California River Research Articles

Disruption of natural disturbance regime decouples habitat and life stage in a keystone species

AbstractAnthropogenic disturbance of stream ecosystems, often chronic in nature, has been studied extensively. However, when disturbance is driven by more than one resource policy over many decades, feedback between habitat evolution and biological adaptation can be disrupted and ecological function affected in unforeseen ways. We analyzed over 100 years of Chinook salmon (Oncorhynchus tshawytscha) length frequency trends associated with fisheries management and changes in available spawning substrate (habitat) linked to flow regulation in a highly altered California river. Over time, salmon lengths generally decreased, fluctuating with exploitation (ocean harvest) and hatchery production rates. Female size reduction, coupled with a degrading and coarsening channel, and perching peripheral habitat related to past mining activity, indicates available spawning substrate may be too large to support the current salmon population. Assuming a salmon can move material ~10% of her body length, length frequency data and current substrate size distribution suggest that increasing salmon sizes to historic distributions could increase available spawning habitat by as much as 13%. Alternatively, decreasing spawning substrate size could support a greater portion of the current population. To test the latter hypothesis and inform future management actions, we monitored two spawning riffles where large and small gravel was placed on top of a cobble. We observed an immediate spawning activity increase that was more pronounced where smaller gravel was deposited. Following a decade of habitat decline, the two sites were both replenished with medium gravel. Elevated spawning use occurred immediately at both sites, commensurate with this intermediate size, further supporting our hypotheses. Sediment coarsening and habitat disconnect below dams, combined with reduced salmon size, indicate the natural spawning process may be decoupled from available habitat below dams in the foreseeable future without continuous intervention. Actively managing salmon population demographics through modified hatchery and size‐selective harvest practices and developing a coarse sediment budget with size‐appropriate material for regulated anadromous rivers could produce immediate benefits for ecosystem services, including salmon populations. However, these management actions will require continued maintenance and informed socio‐ecological goals to remain successful.

Age, growth, and trophic ecology of the Redeye Bass, an alien invader of California rivers

AbstractObjectiveThe Redeye Bass Micropterus coosae is a piscivore introduced into California, which has become a threat to the state's endemic freshwater fishes. It has eliminated native fishes from the middle reaches of the Cosumnes River, our study stream, which is the largest stream without a major dam on its main stem in the Sacramento–San Joaquin River drainage, central California, USA. We thoroughly documented its novel life history and ecology in California to shed light on why it has been such a successful invader despite its relatively small native range.MethodsOver 4000 stable carbon and nitrogen isotope samples were utilized to refine our understanding of fish trophic position within the river food web, along with a stable isotope mixing model that accounts for uncertainty in trophic enrichment data.ResultGrowth was slow, with an adult size range of 9–25 cm standard length (SL), although few were larger than 15‐cm SL (5–6 years old). Stable isotope analyses showed that Redeye Bass dominate the river ecosystem to the exclusion of most native fishes, occupying multiple trophic levels and microhabitats. Adults largely consumed non‐native crayfish and large aquatic insects, while juveniles consumed aquatic insects, the size of prey increasing with Redeye Bass length. There was no evidence of cannibalism. Redeye Bass have effectively occupied the diverse trophic positions of at least four native fish species and have altered the trophic position of Rainbow Trout Oncorhynchus mykiss in sites where they co‐occur with bass.ConclusionThe introduction of Redeye Bass poses a continuing threat to native stream fishes in California and elsewhere.

Mimicking functional elements of the natural flow regime promotes native fish recovery in a regulated river.

Streamflow regimes that maintain vital functions and processes of aquatic ecosystems are critical to sustaining ecosystem health. In rivers with altered flow regimes, restoring components of the natural flow regime is predicted to conserve freshwater biodiversity by supporting ecological functions and geomorphological processes to which native communities are adapted. However, the effectiveness of environmental flow restoration is poorly understood because of inadequate monitoring and uncertainty in ecological responses to managed changes in specific, quantifiable aspects of the annual streamflow regime. Here, we used time series models to analyze 25 years of fish assemblage data collected before and after environmental flow implementation in a dammed river in California, USA. We examined the response of the fish community to changes in individual components of the flow regime known to support ecosystem functions. We found that as functional flow components shifted toward their predicted natural range, the quasi-extinction risk (likelihood of population declines of >80%) decreased for the native fish assemblage. Following environmental flow implementation, observed changes toward natural ranges of dry season duration, fall pulse flow magnitude, and wet season timing each reduced quasi-extinction risk by at least 40% for the native assemblage. However, functional flow components that shifted away from their predicted natural range, including lower spring recession flows and higher dry season baseflow, resulted in greater quasi-extinction risk for native species. In contrast, non-native species decreased in abundance when flow components shifted toward predicted natural ranges and increased when components shifted away from their natural range. Although most functional flow components remained outside of their natural range following environmental flow implementation, our results indicate that even moderate shifts toward a natural flow regime can benefit native and suppress non-native fish species. Overall, this study provides the most compelling evidence to date of the effectiveness of functional environmental flows in supporting native fish recovery in a highly regulated river.

Effects of low temperature on growth and metabolism of larval green sturgeon (Acipenser medirostris) across early ontogeny.

Southern Distinct Population Segment (sDPS) green sturgeon spawn solely in one stretch of the Sacramento River in California. Management of this spawning habitat is complicated by cold water temperature requirements for the conservation of winter-run Chinook salmon. This study assessed whether low incubation and rearing temperatures resulted in carryover effects across embryo to early juvenile life stages on scaling relationships in growth and metabolism in northern DPS green sturgeon used as a proxy for sDPS green sturgeon. Fish were incubated and reared at 11°C and 15°C, with a subset experiencing a reciprocal temperature transfer post-hatch, to assess recovery from cold incubation or to simulate a cold-water dam release which would chillrearing larvae. Growth and metabolic rate of embryos and larvae were measured to 118days post hatch. Reciprocal temperature transfers revealed a greater effect of low temperature exposure during larval rearing rather than during egg incubation. While 11°C eggs hatched at a smaller length, log-transformed length-weight relationships showed that these differences in developmental trajectory dissipated as individuals achieved juvenile morphology. However, considerable size-at-age differences persisted between rearing temperatures, with 15°C fish requiring 60days post-hatch to achieve 1g in mass, whereas 11°C fish required 120days to achieve 1g, resulting in fish of the same age at the completion of the experiment with a ca. 37-fold difference in weight. Consequently, our study suggests that cold rearing temperatures have far more consequential downstream effects than cold embryo incubation temperatures. Growth delays from 11°C rearing temperatures would greatly increase the period of vulnerability to predation in larval green sturgeon. The scaling relationship between log-transformed whole-body metabolism and mass exhibited a steeper slope and thus an increased oxygen requirement with size in 11°C reared fish, potentially indicating an energetically unsustainable situation. Understanding how cold temperatures affect green sturgeon ontogeny is necessary to refine our larval recruitment estimations for this threatened species.

Remnant salmon life history diversity rediscovered in a highly compressed habitat.

Chinook salmon (Oncorhynchus tshawytscha) display remarkable life history diversity, underpinning their ability to adapt to environmental change. Maintaining life history diversity is vital to the resilience and stability of Chinook salmon metapopulations, particularly under changing climates. However, the conditions that promote life history diversity are rapidly disappearing, as anthropogenic forces promote homogenization of habitats and genetic lineages. In this study, we use the highly modified Yuba River in California to understand if distinct genetic lineages and life histories still exist, despite reductions in spawning habitat and hatchery practicesthat have promoted introgression. There is currently a concerted effort to protect federally listed Central Valley spring-run Chinook salmon populations, given that few wild populations still exist. Despite this, we lack a comprehensive understanding of the genetic and life history diversity of Chinook salmon present in the Yuba River. To understand this diversity, we collected migration timing data and GREB1L genotypes from hook-and-line, acoustic tagging, and carcass surveys of Chinook salmon in the Yuba River between 2009 and 2011. Variation in the GREB1L region of the genome is tightly linked with run timing in Chinook salmon throughout their range, but the relationship between this variation and entry on spawning grounds is little explored in California's Central Valley. We found that the date Chinook salmon crossed the lowest barrier to Yuba River spawning habitat (Daguerre Point Dam) was tightly correlated with their GREB1L genotype. Importantly, our study confirms that ESA-listed spring-run Chinook salmon are spawning in the Yuba River, promoting a portfolio of life history and genetic diversity, despite the highlycompressed habitat. This work highlights the need to identify and protect this life history diversity, especially in heavily impacted systems,to maintain healthy Chinook salmon metapopulations. Without protection, we run the risk of losing the last vestiges of important genetic variation.

Back-to-back high category atmospheric river landfalls occur more often on the west coast of the United States

The catastrophic December 2022-January 2023 nine atmospheric rivers in California underscore the urgent need to better understand such high-risk weather extremes. Here we applied a machine learning clustering tool to understand the activity of atmospheric river clusters. Reanalysis results show that clusters with high density, that is the time fraction under atmospheric river conditions within a cluster, exhibit more frequent high-category atmospheric rivers, alongside an increased likelihood for extreme precipitation and severe land surface responses. The key circulation patterns of atmospheric river clusters are primarily attributed to subseasonal variability. Furthermore, the occurrence and density of atmospheric river clusters are modulated by the daily variability of the geopotential height field. Climate model projections suggest that atmospheric river clusters with higher density and higher categories will be more frequent as warming level increases. Our findings emphasize the important role of atmospheric river clusters in the development of climate adaptation and resilience strategies.

Leveraging Next‐Generation Satellite Remote Sensing‐Based Snow Data to Improve Seasonal Water Supply Predictions in a Practical Machine Learning‐Driven River Forecast System

AbstractSeasonal predictions of spring‐summer river flow volume (water supply forecasts, WSFs) are foundational to western US water management. We test a new space‐based remote sensing product, spatially and temporally complete (STC) MODSCAG fractional snow‐covered area (fSCA), as input for the Natural Resources Conservation Service (NRCS) operational US West‐wide WSF system. fSCA data were considered alongside traditional SNOTEL predictors, in both statistical and AI‐based NRCS operational hydrologic models, throughout the forecast season, in four test watersheds (Walker, Wind, Piedra, and Gila Rivers in California, Wyoming, Colorado, and New Mexico). Outcomes from over 200 WSF models suggest fSCA‐enabled accuracy gains are most consistent and explainable for short‐lead, late‐season forecasts (roughly 10%–25% improvements, typically), which in operational practice can be challenging as snowlines rise above in situ measurement sites. Gains are roughly proportional to how thoroughly spring‐summer runoff is dominated by snowmelt, and how poorly in situ networks monitor late‐season snowpack. fSCA also improved accuracy for long‐lead, early‐season forecasts, which are similarly problematic in WSF practice, but not for WSFs issued around the time of peak snow accumulation, when in situ measurements reasonably characterize mountain snowpack available for upcoming spring‐summer snowmelt. The AI‐based hydrologic model generally outperformed the statistical model and, in some cases, better‐capitalized on satellite remote sensing. Additionally, preliminary analyses suggest reasonable WSF skill in many cases using fSCA as the sole predictor, potentially useful in sparsely monitored regions; and that combining satellite and in situ products in data‐driven hydrologic models using genetic algorithm‐based predictor selection could help guide new SNOTEL site selection.

Comparison of environmental DNA and underwater visual count surveys for detecting juvenile Coho Salmon in small rivers

AbstractObjectiveThis study compares the probability of detecting juvenile Coho Salmon Oncorhynchus kisutch using both environmental DNA (eDNA) techniques and underwater visual count (UVC) surveys in northern California rivers. Here, UVC surveys commonly have detection probabilities (p) surpassing 0.90, providing an ideal setting to examine the performance of newer eDNA methods. We also evaluate the potential for using eDNA concentrations to predict the count of Coho Salmon within pool habitats.MethodsWe conducted paired eDNA and UVC surveys in 96 pools across 25 stream reaches within the Smith River basin, California. Method‐specific p and the effect of environmental covariates were estimated using multiscale occupancy modeling. We used generalized linear models to evaluate the relationship of fish counts to eDNA concentrations and habitat covariates.ResultThe eDNA and UVC methods showed a high degree of agreement in detecting the presence of Coho Salmon within a pool (93% agreement) and survey reach (80% agreement). Detection probabilities for eDNA (peDNA) and for UVC (pUVC) were similar and high at median levels of pool residual depth and contributing basin area (peDNA = 91%, pUVC = 89%). Contributing basin area (a proxy for discharge) had a strong, negative effect that was more pronounced for peDNA than for pUVC (e.g., in the largest basins, peDNA = 34% whereas pUVC = 77%). We did not find eDNA concentrations to be a good predictor of Coho Salmon counts in small pools.ConclusionThis study demonstrates that eDNA methods yielded nearly identical results to UVC surveys in catchments <36 km2 and can provide a highly effective approach for determining the distribution of Coho Salmon. However, additional investigation is required before eDNA could be used to estimate relative abundance in small pools.

Canine Schistosomiasis in the West Coast: Heterobilharzia americana in Two Natural Intermediate Hosts Found in the Colorado River, California.

The emergence of infectious diseases presents a significant global health, economic, and security risk. Climate change can unexpectedly lead to the spread of pathogens, vectors, or hosts into new areas, contributing to the rise of infectious diseases. Surveillance plays a crucial role in monitoring disease trends and implementing control strategies. In this study, we document the first discovery of Heterobilharzia americana, a parasitic schistosome of mammals and its intermediate hosts Galba cubensis and Galba humilis along the banks of the Colorado River in California. We conducted multiple samplings of snails from various locations in the region with a previous history of canine schistosomiasis. Nucleotide sequencing of the multiple regions of the snails' and parasites' DNA revealed the coexistence of G. cubensis and G. humilis, both infected with H. americana. Phylogenetic analyses further validate the presence of H. americana in California, suggesting a wider distribution than previously reported. Our findings have implications for public health, veterinary medicine, and biodiversity conservation, contributing to developing effective control strategies to prevent the spread of this emerging infectious disease.

Applying parentage methods to detect gravel augmentation effects on juvenile Chinook Salmon recruitment rates

AbstractQuantifiable measurement of habitat restoration effects on salmonid reproductive performance is limited, although it is necessary for evaluating whether population responses follow management actions. We investigated using close‐kin mark‐recapture methods to partition restoration effects within standard monitoring metrics of juvenile emigrants leaving the natal reach. This approach allowed for statistical comparison of relative juvenile capture rates (recruitment) from Chinook Salmon (Oncorhynchus tshawytscha) naturally reproducing in gravel augmented (restored) and nonaugmented (unrestored) reaches of a highly managed California River. Genetic parentage techniques linked adult females that had spawned in augmented and nonaugmented spawning habitats with juvenile Chinook Salmon sampled the following spring at a trap located below the natal spawning area. Successful recruitment was documented from both augmented and nonaugmented habitats, with no statistical difference between the two habitat types. The capture rate per adult female was low (0.19–0.24 juveniles/female) compared to rates observed in other systems. Within the juvenile collections, most females in the study had 0 or 1 offspring observed; however, one female that spawned in a restored habitat had 25 offspring recovered at the trap. We modeled juvenile capture rates in relation to a range of biological and environmental variables including spawning habitat site, spawning habitat treatment (augmented and nonaugmented), annual spawner abundance, year spawned, female fork length, spawning and hatch day, and flow maximum and variance. There was an inverse relationship between annual adult abundance (escapement obtained from carcass surveys) and recruitment (juvenile recoveries at trap), suggesting habitat limitation may be creating density‐dependent effects. Additionally, female body size was positively associated with recruitment, while spawning day and mean daily temperature were inversely associated with recruitment, suggesting that both biological and environmental factors independent of habitat influenced reproduction potential. This study provides evidence that habitat restoration could have an additive (incremental) positive effect on recruitment rate, informing hatchery management and restoration activities related to population recovery.

Temporal compounding increases economic impacts of atmospheric rivers in California.

Temporally compounding atmospheric river (AR) events cause severe flooding and damage in California. However, the contribution of temporal compounding to AR-induced loss has yet to be systematically quantified. We show that the strongest ARs are more likely to be part of sequences, which are periods of elevated hydrologic hazard associated with temporally clustered ARs. Sequences increase the likelihood of flood-related impacts by 8.3% on AR days and 5.4% on non-AR days, and across two independent loss datasets, we find that ARs within sequences have over three times higher expected losses compared to ARs outside of sequences. Expected losses also increase when the preceding AR is higher intensity, when time since the preceding AR is shorter, and when an AR is the second or later event within a sequence. We conclude that temporal compounding is a critical source of information for predicting an AR's potential consequences.

Chytrid infections exhibit historical spread and contemporary seasonality in a declining stream-breeding frog.

Species with extensive geographical ranges pose special challenges to assessing drivers of wildlife disease, necessitating collaborative and large-scale analyses. The imperilled foothill yellow-legged frog (Rana boylii) inhabits a wide geographical range and variable conditions in rivers of California and Oregon (USA), and is considered threatened by the pathogen Batrachochytrium dendrobatidis (Bd). To assess drivers of Bd infections over time and space, we compiled over 2000 datapoints from R. boylii museum specimens (collected 1897-2005) and field samples (2005-2021) spanning 9° of latitude. We observed a south-to-north spread of Bd detections beginning in the 1940s and increase in prevalence from the 1940s to 1970s, coinciding with extirpation from southern latitudes. We detected eight high-prevalence geographical clusters through time that span the species' geographical range. Field-sampled male R. boylii exhibited the highest prevalence, and juveniles sampled in autumn exhibited the highest loads. Bd infection risk was highest in lower elevation rain-dominated watersheds, and with cool temperatures and low stream-flow conditions at the end of the dry season. Through a holistic assessment of relationships between infection risk, geographical context and time, we identify the locations and time periods where Bd mitigation and monitoring will be critical for conservation of this imperilled species.

Mesoscale and Synoptic Scale Analysis of Narrow Cold Frontal Rainband During a Landfalling Atmospheric River in California During January 2021

AbstractNarrow cold‐frontal rain bands (NCFR) often produce short‐duration and high‐intensity precipitation that can lead to flooding and debris flow in California (CA). On 27 January 2021, an atmospheric river (AR) associated with an intense surface cyclone made landfall over coastal northern CA, which featured a prominent NCFR. This study uses high‐resolution West Weather Research and Forecasting simulations to accurately resolve the gap and core structure of the NCFR and provide reliable precipitation estimations, compensating for limitations of radar and satellite observations. This NCFR was supported by robust synoptic‐scale quasi‐geostrophic (QG) forcing for ascent and frontogenesis. It propagated southward from Cape Mendocino to Big Sur in 12 hr before stalling and rotating counter‐clockwise in central/southern CA due to upstream Rossby wave breaking and an amplifying upper‐tropospheric trough. With the lower to middle tropospheric flow backed considerably to the south‐southwest over the NCFR, the increase of the vertical wind shear caused the transition from parallel to trailing stratiform precipitation. The stall and pivot of the AR and NCFR led to intense rainfall with a 2‐day precipitation accumulation greater than 300 mm over central CA. In addition, under the potential instability and frontogenesis, a moist absolutely unstable layer between 850 and 700 hPa was captured at the leading edge of the NCFR, which indicated slantwise deep layer lifting and high precipitation efficiency. This study reveals synoptic‐scale and mesoscale drivers of rainfall outside orographic lifting and reaffirms the importance of high‐resolution numerical modeling for the prediction of extreme precipitation and related natural hazards.

Hydrology, rather than wildfire burn extent, determines post‐fire organic and black carbon export from mountain rivers in central coastal California

AbstractCoastal mountain rivers export disproportionately high quantities of terrestrial organic carbon (OC) directly to the ocean, feeding microbial communities and altering coastal ecology. To better predict and mitigate the effects of wildfires on aquatic ecosystems and resources, we must evaluate the relationships between fire, hydrology, and carbon export, particularly in the fire‐prone western United States. This study examined the spatiotemporal export of particulate and dissolved OC (POC and DOC, respectively) and particulate and dissolved black carbon (PBC and DBC, respectively) from five coastal mountain watersheds following the 2020 CZU Lightning Complex Fires (California, USA). Despite high variability in watershed burn extent (20–98%), annual POC, DOC, PBC, and DBC concentrations remained relatively stable among the different watersheds. Instead, they correlated significantly with watershed discharge. Our findings indicate that hydrology, rather than burn extent, is a primary driver of post‐fire carbon export in coastal mountain watersheds.

Provenance of modern sands from Baja California rivers (Mexico): petrographic constraints from light and heavy minerals

ABSTRACT We used high-resolution petrographic and dense-mineral data on modern sand to investigate erosion patterns of the El Rosario, San Fernando, and San Vicente river basins of Baja California (Mexico) to better understand the interrelationships between a complex magmatic arc terrane and surface processes. Modern sand composition of these three rivers reflects the nature of the source region, which lies in the central part of the Alisitos arc (Peninsular Ranges, Baja California, Mexico). The sand detrital modes correspond well with the main structural units drained by the El Rosario, San Fernando, and San Vicente rivers: 1) the Early Cretaceous oceanic arc of the Alisitos Group, 2) the Paleozoic to Mesozoic continental-margin metasedimentary rocks, 3) the Cretaceous plutons, 4) the Upper Cretaceous to Tertiary sedimentary rocks, and 5) the Tertiary volcanics. The modern sand of the San Vicente, San Fernando, and El Rosario rivers is fed chiefly from erosion of a magmatic arc and consists mostly of minor feldspatho-lithic (Fl) to quartzo-litho-feldspathic (qFL) sand and dominant quartzo-feldspatho-lithic (qLF) and litho-feldspatho-quartzose (lQF) sand. Framework petrography also suggests a progressive increase in quartz, K-feldspar, sedimentary and metamorphic lithic fragments, and a decrease in volcanic lithic fragments. Sand, in the Lv field, microlitic (Lvmi), felsitic (Lvf) and lathwork (Lvl) types, and trace amounts of vitric grains (Lvv), such as pumice particles. The andesitic volcanic province of the Alisitos arc sheds quartz-poor sand containing mainly microlitic lithic fragments and plagioclase, whereas sand derived from more felsic rhyolites and rhyodacitic and trachyandesitic products contains largely felsitic volcanic lithics and minor lathwork lithics are mainly derived from subordinate basalts. The abundance of intrusive rock fragments and volcanic and sedimentary lithics of the sampled river sands faithfully represents the relative abundance of a heterogeneous bedrock exposure consisting of sedimentary and metasedimentary rocks, as well as volcanic, plutonic, and medium- to high-grade metamorphic rocks in each drainage basin. Transparent heavy-mineral assemblages including major amounts of amphibole, pyroxene, epidote, titanite, zircon, and minor amounts of staurolite, rutile, actinolite, tourmaline, garnet, kyanite, andalusite, sillimanite, and apatite are in good agreement with a mixed provenance characterized mainly by magmatic, primarily volcanic (andesite, rhyolite, and basalt) and secondarily plutonic (granitoid rocks) and metamorphic source rocks. Some labile species such as hornblende and pyroxene grains show mainly corroded to etched morphologies due to dissolution processes and by chemical weathering processes occurring in a paleo and current semiarid climate. The Zircon+Tourmaline+Rutile index of the heavy-mineral modes, coupled with their subrounded to rounded grain surface texture, indicates recycling from the sedimentary source rocks. Heavy-mineral abundance and weathering textures in the San Fernando and San Vincente river sands match predominantly volcanic bedrock lithologies, while the El Rosario river sands match sedimentary and metasedimentary source rocks.

Trends in Chinook salmon spawner abundance and total run size highlight linkages between life history, geography and decline

AbstractChinook salmon (Oncorhynchus tshawytscha, Salmonidae) are foundational to social‐ecological systems of the Northeast Pacific Rim and exhibit a rich diversity of life histories including in their adult migration timing, age at critical life‐history transitions and marine feeding distributions. In recent decades Chinook have experienced declines across much of their native range; however, changes in productivity and abundance have rarely been evaluated in relation to life‐history variation. To understand trends in Chinook salmon production, and how they are related to life history, we compiled time series data from the Fraser River to the Sacramento River on total run size (pre‐fishery abundance) and escapement (post‐fishery spawner abundance) and fit time series models to estimate trends across this bioregion. Our analysis revealed that most Chinook populations are declining, with negative trends in escapement (57 of 79) and total run (16 of 23) size. Trends were most acutely negative for interior spring Chinook in the Fraser, Columbia and Snake Rivers and most populations in California. Summer and fall Chinook had mixed trends, with several summer and fall upriver bright populations in the interior Columbia and Fraser exhibiting increases in abundance from the 1990s to 2019. Our research reveals widespread declines of this important species, but local complexity in trends that are mediated by population‐level life history, migratory behaviours and watershed‐scale restoration actions. Understanding linkages between life histories and resilience should inform rebuilding efforts for Chinook salmon and highlight the need to conserve intraspecific biodiversity.

Limited, asymmetric hybridization between coastal cutthroat trout and steelhead in a Northern California river.

Hybridization between coastal cutthroat trout (Oncorhynchus clarkii clarkii) and steelhead (O. mykiss) was assessed in the Smith River, California. Individuals were categorized as pure or as 1 of 10 hybrid classes using 30 "diagnostic" single-nucleotide polymorphisms positioned on 26 separate chromosomes. Most of the individuals examined (n = 876), were pure coastal cutthroat trout (n = 634) or pure steelhead (n = 213), and 29 individuals were identified as having hybrid ancestry. Among hybrids, first generation hybrids (n = 15) and coastal cutthroat trout backcrosses (n = 12) were the most common. No individuals were identified as backcrosses to SH, suggesting the presence of genetic or behavioral mechanisms constraining such backcrosses, or the growth and survival of their progeny. Mitochondrial DNA of 14 of 15 F1 hybrids was of steelhead origin, suggesting that hybridization was driven primarily by sneak-mating of male coastal cutthroat trout with female steelhead. Evaluation of classical phenotypic characters for coastal cutthroat trout and steelhead (i.e. jaw slash, maxillary length, and hyoid teeth) were not reliable by themselves for identification of either pure parental fish or hybrids. In contrast, analysis with geometric morphometrics revealed distinctive body shapes for pure coastal cutthroat trout and steelhead, and the combination of classical traits and geometric morphology was mostly accurate in distinguishing them. However, first generation hybrids and backcrosses overlapped completely with parental types, highlighting challenges in hybrid identification using phenotypic traits.

Modeling Seasonal Effects of River Flow on Water Temperatures in an Agriculturally Dominated California River

AbstractLow streamflows can increase vulnerability to warming, impacting coldwater fish. Water managers need tools to quantify these impacts and predict future water temperatures. Contrary to most statistical models' assumptions, many seasonally changing factors (e.g., water sources and solar radiation) cause relationships between flow and water temperature to vary throughout the year. Using 21 yr of air temperature and flow data, we modeled daily water temperatures in California's snowmelt‐driven Scott River where agricultural diversions consume most summer surface flows. We used generalized additive models to test time‐varying and nonlinear effects of flow on water temperatures. Models that represented seasonally varying flow effects with intermediate complexity outperformed simpler models assuming constant relationships between water temperature and flow. Cross‐validation error of the selected model was ≤1.2°C. Flow variation had stronger effects on water temperatures in April–July than in other months. We applied the model to predict effects of instream flow scenarios proposed by regulatory agencies. Relative to historic conditions, the higher instream flow scenario would reduce annual maximum temperature from 25.2° to 24.1°C, reduce annual exceedances of 22°C (a cumulative thermal stress metric) from 106 to 51 degree‐days, and delay onset of water temperatures >22°C during some drought years. Testing the same modeling approach at nine additional sites showed similar accuracy and flow effects. These methods can be applied to streams with long‐term flow and water temperature records to fill data gaps, identify periods of flow influence, and predict temperatures under flow management scenarios.

TempMesh – A Flexible Wireless Sensor Network for Monitoring River Temperatures

For a Chinook salmon restoration project in the lower Yuba River in California, we designed and deployed a wireless sensor network to monitor river temperatures at micro-habitat scales. The study required that temperatures be measured along a 3 km study reach, across the channel, and into off-channel areas. To capture diel and seasonal fluctuations, sensors were sampled quarter-hourly for the full duration of the six-month juvenile salmon winter residency. This sampling duration required that nodes minimize power-use. We adopted event-based software on MSP430 micro-controllers with 433 MHz radio and minimized the networking duty-cycle. To address link failures, we included network storage. As the network lacked real-time clocks, data were timestamped at the destination. This, coupled with the storage, yielded timestamp inaccuracies, which we re-aligned using a novel algorithm. We collected over six months of temperature data from 35 sensors across seven nodes. Of the packets collected, we identified 21% as being incorrectly timestamped and were able to re-align 41% of these incorrectly timestamped packets. We collected temperature data through major floods, and the network uploaded data until the flood destroyed the sensors. The network met an important need in ecological sampling with ultra-low power (multi-year battery life) and low-throughput.

Urbanization and Its Potential Impact on the Peak Discharge from the Watershed of the Upper Merced River in California

Urbanization is an unavoidable process that influences many components of a watershed, and thus hydrologic processes are severely affected by changes in land use due to this urbanization. During this study, the objective was to assess the impact of urbanization on the peak discharge of a watershed in accordance with the outcome of this research. For this purpose, Watershed Modeling System (WMS) software and Hydrologic Engineering Center- Hydrologic Modeling System (HEC-HMS) model were used for simulating various land-use scenarios of Merced County, in the central part of California, USA. Simulation results were analyzed to assess the impact of land-use changes on the peak discharge of the watershed. The results showed that approximately 18% peak discharge was increased at the sub-basin level and approximately 2% peak discharge was increased at the final outlet. In the future, the study could help researchers, policymakers, and structural designers to foresee and prevent the unpleasant effects of urbanization so that they can take specific measures to prevent calamities beforehand. Keywords: Watershed-modeling, urbanization, land use, peak discharge, WMS, HEC-HMS. DOI: 10.7176/CER/14-7-02 Publication date: November 30 th 2022