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Alameda Creek Watershed Historical Ecology Study. San Francisco Estuary Institute: Richmond, CA.2013.
An Assessment of the South Bay Historical Tidal-Terrestrial Transition Zone. SFEI Contribution No. 693. San Francisco Estuary Institute: Richmond, CA.2013.
Baylands Ecosystem Habitat Goals. SFEI Contribution No. 330. U. S. Environmental Protection Agency, San Francisco, Calif./S.F. Bay Regional Water Quality Control Board, Oakland, Calif. p 328.1999.
Building a regionally consistent base map for the Bay Area: The National Hydrography Data Set. Abstracts of the 5th Biannual State of the Estuary Conference – San Francisco Estuary: Achievements, trends and the future, pp 108.2001.
Building Ecological Resilience in Highly Modified Landscapes.2018.
Ecological resilience is a powerful heuristic for ecosystem management in the context of rapid environmental change. Significant efforts are underway to improve the resilience of biodiversity and ecological function to extreme events and directional change across all types of landscapes, from intact natural systems to highly modified landscapes such as cities and agricultural regions. However, identifying management strategies likely to promote ecological resilience remains a challenge. In this article, we present seven core dimensions to guide long-term and large-scale resilience planning in highly modified landscapes, with the objective of providing a structure and shared vocabulary for recognizing opportunities and actions likely to increase resilience across the whole landscape. We illustrate application of our approach to landscape-scale ecosystem management through case studies from two highly modified California landscapes, Silicon Valley and the Sacramento–San Joaquin Delta. We propose that resilience-based management is best implemented at large spatial scales and through collaborative, cross-sector partnerships.
Cartographic analysis of historical and modern baylands boundaries for Marin County, California. SFEI Contribution No. 229. Marin County Community Develpment Agency. p 88 pp.1998.
Changing Channels: Regional Information for Developing Multi-benefit Flood Control Channels at the Bay Interface. Flood Control 2.0. SFEI Contribution No. 801. San Francisco Estuary Institute: Richmond, CA.2017.
Over the past 200 years, many of the channels that drain to San Francisco Bay have been modified for land reclamation and flood management. The local agencies that oversee these channels are seeking new management approaches that provide multiple benefits and promote landscape resilience. This includes channel redesign to improve natural sediment transport to downstream bayland habitats and beneficial re-use of dredged sediment for building and sustaining baylands as sea level continues to rise under a changing climate. Flood Control 2.0 is a regional project that was created to help develop innovative approaches for integrating habitat improvement and resilience into flood risk management at the Bay interface. Through a series of technical, economic, and regulatory analyses, the project addresses some of the major elements associated with multi-benefit channel design and management at the Bay interface and provides critical information that can be used by the management and restoration communities to develop long-term solutions that benefit people and wildlife.
This Flood Control 2.0 report provides a regional analysis of morphologic change and sediment dynamics in flood control channels at the Bay interface, and multi-benefit management concepts aimed at bringing habitat restoration into flood risk management. The findings presented here are built on a synthesis of historical and contemporary data that included input from Flood Control 2.0 project scientists, project partners, and science advisors. The results and recommendations, summarized below, will help operationalize many of the recommendations put forth in the Baylands Ecosystem Habitat Goals Science Update (Goals Project 2015) and support better alignment of management and restoration communities on multi-benefit bayland management approaches.
Conceptual models of freshwater influences on tidal marsh form and function, with an historical perspective. SFEI Contribution No. 327. Department of Environmental Services: City of San Jose, CA. p 237 pp.1999.
Coyote Creek Watershed Historical Ecology Study: Historical Conditions and Landscape Change in the Eastern Santa Clara Valley, California. SFEI Contribution No. 426. San Francisco Estuary Institute.2006.
A Delta Renewed: A Guide to Science-Based Ecological Restoration in the Sacramento-San Joaquin Delta. Delta Landscapes Project. Prepared for the California Department of Fish and Wildlife and Ecosystem Restoration Program. A Report of SFEI-ASC’s Resilient Landscapes Program. SFEI Contribution No. 799. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.2016.
This report offers guidance for creating and maintaining landscapes in the Sacramento-San Joaquin Delta that support desired ecological functions, while retaining the overall agricultural character and water-supply service of the region. Based on extensive research into how the Delta functioned historically, how it has changed, and how it is likely to evolve, we discuss where and how to re-establish the dynamic natural processes that can sustain native Delta habitats and wildlife into the future. The approach, building on work others have piloted and championed, is to restore or emulate natural processes where possible, establish an appropriate mosaic of habitat types at the landscape scale, use multi-benefit management strategies to increase support for native species in agricultural and urban areas, and allow the Delta to adapt to future uncertainties of climate change, levee failure, and human population growth. With this approach, it will be critical to integrate ecological improvements with the human landscape: a robust agricultural economy, water infrastructure and diversions, and urbanized areas. Strategic restoration that builds on the history and ecology of the region can contribute to the strong sense of place and recreational value of the Delta.
A Delta Transformed: Ecological Functions, Spatial Metrics, and Landscape Change in the Sacramento-San Joaquin Delta. SFEI Contribution No. 729. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.2014.
Documenting Local Landscape Change: The Bay Area Historical Ecology Project. In The Historical Ecology Handbook: A Restorationist's Guide to Reference Ecosystems.. . The Historical Ecology Handbook: A Restorationist's Guide to Reference Ecosystems. Island Press: Washington D.C.2001.
Documenting Local Landscape Change: The Bay Area Historical Ecology Project. In The HISTORICAL ECOLOGY HANDBOOK: A Restorationist's Guide to Reference Ecosystems. . The HISTORICAL ECOLOGY HANDBOOK: A Restorationist's Guide to Reference Ecosystems. Island Press.2005.
East Contra Costa Historical Ecology Study. SFEI Contribution No. 648. SFEI: Oakland.2011.
East Contra Costa Historical Ecology Study GIS data, GIS data produced for the East Contra Costa County Historical Ecology Study.2011.
Ecological, Geomorphic, and Land Use History of Carneros Creek Watershed: A component of the watershed management plan for the Carneros Creek watershed, Napa County, California. SFEI Contribution No. 70. San Francisco Estuary Institute: Oakland.2004.
Ecological, Geomorphic, and Land Use History of Sulphur Creek Watershed: A component of the watershed management plan for the Sulphur Creek watershed, Napa County, California. SFEI Contribution No. 307. San Francisco Estuary Institute: Oakland.2004.
Ecological implications of modeled hydrodynamic changes in the upper San Francisco Estuary: Phase II Technical Memorandum. SFEI Contribution No. 786.2016.
The physical and ecological environment of the upper San Francisco Estuary has been profoundly altered since the early 1800s. Recent efforts have utilized maps of the upper estuary’s historical habitat types to infer associated changes in desired ecosystem processes and functions. The work presented in this memo builds on these previous efforts, but utilizes a new tool for evaluating change over time: a 3D hydrodynamic model of the pre-development estuary. This model was constructed by Resource Management Associates (RMA) using a new digital elevation model of the pre-development upper estuary generated by SFEI and UC Davis (UCD) and “natural” boundary flows calculated by the California Department of Water Resources (CDWR).
Once completed and calibrated, the pre-development model was paired with a similar model of the contemporary system in order to analyze hydrodynamic changes in the upper estuary. These analyses are presented in a technical memorandum published by RMA (2015). This memorandum takes these analyses and considers the ecological implications of modeled changes (see the “Results” section). Hydrodynamic analyses include analyzing changes in tidal prism, isohaline positions, low-salinity zone habitat, channel velocity, and source water distribution.
In addition to describing the ecological implications of modeled hydrodynamic changes, this memorandum summarizes major ongoing questions about estuarine hydrodynamics that might be explored using these models, including changes in water residence time, temperature, transport pathways, and the connectivity of aquatic and semi-aquatic habitats. Understanding changes in these and other factors would greatly improve our understanding of the desirable ecosystem functions provided by the historical system and, as a result, improve our ability to recover these functions now and into the future.
Estuaries: Life on the edge. In Ecosystems of California. Ecosystems of California. University of California Press: Berkeley, CA. pp 359-388.2016.
From past patterns to future potential: using historical ecology to inform river restoration on an intermittent California river. Landscape Ecology 31 (3), 20.2016.
Context Effective river restoration requires understanding a system’s potential to support desired functions. This can be challenging to discern in the modern landscape, where natural complexity and heterogeneity are often heavily suppressed or modified. Historical analysis is therefore a valuable tool to provide the long-term perspective on riverine patterns, processes, and ecosystem change needed to set appropriate environmental management goals and strategies.
Objective In this study, we reconstructed historical (early 1800s) riparian conditions, river corridor extent, and dry-season flow on the lower Santa Clara River in southern California, with the goal of using this enhanced understanding to inform restoration and management activities.
Method Hundreds of cartographic, textual, and visual accounts were integrated into a GIS database of historical river characteristics.
Results We found that the river was characterized by an extremely broad river corridor and a diverse mosaic of riparian communities that varied by reach, from extensive ([100 ha) willow-cottonwood forests to xeric scrublands. Reach-scale ecological heterogeneity was linked to local variations in dry-season water availability, which was in turn underpinned by regional geophysical controls on groundwater and surface flow.
Conclusions Although human actions have greatly impacted the river’s extent, baseflow hydrology, and riparian habitats, many ecological attributes persist in more limited form, in large part facilitated by these fundamental hydrogeological controls. By drawing on a heretofore untapped dataset of spatially explicit and long-term environmental data, these findings improve our understanding of the river’s historical and current conditions and allow the derivation of reach-differentiated restoration and management opportunities that take advantage of local potential.
Futures Past: Exploring California Landscapes with SFEI. Boom: A Journal of California 4 (3), 24.2014.
Futures Past Exploring California landscapes with the San Francisco Estuary Institute. Boom: The Journal of California . pp 4-27.2014.
A Geographic History of the San Lorenzo Creek Watershed: Landscape Patterns Underlying Human Activities (w / 8.5x11 or 11 x 17 map). SFEI Contribution No. 85. San Francisco Estuary Institute: Oakland, CA.2003.
Historical Ecology and Landscape Change in the Central Laguna de Santa Rosa. SFEI Contribution No. 820. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.2017.
This study synthesizes a diverse array of data to examine the ecological patterns, ecosystem functions, and hydrology that characterized a central portion of the Laguna de Santa Rosa during the mid-19th century, and to analyze landscape changes over the past 150 years. The primary purpose of this study was to help guide restoration actions and other measures aimed at reducing nutrient loads within this portion of the Laguna de Santa Rosa watershed.
Historical Ecology of Lower San Francisquito Creek Phase 1. San Francisco Estuary Institute: Oakland, Ca.2009.
The Historical Ecology of Napa Valley: An Introduction. SFEI Contribution No. 557.2008.
Historical Ecology of the lower Santa Clara River, Ventura River, and Oxnard Plain: an analysis of terrestrial, riverine, and coastal habitats. SFEI Contribution No. 641. SFEI: Oakland.2011.
The Historical Ecology of the Tijuana Estuary & River Valley (Restore America's Estuaries 2018 Conference Presentation).2018.
This talk was given at the 2018 Restore America's Estuary Conference in Long Beach, CA as part of a special session titled "Restoration Perspectives from the Tijuana River National Estuarine Research Reserve." It is based on information from the Tijuana River Valley Historical Ecology Investigation, a report published in 2017.
Though many areas of the binational Tijuana River watershed remain relatively undeveloped, land and water use changes over the past 200 years have resulted in significant ecological impacts, particularly in the more urbanized areas of the lower watershed. Drawing upon a diverse set of historical data, we reconstructed the ecological and hydrogeomorphic conditions of the lower Tijuana River valley prior to major Euro-American modification (ca. 1850) and documented major changes in habitat distribution and physical processes over this time. The river corridor, which was historically dominated by riparian scrub, today instead supports dense stands of riparian forest. The valley bottom surrounding the river corridor, which historically supported extensive seasonal wetlands, has largely been converted to drier habitat types and agricultural uses. The estuary, which historically supported large expanses of salt marsh and mudflat as well as seasonally dry salt flats, has retained much of its former extent and character, but has been altered by increased sediment input and other factors. The new information about the historical landscape presented here is relevant to a number of issues scientists and managers are dealing with today, including the conservation of endangered species, the fate of the valley’s riparian habitats after the recent invasion of invasive shot-hole borer beetles, and the effects on groundwater levels on native plant communities. We will also draw from other historical ecology studies conducted in Southern California to illustrate how the information about the past has been utilized to improve the functioning and resilience of nearby coastal ecosystems.
Presentation recording: available here.
Historical Ecology Reconnaissance for the Lower Salinas River. SFEI Contribution No. 581. San Francisco Estuary Institute: Richmond. p 32.2009.
Historical Evidence of Freshwater Effects on the Plan Form of Tidal Marshlands in the Golden Gate Estuary, University of California: Santa Cruz, p 130 pp.1995.
Historical landscape ecology of an urbanized California valley: wetlands and woodlands in the Santa Clara Valley. Landscape Ecology 103-120.2007.
Historical Wetlands of the Southern California Coast: An Atlas of US Coast Survey T-sheets, 1851-1889. SFEI Contribution No. 586. SFEI: Oakland.2011.
Introduced Tidal Marsh Plants in the San Francisco Estuary: Regional Distribution and Priorities for Control. SFEI Contribution No. 321. San Francisco Estuary Institute: Richmond CA. p 42.1998.
An Introduction to the Historical Ecology of the Sonoma Creek Watershed: a Tool for the Critical Coastal Area Action Plan. San Francisco Estuary Institute.2008.
An Introduction to the Historical Ecology of the Watsonville Sloughs: a Tool for the Critical Coastal Area Action Plan. San Francisco Estuary Institute.2008.
Landscape Patterns and Processes of the McCormack-Williamson Tract and Surrounding Area: A framework for restoring a resilient and functional landscape. SFEI Contribution No. 674. SFEI-ASC: Richmond, CA.2013.
Landscape Resilience Framework: Operationalizing Ecological Resilience at the Landscape Scale. SFEI Contribution No. 752. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.. 2015.
Landscape Scale Management Strategies for Arroyo Mocho and Arroyo Las Positas: Process-Based Approaches for Dynamic, Multi-Benefit Urban Channels. SFEI Contribution No. 714. San Francisco Estuary Institute: Richmond, CA.2014.
Land Use Timeline for Crow Canyon and the San Lorenzo Creek Watershed. SFEI Contribution No. 352. Alameda Countywide Clean Water Program. p 6 pp.2001.
Making Nature's City. SFEI Contribution No. 947. San Francisco Estuary Institute: Richmond, CA.2019.
Mission Bay Historical Ecology Reconnaissance Study: Data Collection Summary (Technical Report). SFEI Contribution No. 777.2016.
The goals of the Mission Bay Historical Ecology Reconnaissance Study were to collect and compile high-priority historical
The goals of the Mission Bay Historical Ecology Reconnaissance Study were to collect and compile high-priority historical
data about the Mission Bay landscape, identify sources that could help to develop a deeper understanding of early
ecological conditions, and to identify future possible research directions based on the available data. This technical
memorandum is intended to document the archives consulted during the reconnaissance study, summarize the collected
and compiled data, and to identify potential next steps. A separate technical presentation to project staff and advisors will
summarize the preliminary findings and questions generated from a review of the historical dataset. Ultimately, this
research is intended to support the San Diego Audubon Society’s Mission Bay Wetlands Conceptual Restoration Plan (CRP)
and the ReWild Mission Bay project.
Mt. Wanda Historical Ecology Investigation. SFEI Contribution No. 743. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 51.2015.
Napa River Sediment TMDL Baseline Study: Geomorphic Processes and Habitat form and function in Soda Creek. SFEI Contribution No. 63. San Francisco Estuary Institute: Oakland, CA.2002.
Napa River Watershed Profile: Past and Present Characteristics with Implications for Future Management of the Changing Napa River Valley. San Francisco Estuary Institute: Richmond, CA. p 172.2012.
Napa Valley Historical Ecology Atlas: Exploring a Hidden Landscape of Transformation and Resilience. UC Press: Berkeley. p 223.2012.
Northern San Diego County Lagoons Historical Ecology Investigation. SFEI Contribution No. 722. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 215.2014.
Novato Creek Baylands Vision: Integrating ecological functions and flood protection within a climate-resilient landscape. SFEI Contribution No. 764.2015.
This report explores the potential for integrating ecological functions into flood risk management on lower Novato Creek. It presents an initial vision of how ecological elements could contribute to flood protection, based on a broad scale analysis and a one day workshop of local and regional experts. The Vision is not intended to be implemented as is, but rather adapted and applied through future projects and analysis. Other actions (e.g., floodwater detention basins) may also need to be implemented in the interim to meet flood risk objectives.
Oak Landscapes in the Recent Past. In Oaks in the Urban Landscape: Selection, Care, and Preservation. . Oaks in the Urban Landscape: Selection, Care, and Preservation. University of California Agriculture and Natural Resources: Richmond, CA.2011.
Petaluma Valley Historical Hydrology and Ecology Study. SFEI Contribution No. 861. San Francisco Estuary Institute: Richmond, CA.2018.
This study reconstructs the historical landscape of the Petaluma River watershed and documents the major landscape changes that have taken place within the watershed over the past two centuries. Prior to Spanish and American settlement of the region, the Petaluma River watershed supported a dynamic and interconnected network of streams, riparian forests, freshwater wetlands, and tidal marshes. These habitats were utilized by a wide range of plant and animal species, including a number of species that are today listed as threatened or endangered such as Ridgway’s Rail, Black Rail, salt marsh harvest mouse, California red-legged frog, Central California Coast steelhead, and soft bird’s beak (CNDDB 2012, SRCD 2015). Agricultural and urban development beginning in the mid-1800s has significantly altered the landscape, degrading habitat for fish and wildlife and contributing to contemporary management challenges such as flooding, pollutant loading, erosion, and sedimentation. While many natural areas and remnant wetlands still exist throughout the watershed—most notably the Petaluma Marsh—their ecological function is in many cases seriously impaired and their long-term fate jeopardized by climate change and other stressors. Multi-benefit wetland restoration strategies, guided by a thorough understanding of landscape history, can simultaneously address a range of chronic management issues while improving the ecological health of the watershed, making it a better place to live for both people and wildlife.
Primary Production in the Delta: Then and Now. San Francisco Estuary and Watershed Science 14 (3).2016.
To evaluate the role of restoration in the recovery of the Delta ecosystem, we need to have clear targets and performance measures that directly assess ecosystem function. Primary production is a crucial ecosystem process, which directly limits the quality and quantity of food available for secondary consumers such as invertebrates and fish. The Delta has a low rate of primary production, but it is unclear whether this was always the case. Recent analyses from the Historical Ecology Team and Delta Landscapes Project provide quantitative comparisons of the areal extent of 14 habitat types in the modern Delta versus the historical Delta (pre-1850). Here we describe an approach for using these metrics of land use change to: (1) produce the first quantitative estimates of how Delta primary production and the relative contributions from five different producer groups have been altered by large-scale drainage and conversion to agriculture; (2) convert these production estimates into a common currency so the contributions of each producer group reflect their food quality and efficiency of transfer to consumers; and (3) use simple models to discover how tidal exchange between marshes and open water influences primary production and its consumption. Application of this approach could inform Delta management in two ways. First, it would provide a quantitative estimate of how large-scale conversion to agriculture has altered the Delta's capacity to produce food for native biota. Second, it would provide restoration practitioners with a new approach—based on ecosystem function—to evaluate the success of restoration projects and gauge the trajectory of ecological recovery in the Delta region.
Relative effects of fluvial processes and historical land use on channel morphology in three sub-basins, Napa River basin, California, USA. IAHS, International Association of Hydrological Sciences 288.2004.