Rachel C JohnsonSouthwest Fisheries Science Center · Fisheries Ecology Division
Rachel C Johnson
Doctor of Philosophy
About
52
Publications
17,194
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
816
Citations
Citations since 2017
Publications
Publications (52)
Context
Cross-boundary subsidies create important growth opportunities for a range of taxa. In modified river systems, remnant patches of floodplain and flood bypasses become ephemeral hotspots of zooplankton production, however, the extent to which these prey items are (or could be) transported downstream is unclear.
Objectives
We investigated th...
Graphical abstract for our recent publication on the use of otoliths in fisheries science.
Chemical analysis of calcified structures continues to flourish, as analytical and technological advances enable researchers to tap into trace elements and isotopes taken up in otoliths and other archival tissues at ever greater resolution. Increasingly, these tracers are applied to refine age estimation and interpretation, and to chronicle respons...
Effective species management depends on accurate estimates of population size. There are, however, no estimates of annual juvenile production for Central Valley spring-run Chinook Salmon (“spring run”), a highly imperiled species in California, making it difficult to evaluate population status and effectively manage key issues such as entrainment o...
Historically, Chinook Salmon in the California Central Valley reared in the vast wetlands of the Sacramento–San Joaquin Delta. However, more than 95% of floodplain, riparian, and wetland habitats in the Delta have become degraded because of anthropogenic factors such as pollution, introduced species, water diversions, and levees. Despite pronounced...
Historically, Chinook Salmon in the California Central Valley reared in the vast wetlands of the Sacramento–San Joaquin Delta. However, more than 95% of floodplain, riparian, and wetland habitats in the Delta have become degraded because of anthropogenic factors such as pollution, introduced species, water diversions, and levees. Despite pronounced...
Riverine ecosystems in their natural state are complex mosaics of habitats whose conditions vary across space and time as landscape features filter prevailing hydrologic forcing. Yet, through anthropogenic alteration many large river systems have become simplified through the construction of levees and dams that reduce lateral connectivity and flow...
Rare phenotypes and behaviours within a population are often overlooked, yet they may serve a heightened role for species imperilled by rapid warming. In threatened spring-run Chinook salmon spawning at the southern edge of the species range, we show late-migrating juveniles are critical to cohort success in years characterized by droughts and ocea...
Estuarine food webs are complex, as marine, freshwater, and terrestrial inputs combine and contribute variable amounts of organic material. Seasonal fluctuations in precipitation amplify the dynamism inherent to estuarine food webs, particularly in lagoonal estuaries, which can be seasonally closed and disconnected from the ocean in low-runoff peri...
Floodplains represent critical nursery habitats for a variety of fish species due to their highly productive food webs, yet few tools exist to quantify the extent to which these habitats contribute to ecosystem-level production. Here we conducted a large-scale field experiment to characterize differences in food web composition and stable isotopes...
Rare phenotypes and behaviours within a population are often overlooked, yet they may serve a heightened role for species imperilled by rapid warming. In threatened spring-run Chinook salmon spawning at the southern edge of the species range, we show late-migrating juveniles are critical to cohort success in years characterized by droughts and ocea...
Warming and hypoxia are two stressors commonly found within natural salmon redds that are likely to co-occur. Warming and hypoxia can interact physiologically, but their combined effects during fish development remain poorly studied, particularly stage-specific effects and potential carry-over effects. To test the impacts of warm water temperature...
Stable isotopes recorded in fish eye lenses are an emerging tool to track dietary shifts coincident with use of diverse habitats over the lifetime of individuals. Eye lenses are metabolically inert, sequentially deposited, archival tissues that can open avenues to chronicle contaminant exposures, diet histories, trophic dynamics and migratory histo...
• Predator–prey systems face intensifying pressure from human exploitation and a warming climate with implications for where and how natural resource management can successfully intervene. We hypothesized young salmon migrating to the Pacific Ocean face a seasonally intensifying predator gauntlet when warming water temperature intensifies a multipl...
Here we summarized the California Central Valley Steelhead Distinct Population Segment (DPS) definition, distribution, status and recovery strategy for a workshop held in February 2021. The goal of this this workshop was to identify collaborations and partnerships that could contribute to the future development of comprehensive monitoring of San Jo...
Tracking habitat use and dietary shifts in migratory species is vital to conservation and management. Yet conventional animal tracking often precludes tracking small juveniles at critical life‐stages where recruitment bottlenecks often manifest. Stable isotope analysis (SIA) in consecutive laminae in eye lenses, a protein‐rich depositional tissue,...
Here we reviewed Central Valley spring-run Chinook
salmon (Oncorhynchus tshawytscha; CVSC) life history diversity, with an emphasis on the juvenile life stage and relevant tools and emerging studies which advance the identification of life history variants, for a workshop held in September 2020. The goal of this workshop was to serve as a public sc...
Chinook Salmon (Oncorhynchus tshawytscha)
are increasingly vulnerable to anthropogenic
activities and climate change, especially at
their most southern range in California’s
Central Valley. There is considerable
interest in understanding stressors that
contribute to population decline and in
identifying management actions that
reduce the effects of...
Chinook Salmon (Oncorhynchus tshawytscha) are increasingly vulnerable to anthropogenic activities and climate change, especially at their most southern species range in California’s Central Valley. There is considerable interest in understanding stressors that contribute to population decline and in identifying management actions that reduce the im...
Bar-built coastal lagoons are dynamic ecosystems at the land-sea interface that are important habitats for a variety of species. This study examined the habitat ecology of two lagoon species, the endangered Tidewater Goby (Eucyclogobius newberryi) and the Prickly Sculpin (Cottus asper) by reconstructing individual life histories from patterns in th...
Fish face many anthropogenic stressors. Authorities in marine, estuarine, and freshwater realms often share interdependent fisheries management goals, but address singular stressors independently. Here, we present a case study suggesting that coordinating stressor relief across management realms may synergize conservation efforts, especially to act...
Aquatic ecosystems worldwide face growing threats from elevated levels of contaminants from human activities. Toxic levels of selenium (Se) shown to cause deformities in birds, fish, and mammals can transfer from parents to progeny during embryonic development or accumulate through Se-enriched diets. For migratory species that move across landscape...
Altered river flows and fragmented habitats often simplify riverine communities and favor non‐native fishes, but their influence on life‐history expression and survival is less clear. Here, we quantified the expression and ultimate success of diverse salmon emigration behaviors in an anthropogenically altered California river system. We analyzed tw...
Estuaries provide critical habitat for a vast array of fish and wildlife but are also a nexus for core economic activities that mobilize and concentrate contaminants that can threaten aquatic species. Selenium (Se), an essential element and potent reproductive toxin, is enriched in parts of the San Francisco Estuary (SFE) to levels known to cause t...
Major ecological realignments are already occurring in response to climate change. To be successful, conservation strategies now need to account for geographical patterns in traits sensitive to climate change, as well as climate threats to species-level diversity. As part of an effort to provide such information, we conducted a climate vulnerabilit...
Ecologists are pressed to understand how climate constrains the timings of annual biological events (phenology). Climate influences on phenology are likely significant in estuarine watersheds because many watersheds provide seasonal fish nurseries where juvenile presence is synched with favorable conditions. While ecologists have long recognized th...
Identification of habitats responsible for the successful production and recruitment of rare migratory species is a challenge in conservation biology. Here, a tool was developed to assess life stage linkages for the threatened potamodromous cyprinid Clear Lake hitch Lavinia exilicauda chi. Clear Lake hitch undertake migrations from Clear Lake (Lake...
Animal migration is the seasonal movement from one region to another and can involve thousands of individuals journeying across continents and oceans. Scientists often use electronic and physical tags to track the movements of migratory fish. However, these tags only work on bigger fish and only give a limited picture of where the fish have been. H...
Fall-run Chinook salmon (Oncorhynchus tshawytscha) from the Sacramento–San Joaquin River system form the backbone of California’s salmon fishery and are heavily subsidized through hatchery production. Identifying temporal trends in the relative contribution of hatchery- versus wild-spawned salmon is vital for assessing the status and resiliency of...
Protecting habitats for imperiled species is central to conservation efforts. However, for migratory species, identifying juvenile habitats that confer success requires tracking individuals to reproduction. Here, we used otolith strontium isotope ratios (87 Sr/ 86 Sr) to reconstruct juvenile habitat use by endangered Sacramento River winter-run Chi...
A robust monitoring network that provides quantitative information about the status of imperiled species at key life stages and geographic locations over time is fundamental for sustainable management of fisheries resources. For anadromous species, management actions in one geographic domain can substantially affect abundance of subsequent life sta...
This conceptual model was compiled to support the development of monitoring studies and plans associated with management and recovery of sturgeon species in the San Francisco Estuary (SFE) watershed. Multiple life stages of the southern Distinct Population Segment (sDPS) of North American green sturgeon (Acipenser medirostris) and the Sacramento-Sa...
This document describes life history and current monitoring of the two endemic sturgeon
species of the San Francisco Estuary watershed: the southern Distinct Population Segment
(sDPS) of North American green sturgeon green sturgeon and the Sacramento-San Joaquin River
white sturgeon. It serves as background information used in the development of th...
California’s Central Valley Interagency Ecology Program (IEP) formed multi-agency Salmon
and Sturgeon Assessment of Indicators by Life Stage (SAIL) synthesis teams to develop a
scientific framework for evaluating existing information on endangered Sacramento River
winter-run Chinook salmon (SRWRC; Oncorhynchus tshawytscha), green sturgeon (Acipense...
The ability of salmon to navigate from the ocean back to their river of origin to spawn acts to reinforce local adaptation and maintenance of unique and heritable traits among salmon populations. Here, the extent to which Chinook salmon Oncorhynchus tshawytscha from the same freshwater breeding groups associate together in the ocean at regional and...
Presentation at the 2014 Bay Delta Science Conference. ABSTRACT: The maintenance of life history diversity within and among populations is thought to be critical for the long-term persistence of salmon stocks. Asynchronous population dynamics can buffer stocks against environmental change and provide a stabilizing ‘portfolio effect’. Preserving and...
The loss of genetic and life history diversity has been documented across many taxonomic groups, and is considered a leading cause of increased extinction risk. Juvenile salmon leave their natal rivers at different sizes, ages and times of the year, and it is thought that this life history variation contributes to their population sustainability, a...
Trace element concentrations in fish earstones (‘otoliths’) are widely used to discriminate spatially discrete populations or individuals of marine fish, based on a commonly held assumption that physiological influences on otolith composition are minor, and thus variations in otolith elemental chemistry primarily reflect changes in ambient water ch...
The Sacramento splittail (Pogonichthys macrolepidotus) is a relatively large (400 mm), long-lived (8 years) demersal cyprinid of conservation importance endemic to the San Francisco Estuary (SFE), California, USA. It exhibits a semi-anadromous life cycle spending adult life in low to moderate salinity (0-12) habitat with migrations into upstream fr...
Background/Question/Methods
The maintenance of life history diversity within and among populations is thought to be critical for the persistence of salmon stocks. Preserving and restoring diversity in life history traits is thus central to many recovery efforts, but it is necessary to first understand the way in which environmental factors affect...
Selective mortality during early life history stages can have significant population-level consequences, yet critical periods when selective mortality occurs, the strength of selection, and under what environmental conditions can be difficult to identify. Here, we used otolith microstructure and chemistry to examine the factors potentially linked t...
The maintenance of life history diversity is critical for the persistence of salmonid populations and central to many recovery efforts. Juvenile Chinook salmon leave their natal rivers at different sizes, ages and times of the year, and it is thought that this life history variation contributes to their population sustainability. Preserving and res...
Maintaining viable populations of salmon in the wild is a primary goal for many conservation and recovery programs. The frequency and extent of connectivity among natal sources defines the demographic and genetic boundaries of a population. Yet, the role that immigration of hatchery-produced adults may play in altering population dynamics and fitne...
Eualus subtilis Carvacho & Olson 1984 is presently considered a synonym of E. lineatus Wicksten & Butler 1983. Comparisons of the two forms revealed differences in the armature of the antennular peduncle, stylocerite, and pereopods, as well as differences in color and maximum size, indicating that E. subtilis is a valid species. Furthermore, E. sub...
Projects
Projects (2)
Climate change is transforming California and is threatening already vulnerable salmon populations. This project will use archival tissues (otolith ear stones) from modern and historical spring-run Chinook Salmon to understand how shifts in migration timing and habitat use allowed salmon to cope with highly variable environmental conditions. We will learn how salmon responded to the recent drought and flood periods (2012-2020 CE), the California Gold Rush Period (~1835-1870 CE), the Little Ice Age (~1560-1780 CE), and the Megadrought Period (~1200-1410 CE). This effort will provide the insights needed for developing climate-adapted conservation actions to support salmon into the future.
Our goal is to better understand how life history diversity within spring-run populations can help them cope with California Volatile climate and future climate change in a highly perturbed environment. We are using a combination of otolith microchemistry and isotope analysis to get to this research question.