds, particulate inorganic material, particulate organic material, and dissolved organic ions (nitrogen and phosphorus) and compounds.

Book chapter↗
USGS2003

Biological effect of low-head sea lamprey barriers: Designs for extensive surveys and the value of incorporating intensive process-oriented research

Four sampling designs for quantifying the effect of low-head sea lamprey (Petromyzon marinus) barriers on fish communities were evaluated, and the contribution of process-oriented research to the overall confidence of results obtained was discussed. The designs include: (1) sample barrier streams post-construction; (2) sample barrier and reference streams post-construction; (3) sample barrier streams pre- and post-construction; and (4) sample barrier and reference streams pre- and post-construction. In the statistical literature, the principal basis for comparison of sampling designs is generally the precision achieved by each design. In addition to precision, designs should be compared based on the interpretability of results and on the scale to which the results apply. Using data collected in a broad survey of streams with and without sea lamprey barriers, some of the tradeoffs that occur among precision, scale, and interpretability are illustrated. Although circumstances such as funding and availability of pre-construction data may limit which design can be implemented, a pre/post-construction design including barrier and reference streams provides the most meaningful information for use in barrier management decisions. Where it is not feasible to obtain pre-construction data, a design including reference streams is important to maintain the interpretability of results. Regardless of the design used, process-oriented research provides a framework for interpreting results obtained in broad surveys. As such, information from both extensive surveys and intensive process-oriented research provides the best basis for fishery management actions, and gives researchers and managers the most confidence in the conclusions reached regarding the effects of sea lamprey barriers.

Conference Paper↗
USGS2012

Monitoring of endangered Roanoke logperch ( Percina rex ) in Smith River upstream from the Philpott Reservoir on U.S. Army Corps of Engineers property near Martinsville, Virginia

The purpose of this study was to continue annual monitoring of Roanoke logperch ( Percina rex ), an endangered fish, in the Smith River immediately upstream from Philpott Reservoir. This river reach is owned by the U.S. Army Corps of Engineers (USACE), which must ensure that appropriate actions are undertaken to aid in recovery of logperch. Monitoring of fish abundance and habitat conditions provides a means for assessing the species’ status and its responses to USACE management actions. The Roanoke logperch is a large darter (Percidae: Etheostomatinae) endemic to the Roanoke, Dan, and Nottoway River basins of Virginia and North Carolina, where it occupies third- to sixth-order streams containing relatively silt-free substrate (Jenkins and Burkhead, 1994). Because of its rarity, small range, and vulnerability to siltation, the Roanoke logperch was listed in 1989 as endangered under the U.S. Endangered Species Act (ESA) (U.S. Federal Register 54:34468-34472). Within the Dan basin, Roanoke logperch have long been known to occupy the Smith River and one of its largest tributaries, Town Creek (Jenkins and Burkhead, 1994). Logperch also recently were discovered in other tributaries of the Dan River, including North Carolina segments of the Mayo River, Cascade Creek, Big Beaver Island Creek, Wolf Island Creek (William Hester, U.S. Fish and Wildlife Service, personal commun., 2012). Within the Smith River, Roanoke logperch are present both upstream and downstream from Philpott Reservoir, a hydroelectric and water storage project owned and operated by the USACE. Although logperch have not been observed in the reservoir itself, the species is relatively abundant in a free-flowing, ≈ 2.5-km-long segment of Smith River upstream from the reservoir on USACE property (Lahey and Angermeier, 2006). This segment is bounded on the downstream end by the lentic conditions of the reservoir and on the upstream end by White Falls, a natural waterfall that presumably allows fish passage during all but the lowest streamflow (Roberts and Angermeier, 2009). The ESA stipulates that USACE must ensure that its actions do not jeopardize Roanoke logperch and ensure that appropriate actions are taken to aid in the recovery of Roanoke logperch. USACE recognized that additional information was needed to assess compliance with these stipulations, including data on baseline population levels, habitat availability, and potential threats to the species on USACE property. USACE therefore contracted with Virginia Tech (VT) and the U.S. Geological Survey via the Virginia Cooperative Fisheries and Wildlife Research Unit (VCFWRU) to continue ecological monitoring that was initiated in a pilot study in 2005 (Lahey and Angermeier, 2006). The VCFWRU is jointly sponsored by the U.S. Geological Survey, Virginia Tech, Virginia Department of Game and Inland Fisheries, and Wildlife Management Institute. This final report summarizes results of biological monitoring performed by VT and the VCFWRU in 2011, and compares these data to data collected during 2006–2010 (Roberts and Angermeier, 2011). Where appropriate, a comparison was made to data on Roanoke logperch collected previously in the study reach (Lahey and Angermeier, 2006) and in the upper Roanoke River (Roberts and Angermeier, 2011). This work was performed under the auspices of VT’s Institutional Animal Care and Use Committee (IACUC) protocol 11-035-FIW. Specifically, the following objectives were addressed: * Estimate population density of Roanoke logperch on USACE property; * Measure and map by suitability class the distribution of habitat suitable for Roanoke logperch in the project area; * Assess water quality relative to Roanoke logperch habitat in the project area; * Use the data on logperch abundance, habitat suitability, and water quality to test the general validity of correlates of logperch abundance from other locations; * Identify opportunities and threats related to protecting and enhancing Roanoke logperch habitat; and * Provide suggestions on the necessity and scale of future studies and monitoring related to logperch in and near USACE waters.

Virginia↗
USGS1960

Bureau of Sport Fisheries and Wildlife Pesticide-Wildlife Review: 1959

Research findings of the Bureau of Sport Fisheries and Wildlife, State agencies and independent research workers in Ala., Ark., Fla., Ga., La., Mass., Mich., Mont., N. Dak., Tex., and Wis. are summarized in this report together with recommendations for reducing damage from pest control operations. Major topics discussed are: Scope of Pesticide-Wildlife Problem; Effects on Wildlife-General; Laboratory Studies and Toxicology; Direct and Indirect Effects of Pesticides on Wildlife; Recent Pesticide Legislation; Value of Wildlife; and Recommendations for Safeguarding Wildlife Values during Pest Control. To avoid undue hazards to wildlife, applications must not exceed the toxicity equivalent of the following concentrations of DDT to the respective forms of wildlife: 0.1 pounds of DDT/acre for crustaceans; 0.2 for fish; 1.0 for amphibians; 2.0 for reptiles and birds; and 5.0 for most mammals. Other suggestions are: 1) Chemical treatment should be used only when entomological research has proved it to be necessary; 2) Before pesticides are used, the effects on different kinds of animals and on animals living in different habitats should be known and carefully considered; 3) Only minimum quantities of chemicals necessary to achieve adequate control of pests should be applied; 4) Pesticides should not be applied to areas that are any larger than is necessary and the chemicals that are used should be the ones whose effects are no more long-lasting than necessary; 5) Whenever possible, chemicals should be applied at the seasons of the year when wildlife damage will be least; 6) Conscientious effort should be made to be sure that pesticides are applied at no more than the intended rates and that no areas receive double doses. Alternates to chemical control are suggested. Among these are biological control, modified agricultural practices, destruction of insect wintering quarters, and the manipulation of water levels.

Circular↗
USGS2009

Kootenai River velocities, depth, and white sturgeon spawning site selection – A mystery unraveled?

The Kootenai River white sturgeon Acipenser transmontanus population in Idaho, US and British Columbia (BC), Canada became recruitment limited shortly after Libby Dam became fully operational on the Kootenai River, Montana, USA in 1974. In the USA the species was listed under the Endangered Species Act in September of 1994. Kootenai River white sturgeon spawn within an 18-km reach in Idaho, river kilometer (rkm) 228.0–246.0. Each autumn and spring Kootenai River white sturgeon follow a ‘short two-step’ migration from the lower river and Kootenay Lake, BC, to staging reaches downstream of Bonners Ferry, Idaho. Initially, augmented spring flows for white sturgeon spawning were thought to be sufficient to recover the population. Spring discharge mitigation enhanced white sturgeon spawning but a series of research investigations determined that the white sturgeon were spawning over unsuitable incubation and rearing habitat (sand) and that survival of eggs and larvae was negligible. It was not known whether post-Libby Dam management had changed the habitat or if the white sturgeon were not returning to more suitable spawning substrates farther upstream. Fisheries and hydrology researchers made a team effort to determine if the spawning habitat had been changed by Libby Dam operations. Researchers modeled and compared velocities, sediment transport, and bathymetry with post-Libby Dam white sturgeon egg collection locations. Substrate coring studies confirmed cobbles and gravel substrates in most of the spawning locations but that they were buried under a meter or more of post-Libby Dam sediment. Analysis suggested that Kootenai River white sturgeon spawn in areas of highest available velocity and depths over a range of flows. Regardless of the discharge, the locations of accelerating velocities and maximum depth do not change and spawning locations remain consistent. Kootenai River white sturgeon are likely spawning in the same locations as pre-dam, but post-Libby Dam water management has reduced velocities and shear stress, thus sediment is now covering the cobbles and gravels. Although higher discharges will likely provide more suitable spawning and rearing conditions, this would be socially and politically unacceptable because it would bring the river elevation to or in excess of 537.66 m, which is flood stage. Thus, support should be given to habitat modifications incorporated into a management plan to restore suitable habitat and ensure better survival of eggs and larvae.

Journal of Applied Ichthyology↗
USGS2022

FishStan: Hierarchical Bayesian models for fisheries

Fisheries managers and ecologists use statistical models to estimate population-level relations and demographic rates (e.g., length-maturity curves, growth curves, and mortality rates). These relations and rates provide insight into populations and inputs for other models. For example, growth curves may vary across lakes showing fish populations differ due to management actions or underlying environmental conditions. A fisheries manager could use this information to set lake-specific harvest limits or an ecologist could use this information to test scientific hypotheses about fish populations. The above example also demonstrates how populations exist within hierarchical structures where sub-populations may be nested within a meta-population. More generally, these hierarchical structures may be both biological (e.g., different lakes or river pools) and statistical (e.g., correlated error structures). Currently, limited options exist for fitting these hierarchical models and people seeking to use them often must program their own implementations. Furthermore, many fisheries managers and researchers may not have Bayesian programming skills, but many can use interactive languages such as R. Additionally, programs such as JAGS often require long run times (e.g., hours if not days) to fit hierarchical models and programs such as Stan can be more difficult to program because it is a compiled language. We created fishStan to share hierarchical models for fisheries and ecology in an easy-to-use R package.

Journal of Open Source Software↗
USGS1992

Transfer of computer software technology through workshops: The case of fish bioenergetics modeling

I recommend a three-part program to promote the availability and use of computer software packages to fishery managers and researchers. The three-part approach consists of journal articles that announce new technologies, technical reports that serve as user's guides, and hands-on workshops that provide direct instruction to new users. Workshops, which allow experienced users to directly instruct novices in software operation and application, are an important, but often neglected, final step in this process. My experience with organizing and conducting bioenergetics modeling workshops suggests the optimal workshop would take 2 days, have 10–15 participants, one computer for every two users, and one instructor for every 5–6 people.

Fisheries↗
USGS2017

Fish Bioenergetics 4.0: An R-based modeling application

Bioenergetics modeling is a widely used tool in fisheries management and research. Although popular, currently available software (i.e., Fish Bioenergetics 3.0) has not been updated in over 20 years and is incompatible with newer operating systems (i.e., 64‐bit). Moreover, since the release of Fish Bioenergetics 3.0 in 1997, the number of published bioenergetics models has increased appreciably from 56 to 105 models representing 73 species. In this article, we provide an overview of Fish Bioenergetics 4.0 (FB4), a newly developed modeling application that consists of a graphical user interface (Shiny by RStudio) combined with a modeling package used in the R computing environment. While including the same capabilities as previous versions, Fish Bioenergetics 4.0 allows for timely updates and bug fixes and can be continuously improved based on feedback from users. In addition, users can add new or modified parameter sets for additional species and formulate and incorporate modifications such as habitat‐dependent functions (e.g., dissolved oxygen, salinity) that are not part of the default package. We hope that advances in the new modeling platform will attract a broad range of users while facilitating continued application of bioenergetics modeling to a wide spectrum of questions in fish biology, ecology, and management.

Fisheries Magazine↗