Goodbye to “Rough Fish”: Paradigm Shift in the Conservation of Native Fishes

American Fisheries Society (AFS) | July 21st, 2021

Goodbye to “Rough Fish”: Paradigm Shift in the Conservation of Native Fishes

American Fisheries Society (AFS) | July 21st, 2021

While sometimes difficult to admit, perspectives of European and white males have overwhelmingly dominated fisheries science and management in the USA. This dynamic is ex

While sometimes difficult to admit, perspectives of European and white males have overwhelmingly dominated fisheries science and management in the USA. This dynamic is exemplified by bias against “rough fish”—a pejorative ascribing low-to-zero value for countless native fishes. One product of this bias is that biologists have ironically worked against conservation of diverse fishes for over a century, and these problems persist today. Nearly all U.S. states retain bag limits and other policies that are regressive and encourage overfishing and decline of native species. Multiple lines of evidence point towards the need for a paradigm shift. These include: (1) native species deliver critical ecosystem services; (2) little demonstration that native fish removals deliver intended benefits; (3) many native fishes are long-lived and vulnerable to overfishing and decline; and (4) fisher values and demographics shifting towards native fish conservation. Overall, existing native fish policies are unacceptable and run counter to the public trust doctrine where government agencies manage natural resources for public use. We encourage agencies to revisit their policies regarding native fishes and provide suggestions for developing more holistic, protective, and inclusive conservation policy.

Guidelines for salmonid passage at stream crossings

National Marine Fisheries Service (NMFS) | August 20th, 2013

This document provides guidelines for design of stream crossings to aid upstream and downstream passage of migrating salmonids. It is intended to facilitate the design of

This document provides guidelines for design of stream crossings to aid upstream and downstream passage of migrating salmonids. It is intended to facilitate the design of a new generation of stream crossings, and assist the recovery of threatened and endangered salmon species. These guidelines are offered by the National Marine Fisheries Service, Southwest Region (NMFS-SWR), as a result of its responsibility to prescribe fishways under the Endangered Species Act, the Magnuson-Stevens Act, the Federal Power Act, and the Fish and Wildlife Coordination Act. The guidelines apply to all public and private roads, trails, and railroads within the range of anadromous salmonids in California.

Habitat-Specific Foraging by Striped Bass (Morone saxatilis) in the San Francisco Estuary, California: Implications for Tidal Restoration

University of California, Davis (UC Davis) | December 1st, 2022

Non-native predatory fish strongly affect aquatic communities, and anthropogenic habitat alterations can exacerbate their effects. Loss of natural habitat, and restorati

Non-native predatory fish strongly affect aquatic communities, and anthropogenic habitat alterations can exacerbate their effects. Loss of natural habitat, and restoration actions that reverse habitat loss, can modify relationships between non-native predators and prey. Predicting how these relationships will change is often difficult because insufficient information exists on the habitat-specific feeding ecology of non-native predators. To address this information gap, we examined diets of non-native Striped Bass (Morone saxatilis; 63 to 671 mm standard length; estimated age 1 to 5 yrs) in the San Francisco Estuary during spring and summer in three habitat types—marsh, shoal, and channel—with the marsh habitat type serving as a model for ongoing and future restoration. Based on a preyspecific index of relative importance, Striped Bass diets were dominated by macroinvertebrates in spring and summer (amphipods in spring, decapods and isopods in summer). In spring, diets were relatively consistent across habitats. In summer, marsh diets were dominated by sphaeromatid isopods and shoal/channel diets by idoteid amphipods and decapods. Striped Bass consumed a variety of native and non-native fishes, primarily Prickly Sculpin (Cottus asper) and Gobiidae. The highest importance of fish prey was in the marsh in spring (~ 40% prey weight), and fish prey comprised less than 25% prey weight in all other season/habitat combinations. Linear discriminant analyses suggested that marsh foraging was prevalent in Striped Bass collected in other habitats, mostly because of the predominance of marsh-associated invertebrates found in the stomachs of individual Striped Bass collected outside the marsh. Striped Bass diets differ across habitats, with marsh foraging important to Striped Bass regardless of collection location. This information can be used to forecast the potential utilization of restored habitats by this non-native piscivore.

Humboldt County | Near-Stream Recharge: Reconnecting Surface and Groundwater

Nature Conservancy | January 1st, 2019

Baker Creek, a tributary to the Mattole River, is a key stream for the federally and state protected coho salmon, however portions of the river were running dry

Baker Creek, a tributary to the Mattole River, is a key stream for the federally and state protected coho salmon, however portions of the river were running dry due to drought, impeding salmon migration and deteriorating habitat. A partnership of federal and state agencies, consultants and NGOs are working to increase groundwater levels with both instream and offchannel projects to ensure year-round water in the creek and floodplain wetlands for salmon habitat. Salmon now returning to the stream, with Phase 1 of the project complete, 1,300 juvenile coho have been counted in Baker Creek after the previous five years saw zero juveniles. Stream restoration in Baker Creek in the Mattole River watershed is an excellent example of a multi- benefit project recharging groundwater, as well as providing the instream coho salmon habitat that has been disappearing.

Hydrodynamics and habitat interact to structure fish communities within terminal channels of a tidal freshwater delta

Ecological Society of America (Wiley) | January 13th, 2023

Terminal channels were historically a common feature of tidal delta ecosystems but have become increasingly rare as landscapes have been modified. Tidal hydrodynamics are

Terminal channels were historically a common feature of tidal delta ecosystems but have become increasingly rare as landscapes have been modified. Tidal hydrodynamics are a defining feature in tidal terminal channel ecosystems from which native aquatic communities have evolved. However, few studies have explored the relationship between fish community structure and hydrodynamics in these tidal terminal channel ecosystems. We sampled fish communities throughout a network of terminal channels within the northeasternmost region of the San Francisco Estuary to determine the relationship between fish community structure and hydrodynamics within these environments. We collected two years (2017 and 2018) of fish community samples using gill nets and analyzed data using multivariate community analyses and count models. We found metrics of fish diversity and counts of native fishes to be greatest upstream (farthest from tidal influence) of the tidal excursion within terminal channels. Counts of non-native fishes were less affected by this hydrodynamic feature of terminal channels and more tightly correlated to local habitat conditions (e.g., water temperature, depth). Our results suggest that channel hydrodynamics plays a role in structuring fish communities within terminal channels, particularly native fishes. These results indicate that hydrodynamics in tidal delta ecosystems may be able to be altered in ways that benefit native fishes without the cost of water pumping.

Hydrology and Hydrodynamics on the Sacramento River Near the Fremont Weir, California—Implications for Juvenile Salmon Entrainment Estimates

U.S. Geological Survey (USGS) | November 9th, 2018

Estimates of fish entrainment on the Sacramento River near the Fremont Weir are a critical component in determining the feasibility and design of a proposed notch in the

Estimates of fish entrainment on the Sacramento River near the Fremont Weir are a critical component in determining the feasibility and design of a proposed notch in the weir to increase access to the Yolo Bypass, a seasonal floodplain of the Sacramento River. Detailed hydrodynamic and velocity measurements were made at a river bend near the Fremont Weir in the winter and spring of 2016 to examine backwater conditions and estimate the hydraulic entrainment zone, a zone where fish would be predicted to be entrained into the notch. Secondary circulation near the river bend was shown to shift the velocity and discharge distributions toward the outside of the bend. Variability in the stage-discharge relation was shown to be the biggest source of uncertainty in determining the location of the hydraulic entrainment zone. Outflow from the Sutter Bypass and high flow on the Feather River resulted in backwater conditions near the Fremont Weir about 25 percent of the time over the 27-year period from April 1990–April 2017. Velocity measurements used to estimate the critical streakline position (the outer edge of the hydraulic entrainment zone) were not made over a sufficient range of conditions to explicitly quantify the variability in the location of the critical streakline. The variability in the critical streakline position was therefore represented stochastically with a random effects model. The estimated position of the critical streakline and the random effects model are input parameters used in a simulation designed to estimate fish entrainment over a 15-year period. The estimates of the critical streakline and likely fish entrainment could be much improved with velocity measurements over a broader range of stage and discharge conditions. 

Hydrology, Ecology, and Fishes of the Klamath River Basin (2008)

National Academy of Sciences (NAS) | January 1st, 2008

The Klamath River basin, which spans parts of southern Oregon and northern California, has been the focus of a prominent conflict over competing uses for water. Manag

The Klamath River basin, which spans parts of southern Oregon and northern California, has been the focus of a prominent conflict over competing uses for water. Management actions to protect threatened and endangered fish species in the basin have left less water available for irrigation in dry years and heightened tensions among farmers and other stakeholders including commercial fishermen, Native Americans, conservationists, hunters, anglers, and hydropower producers. This National Research Council report assesses two recent studies that evaluate various aspects of flows in the Klamath basin: (1) the Instream Flow Phase II study (IFS), conducted by Utah State University, and (2) the Natural Flow of the Upper Klamath Basin study (NFS), conducted by the U.S. Bureau of Reclamation (USBR). The report concludes that both studies offer important new information but do not provide enough information for detailed management of flows in the Klamath River, and it offers many suggestions for improving the studies. The report recommends that a comprehensive analysis of the many individual studies of the Klamath river basin be conducted so that a big picture perspective of the entire basin and research and management needs can emerge. Key Messages If these conclusions were borne out by studies incorporating experimental flows and monitored responses, managers would be able to have greater confidence that decisions to increase flows would have a beneficial effect on anadromous fishes in the lower river The Instream Flow Study Phase II did not include important water-quality attributes, such as dissolved oxygen levels, nutrient loadings, contaminants, and sediment concentrations, although each has important implications for the vitality of the fish populations of the Klamath River. The Natural Flow Study and the Instream Flow Study Phase II were major science and engineering investigations, but the linkage of one to the other was only partially achieved. The Natural Flow Study was seriously compromised by several fundamental issues, including its choice of a basic approach for understanding natural flows, choices of the models for calculations, and serious omissions of factors likely to influence river flows at the Iron Gate Dam gauge site. The basin and its biota have changed so much in the past century that the implications for the fishes of restoring natural flows are not clear. The committee concluded that the Natural Flow Study includes calculated flows that are at best first approximations to useful estimates of such flows. The committee found important shortcomings in the Instream Flow Study Phase II and its use of various models and data. Two major shortcomings use of monthly data and lack of tributary analyses are so severe that that they should be addressed before decision makers can use the outputs of the study to establish precise flow regimes with confidence. The most important outcome of the Instream Flow Study was that it indicated that increases in existing flows downstream from Iron Gate Dam probably would benefit fish populations through improved physical habitat associated with more water and through reduced water temperatures. There was a lack of a thorough assessment of the relationship between flow-data time series and the behavior of different species and life stages and the population dynamics of coho and Chinook salmon When the science needs for the basin are better characterized, the individual studies necessary to create a sound science-based body of knowledge for decision makers and managers will be more easily identified. current flow regime. These are improvements in flow because they include intra- and inter-annual variations and probably will enhance Chinook salmon growth and young-of-the-year production. is not possible to know how well the recommendations apply to any one species or to all the species as a whole. Indeed, most of the information was from Chinook salmon, which suggests that confidence in its applicability to that species would be greater than to other species. of the representativeness of the reaches used for detailed study, and the statistical approach to analyze the calculated set of instream flows did not use normalized data and did not have provisions for identifying serial autocorrelations.

Independent Panel Review of the Bay Delta Conservation Plan prepared for The Nature Conservancy and American Rivers

Nature Conservancy | September 19th, 2013

Two non-­governmental organizations, The Nature Conservancy (TNC) and American Rivers (AR), are evaluating their options for engagement with the Bay Delta Conservation P

Two non-­governmental organizations, The Nature Conservancy (TNC) and American Rivers (AR), are evaluating their options for engagement with the Bay Delta Conservation Plan (BDCP). If approved, the Plan would become a Habitat Conservation Plan (HCP) under the federal Endangered Species Act and a Natural Communities Conservation Plan (NCCP) under California law. The purpose of the Plan is to allow for construction of new water diversion facilities in the Sacramento-­San Joaquin Delta while also protecting aquatic and terrestrial species that may be adversely affected by the project and accompanying changes in the State Water Project (SWP) and Central Valley Project (CVP) operations. The Plan also includes habitat restoration and a commitment to assist in the conservation and recovery of species that are listed for protection under the federal and state Endangered Species Acts. With financial support from the S.D. Bechtel, Jr. Foundation, Saracino and Mount, LLC, convened an independent panel of experts, with technical support from NewFields, Inc., to evaluate portions of the Plan. The panel, working jointly with TNC and AR, developed a series of technical and legal questions about the Plan. This report provides answers to these questions, along with limited recommendations on how to improve BDCP. To simplify analysis, this review focuses on conditions for federally listed fishes during the Early Long Term (ELT), a decade after a permit would be issued (approximately year 2025). These are described in detail in the BDCP Effects Analysis and accompanying Environmental Impact Statement/Environmental Impact Report. We compared the performance of three different scenarios: a No Action Alternative (NAA) where no new North Delta diversion facility is constructed, a High Outflow Scenario (HOS) where the facilities are operated in a way that allows for occasional high spring and fall outflows, and a Low Outflow Scenario (LOS) with lower spring and fall outflows. The review also emphasizes in-­Delta and Sacramento River watershed conditions during the ELT, with less attention to San Joaquin River conditions and fishes. Although multiple data sources were used in this analysis, most hydrologic data came from CALSIM simulations conducted by BDCP consultants. The Panel strongly cautions about the conclusions drawn from these simulations. Flow simulations have three compounding uncertainties that can lead to significant error: (1) uncertainty in system understanding and future conditions, (2) model uncertainties (particularly the relationships between 1-­, 2-­, and 3-­dimensional models), and (3) behavioral/regulatory uncertainty where the models cannot capture the scope of human behavior in operating the projects under various conditions. These uncertainties, which are not described in BDCP documents well, makes all of our conclusions contingent on the projects actually being operated as simulated.

Independent Review Panel (IRP) Report for the 2014 Long-Term Operations Biological Opinions (LOBO) Annual Science Review

Delta Stewardship Council (Delta Council) | December 1st, 2014