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IEP Publications

The IEP Lead Scientist is happy to receive notice of publications involving the IEP Community and will periodically post a listing of those items received here. 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 here.

The IEP Lead Scientist shares this listing with IEP Directors and Coordinators on a quarterly basis and 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. 

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

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.