IEP Publications

IEP is happy to receive notice of publications involving the IEP Community. IEP Program Support will periodically post a listing of those items received. We welcome refereed literature notices from IEP scientists, studies using IEP-derived data, IEP-sponsored studies, and members of the broader Bay-Delta Estuarine community who would like to display research-related publication notices.

IEP Program Support shares this listing with IEP Directors and Coordinators on a quarterly basis and we would be grateful to receive file copies or locations of open access articles as available. Please contact IEP@wildlife.ca.gov for more information. This is not a comprehensive listing, nor does inclusion infer any endorsement whatsoever of findings or conclusions.

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Bibliography by Year

2023 Bibliography

  • Baerwald, M. R., N. Kwan, C. Pien, G. Auringer, E. W. Carson, D. E. Cocherell, L. Ellison, N. A. Fangue, A. J. Finger, D. A. Gille, H. Hudson, T. C. Hung, T. Sommer, T. Stevenson and B. M. Schreier (2023). "Captive-reared Delta Smelt (Hypomesus transpacificus) exhibit high survival in natural conditions using in situ enclosures." PLoS One 18(5): e0286027.
  • Boyer, K., S. Safran, S. Khanna and M. Patten (2023). "Landscape Transformation and Variation in Invasive Species Abundance Drive Change in Primary Production of Aquatic Vegetation in the Sacramento–San Joaquin Delta." San Francisco Estuary and Watershed Science 20(4).
  • Christman, M., S. Khanna, J. Drexler and M. Young (2023). "Ecology and Ecosystem Impacts of Submerged and Floating Aquatic Vegetation in the Sacramento–San Joaquin Delta." San Francisco Estuary and Watershed Science 20(4).
  • Conrad, J. L., M. Thomas, K. Jetter, J. Madsen, P. Pratt, P. Moran, J. Takekawa and G. Darin (2023). "Invasive Aquatic Vegetation in the Sacramento–San Joaquin Delta and Suisun Marsh: The History and Science of Control Efforts and Recommendations for the Path Forward." San Francisco Estuary and Watershed Science 20(4).
  • Ellison, L., M. M. Rahman, A. J. Finger, M. Sandford, C. H. Hsueh, A. A. Schultz and T. C. Hung (2023). "Size, fecundity and condition factor changes in endangered delta smelt Hypomesus transpacificus over 10 generations in captivity." Aquaculture, Fish and Fisheries.
  • Graham-Bruno, R., M. A. Stickrod and V. T. Parker (2023). "Constraints on Cirsium hydrophilum var. hydrophilum, the Suisun thistle, an endangered tidal wetland species." Wetlands Ecology and Management.
  • Gross, E., R. Holleman, W. Kimmerer, S. Munger, S. Burdick and J. Durand (2023). "Using Age Tracers to Estimate Ecological Rates in a Phytoplankton Model." Water 15(11).
  • Gustine, R. N., C. L. Nickles, C. M. Lee, B. A. Crawford, E. L. Hestir and S. Khanna (2023). "Evaluating Habitat Suitability and Tidal Wetland Restoration Actions With ECOSTRESS." Journal of Geophysical Research: Biogeosciences 128(9).
  • Halpern, B. S., C. Boettiger, M. C. Dietze, J. A. Gephart, P. Gonzalez, N. B. Grimm, P. M. Groffman, J. Gurevitch, S. E. Hobbie, K. J. Komatsu, K. J. Kroeker, H. J. Lahr, D. M. Lodge, C. J. Lortie, J. S. S. Lowndes, F. Micheli, H. P. Possingham, M. H. Ruckelshaus, C. Scarborough, C. L. Wood, G. C. Wu, L. Aoyama, E. E. Arroyo, C. A. Bahlai, E. E. Beller, R. E. Blake, K. S. Bork, T. A. Branch, N. E. M. Brown, J. Brun, E. M. Bruna, L. B. Buckley, J. L. Burnett, M. C. N. Castorani, S. H. Cheng, S. C. Cohen, J. L. Couture, L. B. Crowder, L. E. Dee, A. S. Dias, I. J. Diaz‐Maroto, M. R. Downs, J. C. Dudney, E. C. Ellis, K. A. Emery, J. G. Eurich, B. E. Ferriss, A. Fredston, H. Furukawa, S. A. Gagné, S. R. Garlick, C. J. Garroway, K. M. Gaynor, A. L. González, E. M. Grames, T. Guy‐Haim, E. Hackett, L. M. Hallett, T. K. Harms, D. E. Haulsee, K. J. Haynes, E. L. Hazen, R. M. Jarvis, K. Jones, G. S. Kandlikar, D. W. Kincaid, M. L. Knope, A. Koirala, J. Kolasa, J. S. Kominoski, J. Koricheva, L. T. Lancaster, J. A. Lawlor, H. E. Lowman, F. E. Muller‐Karger, K. E. A. Norman, N. Nourn, C. C. O'Hara, S. X. Ou, J. L. Padilla‐Gamino, P. Pappalardo, R. A. Peek, D. Pelletier, S. Plont, L. C. Ponisio, C. Portales‐Reyes, D. B. Provete, E. J. Raes, C. Ramirez‐Reyes, I. Ramos, S. Record, A. J. Richardson, R. Salguero‐Gómez, E. V. Satterthwaite, C. Schmidt, A. J. Schwartz, C. R. See, B. D. Shea, R. S. Smith, E. R. Sokol, C. T. Solomon, T. Spanbauer, P. V. Stefanoudis, B. W. Sterner, V. Sudbrack, J. D. Tonkin, A. R. Townes, M. Valle, J. A. Walter, K. I. Wheeler, W. R. Wieder, D. R. Williams, M. Winter, B. Winterova, L. C. Woodall, A. S. Wymore and C. Youngflesh (2023). "Priorities for synthesis research in ecology and environmental science." Ecosphere 14(1).
  • Hassrick, J. L., J. Korman, W. J. Kimmerer, E. S. Gross, L. F. Grimaldo, C. Lee and A. A. Schultz (2023). "Freshwater Flow Affects Subsidies of a Copepod (Pseudodiaptomus forbesi) to Low-Salinity Food Webs in the Upper San Francisco Estuary." Estuaries and Coasts 46(2): 450-462.
  • Hestir, E. and I. Dronova (2023). "Remote Sensing of Primary Producers in the Bay-Delta." San Francisco Estuary and Watershed Science 20(4).
  • Huntsman, B. M., M. J. Young, F. V. Feyrer, P. R. Stumpner, L. R. Brown and J. R. Burau (2023). "Hydrodynamics and habitat interact to structure fish communities within terminal channels of a tidal freshwater delta." Ecosphere 14(1).
  • Hutton, P. and S. Roy (2023). "A Note on Conservative Mixing: Implications for Selecting Salinity-Transport Model Constituents in the San Francisco Estuary." San Francisco Estuary and Watershed Science 21(2).
  • Khanna, S., J. W. Gaeta, J. L. Conrad and E. S. Gross (2023). "Multi-year landscape-scale efficacy analysis of fluridone treatment of invasive submerged aquatic vegetation in the Sacramento–San Joaquin Delta." Biological Invasions.
  • Kudela, R., M. Howard, S. Monismith and H. Paerl (2023). "Status, Trends, and Drivers of Harmful Algal Blooms Along the Freshwater-to-Marine Gradient in the San Francisco Bay–Delta System." San Francisco Estuary and Watershed Science 20(4).
  • Lacy, J., E. Dailey and T. Morgan–King (2023). "What Controls Suspended-Sediment Concentration and Export in Flooded Agricultural Tracts in the Sacramento–San Joaquin Delta?" San Francisco Estuary and Watershed Science 21(1).
  • Larsen, L., S. Bashevkin, M. Christman, J. L. Conrad, C. Dahm and J. Thompson (2023). "Ecosystem Services and Disservices of Bay-Delta Primary Producers: How Plants and Algae Affect Ecosystems and Respond to Management of the Estuary and Its Watershed." San Francisco Estuary and Watershed Science 20(4).
  • Lee, C., A. Smith, J. Hassrick, A. Kalmbach, M. Sabal, D. Cox, L. Grimaldo and A. Schultz (2023). "Flow Augmentations Modify an Estuarine Prey Field." San Francisco Estuary and Watershed Science 21(2).
  • Mauduit, F., A. Segarra, J. R. Sherman, M. L. Hladik, L. Wong, T. M. Young, L. S. Lewis, T. C. Hung, N. A. Fangue and R. E. Connon (2023). "Bifenthrin, a Ubiquitous Contaminant, Impairs the Development and Behavior of the Threatened Longfin Smelt during Early Life Stages." Environ Sci Technol 57(26): 9580-9591.
  • Mussen, T., S. Driscoll, M. Cook, J. Nordin, M. Guerin, R. Rachiele, D. Smith, G. Berg and L. Thompson (2023). "Investigating Factors Contributing to Phytoplankton Biomass Declines in the Lower Sacramento River." San Francisco Estuary and Watershed Science 21(1).
  • Pak, N., D. D. Colombano, T. Greiner, J. A. Hobbs, S. M. Carlson and A. Ruhi (2023). "Disentangling abiotic and biotic controls of age‐0 Pacific herring population stability across the San Francisco Estuary." Ecosphere 14(5).
  • Pasparakis, C., T. Lohroff, F. Biefel, D. E. Cocherell, E. W. Carson, T. C. Hung, R. E. Connon, N. A. Fangue and A. E. Todgham (2023). "Effects of turbidity, temperature and predation cue on the stress response of juvenile delta smelt." Conserv Physiol 11(1): coad036.
  • Polansky, L., L. Mitchell and K. B. Newman (2023). "Combining multiple data sources with different biases in state-space models for population dynamics." Ecol Evol 13(6): e10154.
  • Raposa, K. B., A. Woolfolk, C. A. Endris, M. C. Fountain, G. Moore, M. Tyrrell, R. Swerida, S. Lerberg, B. J. Puckett, M. C. Ferner, J. Hollister, D. M. Burdick, L. Champlin, J. R. Krause, D. Haines, A. B. Gray, E. B. Watson and K. Wasson (2023). "Evaluating Thin-Layer Sediment Placement as a Tool for Enhancing Tidal Marsh Resilience: a Coordinated Experiment Across Eight US National Estuarine Research Reserves." Estuaries and Coasts 46(3): 595-615.
  • Schacter, C., C. A. Hartman, M. Herzog, S. Peterson, L. M. Tarjan, Y. Wang, C. Strong, R. Tertes, N. Warnock and J. Ackerman (2023). "Habitat Use by Breeding Waterbirds in Relation to Tidal Marsh Restoration in the San Francisco Bay Estuary." San Francisco Estuary and Watershed Science 21(2).
  • Smith, W. E. and M. L. Nobriga (2023). "A bioenergetics‐based index of habitat suitability: Spatial dynamics of foraging constraints and food limitation for a rare estuarine fish." Transactions of the American Fisheries Society.
  • Smits, A. P., L. C. Loken, E. E. Van Nieuwenhuyse, M. J. Young, P. R. Stumpner, L. E. K. Lenoch, J. R. Burau, R. A. Dahlgren, T. Brown and S. Sadro (2023). "Hydrodynamics structure plankton communities and interactions in a freshwater tidal estuary." Ecological Monographs.
  • Sommer, T., J. L. Conrad and S. Culberson (2023). "Data to Decisions: How to Make Science More Relevant for Management of the San Francisco Estuary." San Francisco Estuary and Watershed Science 21(1).
  • Stein, E. D., C. L. Jerde, E. A. Allan, A. J. Sepulveda, C. L. Abbott, M. R. Baerwald, J. Darling, K. D. Goodwin, R. S. Meyer, M. A. Timmers and P. M. Thielen (2023). "Critical considerations for communicating environmental DNA science." Environmental DNA.
  • Stompe, D. K., P. B. Moyle, K. L. Oken, J. A. Hobbs and J. R. Durand (2023). "A Spatiotemporal History of Key Pelagic Fish Species in the San Francisco Estuary, CA." Estuaries and Coasts.
  • Windham–Myers, L., P. Oikawa, S. Deverel, D. Chapple, J. Drexler and D. Stern (2023). "Carbon Sequestration and Subsidence Reversal in the Sacramento-San Joaquin Delta and Suisun Bay: Management Opportunities for Climate Mitigation and Adaptation." San Francisco Estuary and Watershed Science 20(4).

2022 Bibliography

  • Barros, A., J. A. Hobbs, M. Willmes, C. M. Parker, M. Bisson, N. A. Fangue, A. L. Rypel and L. S. Lewis (2022). "Spatial Heterogeneity in Prey Availability, Feeding Success, and Dietary Selectivity for the Threatened Longfin Smelt." Estuaries and Coasts.
  • Barton, C. M., A. Lee, M. A. Janssen, S. van der Leeuw, G. E. Tucker, C. Porter, J. Greenberg, L. Swantek, K. Frank, M. Chen and H. R. A. Jagers (2022). "How to make models more useful." Proc Natl Acad Sci U S A 119(35): e2202112119.
  • Bashevkin, S. (2022). "A Framework for Evaluating the Effects of Reduced Spatial or Temporal Monitoring Effort." San Francisco Estuary and Watershed Science 20(3).
  • Bashevkin, S. M., R. Hartman, M. Thomas, A. Barros, C. E. Burdi, A. Hennessy, T. Tempel and K. Kayfetz (2022). "Five decades (1972-2020) of zooplankton monitoring in the upper San Francisco Estuary." PLoS One 17(3): e0265402.
  • Bashevkin, S. M. and B. Mahardja (2022). "Seasonally variable relationships between surface water temperature and inflow in the upper San Francisco Estuary." Limnology and Oceanography.
  • Bashevkin, S. M., B. Mahardja and L. R. Brown (2022). "Warming in the upper San Francisco Estuary: Patterns of water temperature change from five decades of data." Limnology and Oceanography.
  • Brennan, C., J. Hassrick, A. Kalmbach, D. Cox, M. Sabal, R. Zeno, L. Grimaldo and S. Acuña (2022). "Estuarine Recruitment of Longfin Smelt (Spirinchus thaleichthys) north of the San Francisco Estuary." San Francisco Estuary and Watershed Science 20(3).
  • Colborne, S. F., L. W. Sheppard, D. R. O'Donnell, D. C. Reuman, J. A. Walter, G. P. Singer, J. T. Kelly, M. J. Thomas and A. L. Rypel (2022). "Intraspecific variation in migration timing of green sturgeon in the Sacramento River system." Ecosphere 13(6).
  • Coleman, L., R. Johnson, F. Cordoleani, C. Phillis and A. Sturrock (2022). "Variation in Juvenile Salmon Growth Opportunities Across a Shifting Habitat Mosaic." San Francisco Estuary and Watershed Science 20(1).
  • Colombano, D. D., S. M. Carlson, J. A. Hobbs and A. Ruhi (2022). "Four decades of climatic fluctuations and fish recruitment stability across a marine-freshwater gradient." Glob Chang Biol 28(17): 5104-5120.
  • Cordoleani, F., E. Holmes, M. Bell-Tilcock, R. C. Johnson and C. Jeffres (2022). "Variability in foodscapes and fish growth across a habitat mosaic: Implications for management and ecosystem restoration." Ecological Indicators 136.
  • Davis, B., J. Adams, L. Lewis, J. Hobbs, N. Ikemiyagi, C. Johnston, L. Mitchell, A. Shakya and B. Schreier (2022). "Wakasagi in the San Francisco Bay Delta Watershed: Comparative Trends in Distribution and Life-History Traits with Native Delta Smelt." San Francisco Estuary and Watershed Science 20(3).
  • Ehrlich, P. R. and A. H. Ehrlich (2022). "Returning to "Normal"? Evolutionary Roots of the Human Prospect." Bioscience 72(8): 778-788.
  • Eschenroeder, J., M. Peterson, M. Hellmair, T. Pilger, D. Demko and A. Fuller (2022). "Counting the Parts to Understand the Whole: Rethinking Monitoring of Steelhead in California’s Central Valley." San Francisco Estuary and Watershed Science 20(1).
  • Gille, D., B. Barney, A. Segarra, M. Baerwald, A. Schreier and R. Connon (2022). "Investigation of Molecular Pathogen Screening Assays for Use in Delta Smelt." San Francisco Estuary and Watershed Science 20(1).
  • Glibert, P. M., F. P. Wilkerson, R. C. Dugdale and A. E. Parker (2022). "Ecosystem Recovery in Progress? Initial Nutrient and Phytoplankton Response to Nitrogen Reduction from Sewage Treatment Upgrade in the San Francisco Bay Delta." Nitrogen 3(4): 569-591.
  • Gross, E., W. Kimmerer, J. Korman, L. Lewis, S. Burdick and L. Grimaldo (2022). "Hatching distribution, abundance, and losses to freshwater diversions of longfin smelt inferred using hydrodynamic and particle-tracking models." Marine Ecology Progress Series 700: 179-196.
  • Halverson, G. H., C. M. Lee, E. L. Hestir, G. C. Hulley, K. Cawse-Nicholson, S. J. Hook, B. A. Bergamaschi, S. Acuna, N. B. Tufillaro, R. G. Radocinski, G. Rivera and T. R. Sommer (2022). "Decline in Thermal Habitat Conditions for the Endangered Delta Smelt as Seen from Landsat Satellites (1985-2019)." Environ Sci Technol 56(1): 185-193.
  • Hamilton, S. A. and D. D. Murphy (2022). "Identifying Environmental Factors Limiting Recovery of an Imperiled Estuarine Fish." Frontiers in Ecology and Evolution 10.
  • Hartman, R., A. Barros, M. Avila, C. Bowles, D. Ellis, T. Tempel and S. Sherman (2022). "I’m not that Shallow – Different Zooplankton Abundance but Similar Community Composition Between Habitats in the San Francisco Estuary." San Francisco Estuary and Watershed Science 20(3).
  • Hauer, F. R., M. S. Lorang and T. Gonser (2022). "Remote Sensing to Characterize River Floodplain Structure and Function." Remote Sensing 14(5).
  • Hendrix, A. N., E. Fleishman, M. W. Zillig and E. D. Jennings (2022). "Relations Between Abiotic and Biotic Environmental Variables and Occupancy of Delta Smelt (Hypomesus transpacificus) in Autumn." Estuaries and Coasts.
  • Herbold, B., E. Bush, G. Castillo, D. Colombano, R. Hartman, P. Lehman, B. Mahardja and T. Sommer (2022). "Climate Change Impacts on San Francisco Estuary Aquatic Ecosystems: A Review." San Francisco Estuary and Watershed Science 20(2).
  • Howard, M. D. A., J. Smith, D. A. Caron, R. M. Kudela, K. Loftin, K. Hayashi, R. Fadness, S. Fricke, J. Kann, M. Roethler, A. Tatters and S. Theroux (2022). "Integrative monitoring strategy for marine and freshwater harmful algal blooms and toxins across the freshwater-to-marine continuum." Integr Environ Assess Manag.
  • Hung, T. C., L. Ellison, T. Stevenson, M. Sandford, A. A. Schultz and A. R. Eads (2022). "Early Weaning in Endangered Delta Smelt: Effect of Weaning Time on Growth and Survival." North American Journal of Aquaculture.
  • Hung, T. C., B. G. Hammock, M. Sandford, M. Stillway, M. Park, J. C. Lindberg and S. J. Teh (2022). "Temperature and salinity preferences of endangered Delta Smelt (Hypomesus transpacificus, Actinopterygii, Osmeridae)." Sci Rep 12(1): 16558.
  • Huntsman, B., B. Mahardja and S. Bashevkin (2022). "Relative Bias in Catch Among Long-Term Fish Monitoring Surveys Within the San Francisco Estuary." San Francisco Estuary and Watershed Science 20(1).
  • Keeley, A. T. H., A. K. Fremier, P. A. L. Goertler, P. R. Huber, A. M. Sturrock, S. M. Bashevkin, B. A. Barbaree, J. L. Grenier, T. E. Dilts, M. Gogol-Prokurat, D. D. Colombano, E. E. Bush, A. Laws, J. A. Gallo, M. Kondolf and A. T. Stahl (2022). "Governing Ecological Connectivity in Cross-Scale Dependent Systems." BioScience.
  • Kimmerer, W. and E. Gross (2022). "Population Abundance and Diversion Losses in a Threatened Estuarine Pelagic Fish." Estuaries and Coasts.
  • Kurobe, T., B. G. Hammock, L. J. Damon, T. C. Hung, S. Acuna, A. A. Schultz and S. J. Teh (2022). "Reproductive strategy of Delta Smelt Hypomesus transpacificus and impacts of drought on reproductive performance." PLoS One 17(3): e0264731.
  • Lehman, P. (2022). "The increase of cyanobacteria and benthic diatoms over 43 years in upper San Francisco Estuary, California." Estuarine, Coastal and Shelf Science 275.
  • Lojkovic Burris, Z. P., R. D. Baxter and C. E. Burdi (2022). "Larval and juvenile Longfin Smelt diets as a function of fish size and prey density in the San Francisco Estuary." California Fish and Wildlife Journal 108(2).
  • Loken, L. C., S. Sadro, L. E. K. Lenoch, P. R. Stumpner, R. A. Dahlgren, J. R. Burau and E. E. Van Nieuwenhuyse (2022). "Whole-Ecosystem Experiment Illustrates Short Timescale Hydrodynamic, Light, and Nutrient Control of Primary Production in a Terminal Slough." Estuaries and Coasts.
  • Mahardja, B., S. M. Bashevkin, C. Pien, M. Nelson, B. E. Davis and R. Hartman (2022). "Escape from the heat: thermal stratification in a well-mixed estuary and implications for fish species facing a changing climate." Hydrobiologia 849(13): 2895-2918.
  • Moyle, P. B. and M. A. Campbell (2022). "Cryptic Species of Freshwater Sculpin (Cottidae: Cottus) in California, USA." Zootaxa 5154(5): 501-527.
  • Nagarajan, R. P., M. Bedwell, A. E. Holmes, T. Sanches, S. Acuña, M. Baerwald, M. A. Barnes, S. Blankenship, R. E. Connon, K. Deiner, D. Gille, C. S. Goldberg, M. E. Hunter, C. L. Jerde, G. Luikart, R. S. Meyer, A. Watts and A. Schreier (2022). "Environmental DNA Methods for Ecological Monitoring and Biodiversity Assessment in Estuaries." Estuaries and Coasts.
  • Nelson, P., M. Baerwald, O. Burgess, E. Bush, A. Collins, F. Cordoleani, H. DeBey, D. Gille, P. Goertler, B. Harvey, R. Johnson, J. Kindopp, E. Meyers, J. Notch, C. Phillis, G. Singer and T. Sommer (2022). "Considerations for the Development of a Juvenile Production Estimate for Central Valley Spring-Run Chinook Salmon." San Francisco Estuary and Watershed Science 20(2).
  • Pathak, D., M. Hutchins, L. E. Brown, M. Loewenthal, P. Scarlett, L. Armstrong, D. Nicholls, M. Bowes, F. Edwards and G. Old (2022). "High‐resolution water‐quality and ecosystem‐metabolism modeling in lowland rivers." Limnology and Oceanography 67(6): 1313-1327.
  • Rachid, N., N. Issam, B. Abdelkrim, A. Abdelhamid and H. Amina (2022). "Pond Energy Dynamics, Evaporation Rate and Ensemble Deep Learning Evaporation Prediction: Case Study of the Thomas Pond—Brenne Natural Regional Park (France)." Water 14(6).
  • Richardson, C., J. Fackrell, T. E. C. Kraus, M. Young and A. Paytan (2022). "Nutrient and Trace Element Contributions from Drained Islands in the Sacramento–San Joaquin Delta, California." San Francisco Estuary and Watershed Science 20(2).
  • Rollwagen-Bollens, G., K. A. Connelly, S. M. Bollens, J. Zimmerman and A. Coker (2022). "Nutrient Control of Phytoplankton Abundance and Biomass, and Microplankton Assemblage Structure in the Lower Columbia River (Vancouver, Washington, USA)." Water 14(10).
  • Sellheim, K., M. Willmes, L. S. Lewis, J. Sweeney, J. Merz and J. A. Hobbs (2022). "Diversity in Habitat Use by White Sturgeon Revealed Using Fin Ray Geochemistry." Frontiers in Marine Science 9.
  • Sturrock, A. M., M. Ogaz, K. Neal, N. J. Corline, R. Peek, D. Myers, S. Schluep, M. Levinson, R. C. Johnson and C. A. Jeffres (2022). "Floodplain trophic subsidies in a modified river network: managed foodscapes of the future?" Landscape Ecology.
  • Thomas, M. J., A. L. Rypel, G. P. Singer, A. P. Klimley, M. D. Pagel, E. D. Chapman and N. A. Fangue (2022). "Movement patterns of juvenile green sturgeon (Acipenser medirostris) in the San Francisco Bay Estuary." Environmental Biology of Fishes.
  • Tillotson, M., J. Hassrick, A. Collins and C. Phillis (2022). "Machine Learning Forecasts to Reduce Risk of Entrainment Loss of Endangered Salmonids at Large-Scale Water Diversions in the Sacramento–San Joaquin Delta, California." San Francisco Estuary and Watershed Science 20(2).
  • Wulff, M., F. Feyrer and M. Young (2022). "Gill Net Selectivity for Fifteen Fish Species of the Upper San Francisco Estuary." San Francisco Estuary and Watershed Science 20(2).
  • Yelton, R., A. M. Slaughter and W. J. Kimmerer (2022). "Diel Behaviors of Zooplankton Interact with Tidal Patterns to Drive Spatial Subsidies in the Northern San Francisco Estuary." Estuaries and Coasts.
  • Young, M., F. Feyrer, C. Smith and D. Valentine (2022). "Habitat-Specific Foraging by Striped Bass (Morone saxatilis) in the San Francisco Estuary, California: Implications for Tidal Restoration." San Francisco Estuary and Watershed Science 20(3).

Summer/Fall 2021 Bibliography

  • Aha, N. M., et al. (2021). "Managed Wetlands Can Benefit Juvenile Chinook Salmon in a Tidal Marsh." Estuaries and Coasts 44(5): 1440-1453.
  • Blackburn, S. E., et al. (2019). "Population Dynamics and Evaluation of Management Scenarios for White Sturgeon in the Sacramento–San Joaquin River Basin." North American Journal of Fisheries Management 39(5): 896-912.
  • Brandl, S., et al. (2021). "Enumerating Predation on Chinook Salmon, Delta Smelt and other San Francisco Estuary Fishes using Genetics." North American Journal of Fisheries Management.
  • Ciotti, D. C., et al. (2021). "Design Criteria for Process-Based Restoration of Fluvial Systems." Bioscience 71(8): 831-845.
  • Colombano, D. D., et al. (2021). "Complex Tidal Marsh Dynamics Structure Fish Foraging Patterns in the San Francisco Estuary." Estuaries and Coasts.
  • Colombano, D. D., et al. (2021). "Climate Change Implications for Tidal Marshes and Food Web Linkages to Estuarine and Coastal Nekton." Estuaries and Coasts.
  • Day, J. W., et al. (2021). "Diminishing Opportunities for Sustainability of Coastal Cities in the Anthropocene: A Review." Frontiers in Environmental Science 9.
  • Dierssen, H. M., et al. (2021). "Living up to the Hype of Hyperspectral Aquatic Remote Sensing: Science, Resources and Outlook." Frontiers in Environmental Science 9.
  • Drexler, J. Z., et al. (2021). "Carbon storage and sediment trapping by Egeria densa Planch., a globally invasive, freshwater macrophyte." Science of the Total Environment 755(Pt 1): 142602.
  • Fangue, N. A., et al. (2021). "Juvenile Chinook salmon use of sandbar willows in a large-scale, simulated riparian floodplain: microhabitat and energetics." Environmental Biology of Fishes 104(7): 867-879.
  • Finger, A. J., et al. (2018). "A conservation hatchery population of Delta Smelt shows evidence of genetic adaptation to captivity after 9 generations." J Hered.
  • Ghalambor, C., et al. (2020). "Ecological Effects of Climate-Driven Salinity Variation in the San Francisco Estuary: Can We Anticipate and Manage the Coming Changes?" San Francisco Estuary and Watershed Science 19(2).
  • Huntsman, B., et al. (2020). "Use of the SmeltCam as an Efficient Fish Sampling Alternative Within the San Francisco Estuary." San Francisco Estuary and Watershed Science 19(2).
  • Huntsman, B. M., et al. (2021). "Recruitment dynamics of non-native largemouth bass within the Sacramento–San Joaquin Delta." Canadian Journal of Fisheries and Aquatic Sciences 78(5): 505-521.
  • Lee, C. M., et al. (2021). "Monitoring Turbidity in San Francisco Estuary and Sacramento–San Joaquin Delta Using Satellite Remote Sensing." JAWRA Journal of the American Water Resources Association.
  • Lehman, P. W., et al. (2021). "Covariance of Phytoplankton, Bacteria, and Zooplankton Communities Within Microcystis Blooms in San Francisco Estuary." Front Microbiol 12: 632264.
  • Liu, H., et al. (2021). "A hybrid neural network model for marine dissolved oxygen concentrations time-series forecasting based on multi-factor analysis and a multi-model ensemble." Engineering.
  • Mahardja, B., et al. (2021). "Leveraging Delta Smelt Monitoring for Detecting Juvenile Chinook Salmon in the San Francisco Estuary." San Francisco Estuary and Watershed Science 19(1).
  • McCord, S. E., et al. (2021). "Provoking a Cultural Shift in Data Quality." Bioscience 71(6): 647-657.
  • Merz, J. E., et al. (2021). "A New Method for Standardizing Inland Fish Community Surveys: Characterizing Habitat Associated with Small-Bodied Fish Species, Abundance, and Size Distributions in a Highly Modified Estuary." Frontiers in Environmental Science 9.
  • Mitchell, L. and R. Baxter (2020). "Examining Retention-at-Length of Pelagic Fishes Caught in the Fall Midwater Trawl Survey." San Francisco Estuary and Watershed Science 19(2).
  • Munsch, S. H., et al. (2020). "Science for integrative management of a diadromous fish stock: interdependencies of fisheries, flow, and habitat restoration." Canadian Journal of Fisheries and Aquatic Sciences 77(9): 1487-1504.
  • Nobriga, M. L., et al. (2021). "Coldwater fish in a warm water world: Implications for predation of salmon smolts during estuary transit." Ecol Evol 11(15): 10381-10395.
  • Parker, A. E. and P. W. Lehman (2021). "Powering Life in the Water: Phytoplankton in the San Francisco Estuary." Frontiers for Young Minds 9.
  • Patton, O., et al. (2020). "Estuarine Habitat Use by White Sturgeon (Acipenser transmontanus)." San Francisco Estuary and Watershed Science 18(4).
  • Romine, J., et al. (2020). "Effects of Tidally Varying River Flow on Entrainment of Juvenile Salmon into Sutter and Steamboat Sloughs." San Francisco Estuary and Watershed Science 19(2).
  • Smith, W. E., et al. (2021). "Disentangling risks to an endangered fish: using a state-space life cycle model to separate natural mortality from anthropogenic losses." Canadian Journal of Fisheries and Aquatic Sciences 78(8): 1008-1029.
  • Stumpner, P. R., et al. (2020). "A Lagrangian-to-Eulerian Metric to Identify Estuarine Pelagic Habitats." Estuaries and Coasts.
  • Tempel, T. L., et al. (2021). "The value of long-term monitoring of the San Francisco Estuary for Delta Smelt and Longfin Smelt." California Fish and Wildlife Journal(CESA Special Issue): 148-171.
  • Triana-Garcia, P. A., et al. (2021). "Gross morphology, histology, and ultrastructure of the olfactory rosette of a critically endangered indicator species, the Delta Smelt, Hypomesus transpacificus." J Comp Physiol A Neuroethol Sens Neural Behav Physiol.
  • Valentine, D. A., et al. (2020). "Sacramento Pikeminnow Migration Record." Journal of Fish and Wildlife Management 11(2): 588-592.
  • Work, P. A., et al. (2020). "Trapping of Suspended Sediment by Submerged Aquatic Vegetation in a Tidal Freshwater Region: Field Observations and Long-Term Trends." Estuaries and Coasts.
  • Young, M. J., et al. (2020). "Hydrodynamics drive pelagic communities and food web structure in a tidal environment." International Review of Hydrobiology 106(2): 69-85.

Summer/Fall 2020 Bibliography

  • Archdeacon, T. P. and J. K. Reale (2020). "No quarter: Lack of refuge during flow intermittency results in catastrophic mortality of an imperiled minnow." Freshwater Biology.
  • Bogard, M. J., B. A. Bergamaschi, D. E. Butman, F. Anderson, S. H. Knox and L. Windham‐Myers (2020). "Hydrologic Export Is a Major Component of Coastal Wetland Carbon Budgets." Global Biogeochemical Cycles 34(8).
  • Cloern, J. E., T. S. Schraga, E. Nejad and C. Martin (2020). "Nutrient Status of San Francisco Bay and Its Management Implications." Estuaries and Coasts 43(6): 1299-1317.
  • Connelly, K. A., G. Rollwagen-Bollens and S. M. Bollens (2020). "Seasonal and longitudinal variability of zooplankton assemblages along a river-dominated estuarine gradient." Estuarine, Coastal and Shelf Science 245.
  • Delaney, C. J., R. K. Hartman, J. Mendoza, M. Dettinger, L. Delle Monache, J. Jasperse, F. M. Ralph, C. Talbot, J. Brown, D. Reynolds and S. Evett (2020). "Forecast Informed Reservoir Operations Using Ensemble Streamflow Predictions for a Multipurpose Reservoir in Northern California." Water Resources Research 56(9).
  • Drexler, J. Z., M. J. Davis, I. Woo and S. De La Cruz (2020). "Carbon Sources in the Sediments of a Restoring vs. Historically Unaltered Salt Marsh." Estuaries and Coasts 43(6): 1345-1360.
  • Gilby, B. L., M. P. Weinstein, R. Baker, J. Cebrian, S. B. Alford, A. Chelsky, D. Colombano, R. M. Connolly, C. A. Currin, I. C. Feller, A. Frank, J. A. Goeke, L. A. Goodridge Gaines, F. E. Hardcastle, C. J. Henderson, C. W. Martin, A. E. McDonald, B. H. Morrison, A. D. Olds, J. S. Rehage, N. J. Waltham and S. L. Ziegler (2020). "Human Actions Alter Tidal Marsh Seascapes and the Provision of Ecosystem Services." Estuaries and Coasts.
  • Grimaldo, L., J. Burns, R. E. Miller, A. Kalmbach, A. Smith, J. Hassrick and C. Brennan (2020). "Forage Fish Larvae Distribution and Habitat Use During Contrasting Years of Low and High Freshwater Flow in the San Francisco Estuary." San Francisco Estuary and Watershed Science 18(3).
  • Hammock, B. G., W. F. Ramirez-Duarte, P. A. Triana Garcia, A. A. Schultz, L. I. Avendano, T. C. Hung, J. R. White, Y. T. Bong and S. J. Teh (2020). "The health and condition responses of Delta Smelt to fasting: A time series experiment." PLoS One 15(9): e0239358.
  • Hatchett, B. J., Q. Cao, P. B. Dawson, C. J. Ellis, C. W. Hecht, B. Kawzenuk, J. T. Lancaster, T. C. Osborne, A. M. Wilson, M. L. Anderson, M. D. Dettinger, J. F. Kalansky, M. L. Kaplan, D. P. Lettenmaier, N. S. Oakley, F. M. Ralph, D. W. Reynolds, A. B. White, M. Sierks and E. Sumargo (2020). "Observations of an Extreme Atmospheric River Storm With a Diverse Sensor Network." Earth and Space Science 7(8).
  • Jahn, A. and W. Kier (2020). "Reconsidering the Estimation of Salmon Mortality Caused by the State and Federal Water Export Facilities in the Sacramento–San Joaquin Delta, San Francisco Estuary." San Francisco Estuary and Watershed Science 18(3).
  • Lehman, B., R. C. Johnson, M. Adkison, O. T. Burgess, R. E. Connon, N. A. Fangue, J. S. Foott, S. L. Hallett, B. Martinez–López, K. M. Miller, M. K. Purcell, N. A. Som, P. Valdes–Donoso and A. A. Collins (2020). "Disease in Central Valley Salmon: Status and Lessons from Other Systems." San Francisco Estuary and Watershed Science 18(3).
  • Lucas, L. V. and E. Deleersnijder (2020). "Timescale Methods for Simplifying, Understanding and Modeling Biophysical and Water Quality Processes in Coastal Aquatic Ecosystems: A Review." Water 12(10).
  • Major, K. M., B. M. DeCourten, J. Li, M. Britton, M. L. Settles, A. C. Mehinto, R. E. Connon and S. M. Brander (2020). "Early Life Exposure to Environmentally Relevant Levels of Endocrine Disruptors Drive Multigenerational and Transgenerational Epigenetic Changes in a Fish Model." Frontiers in Marine Science 7.
  • Martin, B. T., P. N. Dudley, N. S. Kashef, D. M. Stafford, W. J. Reeder, D. Tonina, A. M. Del Rio, J. Scott Foott and E. M. Danner (2020). "The biophysical basis of thermal tolerance in fish eggs." Proc Biol Sci 287(1937): 20201550.
  • Matica, Z. (2020). "Considerations for Multi-Species Fish Passage in California: A Literature Review." San Francisco Estuary and Watershed Science 18(3).
  • Mundy, P. C., M. F. Carte, S. M. Brander, T. C. Hung, N. Fangue and R. E. Connon (2020). "Bifenthrin exposure causes hyperactivity in early larval stages of an endangered fish species at concentrations that occur during their hatching season." Aquat Toxicol 228: 105611.
  • Nielsen, M. C. and S. C. Jiang (2020). "Can cyanotoxins penetrate human skin during water recreation to cause negative health effects?" Harmful Algae 98.
  • Ouellet, V., A. St-Hilaire, S. J. Dugdale, D. M. Hannah, S. Krause and S. Proulx-Ouellet (2020). "River temperature research and practice: Recent challenges and emerging opportunities for managing thermal habitat conditions in stream ecosystems." Sci Total Environ 736: 139679.
  • Sommer, T. (2020). "How to Respond? An Introduction to Current Bay–Delta Natural Resources Management Options." San Francisco Estuary and Watershed Science 18(3).
  • Sommer, T., B. Schreier, J. L. Conrad, L. Takata, B. Serup, R. Titus, C. Jeffres, E. Holmes and J. Katz (2020). "Farm to Fish: Lessons from a Multi-Year Study on Agricultural Floodplain Habitat." San Francisco Estuary and Watershed Science 18(3).
  • Stern, M. A., L. E. Flint, A. L. Flint, N. Knowles and S. A. Wright (2020). "The Future of Sediment Transport and Streamflow Under a Changing Climate and the Implications for Long‐Term Resilience of the San Francisco Bay‐Delta." Water Resources Research 56(9).
  • Stewart, A. R., F. Feyrer and R. C. Johnson (2020). "Resolving selenium exposure risk: Spatial, temporal, and tissue-specific variability of an endemic fish in a large, dynamic estuary." Science of The Total Environment 707.
  • Wang, Z., F. Chai, R. Dugdale, Q. Liu, H. Xue, F. Wilkerson, Y. Chao, Y. Zhang and H. Zhang (2020). "The interannual variabilities of chlorophyll and nutrients in San Francisco Bay: a modeling study." Ocean Dynamics 70(8): 1169-1186.
  • Work, P. A., M. Downing-Kunz and J. Z. Drexler (2020). "Trapping of Suspended Sediment by Submerged Aquatic Vegetation in a Tidal Freshwater Region: Field Observations and Long-Term Trends." Estuaries and Coasts.
  • Zeug, S. C., M. Beakes, J. Wiesenfeld, M. Greenwood, L. Grimaldo, J. Hassrick, A. Collins, S. Acuña and M. Johnston (2020). "Experimental Quantification of Piscivore Density and Habitat Effects on Survival of Juvenile Chinook Salmon in a Tidal Freshwater Estuary." Estuaries and Coasts.