Geology topics

Ted Sommer

Publications and source records attributed to Ted Sommer.

7 recordsLinked to original sources

USGS2024

Estimating the benefits of floodplain restoration to juvenile Chinook salmon in the upper San Francisco Estuary, United States, under future climate scenarios

Many river systems within the Central Valley of California have been disconnected from their floodplains, hypothesized to be partially responsible for declining Chinook salmon populations ( Oncorhynchus tshawytscha ). The primary floodplain of the system, Yolo By-Pass (known regionally as “Yolo Bypass”), offered an opportunity to examine whether improved connectivity between the floodplain and river could limit negative climate change effects on salmon populations. Specifically, the top of the floodplain (Fremont Weir) is being modified to provide Sacramento River Chinook salmon better access to floodplain rearing habitat. We estimated restoration effects on the Yolo By-Pass flood regime now and under future climate scenarios using flow rating curves. Additionally, we used temperature and flow-specific effects on Chinook salmon population dynamics within the Yolo By-Pass and Sacramento River complex to describe how the restoration project and climate change may interact to affect juvenile Chinook salmon biomass production. Our results indicate that the Fremont Weir restoration project will extend the frequency, timing, and duration of Yolo By-Pass flooding. Our production model indicates that the modification will result in greater salmon entrainment rates into the Yolo By-Pass, where salmon growth rates, survival rates, and biomass production were higher when compared to the Sacramento River main stem. The project appears to benefit all regional runs of Chinook salmon, which should help support life history diversity. Our results suggest that the weir modification should benefit native fish from the Central Valley that use floodplain habitat and that these benefits may be resilient to challenges created by a changing climate.

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USGS2021

Resistance and resilience of pelagic and littoral fishes to drought in the San Francisco Estuary

Many estuarine ecosystems and the fish communities that inhabit them have undergone substantial changes in the past several decades, largely due to multiple interacting stressors that are often of anthropogenic origin. Few are more impactful than droughts, which are predicted to increase in both frequency and severity with climate change. In this study, we examined over five decades of fish monitoring data from the San Francisco Estuary, California, USA, to evaluate the resistance and resilience of fish communities to disturbance from prolonged drought events. High resistance was defined by the lack of decline in species occurrence from a wet to a subsequent drought period, while high resilience was defined by the increase in species occurrence from a drought to a subsequent wet period. We found some unifying themes connecting the multiple drought events over the 50‐yr period. Pelagic fishes consistently declined during droughts (low resistance), but exhibit a considerable amount of resiliency and often rebound in the subsequent wet years. However, full recovery does not occur in all wet years following droughts, leading to permanently lower baseline numbers for some pelagic fishes over time. In contrast, littoral fishes seem to be more resistant to drought and may even increase in occurrence during dry years. Based on the consistent detrimental effects of drought on pelagic fishes within the San Francisco Estuary and the inability of these fish populations to recover in some years, we conclude that freshwater flow remains a crucial but not sufficient management tool for the conservation of estuarine biodiversity.

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USGS2021

Synthesis of data and studies relating to Delta Smelt biology in the San Francisco Estuary, emphasizing water year 2017

In the San Francisco Estuary (SFE), the effects of freshwater flow on the aquatic ecosystem have been studied extensively over the years and remains a contentious management issue. It is especially contentious with regards to the Delta Smelt (Hypomesus transpacificus), a species endemic to the SFE that has been listed as threatened under the Federal Endangered Species Act and endangered by the State of California. Early studies of Delta Smelt distribution within the SFE suggested that Delta Smelt habitat is determined largely by freshwater flow; however, the exact mechanisms and processes producing such benefits remained unclear. In the summer of 2017, the Flow Alteration Management, Analysis, and Synthesis Team (FLOAT-MAST) was established to analyze, synthesize, and summarize the data collected from the various flow-related monitoring and special studies occurring in 2017(see Table Intro 4). This report will focus on the 2017 summer-fall status of Delta Smelt and its habitat following a record wet year. There has been a long-term decline in the abundance of Delta Smelt associated with a decline in other pelagic fishes. Investigators concluded that the decline has likely been caused by the interactive effects of several causes, including changes in both physical and biotic habitats, many of which are tied to amount and timing of freshwater flow. For this report, we formulated a number of basic predictions about the likely effects of high flows in 2017 on Delta Smelt and their habitat (Table 3). We use a qualitative weight of evidence approach to evaluate whether these predictions were supported by available data. Data sources included a variety of long-term monitoring surveys conducted by Interagency Ecological Program (IEP) agencies, as well as model outputs. Delta Smelt population, health, and life history metrics rarely responded as predicted. Water temperature appears to have a stronger effect on Delta Smelt growth rate and some metrics of life history diversity than outflow or X2 position. Other life history diversity attributes varied but did not appear to be driven by outflow or temperature. Health status was difficult to interpret. Low prevalence of lesions and improved nutritional condition during the drought was contradicted by declining overall population levels. Because of the sparse catches of Delta Smelt in the post-POD years, we consider the data insufficient to reach firm conclusions about the predictions concerning range and distribution of Delta Smelt, especially in the fall. The prediction of high survival was not supported. The 2017 Delta Smelt year class began with poor recruitment in spring of 2017 and below average survival for spring to summer and summer to fall. Thus, low production and low survival led to low abundance of all life stages. During the fall to winter period survival improved, yet the resulting adults were low in number. Foraging success of the fish captured, as measured by stomach fullness, was high for juveniles and adults in 2017 relative to recent years associated with the higher densities of common zooplankton prey that occurred in 2017.

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USGS2020

Ecological effects of climate-driven salinity variation in the San Francisco Estuary: Can we anticipate and manage the coming changes?

Climate change-driven sea level rise and altered precipitation regimes are predicted to alter patterns of salt intrusion within the San Francisco Estuary. A central question is: Can we use existing knowledge and future projections to predict and manage the anticipated ecological impacts? This was the subject of a 2018 symposium entitled “Ecological and Physiological Impacts of Salinization of Aquatic Systems from Human Activities.” The symposium brought together an inter-disciplinary group of scientists and researchers, resource managers, and policy-makers. Here, we summarize and review the presentations and discussions that arose during the symposium. From a historical perspective, salt intrusion has changed substantially over the past 10,000 years as a result of changing climate patterns, with additional shifts from recent anthropogenic effects. Current salinity patterns in the San Francisco Estuary are driven by a suite of hydrodynamic processes within the given contexts of water management and geography. Based on climate projections for the coming century, significant changes are expected in the processes that determine the spatial and temporal patterns of salinity. Given that native species—including fishes such as the Delta Smelt and Sacramento Splittail—track favorable habitats, exhibit physiological acclimation, and can adaptively evolve, we present a framework for assessing their vulnerability to altered salinity in the San Francisco Estuary. We then present a range of regulatory and structural management tools that are available to control patterns of salinity within the San Francisco Estuary. Finally, we identify major research priorities that can help fill critical gaps in our knowledge about future salinity patterns and the consequences of climate change and sea level rise. These research projects will be most effective with strong linkages and communication between scientists and researchers, resource managers, and policy-makers.

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USGS2015

Delta smelt habitat in the San Francisco Estuary: A reply to Manly, Fullerton, Hendrix, and Burnham’s “Comments on Feyrer et al. Modeling the effects of future outflow on the abiotic habitat of an imperiled estuarine fish"

Manly et al. (2015) commented on the approach we (Feyrer et al. 2011) used to calculate an index of the abiotic habitat of delta smelt Hypomesus transpacificus. The delta smelt is an annual fish species endemic to the San Francisco Estuary (SFE) in California, USA. Conserving the delta smelt population while providing reliability to California’s water supply with water diverted from the SFE ecosystem is a major management and policy issue. Feyrer et al. (2011) evaluated historic and projected future abiotic habitat conditions for delta smelt. Manly et al. (2015) specifically commented regarding the following: (1) use of an independent abundance estimate, (2) spatial bias in the habitat index, and (3) application of the habitat index to future climate change projections. Here, we provide our reply to these three topics. While we agree that some of the concepts raised by Manly et al. (2015) have the potential to improve habitat assessments and their application to climate change scenarios as knowledge is gained, we note that the Feyrer et al. (2011) delta smelt habitat index is essentially identical to one reconstructed using Manly et al.’s (2015) preferred approach (their model 8), as shown here in Fig. 1.

Estuaries and Coasts↗

USGS2015

An updated conceptual model of Delta Smelt biology: Our evolving understanding of an estuarine fish

The main purpose of this report is to provide an up-to-date assessment and conceptual model of factors affecting Delta Smelt (Hypomesus transpacificus) throughout its primarily annual life cycle and to demonstrate how this conceptual model can be used for scientific and management purposes. The Delta Smelt is a small estuarine fish that only occurs in the San Francisco Estuary. Once abundant, it is now rare and has been protected under the federal and California Endangered Species Acts since 1993. The Delta Smelt listing was related to a step decline in the early 1980s; however, population abundance decreased even further with the onset of the “pelagic organism decline” (POD) around 2002. A substantial, albeit short-lived, increase in abundance of all life stages in 2011 showed that the Delta Smelt population can still rebound when conditions are favorable for spawning, growth, and survival. In this report, we update previous conceptual models for Delta Smelt to reflect new data and information since the release of the last synthesis report about the POD by the Interagency Ecological Program for the San Francisco Estuary (IEP) in 2010. Specific objectives include: 1. Provide decision makers with a practical tool for evaluating difficult trade-offs associated with management and policy decisions. 2. Provide scientists with a framework from which they can formulate and evaluate hypotheses using qualitative or quantitative models. 3. Provide the general public with a new way of learning about Delta Smelt and their habitat. Our updated conceptual model describes the habitat conditions and ecosystem drivers affecting each Delta Smelt life stage, across seasons and how the seasonal effects contribute to the annual success of the species. The conceptual model consists of two nested and linked levels of increasing specificity. The general life cycle conceptual model for four Delta Smelt life stages (adults, eggs and larvae, juveniles, and subadults) includes stationary ecosystem components and dynamic environmental drivers, habitat attributes, and Delta Smelt responses. The more detailed life stage transition conceptual models for each of the four Delta Smelt life stages describe relationships between environmental drivers, key habitat attributes, and the responses of Delta Smelt to habitat attributes as they transition from one life stage to the next. Our analyses and conceptual model show that good larval recruitment is essential for setting the stage for a strong year class; however, increased growth and survival through subsequent life stages are also needed to achieve and sustain higher population abundance. We used our conceptual model to generate 16 hypotheses about the factors that may have contributed to the 2011 increase in Delta Smelt relative abundance. We then evaluated these hypotheses by comparing habitat conditions and Delta Smelt responses in the wet year 2011 to those in the prior wet year 2006 and in the drier years 2005 and 2010. Larval recruitment was similarly high in both wet years and lower in the drier antecedent years, but juvenile and adult abundance increased only in 2011. In 2005 and 2006, the population was limited by very poor survival from the larval to the juvenile life stage. We found that in 2011, Delta Smelt may have benefitted from a combination of favorable habitat conditions throughout the year, including: 1. Adults and larvae benefitted from prolonged cool spring water temperatures, high 2011 winter and spring outflows which reduced entrainment risk and possibly improved other habitat conditions, and possibly enhanced food availability in late spring. 2. Juveniles benefitted from cool water temperatures in late spring and early summer as well as from improved food availability and low levels of harmful Microcystis. 3. Subadults also benefitted from improved food availability and from favorable habitat conditions in the large, low salinity zone (salinity 1-6) located more toward Suisun Bay,

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USGS2014

Synthesis of studies in the fall low-salinity zone of the San Francisco Estuary, September-December 2011

In fall 2011, a large-scale investigation (fall low-salinity habitat investigation) was implemented by the Bureau of Reclamation in cooperation with the Interagency Ecological Program to explore hypotheses about the ecological role of low-salinity habitat in the San Francisco Estuary—specifically, hypotheses about the importance of fall low-salinity habitat to the biology of delta smelt Hypomesus transpacificus , a species endemic to the San Francisco Estuary and listed as threatened or endangered under federal and state endangered species legislation. The Interagency Ecological Program is a consortium of 10 agencies that work together to develop a better understanding of the ecology of the Estuary and the effects of the State Water Project and Federal Central Valley Project operations on the physical, chemical, and biological conditions of the San Francisco Estuary. The fall low-salinity habitat investigation constitutes one of the actions stipulated in the Reasonable and Prudent Alternative issued with the 2008 Biological Opinion of the U.S. Fish and Wildlife Service, which called for adaptive management of fall Sacramento-San Joaquin Delta outflow following “wet” and “above normal” water years to alleviate jeopardy to delta smelt and adverse modification of delta smelt critical habitat. The basic hypothesis of the adaptive management of fall low-salinity habitat is that greater outflows move the low-salinity zone (salinity 1–6), an important component of delta smelt habitat, westward and that moving the low-salinity zone westward of its position in the fall of recent years will benefit delta smelt, although the specific mechanisms providing such benefit are uncertain. An adaptive management plan was prepared to guide implementation of the adaptive management of fall low-salinity habitat and to reduce uncertainty. This report has three major objectives: • To provide a summary of the results from the first year of coordinated fall low-salinity habitat studies and monitoring. • To provide a synthesis of the results of the fall low-salinity habitat studies and other ongoing research and monitoring, to determine if the available information supports the hypotheses behind the adaptive management of fall low-salinity habitat as set forth in the adaptive management plan. • To begin to put the results from the fall low-salinity habitat studies into context within the larger body of knowledge regarding the San Francisco Estuary and, in particular, the upper San Francisco Estuary, including the Sacramento-San Joaquin Delta, Suisun Bay, and associated embayments. The basic approach of this report is to evaluate predictions derived from the hypotheses included in the conceptual model developed within the adaptive management plan. All available data from studies and monitoring conducted in fall 2011 and similar data from fall 2006, which was the most recent wet year preceding 2011, were considered. Data from 2005 and 2010 were also considered, to include the conditions antecedent to those years. Many of the predictions either could not be evaluated with the data available, or the needed data were not collected. Most of the predictions that could be addressed involved either the abiotic habitat components (that is, the physical environment) or delta smelt responses. In general, the fall low-salinity habitat investigation has been largely inconclusive as of the writing of this report. This is not to be unexpected in the first year of what is intended to be a multi-year adaptive-management effort. This report can be viewed as the first chapter of a “living document” that is to be continually updated as part of the adaptive management cycle. The results of this report, especially predictions with insufficient data for evaluation, indicate a number of science-based approaches to improve the fall low-salinity habitat investigations: • Develop a method of measuring “hydrodynamic complexity.” This concept is central to a number of the predictions that could not be evaluated. • Determine if wind speed warrants a stand-alone prediction. The wind-speed prediction is directly related to the turbidity predictions, and wind is only one of several factors important for determining turbidity. • Determine the correct spatial and temporal scale or scales necessary for monitoring and for studies to address the predicted abiotic and biotic responses. Many of the assessments in this report were based on monthly sampling of dynamic habitat components, such as phytoplankton and zooplankton populations, that can change on daily scales. • Address the nutrient predictions as part of developing a phytoplankton production model that includes nutrient cycling and other important processes, if feasible. At a minimum develop a mechanistic conceptual model to support more processed-based interpretations of data or design of new studies, rather than making simple predictions of increase or decrease. • Determine if studies of predation rates are feasible in areas where there are delta smelt.

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