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Cohen, A. N. 1997. Have claw, will travel. Aquatic Nuisance Species Digest 2, 1, 16-17. . SFEI Contribution No. 200.
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Cohen, A. N. 1994. The hidden costs of California's water. In Life on the Edge: A Resource Guide to California's Endangered Wildlife. Life on the Edge: A Resource Guide to California's Endangered Wildlife. Biosystems Books: Santa Cruz, CA. pp 288-302.
Cohen, A. N. 2002. The highly invaded ecosystem of San Francisco Bay. Cawthron Institute, Nelson, New Zealand.
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Baumgarten, S.; Grossinger, R. M.; Beller, E. E.; Trowbridge, W.; Askevold, R. A. 2017. 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.

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.

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Program, H. Ecology. 2012. Historical Ecology of the McCormack-Williamson Tract: A Landscape Framework for Restoration. SFEI Contribution No. 674. Aquatic Science Center / San Francisco Estuary: Richmond, CA.
Safran, S. M.; Baumgarten, S. A.; Beller, E. E.; Bram, D. L.; Crooks, J. A.; Dark, S. J.; Grossinger, R. M.; Longcore, T. R.; Lorda, J.; Stein, E. D. 2018. The Historical Ecology of the Tijuana Estuary & River Valley (Restore America's Estuaries 2018 Conference Presentation).

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.

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Beller, E. E.; Grossinger, R. M.; Whipple, A. 2009. Historical Ecology Reconnaissance for the Lower Salinas River. SFEI Contribution No. 581. San Francisco Estuary Institute: Richmond. p 32.
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2005. Historical Landscape Analysis (full title to come from Robin). SFEI Contribution No. 396. San Francisco Estuary Institute.
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Dusterhoff, S. D.; Doehring, C.; Shusterman, G. 2014. How Creeks Meet the Bay: Changing Interfaces (Interactive web map).

San Francisco Bay’s connections to local creeks are integral to its health. These fluvial-tidal (F-T) interfaces are the points of delivery for freshwater, sediment, contaminants, and nutrients. The ways in which the F-T interface has changed affect flooding dynamics, ecosystem functioning, and resilience to a changing climate. As the historical baylands have been altered, the majority of contemporary F-T interface types have changed leading to additional F-T interface types within the present-day landscape. Illustrations of each F-T interface type and methods for classification are available here

This project is part of Flood Control 2.0. For further information please visit this project page

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David, N.; Oros, D. R. 2002. Identification and evaluation of unidentified organic contaminants in the San Francisco Estuary. SFEI Contribution No. 45. San Francisco Estuary Institute: Oakland, CA.
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Cohen, A. N.; Nordby, J. C.; Beissinger, S. R. 2002. The impact of an invasive Atlantic cordgrass (Spartina alterniflora) on San Francisco Bay Song Sparrow populations: direct and indirect influence. In Terrestrial Vertebrates of Tidal Marshes: Evolution, Ecology and Conservation. Terrestrial Vertebrates of Tidal Marshes: Evolution, Ecology and Conservation. Silver Spring, MD.
Cohen, A. N. 2001. Impacts from the Asian clam Potamocorbula amurensis. In National Management Plan. National Management Plan. National Invasive Species Council: Washington DC.
Cohen, A. N. 1994. Impacts of invasions in the Bay and Delta. Abs. Proc. 75th Ann. Mtg., Pac. Div. Amer. Assoc. Adv. Sci..
Fiorillo, J. T. 1994. Implementation Manual for the San Leandro Creek Watershed Awareness Program, 1993-1994. SFEI Contribution No. 177. San Francisco Estuary Institute: Richmond, Ca. p 75.
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Hatje, V.; Bruland, K. W.; A. Flegal, R. 2016. Increases in Anthropogenic Gadolinium Anomalies and Rare Earth Element Concentrations in San Francisco Bay over a 20 Year Record. Environ. Sci. Technol. 50 (8).

We evaluated both the spatial distribution of gadolinium (Gd) and other rare earth elements (REE) in surface waters collected in a transect of San Francisco Bay (SFB) and their temporal variations within the Bay over two decades. The REE were preconcentrated using the NOBIAS PA-1 resin prior to analysis by high-resolution inductively coupled plasma mass spectrometry. Measurements revealed a temporal increase in the Gd anomaly in SFB from the early 1990s to the present. The highest Gd anomalies were observed in the southern reach of SFB, which is surrounded by several hospitals and research centers that use Gd-based contrast agents for magnetic resonance imaging. Recent increases in that usage presumably contributed to the order of magnitude increase in anthropogenic Gd concentrations in SFB, from 8.27 to 112 pmol kg–1 over the past two decades, and reach the northeast Pacific coastal waters. These measurements (i) show that “exotic” trace elements used in new high-tech applications, such as Gd, are emerging contaminants in San Francisco Bay and that anthropogenic Gd concentrations increased substantially over a 20 year period; (ii) substantiate proposals that REE may be used as tracers of wastewater discharges and hydrological processes; and (iii) suggest that new public policies and the development of more effective treatment technologies may be necessary to control sources and minimize future contamination by REE that are critical for the development of new technologies, which now overwhelm natural REE anomalies.

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Cohen, A. N.; Carlton, J. T. 2007. Introduced Marine and Estuarine Invertebrates. In The Light & Smith Manual: Intertidal Invertebrates of the California and Oregon Coast. Carlton, J. T., Ed.. The Light & Smith Manual: Intertidal Invertebrates of the California and Oregon Coast. University of California Press: Berkeley, Ca.
Cohen, A. N. 1995. Introduced Species. Prepared for: California's Ocean Resources: An Agenda for the Future, California Resources Agency: Sacramento, CA.
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Cohen, A. N.; Schaeffer, K.; McGourty, K.; Cosentino-Manning, N.; De La Cruz, S. E. Wainwri; Elliot, M.; Allen, S. 2007. Introduction for Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. In Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. NOAA National Marine Fisheries Service. p 35.
Hale, T.; Grosso, C. 2016. An Introduction to EcoAtlas: Applied Aquatic Science. San Francisco Estuary Institute: Richmond, CA. p 16 pages.

This memo was developed by SFEI to introduce the EcoAtlas tools, their intended (target) user community, and the short- and long-term intended applications. 

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