Using the Distinct Population Segment concept to protect fishes with low levels of genomic differentiation: conservation of an endemic minnow (Hitch, Lavinia exilicauda)

American Fisheries Society (AFS) | December 23rd, 2018

In the United States, the Endangered Species Act (ESA) of 1973 was enacted to conserve species that are endangered or threatened throughout all or a portion of their rang

In the United States, the Endangered Species Act (ESA) of 1973 was enacted to conserve species that are endangered or threatened throughout all or a portion of their range. The definition of “species” includes subspecies and distinct population segments (DPSs). Among freshwater fishes, the use of DPS designations has largely been restricted to salmonids, although the DPS concept is increasingly applied to other fishes as well. As more taxa approach threatened status, the difficult question becomes what to do when genetic evidence does not strongly support formal taxonomic designations (full species or subspecies). We examine the potential application of the DPS concept to protect fishes by using the example of the Hitch Lavinia exilicauda, a cyprinid fish that is endemic to California. The Hitch is divided into three formally described, geographically separate subspecies (the Sacramento, Monterey, and Clear Lake Hitches). However, genomic studies (i.e., restriction site‐associated DNA sequencing), presented here with three independent analyses using a large data set, only weakly supported subspecies designations. Results suggested population structure but not subspecies structure. Nevertheless, conventional taxonomic methods, strong contemporary isolation, the importance of protecting genetic diversity, and high cultural value still qualify all three designated subspecies for DPS status and demonstrate how taxa such as the Clear Lake Hitch can warrant protection under the ESA.

Variable coastal hypoxia exposure and drivers across the southern California Current

Nature Portfolio (Springer Nature) | May 25th, 2021

Declining oxygen is one of the most drastic changes in the ocean, and this trend is expected to worsen under future climate change scenarios. Spatial variability in disso

Declining oxygen is one of the most drastic changes in the ocean, and this trend is expected to worsen under future climate change scenarios. Spatial variability in dissolved oxygen dynamics and hypoxia exposures can drive differences in vulnerabilities of coastal ecosystems and resources, but documentation of variability at regional scales is rare in open-coast systems. Using a regional collaborative network of dissolved oxygen and temperature sensors maintained by scientists and fishing cooperatives from California, USA, and Baja California, Mexico, we characterize spatial and temporal variability in dissolved oxygen and seawater temperature dynamics in kelp forest ecosystems across 13° of latitude in the productive California Current upwelling system. We find distinct latitudinal patterns of hypoxia exposure and evidence for upwelling and respiration as regional drivers of oxygen dynamics, as well as more localized effects. This regional and small-scale spatial variability in dissolved oxygen dynamics supports the use of adaptive management at local scales, and highlights the value of collaborative, large-scale coastal monitoring networks for informing effective adaptation strategies for coastal communities and fisheries in a changing climate.

Variation in Salmon Migration Phenology Bolsters Population Stability but Is Threatened by Drought

Wiley Online Library | February 23rd, 2025

Intrapopulation variation in movement is common in nature but its effects on population dynamics are poorly understood. Using movement data from 3270 individually-marked

Intrapopulation variation in movement is common in nature but its effects on population dynamics are poorly understood. Using movement data from 3270 individually-marked fish representing nine cohorts of coho salmon (Oncorhynchus kisutch) in California, we show that bimodal intrapopulation variation in the timing of juvenile down-migration from their natal habitat and subsequent residence in non-natal habitat affects growth, emigration timing, and the abundance and stability of adult returns. Non-natal fish (early down-migrants) exhibited more variable growth and more variable but earlier emigration to the estuary than natal fish (late down-migrants). While natal rearing was more common, non-natal fish were overrepresented among adult returns, and total returns were 1.4 times more stable than natal returns alone. Our results demonstrate that variation in migratory behaviour bolsters population stability. However, non-natal rearing is reduced in low water years, suggesting that drought exacerbates population instability by reducing critical intrapopulation variation.

Viability assessment for Pacific salmon and steelhead listed under the Endangered Species Act

National Marine Fisheries Service (NMFS) | July 25th, 2016

The Endangered Species Act (ESA) requires that the National Marine Fisheries Service (NMFS) review the status of listed species under its authority at least every five ye

The Endangered Species Act (ESA) requires that the National Marine Fisheries Service (NMFS) review the status of listed species under its authority at least every five years and determine whether any species should be removed from the list or have its listing status changed. Assessments of the viability of ESA-listed Pacific salmonids were conducted by the Southwest Fisheries Science Center and the Northwest Fisheries Science Center. The information from these assessments is incorporated into the West Coast Region’s status review, and the NMFS West Coast Region will make final determinations about any proposed changes in listing status, taking into account not only biological information (viability assessments) but also threats to the species and ongoing or planned protective efforts. This report from the Southwest Fisheries Science Center covers 10 ESA-listed Evolutionarily Significant Units (ESUs) and Distinct Population Segments (DPSs) that lie wholly or partially in California. In this review, we consider 1) new information relevant to the delineation of ESU/DPS boundaries, and 2) new information on status and trends in abundance, productivity, spatial structure and diversity specifically addressed by viability criteria previously developed by Technical Recovery Teams (TRTs). These viability assessments summarize current information (through the 2014–2015 spawning year where available) with respect to the viability criteria developed by the TRTs.  Consequently, the current assessments consider not only changes in populations that have occurred since the 2010 assessments but also the status of populations and ESUs/DPSs in relation to the viability criteria developed by the TRTs. For eight of the ESUs/DPSs (Southern Oregon/Northern California Coho Salmon, Central California Coast Coho Salmon, California Coastal Chinook Salmon, Northern California Steelhead, Central California Coast Steelhead, South-central California Steelhead, Southern California Steelhead, and California Central Valley Steelhead) the new information suggests that there has been no change in extinction risk since 2010 viability assessments. For two ESUs (Central Valley Spring-run Chinook Salmon, and Sacramento River Winter-run Chinook Salmon) the new information suggests a change in extinction risk. The viability of Central Valley Spring-run Chinook salmon appears to have improved since the 2010 assessment, but this ESU is far from being viable and is still facing relatively high extinction risk. The viability of Sacramento River Winter-run Chinook Salmon has been reduced and the ESU faces greater extinction risk since the 2010 assessment.

Visual, spectral, and microchemical quantification of crystalline anomalies in otoliths of wild and cultured delta smelt

Nature Portfolio (Springer Nature) | December 1st, 2022

Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in oto

Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in otoliths of delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the San Francisco Estuary. Left–right asymmetry and anomalous crystalline polymorphs (i.e., vaterite) were quantified and compared between wild and cultured populations using digital image analysis. Visual estimates of vaterite were validated using X-ray diffraction, Raman spectroscopy, laser ablation ICPMS, and electron probe microanalysis. Results indicated that cultured delta smelt were 80 times more likely to contain a vateritic otolith and 18 times more likely to contain relatively large (≥ 15%) amounts of vaterite. Similarly, cultured fish exhibited 30% greater asymmetry than wild fish. These results indicate that cultured delta smelt exhibit a significantly higher frequency of vestibular abnormalities which are known to reduce fitness and survival. Such hatchery effects on otolith development could have important implications for captive culture practices and the supplementation of wild fish populations with cultured individuals.

Water and the Future of the San Joaquin Valley

Public Policy Institute of California (PPIC) | February 14th, 2019

The San Joaquin Valley—California’s largest agricultural region and an important contributor to the nation’s food supply—is in a time of great change. The valle

The San Joaquin Valley—California’s largest agricultural region and an important contributor to the nation’s food supply—is in a time of great change. The valley is ground zero for many of California’s most difficult water management problems—including groundwater overdraft, drinking water contamination, and declines in habitat and native species. Local water supplies are limited, particularly in the southern half of the region. To irrigate their crops, many farmers use water imported from the Sacramento–San Joaquin Delta. But in many places farmers have also relied on groundwater overdraft—pumping groundwater in excess of the rate at which it is replenished. Worsening droughts, increasing regulations to protect endangered native fishes, and growing demand by Southern California for Delta imports have compounded surface water scarcity. The state’s Sustainable Groundwater Management Act (SGMA) requires local water users to bring groundwater use to sustainable levels by the early 2040s. This will have a broad impact on valley agriculture and the regional economy in coming years—likely including some permanent idling of farmland. This report explores three key challenges facing the San Joaquin Valley and reviews the most promising approaches to address them:  Balancing water supplies and demands. To close the groundwater deficit, groundwater sustainability agencies in the valley’s overdrafted basins will have to augment supplies, reduce demands, or use some combination of these two approaches. A range of options are under consideration but they are not equally effective or practical.  Addressing groundwater quality challenges. Poor groundwater quality impairs drinking water supplies in disadvantaged rural communities, reduces long-term agricultural prosperity, and degrades ecosystems. Providing safe drinking water is an urgent priority. Over the longer term, parties will also need to manage water quantity and quality together, to take advantage of synergies and avoid unintended consequences. The necessary coordination will be challenging because the various programs addressing valley water quality issues are carried out by numerous local and regional entities, whose lines of responsibility and geographic boundaries do not neatly align.  Fostering beneficial water and land use transitions. Effectively addressing water scarcity and the resulting land use changes in the San Joaquin Valley offers opportunities to put lands coming out of production to good use—and gain “more pop per drop” from limited water resources. Multiple-benefit approaches to water and land management can enhance groundwater recharge and improve air and water quality. They can also promote healthier soils, new recreational opportunities, additional flood protection, improved habitat, and new revenue streams for private landowners engaging in conservation-oriented management. Addressing these complex and intertwined issues requires significant changes in water and land management and a major ramp-up in cooperation and coordination among a wide circle of stakeholders. Pursuing solutions that deliver multiple benefits will boost the chances of success overall. The entire region—and California as a whole—will benefit if solutions to these challenges are cost-effective and support the valley’s economy while improving public health and the natural environment.

Water Features of the Smith River Plain, Del Norte County, California

U.S. Geological Survey (USGS) | December 1st, 1957

Water Wasted to the Sea?

University of California, Davis (UC Davis) | July 15th, 2017

Watershed Condition, Turbidity, and Implications for Anadromous Salmonids in North Coastal California Streams

California State Water Resources Control Board (SWRCB) | May 21st, 2008

It is widely acknowledged that historically intensive human disturbances increased erosion and sediment delivery rates to extreme levels in the 1950s through the 1970s ac

It is widely acknowledged that historically intensive human disturbances increased erosion and sediment delivery rates to extreme levels in the 1950s through the 1970s across the north coast, and are likely continuing to affect turbidity durations to some degree. A more controversial question is to what extent contemporary land use is affecting present-day erosion, sediment delivery and turbidity. Using turbidity exceedence levels to indicate watershed disturbance, we approached this question from several perspectives. Part A of this report follows up and expands on an earlier analysis (Klein, 2003) for which turbidity data sets from only eight sites were available. In the present study, annual turbidity data sets were assembled from up to 28 continuous turbidity and stage recording stations located on small streams in the northcoast region from Del Norte County in the north to Mendocino County in the south. Data spanning three water years (WY2003-2005) were processed to calculate lengths of time turbidity was higher than several thresholds. Turbidity thresholds ranged from 25 (frequently cited in the salmonid literature as causing ill effects when exceeded) to 1000 FNU. Turbidity exceedence analyses, similar to conventional flow exceedence analyses, were also performed, allowing comparison of turbidity levels at various exceedence probabilities. Part B of this report uses turbidity relationships to harvest rate to model potential effects on anadromous salmonids within a cumulative watershed effects (CWE) framework. To evaluate CWEs on anadromous salmonids and the stream ecosystem, annual turbidigraphs were produced from WY1991 through WY2005 at annual average harvest rates of 0% to 6% for an 8 mi2 old second-growth watershed in North Coastal California. The turbidigraphs were very conservative in that they used the ‘Lower Bound Lines’ to estimate turbidity from discharge, rather than a line of best fit. Turbidity thresholds established at 10, 25, and 50 FNU were applied to assess chronic background, moderate, and severe stress to stream ecosystems in each water year. A simple model of smolt growth and survival-to-adult-return (SAR), as influenced by the annual turbidigraph, indicated the minimum supportable adult steelhead population size could be more than halved at the 2% average annual timber harvest rate compared to that supported by an old second-growth watershed.

Wetland geomorphology and tidal hydrodynamics drive fine‑scale fish community composition and abundance

Environmental Biology of Fishes (Springer) | January 19th, 2024