@article {83011, title = {Expansion and systematics redefinition of the most threatened freshwater mussel family, the Margaritiferidae}, journal = {Molecular Phylogenetics and Evolution}, volume = {127}, year = {2018}, note = {In this article, the evolution, distribution and taxonomy of the freshwater pearl mussel family, Margaritiferidae, is explored. Fossils as well as genetic data were used to model the diversification of this family. Maps, charts.}, month = {2018, Oct.}, pages = {p.98-118}, keywords = {aquatic invertebrates, bivalves, evolution, general, genetics, geographic distribution, molluscs, morphology, mussels, phylogeny, taxonomy}, doi = {https://doi.org/10.1016/j.ympev.2018.04.041 }, author = {Lopes-Lima, Manuel and Bolotov, Ivan N. and Do, Van Tu and Aldridge, David C. and Fonseca, Miguel M. and Gan, Han Ming and Gofarov, Mikhail Y. and Kondakov, Alexander V. and Pri{\'e}, Vincent and Sousa, Ronaldo and Varandas, Simone and Vikhrev, Ilya V. and Teixeira, Amilcar and Wu, Rui-Wen and Wu, Xiaoping and Zieritz, Alexandra and Froufe, Elsa and Bogan, Arthur E.} } @article {76876, title = {Landscape genetics and genetic structure of the southern torrent salamander, Rhyacotriton variegatus}, journal = {Conservation Genetics }, volume = {16}, year = {2015}, note = {Rhyacotriton variegatus is a salamander species in the Pacific Northwest. It is notable for its low tolerance for desiccation. Its need for a moist environment has caused it to be listed as Vulnerable in the Oregon Sensitive Species List. In this study, the authors used landscape genetics techniques to identify the best conservation measures for this animal. The southern torrent salamander needs streamside canopies for the best genetic dispersal, and unfortunately the streamside habitat is often fragmented and broken. The authors suggest that, {\textquotedblleft}Maintaining stream corridors with buffers of dense canopy cover may maximize connectivity despite the pressures of timber harvest and urbanization.{\textquotedblright} (from the Abstract)}, pages = {p.209{\textendash}221}, keywords = {Alsea River, Big Elk Creek (Yaquina), genetics, habitats, Neskowin Creek, Panther Creek (Salmon), population dynamics, riparian areas, Rock Creek (Alsea), Salmon Creek (Yaquina), Salmon River, Southern torrent salamander = Rhyacotriton variegatus, Tenmile Creek}, doi = {10.1007/s10592-014-0653-5}, author = {Emel, Sarah L. and Storfer, Andrew} } @article {54926, title = {Evaluating the Population Genetic Structure of Dungeness Crab (Cancer magister) off the Oregon Coast}, year = {2014}, note = {{\textquotedblleft}The goal of this study was to evaluate the genetic diversity and population genetic structure of Dungeness crab off the Oregon coast and provide baseline data that could be used to help inform decisions on marine spatial planning. From a conservation and management standpoint, it is critical to determine the population genetic structure and genetic diversity within subpopulations to ensure the long term viability of a species.{\textquotedblright} (p.4-5) There are clear and helpful explanations of the concepts and issues involved in this study. Nicely done.}, pages = {20 p.}, institution = {Oregon Wave Energy Trust,}, address = {Portland, Or.}, keywords = {Astoria, Brookings, Coos Bay, Dungeness crab = Metacarcinus magister (Cancer magister), Garibaldi, general, genetics, Newport (Or.), population biology, Port Orford}, url = {https://ir.library.oregonstate.edu/concern/technical_reports/w0892g295}, author = {O{\textquoteright}Malley, Kathleen and Roegner, Curtis and Oregon. Wave Energy Trust, and Oregon. Dungeness Crab Commission,} } @article {11881, title = {Recovery of wild coho salmon in Salmon River Basin, 2008-2010}, volume = {no.OPSW-ODFW-2011-10}, year = {2011}, note = {In 2007, after 30 years of artificially producing fish, the Salmon River Hatchery was closed. This study reports on coho salmon in the Salmon River three years after the closure of the hatchery. Favorable ocean conditions helped, but dangers such as high flow levels in winter remain. "In the absence of intensive hatchery pressure, we hypothesize that the stream and estuary habitats in Salmon River will have sufficient connectivity, capacity, and quality to recover and sustain a resilient population of wild coho salmon." (p.33)}, pages = {53 p.}, institution = {Oregon Dept. of Fish and Wildlife}, address = {Salem, Or.}, keywords = {Coho salmon = Oncorhynchus kisutch, depleted populations, genetics, hatcheries, hatchery salmonids, Salmon River, wild salmonids}, url = {https://odfw-static.forestry.oregonstate.edu/freshwater/inventory/pdffiles/Salmon\%20River\%20ODFW-OPSW\%202011-10\%20final.pdf}, author = {Jones, Kim K. and Cornwell, Trevan J. and Bottom, Daniel L. and Stein, Staci and Kelly, Holly Wellard and Campbell, Lance A.} } @mastersthesis {26726, title = {Patterns of Natural Selection and Demography in Coastal Oregon Coho Salmon (Oncorhynchus kisutch) Populations: Evidence from Neutral and Olfactory Receptor Gene-Linked Markers}, year = {2009}, note = {"For Pacific salmon, the evolution of local adaptations depends upon the species{\textquoteright} propensity to return, or {\textquotedblleft}home{\textquotedblright}, to natal streams at time of reproduction. Pacific salmon use olfactory cues to guide homing behavior, yet little is known about the genetics of olfaction in salmon. In this study, I use putatively neutral microsatellite markers to estimate demographic parameters and describe the population genetic structure of Oregon Coastal coho salmon (Oncorhynchus kisutch). . . I then used genomic sequence data from nine species of salmon and trout to infer the evolutionary history for eight olfactory receptor genes. . . Finally, I used molecular markers linked to olfactory receptor genes to test for a signal of selection among coho salmon populations from different rivers." (from the Abstract) Found the Coos Bay salmon were the major source of straying in the south coast, while Nehalem River salmon did most of the straying on the north coast. Major professor was Michael A. Banks.}, pages = {111 p.}, school = {Oregon State University}, type = {Doctoral Dissertation}, edition = {Ph. D.}, chapter = {Dept. of Fisheries and Wildlife}, address = {Corvallis, Or.}, keywords = {Coho salmon = Oncorhynchus kisutch, genetics, geographic distribution, population biology, theses}, url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/gh93h230k}, author = {Johnson, Marc Aaron} } @article {11956, title = {Salmon River Hatchery Operations Plan: 2010}, year = {2009}, keywords = {Chinook salmon = Oncorhynchus tshawytscha, Coho salmon = Oncorhynchus kisutch, genetics, hatcheries, hatchery salmonids, steelhead trout = Oncorhynchus mykiss, wild salmonids}, url = {https://digital.osl.state.or.us/islandora/object/osl\%3A45556}, author = {Oregon. Dept. of Fish and Wildlife,} } @article {12141, title = {Updated status of federally listed ESUs of west coast salmon and steelhead}, volume = {no.66}, year = {2005}, pages = {598 p.}, institution = {U.S. Dept. of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center,}, address = {Seattle, Wash.}, keywords = {Alsea River, Beaver Creek, Chinook salmon = Oncorhynchus tshawytscha, chum salmon = Oncorhynchus keta, Coho salmon = Oncorhynchus kisutch, Coos Bay, Coquille River, depleted populations, Devil{\textquoteright}s Lake, fecundity, genetics, hatcheries, human impacts, hybridization, Necanicum River, Nehalem River, Nestucca River, population biology, population count, reproductive behavior, Rogue River, Salmon River, salmonid species, Sand Lake, Siletz River, Siuslaw River, statistical analysis, steelhead trout = Oncorhynchus mykiss, Tenmile Lake, Tillamook Bay, Umpqua River Basin, Yachats River, Yaquina River}, url = {https://repository.library.noaa.gov/view/noaa/3413}, editor = {Good, Thomas P. and Waples, Robin S. and Adams, Pete} } @book {36746, title = {Status review of coastal cutthroat trout from Washington, Oregon, and California}, series = {NOAA Technical Memorandum NMFS-NWFSC}, year = {1999}, note = {The Biological Review Team concluded that coastal stocks of cutthroat trout were not presently at risk of extinction. Appendix 1-A gives the known history of hatchery releases in streams and lakes.}, month = {1999}, publisher = {Northwest Fisheries Science Center}, organization = {Northwest Fisheries Science Center}, address = {[Seattle, Wash.]}, keywords = {Alsea Fish Hatchery, Alsea River, Chetco River, Coos Bay, Coos River, Coquille River, cutthroat trout = Oncorhynchus clarki, Devils Lake, endangered species, environmental policy and law, general ecosystem description, genetics, hatcheries, history, Kilchis River, life history information, Miami River, Millicoma River, natural resource management, Necanicum River, Nehalem River, Nestucca River, population biology, population count, Rogue River, Salmon River, salmonid species, Sand Creek, Siltcoos Lake, Siuslaw River, Smith River, statistics, Tahkenitch Lake, Tenmile Creek, Tillamook River, Trask River, Umpqua River, Wilson River, Yachats River, Yaquina River}, url = {https://repository.library.noaa.gov/view/noaa/3066}, author = {Johnson, Orlay W. and Ruckelshaus, Mary H. and Grant, W. Stewart and Waknitz, F. William and Garrett, Ann M. and Bryant, Gregory J. and Neely, Kathleen and Hard, Jeffrey J. and Northwest Fisheries Science Center (U.S.),} } @article {12361, title = {Status review of chinook salmon from Washington, Idaho, Oregon, and California}, volume = {no.35}, year = {1998}, note = {The team studying Chinook salmon felt that for the Oregon Coast this species is not in danger of extinction, nor thought to become extinct "in the forseeable future" (p.249). Appendix D gives the known history of hatchery releases. }, pages = {443 p.}, institution = {U.S. Dept. of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service}, address = {[Seattle, Wash.] }, keywords = {Alsea River, Chinook salmon = Oncorhynchus tshawytscha, Coquille River, endangered species, environmental policy and law, general ecosystem description, genetics, hatcheries, historical, Kilchis River, life history information, Miami River, Millicoma Rive, natural resource management, Necanicum River, Nehalem River, Nestucca River, population biology, population count, r Coos River, Salmon River, salmonid species, Siletz River, Siuslaw River, statistics, Tillamook River, Trask River, Umpqua River, Wilson River, Yachats River, Yaquina River}, url = {https://repository.library.noaa.gov/view/noaa/3034}, author = {Myers, James M. and Kope, Robert G. and Bryant, Gregory J. and Teel, David; and Lierheimer, Lisa J. and Wainwright, Thomas C. and Grant, W. Stewart and Waknitz, F. William and Neely, Kathleen and Lindley, Steven T. and Waples, Robin S.} } @article {12446, title = {Status review of coho salmon from Washington, Oregon, and California}, volume = {no.24}, year = {1995}, note = {The Biological Review Team concluded that "coho salmon in this ESU are not at immediate risk of extinction but are likely to become endangered in the future if present trends continue." The Team noted that "spawning escapements have declined substantially during this century and may now be at less than 5\% of their abundance in the early 1900s." (p.128) }, pages = {258 p.}, institution = {U.S. Dept. of Commerce, National Oceanic and Atmoospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center }, address = {Seattle, Wash.}, keywords = {Coho salmon = Oncorhynchus kisutch, Coos River, Coquille River, endangered species, environmental policy and law, general ecosystem description, genetics, hatcheries, historical, life history information, Miami River, natural resource management, Necanicum River, Nehalem River, Nestucca River, population biology, population count, Salmon River, salmonid species, Siletz River, Siuslaw River, statistics, Tillamook River, Umpqua River, Wilson River, Yaquina River}, url = {https://www.nwfsc.noaa.gov/assets/25/5585_06172004_123333_coho.pdf}, author = {Weitcamp, Laurie A. and Wainwright, Thomas C. and Bryant, Gregory J. and Milner, George B. and Teel, David J. and Kope, Robert G. and Waples, Robin S.} } @mastersthesis {36141, title = {Cytophaga psychrophila, 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} } @article {12771, title = {Phenotypic differences among stocks of hatchery and wild coho salmon, Oncorhynchus kisutch, in Oregon, Washington, and California}, journal = {Fishery bulletin}, volume = {80}, number = {1}, year = {1982}, month = {1982}, pages = {p.105-119}, keywords = {Alsea River, Beaver Creek, Coho salmon = Oncorhynchus kisutch, Columbia River, Coquille River, genetics, hatchery salmonids, life history information, Nehalem River, Nestucca River, North Nehalem River, physiology, Rogue River, Salmon River, Siletz River, Smith River, Tenmile Lakes, Trask River, Umpqua River, wild salmonids}, url = {https://spo.nmfs.noaa.gov/sites/default/files/pdf-content/1982/801/hjort.pdf}, author = {Hjort, Randy Carl and Schreck, Carl B.} } @mastersthesis {12836, title = {Phenotypic Comparison of Hatchery and Wild Coho Salmon (Oncorhynchus kisutch) in Oregon, Washington, and California}, year = {1979}, note = {"Phenotypic similarities of coho salmon (Oncorhynchus kisutch) stocks from Oregon, Washington, and California were compared using agglomerative and divisive cluster analyses. The phenotypic characters evaluated included the following: 1) the isozyme gene frequencies of transferrin and phosphoglucose isomerase; 2) the life history characters time of peak spawning and proportion of females in the population; and 3) the morphological characters scales in the lateral series, scales above the lateral line, anal rays, gill rakers, branchiostegal rays and vertebrae." (from the Abstract) }, pages = {50 pp,}, school = {Oregon State University}, type = {Masters Thesis}, edition = {M. S.}, chapter = {Dept. of Fisheries and Wildlife}, address = {Corvallis, Or.}, keywords = {Alsea River, Beaver Creek, Coho salmon = Oncorhynchus kisutch, Columbia River, Coquille River, genetics, hatchery salmonids, life history information, Nehalem River, Nestucca River, North Nehalem River, physiology, Rogue River, Salmon River, Siletz River, Smith River, Tenmile Lakes, theses, Trask River, Umpqua River, wild salmonids}, url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/tm70mx49x}, author = {Hjort, Randy Carl} } @article {12991, title = {Research on anadromous fish in coastal watersheds of Oregon}, year = {1976}, note = {"Annual Report, July 1, 1975 - June 30, 1976. Completion Reports, July 1, 1973 - June 30, 1976." Reports on various studies of Coastal Rivers Investigations including rearing spring Chinook, fall Chinook ecology, sport fishery survey, accelerated growth and release, coastal fall Chinook stock assessment, and shad and striped bass studies. Included work to develop and evaluate the new Salmon River hatchery. }, address = {Portland, Or.}, keywords = {Alsea River, Alsea Salmon Hatchery, Chetco River, Chinook salmon = Oncorhynchus tshawytscha, Coho salmon = Oncorhynchus kisutch, Coos River, Coquille River, Elk River, genetics, habitats, hatcheries, hatchery salmonids, natural resource management, Nestucca River, New River, Salmon River, Shad = Alosa sapidissima, Siuslaw River, Smith River, Striped Bass = Morone saxatilis, Tenmile Lakes, Trask River, Umpqua River, wild salmonids}, url = {https://ir.library.oregonstate.edu/concern/technical_reports/5712m731k}, author = {McGie, Alan M.} } @article {13031, title = {Research on anadromous fish in coastal watersheds of Oregon}, year = {1975}, note = {"Annual Report, July 1, 1974 - June 30, 1975." Reports on various studies of Coastal Rivers Investigations including rearing spring Chinook, fall Chinook ecology, sport fishery survey, accelerated growth and release, coastal fall Chinook stock assessment, and shad and striped bass studies. Describes the beginning of the Salmon River Project.}, month = {1974/1975}, address = {Portland, Or.}, keywords = {Alsea River, Alsea Salmon Hatchery, Chetco River, Chinook salmon = Oncorhynchus tshawytscha, Coho salmon = Oncorhynchus kisutch, Coos River, Coquille River, Elk River, Fall Creek, genetics, habitats, hatcheries, hatchery salmonids, natural resource management, Nestucca River, New River, Salmon River, Shad = Alosa sapidissima, Siuslaw River, Smith River, South Fork Alsea River, Striped Bass = Morone saxatilis, Tenmile Lakes, Trask River, Umpqua River, wild salmonids}, url = {https://ir.library.oregonstate.edu/concern/defaults/5t34sk05j}, author = {McGie, Alan M. and Oregon. Fish Commission Division of Management and Research,} }