Geology topics

Research about California

Source-linked reports with geographic coverage including California.

At least 487 records · Page 27Linked to original sources

USGS2023

Increasing salt marsh elevation using sediment augmentation: Critical insights from surface sediments and sediment cores

Sea-level rise is particularly concerning for tidal wetlands that reside within an area with steep topography or are constrained by human development and alteration of sedimentation. Sediment augmentation to increase wetland elevations has been considered as a potential strategy for such areas to prevent wetland loss over the coming decades. However, there is little information on the best approaches and whether adaptive management actions can mimic natural processes to build sea-level rise resilience. In addition, the lack of information on long-term marsh characteristics, processes, and variability can hamper development of effective augmentation strategies. Here, we assess a case study in a southern California marsh to determine the nature of the pre-existing sediments and variability of the site in relation to sediments applied during an augmentation experiment. Although sediment cores revealed natural variations in the grain size and organic content of sediments deposited at the site over the past 1500 years, the applied sediments were markedly coarser in grain size than prehistoric sediments at the site (100% maximum sand versus 76% maximum sand). The rate of the experimental sediment application (25.1 ± 1.09 cm in ~2 months) was also much more rapid than natural accretion rates measured for the site historically. In contrast, post-augmentation sediment accretion rates on the augmentation site have been markedly slower than pre-augmentation rates or current rates on a nearby control site. The mismatch between the characteristics of the applied sediment and thickness of application and the historic conditions are likely strong contributors to the slow initial recovery of vegetation. Sediment augmentation has been shown to be a useful strategy in some marshes, but this case study illustrates that vegetation recovery may be slow if applied sediments are not similar or at a thickness similar to historic conditions. However, testing adaptation strategies to build wetland elevations is important given the long-term risk of habitat loss with sea-level rise. Lessons learned in the case study could be applied elsewhere.

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USGS2023

A novel boat-based field application of a high-frequency conductometric ammonium analyzer to characterize spatial variation in aquatic ecosystems

Documenting dissolved inorganic nitrogen (DIN) concentration and form at appropriate temporal and spatial scales is key to understanding aquatic ecosystem health, particularly as DIN fuels primary productivity. In addition to point and non-point source nutrient inputs, factors such as hydrology, geomorphology, temperature, light, and biogeochemical transformations influence nutrient dynamics in surface waters, allowing for the formation of steep spatial gradients and patchiness. Documenting nutrient variability is also necessary to identify sources, quantify transformation rates, and understand drivers. Due to logistical and cost constraints, it is often unfeasible to measure concentrations of nutrients in surface waters using discrete sampling followed by laboratory analysis at a resolution high enough to identify steep spatial gradients and patchiness. Because of these constraints, data generated from discrete sampling are limited in space and time, often missing key variabilities. Recent advancements of in situ nitrate plus nitrite (NO3- and NO2-) sensor technology has enabled highly temporally and spatially resolved NO3- concentration measurements in aquatic ecosystems. However, comparable information about ammonium (NH4+) concentrations remains unavailable. To address this need, U.S. Geological Survey collaborated with Timberline Instruments to modify their commercially available benchtop TL-2800 ammonia analyzer to collect high-frequency continuous (1 unique sample measurement per second) NH4+ concentration measurements at a micromolar (0.5 µM) resolution in flow-through mode while receiving water pumped from a moving boat. Although the utility of this method is described for spatial surveys, we anticipate that it would be adaptable to installation at a fixed station for continuous monitoring of NH4+ concentration.

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USGS2023

Multiple-well monitoring site adjacent to the Elk Hills Oil Field, Kern County, California

Introduction The Elk Hills Oil Field is one of the many fields selected for regional groundwater mapping and monitoring by the California State Water Resources Control Board as part of the Oil and Gas Regional Monitoring Program (California State Water Resources Control Board, 2015, 2022b; U.S. Geological Survey, 2022a). The U.S. Geological Survey (USGS), in cooperation with the California State Water Resources Control Board, is evaluating groundwater resources near areas of oil and gas development in California, including (1) the location of groundwater resources near oil fields; (2) the proximity of oil and gas operations to groundwater, and the geologic materials between them; (3) evidence (or lack of evidence) of fluids from oil and gas sources in groundwater; and (4) the pathways or processes responsible when fluids from oil and gas sources are present in groundwater (U.S. Geological Survey, 2022a). As part of this evaluation, the USGS installed a multiple-well monitoring site near the administrative boundary of the Elk Hills Oil Field in the southern San Joaquin Valley about 6 miles northeast of Taft, California (California Department of Water Resources, 2020; fig. 1). Data collected at the Elk Hills multiple-well monitoring site (ELKH) provide information about the geology, hydrology, geophysical properties, and water quality of the aquifer system, thus enhancing the understanding of relations between adjacent groundwater and the Elk Hills Oil Field in an area where groundwater data are limited, particularly at different depths in the aquifer. This report presents construction information for the ELKH and initial geohydrologic data collected from the site. Similar sites installed on the east side of the Lost Hills Oil Field, on the east side of the North and South Belridge Oil Fields, and within the Poso Creek Oil Field were described by Everett and others (2020a, b, 2023).

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USGS2023

Effects of solar energy development on ants in the Mojave Desert

Land-use change from solar energy development may affect desert ecosystems and the soils, plants, and animals therein, yet our understanding of these interactions is nascent. With their ubiquity, criticality as ecosystem constituents, and sensitivity to environmental variation, ants may be useful study organisms for elucidating ecological effects of solar energy development in deserts. Our objectives were to disentangle the response of a desert ant community to solar energy development decisions and test the efficacy of ants as bioindicators at a solar power facility (392 MW) in the Mojave Desert, USA. We used pitfall traps to collect ants in treatments representing different solar energy development decisions, including variably intense site preparation practices: blading (i.e., bulldozing) and mowing, and establishment of undeveloped patches in solar fields, replicated across three power blocks comprising the facility and in undeveloped control sites surrounding the facility. We determined that ant abundance, species richness, Shannon Diversity Index, and functional richness were lower in bladed treatments than in all other treatments and controls. For most taxonomic and functional ant responses, we detected no difference between nonbladed treatments and controls; these results suggest that less intensive site preparation and increased spatial heterogeneity (i.e., undeveloped patches in solar fields) can reduce the negative effects of solar energy development on desert ants. However, our results indicate that ants may serve as useful bioindicators of the severity of anthropogenic disturbance from solar energy development in deserts, and indicator analysis signifies that solar energy infrastructure may negatively affect some species with high ecological value (e.g., harvester ants). Negative effects of solar energy development on ants can have significant implications for desert ecosystem function and integrity, but conservation-minded solar facility design and construction may lead to avoidance of “bottom-up” ecological ramifications of increased solar production during the renewable energy transition.

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USGS2023

Movement behavior, habitat selection, and functional responses to habitat availability among four species of wintering waterfowl in California

Habitat selection analyses provide a window into the perceived value of habitats by animals and how those perceptions compare with other animals, change across time, or change in relation to availability (termed functional responses). Habitat selection analysis and functional responses can be used to develop strategies to avoid habitat limitations, guide habitat management, and set attainable conservation goals. GPS relocations of marked animals are the principal data used in habitat selection analysis. The accuracy and frequency with which tracking devices collect data are increasing and may result in non-stationary point processes that result from latent behaviors previously unidentifiable in sparse data.

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USGS2023

The Mojave section of the San Andreas fault (California), 1: Shaping the terrace stratigraphy of Littlerock Creek through the competition between rapid strike-slip faulting and lateral stream erosion over the last 40ka.

To determine the post-40 ka slip-rate along the Mojave section of the San Andreas Fault (MSAF) we re-analyze the sedimentary record preserved where Little Rock (LR) Creek flows across the fault. At this location, interaction between the northeast-flowing stream and right-lateral fault has resulted in the abandonment and preservation of 11 strath terraces and one paleo-floodplain in the downstream trailing corner of the river, two of which are also preserved upstream to provide cross-fault matches. A new model of fault-induced river deflection, together with standard terrace riser restoration, yields strike-slip displacements of 1,140 ± 160 m for the older terrace and 360 ± 70 m for the younger one. When combined with new 10 Be dating and reinterpretation of prior measurements the displaced terraces yield right-lateral slip-rates of 27.7 +6.9/−3.5 and 26.8 +3.4/−3.0 mm/yr over the last 23 k.y. and last 40 k.y., where uncertainties are at 95% credible intervals. These new rate determinations are consistent with independent late Holocene estimates, indicating that the long-term rate of strain accumulation along the MSAF is relatively fast and does not vary significantly when averaged over timescales of 15–20 k.y. Using our new model of stream deflection, we find that the fluvial sequence was emplaced in two distinct periods, each characterized by a temporally stable but markedly different deflected river geometry. Each period coincides with a distinct stage of erosive power along LR Creek determined from independent paleoclimate proxies. Importantly, application of the new river-deflection model allows strike-slip displacements to be determined in the absence of upstream piercing points.

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USGS2023

Arsenic, chromium, uranium, and vanadium in rock, alluvium, and groundwater, Mojave River and Morongo Areas, western Mojave Desert, southern California

Trace elements within groundwater that originate from aquifer materials and pose potential public-health hazards if consumed are known as geogenic contaminants. The geogenic contaminants arsenic, chromium, and vanadium can form negatively charged ions with oxygen known as oxyanions. Uranium complexes with bicarbonate and carbonate to form negatively charged ions having aqueous chemistry similar to oxyanions. The concentrations of arsenic, chromium, uranium, and vanadium in groundwater result from the combined effects of (1) geologic abundance within aquifer materials; (2) the fraction of these elements that have weathered from and sorbed to the surfaces of mineral grains and are potentially available to groundwater; and (3) the aqueous chemistry of dissolved oxyanions in groundwater during different redox conditions and pH, both of which are affected by hydrogeology, including the length of time groundwater has been in contact with aquifer materials. Concentrations of arsenic, chromium, uranium, and vanadium were measured in samples of (1) rock, surficial alluvium, and drill cuttings using portable (handheld) X-ray fluorescence (pXRF); (2) operationally defined fractions extractable from these materials; and (3) water from wells sampled between 2000 and 2018 within the 3,500 square mile Mojave River area and Morongo area of the western Mojave Desert, southern California. Regionally, rock and surficial alluvium in the Mojave River and Morongo areas are high in arsenic, low in chromium and uranium, and near the average bulk continental crust concentration for vanadium. Locally, high chromium concentrations are present in mafic rock within the San Gabriel Mountains; high uranium concentrations are present in felsic rock within the San Bernardino Mountains; and high arsenic, uranium, and vanadium concentrations are present in extrusive (volcanic) felsic rock within uplands surrounding groundwater basins along the Mojave River downstream from Barstow, California. Elemental assemblages identified using principal component analyses (PCA) of pXRF data were used to characterize felsic, mafic, and felsic volcanic source terranes in rock, surficial alluvium, and in geologic material penetrated by selected monitoring wells drilled between 1994 and 2018. Highly felsic alluvium associated with recent deposition from the Mojave River was identified along the 90-mile length of the floodplain aquifer along the river. The thickness of these highly felsic alluvial deposits ranged from 200 feet (ft) near Victorville and near Barstow to a thin veneer about 30 ft thick downstream from Victorville and downstream portions of the floodplain aquifer within the Mojave Valley. Groundwater in the Mojave River and Morongo areas was generally oxic and alkaline (pH≥7.5). Maximum concentrations of arsenic, hexavalent chromium [Cr(VI)], uranium, and vanadium in water from as many as 498 wells sampled between 2000 and 2018 were 360, 140, 1,470, and 690 micrograms per liter (μg/L), respectively. Water from 22 percent of sampled wells exceeded the U.S. Environmental Protection Agency (EPA) maximum contaminant level (MCL) for arsenic of 10 μg/L, with arsenic concentrations commonly exceeding the MCL in water from wells east of Barstow, deep wells in the Victorville fan, and in suboxic or reduced groundwater within the floodplain aquifer. Water from about 1 percent of sampled wells had Cr(VI) concentrations greater than the California MCL for total chromium of 50 μg/L, whereas 13 percent of sampled wells had Cr(VI) concentrations greater than the former California MCL of 10 μg/L. Hexavalent chromium concentrations were highest in water from wells in the Sheep Creek alluvial fan, eroded from mafic rock in the San Gabriel Mountains, although Cr(VI) concentrations greater than the former California MCL also were present elsewhere in the study area where mafic materials or older groundwater were present. Water from about 9 percent of sampled wells exceeded the EPA MCL for uranium of 30 μg/L, with concentrations exceeding the MCL commonly associated with irrigation return from agricultural land overlying the floodplain aquifer. Water from about 7 percent of sampled wells had vanadium concentrations greater than the California notification level of 50 μg/L; most of these wells were in the Victorville fan within the Mojave River area. In general, arsenic concentrations were higher in suboxic or reduced water; chromium concentrations were higher in oxic, alkaline (pH≥7.5) water; uranium concentrations were higher in circumneutral to slightly alkaline water (pH≤7.4); and vanadium concentrations were higher in highly alkaline (pH≥8.0) water, independent of redox status. Concentrations within geologic source terranes are not the sole factor controlling the concentrations of geogenic elements in groundwater. Differences in mineral weathering, pH-dependent sorption to surface-exchange sites on mineral grains, and aqueous geochemistry (especially redox status and pH) affect geogenic element concentrations in groundwater. Consequently, the relative abundances of arsenic, Cr(VI), uranium, and vanadium in groundwater differ from their relative abundances in the average bulk continental crust and their regional abundances in rock and surficial alluvium within groundwater basins of the western Mojave Desert. Processes that control the concentrations of arsenic, chromium, uranium, and vanadium in groundwater operate at the mineral-grain and aquifer scale. At the mineral-grain scale, sequential chemical extraction data show arsenic and uranium are more available to groundwater (under specific geochemical conditions) than chromium or vanadium, which largely are unavailable within unweathered mineral grains. Additionally, chromium and vanadium form few aqueous complexes and bind tightly with iron minerals within surface coatings on mineral grains making them less available to groundwater, whereas complexation with other dissolved ions enhances the solubility of uranium and, to a lesser extent, arsenic. Complexation also increases the valence (less negative charge) and increases the size of dissolved oxyanions and uranium complexes with bicarbonate and carbonate making them less readily sorbed to aquifer materials. At the aquifer scale, hydrogeology (including isolation of water in aquifers from surface sources of recharge, older groundwater age, and long contact times between groundwater and aquifer materials) combined with geochemical processes (such as silicate weathering) to produce alkaline groundwater. Desorption from sorption sites on the surfaces of mineral grains with increasing pH increases arsenic, chromium, and vanadium concentrations in water from wells and increases Cr(VI) concentrations as long as water remains oxic. Aqueous geochemistry and concentrations of geogenic contaminants also are affected by anthropogenic activities including (1) discharge of treated municipal wastewater, which may change the redox status of groundwater; (2) return from irrigated agriculture, which may alter the chemistry of groundwater and increase the solubility of trace elements such as uranium; and (3) groundwater pumping and subsequent water-level declines, which may change the source of water yielded by wells. The quality of water imported from northern California and infiltrated from ponds for groundwater recharge may be altered by naturally present trace elements, especially uranium in areas of agricultural land use or chromium within mafic alluvium.

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USGS2023

Application of the Stream Salmonid Simulator (S3) model to assess fall Chinook salmon (Oncorhynchus tshawytscha) production in the American River, California

Executive Summary Anadromous fish returning to the lower American River are restricted to 36 kilometers of free-flowing river between Nimbus Dam and American River’s confluence with the Sacramento River, California. Salmon in the American River provide an important freshwater recreational fishery. However, annual salmon production in the American River in recent years has been low relative to the mid-1990s (Surface Water Resources, Inc., 2001). To investigate the low production of fall-run Chinook salmon ( Oncorhynchus tshawytscha ), the Bureau of Reclamation requested that the U.S. Geological Survey apply the Stream Salmonid Simulator (S3) model to the population of fall-run Chinook salmon on the American River. The American River was chosen among seven candidate Sacramento Basin rivers for S3 application. The American River was selected because of its management and public interest, recently low anadromous fish production, and rich time series of key demographic data needed for S3 application. Data that were not available, however, were empirical estimates on juvenile salmon habitat suitability in the American River. Therefore, a large component of applying S3 to the American River was devoted to the estimation of juvenile salmon habitat suitability and capacity. This entailed snorkeling the lower American River for 3 weeks in March 2021 during the early out-migration period for juvenile Chinook salmon. These efforts were fruitful and showed that the typically small fish (<55 millimeters) in the American River preferred much shallower depths than predicted by habitat suitability criteria derived from the literature for this population. Having empirical estimates on juvenile salmon in the American River provided a solid foundation from which to simulate the population using the S3 model. The S3 model is a spatially explicit population model that runs on a daily time step to simulate redd superimposition, egg maturation, fry emergence and the subsequent growth, survival, and emigration of juvenile Chinook salmon from the river. The key features of this model relevant to this report include (1) a temperature-dependent bioenergetics model driving daily growth rates; (2) density-dependent dynamics that are influenced by the effect of flow on suitable habitat area; and (3) within-year habitat, river flow, and water temperature effects specific to spawning, egg incubation, and fry, parr, and smolt life stages. We used estimates of spawning escapement and geo-referenced redd locations to quantify the spatial and temporal distribution of female spawners for brood years 2014–19. These estimates of female spawners initiate the simulation of each year’s juvenile salmon emergence and emigration over a spatial domain extending from Nimbus Dam to the river’s confluence with the Sacramento River. Using weekly estimates of juvenile salmon abundance and size (fork length) that passed the Watt Avenue fish trap (river kilometer 14.7), we calibrated the S3 model by estimating three key demographic parameters for each year, y : (1) S y , the average daily survival probability, (2) M 0y , the intercept for density-dependence in movement, representing the average daily probability of remaining in a habitat at zero abundance, and (3) C y , the average daily proportion of maximum consumption. These parameters were obtained by minimizing the Mallow’s distance (Lupu and others, 2017) between distributions of weekly abundances and sizes of fish at the traps and weekly simulated abundances and sizes (by S3). Investigation of model fit showed excellent agreement between simulated annual abundances and the abundance of fish passing the fish trap. However, when we compared weekly abundances at the fish trap, S3 under-predicted peaks and over-predicted troughs in the time series of weekly abundances at the fish trap. Thus, some unknown within-year effects have yet to be identified and incorporated in the S3 model. Identifying these important effects and incorporating them in the S3 model would help explain the lack of fit between estimated and simulated weekly abundances. We estimated parameters for 6 years that included a wide range of female spawner abundances (3,057–10,753) and water year types (Critical–Wet). We contrast our estimated parameters to the corresponding number of female spawners and the water year type for the Sacramento Valley. By happenstance, years having higher annual spawner abundances concurred with Critical to Dry water year types. Estimates of survival trended lower with higher spawner abundances and Critical to Dry conditions. In contrast, the extremely wet water year of 2017 had the lowest M 0y , suggesting less density-dependence in fish movement, and the lowest C y , suggesting lower average consumption in this year. When this high-flow year was excluded, a trend towards higher probabilities of fish remaining in a habitat at low abundance and lower proportions of maximum consumption was apparent from Critical to Wet conditions, but only 5 years of data were included. Except for 2017, daily proportions of maximum consumption were relatively high ( C y > 0.83), suggesting that fish were feeding at reasonably high proportions relative to the expected maximum consumption as defined by the “Wisconsin” bioenergetics model (Stewart and Ibarra, 1991). Survival estimates from fry emergence to outmigration at the Sacramento River confluence were generally low when integrated over time. The highest daily survival probability was S y = 0.93 in 2019, or 50 percent total mortality after 10 days. In contrast, our lowest daily survival probability was S y = 0.74 in 2015, or 95 percent total mortality after 10 days. Consequently, even our highest estimated daily survival probability might be considered low. This is especially true given that S y was estimated over a relatively short distance (<14.7 kilometers) from emergence to the Watt Avenue fish trap. Several factors, including our assumed and relatively high daily egg survival rate of 0.9975, could influence juvenile survival estimates. For example, an egg survival rate of 0.9975 results in 3-percent total mortality after 10 days. Egg mortality estimates used in S3 calibration were approximated from egg survivorship studies in the Yakima River, Washington (Johnson and others, 2012), and remains one of the greater uncertainties in S3 when estimating survival across life stages. By including bona fide estimates of egg survival in S3 simulations, the validity of the S3’s current daily egg survival rate could be assessed specifically for the American River. Tagging studies also could provide S3 with direct estimates of juvenile survival and movement; survival during egg incubation then could be estimated indirectly via model fitting.

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USGS2023

Spatially explicit models of seed availability improve predictions of conifer regeneration following the 2018 Carr Fire in northern California

For many conifer species in dry conifer forests of North America, seeds must be present for postfire regeneration to occur, suggesting that seed dispersal from surviving trees plays a critical role in postfire forest recovery. However, the application of tree fecundity and spatial arrangement to postfire conifer recovery predictions have only recently become more common, and is often included at relatively coarse scales (i.e., 30 meters). In this study, we mapped surviving trees using lidar and created a spatially explicit estimate of seed density (seed shadows) with 10 m, 50 m, and 100 m median dispersal distances. We estimated the number of seeds produced by each tree using allometric relationships between tree size and fecundity. Along with the seed shadows, we used a suite of topographic variables as inputs to negative binomial hurdle models to predict conifer seedling abundance in 131 plots following the 2018 Carr Fire in northern California, USA. We compared models using each of the seed shadows to each other as well as to a model using the distance to the nearest surviving tree, which served as a baseline. All model formulations indicated that estimated seed availability was positively associated with conifer regeneration. Despite the importance of seed availability plays in regeneration and the substantial differences in seed availability represented by the different seed shadows in our analysis, we found surprisingly little difference in model performance regardless of which seed shadow was used. However, the models employing seed shadows outperformed the models with distance to the nearest live tree. Although we have demonstrated a modest improvement in predicting postfire conifer regeneration, the uncertainty in our results highlights the importance of tree detection and classification in future studies of this kind. Future studies may find it useful to consider other factors such as predation, site suitability, and seed mortality as potential drivers of discrepancies between total and realized dispersal kernels.

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USGS2023

Crop water productivity from cloud-Based landsat helps assess California’s water savings

Demand for food and water are increasing while the extent of arable land and accessible fresh water are decreasing. This poses global challenges as economies continue to develop and the population grows. With agriculture as the leading consumer of water, better understanding how water is used to produce food may help support the increase of Crop Water Productivity (CWP; kg/m 3 ), the ratio of crop output per unit of water input (or crop per drop). Previous large-scale CWP studies have been useful for broad water use modeling at coarser resolutions. However, obtaining more precise CWP, especially for specific crop types in a particular area and growing season as outlined here are important for informing farm-scale water management decision making. Therefore, this study focused on California’s Central Valley utilizing high-spatial resolution satellite imagery of 30 m (0.09 hectares per pixel) to generate more precise CWP for commonly grown and water-intensive irrigated crops. First, two products were modeled and mapped. 1. Landsat based Actual Evapotranspiration (ET a ; mm/d) to determine Crop Water Use (CWU; m 3 /m 2 ), and 2. Crop Productivity (CP; kg/m 2 ) to estimate crop yield per growing season. Then, CWP was calculated by dividing CP by CWU and mapped. The amount of water that can be saved by increasing CWP of each crop was further calculated. For example, in the 434 million m 2 study area, a 10% increase in CWP across the 9 crops analyzed had a potential water savings of 31.5 million m 3 of water. An increase in CWP is widely considered the best approach for saving maximum quantities of water. This paper proposed, developed, and implemented a workflow of combined methods utilizing cloud computing based remote sensing data. The environmental implications of this work in assessing water savings for food and water security in the 21st century are expected to be significant.

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USGS2023

The long shadow of a major disaster: Modeled dynamic impacts of the hypothetical HayWired earthquake on California’s economy

We develop and apply a dynamic economic simulation model to analyze the multi-regional impacts of, and mechanisms of recovery from, a major disaster, the HayWired scenario — a hypothetical Magnitude 7.0 earthquake affecting California’s San Francisco Bay Area. The model integrates loss pathways: capital stock damage, labor supply shocks due to short-term population displacement and longer-run out-migration from damaged areas, and the exacerbating effects of damage to transportation infrastructure capital, as well as various aspects of static and dynamic economic resilience. With input substitution-based static inherent resilience and dynamic resilience in the form of optimal intertemporal and spatial investment allocation, gross output losses range from 0.5 percent to 6 percent across regions, and welfare losses are 0.4 percent statewide but can be ten times as large in hardest-hit areas. Large-scale reconstruction investment is supported by substantial interregional transfers of resources through intra-state trade. Increased output via firms engaging in the key adaptive resilience tactic of production recapture can alleviate a substantial fraction of losses—but only if upstream and downstream barriers to recovery can be lowered quickly.

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USGS2023

Revisiting conservation units for the endangered mountain yellow-legged frog species complex (Rana muscosa, Rana sierrae) using multiple genomic methods

Insights from conservation genomics have dramatically improved recovery plans for numerous endangered species. However, most taxa have yet to benefit from the full application of genomic technologies. The mountain yellow-legged frog species complex, Rana muscosa and Rana sierrae, inhabits the Sierra Nevada mountains and Transverse/Peninsular Ranges of California and Nevada. Both species have declined precipitously throughout their historical distributions. Conservation management plans outline extensive ongoing recovery efforts but are still based on the genetic structure determined primarily using a single mitochondrial sequence. Our study used two different sequencing strategies – amplicon sequencing and exome capture – to refine our understanding of the population genetics of these imperiled amphibians. We used buccal swabs, museum tissue samples, and archived skin swabs to genotype frog populations across their range. Using the amplicon sequencing and exome capture datasets separately and combined, we document five major genetic clusters. Notably, we found evidence supporting previous species boundaries within Kings Canyon National Park with some exceptions at individual sites. Though we see evidence of genetic clustering, especially in the R. muscosa clade, we also found evidence of some admixture across cluster boundaries in the R. sierrae clade, suggesting a stepping-stone model of population structure. We also find that the southern R. muscosa cluster had large runs of homozygosity and the lowest overall heterozygosity of any of the clusters, consistent with previous reports of marked declines in this area. Overall, our results clarify management unit designations across the range of an endangered species and highlight the importance of sampling the entire range of a species, even when collecting genome-scale data.

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USGS2023

Monitoring nesting waterbirds for the South Bay Salt Pond Restoration Project—2022 breeding season

The San Francisco Bay supports thousands of breeding waterbirds annually and hosts large populations of American avocets ( Recurvirostra americana ), black-necked stilts ( Himantopus mexicanus ), and Forster’s terns ( Sterna forsteri ). These three species have relied largely on former commercial salt ponds in South San Francisco Bay, which provide wetland foraging habitat and island nesting habitat. The South Bay Salt Pond Restoration Project is in the process of restoring 50–90 percent of 15,100 acres of these former salt ponds to tidal marsh and tidal mudflats. Although this restoration is expected to have numerous benefits, including providing habitat for tidal wetland-dependent species, improving water quality, buffering against storm surge, and protecting inland areas from sea level rise, the reduction in former salt pond habitat and nesting islands may negatively affect breeding waterbirds. To address the reduction in former salt pond habitat available to waterbirds, the South Bay Salt Pond Restoration Project also includes enhancements to remaining pond habitat, such as the construction of new islands for nesting. Moreover, the South Bay Salt Pond Restoration Project follows an adaptive management plan in which waterbird response to the changing landscape is monitored over time to ensure that existing breeding waterbird populations are maintained. In this report, we provide results of waterbird nest monitoring in South San Francisco Bay during the 2022 breeding season and present these results in the context of annual nest monitoring in South San Francisco Bay since 2005. Overall, nest abundance in 2022 remained at or near 18-year lows for American avocets (176 nests) and black-necked stilts (97 nests), but Forster’s tern nest abundance (1,727 nests) was at an 18-year high, reversing historically low abundance observed during 2015–2017. In 2022, there were only 6 American avocet, 4 black-necked stilt, and 4 Forster’s tern major colony nesting sites, which is down from annual averages of 12.4, 6.6, and 6.6 observed during 2005–2009. Nest success (30 percent for American avocets, 29 percent for black-necked stilt, and 53 percent for Forster’s terns) was below the 2005–2007 baseline values established for the South Bay Salt Pond Restoration Project. Average egg-hatching success (98 percent, 100 percent, and 90 percent), and clutch sizes (3.68, 3.70, and 2.63 eggs) of American avocets, black-necked stilts, and Forster’s terns, respectively, were similar to values observed during 2005–2010. All three species displayed notable shifts in nest initiation dates in 2022, with American avocets and Forster’s terns nesting 10–11 days earlier and black-necked stilts nesting 10 days later than during 2005–2010. Finally, the enhanced, managed ponds with newly constructed islands (Ponds A16 and SF2) supported 86 percent of all the Forster’s tern nests recorded in South San Francisco Bay in 2022, which is the first time these managed ponds have hosted such a substantial number of tern nests.

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USGS2023

Fecal metabarcoding of the endangered Pacific pocket mouse (Perognathus longimembris pacificus) reveals a diverse and forb rich diet that reflects local habitat availability

Information on diet breadth and preference can assist in understanding links between food resources and population growth and inform habitat restoration for rare herbivores. We assessed the diet of the endangered Pacific pocket mouse using metabarcoding of fecal samples and compared it to plant community composition in long-term study plots in two populations on Marine Corps Base Camp Pendleton, San Diego County, CA. Fecal samples ( n = 221) were collected between spring 2016 and fall 2017 during monthly live-trap surveys. Concurrently, percent cover and plant phenology were measured in plots centered on trap locations. Fecal samples were sequenced with paired-end reads of the internal transcribed spacer 2 region of the nuclear ribosomal gene, and the resulting amplicons were matched to a regionally specific database. Seventy-three plant taxa were detected, which were mostly forbs and perennial herbs (70–90%). Diet composition differed between populations, years, seasons, and plots. Overall, diet and local habitat composition in plots were significantly correlated. However, we detected some differences in above-ground seed availability and proportion in fecal samples that indicate diet preferences for some forbs, perennial herbs, and native bunch grasses over perennial shrubs and non-native grasses. This is the first study of PPM to pair plant phenology surveys with diet metabarcoding to estimate resource selection, and results suggest that managing habitat for diverse native forb communities and reducing non-native grass cover may be beneficial for this critically endangered species.

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USGS2023

Salinity trends in a groundwater system supplemented by 50 years of imported Colorado River water

The Indio subbasin of the Coachella Valley is a desert area of southern California where a growing population depends primarily on groundwater for drinking and agricultural uses. The aquifer system has been supplemented with Colorado River water through managed recharge and widespread irrigation since the mid-20th century. We use a combination of geochemical modeling and trend analysis to identify changes in total dissolved solids through time, elucidate the sources of dissolved solids, and quantify the extent of contributions from those sources throughout the Indio subbasin. We conclude that recharged Colorado River water is the primary source and driver of increasing salinity, particularly in areas immediately downgradient from the recharge locations and in the eastern part of the subbasin away from the recharge ponds due to irrigation using imported water. Other contributions of dissolved solids to groundwater resources include geothermal waters, wastewater effluent, and agricultural return flow, although their effects are more localized. This study presents a broadly applicable framework for identifying sources of dissolved solids in groundwater wells and salinity trends at a regional scale in a large data set.

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USGS2023

Future marsh evolution due to tidal changes induced by human adaptation to sea level rise

With sea level rise threatening coastal development, decision-makers are beginning to act by modifying shorelines. Previous research has shown that hardening or softening shorelines may change the tidal range under future sea level rise. Tidal range can also be changed by natural factors. Coastal marshes, which humans increasingly depend on for shoreline protection, are ecologically sensitive to tidal range. Therefore, it is critical to examine how changes in tidal range could influence marsh processes. A marsh accretion model was used to investigate the ecological response of a San Francisco Bay, California, USA marsh to multiple tidal range scenarios and sea level rise from 2010 to 2100. The scenarios include a baseline scenario with no shoreline modifications in the estuary, a shoreline hardening scenario that amplifies the tidal range, and 14 tidal range scenarios as a sensitivity analysis that span tidal amplification and reduction of the baseline scenario. The modeling results expose key tradeoffs to consider when planning for sea level rise. Compared to the baseline, the hardening scenario shows minor differences. However, further tidal amplification prolongs marsh survival but decreases Sarcocornia pacifica cover, an important species for certain threatened wildlife and an effective attenuator of wave energy. Conversely, tidal reduction precipitates marsh drowning but shows gains in Sarcocornia pacifica cover. These mixed impacts of tidal amplification and reduction shown by the model indicate potential tradeoffs in relation to marsh survival, habitat characteristics, and shoreline protection. This study suggests the need for a cross-sectoral, regional approach to sea level rise adaptation.

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USGS2023

Native amphibian toxin reduces invasive crayfish feeding with potential benefits to stream biodiversity

Background Biodiversity is generally reduced when non-native species invade an ecosystem. Invasive crayfish, Procambarus clarkii , populate California freshwater streams, and in the Santa Monica Mountains (Los Angeles, USA), their introduction has led to trophic cascades due to omnivorous feeding behavior and a rapid rate of population growth. The native California newt, Taricha torosa , possesses a neurotoxin, tetrodotoxin (TTX), that affects freshwater animal behavior. Given P. clarkii has a limited evolutionary history with TTX, we hypothesized that TTX may affect crayfish feeding behaviors. To determine if TTX affects P. clarkii behavior, we measured cumulative movement and various feeding behaviors of P. clarkii exposed to (i) waterborne, ecologically realistic concentrations of TTX (~ 3.0 × 10 − 8 moles/L), (ii) an anuran chemical cue to account for intraguild cues, or (iii) a T. torosa chemical cue with quantitated TTX in it (~ 6.2 × 10 − 8 moles/L). Results We found that the presence of TTX in any form significantly reduced crayfish movement and decreased the amount of food consumed over time. Crayfish responses to the anuran treatment did not significantly differ from controls. Conclusion Our laboratory results show that naturally occurring neurotoxin from native California newts limits invasive crayfish foraging and feeding rates, which may play a role in preserving local stream ecosystems by limiting invasive crayfish behaviors that are detrimental to biodiversity.

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USGS2023

Southern (California) sea otter population status and trends at San Nicolas Island, 2020–2023

The population of southern sea otters ( Enhydra lutris nereis ) at San Nicolas Island, California, has been monitored annually since the translocation of 140 southern sea otters to the island was completed in 1990. Monitoring efforts have varied in frequency and type across years. In 2017, the U.S. Navy and the U.S. Fish and Wildlife Service initiated a southern sea otter monitoring and research plan to determine the effects of military readiness activities on the growth or decline of the southern sea otter population at San Nicolas Island. The southern sea otter is the only subspecies of sea otter in California (hereafter, “sea otter"). The monitoring program, at its basic level, includes seasonal surveys of population abundance, distribution, and foraging activity. From 2020 to 2023, we measured a 10-percent per annum increase in population abundance (95-percent confidence interval =0–20 percent), with 146 total individuals as of April 2023. Coinciding with the recent population growth, the sea otter distribution, which previously tended to concentrate on the island’s west end during 2003–2006 before shifting toward more use in the north and south sides during 2017–2019, appears to have shifted again during 2020–2023 to concentrate at the island’s east end. Forage data were collected between February 2020 and April 2023. There was a total of 773 forage dives in 60 forage bouts, with most of the identified prey on successful dives (n=401) recorded as sea urchins (66 percent), followed by bivalves (15 percent), snails (12 percent), and crabs (5.2 percent). Two lobsters and three abalone also were identified among the sea otter prey. Estimates of energy intake rates averaged 14.0 kilocalories per minute (95-percent confidence interval =10.8–17.2 kilocalories per minute). Monitoring data from the past two decades indicate that sea otters at San Nicolas Island have maintained a steady pattern of energy intake and population growth characteristic of a robust population, including a sixfold growth between 2000 and 2023. There was no conclusive evidence of density-dependent effects based on these patterns; however, estimates of energy intake rates for 2020–2023 were slightly lower than previous estimates from 2017 to 2019. Additionally, subtidal monitoring results at four sites around San Nicolas Island indicated that counts of purple sea urchins ( Strongylocentrotus purpuratus ) have increased between 2003 and 2023, whereas sea otter foraging surveys completed during the same period revealed that some sea otters have shifted toward higher consumption of purple sea urchins and bivalves compared to red sea urchins ( S. fransicanus ), which generally are the preferred larger prey of sea otters. These results contribute to the understanding of population dynamics and to the conservation and planning of future monitoring and research of sea otters at San Nicolas Island.

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