Alpine, A.E., and J.E. Cloern. 1992. Trophic interactions and direct physical effects control phytoplankton biomass and production in an estuary. Limnology and Oceanography 37 (5): 946–955.
Google Scholar
Barbier, E.B., S.D. Hacker, C. Kennedy, E.W. Koch, A.C. Stier, and B.R. Silliman. 2011. The value of estuarine and coastal ecosystem services. Ecological Monographs 81 (2): 169–193.
Google Scholar
Bates, D., M. Mächler, B. Bolker, and S. Walker. 2015. Fitting linear mixed effects models using lme4. Journal of Statistical Software 67 (1): 1–48.
Google Scholar
Baumgartner, L., B. Zampatti, M. Jones, I. Stuart, and M. Mallen-Cooper. 2014. Fish passage in the Murray-Darling Basin, Australia: Not just an upstream battle. Ecological Management & Restoration 15: 28–39.
Google Scholar
Bolker, B.M. 2008. Ecological models and data in R. Princeton University Press.
Borja, Á., D.M. Dauer, M. Elliott, and C.A. Simenstad. 2010. Medium-and long-term recovery of estuarine and coastal ecosystems: Patterns, rates and restoration effectiveness. Estuaries and Coasts 33 (6): 1249–1260.
Google Scholar
Bottom, D.L., K.K. Jones, T.J. Cornwell, A. Gray, and C.A. Simenstad. 2005. Patterns of Chinook salmon migration and residency in the Salmon River estuary (Oregon). Estuarine, Coastal and Shelf Science 64 (1): 79–93.
Google Scholar
Brophy, L.S., C.M. Greene, V.C. Hare, B. Holycross, A. Lanier, W.N. Heady, K. O’Connor, H. Imaki, T. Haddad, and R. Davis. 2019. Insights into estuary habitat loss in the western United States using a new method for mapping maximum extent of tidal wetlands. PLoS One 14 (8): e0218558. https://doi.org/10.1371/journal.pone.0218558.
CAS
Article
Google Scholar
Burnham, K.P., D.R. Anderson, and K.P. Huyvaert. 2011. AIC model selection and multimodel inference in behavioral ecology: Some background, observations, and comparisons. Behavioral Ecology and Sociobiology 65 (1): 23–35.
Google Scholar
Carlson, S.M., and W.H. Satterthwaite. 2011. Weakened portfolio effect in a collapsed salmon population complex. Canadian Journal of Fisheries and Aquatic Sciences 68 (9): 1579–1589.
Google Scholar
Colombano, D.D., A.D. Manfree, T.A. O’Rear, J.R. Durand, and P.B. Moyle. 2020. Estuarine-terrestrial habitat gradients enhance nursery function for resident and transient fishes in the San Francisco Estuary. Marine Ecology Progress Series 637: 141–157.
Google Scholar
Corline, N.J., T. Sommer, C.A. Jeffres, and J. Katz. 2017. Zooplankton ecology and trophic resources for rearing native fish on an agricultural floodplain in the Yolo bypass California, USA. Wetlands Ecology and Management 25 (5): 533–545.
Google Scholar
Costanza, R., R. d'Arge, R. De Groot, S. Farber, M. Grasso, B. Hannon, K. Limburg, et al. 1997. The value of the world’s ecosystem services and natural capital. Nature 387 (6630): 253–260.
CAS
Google Scholar
David, A.T., C.A. Simenstad, J.R. Cordell, J.D. Toft, C.S. Ellings, A. Gray, and H.B. Berge. 2016. Wetland loss, juvenile salmon foraging performance, and density dependence in Pacific Northwest estuaries. Estuaries and Coasts 39 (3): 767–780.
Google Scholar
Dumont, H.J., I. Van de Velde, and S. Dumont. 1975. The dry weight estimate of biomass in a selection of Cladocera, Copepoda and Rotifera from the plankton, periphyton and benthos of continental waters. Oecologia 19 (1): 75–97.
Google Scholar
Durand, J.R. 2017. Evaluating the aquatic habitat potential of flooded polders in the Sacramento-San Joaquin Delta. San Francisco Estuary and Watershed Science 15 (4). https://doi.org/10.15447/sfews.2017v15iss4art4.
Edgar, G.J., N.S. Barrett, D.J. Graddon, and P.R. Last. 2000. The conservation significance of estuaries: A classification of Tasmanian estuaries using ecological, physical and demographic attributes as a case study. Biological Conservation 92 (3): 383–397.
Google Scholar
Enright, C., S.D. Culberson, and J.R. Burau. 2013. Broad timescale forcing and geomorphic mediation of tidal marsh flow and temperature dynamics. Estuaries and Coasts 36 (6): 1319–1339.
Google Scholar
Forrester, G.E., B.I. Fredericks, D. Gerdeman, B. Evans, M.A. Steele, K. Zayed, L.E. Schweitzer, I.H. Suffet, R.R. Vance, and R.F. Ambrose. 2003. Growth of estuarine fish is associated with the combined concentration of sediment contaminants and shows no adaptation or acclimation to past conditions. Marine Environmental Research 56 (3): 423–442.
CAS
Google Scholar
Gedan, K.B., B.R. Silliman, and M.D. Bertness. 2009. Centuries of human-driven change in salt marsh ecosystems. Annual Review of Marine Science 1 (1): 117–141.
Google Scholar
Geist, D.R., C.S. Abernethy, K.D. Hand, V.I. Cullinan, J.A. Chandler, and P.A. Groves. 2006. Survival, development, and growth of fall Chinook salmon embryos, alevins, and fry exposed to variable thermal and dissolved oxygen regimes. Transactions of the American Fisheries Society 135 (6): 1462–1477.
CAS
Google Scholar
Goertler, P.A.L., T.R. Sommer, W.H. Satterthwaite, and B.M. Schreier. 2018. Seasonal floodplain-tidal slough complex supports size variation for juvenile Chinook salmon (Oncorhynchus tshawytscha). Ecology of Freshwater Fish 27 (2): 580–593.
Google Scholar
Gotelli, N.J., and A.M. Ellison. 2004. A primer of ecological statistics. Sunderland: Sinauer Associates, Inc..
Google Scholar
Healey, M. 1980. Utilization of the Nanaimo River estuary by juvenile Chinook salmon, Oncorhynchus tshawytscha. Fishery Bulletin 77 (3): 653–668.
Google Scholar
Heath, A.G., B.J. Turner, and W.P. Davis. 1993. Temperature preferences and tolerances of three fish species inhabiting hyperthermal ponds on mangrove islands. Hydrobiologia 259 (1): 47–55.
Google Scholar
Hemes, K.S., E. Eichelmann, S. Chamberlain, S.H. Knox, P.Y. Oikawa, C. Sturtevant, J. Verfaillie, D. Szutu, and D.D. Baldocchi. 2018. A unique combination of aerodynamic and surface properties contribute to surface cooling in restored wetlands of the Sacramento-San Joaquin Delta, California. Journal of Geophysical Research – Biogeosciences 123 (7): 2072–2090.
Google Scholar
Herbold, B., S.M. Carlson, R. Henery, R.C. Johnson, N. Mantua, M. McClure, P.B. Moyle, and T. Sommer. 2018. Managing for Salmon resilience in California’s variable and changing climate. San Francisco Estuary and Watershed Science 16 (2). https://doi.org/10.15447/sfews.2018v16iss2art3.
Hering, D.K., D.L. Bottom, E.F. Prentice, K.K. Jones, and I.A. Fleming. 2010. Tidal movements and residency of subyearling Chinook salmon (Oncorhynchus tshawytscha) in an Oregon salt marsh channel. Canadian Journal of Fisheries and Aquatic Sciences 67 (3): 524–533.
Google Scholar
Herrmann, R.B., C.E. Warren, and P. Doudoroff. 1962. Influence of oxygen concentration on the growth of juvenile coho salmon. Transactions of the American Fisheries Society 91 (2): 155–167.
CAS
Google Scholar
Hyslop, E.J. 1980. Stomach contents analysis—A review of methods and their application. Journal of Fish Biology 17 (4): 411–429.
Google Scholar
Jassby, A. 2008. Phytoplankton in the upper San Francisco Estuary: Recent biomass trends, their causes, and their trophic significance. San Francisco Estuary and Watershed Science 6 (1). https://doi.org/10.15447/sfews.2008v6iss1art2.
Jeffres, C.A., J.J. Opperman, and P.B. Moyle. 2008. Ephemeral floodplain habitats provide best growth conditions for juvenile Chinook salmon in a California river. Environmental Biology of Fishes 83 (4): 449–458.
Google Scholar
Jones, M.J., and I.G. Stuart. 2008. Regulated floodplains—a trap for unwary fish. Fisheries Management and Ecology 15 (1): 71–79.
Google Scholar
Jude, D.J., and J. Pappas. 1992. Fish utilization of Great Lakes coastal wetlands. Journal of Great Lakes Research 18 (4): 651–672.
Google Scholar
Junk, W. J., P. B. Bayley, and R. E. Sparks. 1989. The flood-pulse concept in river-floodplain systems. In: Dodge, D.P., Ed., Proceedings of the international large river symposium (LARS), Canadian Journal of Fisheries and Aquatic Sciences special publication 106, NRC research press, Ottawa, 110–127.
Katz, J.V.E., C. Jeffres, L. Conrad, T.R. Sommer, J. Martinez, S. Brumbaugh, N. Corline, and P.B. Moyle. 2017. Floodplain farm fields provide novel rearing habitat for Chinook salmon. PLoS One 12 (6): e0177409. https://doi.org/10.1371/journal.pone.0177409.
CAS
Article
Google Scholar
Kimmerer, W.J., A.E. Parker, U.E. Lidström, and E.J. Carpenter. 2012. Short-term and interannual variability in primary production in the low-salinity zone of the San Francisco Estuary. Estuaries and Coasts 35 (4): 913–929.
CAS
Google Scholar
Kirwan, M.L., and J.P. Megonigal. 2013. Tidal wetland stability in the face of human impacts and sea-level rise. Nature 504 (7478): 53–60.
CAS
Google Scholar
Kjelson, M.A., P.F. Raquel, and F.W. Fisher. 1982. Life history of fall-run juvenile Chinook salmon, Oncorhynchus tshawytscha, in the Sacramento-San Joaquin Estuary, California. In Estuarine comparisons, ed. V.S. Kennedy, 393–411. New York: Academic Press.
Google Scholar
Levy, D.A., and T.G. Northcote. 1982. Juvenile salmon residency in a marsh area of the Fraser River estuary. Canadian Journal of Fisheries and Aquatic Sciences 39 (2): 270–276.
Google Scholar
Lucas, L.V., J.K. Thompson, and L.R. Brown. 2009. Why are diverse relationships observed between phytoplankton biomass and transport time? Limnology and Oceanography 54 (1): 381–390.
Google Scholar
Lund, J. 2017. After drought, California urgently needs to focus on big picture of water management. Sacramento Bee, Op-Ed. https://sacbee.relaymedia.com/amp/opinion/op-ed/soapbox/article129221644.html. Accessed 20 August 2018.
Lund, J. R., E. Hanak, W. Fleenor, R. Howitt, J. Mount, and P. Moyle. 2007. Envisioning futures for the Sacramento-San Joaquin Delta. San Francisco, CA: Public Policy Institute of California. http://www.ppic.org/main/publication.asp?i=671. Accessed 22 August 2020.
Lusardi, R.A., B.G. Hammock, C.A. Jeffres, R.A. Dahlgren, and J.D. Kiernan. 2019. Oversummer growth and survival of juvenile coho salmon (Oncorhynchus kisutch) across a natural gradient of stream water temperature and prey availability: An in situ enclosure experiment. Canadian Journal of Fisheries and Aquatic Sciences 77 (2): 413–424. https://doi.org/10.1139/cjfas-2018-0484.
Article
Google Scholar
Ma, Z., Y. Cai, B. Li, and J. Chen. 2010. Managing wetland habitats for waterbirds: An international perspective. Wetlands 30 (1): 15–27.
CAS
Google Scholar
MacFarlane, R.B., and E.C. Norton. 2002. Physiological ecology of juvenile Chinook salmon (Oncorhynchus tshawytscha) at the southern end of their distribution, the San Francisco Estuary and Gulf of the Farallones, California. Fishery Bulletin 100 (2): 244–257.
Google Scholar
Marine, K.R., and J.J. Cech Jr. 2004. Effects of high water temperature on growth, smoltification, and predator avoidance in juvenile Sacramento River Chinook Salmon. North American Journal of Fisheries Management 24 (1): 198–210.
Google Scholar
McCullough, D.A., J.M. Bartholow, H.I. Jager, R.L. Beschta, E.F. Cheslak, M.L. Deas, J.L. Ebersole, J.S. Foott, S.L. Johnson, K.R. Marine, M.G. Mesa, J.H. Petersen, Y. Souchon, K.F. Tiffan, and W.A. Wurtsbaugh. 2009. Research in thermal biology: Burning questions for coldwater stream fishes. Reviews in Fisheries Science 17 (1): 90–115.
Google Scholar
Meeuwig, M.H., J.B. Dunham, J.P. Hayes, and G.L. Vinyard. 2004. Effects of constant and cyclical thermal regimes on growth and feeding of juvenile cutthroat trout of variable sizes. Ecology of Freshwater Fish 13 (3): 208–216.
Google Scholar
Monroe, M., P. R. Olofson, J. N. Collins, R. M. Grossinger, J. Haltiner, and C. Wilcox. 1999. Baylands ecosystem habitat goals; San Francisco Bay Area Wetlands Ecosystem Goals Project. U.S. Environmental Protection Agency, San Francisco, California/S.F. Bay Regional Water Quality Control Board, Oakland, California. https://sfestuary.org/wp-content/uploads/2012/12/1Habitat_Goals.pdf. Accessed 25 November 2019.
Moore, J.W., J. Gordon, C. Carr-Harris, A.S. Gottesfeld, S.M. Wilson, and J. Harvey Russell. 2016. Assessing estuaries as stopover habitats for juvenile Pacific salmon. Marine Ecology Progress Series 559: 201–215.
Google Scholar
Mount, J., W. Bennett, J. Durand, W. Fleenor, E. Hanak, J. Lund, and P. Moyle. 2012. Aquatic ecosystem stressors in the Sacramento-san Joaquin Delta. Public Policy Institute of California. https://www.ppic.org/content/pubs/report/R_612JMR.pdf. Accessed 24 November 2019.
Moyle, P.B., A.D. Manfree, and P.L. Fiedler, eds. 2014. Suisun marsh: Ecological history and possible futures. Berkeley: Univ of California Press.
Google Scholar
Moyle, P.B., J. Durand, and C. Jeffres. 2018. Making the delta a better place for native fishes. Orange County Coast Keeper. https://www.coastkeeper.org/wp-content/uploads/2018/03/Delta-White-Paper_completed-3.6.pdf. Accessed 23 January 2020.
Nagelkerken, I., M. Sheaves, R. Baker, and R.M. Connolly. 2015. The seascape nursery: A novel spatial approach to identify and manage nurseries for coastal marine fauna. Fish and Fisheries 16 (2): 362–371.
Google Scholar
Needles, L.A., S.E. Lester, R. Ambrose, A. Andren, M. Beyeler, M. Connor, J. Eckman, B. Costa-Pierce, S.D. Gaines, K. Lafferty, H. Lenihan, J. Parrish, M.S. Peterson, A. Scaroni, J. Weis, and D.E. Wendt. 2015. Managing bay and estuarine ecosystems for multiple services. Estuaries and Coasts 38 (Supplemental 1): S35–S48. https://doi.org/10.1007/s12237-013-9602-7.
Article
Google Scholar
Nehlsen, W., J.E. Williams, and J.A. Lichatowich. 1991. Pacific salmon at the crossroads: Stocks at risk from California, Oregon, Idaho, and Washington. Fisheries 16 (2): 4–21.
Google Scholar
Nicieza, A.G., and N.B. Metcalfe. 1997. Growth compensation in juvenile Atlantic salmon: Responses to depressed temperature and food availability. Ecology 78 (8): 2385–2400.
Google Scholar
O’Rear, T. A., and P. B. Moyle. 2018. Suisun marsh fish study: Trends in fish and invertebrate populations of Suisun marsh. Center for Watershed Sciences, University of California, Davis. https://watershed.ucdavis.edu/files/biblio/Suisun Marsh Fish Report 2016 Final.pdf. Accessed 25 November 2019.
O’Rear, T. A., P. B. Moyle, and J. R. Durand. 2019. Trends in fish and invertebrate populations of Suisun marsh. Center for Watershed Sciences, University of California, Davis. https://watershed.ucdavis.edu/files/biblio/Suisun Marsh Fish Report 2017 Final No Appendix (low res).pdf. Accessed 25 November 2019.
Peierls, B.L., N.S. Hall, and H.W. Paerl. 2012. Non-monotonic responses of phytoplankton biomass accumulation to hydrologic variability: A comparison of two coastal plain North Carolina estuaries. Estuaries and Coasts 35 (6): 1376–1392.
Google Scholar
Pendleton, L., D.C. Donato, B.C. Murray, S. Crooks, W.A. Jenkins, S. Sifleet, C. Craft, J.W. Fourqurean, J.B. Kauffman, N. Marbà, P. Megonigal, E. Pidgeon, D. Herr, D. Gordon, and A. Baldera. 2012. Estimating global “blue carbon” emissions from conversion and degradation of vegetated coastal ecosystems. PLoS One 7 (9): e43542. https://doi.org/10.1371/journal.pone.0043542.
CAS
Article
Google Scholar
R Core Team. 2020. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. https://www.R-project.org/.
Reimers, P. E. 1971. The length of residence of juvenile fall Chinook salmon in Sixes River, Oregon. Dissertation, Oregon State University. http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/9z903242m. Accessed 21 August 2018.
Ritter, A.F., K. Wasson, S.I. Lonhart, R.K. Preisler, A. Woolfolk, K.A. Griffith, S. Connors, and K.W. Heiman. 2008. Ecological signatures of anthropogenically altered tidal exchange in estuarine ecosystems. Estuaries and Coasts 31 (3): 554–571.
Google Scholar
Rountree, R.A., and K.W. Able. 2007. Spatial and temporal habitat use patterns for salt marsh nekton: Implications for ecological functions. Aquatic Ecology 41 (1): 25–45.
CAS
Google Scholar
Rypel, A.L., and C.A. Layman. 2008. Degree of aquatic ecosystem fragmentation predicts population characteristics of gray snapper (Lutjanus griseus) in Caribbean tidal creeks. Canadian Journal of Fisheries and Aquatic Sciences 65 (3): 335–339.
Google Scholar
Rypel, A.L., K.M. Pounds, and R.H. Findlay. 2012. Spatial and temporal trade-offs by bluegills in floodplain river ecosystems. Ecosystems 15 (4): 555–563.
Google Scholar
Sass, G.G., A.L. Rypel, and J.D. Stafford. 2017. Inland fisheries habitat management: Lessons learned from wildlife ecology and a proposal for change. Fisheries 42 (4): 197–209.
Google Scholar
Satterthwaite, W.H., and S.M. Carlson. 2015. Weakening portfolio effect strength in a hatchery-supplemented Chinook salmon population complex. Canadian Journal of Fisheries and Aquatic Sciences 72 (12): 1860–1875.
Google Scholar
Schindler, D.E., R. Hilborn, B. Chasco, C.P. Boatright, T.P. Quinn, L.A. Rogers, and M.S. Webster. 2010. Population diversity and the portfolio effect in an exploited species. Nature 465 (7298): 609–612.
CAS
Google Scholar
Shreffler, D.K., C.A. Simenstad, and R.M. Thom. 1992. Foraging by juvenile salmon in a restored estuarine wetland. Estuaries 15 (2): 204–213.
Google Scholar
Simenstad, C.A., and J.R. Cordell. 2000. Ecological assessment criteria for restoring anadromous salmonid habitat in Pacific Northwest estuaries. Ecological Engineering 15 (3–4): 283–302.
Google Scholar
Sommer, T.R., M.L. Nobriga, W.C. Harrell, W. Batham, and W.J. Kimmerer. 2001. Floodplain rearing of juvenile Chinook salmon: Evidence of enhanced growth and survival. Canadian Journal of Fisheries and Aquatic Sciences 58 (2): 325–333.
Google Scholar
Tamisier, A., and P. Grillas. 1994. A review of habitat changes in the Camargue: An assessment of the effects of the loss of biological diversity on the wintering waterfowl community. Biological Conservation 70 (1): 39–47.
Google Scholar
Valentine-Rose, L., C.A. Layman, D.A. Arrington, and A.L. Rypel. 2007. Habitat fragmentation decreases fish secondary production in Bahamian tidal creeks. Bulletin of Marine Science 80 (3): 863–877.
Google Scholar
Volk, E.C., D.L. Bottom, K.K. Jones, and C.A. Simenstad. 2010. Reconstructing juvenile Chinook salmon life history in the Salmon River estuary, Oregon, using otolith microchemistry and microstructure. Transactions of the American Fisheries Society 139 (2): 535–549.
Google Scholar
Williams, J.G. 2012. Juvenile Chinook salmon (Oncorhynchus tshawytscha) in and around the San Francisco estuary. San Francisco Estuary and Watershed Science 10 (3). https://doi.org/10.15447/sfews.2012v10iss3art2.
Yoshiyama, R.M., F.W. Fisher, and P.B. Moyle. 1998. Historical abundance and decline of Chinook Salmon in the Central Valley region of California. North American Journal of Fisheries Management 18 (3): 487–521.
Google Scholar