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.

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 management in mediterranean river basins: a comparison of management frameworks, physical impacts, and ecological responses

Hydrobiologia (Springer) | September 11th, 2012

Rivers in mediterranean climates have been extensively modified by water management infrastructure and practices, yet patterns of development and consequent effec

Rivers in mediterranean climates have been extensively modified by water management infrastructure and practices, yet patterns of development and consequent effects on freshwater ecosystems have not been compared across multiple regions. To evaluate the influence of water management on mediterranean-climate rivers, we compare the historic progression of management policies, institutions, and ecosystem impacts in the Sacramento River (California, USA), Ebro River (Spain), and Biobío River (Chile) basins. There are broad similarities in patterns of ecosystem alterations related to the extensive development of dams and water management infrastructure in the three study basins. Flow regimes have been altered by the reduction of winter peak flows and increased summer baseflows. There are also common patterns of disturbance from sediment transport alteration, water quality degradation, and declines in freshwater biodiversity. Current approaches are inadequate for addressing the formidable water management challenges in California, Spain, and Chile, yet the dramatic evolution of water policies and institutions over the past 150 years suggests that further adaptation is possible. Advances toward integrated and sustainable water management models are likely to occur through incremental change, driven by growing awareness of climate change effects and public demands for water-use efficiency and improved environmental quality.  

Water storage decisions will determine the distribution and persistence of imperiled river fishes

Ecological Society of America (Wiley) | December 17th, 2020

Managing the world’s freshwater supply to meet societal and environmental needs in a changing climate is one of the biggest challenges for the 21st century. Dams provid

Managing the world’s freshwater supply to meet societal and environmental needs in a changing climate is one of the biggest challenges for the 21st century. Dams provide water security; however, the allocation of dwindling water supply among reservoirs could exacerbate or ameliorate the effects of climate change on aquatic communities. Here, we show that the relative sensitivity of river thermal regimes to direct impacts of climate change and societal decisions concerning water storage vary substantially throughout a river basin. In the absence of interspecific interactions, future Colorado River temperatures would appear to benefit both endemic and nonnative fish species. However, endemic species are already declining or extirpated in locations where their ranges overlap with warmwater nonnatives and changes in water storage may lead to warming in some of the coolest portions of the river basin, facilitating further nonnative expansion. Integrating environmental considerations into ongoing water storage negotiations may lead to better resource outcomes than mitigating nonnative species impacts after the fact.

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.