Pub Date : 2024-06-11DOI: 10.15447/sfews.2024v22iss2art4
Ryan McKenzie, Christian Gredzens, B. Mahardja
The loss of biodiversity and biotic homogenization are on the rise in ecosystems around the world as a result of species invasions, habitat degradation, and the effects of climate change. In the Sacramento–San Joaquin Delta, non-native species make up the majority of the fish community, and declines in native species have been well documented; however, little is known about whether these trends have resulted in biotic homogenization. In this study, we used data from a long-term beach seine survey to analyze regional beta diversity trends of nearshore fish assemblages in the Delta from 1995 to 2019. Overall, we found no evidence of regional biotic homogenization occurring over the study period. Regional beta diversity increased moderately over time and was significantly influenced by the high interannual variability of freshwater inflow. These beta diversity patterns were driven by the non-native Mississippi Silverside that has proliferated in the system in recent years, but also by a handful of native fish species such as the Sacramento Sucker, Tule Perch, and Splittail. Overall, our results offer a contrast to other highly invaded ecosystems around the world and suggest that despite the near extinction of some native fish species, there remain pockets of suitable habitat in the Delta that may play a key role in the conservation of remnant native fish diversity.
{"title":"Regional Diversity Trends of Nearshore Fish Assemblages of the Upper San Francisco Estuary","authors":"Ryan McKenzie, Christian Gredzens, B. Mahardja","doi":"10.15447/sfews.2024v22iss2art4","DOIUrl":"https://doi.org/10.15447/sfews.2024v22iss2art4","url":null,"abstract":"The loss of biodiversity and biotic homogenization are on the rise in ecosystems around the world as a result of species invasions, habitat degradation, and the effects of climate change. In the Sacramento–San Joaquin Delta, non-native species make up the majority of the fish community, and declines in native species have been well documented; however, little is known about whether these trends have resulted in biotic homogenization. In this study, we used data from a long-term beach seine survey to analyze regional beta diversity trends of nearshore fish assemblages in the Delta from 1995 to 2019. Overall, we found no evidence of regional biotic homogenization occurring over the study period. Regional beta diversity increased moderately over time and was significantly influenced by the high interannual variability of freshwater inflow. These beta diversity patterns were driven by the non-native Mississippi Silverside that has proliferated in the system in recent years, but also by a handful of native fish species such as the Sacramento Sucker, Tule Perch, and Splittail. Overall, our results offer a contrast to other highly invaded ecosystems around the world and suggest that despite the near extinction of some native fish species, there remain pockets of suitable habitat in the Delta that may play a key role in the conservation of remnant native fish diversity.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":"10 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141356143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-11DOI: 10.15447/sfews.2024v22iss2art1
John Helly, Daniel Cayan, Jennifer Stricklin, Laurel Dehaan
Spatial and temporal patterns of water supply and water use were analyzed from 475 Detailed Analysis Units by County (DAUCOs) spatial units across California over 2002 to 2016 to evaluate how precipitation variability affected the water balance. Many DAUCOs have relatively low total water supply variability compared to state-wide precipitation. Such low variability is the result of switching between water supply sources as needed to maintain a reliable total supply. We used multiple approaches to explore these variations which involved four categories of water supply (local, groundwater, imported, and other) and two categories of water use (agricultural and urban). First, a cluster analysis of the volumetric water balance data identified a small set of clusters having similar magnitudes and proportions of water supply sources and water use—some of them composed of only a few DAUCOs but accounting for a disproportionate amount of the state’s water use. Second, a principal components analysis identified leading modes of anomalous water supply and water use among the 475 DAUCOs, capturing most of the time variation during 2002 to 2016. The most prominent mode exhibits a multi-year trend, most strongly involving increasing groundwater supply and agricultural water use, and decreasing urban water use and imported water supply. Over the study period, trends in both supply and use were pronounced, but differed considerably across California DAUCOs. One predominant subset of DAUCOs grew their agricultural water use with increased groundwater supply; in contrast to a widespread group of DAUCOs which reduced their urban water use. An important result for planners is our finding that variation in precipitation—itself important—is amplified by the human response to water supply availability and regulatory policy.
{"title":"Spatial Patterns of Water Supply and Use in California","authors":"John Helly, Daniel Cayan, Jennifer Stricklin, Laurel Dehaan","doi":"10.15447/sfews.2024v22iss2art1","DOIUrl":"https://doi.org/10.15447/sfews.2024v22iss2art1","url":null,"abstract":"Spatial and temporal patterns of water supply and water use were analyzed from 475 Detailed Analysis Units by County (DAUCOs) spatial units across California over 2002 to 2016 to evaluate how precipitation variability affected the water balance. Many DAUCOs have relatively low total water supply variability compared to state-wide precipitation. Such low variability is the result of switching between water supply sources as needed to maintain a reliable total supply. We used multiple approaches to explore these variations which involved four categories of water supply (local, groundwater, imported, and other) and two categories of water use (agricultural and urban). First, a cluster analysis of the volumetric water balance data identified a small set of clusters having similar magnitudes and proportions of water supply sources and water use—some of them composed of only a few DAUCOs but accounting for a disproportionate amount of the state’s water use. Second, a principal components analysis identified leading modes of anomalous water supply and water use among the 475 DAUCOs, capturing most of the time variation during 2002 to 2016. The most prominent mode exhibits a multi-year trend, most strongly involving increasing groundwater supply and agricultural water use, and decreasing urban water use and imported water supply. Over the study period, trends in both supply and use were pronounced, but differed considerably across California DAUCOs. One predominant subset of DAUCOs grew their agricultural water use with increased groundwater supply; in contrast to a widespread group of DAUCOs which reduced their urban water use. An important result for planners is our finding that variation in precipitation—itself important—is amplified by the human response to water supply availability and regulatory policy.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":"99 42","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141359102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-11DOI: 10.15447/sfews.2024v22iss2art3
Lydia Vaughn, S. Deverel, Stephanie Panlasigui, Judith Drexler, Marc Olds, José Díaz, Kendall Harris, James Morris, J. L. Grenier, April Robinson, Donna Ball
In the Sacramento–San Joaquin Delta (Delta), widespread drainage of historical wetlands has led to extensive subsidence and peat carbon losses, as well as high ongoing greenhouse gas (GHG) emissions. Large-scale wetland restoration and conversion to rice fields has the potential to mitigate these effects while conferring flood protection and creating habitat for wetland species. To explore the scale of these potential benefits, this study evaluated the effects of seven Delta-wide land-use scenarios on carbon stocks, land-surface elevation, GHG emissions, and habitat. Peat mapping and data from peat cores indicate that soil carbon stocks have decreased between the early 1800s and 2010s from 288 ± 15 to 145 ± 14 million metric tons (megatonnes; Mt) of carbon (C). If existing land uses continue, the Delta could lose an additional 8.3 Mt C during the coming 40 years, equal to average GHG emissions of 1.2 Mt CO2 equivalents (CO2e) yr-1. Future restoration and rice-farming scenarios indicate that wetland restoration could theoretically halt GHG emissions, converting the Delta from a large GHG source to a weak net source or sink. Across three future scenarios based on existing restoration targets, wetland creation and conversion to rice fields reduced GHG emissions by 0.39 to 0.67 Mt CO2e yr-1, with per-area benefits of 16 to 28 metric tons (tonnes; t) CO2e per hectare (ha) yr-1. Differences among scenarios in extents of wetland types influenced their relative benefits for different management goals. Tidal restoration and conversion to rice fields enhanced habitat benefits and offered a source of agricultural income, but with reduced GHG mitigation compared with conversion to peat-building wetlands. This highlights the importance of clear objectives when developing land-use plans. A strategic land-management portfolio that includes rice fields and both impounded and tidal wetlands could be designed to provide GHG and subsidence mitigation while offering a diverse suite of benefits for ecosystems and people.
{"title":"Managed Wetlands for Climate Action: Potential Greenhouse Gas and Subsidence Mitigation in the Sacramento–San Joaquin Delta","authors":"Lydia Vaughn, S. Deverel, Stephanie Panlasigui, Judith Drexler, Marc Olds, José Díaz, Kendall Harris, James Morris, J. L. Grenier, April Robinson, Donna Ball","doi":"10.15447/sfews.2024v22iss2art3","DOIUrl":"https://doi.org/10.15447/sfews.2024v22iss2art3","url":null,"abstract":"In the Sacramento–San Joaquin Delta (Delta), widespread drainage of historical wetlands has led to extensive subsidence and peat carbon losses, as well as high ongoing greenhouse gas (GHG) emissions. Large-scale wetland restoration and conversion to rice fields has the potential to mitigate these effects while conferring flood protection and creating habitat for wetland species. To explore the scale of these potential benefits, this study evaluated the effects of seven Delta-wide land-use scenarios on carbon stocks, land-surface elevation, GHG emissions, and habitat. Peat mapping and data from peat cores indicate that soil carbon stocks have decreased between the early 1800s and 2010s from 288 ± 15 to 145 ± 14 million metric tons (megatonnes; Mt) of carbon (C). If existing land uses continue, the Delta could lose an additional 8.3 Mt C during the coming 40 years, equal to average GHG emissions of 1.2 Mt CO2 equivalents (CO2e) yr-1. Future restoration and rice-farming scenarios indicate that wetland restoration could theoretically halt GHG emissions, converting the Delta from a large GHG source to a weak net source or sink. Across three future scenarios based on existing restoration targets, wetland creation and conversion to rice fields reduced GHG emissions by 0.39 to 0.67 Mt CO2e yr-1, with per-area benefits of 16 to 28 metric tons (tonnes; t) CO2e per hectare (ha) yr-1. Differences among scenarios in extents of wetland types influenced their relative benefits for different management goals. Tidal restoration and conversion to rice fields enhanced habitat benefits and offered a source of agricultural income, but with reduced GHG mitigation compared with conversion to peat-building wetlands. This highlights the importance of clear objectives when developing land-use plans. A strategic land-management portfolio that includes rice fields and both impounded and tidal wetlands could be designed to provide GHG and subsidence mitigation while offering a diverse suite of benefits for ecosystems and people.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":"88 11","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141359556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-11DOI: 10.15447/sfews.2024v22iss2art5
Marie E Stillway, B. Hammock, Shawn Acuńa, Amanda McCormick, Tien‐Chieh Hung, Andrew Schultz, Thomas Young, S. Teh
The Delta Smelt is a largely zooplanktivorous, endangered fish endemic to the San Francisco Estuary (the estuary). High flows increase the availability of fresh and brackish water habitat for Delta Smelt, but also may mobilize contaminants, potentially increasing toxicological stress. Here, we examine the association between contaminants and Delta Smelt health across contrasting water year types and flow-related management actions. Our study spanned the fall season of three years: 1 dry year (2018) bracketed by 2 wet years (2017 and 2019) and coincided with several management actions meant to benefit Delta Smelt. We collected field water from six sites in the estuary that encompass the freshwater and low-salinity habitat of Delta Smelt and analyzed the water for contaminant concentrations. After a 96-hour exposure to the field water, we assessed cultured Delta Smelt survival and the histopathological condition of the gill and liver. Insecticides, particularly fipronil metabolites, were the most prevalent contaminants detected in 2017 and 2018, and a variety of contaminants associated with the rice harvest were detected in 2019. No acute toxicity was observed during any exposure, but we observed negative effects in the livers of Delta Smelt exposed to agricultural water from the Toe Drain and Cache Slough during a 2019 pulse flow action, which coincided with elevated detections and concentrations of organic pesticides. Other noteworthy sub-lethal effects, likely occurring in response to contaminant mixtures, included severe gill lesions in Delta Smelt exposed to Decker Island water in 2019. In the drier year of 2018, lesions were generally mild or absent. Thus, the trade-offs between increased habitat availability and contaminant loading may provide one explanation for why Delta Smelt abundance does not consistently respond positively to outflow.
{"title":"Sub-Lethal Responses of Delta Smelt to Contaminants Under Different Flow Conditions","authors":"Marie E Stillway, B. Hammock, Shawn Acuńa, Amanda McCormick, Tien‐Chieh Hung, Andrew Schultz, Thomas Young, S. Teh","doi":"10.15447/sfews.2024v22iss2art5","DOIUrl":"https://doi.org/10.15447/sfews.2024v22iss2art5","url":null,"abstract":"The Delta Smelt is a largely zooplanktivorous, endangered fish endemic to the San Francisco Estuary (the estuary). High flows increase the availability of fresh and brackish water habitat for Delta Smelt, but also may mobilize contaminants, potentially increasing toxicological stress. Here, we examine the association between contaminants and Delta Smelt health across contrasting water year types and flow-related management actions. Our study spanned the fall season of three years: 1 dry year (2018) bracketed by 2 wet years (2017 and 2019) and coincided with several management actions meant to benefit Delta Smelt. We collected field water from six sites in the estuary that encompass the freshwater and low-salinity habitat of Delta Smelt and analyzed the water for contaminant concentrations. After a 96-hour exposure to the field water, we assessed cultured Delta Smelt survival and the histopathological condition of the gill and liver. Insecticides, particularly fipronil metabolites, were the most prevalent contaminants detected in 2017 and 2018, and a variety of contaminants associated with the rice harvest were detected in 2019. No acute toxicity was observed during any exposure, but we observed negative effects in the livers of Delta Smelt exposed to agricultural water from the Toe Drain and Cache Slough during a 2019 pulse flow action, which coincided with elevated detections and concentrations of organic pesticides. Other noteworthy sub-lethal effects, likely occurring in response to contaminant mixtures, included severe gill lesions in Delta Smelt exposed to Decker Island water in 2019. In the drier year of 2018, lesions were generally mild or absent. Thus, the trade-offs between increased habitat availability and contaminant loading may provide one explanation for why Delta Smelt abundance does not consistently respond positively to outflow.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":"29 24","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141357341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-21DOI: 10.15447/sfews.2023v21iss4art5
Emily T. Richardson, Keith Bouma-Gregson, Katy O’Donnell, Brian Bergamaschi
The diffuse attenuation coefficient of photosynthetically active radiation (KdPAR) is commonly used to predict light attenuation in aquatic productivity models, but obtaining measurements of PAR to compute KdPAR is difficult. In situ calculations of KdPAR require multiple measurements of PAR through the water column, and these measurements are infeasible for real-time recording. Instead, predictive models using surface-water measurements may be used. Traditional KdPAR models are based on open-ocean habitats and rely on chlorophyll—as a proxy measurement for phytoplankton abundance—as the main predictive parameter. However, elevated suspended sediments and dissolved organic materials may also affect KdPAR values of inland water bodies and estuaries. In this study, we leverage KdPAR calculations derived from in situ light measurements collected along with surface-water-quality parameters across the Sacramento-San Joaquin River Delta in California, USA (the Delta). Sampling occurred between January of 2013 and May of 2014. We also explored regional and seasonal effects, but these did not clearly affect the model. Ultimately, the best-performing model included surface-level turbidity only (R2 = 0.91). The simplicity of the model facilitates use of KdPAR estimates for a variety of purposes throughout the Delta, including euphotic depth calculations, and as inputs to primary-productivity and habitat-suitability models. We demonstrate the model’s usability with two open-sources data sets (one spatially dense, and one temporally dense), and estimate KdPAR, euphotic depth, and primary productivity within the Delta. We provide calculations for each estimation, allowing users to easily adopt these models and apply them to their own data or with open-sourced data, which are abundant.
{"title":"A Simple Approach to Modeling Light Attenuation in the Sacramento–San Joaquin Delta Using Commonly Available Data","authors":"Emily T. Richardson, Keith Bouma-Gregson, Katy O’Donnell, Brian Bergamaschi","doi":"10.15447/sfews.2023v21iss4art5","DOIUrl":"https://doi.org/10.15447/sfews.2023v21iss4art5","url":null,"abstract":"The diffuse attenuation coefficient of photosynthetically active radiation (KdPAR) is commonly used to predict light attenuation in aquatic productivity models, but obtaining measurements of PAR to compute KdPAR is difficult. In situ calculations of KdPAR require multiple measurements of PAR through the water column, and these measurements are infeasible for real-time recording. Instead, predictive models using surface-water measurements may be used. Traditional KdPAR models are based on open-ocean habitats and rely on chlorophyll—as a proxy measurement for phytoplankton abundance—as the main predictive parameter. However, elevated suspended sediments and dissolved organic materials may also affect KdPAR values of inland water bodies and estuaries. In this study, we leverage KdPAR calculations derived from in situ light measurements collected along with surface-water-quality parameters across the Sacramento-San Joaquin River Delta in California, USA (the Delta). Sampling occurred between January of 2013 and May of 2014. We also explored regional and seasonal effects, but these did not clearly affect the model. Ultimately, the best-performing model included surface-level turbidity only (R2 = 0.91). The simplicity of the model facilitates use of KdPAR estimates for a variety of purposes throughout the Delta, including euphotic depth calculations, and as inputs to primary-productivity and habitat-suitability models. We demonstrate the model’s usability with two open-sources data sets (one spatially dense, and one temporally dense), and estimate KdPAR, euphotic depth, and primary productivity within the Delta. We provide calculations for each estimation, allowing users to easily adopt these models and apply them to their own data or with open-sourced data, which are abundant.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":"72 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138951512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-21DOI: 10.15447/sfews.2023v21iss4art4
Matthew L. Peterson, Tyler J. Pilger, Jason Guignard, Andrea Fuller, D. Demko
The fish communities of the Sacramento–San Joaquin Delta and its tributaries in California’s Central Valley have been irreparably altered through introductions of numerous fish species, including Striped Bass (Morone saxatilis), black bass (Micropterus spp.), and catfishes (Ameiurus spp. and Ictalurus spp.). Research into how predation by non-native piscivores affects native anadromous species has focused on the Sacramento and San Joaquin river mainstems and Delta habitats, through which all anadromous species must pass. Yet, the ranges of non-native fishes extend into upstream tributaries. We collected diets from native and non-native piscivores in the Stanislaus River, a tributary to the San Joaquin River and a remaining stronghold for native fishes. Piscivorous fishes primarily consumed invertebrates and the native species fall-run Chinook Salmon (Oncorhynchus tshawytscha) and Pacific Lamprey (Entosphenus tridentatus). Juvenile Chinook Salmon and Pacific Lamprey were consumed at higher frequencies than any other potential fish prey species, particularly by Striped Bass and black bass. The frequency of native fishes in predator diets was similar across years, despite contrasting hydrologic conditions; 2019 (wet year), 2020 (dry year), and 2021 (critically dry year). Our results show that Pacific Lamprey were frequently consumed by native and non-native piscivores, and that juvenile Chinook Salmon experience substantial predation early in their migration, regardless of hydrologic conditions.
{"title":"Diets of Native and Non-Native Piscivores in the Stanislaus River, California, Under Contrasting Hydrologic Conditions","authors":"Matthew L. Peterson, Tyler J. Pilger, Jason Guignard, Andrea Fuller, D. Demko","doi":"10.15447/sfews.2023v21iss4art4","DOIUrl":"https://doi.org/10.15447/sfews.2023v21iss4art4","url":null,"abstract":"The fish communities of the Sacramento–San Joaquin Delta and its tributaries in California’s Central Valley have been irreparably altered through introductions of numerous fish species, including Striped Bass (Morone saxatilis), black bass (Micropterus spp.), and catfishes (Ameiurus spp. and Ictalurus spp.). Research into how predation by non-native piscivores affects native anadromous species has focused on the Sacramento and San Joaquin river mainstems and Delta habitats, through which all anadromous species must pass. Yet, the ranges of non-native fishes extend into upstream tributaries. We collected diets from native and non-native piscivores in the Stanislaus River, a tributary to the San Joaquin River and a remaining stronghold for native fishes. Piscivorous fishes primarily consumed invertebrates and the native species fall-run Chinook Salmon (Oncorhynchus tshawytscha) and Pacific Lamprey (Entosphenus tridentatus). Juvenile Chinook Salmon and Pacific Lamprey were consumed at higher frequencies than any other potential fish prey species, particularly by Striped Bass and black bass. The frequency of native fishes in predator diets was similar across years, despite contrasting hydrologic conditions; 2019 (wet year), 2020 (dry year), and 2021 (critically dry year). Our results show that Pacific Lamprey were frequently consumed by native and non-native piscivores, and that juvenile Chinook Salmon experience substantial predation early in their migration, regardless of hydrologic conditions.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":"26 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138951380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-21DOI: 10.15447/sfews.2023v21iss4art2
Jacob Stagg, Andrew Goodman, Lara Mitchell, Emily Funk, Andrea Schreier
Accurate species identification is critical to monitoring programs because mis-identifications can lead to incorrect assessments of population status and trends. In the San Francisco Estuary, efforts to monitor the imperiled osmerid Delta Smelt (Hypomesus transpacificus) using morphology can be challenging because of the presence of the similar-looking non-native osmerid Wakasagi (Hypomesus nipponensis). In 2017, the US Fish and Wildlife Service’s field office in Lodi implemented a two-stage verification process for Wakasagi to help prevent Delta Smelt from being mis-identified as Wakasagi. Under this process, Wakasagi are initially identified in the field, independently identified a second time by an experienced staff member in the laboratory, then stored on-site where they can be made available for future studies. Using the recently developed Specific High-sensitivity Enzymatic Reporter un-LOCKing (SHERLOCK) assay for Wakasagi, we evaluated how well verification protocols performed by genetically identifying a subset of Wakasagi collected during routine sampling between 2017 and 2021. Through this study, we found that the protocols have served as an effective quality control measure for over 4 years and across multiple surveys. With the development of field-deployable genetics tools such as SHERLOCK, genetic identification will likely play an increasingly important role in ecological monitoring. We expect that hybrid approaches that combine morphological identifications by trained field crew with application of field-based genetic tools may offer an effective and efficient approach to ensuring data accuracy in the future.
{"title":"Proofing Field and Laboratory Species Identification Procedures Developed for the Non-Native Osmerid Species Wakasagi (Hypomesus nipponensis) Using SHERLOCK-Based Genetic Verification","authors":"Jacob Stagg, Andrew Goodman, Lara Mitchell, Emily Funk, Andrea Schreier","doi":"10.15447/sfews.2023v21iss4art2","DOIUrl":"https://doi.org/10.15447/sfews.2023v21iss4art2","url":null,"abstract":"Accurate species identification is critical to monitoring programs because mis-identifications can lead to incorrect assessments of population status and trends. In the San Francisco Estuary, efforts to monitor the imperiled osmerid Delta Smelt (Hypomesus transpacificus) using morphology can be challenging because of the presence of the similar-looking non-native osmerid Wakasagi (Hypomesus nipponensis). In 2017, the US Fish and Wildlife Service’s field office in Lodi implemented a two-stage verification process for Wakasagi to help prevent Delta Smelt from being mis-identified as Wakasagi. Under this process, Wakasagi are initially identified in the field, independently identified a second time by an experienced staff member in the laboratory, then stored on-site where they can be made available for future studies. Using the recently developed Specific High-sensitivity Enzymatic Reporter un-LOCKing (SHERLOCK) assay for Wakasagi, we evaluated how well verification protocols performed by genetically identifying a subset of Wakasagi collected during routine sampling between 2017 and 2021. Through this study, we found that the protocols have served as an effective quality control measure for over 4 years and across multiple surveys. With the development of field-deployable genetics tools such as SHERLOCK, genetic identification will likely play an increasingly important role in ecological monitoring. We expect that hybrid approaches that combine morphological identifications by trained field crew with application of field-based genetic tools may offer an effective and efficient approach to ensuring data accuracy in the future.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":"24 23","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138950219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-21DOI: 10.15447/sfews.2023v21iss4art6
Paul Hutton, Arushi Sinha, Sujoy Roy, Richard Denton
This work presents a simplified approach for estimating ionic concentrations from specific electrical conductance (EC) data in the San Francisco Estuary. Monitoring the EC of water through electrodes is simple and inexpensive. As a result, a wealth of high-resolution time-series data is available to indirectly estimate salinity concentrations and, by extension, seawater intrusion throughout the study domain. However, scientists and managers are also interested in quantifying ionic (e.g., bromide, chloride) and total dissolved solids (TDS) concentrations to meet water-quality regulations, protect beneficial uses, support environmental analyses, and track source-water dominance. These constituent concentrations, reported with lower spatial and temporal resolution than EC, are typically measured in the laboratory from discrete (grab) water samples. We divided the study domain into four unique regions to estimate concentrations of major ions and TDS as mathematical functions of measured or model-simulated EC. Salinity relationships in three of the four regions—regions that represent Sacramento-San Joaquin Delta (Delta) inflow and seawater-dominated boundaries—reflect ionic make-ups that are either independent of or weakly dependent on season and hydrologic condition, and are highly correlated with EC. The fourth region—represented by the interior Delta—exhibits salinity characteristics associated with complex-boundary source-water mixing that varies by season and hydrologic condition. We introduce a novel method to estimate ionic and dissolved solids concentrations within this fourth region, given month, water year type, and (optionally) X2 isohaline position, which allows for more accurate EC-based estimates than previously available. The resulting approach, while not a substitute for hydrodynamic modeling, can provide useful information under constrained schedules and budgets.
{"title":"A Simplified Approach for Estimating Ionic Concentrations from Specific Conductance Data in the San Francisco Estuary","authors":"Paul Hutton, Arushi Sinha, Sujoy Roy, Richard Denton","doi":"10.15447/sfews.2023v21iss4art6","DOIUrl":"https://doi.org/10.15447/sfews.2023v21iss4art6","url":null,"abstract":"This work presents a simplified approach for estimating ionic concentrations from specific electrical conductance (EC) data in the San Francisco Estuary. Monitoring the EC of water through electrodes is simple and inexpensive. As a result, a wealth of high-resolution time-series data is available to indirectly estimate salinity concentrations and, by extension, seawater intrusion throughout the study domain. However, scientists and managers are also interested in quantifying ionic (e.g., bromide, chloride) and total dissolved solids (TDS) concentrations to meet water-quality regulations, protect beneficial uses, support environmental analyses, and track source-water dominance. These constituent concentrations, reported with lower spatial and temporal resolution than EC, are typically measured in the laboratory from discrete (grab) water samples. We divided the study domain into four unique regions to estimate concentrations of major ions and TDS as mathematical functions of measured or model-simulated EC. Salinity relationships in three of the four regions—regions that represent Sacramento-San Joaquin Delta (Delta) inflow and seawater-dominated boundaries—reflect ionic make-ups that are either independent of or weakly dependent on season and hydrologic condition, and are highly correlated with EC. The fourth region—represented by the interior Delta—exhibits salinity characteristics associated with complex-boundary source-water mixing that varies by season and hydrologic condition. We introduce a novel method to estimate ionic and dissolved solids concentrations within this fourth region, given month, water year type, and (optionally) X2 isohaline position, which allows for more accurate EC-based estimates than previously available. The resulting approach, while not a substitute for hydrodynamic modeling, can provide useful information under constrained schedules and budgets.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":"9 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138950303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-21DOI: 10.15447/sfews.2023v21iss4art1
Michael Dettinger, Anna Wilson, Garrett McGurk
Climate-change projections for California confidently describe a future with warmer temperatures, more evaporative demand, less snow, more rain, earlier and flashier runoff and streamflow, and drier summer conditions. The future of annual precipitation is much less certain, but a fairly unanimous projection of drier, more drought-prone conditions punctuated by occasional stronger-than-historical storms is almost as common among projections as is the warming itself. Rather than focusing on the less certain annual precipitation changes, we recommend more focus on keeping water in the headwaters longer. Doing so will involve reducing winter flood flows from headwater catchments, reducing the summer aridification (and wildfire risks) there, salvaging some groundwater recharge that would likely otherwise be lost, and overall, perpetuating headwater (and downstream) hydrologies under more historical and natural conditions. Among the available near-term adaptation strategies for keeping water in the headwaters longer, we discuss several examples here: (1) an increased emphasis on soils and percolation management as a priority and co-benefit in forest-health restoration activities; (2) beaver-population restoration or proliferation of beaver-inspired infrastructures; and (3) upstream-focused, forecast-informed reservoir-operation (FIRO) strategies.
{"title":"Keeping Water in Climate-Changed Headwaters Longer","authors":"Michael Dettinger, Anna Wilson, Garrett McGurk","doi":"10.15447/sfews.2023v21iss4art1","DOIUrl":"https://doi.org/10.15447/sfews.2023v21iss4art1","url":null,"abstract":"Climate-change projections for California confidently describe a future with warmer temperatures, more evaporative demand, less snow, more rain, earlier and flashier runoff and streamflow, and drier summer conditions. The future of annual precipitation is much less certain, but a fairly unanimous projection of drier, more drought-prone conditions punctuated by occasional stronger-than-historical storms is almost as common among projections as is the warming itself. Rather than focusing on the less certain annual precipitation changes, we recommend more focus on keeping water in the headwaters longer. Doing so will involve reducing winter flood flows from headwater catchments, reducing the summer aridification (and wildfire risks) there, salvaging some groundwater recharge that would likely otherwise be lost, and overall, perpetuating headwater (and downstream) hydrologies under more historical and natural conditions. Among the available near-term adaptation strategies for keeping water in the headwaters longer, we discuss several examples here: (1) an increased emphasis on soils and percolation management as a priority and co-benefit in forest-health restoration activities; (2) beaver-population restoration or proliferation of beaver-inspired infrastructures; and (3) upstream-focused, forecast-informed reservoir-operation (FIRO) strategies.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":"16 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138952196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-21DOI: 10.15447/sfews.2023v21iss4art3
William Satterthwaite, Emily Chen, Tracy McReynolds, Audrey Dean, Shanae Allen, Michael O'Farrell
Central Valley Spring-run Chinook (CVSC) are listed as threatened under the California and federal Endangered Species Acts, but how ocean fisheries affect CVSC is not routinely monitored or managed, largely because of data limitations. Most tag data for CVSC are from a hatchery program that may not sufficiently represent natural-origin fish in ocean and inland fishery recovery data. However, a discontinued tagging program for Butte Creek Wild Spring-run Chinook (BCWSC) provides for estimation of fishery impacts and maturation schedules for a limited set of years, which we compared with estimates for hatchery-origin fish for common years, while extending the hatchery-origin estimates over a wider time-frame. Additional scale-age data from BCWSC allow inferences about more recent maturation rates, conditional on harvest-rate estimates borrowed from other stocks. Overall, CVSC appear to experience low age-3 ocean fishery impact rates, but age-4 impact rates can be comparable to ocean harvest rates estimated for Sacramento River Fall Chinook. Tagging data from the years available indicate that ocean fisheries may reduce spawning run sizes (all ages combined) by 40% to 60% during periods of high fishing effort. Effects of ocean fishing on spawner abundance are weaker in years of reduced fishing or for cohorts displaying earlier maturation. It appears that maturation rates of hatchery-origin CVSC may have increased (i.e., earlier maturation) over the full time-period examined, and there may be indications of increasing maturation rates for BCWSC as well.
{"title":"Comparing Fishery Impacts and Maturation Schedules of Hatchery-Origin vs. Natural-Origin Fish from a Threatened Chinook Salmon Stock","authors":"William Satterthwaite, Emily Chen, Tracy McReynolds, Audrey Dean, Shanae Allen, Michael O'Farrell","doi":"10.15447/sfews.2023v21iss4art3","DOIUrl":"https://doi.org/10.15447/sfews.2023v21iss4art3","url":null,"abstract":"Central Valley Spring-run Chinook (CVSC) are listed as threatened under the California and federal Endangered Species Acts, but how ocean fisheries affect CVSC is not routinely monitored or managed, largely because of data limitations. Most tag data for CVSC are from a hatchery program that may not sufficiently represent natural-origin fish in ocean and inland fishery recovery data. However, a discontinued tagging program for Butte Creek Wild Spring-run Chinook (BCWSC) provides for estimation of fishery impacts and maturation schedules for a limited set of years, which we compared with estimates for hatchery-origin fish for common years, while extending the hatchery-origin estimates over a wider time-frame. Additional scale-age data from BCWSC allow inferences about more recent maturation rates, conditional on harvest-rate estimates borrowed from other stocks. Overall, CVSC appear to experience low age-3 ocean fishery impact rates, but age-4 impact rates can be comparable to ocean harvest rates estimated for Sacramento River Fall Chinook. Tagging data from the years available indicate that ocean fisheries may reduce spawning run sizes (all ages combined) by 40% to 60% during periods of high fishing effort. Effects of ocean fishing on spawner abundance are weaker in years of reduced fishing or for cohorts displaying earlier maturation. It appears that maturation rates of hatchery-origin CVSC may have increased (i.e., earlier maturation) over the full time-period examined, and there may be indications of increasing maturation rates for BCWSC as well.","PeriodicalId":38364,"journal":{"name":"San Francisco Estuary and Watershed Science","volume":"139 23","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138953340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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