@article {83097, title = {Differences in mate pairings of hatchery- and natural-origin coho salmon inferred from offspring genotypes}, journal = {Integrative Organismal Biology}, volume = {3}, number = {1}, year = {2021}, note = {In this open-access article, the authors explore the relationship between genetics and mate selection, potentially quite important in managing hatchery salmonids. {\textquotedblleft}Using genotyping-by-sequencing, we identify single-nucleotide polymorphisms (SNPs) associated with variation in mate pairings from a natural context involving hatchery- and natural-origin coho salmon (Oncorhynchus kisutch){\textquotedblright} (from the Abstract).}, pages = {Article obab020}, keywords = {Calapooya Creek, Coho salmon = Oncorhynchus kisutch, genetics, hatchery salmonids, reproductive behavior, Umpqua River, wild salmonids}, doi = {https://doi.org/10.1093/iob/obab020}, url = {https://academic.oup.com/iob/article/3/1/obab020/6308823 }, author = {Auld, H. L. and Jacobson, D. P. and Rhodes, A. C. and Banks, M. A.} } @article {83269, title = {Landscape genetics of American beaver in coastal Oregon}, journal = {The Journal of Wildlife Management}, volume = {85}, number = {7}, year = {2021}, note = {American beavers have often been moved from one location, where their dams and flooding might be a nuisance, to another, where they help with stream and water table restoration. The authors review the history of trapping and translocations of beavers in the Oregon Coast Range. {\textquotedblleft}Management requires a better understanding of the ability of beaver to disperse and colonize empty habitat, and the distances or landscapes over which a beaver, if translocated, is unlikely to return. We evaluated genetic structure and applied a landscape genetic approach to characterize landscape features that influence genetic flow for beaver in the Coast Range of Oregon.{\textquotedblright} (p.1464)}, month = {2021, Sep.}, pages = {p.1462-1475}, keywords = {Alsea River, Coos River, Coquille River, genetics, geographical distribution, habitats, human impacts, Necanicum River, Nehalem River, Nestucca River, North American beaver = Castor canadensis, North Umpqua River, Siletz River, Siltcoos River, Siuslaw River, Sixes River, South Umpqua River, topography, Trask River, Umpqua River, Wilson River, Yaquina River}, doi = {https://doi.org/10.1002/jwmg.22102}, author = {Epps, Clinton W. and Petro, Vanessa M. and Creech, Tyler G. and Crowhurst, Rachel S. and Weldy, Matthew J. and Taylor, Jimmy D.} } @article {83130, title = {Landscape genetics of American beaver in coastal Oregon}, journal = {The Journal of Wildlife Management}, volume = {85}, number = {7}, year = {2021}, note = {American beavers have often been moved from one location, where their dams and flooding might be a nuisance, to another, where they help with stream and water table restoration. The authors review the history of trapping and translocations of beavers in the Oregon Coast Range. {\textquotedblleft}Management requires a better understanding of the ability of beaver to disperse and colonize empty habitat, and the distances or landscapes over which a beaver, if translocated, is unlikely to return. We evaluated genetic structure and applied a landscape genetic approach to characterize landscape features that influence genetic flow for beaver in the Coast Range of Oregon.{\textquotedblright} (p.1464)}, month = {2021, Sep.}, pages = {p.1462-1475}, keywords = {Alsea River, Coos River, Coquille River, genetics, geographical distribution, habitats, human impacts, Necanicum River, Nehalem River, Nestucca River, North American beaver = Castor canadensis, North Umpqua River, Siletz River, Siltcoos River, Siuslaw River, Sixes River, South Umpqua River, topography, Trask River, Umpqua River, Wilson River, Yaquina River}, doi = {https://doi.org/10.1002/jwmg.22102}, author = {Epps, Clinton W. and Petro, Vanessa M. and Creech, Tyler G. and Crowhurst, Rachel S. and Weldy, Matthew J. and Taylor, Jimmy D.} } @mastersthesis {83199, title = {Marine Mammals Before Extirpation: Using Archaeology to Understand Native American Use of Sea Otters and Whales in Oregon Prior to European Contact}, year = {2021}, note = {In this doctoral dissertation, the author explores Native American exploitation of marine mammals, particularly sea otters. DNA analysis was performed on 20 ancient sea otter specimens from archeological sites at Seaside. Additionally, analysis was performed on 158 cetacean specimens. {\textquotedblleft}These analyses provided new insight regarding precontact ancestral tribal use of sea otters and cetaceans and the historical ecologies of the animals. This dissertation provides a socio-ecological dataset with
implications for potential reintroductions of sea otters and the conservation of cetaceans in Oregon today{\textquotedblright} (from the Abstract).}, pages = {158 p.}, school = {University of Oregon}, type = {Doctoral Dissertation}, edition = {Ph. D.}, chapter = {Dept. of Anthropology}, address = {Eugene, Or.}, keywords = {archeology, Blue whale = Balaenoptera musculus, genetics, Gray whale = Eschrichtius robustus, human impacts, Humpback whale = Megaptera novaeangliae, Lower Umpqua River, Native Americans, Palmrose Site, Par-Tee Site, Sea otter = Enhydra lutris, Seaside (Or.), Tahkenitch Lake, Tahkenitch Landing}, url = {https://scholarsbank.uoregon.edu/xmlui/handle/1794/26714 }, author = {Wellman, Hannah P.} } @article {83030, title = {Assessing the diversity of Western North American Juga (Semisulcospiridae, Gastropoda)}, journal = {Molecular Phylogenetics and Evolution}, volume = {136}, year = {2019}, note = {Before genetic analysis, taxonomists relied on differences in morphology to identify different species. This practice had its limitations. Genetic science has revolutionized taxonomy. In this article, the authors describe their use of genetic analysis to test the diversity of freshwater snails in the genus Juga. These snails are slow to mature, reproduce at a low rate, and do not disperse their offspring widely. These factors make them vulnerable to habitat loss. It is important to identify unique species that may be threatened by changing environmental conditions. Surprisingly, the authors found less genetic diversity within morphological variation than was expected. One author was a Federal employee: therefore, this is an Open Access publication.}, month = {2019, Jul.}, pages = {p.87-103}, keywords = {genetics, Juga spp., North Fork Umpqua River, population biology, Sawyer{\textquoteright}s Rapids, Siuslaw River, taxonomy, Umpqua River, Yoncalla Creek}, doi = {https://doi.org/10.1016/j.ympev.2019.04.009}, url = {https://www.researchgate.net/publication/332279100_Assessing_the_diversity_of_Western_North_American_Juga_Semisulcospiridae_Gastropoda }, author = {Strong, Ellen E. and Whelan, Nathan V.} } @article {83153, title = {Assessing the Feasibility of a Sea Otter Reintroduction to Oregon through a Coupled Natural-Human Lens}, year = {2019}, note = {This report is the product of a National Science Foundation grant designed to encourage interdisciplinary studies among graduate students. The authors assess various locations on the Oregon Coast for suitable sites for reintroducing sea otters. An earlier attempt to reintroduce sea otters from Alaska to Oregon failed, perhaps because the historic Oregon population was more closely related to California sea otters than to the Alaskan otters. Public opinion, possible conflicts and habitat suitability are considered.}, pages = {57 p.}, institution = {Oregon State University}, address = {Corvallis, Or.}, keywords = {archeology, Cape Blanco, commercial fisheries, genetics, habitats, human impacts, population biology, Port Orford, reintroduced species, Sea otter = Enhydra lutris, tourism, Umpqua River, Yaquina River}, url = {https://ir.library.oregonstate.edu/concern/technical_reports/c821gs71d }, author = {Curran, Lorne S. and Kone, Dominique V. and Wickizer, Benjamin J.} } @article {82546, title = {Genetic divergence outpaces phenotypic evolution among threespine stickleback populations in old freshwater habitats}, journal = {Biological Journal of the Linnean Society}, volume = {128}, number = {2}, year = {2019}, note = {The three-spined stickleback is a highly adaptive species, capable of thriving in oceanic, estuarine and freshwater environments. Its abundance and differing life histories make it a good subject for studying the interplay between environment and genetics. In this paper, the authors exhaustively examine the genetic and physiological characteristics of this species. {\textquotedblleft}To address the degree of congruence between genetic and phenotypic divergence, we directly compared Oregon stickleback to much younger (post-glacial) Alaskan populations. We found phenotypic variation in Oregon Stickleback to be primarily partitioned between oceanic and freshwater habitats . . . However, the main axis of genetic divergence was between coastal and inland regions regardless of habitat type{\textquotedblright} (from the Abstract). Interestingly, scattered populations of inland fish retain physical characteristics typical of the oceanic residents.}, month = {2019, Oct.}, pages = {p.415{\textendash}434}, keywords = {Alaska, Columbia River, Coos River Basin, Crooked River, Cushman Slough (Siuslaw), Dean Creek (Umpqua), Deschutes River Basin,, evolution, genetics, geography, Lily Lake (Siuslaw), Luckiamute River Basin, McKenzie River Basin, Millport Slough (Siletz), Molalla River, morphology, Oregon, Page Road (Umpqua), phenology, population biology, Santiam River Basin, Siletz River Basin, Siuslaw River Basin, South Jetty (Siuslaw), Ten Mile Creek Basin, Three-spined stickleback = Gasterosteus aculeatus, Umpqua River Basin, Willamette River Basin}, doi = {https://doi.org/10.1093/biolinnean/blz106}, author = {Currey, Mark C. and Bassham, Susan L. and Cresko, William A.} } @mastersthesis {83031, title = {Natural Chimerism in the Invasive Colonial Ascidian Didemnum vexillum}, volume = {M.S.}, year = {2019}, note = {{\textquotedblleft}Colonial, asexually reproducing organisms are typically treated as genetically homogenous entities composed of clonal units. However, processes such as fusion and somatic mutation may lead to the integration of multiple genetic lines in a single physiologically continuous organism. This state, known as chimerism, has been documented in a broad range of sessile modular taxa, including plants, fungi, slime molds, and colonial metazoans such as ascidians.{\textquotedblright} (from the Abstract) This thesis describes a process to quantify how much chimerism was present in a given colony. Twenty tunicate colonies were studied in Winchester Bay, and fifteen colonies in Half Moon Bay, California. The Umpqua River estuary colonies had about 70\% chimerism, which is the highest percentage of chimerism identified in colonies studied to date.}, pages = {63 p.}, school = {San Francisco State University}, address = {San Francisco, Ca.}, keywords = {aquatic invertebrates, genetics, introduced species, molecular biology, sea vomit = Didemnum vexillum, taxonomy, tunicates, Umpqua River estuary, Umpqua triangle, Winchester Bay}, url = {https://scholarworks.calstate.edu/concern/theses/2227mr486}, author = {Weinberg, Rachel Beth} } @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 {83014, title = {Formation of population genetic structure following the introduction and establishment of non-native American shad (Alosa sapidissima) along the Pacific Coast of North America}, journal = {Biological Invasions }, volume = {20}, year = {2018}, note = {American shad is a kind of herring native to the Atlantic coast of North America. Like the salmon, it is anadromous, spending part of its life cycle in freshwater and part in the ocean. Between 1871 and 1886, shad were introduced to the Sacramento River in California and to the Columbia River. These introductions were enough to allow the fish to spread along the west coast, and there is a significant population resident in the Umpqua River. In this article, the authors explain how they were able to use genetic microsatellite locations to identify different populations of shad. They explore what genetic differences can tell them about the different populations. It is interesting to note that some shad in the Columbia River have adopted unique freshwater life cycles, and one landlocked population also has a freshwater life cycle. The data tends to show that most shad are faithful to the locations where they have spread, and tend not to stray much beyond the original founding event. This is true of the shad in the Umpqua River. }, month = {2018, Nov.}, pages = {p.3123{\textendash}3143}, keywords = {Columbia River, genetics, geographic distribution, introduced species, Klamath River, life history, population biology, Rogue River, Shad = Alosa sapidissima, Umpqua River}, doi = {https://doi.org/10.1007/s10530-018-1763-7 }, author = {Hasselman, Daniel J. and Bentzen, Paul and Narum, Shawn R. and Quinn, Thomas P.} } @article {83020, title = {Two additional western United States freshwater snails named for Terrence Frest}, journal = {The Dredgings }, volume = {58 }, year = {2018}, note = {This article describes several molluscan species including some named after Terrence Frest. Among the snails described are two species of pebblesnails found in the Umpqua River drainage. Color photographs.}, pages = {p.3-5 }, keywords = {aquatic invertebrates, Fluminicola umpquaensis = Jade pebblesnail, Fluminicola fresti = Frest{\textquoteright}s pebblesnail, gastropods, genetics, molluscs, new species description, North Umpqua River, South Umpqua River, taxonomy}, url = {https://www.bily.com/pnwsc/web-content/Articles/Two-additional-western-United-States-freshwater-snails-named-for-Terrence-Frest.pdf}, author = {Johannes, Edward J.} } @article {83085, title = {Umpqua River spring Chinook}, year = {2016}, note = {In two parts. Part 2 may be obtained from the State Library website. Subtitled: Stock 55. The original (2006) version of this report is available at: https://digital.osl.state.or.us/islandora/object/osl\%3A951412}, month = {2016, Aug.23}, institution = {Oregon Dept. of Fish and Wildlife}, address = {[Salem, Or.?]}, keywords = {Chinook salmon = Oncorhynchus tshawytscha, genetics, hatcheries, hatchery salmonids, North Umpqua River, Rock Creek, wild salmonids}, url = {https://digital.osl.state.or.us/islandora/object/osl\%3A951411 }, author = {Oregon. Dept. of Fish and Wildlife,} } @inbook {77161, title = {Historical biogeography of Pacifastacus crayfishes and their branchiobdellidan and entocytherid ectosymbionts in western North America}, booktitle = {Freshwater Crayfish: A Global Overview}, year = {2015}, note = {This book chapter discusses some freshwater crayfish that are common in coastal streams. It goes extensively into the biogeography of signal crayfish and events that influenced their distribution, including volcanism, glaciation, glacial-era floods, and stream captures. The fossil record is considered. The Columbia River signal crayfish (P leniusculus trowbridgii) is the subspecies found in most Oregon coastal streams.}, pages = {p.404-447}, publisher = {CRC Press}, organization = {CRC Press}, keywords = {aquatic invertebrates, Columbia River signal crayfish = Pacifastacus leniusculus trowbridgii, crawdads, crustaceans, genetics, geographical distribution, morphology, Signal crayfish = Pacifastacus leniusculus leniusculus, Siuslaw River, taxonomy, Umpqua River}, author = {Larson, Eric R. and Williams, B.W.}, editor = {Kawai, T. and Faulkes, Z. and Scholtz, G.} } @article {77011, title = {Influence of immune-relevant genotype on the reproductive success of a salmonid alternative mating strategy}, journal = {Journal of Fish Biology }, volume = {86}, year = {2015}, note = {Jack coho salmon mature a year early and are smaller than normally mature spawning male salmon. They tend to use a {\textquotedblleft}sneaker{\textquotedblright} mating strategy, rather than fighting for the attentions of females. Olfactory cues enable salmon to identify other salmon with compatible immune defenses. This study looks at {\textquotedblleft}the major histocompatibility complex (MHC), the central component of the vertebrate immune system,{\textquotedblright} to see if compatibility with this system influences mate choices and reproductive success. (p.872), and if there were differences in these reproductive strategies between wild and hatchery salmon.}, pages = {p.871{\textendash}881}, keywords = {Calapooya Creek, Coho salmon = Oncorhynchus kisutch, genetics, Nonpareil Dam, reproductive behavior, Umpqua River}, doi = {doi:10.1111/jfb.12597}, author = {O{\textquoteright}Malley, Kathleen G. and Perales, B. and Whitcomb, A. C.} } @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 {51351, title = {Geographic range and structure of cryptic genetic diversity among Pacific North American populations of the non-native amphipod Grandidierella japonica}, journal = {Biological Invasions}, volume = {15}, year = {2013}, note = {In this article, the authors attempt to reconstruct the invasion history of the introduced amphipod Gradidierella japonica. DNA analysis shows two distinct groups {\textendash} one from San Francisco south, and the other north of San Francisco. There are significant genetic differences between the two groups, which, coupled with low genetic diversity within each group, suggests that there were two separate introductions of this species to the West Coast.}, month = {2013}, pages = {p.2415{\textendash}2428}, keywords = {amphipods, Columbia River estuary, Coos Bay, crustaceans, genetics, Grandidierella japonica, introduced species, Puget Sound, San Francisco Bay, Umpqua River estuary, Winchester Bay, Yaquina Bay}, doi = {10.1007/s10530-013-0462-7}, author = {Pilgrim, Erik M. and Blum, Michael J. and Reusser, Deborah A. and Lee II, Henry and Darling, John A.} } @article {36401, title = {Geography of the circadian gene clock and photoperiodic response in western North American populations of the three-spined stickleback Gasterosteus aculeatus}, journal = {Journal of Fish Biology}, volume = {82}, number = {3}, year = {2013}, note = {Many animals use the timing of day length to anticipate changes in their environments. Day length is closely linked to seasonal activities such as reproduction. This article describes a study of a specific gene, the clock gene, and looked at variations in length of the polyglutamine domain of the clock protein in the three-spined stickleback. Sticklebacks from widely varying latitudes (northern Alaska and southern Oregon) were examined to see if variations in length of the polyglutamine domain corresponded with different latitudes. The study found no significant variation in length, and photoperiodic responses were similar in the differing latitudes.. }, month = {2013, Mar.}, pages = {p.827{\textendash}839}, keywords = {circadian clock, Eel Creek, genetics, light, Miner Creek, Prosser Slough (Cushman Slough), reproductive behavior, Siuslaw River, Smith River, Three-spined stickleback = Gasterosteus aculeatus, Umpqua River, Winchester Marsh}, doi = {doi:10.1111/jfb.12024}, author = {O{\textquoteright}Brien, C. and Unruh, L. and Zimmerman, C. and Bradshaw, W. E. and Holzapfel, C. M. and Cresko, W. A.} } @article {36186, title = {Timing of population fragmentation in a vulnerable minnow, the Umpqua chub, and the role of nonnative predators}, journal = {Transactions of the American Fisheries Society}, volume = {14}, number = {2}, year = {2013}, note = {This is a study of the effects of population fragmentation on the genetic diversity of the Umpqua chub, a sensitive-threatened native species in Oregon.}, month = {2013, Mar.}, pages = {p.447-457}, keywords = {Calapooya Creek, Cow Creek, depleted populations, Elk Creek, genetics, invasive species, Olalla Creek, population biology, Smallmouth Bass = Micropterus dolomieu, Smith River, South Umpqua River, Umpqua chub = Oregonichthys kalawatseti, Umpqua River}, doi = {10.1080/00028487.2012.728166}, author = {O{\textquoteright}Malley, Kathleen G. and Markle, Douglas F. and Ardren, William R.} } @article {36511, title = {Umpqua Coho Salmon Genetic Pedigree}, year = {2013}, note = {{\textquotedblleft}Data, pedigrees, reports and manuscripts herein are from an investigation conducted with coho salmon of the Umpqua River in southern Oregon from 2001-2009. They relate to a study investigating several areas of uncertainty about the use of salmon hatcheries to increase the abundance of wild populations{\textellipsis}{\textquotedblright} (from the Abstract) Four files are included here: a general description, a file of metadata for field names, a file of genetic data, and a completion report.}, keywords = {Calapooya Creek, Coho salmon = Oncorhynchus kisutch, dataset, fecundity, genetics, hatchery salmonids, Rock Creek Fish Hatchery, Umpqua River, wild salmonids}, url = {https://ir.library.oregonstate.edu/concern/datasets/8336h610p}, author = {Banks, Michael A. and Blouin, Michael S. and Moyer, Gregory R. and Theriault, Veronique and Whitcomb, Amelia and Loomis, David and Jackson, Laura S.} } @mastersthesis {38651, title = {Variation in the Timing of Coho Salmon (Oncorhynchus kisutch) Migration and Spawning Relative to River Discharge and Temperature}, year = {2013}, note = {This very interesting study examines different factors that induce salmon to begin their migrations towards spawning grounds. {\textquotedblleft}This study compares interannual patterns in the timing of coho mid-river migration in the North Umpqua (180 km up river from the estuary) and the initiation of spawn timing in the Smith River basins (Oregon) with river discharge and water temperature data to ascertain whether these behaviors are driven by fluvial conditions. Additionally, we used this data to identify the window over which most migration and spawning takes place in our test systems.{\textquotedblright} (from the Abstract) The North Umpqua study used Winchester Dam passage data for 1998-2010. In the Smith River study, the author contrasted data from stream gauging stations at five locations in the basin with observations of run timing. The major professor was Mary V. Santelmann.}, pages = {146 p.}, school = {Oregon State University}, type = {Masters Thesis}, edition = {M.S.}, chapter = {Water Resources Science}, address = {Corvallis, Or.}, keywords = {Beaver Creek (Smith River), climate, Coho salmon = Oncorhynchus kisutch, genetics, Mosetown Creek (Smith River), North Sister Creek (Smith River), North Umpqua River, Panther Creek (Smith River), phenology, precipitation, reproductive behavior, Smith River Basin, spatial distribution, temporal distribution, water temperature, West Fork Smith River, Winchester Dam}, url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/ff365880x}, author = {LovellFord, Rachel M.} } @article {34526, title = {Genetic diversity, endemism and phylogeny of lampreys within the genus Lampetra sensu stricto (Petromyzontiformes: Petromyzontidae) in western North America}, journal = {Journal of Fish Biology}, volume = {81}, number = {6}, year = {2012}, note = {Describes the phylogenetic relationships between West Coast lamprey populations. The Siuslaw River brook lamprey population was among the most genetically distinct.}, month = {2012, Nov.}, pages = {p.1891-1914}, keywords = {Alsea River, Coos River, Cow Creek, East Fork Millicoma River, Fishawk Creek, genetics, Mill Creek, Necanicum River, Nehalem River, North Fork Siuslaw River, Pacific lamprey = Entosphenus tridentatus (Lampetra tridentata), River lamprey = Lampetra ayresi, Siuslaw River, taxonomy, Umpqua River, Western brook lamprey = Lampetra richardsoni, Wilson River, Yaquina River}, doi = {10.1111/j.1095-8649.2012.03417.x}, author = {Boguski, D. A. and Reid, S. B. and Goodman, D. H. and Docker, M. F.} } @mastersthesis {36151, title = {Genetic Population Structure and Cryptic Speciation of Ghost Shrimp (Neotrypaea californiensis) in North American West Coast Estuaries}, year = {2012}, note = {Surveyed the West Coast from Puget Sound to San Diego to study the genetics of the ghost shrimp population and thereby infer the potential for larval dispersal in ghost shrimp. {\textquotedblleft}Multiple haplotypes were shared among 346 adult ghost shrimp specimens collected from estuaries in Washington, Oregon, and California indicated that larvae of this species are transported across great distances during the pelagic dispersal phase of development.{\textquotedblright} The author also found the population structure was influenced by {\textquotedblleft}the presence of three putative cryptic species that were deeply divergent from N. californiensis.{\textquotedblright} (from the Abstract) Paper 4232.}, month = {2012, Dec.}, pages = {52 p.}, school = {San Jose State University}, type = {Masters Thesis}, edition = {M.S.}, chapter = {Dept. of Biological Sciences}, address = {San Jose, Calif.}, keywords = {Alsea Bay, Columbia River, Coos Bay, genetics, Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis), Heceta Head, life history information, Nestucca Bay, population biology, theses, Tillamook Bay, Umpqua River estuary, Winchester Bay, Yaquina Bay, Yaquina Head}, doi = {https://doi.org/10.31979/etd.p76q-dprs }, url = {https://scholarworks.sjsu.edu/etd_theses/4232/}, author = {Gille, Daphne Anne} } @mastersthesis {34641, title = {Mate Choice of Wild Spawning Coho Salmon (Oncorhynchus kisutch) in the Umpqua River, Oregon}, year = {2012}, note = {When hatchery-reared salmon spawn in the wild, there is evidence that they have less reproductive success than wild salmon. This study considers mate choice as a possible mechanism that contributes to greater or less reproductive success in salmonids. Wild-spawning coho salmon from the Umpqua River were examined in 2005 and 2006. {\textquotedblleft}We tested for: (1) a departure from random expectations with regard to mate pair allelic diversity at immune-relevant markers, (2) a correlation between immune-relevant gene diversity and mate pair RS [reproductive success], and (3) distinguishable differences between mate choice strategies used by hatchery-reared and wild origin coho.{\textquotedblright} (from the Abstract)}, pages = {91 p.}, school = {Oregon State University}, type = {Masters Thesis}, edition = {M.S.}, chapter = {Dept. of Fisheries and Wildlife, Fisheries Science}, address = {Corvallis, Or.}, keywords = {Calapooya Creek, Coho salmon = Oncorhynchus kisutch, depleted populations, fecundity, genetics, hatchery salmonids, Nonpareil Dam, reproductive behavior, statistical analysis, Umpqua River, wild salmonids}, url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/zs25xc94n}, author = {Whitcomb, Amelia C.} } @article {26906, title = {Electronic tagging of green sturgeon reveals population structure and movement among estuaries}, journal = {Transactions of the American Fisheries Society}, volume = {140}, number = {1}, year = {2011}, note = {Green sturgeon spawn in a limited number of streams on the West Coast, including the Columbia, Rogue and Klamath rivers. In this study, young sturgeon were tagged and followed to see where they went. After spawning, they migrate and use many Pacific Coast estuaries, including the Umpqua River. Heaviest sturgeon use on the Umpqua is in the summer with some autumn use. Most Umpqua River green sturgeon spawned in the Rogue and Klamath rivers, although two sturgeon from the Sacramento River were found in the Umpqua. The study points out that sturgeon can use a variety of habitats and that keeping different habitats usable is important for their survival. }, pages = {p.108-122}, keywords = {Alsea Bay, Columbia River, Coos Bay, Coquille River, feeding behavior, genetics, Gray{\textquoteright}s Harbor, Green sturgeon = Acipenser medirostris, habitats, Humboldt Bay, Klamath River, life history information, Puget Sound, Rogue River, Sacramento River, San Francisco Bay, San Pablo Bay, Siuslaw River, spatial distribution, temporal distribution, Umpqua River, Willapa Bay, Yaquina Bay}, doi = {10.1080/00028487.2011.557017}, author = {Lindley, Steven T. and Erickson, Daniel L. and Moser, Mary L. and Williams, Greg and Langness, Olaf P. and McCovey, Barry W., Jr. and Belchik, Michael and Vogel, Dave and Pinnix, William and Kelly, John T. and Heublein, Joseph C. and Klimley, A. Peter} } @article {26901, title = {Rangewide phylogeography and landscape genetics of the Western U.S. endemic frog Rana boylii (Ranidae): implications for the conservation of frogs and rivers}, journal = {Conservation Genetics}, volume = {12}, number = {1}, year = {2011}, note = {The foothill yellow-legged frog is a species with a declining population, and is listed as a Species of Special Concern in California. This paper looks at genetic analysis to identify distinct subpopulations. The Umpqua Basin population is interesting in that it is more closely related to California populations than to Oregon groups. The authors urge that genetic biodiversity be considered in conservation plans, and that unique populations be preserved.}, month = {2011, Feb.}, pages = {p.269-284}, keywords = {conservation, Depleted population, foothill yellow-legged frog=Rana boylii, genetics, Umpqua River Basin}, doi = {10.1007/s10592-010-0138-0}, author = {Lind, Amy J. and Spinks, Phillip Q. and Fellers, Gary M. and Sjaffer. H. Bradley} } @article {26931, title = {Reduced reproductive success of hatchery coho salmon in the wild: insights into most likely mechanisms}, journal = {Molecular Ecology}, volume = {20}, number = {9}, year = {2011}, note = {Hatchery salmonids have been shown to have less reproductive success than wild salmonids. This phenomenon has been extensively documented in steelhead. In this paper, the authors examine a hatchery program on the North Umpqua River to see if hatchery coho salmon also are less successful at breeding. Mature coho are less successful, particularly males, although hatchery jack salmon were about as successful as wild jacks. Even the most up-to-date hatchery practices such as using wild brood stock and allowing mating by pairs of fish were not enough to overcome the disadvantage suffered by hatchery coho. Possible mechanisms for the lack of reproductive success in hatchery coho are explored.}, month = {2011, May}, pages = {p.1860-1869}, keywords = {Calapooya Creek, Coho salmon = Oncorhynchus kisutch, Elk Creek, fecundity, genetics, hatcheries, hatchery salmonids, Nonpareil Dam, North Umpqua River, reproductive behavior, Rock Creek Hatchery, Umpqua River, wild salmonids, Winchester Dam}, doi = {10.1111/j.1365-294X.2011.05058.x}, author = {Th{\'e}riault, V{\'e}ronique and Moyer, Gregory R. and Jackson, Laura S. and Blouin, Michael S. and Banks, Michael A.} } @article {83282, title = {Umpqua Chub Population Estimate: Final Report}, year = {2011}, note = {"Over the past several decades the distribution of Umpqua chub has contracted such that there are now six fragmented populations. Because there is little information on the biology of Umpqua chub and concern has been raised about their ability to persist in the presence of smallmouth bass, we began a collaborative effort to better understand their demographics and genetics." In 2008, the authros took 25 specimens from each of the sic isolated populations for genetic analysis, and repeated the procedure in 2010 "for potential future analysis." (p.2) "USFWS Grant $\#$ E-2-54"}, pages = {27 p.}, institution = {Oregon State University}, address = {Corvallis, Or.}, keywords = {Calapooya Creek, Cow Creek, demographics, depleted populations, Elk Creek, genetics, geographic distribution, Olalla Creek, population biology, predation, Smallmouth Bass = Micropterus dolomieu, Smith River, South Umpqua River, species list, Umpqua chub = Oregonichthys kalawatseti}, url = {https://agsci.oregonstate.edu/sites/agscid7/files/umpqua_chub_final_report_01_04_11.pdf}, author = {Markle, Douglas F. and O{\textquoteright}Malley, Kathleen and Terwilliger, Mark and Baki, Pete and Truemper, Holly and Simon, David C.} } @article {26776, title = {Polyphyly of the pikeminnows (Teleostei: Cyprinidae) inferred using mitochondrial DNA sequences}, journal = {Transactions of the American Fisheries Society}, volume = {139}, number = {1}, year = {2010}, note = {Genetic relationships between Colorado pikeminnow, northern (or Oregon) pikeminnow, Sacramento pikeminnow, Umpqua pikeminnow and hardhead are explored and related to geologic events in the western United States.}, pages = {p.303-315}, keywords = {Elk Creek, evolution, genetics, geology, morphology, Oregon pikeminnow = Ptychocheilus oregonensis, Siuslaw River, spatial distribution, taxonomy, Umpqua pikeminnow = Ptychocheilus umpquae}, doi = {10.1577/T09-075.1}, author = {Houston, Derek D. and Ogden, T. Heath and Whiting, Michael F. and Shiozawa, Dennis K.} } @article {26836, title = {Survival and life history characteristics among wild and hatchery coho salmon (Oncorhynchus kisutch) returns: how do unfed fry differ from smolt releases?}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, volume = {67}, number = {3}, year = {2010}, note = {Is it better to release hatchery salmon when they are younger (fry) or more mature (smolts)? This study found that releasing hatchery coho salmon as unfed fry produced results closer to the behavior of wild coho. Behavior of jack salmon and run timing are also discussed.}, month = {2010, Mar.}, pages = {p.486-497}, keywords = {Calapooya Creek, Coho salmon = Oncorhynchus kisutch, Coon Creek, Elk Creek, fecundity, Gassy Creek, genetics, hatcheries, hatchery salmonids, juvenile fish, life history information, Nonpareil Dam, North Umpqua River, reproductive behavior, Rock Creek Hatchery, wild salmonids, Winchester Dam}, doi = {10.1139/cjfas-2013-0501}, author = {Th{\'e}riault, V{\'e}ronique and Moyer, Gregory R. and Banks, Michael 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 {26736, title = {Phylogeography of the longnose dace (Rhinichthys cataractae) species group in northwestern North America {\textemdash} the origin and evolution of the Umpqua and Millicoma dace}, journal = {Canadian Journal of Zoology}, volume = {87}, number = {6}, year = {2009}, note = {Did the Millicoma dace and its morphologically different close relative the Umpqua dace descend from a common ancestor, or did the Millicoma dace descend from the Umpqua dace? The authors use genetic sequences to find data that support the latter hypothesis.}, month = {2009, Jun.}, pages = {p.491-497}, keywords = {Columbia River, Coos River, evolution, genetics, Millicoma dace = Rhinicthys cataractae ssp., morphology, North Fork Umpqua River, Smith River, South Fork Umpqua River, spatial distribution, taxonomy, Umpqua dace = Rhinicthys cataractae, Umpqua River, Willamette River}, doi = {10.1139/Z09-036}, author = {McPhail, J. D. and Taylor, E. B.} } @article {26641, title = {Genetic structure, migration, and patterns of allelic richness among coho salmon (Oncorhynchus kisutch) populations of the Oregon coast}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, volume = {65}, number = {7}, year = {2008}, note = {Studied genotypic data from eight microsatellite loci to characterize Oregon coastal coho salmon. "The Coos, Umpqua, Smith and Coquille rivers appear to form a southern group, whereas the Nehalem, Tillamook, Wilson, Necanicum, Nestucca, Trask, and Salmon rivers form a loosely defined northern group.""...the coastal lakes flanking the mouth of the Umpqua River form a clade together with the lower reaches of this river." (p.1278) }, pages = {p.1274-1285}, keywords = {Coho salmon = Oncorhynchus kisutch, genetics, geographic distribution, population biology}, doi = {10.1139/F08-044}, author = {Johnson, Marc Aaron and Banks, Michael A.} } @mastersthesis {26646, title = {The Oregon Coastal Subprovince, a New Biogeographic Subprovince for Primary Freshwater Fishes in Oregon}, year = {2008}, note = {"The goals of this study were: 1) to describe fishes in the genera Catostomus and Ptychocheilus in the Oregon Coastal Subprovince using morphological data and mitochondrial cytochrome b sequences; 2) to investigate the relationships of fishes in the Oregon Coastal Subprovince to nearby provinces; and 3) to address competing distribution theories." (from the Abstract) The author proposes that, based on the endemic distribution of freshwater fishes, the Oregon coast may deserve designation as a biogeographic subprovince, ranging from the Miami River in the north to the Sixes River in the south. Possible explanations for the distribution of these fishes are considered. The major professor was Douglas Markle.}, pages = {194 p.}, school = {Oregon State University}, type = {Doctoral Dissertation}, edition = {Ph. D.}, chapter = {Dept. of Fisheries and Wildlife, Fisheries Science}, address = {Corvallis, Or.}, keywords = {Colorado pikeminnow = Ptychocheilus lucius, Coos River, Coquille River, genetics, geology, Klamath smallscale sucker = Catostomus rimiculus, Largescale sucker = Catostomus macrocheilus, Nehalem River, Oregon pikeminnow = Ptychocheilus oregonensis, paleosciences, Ptychocheilus grandis = Sacramento pikeminnow, Siuslaw River, Sixes River, spatial distribution, taxonomy, theses, Tyee sucker = Catostomus tsiltcoosensis, Umpqua River, Umpqua River Basin, Umpqua squawfish = Ptychocheilus umpquae}, url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/76537380b}, author = {Kettratad, Jes} } @article {26566, title = {Characterization of 16 highly variable tetranucleotide microsatellite loci for Oregon chub (Oregonichthys crameri) and cross amplification in Umpqua chub (O. kalawatseti)}, journal = {Molecular Ecology Notes}, volume = {7}, number = {5}, year = {2007}, note = {"We describe the isolation and development of 16 polymorphic tetranucleotide microsatellite loci for the endangered Oregon chub (Oregonichthys crameri)." (from the Abstract)}, month = {2007, Sep.}, pages = {p.808-810}, keywords = {genetics, Oregon chub = Oregonichthys crameri, Umpqua chub = Oregonichthys kalawatseti}, isbn = {1471-8278}, doi = {10.1111/j.1471-8286.2007.01711.x}, author = {Ardren, William R. and Amata, Lara and Whelen, Jennifer and Dehaan, Patrick W.} } @article {26611, title = {Oregon Coast Coho Conservation Plan for the State of Oregon}, year = {2007}, note = {"The purpose of this Conservation Plan is to ensure the continued viability of the Oregon Coast Coho Evolutionary Significant Unit (ESU) and to achieve a desired status that provides substantial ecological and societal benefits." (p.10) Date from cover, "March 16, 2007."}, keywords = {Coho salmon = Oncorhynchus kisutch, genetics, habitats, hatcheries, hatchery salmonids, Lower Umpqua River, Middle Umpqua River, natural resource management, North Umpqua River, South Umpqua River, water quality, water use, wild salmonids}, url = {https://digital.osl.state.or.us/islandora/object/osl\%3A942595}, author = {Oregon. Dept. of Fish and Wildlife,} } @book {26451, title = {Umpqua River spring Chinook}, series = {Hatchery and Genetic Management Plan }, year = {2006}, note = {Subtitled: Stock 55. An updated (2016) version of this report is available at: https://digital.osl.state.or.us/islandora/object/osl\%3A951411 }, month = {2006, Jan.24}, pages = {44 p.}, publisher = {Oregon Dept. of Fish and Wildlife}, organization = {Oregon Dept. of Fish and Wildlife}, address = {[Salem, Or.?]}, keywords = {Chinook salmon = Oncorhynchus tshawytscha, genetics, hatcheries, hatchery salmonids, North Umpqua River, Rock Creek, wild salmonids}, url = {https://digital.osl.state.or.us/islandora/object/osl\%3A951412}, author = {Oregon. Dept. of Fish and Wildlife,} } @article {26356, title = {Green Sturgeon (Acipenser medirostris) Status Review Update}, year = {2005}, note = {This is an update to the original (2002) status review. There seems to be a division between the Rogue and Klamath River green sturgeon, and Sacramento River stugeon and more southern rivers. The Umpqua stock is actually a blend of these two discrete population segments, but is genetically closer to the Rogue and Klamath sturgeons. "Spawning does appear to take place in the Umpqua River, but is probably rare." (p.12)}, pages = {35 p.}, institution = {National Marine Fisheries Service}, address = {Santa Cruz, Ca.}, keywords = {depleted populations, genetics, Green sturgeon = Acipenser medirostris, natural resource management, spatial distribution, temporal distribution, Umpqua River}, url = {https://tinyurl.com/2p85w85v} } @article {26256, 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, Calapooya Creek, Chinook salmon = Oncorhynchus tshawytscha, chum salmon = Oncorhynchus keta, Coho salmon = Oncorhynchus kisutch, Coos Bay, Coquille River, Cow Creek, depleted populations, Devil{\textquoteright}s Lake, Elk Creek, fecundity, genetics, hatcheries, human impacts, hybridization, Kilchis River, Miami River, Necanicum River, Nehalem River, Nestucca River, Oncorhynchus species, population biology, population count, reproductive behavior, Rogue River, Salmon River, salmonid species, Siletz River, Siuslaw River, Smith River, South Umpqua River, statistical analysis, steelhead trout = Oncorhynchus mykiss, Tenmile Lake, Tillamook Bay, Tillamook River, Trask River, Umpqua River, Wilson River, Yaquina River}, url = {http://www.nwfsc.noaa.gov/assets/25/203_08302005_132955_brttechmemo66final2.pdf}, author = {Northwest Fisheries Science Center (U.S.).}, editor = {Good, Thomas P. and Waples, Robin S. and Adams, Pete} } @article {26156, title = {Genetic population structure of central Oregon Coast coho salmon (Oncorhynchus kisutch)}, journal = {Conservation Genetics}, volume = {5}, number = {6}, year = {2004}, note = {The "Umpqua Complex" includes the Smith River, Elk River, Calapooya Creek and Rock Creek. These coho populations are closely related. Umpqua River coho seem to be genetically distinct.}, month = {2004, Nov.}, pages = {p.797-812}, keywords = {Coho salmon = Oncorhynchus kisutch, genetics, population biology}, doi = {10.1007/s10592-004-1983-5}, author = {Ford, Michael J. and Teel, David J. and Van Doornik, Donald M. and Kuligowski, David and Lawson, Peter W.} } @mastersthesis {26161, title = {Landscape-Scale Evaluation of Genetic Structure among Barrier-Isolated Populations of Coastal Cutthroat Trout, Oncorhynchus clarki clarki}, year = {2004}, note = {Studied populations of coastal cutthroat trout, all of which were isolated above significant barriers to downstream travel (waterfalls). Among the findings were that Cascade headwater fish tended to live in a single channel and be more vulnerable to habitat disruptions such as landslides, while coastal streams "tended to have more complex drainage patterns and fewer within-watershed obstacles to dispersal..." and were therefore more likely to retain genetic diversity. More genetic diversity was found than expected.}, pages = {43 p.}, school = {Oregon State University}, type = {Masters Thesis}, edition = {M.S.}, chapter = {Dept. of Fisheries and Wildlife, Fisheries Science}, address = {Corvallis, Or.}, keywords = {Buckeye Creek, Camp Creek, Cavitt Creek, Coffee Creek, Coos River Basin, Coquille River Basin, cutthroat trout = Oncorhynchus clarki, genetics, habitats, Miller Creek, population biology, Rock Creek, Rogue River Basin, theses, Umpqua River Basin, Willamette River Basin}, url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/2227ms51q}, author = {Guy, Troy J.} } @mastersthesis {26146, title = {Factors Influencing Within-Watershed Genetic Variation of Coastal Cutthroat Trout in Camp Creek, Oregon}, year = {2003}, note = {Headwater streams often have fragmented habitats and barriers to migration such as waterfalls and culverts that cause fish populations to be isolated. This study showed that cutthroat trout in Camp Creek "exist as many small, partially independent populations connected by low to moderate levels of gene flow." The isolation can lead to "reduced cutthroat trout genetic diversity" and can compromise the potential of the population to persist. (from the Abstract) Major professor was Robert Gresswell.}, pages = {52 p.}, school = {Oregon State University}, type = {Masters Thesis}, edition = {M.S.}, chapter = {Dept. of Fisheries and Wildlife, Fisheries Science}, address = {Corvallis, Or.}, keywords = {Camp Creek, cutthroat trout = Oncorhynchus clarki, genetics, geographic distribution, habitats, Lower Umpqua River, Mill Creek, theses}, url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/1n79h791s}, author = {Wofford, John E.B.} } @article {25931, title = {Status Review for North American Green Sturgeon, Acipensis medirostris}, year = {2002}, note = {Reviews the 2001 petition to give green sturgeon threatened or endangered status. For both the northern and southern "distinct population segments," the review committee concluded "that there is not sufficient information that shows green sturgeon in this DPS are in danger of extinction or would be likely to become so in the foreseeable future." (p.18-19)}, month = {2002, Jun.}, pages = {49 p.}, keywords = {commercial fisheries, Coos Bay, depleted populations, fecundity, feeding behavior, genetics, Green sturgeon = Acipenser medirostris, growth, habitats, juvenile fish, life history information, natural resource management, predation, recreational fisheries, reproductive behavior, Rogue River, Smith River, statistical analyses, taxonomy, Umpqua River}, url = {https://repository.library.noaa.gov/view/noaa/16288}, author = {Adams, Peter B. and Grimes, Churchill B. and Hightower, Joseph E. and Lindley, Steven T. and Moser, Mary L. and U.S. National Marine Fisheries Service,} } @article {25876, title = {Reducing impacts of hatchery steelhead programs}, volume = {no.2001-01}, year = {2001}, note = {Attempts to determine how many hatchery steelhead were straying into other rivers to spawn, also if the timing of their spawning increased the risk of hatchery steelhead interbreeding with wild fish. Investigated the use of local broodstock in hatcheries, and some methods of reducing interbreeding between hatchery and wild steelhead.}, pages = {88 p.}, institution = {Oregon Dept. of Fish and Wildlife, Fish Division}, address = {Portland, Or.}, keywords = {Alsea River, Chetco River, Coquille River, genetics, hatcheries, hatchery salmonids, Necanicum River, Nehalem River, Nestucca River, reproductive behavior, Rogue River, Siletz River, Siuslaw River, Sixes River, steelhead trout = Oncorhynchus mykiss, Tenmile Creek, Trask River, Umpqua River, wild salmonids, Yachats River, Yaquina River}, url = {https://digital.osl.state.or.us/islandora/object/osl\%3A18493}, author = {Lindsay, Robert Bryan. and Kenaston, K.R. and Schroeder, R. K. and Oregon. Fish Division} } @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.),} } @book {25706, title = {Status review of coastal cutthroat trout from Washington, Oregon, and California}, series = {NOAA Technical Memorandum NMFS-NWFSC}, number = {no.37}, 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}, pages = {292 p.}, 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 {25631, 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. National Marine Fisheries Service}, address = {[Seattle, Wash.] }, keywords = {Alsea River, Chinook salmon = Oncorhynchus tshawytscha, Coos River, Coquille River, 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, Salmon River, salmonid species, Siletz River, Siuslaw River, statistics, Tillamook River, Trask River, Umpqua River, Wilson River, Yachats River, Yaquina River}, url = {https://www.webapps.nwfsc.noaa.gov/assets/25/7190_07042012_124647_Myers.et.al.1998-rev.pdf}, author = {Myers, James M. and Kope, Robert G. and Bryant, Gregory J. and Teel, David J. 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 {25476, 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. 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, history, 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://repository.library.noaa.gov/view/noaa/6218}, 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.} } @proceedings {25406, title = {Summary of biological status review of Umpqua River sea-run cutthroat trout}, year = {1995}, note = {Winchester Dam fish counts show, "From 1946 to 1956, an average of 950 adults passed the dam per year. The run declined precipitously in the late 1950s, followed by a sharp increase in the 1960s and early 1970s during the period when natural fish were supplemented with hatchery releases. In the late 1970s, the run precipitously declined again, and has averaged only 62 adults per year since 1977." (Abstract, p.87) This species was listed as endangered in August, 1966.}, pages = {p.87-102}, publisher = {Oregon Chapter of the American Fisheries Society}, address = {Reedsport, Oregon}, keywords = {Alsea Fish Hatchery, Calapooya Creek, Canton Creek, Canyon Creek, Cavitt Creek, climate, Copeland Creek, Cow Creek, Cutthroat trout = Oncorhynchus clarki clarki, dams, depressed populations, Elk Creek, fecundity, Fish Lake, general ecosystem description, genetics, hatcheries, hybridization, hydrology, Lake Creek, Lemolo Lake, life history information, Little River, Lower Umpqua River, Maideu Lake, North Umpqua River, population biology, population count, reproductive behavior, Scholfield Creek, Smith River, South Umpqua River, Steamboat Creek, Sutherlin Creek, Umpqua River Basin, water temperature, Winchester Dam}, isbn = {0913235997}, author = {Johnson, Orlay W. and Waples, Robin S. and Wainwright, Thomas C. and Neely, Kathleen G. and Waknitz, F. William and Parker, L. Ted}, editor = {Hall, J. D. and Bisson, P. A. and Gresswell, R. E.} } @article {25326, title = {Chromosomal NOR karyotypes and genome size variation among squawfishes of the genus Ptychocheilus (Teleostei: Cyprinidae)}, journal = {Copeia}, number = {1}, year = {1994}, month = {1994}, pages = {p.60-65}, keywords = {genetics, Squafish = Ptychocheilus spp.}, isbn = {0045-8511}, author = {Gold, J. R. and Li, Y.} } @book {25351, title = {Status review for Oregon{\textquoteright}s Umpqua River sea-run cutthroat trout}, series = {NOAA Technical Memorandum NMFS-NWFSC}, number = {15}, year = {1994}, note = {"Although the pattern of abundance and tag/recovery data during the period of supplementation indicated that Alsea River hatchery fish returned as adults to Winchester Dam in some numbers, it is apparent that 15 years of hatchery releases did not result in a viable, self-sustaining population of naturally spawning fish. The unresolved issue is, What do the few remaining anadromous O. clarki represent: remnants of the original Umpqua River gene pool, descendants of the Alsea River hatchery fish, or a mixed lineage? The run-timing shift suggested that an indigenous component may remain." (from the Abstract) This publication discusses the issues surrounding a possible listing of Umpqua River sea-run cutthroat trout. The species was listed as endangered in August, 1996.}, month = {1994}, pages = {122 p.}, publisher = {U.S. Dept. of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service}, organization = {U.S. Dept. of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service}, address = {Seattle, Wash.}, keywords = {Alsea Fish Hatchery, Calapooya Creek, Canton Creek, Canyon Creek, Cavitt Creek, Copeland Creek, Cow Creek, Cutthroat trout = Oncorhynchus clarki clarki, Diamond Lake, Elk Creek, endangered species, genetics, hatcheries, history, Lake Creek, Lemolo Lake, life history information, Little River, natural resource management, North Umpqua River, population biology, population count, Rock Creek, salmonid species, Scholfield Creek, Smith River, South Umpqua River, statistics, Steamboat Creek, Sutherlin Creek, Umpqua River, Umpqua River Basin, Winchester Dam}, url = {https://repository.library.noaa.gov/view/noaa/6171}, author = {Johnson, Orlay W. and Waples, Robin S. and Wainwright, Thomas C. and Neely, Kathleen G. and Waknitz, F. William and Parker, L. Ted} } @article {25096, title = {Geographic variation in population genetic structure of chinook salmon from California and Oregon}, journal = {Fishery Bulletin}, volume = {90}, number = {1}, year = {1991}, note = {Used genetic characteristics to classify Northern California and Southern Oregon hatchery Chinook salmon into five distinct groups. Umpqua Chinook fall into the "Middle Oregon" group, along with Alsea, Coos and Coquille salmon.}, pages = {77-100}, keywords = {Chinook salmon = Oncorhynchus tshawytscha, genetics, straying}, url = {https://spo.nmfs.noaa.gov/sites/default/files/pdf-content/1992/901/gall.pdf}, author = {Gall, Graham A. E. and Bartley, Devin and Bentley, Boyd and Brodziak, Jon and Gomulklewicz, Richard and Mangel, Marc} } @mastersthesis {55366, title = {A Phenotypic Comparison of Thirty-Eight Steelhead (Oncorhynchus mvkiss) Populations from Coastal Oregon}, year = {1990}, note = {Shifts in fish genetics can show how fish interact with their environment. Here, the author looks at coastal steelhead and finds some differences, both in terms of basin size and geographical area. The author notes that, {\textquotedblleft}Steelhead allelic frequencies for several isozymes gradually change in a north to south pattern in populations along the Oregon coast. . . . Small basin populations were shown to have some distinct differences from the large basin populations. While the cause of the differences is not known, the effects of genetic drift on these small, relatively isolated populations is suggested.{\textquotedblright} (p.42) Major professor was Hiram W. Li.}, pages = {55 p.}, school = {Oregon State University}, type = {Masters Thesis}, edition = {M.S.}, chapter = {Dept. of Fisheries and Wildlife}, address = {Corvallis, Or.}, keywords = {Alsea River, Big Creek, Chetco River, Coos River, Coquille River, Cummins Creek, Elk River, Floras Creek, genetics, geographical distribution, hatcheries, hatchery salmonids, Hunter Creek, Miami River, Nehalem River, Nestucca River, Pistol River, Rogue River, Sand Lake Creek, Siletz River, Siuslaw River, Sixes River, Smith River, steelhead trout = Oncorhynchus mykiss, theses, Umpqua River, wild salmonids, Wilson River}, url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/qb98mj12n}, author = {Hatch, Keith Martin} } @mastersthesis {36676, title = {Taxonomic Analyses of the Oregon Chub, Oregonichthys crameri}, year = {1989}, note = {In this thesis, the author examines two populations of the Oregon chub, one group from the Willamette River, and another from the Umpqua River, to see if they might be different species. She concludes that they are sub-species and formally describes them. The two groups have been subsequently recognized as different species. The major professor was Douglas F. Markle.}, pages = {91 p.}, school = {Oregon State University}, type = {Masters Thesis}, edition = {M.S.}, chapter = {Dept. of Fisheries and Wildlife}, address = {Corvallis, Or.}, keywords = {genetics, Oregon chub = Oregonichthys crameri, statistical analysis, taxonomy, theses, Umpqua chub = Oregonichthys kalawatseti, Umpqua River, Willamette River}, url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/2v23vz04m}, author = {Bills, Debra T.} } @mastersthesis {24791, title = {The Relative Effects of Ceratomyxa shasta on Crosses of Resistant and Susceptible Stocks of Summer Steelhead}, year = {1986}, note = {In 1971, after a new fishway was built at Willamette Falls, ODFW introduced summer steelhead into the Upper Willamette River, from stocks from the Siletz and Skamania rivers. The Skamania fish returned, but the steelhead that originated from Siletz River stock did not, due to infection by a myxosporean parasite, Ceratomyxa shasta. Subeequent testing for resistance to infection showed that the Siletz and Umpqua River stocks are susceptible to this infection. This thesis shows that even disease-resistant stocks can have their resistance weakened by interbreeding with less-resistant strains, a potentially dangerous side-effect of hatcheries. The major professor was Hiram Li.}, pages = {19 p.}, school = {Oregon State University}, type = {Masters Thesis}, edition = {M.S.}, chapter = {Dept. of Fisheries and Wildlife}, address = {Corvallis, Or.}, keywords = {Ceratomyxa shasta, genetics, hatcheries, natural resource management, parasites, Siletz River, Skamania River, steelhead trout = Oncorhynchus mykiss, theses, Umpqua River}, url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/zp38wf73f}, author = {Wade, Mark} } @book {24796, title = {The relative effects of Ceratomyxa shasta on crosses of resistant and susceptible stocks of summer steelhead}, series = {Information Reports (Oregon. Fish Division) }, number = { 86-8.}, year = {1986}, note = {In 1971, after a new fishway was built at Willamette Falls, ODFW introduced summer steelhead into the Upper Willamette River, from stocks from the Siletz and Skamania rivers. The Skamania fish returned, but the steelhead that originated from Siletz River stock did not, due to infection by a myxosporean parasite, Ceratomyxa shasta. Subeequent testing for resistance to infection showed that the Siletz and Umpqua River stocks are susceptible to this infection. This work (essentially, the author{\textquoteright}s M.S. thesis) shows that even disease-resistant stocks can have their resistance weakened by interbreeding with less-resistant strains, a potentially dangerous side-effect of hatcheries.}, month = {1986}, pages = {16 p.}, publisher = {Oregon Dept. of Fish and Wildlife, Research and Development Section}, organization = {Oregon Dept. of Fish and Wildlife, Research and Development Section}, address = {Portland, Or.}, keywords = {Ceratomyxa shasta, genetics, hatcheries, natural resource management, parasites, Siletz River, Skamania River, steelhead trout = Oncorhynchus mykiss, Umpqua River}, url = {https://digital.osl.state.or.us/islandora/object/osl:18355}, author = {Wade, M.G.} } @article {24536, 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 {24376, 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) The major professor was Carl B. Schreck.}, pages = {50 p.}, 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} } @proceedings {24276, title = {Life history differences between sympatric populations of rainbow trout and cutthroat trout in relation to fisheries management strategy}, year = {1978}, pages = {p.181-188}, publisher = {Oregon Dept. of Fish and Wildlife, Research and Development Section}, address = {Eugene, Or.}, keywords = {genetics, life history information, population biology, Rainbow trout = Oncorhynchus mykiss}, author = {Nicholas, J. W.}, editor = {Moring, John R.} } @article {24201, 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. Includes table showing shad and striped bass landings on the Umpqua and Smith Rivers in 1975.}, pages = {27 p.}, 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 {24096, title = {Research on Anadromous Fish in Castal 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. }, month = {1974/1975}, pages = {18 p.}, 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, 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,} } @article {23981, title = {Research on Anadromous Fish in Coastal Watersheds of Oregon}, year = {1974}, note = {"Annual Report, July 1, 1973 - June 30, 1974." 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. }, month = {1973/1974}, pages = {22 p.}, 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, 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/r781wg601}, author = {McGie, Alan M. and Oregon. Fish Commission Division of Management and Research,} }