@article {83191,
	title = {Estimating juvenile salmon estuarine carrying capacities to support restoration planning and evaluation},
	journal = {Estuaries and Coasts },
	volume = {46},
	year = {2023},
	note = {What is the carrying capacity of salmon habitat in a time of global warming and rising sea levels? To answer this question, the authors of this paper took a hard dive into the literature, involving over 4,500 printed estimates of densities of juvenile salmonids in estuaries and floodplains. This data was then used in a habitat expansion approach to estimate historic, current potential and predicted population densities after sea level rise. {\textquotedblleft}We demonstrate the habitat expansion approach by applying the quantiles of observed juvenile Chinook salmon (Oncorhynchus tshawytscha) and coho salmon (O. kisutch) densities (fish/ha) to spatial data describing current, historical or potential, and predicted (based on seal level rise) habitat extents for 16 coastal Oregon estuaries to estimate carrying capacities{\textquotedblright} (from the Abstract). This information will be important in the design and evaluation of restoration projects. This is an open-access article.},
	month = {2023},
	pages = {p.1046{\textendash}1066},
	keywords = {Alsea Bay, Chetco River, Chinook salmon = Oncorhynchus tshawytscha, Coho salmon = Oncorhynchus kisutch, Coos Bay, Coquille River, Elk River, juvenile fish, natural resource management, Necanicum River, Nehalem River, Nestucca Bay, Rogue River, Salmon River, sea levels, Siletz Bay, Siuslaw River, Sixes River, Tillamook Bay, Umpqua River, Yaquina Bay},
	doi = {https://doi.org/10.1007/s12237-023-01185-y },
	url = {https://link.springer.com/article/10.1007/s12237-023-01185-y},
	author = {Hall, Jason and Roni, Phil and Ross, Kai and Camp, Meghan J. and Nuckols, Jason and Ruffing, Claire}
}
@article {83219,
	title = {Salmonid egg-to-fry survival and capture methods:  Bibliography},
	volume = {no.2023-02},
	year = {2022},
	note = {"Fish biologists at NMFS{\textquoteright} California Central Valley Division are interested in the variety of methods used to examine the survival of fish eggs in a rivers where salmonids dig nests in gravel. They are also interested in how salmonid egg-to-fry survival is calculated. To that end, the NOAA Central Library conducted a literature search and present their findings in this bibliography." (Background \& Scope)},
	month = {2022, Dec.},
	pages = {126 p.},
	keywords = {bibliography, Chinook salmon = Oncorhynchus tshawytscha, chum salmon  = Oncorhynchus keta, Coho salmon = Oncorhynchus kisutch, cutthroat trout = Oncorhynchus clarki, developmental stages, juvenile fish, life history information, Pink salmon (humpback) = Oncorhynchus gorbuscha, steelhead trout = Oncorhynchus mykiss},
	doi = {https://doi.org/10.25923/wp1n-xt62 },
	url = {https://repository.library.noaa.gov/view/noaa/48004/},
	author = {Shinn, Hope}
}
@article {82506,
	title = {Detecting the effects of management regime shifts in dynamic environments using multi-population state-space models},
	journal = {Biological Conservation},
	volume = {221},
	year = {2018},
	note = {Oregon populations of wild coho salmon were in decline until they were listed by the Federal Government as threatened populations in 1998.  Subsequent efforts to restore coho included reducing hatchery production, restoring habitats and cutting allowable harvests. At the same time, ocean conditions improved, favoring adult salmon survival. In this paper, the authors{\textquoteright} objective {\textquotedblleft}was to assess change in the freshwater production of juvenile production of juveniles (smolts) through time in order to determine if recent increases in adult abundance could be related to management affecting the freshwater juvenile production{\textquotedblright} (from the Abstract).   Interestingly, the authors did not find any improvement in the survival of juvenile fish per spawning salmon. Instead, they attribute the rebound in coho population to improved ocean conditions.  Various aspects of this complex fishery management issue are discussed.},
	month = {2018, May},
	pages = {p.34-43},
	keywords = {Alsea River Basin, Beaver Creek, Coho salmon = Oncorhynchus kisutch, Coos River Basin, depleted populations, habitats, human impacts, juvenile fish, Lower Umpqua River Basin, mathematical modeling, natural resource management, Nehalem River Basin, Siletz River Basin, statistical analysis, Yaquina River Basin},
	doi = {https://doi.org/10.1016/j.biocon.2018.02.026 },
	author = {Falcy, Matthew R. and Suring, Erik}
}
@article {76321,
	title = {The contribution of estuary-resident life histories to the return of adult <i>Oncorhynchus kisutch</i>},
	journal = {Journal of Fish Biology           },
	volume = {85},
	year = {2014},
	note = {The conventional model of coho salmon life history assumes that that young coho salmon rear in the streams where they were born, and return to their natal streams as adults in their third year. More recent research has shown that there is a wider variety of life history patterns, and that estuaries may be more important for some coho salmon than was previously known. {\textquotedblleft}This research reconstructs freshwater and estuarine rearing and migration pathways of juvenile O. kisutch in the Salmon River basin on the central Oregon coast. It then quantifies the contribution of each juvenile life-history type to adult returns.{\textquotedblright} (p.53)},
	pages = {p.52-80},
	keywords = {Coho salmon = Oncorhynchus kisutch, habitats, juvenile fish, life history information, marsh restoration, salinity, Salmon River Estuary, wetland restoration, wetland vegetation},
	doi = {10.1111/jfb.12380},
	author = {Jones, Kim K. and Cornwell, Trevan J. and Bottom, Daniel L. and Campbell, Lance A. and Stein, Staci}
}
@article {76436,
	title = {Nursery Functions of U.S. West Coast Estuaries:  The State of Knowledge for Juveniles of Focal Invertebrate and Fish Species},
	year = {2014},
	note = {This report summarizes what is known about the role of estuaries as nurseries for important aquatic species. The authors inventoried 303 West Coast estuaries and categorized each by class (lagoonal, riverine, embayment and sound) and subclass (estuarine coastal subtidal, tidal channel/creek, slough and lagoon). They examined 15 different species that used estuaries and noted what is known and not known about their life cycles and use of estuaries. {\textquotedblleft}Together with the estuary inventory and the geodatabase, this report represents the first stage in a larger effort to better understand the nursery functions of West Coast estuaries for fish and invertebrates.{\textquotedblright} (p.3)},
	pages = {168 p.},
	institution = {The Nature Conservancy},
	address = {Arlington, Va.},
	keywords = {aquatic invertebrates, Bat stingray = Myliobatus californicus (Aetobatus californicus), Bay shrimp = Crangon franciscorum, Brown rockfish = Sebastes auriculatus, California halibut = Paralichthys californicus, Chinook salmon = Oncorhynchus tshawytscha, Coho salmon = Oncorhynchus kisutch, crustaceans, Dungeness crab =   Metacarcinus magister (Cancer magister), eelgrass = Zostera marina, English sole = Parophrys vetulus, estuaries, fishes, general, geographic distribution, Green sturgeon = Acipenser medirostris, habitats, juvenile fish, Leopard shark = Triakis semifasciata, life history information, Oregon, Pacific Coast, Pacific herring =  Clupea pallasi, Pacific staghorn sculpin = Leptocottus armatus, Shiner perch = Cymatogaster aggregate, Starry flounder = Platichthys stellatus, steelhead trout = Oncorhynchus mykiss},
	url = {https://www.scienceforconservation.org/products/nursery-functions-of-estuaries},
	author = {Hughes, Brent B. and Levey, Matthew D. and Brown, Jennifer A. and Fountain, Monique C. and Carlisle, Aaron B. and Litvin, Steven Y. and Greene, Correigh M. and Heady, Walter N. and Gleason, Mary G.}
}
@article {76906,
	title = {Variation in juvenile Chinook salmon diet composition and foraging success between two estuaries with contrasting land-use histories [PowerPoint presentation]},
	journal = {Salish Sea Ecosystem Conference. },
	number = {Paper 70},
	year = {2014},
	note = {This is a .pdf of a PowerPoint presentation at a conference.  Estuaries may offer attractive opportunities for foraging for juvenile Chinook salmon.  Human intervention can cause wetland losses, however, which may disrupt or reduce invertebrate assemblages, leading to less successful foraging, less growth and lower survival rates for young fish.  Since most of the wetlands in the Salmon River have been restored, it serves as a reference point when this issue is studied.  The authors found that {\textquotedblleft}wetland loss appeared to mediate the effect of density on salmon foraging performance.{\textquotedblright} (slide 20)},
	keywords = {Chinook salmon = Oncorhynchus tshawytscha, Duwamish River, feeding behavior, food availability, habitats, human impacts, juvenile fish, life history information, Nisqually River, physical modifications, Salmon River Estuary, wetlands},
	url = {https://cedar.wwu.edu/cgi/viewcontent.cgi?referer=\&httpsredir=1\&article=1531\&context=ssec},
	author = {David, Aaron and Simenstad, Charles and Cordell, Jeffrey and Toft, Jason and Ellings, Christopher}
}
@article {34486,
	title = {Juvenile salmonid monitoring in coastal Oregon and lower Columbia streams, 2011},
	volume = {no.OPSW-ODFW-2013-1},
	year = {2012},
	note = {These reports give broad trends only. Since we don{\textquoteright}t know what streams are monitored, and cannot contrast the water quality trends of those streams with the population data, these reports are of limited utility.},
	pages = {25 p.},
	address = {Salem, Or.},
	keywords = {Coho salmon =  Oncorhynchus kisutch, depleted populations, juvenile fish, population count, spatial distribution, steelhead trout = Oncorhynchus mykiss, temporal distribution},
	url = {https://digital.osl.state.or.us/islandora/object/osl:43833},
	author = {Constable, Ronald J., Jr. and Suring, Erik and Tippery, Sharon and Oregon. Department of Fish and Wildlife. Western Oregon Rearing Project,}
}
@article {11861,
	title = {Life history variability, habitat use, and migratory behavior of coastal cutthroat trout in the Salmon River, Oregon},
	volume = {no.OPSW-ODFW-2012-10},
	year = {2012},
	note = {Reports on results of tagging cutthroat trout in the Salmon River in 2004, 2009 and 2010. Used trapping, electrofishing, beach seining and acoustic telemetry to study the population and its life history.  This study "complements" Lisa K. Krentz{\textquoteright}s 2007 study of coastal cutthroat trout life history patterns,  "while providing a novel perspective on selected aspects of cutthroat life history, growth, and survival." (p.22) There were high annual variations in migratory and residence patterns. "Although we have found it difficult to ascribe individual fish to estuary or ocean rearing strategies, it appears that cutthroat use one or moer rearing strategies before returning to freshwater in the fall." (p.25) },
	pages = {29 p.},
	institution = {Oregon Dept. of Fish and Wildlife},
	address = {Salem, Or.},
	keywords = {abundance, Bear Creek, Coastal cutthroat trout = Oncorhynchus clarki clarki, geographic distribution, juvenile fish, life history information, population biology, population count, Salmon River, Slick Rock Creek, temporal distribution, Trout Creek},
	url = {https://tinyurl.com/mrxs5xnm},
	author = {Stein, Staci and Cornwell, Trevan J. and Jones, Kim K.}
}
@article {11906,
	title = {Life History Variability, Habitat Use, and Migratory Behavior of Coastal Cutthroat Trout in the Salmon River, Oregon},
	year = {2010},
	note = {Reports on results of tagging cutthroat trout in the Salmon River in 2004 and 2009.  This study calls into question Lisa K. Krentz{\textquoteright}s 2007 study of coastal cutthroat trout life history patterns.  "In contrast to life history patterns in other Oregon estuaries", Krentz had found that cutthroat trout of varying sizes spent long periods of time in channels in the Salmon River. This study did not find that cutthroat trout had extended stays in the estuary:  either the fish stayed in freshwater, or, if they migrated into the estuary, they soon moved out to the ocean.  Future research and analysis will be directed towards resolving differences between the two studies. Charts, maps, infrared aerial photograph.},
	pages = {21 pp},
	institution = {Oregon Dept. of Fish and Wildlife},
	address = {Salem, Or.},
	keywords = {Coastal cutthroat trout = Oncorhynchus clarki clarki, geographic distribution, juvenile fish, life history information, Salmon River, temporal distribution},
	url = {https://digital.osl.state.or.us/islandora/object/osl\%3A989898},
	author = {Cornwell, Trevan J. and Jones, Kim K. and Stein, Staci}
}
@mastersthesis {11936,
	title = {Growth, Residence, and Movement of Juvenile Chinook Salmon within Restored and Reference Estuarine Marsh Channels in Salmon River, Oregon},
	year = {2009},
	note = {One life history strategy for Chinook salmon is the "sea-type" or "ocean-type" strategy. The young salmon adopting this strategy move from freshwater into the estuary and forage for food in estuarine channels.  This pattern makes these salmon vulnerable to habitat degradation in estuaries. "Understanding how juvenile salmon use estuarine habitat and the costs and benefits derived from estuarine rearing is essential to effective conservation and restoration of coastal Chinook salmon populations throughout the Pacific Northwest and is the topic of this thesis."  Co-major professors were Ian K. Fleming and Dan Bottom. },
	pages = {150 p.},
	school = {Oregon State University},
	type = {Masters Thesis},
	edition = {M.S.},
	chapter = {Dept. of Fisheries and Wildlife, Fisheries},
	address = {Corvallis, Or.},
	keywords = {Chinook salmon = Oncorhynchus tshawytscha, feeding behavior, geographic distribution, habitats, juvenile fish, life history information, marshes, Salmon River Estuary, temporal distribution, theses},
	url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/dv13zz42s},
	author = {Hering, David K.}
}
@article {83220,
	title = {Contaminant exposure in outmigrant juvenile salmon from Pacific Northwest estuaries of the United States},
	journal = {Environmental Monitoring and Assessment},
	volume = {124},
	number = {1-3},
	year = {2007},
	note = {When juvenile salmonids migrate downstream towards the ocean, they can encounter and absorb harmful chemicals such as DDT, polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs) and pesticides. The authors of this paper measured harmful chemicals in tissues of juvenile salmonids, and in their prey.  They also measured stomach contents of salmon from estuaries and hatcheries. Results were not surprising:  industrial estuaries such as the Columbia River, Coos Bay and Yaquina Bay showed high contaminant exporsure (Yaquina Bay was high in PCBs in Chinook salmon), while natural estuaries like the Salmon and Elk River estuaries, had low exposures to harmful chemicals. Some of the conservation estuaries, including Alsea Bay, had relatively high exposures to contaminants. . Juvenile Chinook were more vulnerable than coho salmon.},
	pages = {p.167-194},
	keywords = {Alsea Bay, Chinook salmon = Oncorhynchus tshawytscha, Coho salmon = Oncorhynchus kisutch, Columbia River, Coos Bay, Coquille River estuary, DDT, Elk River, juvenile fish, migration, pesticides, Salmon River, Salmon River Hatchery, Tillamook Bay, water pollution, Yaquina Bay},
	doi = {https://doi.org/10.1007/s10661-006-9216-7 },
	author = {Johnson, Lyndal L. and Ylitalo, Gina M. and Arkoosh, Mary R. and Kagley, Anna N. and Stafford, Coral and Bolton, Jennie L. and Buzitis, Jon and Anulacion, Bernadita F. and Collier, Tracy K.}
}
@proceedings {12096,
	title = {Feeding ecology of cutthroat trout in the Salmon River Estuary, Oregon},
	year = {2005},
	note = {Another paper on life history strategies of coastal cutthroat trout, finding they were resident in the Salmon River Estuary for long periods of time, and noting their diet. Lisa McLaughlin, formerly known as Lisa Krentz, who initially asserted the previously unknown estuarine stay for cutthroat trout, co-authored this study. },
	pages = {p.144-151},
	publisher = {Oregon Chapter of the American Fisheries Society},
	address = {Port Townsend, Wash.},
	keywords = {aquatic invertebrates, Coastal cutthroat trout = Oncorhynchus clarki clarki, feeding behavior, fishes, habitats, juvenile fish, life history information, marshes, Salmon River Estuary},
	author = {Jones, David S. and Fleming, Ian A. and McLaughlin, Lisa K.},
	editor = {Connolly, Patrick J. and Williams, T. H. (Thomas Herbert) and Gresswell, Robert E and American Fisheries Society. Oregon Chapter.}
}
@mastersthesis {12116,
	title = {Passage of juvenile cutthroat trout and steelhead through retrofitted culverts},
	year = {2005},
	note = {Studied movements of steelhead and cutthroat trout through culverts in Oregon coastal streams. Found that using baffles in culverts increased the chances of salmonid movement through culverts both in high water and low water flow periods. Baffles did not totally remove the detrimental effects of culverts on fish passage. Some designs were more helpful to fish than others.},
	pages = {62 p.},
	school = {Oregon State University},
	type = {Masters Thesis},
	edition = {M.S.},
	chapter = {Dept. of  Fisheries and Wildlife, Fisheries Science},
	address = {Corvallis, Or.},
	keywords = {Alder Brook (Salmon), Alsea River, Canyon Creek, cutthroat trout = Oncorhynchus clarki, geographic distribution, Hayden Creek, Hough Creek (Siletz), human impacts, hydrology, juvenile fish, Little Lobster Creek (Alsea), migration, precipitation, Salmon River, Siletz River, steelhead trout = Oncorhynchus mykiss, Stemple Creek (Siletz), theses, Umpqua River},
	url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/2v23vx11t},
	author = {McEnroe, Jeffrey R.}
}
@article {12221,
	title = {Contrasting functional performance of juvenile salmon habitat in recovering wetlands in the Salmon River estuary, Oregon, U.S.A.},
	journal = {Restoration Ecology},
	volume = {10},
	number = {3},
	year = {2002},
	note = {Looks at marsh restoration in the Salmon River following the breaching of dikes in 1978, 1987 and 1996 to examine "fish density, available prey resources, and diet composition of wild juvenile Oncorhynchus tshawytscha (chinook salmon).""Tracking the development of recovering emergent marsh ecosystems in the Salmon River estuary reveals significant fish and invertebrate response in the first 2 to 3 years after marsh restoration. This pulse of productivity in newly restored systems is part of the trajectory of development and indicates some level of early functionality and the efficacy of restoring estuarine marshes for juvenile salmon habitat." (from the Abstract)},
	pages = {p.514-526},
	keywords = {amphipods, Chinook salmon = Oncorhynchus tshawytscha, feeding behavior, geographic distribution, insects, juvenile fish, Salmon River Estuary, temporal distribution},
	doi = {10.1046/j.1526-100X.2002.01039.x},
	author = {Gray, Ayesha and Simenstad, Charles A. and Bottom, Daniel L. and Cornwell, Trevan J.}
}
@booklet {12581,
	title = {Chinook salmon populations in Oregon coastal river basins : description of life histories and assessment of recent trends in run strengths},
	year = {1989},
	note = {"This is a reprint of Oregon Department of Fish and Wildlife Information Reports 88-1, with the same title. The Addendum, pages vii-xx, was prepared for this edition." -- p.4 of cover."  Nice life history data.  Estimates catch, run strength, population size, run timing.},
	publisher = {Oregon State University Extension Service},
	address = {Corvallis, Or.},
	keywords = {age composition, Alsea River, Chinook salmon = Oncorhynchus tshawytscha, commercial fisheries - salmon, Coos Rive, fecundity, geographic distribution, hatcheries, juvenile fish, life history information, mathematical modeling, Nehalem River, Nestucca River, population count, r Chetco River, r Coquille River, recreational fisheries - salmon, Rogue River, Salmon River, Siletz River, Siuslaw River, Sixes Rive, size composition, temporal distribution, Tillamook Bay, Umpqua River, Winchester Dam, Yachats River, Yaquina River},
	url = {https://ir.library.oregonstate.edu/concern/open_educational_resources/8910jv041},
	author = {Nicholas, Jay W. and Hankin, David G. and Oregon State University. Extension Service and Oregon. Fish Division and Oregon. Dept. of Fish and Wildlife Research and Development Section,}
}
@article {12601,
	title = {Species Profiles : Life Histories and Environmental Requirements of Coastal Fishes and Invertebrates (Pacific Northwest) : English Sole},
	volume = {no. 82-11.101.},
	year = {1989},
	note = {Estuaries serve as nurseries for young English sole, although adult fish migrate to the ocean. This is a classic overview of the biology and life history of English sole in the Pacific Northwest. Good bibliography, if a bit dated.Map, charts, line drawings.},
	keywords = {Alsea Bay, commercial fisheries, Coos Bay, Coquille Bay, English sole = Parophrys vetulus  taxonomy, fecundity, growth, juvenile fish, life history information, Nestucca Bay, Netarts Bay, recreational fisheries, reproductive behavior, Salmon River Estuary, Sand Lake, Siletz Bay, Siuslaw Bay, Tillamook Bay, Umpqua River estuary, Winchester Bay, Yaquina Bay},
	url = {https://tinyurl.com/qogv2ul},
	author = {Lassuy, Dennis R. and U.S. Army Engineer Waterways Experiment Station. Coastal Ecology Group, and U.S.National Wetlands Research Center}
}
@book {12616,
	title = {Chinook salmon populations in Oregon coastal river basins : description of life histories and assessment of recent trends in run strengths},
	series = {Information Reports (Oregon. Fish Division) },
	volume = {no.88-1},
	year = {1988},
	publisher = {Oregon Dept. of Fish and Wildlife, Research and Development Section,},
	organization = {Oregon Dept. of Fish and Wildlife, Research and Development Section,},
	chapter = {359 pp.},
	address = {Portland, Or},
	keywords = {age composition, Alsea River, Chetco River, Chinook salmon = Oncorhynchus tshawytscha, commercial fisheries - salmon, Coos River, Coquille River, fecundity, geographic distribution, hatcheries, juvenile fish, life history information, mathematical modeling, Nehalem River, Nestucca River, population count, recreational fisheries - salmon, Rogue River, Salmon River, Siletz River, Siuslaw River, Sixes River, size composition, temporal distribution, Tillamook Bay, Umpqua River, Winchester Dam, Yachats River, Yaquina River},
	url = {https://digital.osl.state.or.us/islandora/object/osl\%3A35565},
	author = {Nicholas, Jay W. and Hankin, David G. and Oregon State University. Extension Service and Oregon. Fish Division and Oregon. Dept. of Fish and Wildlife. Research and Development Section,}
}
@mastersthesis {36141,
	title = {<i>Cytophaga psychrophila</i>, the Causative Agent of Bacterial Cold-Water Disease in Salmonid Fish},
	year = {1987},
	note = {This work is an important exploration of an issue for Oregon fish hatcheries.  {\textquotedblleft}Bacterial cold-water disease {\textellipsis} is a serious septicemic infection of hatchery-reared salmonids especially young coho salmon{\textellipsis} in the Pacific Northwest.{\textquotedblright} (p.1)  Includes b+w photographs, including micrographs and scanning electron micrographs.  Major professor was J. L. Fryer. },
	pages = {166 p.},
	school = {Oregon State University},
	type = {Doctoral dissertation},
	edition = {Ph. D.},
	chapter = {Dept. of Microbiology},
	address = {Corvallis, Or.},
	keywords = {bacteria, bacterial cold-water disease, biochemistry, Chinook salmon = Oncorhynchus tshawytscha, Coho salmon = Oncorhynchus kisutch, Cytophaga psychrophila, Fall Creek Fish Hatchery (Alsea River), fish disease, genetics, juvenile fish, Nehalem River Fish Hatchery, Pacific salmonids = Oncorhynchus spp., Salmon River Fish Hatchery, Siletz River Fish Hatchery, steelhead trout = Oncorhynchus mykiss, theses, Trask River Fish Hatchery, water temperature},
	url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/z029p826n},
	author = {Holt, Richaed Allen}
}
