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DRERIP Ecosystem Conceptual Model: Floodplain

California Department of Fish and Wildlife (CDFW) | January 22nd, 2008

Summary

Elements common to all models (Figure 1). Gray shapes (“plaques” in Word parlance) are other DRERIP models. Brown polygons are modifying factors. Pink rectangles are

Elements common to all models (Figure 1). Gray shapes (“plaques” in Word parlance) are other DRERIP models. Brown polygons are modifying factors. Pink rectangles are primary outputs of direct interest to Delta restoration planners (e.g., splittail). Blue rectangles are hydrological characteristics or variables, primarily pertaining to the primary river that is the source of inundation to the floodplain of interest but some rectangles represent “secondary hydrology” such as water deriving from direction precipitation on the floodplain, and groundwater and tributary inputs. Blue-green rectangles represent inundated habitat characteristics – properties of the floodplain during periods of inundation. Model 1 (Creating the Template) captures the linkages and processes that create the habitat mosaic—the physical template of a given floodplain, such as topography and vegetative communities (Figure 2). Note that habitat mosaic is more than vegetative communities as it also includes topographic features like side channels, oxbows, and wetlands. This is a very basic model, so we didn’t attempt to use the information-coded arrows to indicate importance, predictability, etc. This model describes how floodplain topography and vegetation, important features treated as more or less static in the other models, are created and maintained. This model encompasses time scales ranging from a single flood event (e.g., bank erosion) to decades or centuries (successional processes in a floodplain forest). Delta restoration planners can use model 1 to understand management options for creating and maintaining habitat mosaics on a given floodplain. Model 2 (Inundating the template) depicts how a given floodplain, with topography and vegetation created within Model 1, is inundated by river flows and other sources of water to create specific conditions within the inundated floodplain that are important to the species or processes described in model set 3 (Figure 3). The hydrology first encounters river-floodplain topography (e.g., the relative elevations of floodplain to river stage) to determine if the floodplain becomes inundated; the other linkages only occur if flow magnitude is capable of exceeding the inundation threshold. Inundation is a function of flow magnitude in the river, along with contributions from other hydrological sources (e.g., local tributaries, high water table), and the relative elevation and connectivity of the river-floodplain topography. If inundation occurs, the floodwaters interact with the topography and vegetation created in Model 1. As inundation occurs across this mosaic it results in a variety of inundated habitat characteristics—conditions that directly affect biota and processes during the period of inundation. These inundated habitat characteristics are the primary inputs for Model Set 3. This model is primarily focused at the temporal scale of a single flood season. Delta restoration planners can use model 2 to evaluate how management actions can influence the inundation of floodplain habitat mosaics and characteristics of the inundated habitat. Model Set 3 (Management outputs) illustrates how the inundated habitat characteristics, developed in Model 2, interact with a few other key elements to influence the production of biota of direct interest to delta restoration planners, including algae, zooplankton, splittail, and juvenile Chinook salmon (Figures 4 - 7). Model Set 3 encompasses a temporal scale of a single flood season. Model Set 3 can be used to evaluate how specific characteristics of the inundated floodplain affect specific outputs of management interest. Figure 4 provides a basic overview of the inputs and outputs and relationships between the models in Model Set 3. Figure 5 focuses on the production of algae (phytoplankton and epibenthic algae) and zooplankton, structured as a food web. Figures 6 and 7 show how the inundated habitat characteristics and base of the food web (algae and zooplankton) affect the production of splittail and Chinook salmon, respectively. Primary management outputs from floodplain models: 1. Primary productivity, in terms of phytoplankton, the most nutritious organic matter for the downstream delta (Muller-Solger et al. 2002) and secondary productivity (zooplankton and macroinvertebrates). Because several important species in the delta are food-limited, as indicated by low first-year survival, floodplain restoration has been promoted as a means of increasing productivity to these species and ecosystems (Jassby and Cloern 2000). 2. Juvenile Chinook 3. Splittail 4. Habitat mosaic and riparian structure for a variety of species. The first three management outputs are Model 3 outputs. For these a user can work backwards through the models to understand how management options can increase the productivity of a specific desired output. For example, if the desired output is biologically available Carbon for downstream ecosystems (algae), then Figure 5 (Model 3) indicates that residence time and intra-annual frequency are important characteristics; for these characteristics of inundation to occur, Figure 3 (Model 2) indicates that the frequency of inundation can be influenced either through hydrologic or topographic manipulations, and the narrative for Model 1 provides background information on the processes that create and maintain floodplain topography. The management output ‘riparian structure’ is a Model 1 output.

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DRERIP Ecosystem Conceptual Model: Green sturgeon

California Department of Fish and Wildlife (CDFW) | December 27th, 2008

Summary

The purpose of this report is to develop a conceptual life history model of North American green sturgeon (Acipenser medirostris) and the factors that affect reproduction

The purpose of this report is to develop a conceptual life history model of North American green sturgeon (Acipenser medirostris) and the factors that affect reproduction, growth, and survival in the Sacramento and San Joaquin rivers and San Francisco Bay-Delta. This model can be used to organize, visualize, and evaluate how the complex life history of green sturgeon relates to the spatial and temporal variability of riverine and estuarine ecosystems and potential consequences of ecosystem restoration and water management alternatives. This model is compatible with the suite of environmental and species models developed by the Department of Fish and Game Ecosystem Restoration Program (ERP) to assess and prioritize proposed restoration actions for the Delta. The model has a geographic emphasis on the Sacramento River and Bay-Delta regions, though the entire distribution of green sturgeon must be considered when population level responses are of concern, due to the unique, highly-migratory life history of this species. The conceptual life history model incorporates information from numerous sources about green sturgeon, often relying upon life history information from populations outside the Southern Distinct Population Segment (DPS) and occasionally considering information from the sympatric white sturgeon (A. transmontanus). While surrogate information from other North American sturgeon could have been used in the model, the distinctive anadromous and ecological characteristics of green sturgeon limited the utility of these species’ information. Due to the limits of quantitative information about green sturgeon, this model is presented in a qualitative narrative with numerical information provided, when available. While it will not provide quantitative limits on species take relative to maintaining a stable population size, it could be further developed into a population forecasting model since it divides the life history into life history stages, transition probabilities, and factors whose affects on reproduction and survival could be quantified. Life history stage transitions are visualized in a series of life stage submodels highlighting the processes and relationships among ecological factors influencing the transition between stages (Figures 1 and 2). A complex set of conditions and processes are necessary to determine whether an individual fish completes the transition from one life stage to the next. Our knowledge of green sturgeon life history remains limited as to the relative importance of biotic and abiotic factors critical for maintaining self-sustaining populations of green sturgeon. Thus, the importance, predictability, and understanding of each of these linkages are identified in the model. Lastly, a similar characterization of independent stressors is undertaken to describe potential factors affecting survival during each life history stage in a known geographic region. This model is dynamic and not intended to be a final version. As new information becomes available, the model should be refined so managers and biologists have the most current information available.

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DRERIP Ecosystem Conceptual Model: Longfin smelt

California Department of Fish and Wildlife (CDFW) | May 1st, 2010

Summary

This model describes the importance of stressors on the life history of longfin smelt in the San Francisco Estuary. In addition, the model identifies the degree to which

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DRERIP Ecosystem Conceptual Model: Mercury

California Department of Fish and Wildlife (CDFW) | January 24th, 2008

Summary

Mercury has been identified as an important contaminant in the Delta, based on elevated concentrations of methylmercury (a toxic, organic form that readily bioaccumulates

Mercury has been identified as an important contaminant in the Delta, based on elevated concentrations of methylmercury (a toxic, organic form that readily bioaccumulates) in fish and wildlife. There are health risks associated with human exposure to methylmercury by consumption of sport fish, particularly top predators such as bass species. Original mercury sources were upstream tributaries where historical mining of mercury in the Coast Ranges and gold in the Sierra Nevada and Klamath-Trinity Mountains caused contamination of water and sediment on a regional scale. Remediation of abandoned mine sites may reduce local sources in these watersheds, but much of the mercury contamination occurs in sediments stored in the riverbeds, floodplains, and the Bay-Delta, where scouring of Gold-Rush-era sediment represents an ongoing source. Conversion of inorganic mercury to toxic methylmercury occurs in anaerobic environments including some wetlands. Wetland restoration managers must be cognizant of potential effects on mercury cycling so that the problem is not exacerbated. Recent research suggests that wetting-drying cycles can contribute to mercury methylation. For example, high marshes (inundated only during the highest tides for several days per month) tend to have higher methylmercury concentrations in water, sediment, and biota compared with low marshes, which do not dry out completely during the tidal cycle. Seasonally inundated flood plains are another environment experiencing wetting and drying where methylmercury concentrations are typically elevated. Stream restoration efforts using gravel injection or other reworking of coarse sediment in most watersheds of the Central Valley involve tailings from historical gold mining that are likely to contain elevated mercury in associated fines. Habitat restoration projects, particularly those involving wetlands, may cause increases in methylmercury exposure in the watershed. This possibility should be evaluated. The DRERIP mercury conceptual model and its four submodels (1. Methylation, 2. Bioaccumulation, 3. Human Health Effects, and 4. Wildlife Heath Effects) can be used to understand the general relationships among drivers and outcomes associated with mercury cycling in the Delta. Several linkages between important drivers and outcomes have been identified as important but highly uncertain (i.e. poorly understood). For example, there may be significant wildlife health effect of mercury on mammals and reptiles in the Delta, but there is currently very little or no information about it. The characteristics of such linkages are important when prioritizing and funding restoration projects and associated monitoring in the Delta and its tributaries.

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DRERIP Ecosystem Conceptual Model: Potamcorbula amurensis

California Department of Fish and Wildlife (CDFW) | ?

Summary

Potamocorbula amurensis is a pest in the San Francisco Estuary (hereafter SFE) due to its ability to heavily graze pelagic food resources and its accumulation of toxic su

Potamocorbula amurensis is a pest in the San Francisco Estuary (hereafter SFE) due to its ability to heavily graze pelagic food resources and its accumulation of toxic substances that are then moved into the food web through its predators. We begin by describing what we know of its life history and establish its life cycle within the framework of the ecological setting of the SFE. This model should be used within the context of a thought experiment, as there is not enough known about the species to design a strategy to control it in the SFE or Delta. The ultimate purpose of this conceptual model of Potamocorbula amurensis is to explore its weaknesses. The geographic focus of the DRERIP models is the Delta. However we examine the life history patterns of Potamocorbula amurensis as far down bay as San Pablo Bay for two reasons. First, because some of the largest ecosystem effects attributed to P. amurensis are its consumption of pelagic carbon resources, it is necessary to include areas adjacent to the Delta due to the effects of tidal dispersion. Second, many of the life cycle patterns that are visible in San Pablo Bay are transferrable to upstream locations during drought periods. Finally, we expect this model to evolve as a result of the many ongoing studies on P. amurensis. Some of the data shown in this discussion are the direct result of current CALFED studies being done jointly by California Department of Water Resources (EMP Program D. Messer and K. Gerhts) and the USGS (Analysis of Archived Samples to Assess Patterns of Historic Invasive Bivalve Biomass). Our co-investigators on that study have been gracious in allowing us to show some of that data here, before it has been published. We start the model discussion with a brief description of the taxonomic status of this bivalve because the utility of the literature available to us is based on assumptions of the correct identification. We also very briefly describe its introduction into the SFE as a reminder of the facts about its invasion.

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DRERIP Ecosystem Conceptual Model: Pyrethroids

California Department of Fish and Wildlife (CDFW) | February 27th, 2008

Summary

To illustrate the applicability of the general model outlined in Delta Chemical Stressors conceptual model Werner et al. (2008), we are providing an example of its implem

To illustrate the applicability of the general model outlined in Delta Chemical Stressors conceptual model Werner et al. (2008), we are providing an example of its implementation for a specific group of contaminants, synthetic pyrethroid insecticides. Although numerous different pyrethroids exist, the members of this group share many chemical and toxicological characteristics. The US EPA’s decision to phase out certain uses of organophosphate insecticides because of their potential for causing toxicity in humans has led to their gradual replacement by pyrethroids, a class of synthetic insecticides applied in both urban and agricultural areas. They are applied in urban areas primarily for structural pest control, in agricultural areas on crops such as almonds, alfalfa, cotton, lettuce, pistachios, and peaches, and in the home in pet sprays and shampoos. In 2005, five pyrethroids were among the top 21 agricultural insecticides by acres treated in California: lambdacyhalothrin (rank 7), permethrin (rank 9), esfenvalerate (rank 11), cypermethrin (rank 14) and cyfluthrin (rank 21) (California Department of Pesticide Regulation, Pesticide Use Reporting database: www.cdpr.ca.gov). Both winter storm runoff, as well as irrigation return water may be important routes of transport into aquatic systems. Pyrethroids at toxic concentrations have been detected in the majority of sediment samples collected from water bodies draining agricultural areas in the Central Valley (Weston et al., 2004; California Regional Water Quality Control Board Agricultural Waiver Program, 2007), as well as from urban creeks in the Bay/Delta region (Amweg et al., 2006; Woudneh and Oros, 2006 a, b). Pyrethroid concentrations toxic to aquatic life were detected in water samples from Central Valley agricultural drains and creeks (Central Valley Regional Water Quality Control Board, 2005; Bacey et al., 2005), and tributaries to San Francisco Bay (Woudneh and Oros, 2006 a, b). Aquatic organisms, in particular insects, crustaceans and fish, are highly sensitive to pyrethroid insecticides (Oros and Werner, 2005). Acute toxicity to fish and aquatic invertebrates is generally observed at concentrations below 1 ?g/L, and sublethal effects have been reported at low ng/L concentrations. Although it is difficult to model sublethal responses to toxicants and predict ecotoxicological impact or risk, measures of sublethal effects are likely to be as important, or more important, than the measures of acute or chronic lethal effects to accurately assess the consequences of contaminant exposure. All pyrethroids are potent neurotoxicants (Bradbury and Coats, 1989; Shafer and Meyer, 2004), can inhibit ATPases (Litchfield, 1985), and have immunosuppressive effects (Madsen et al., 1996; Clifford et al., 2005). In addition, these compounds and their breakdown products can disrupt hormone-related functions (Go et al., 1999; Tyler et al., 2000; Perry et al., 2006; Sun et al., 2007). As pyrethroid concentrations in the Delta would be expected to peak during the winter/spring storm season (Werner et al. 2004, 2006), as well as after peak agricultural application in the summer and fall (Weston et al., 2004), early life-stages of important Delta fish species or their prey may be directly exposed to these contaminants. The storm season coincides with the spawning and rearing period of several important fish such as the delta smelt, which spawns from February to June (Moyle, 1976). Juvenile fish depend on planktonic crustaceans, small insect larvae, and mysid shrimp as their major food items (Moyle 1976), which are highly sensitive to pyrethroids. It has been suggested that urban and agricultural pesticide use in the Central Valley and Delta region might play a role in the pelagic organism declines observed in the upper estuary (Oros and Werner, 2005).

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DRERIP Ecosystem Conceptual Model: Riparian vegetation

California Department of Fish and Wildlife (CDFW) | November 14th, 2008

Summary

The Sacramento-San Joaquin Delta has immense municipal, agricultural, biological and industrial importance to the economy and livelihood of California and in turn to the

The Sacramento-San Joaquin Delta has immense municipal, agricultural, biological and industrial importance to the economy and livelihood of California and in turn to the United States. Plans to improve conditions in the Delta must address both human and biological communities. The region has been altered extensively over the past 200 years from land conversion to agriculture, fluxes in sedimentation rates, levee construction, and a completely re-plumbed network of waterways and hydrology (Thompson, 1957). Remnant, native riparian and wetland plant communities are almost completely removed and there is some question of whether the natural processes that create and maintain them can be restored (Mount and Twiss, 2005). Restoration implementation will be difficult considering the extent of alteration and complexity of both the natural system and cultural setting. The scientific approach to resolve these issues needs to reflect system complexity and represent the many potential response pathways that lead from proposed alterations. Development of conceptual models to understand these potential pathways is an important first step in understanding restoration implementation (and other management actions) in light of the complexity of the natural system and existing management scheme. The CALFED program is interested in restoring the Delta ecosystem to the extent possible. Riparian Vegetation (RV2) is but one of the natural systems of interest; others include fisheries, wildlife, and other plant communities. The conceptual model presented here deals exclusively with those physical, chemical, and ecological processes relevant to riparian vegetation. Riparian vegetation is important not only for biological conservation of the plant species themselves, but also the other flora and fauna species—and the physical and ecological processes—that depend upon riparian vegetation. Although the restoration of riparian vegetation as a component of a healthy riverine landscape has cultural and economic importance, these aspects are not included in this model. The conceptual model of riparian vegetation presented here is actually a sub-model of the larger floodplain processes/habitat model (Figure 1). The RV Sub-model is general by design, and is intended to provide a framework for potential expansion or adaptation to more-refined models of individual species, habitats, and/or entire landscapes. Spatially, we focus specifically on the floodplain or land area beginning at the upper edge of the emergent vegetation zone, then moving up in elevation and inland from the water, ending when non-floodplain areas, open water, or marsh is encountered. Together, the Floodplain model and the RV Sub-model can be used to analyze various “scenarios,” ranging from potential restoration or research actions, to water management decisions, to placement of bank protection at a specific Delta levee site. In addition, to highlight key differences in conditions that occur in the Delta, we present here two specific applications of the RV Sub-model that we generalize as a being dominated by tidal processes and another dominated by more riverine processes.

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DRERIP Ecosystem Conceptual Model: Sacramento splittail

California Department of Fish and Wildlife (CDFW) | September 3rd, 2008

Summary

Model has not yet fully completed the peer review and collegial review process and final modifications may be required of the developers. Model may not be cited or circul

Model has not yet fully completed the peer review and collegial review process and final modifications may be required of the developers. Model may not be cited or circulated until that process is complete. It may be used in identifying and evaluating restoration actions with assistance from content experts. Model is appropriate for use by experienced evaluation team with input from content experts as necessary. The purpose of this conceptual model is to aid management decisions for the continued persistence and recovery of Sacramento splittail. This model, along with the suite of models developed through ERP as well as other information and tools, is intended to be used for evaluating proposed restoration actions for the Delta and throughout the species geographic range. It is a qualitative life-cycle conceptual model that attempts to bring together many sources of information to build a comprehensive document that represents the current state of knowledge for the species. It is not a quantitative model however. It will not provide quantitative limits on species take or population number outcomes. It will only provide an indication of anticipated population response (i.e. increase or decrease with a magnitude of x or y) based on the most current scientific knowledge. With this knowledge, proposed restoration actions can be grouped and a positive population response can be developed through an adaptive management framework. The model must be read and understood in its entirety and does not provide users/readers quick solutions or answers. The entire life-cycle of the animal must be understood by decision makers if they intend to make sound choices in the future. The conceptual model diagram and associated tables can be used to focus the reader on potential species and population limiting factors given the current scientific understanding under current conditions. The model has a specific emphasis on the Delta; however the entire species range must be considered when population level responses are of concern. For this reason the geographic scope of this document is beyond the legal boundaries of the “Delta”. This is not intended to be the final version of this conceptual model. As new information becomes available through research and in the scientific literature, this model will be updated as time allows providing managers with the most current information available. This conceptual model relies heavily on the extensive work done by Peter Moyle and others in their 2004 white paper Biology and Population Dynamics of Sacramento Splittail (Pogonichthys macrolepidotus) in the San Francisco Estuary: A Review which was published in the San Francisco Estuary and Watershed Science online journal. Content in the model is taken from that review unless otherwise indicated. These sections will be introduced with a citation to Moyle et al. 2004. This model also takes into account new research on Sacramento splittail which has occurred subsequent to the white paper.

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DRERIP Ecosystem Conceptual Model: Sedimentation

California Department of Fish and Wildlife (CDFW) | November 13th, 2007

Summary

1) Sediment supply: The supply of sediment from the watershed to the Delta is limited. Sediment supply is decreasing due to trapping behind dams and diminishment of the

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DRERIP Ecosystem Conceptual Model: White sturgeon

California Department of Fish and Wildlife (CDFW) | April 25th, 2011

Summary

The purpose of this report is to develop a conceptual life history model of white sturgeon (Acipenser transmontanus) and the factors that affect reproduction, growth, and

The purpose of this report is to develop a conceptual life history model of white sturgeon (Acipenser transmontanus) and the factors that affect reproduction, growth, and survival in the Sacramento-San Joaquin Rivers and San Francisco bay-delta. This model can be used to organize, visualize, and evaluate how the complex life history of white sturgeon relates to the spatial and temporal variability of riverine and estuarine ecosystems and potential consequences of ecosystem restoration and water management alternatives. This model is compatible with the suite of environmental and species models developed by the Department of Fish and Game Ecosystem Restoration Program (ERP) to assess and prioritize proposed restoration actions for the delta. The model has a geographic emphasis on the Sacramento River and bay-delta regions, though the entire distribution of white sturgeon should be considered when population level responses are of concern, due to the migratory life history of this species. The conceptual life history model incorporates information from numerous sources about white sturgeon, often relying upon life history information from populations outside California. While additional surrogate information from other North American sturgeons could have been used in the model, the distinctive diadromous and ecological characteristics of California white sturgeon limited the utility of these species’ information, thus information from other diadromous sturgeon species is only occasionally considered. Due to the limits of quantitative information about white sturgeon, this model is presented in a qualitative narrative, though numerical information is provided when available. While it will not provide quantitative limits on species take relative to maintaining a stable population size, it could be further developed into a population forecasting model since it divides the life history into life history stages, transition probabilities, and factors whose effects on reproduction and survival could be quantified. Life history stage transitions are visualized in a series of life stage submodels highlighting the processes and relationships among ecological factors influencing the transition between stages (Figures 1 and 2). A complex set of conditions and processes are necessary to determine whether an individual white sturgeon completes the transition from one life stage to the next. Our knowledge of how biotic and abiotic factors are critical for maintaining healthy populations is fairly basic. Thus, the importance, predictability, and understanding of each of these linkages are identified in the model. Lastly, a similar characterization of independent stressors is undertaken to describe potential factors affecting survival during each life history stage in a known geographic region. This model is dynamic and not intended to be a final version. As new data become available, the model should be refined so managers and biologists have the most current information available.

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DRERIP Ecosystem Conceptual Model: Floodplain

DRERIP Ecosystem Conceptual Model: Green sturgeon

DRERIP Ecosystem Conceptual Model: Longfin smelt

DRERIP Ecosystem Conceptual Model: Mercury

DRERIP Ecosystem Conceptual Model: Potamcorbula amurensis

DRERIP Ecosystem Conceptual Model: Pyrethroids

DRERIP Ecosystem Conceptual Model: Riparian vegetation

DRERIP Ecosystem Conceptual Model: Sacramento splittail

DRERIP Ecosystem Conceptual Model: Sedimentation

DRERIP Ecosystem Conceptual Model: White sturgeon

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