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Abstract -- Many salmonids exhibit partial migration: the phenomenon of populations partitioned into migratory and non-migratory individuals (Jonsson and Jonsson 1993). Oncorhynchus mykiss exhibit a complex ...
Citation Citation
- Title:
- Performance of Progeny From Steelhead and Rainbow Trout Crosses - Final Report 2009
Abstract -- Many salmonids exhibit partial migration: the phenomenon of populations partitioned into migratory and non-migratory individuals (Jonsson and Jonsson 1993). Oncorhynchus mykiss exhibit a complex of life-history strategies ranging from residency in small headwater streams to anadromy involving migrations of hundreds of kilometers. In the Grande Ronde River basin of northeast Oregon, both resident and anadromous life-history forms coexist, and thus populations found there likely exhibit partial migration. Partial migration may have important consequences for anadromous species listed under the Endangered Species Act (ESA). The recent decline of summer steelhead (Oncorhynchus mykiss) populations in the lower Snake River has prompted their listing under the ESA. Declines in steelhead are potentially due to elevated mortality rates associated with anadromous migrations. If resident and anadromous life-history characteristics result from a phenotypically plastic trait (i.e. a genetic trait that is highly variable due to influences from environmental factors), then elevated mortality associated with the anadromous type may be shifting the populations towards residency. Further, although the anadromous expression of the trait may be declining, the trait would not necessarily be lost. Identification of the plasticity of these traits would then be important for the management of these populations. We investigated life history traits of O. mykiss with studies in both the hatchery and natural environment. We anticipated that these complimentary approaches would allow us to evaluate the relationship between the two life-history forms. They should further allow us to explore the feasibility of using hatcheries to produce anadromous progeny from resident parents if the number of anadromous life-history forms becomes severely depressed. The overall goal of this study was to determine the plasticity of life history forms, specifically the ability of resident adults to produce anadromous progeny. Lower Snake River Compensation Plan (LSRCP) ODFW- Eastern Oregon Fish Research (EOFR)
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Abstract -- Bacterial kidney disease (BKD) is a major health problem of cultured Pacific salmon, Oncorhynchus sp. It has been particularly problematic in captive broodstock programs, where the interests ...
Citation Citation
- Title:
- Prevalence of Bacterial Kidney Disease in Natural vs. Hatchery-Reared Adult Chinook Salmon Spawned in a Hatchery and in Nature Information Reports number 2009-06
Abstract -- Bacterial kidney disease (BKD) is a major health problem of cultured Pacific salmon, Oncorhynchus sp. It has been particularly problematic in captive broodstock programs, where the interests of gene conservation and fish health can conflict when spawning females with signs of BKD. Not rearing those fish reduces the genetic diversity of an already depleted population, while rearing those fish may increase the prevalence of BKD in the natural population. We used data collected during spawning at Lookingglass Fish hatchery and on spawning ground surveys to examine the prevalence of BKD, based on enzyme-linked immunosorbent assay optical density (ELISA OD) values, to monitor the prevalence of BKD in natural and hatchery-reared Chinook salmon O. tshawytscha from Grande Ronde and Imnaha basin streams in northeast Oregon. Mean ELISA OD levels differed among all sampled streams from 2004-2008 and was lowest in the Imnaha River salmon (0.0839) and highest in the Minam River (0.1750). Salmon spawned at LFH had a lower mean ELISA OD level (0.086) than those collected from carcasses on spawning ground surveys (0.118). Natural salmon mean ELISA OD level was 0.1058 and 97% were from salmon with ELISA OD level <0.2 and in hatchery salmon, 96% had an ELISA OD level <0.2 and mean ELISA OD level was 0.1138, with no difference between the groups. Over 17 years in the Imnaha River we see no difference in mean ELISA OD levels between natural and hatchery Chinook salmon. There was no difference in mean ELISA OD levels between adult Chinook salmon from wilderness (0.1663) vs. supplemented (0.1184) streams. However, when comparing mean ELISA OD for only natural Chinook salmon carcasses recovered in these streams, we found that mean ELISA OD level was higher in the wilderness streams (0.1676) than in the supplemented streams. Returning adults from the Captive Broodstock F1 generation had a higher mean ELISA OD level (0.1349) than those of Conventional Hatchery Program offspring (0.0957). Annual mean ELISA OD level decreased over time in the Lostine River stock but did not change for any of the other stocks. The data for BKD in Chinook salmon from northeast Oregon streams and hatcheries show that this disease is not prevalent and we found no evidence that the release of hatchery salmon is causing an increase in BKD prevalence in the monitored streams. However, we will continue to monitor this disease.
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Geologic mapping of the Longview-Kelso area and the measurement and description of a composite 650-meter thick stratigraphic section of the Cowlitz Formation (Tc) in Coal Creek using bio-, magneto-, litho-, ...
Citation Citation
- Title:
- Stratigraphy and sedimentology of the middle eocene Cowlitz Formation and adjacent sedimentary and volcanic units in the Longview-Kelso area, southwest Washington
- Author:
- McCutcheon, Mark S.
Geologic mapping of the Longview-Kelso area and the measurement and description of a composite 650-meter thick stratigraphic section of the Cowlitz Formation (Tc) in Coal Creek using bio-, magneto-, litho-, and sequence stratigraphy reveals a complex interplay of Cowlitz micaceous, lithic arkosic shelf to tidal/estuarine to delta plain facies associations, and Grays River basalt lava flows and interbedded basalt volcaniclastics from nearby Grays River eruptive centers (e.g., Mt. Solo and Rocky Point). The lower 100 meters of the Coal Creek section (informal unit 1, Chron 18r) consists of micaceous, lithic arkosic sandstone and siltstone and minor coals, was deposited as part of a highstand system tract (HST) at the base of 3rd order cycle number 3. This unit consists of four dominantly tidal shoaling-upward arkosic sandstone parasequences reflecting upper shoreface to delta plain depositional environments. The overlying unit 2 (Chron 18n) is defined by abundant Grays River basalt volcaniclastic interbeds that intertongue with Cowlitz lithic arkoses. This unit represents the latter part of 3rd order cycle 3, and consists of mostly fining- and thinning-upward parasequences of middle shoreface to delta plain successions of an aggradational to transgressive parasequence set. Near the top of unit 2 is a maximum marine flooding surface depositing lower shoreface lithic arkosic sandstone to shelf siltstones over upper shoreface micaceous lithic arkose. Unit 3 comprises 3rd order cycle 4 (Chron 17r), a lowstand system tract, and consists of 6 mostly fining- and thinning-upward parasequences of lower shoreface to delta plain facies associations. A parasequence or erosional boundary at the base of unit 5 (Chron 17r) consists of submarine channel-fill scoured into underlying micaceous siltstones, produced during a lowstand system tract (LST) of 3rd order cycle 5. This deep marine channel-fill sequence is overlain by thinlybedded to laminated overbank distal turbidites and hemipelagic siltstones that define the top of the Coal Creek section. These 5 informal units in Coal Creek lithologically and chronologically correlate to 5 similar informal units defined by Payne (1998) in the type section of Cowlitz Formation in Olequa Creek near Vader -30 km to the north. Middle Eocene Grays River Volcanics of the study area are mapped as two separate units: a lower unit over 150 meters thick in places, consisting of subaerial basaltic flows and invasive flows (Tgvl), intrusions (Tgvis and Tgvid), and volcaniclastics (Tgvsl); and an upper unit consisting of commonly mollusk-bearing, shallow marine basaltic sedimentary interbeds that intertongue with the Cowlitz Formation (Tgvs2), particularly Cowlitz unit 2 of the Coal Creek section. These volcaniclastic deposits are intrabasinal, derived from volcanic highlands to the west and northwest, and local phreatomagmatic tuff cones. The lower Grays River volcaniclastic unit typically overlies Grays River flows in the study area and is divided into 5 informal facies. Geochemically, Grays River flows in the study area fall within normal parameters (3 to 4% TiO2 and high iron tholeiitic basalts). However, basalt flows and bedded scoriaceous breccias near Rocky Point are anomalously low in TiO2 and are considered in this study to be a separate volcanic subunit (Rocky Point Basalts), time equivalent to and interfingering with Grays River lavas, but may represent mixing with shallower western Cascade calc-alkaline magma. Over 60 younger Grays River dikes intrude the Cowlitz Formation in Coal Creek. A dike low in the Coal Creek section is dated at 40 ± 0.36 Ma, and an invasive flow at Mt. Solo is dated at 36.98 ±.78 Ma. Volcanics capping the hills east of the Cowlitz River are chemically distinct as slightly younger western Cascade basaltic andesite flows, and two dikes east of the river are chemically distinct as western Cascade andesite. Overlying Grays River Volcanics and Cowlitz Formation in much of the study area, are clayey and commonly tuffaceous siltstones and silty sandstones, possibly of the late Eocene-early Oligocene Toutle Formation, a new unit to this area. The Toutle Formation is a mixture of wave and stream reworked micaceous and arkosic Cowlitz Formation and fresh silicic pyroclastic ash and pumice from the active western Cascade arc. An angular unconformity separates the Paleogene Grays River Volcanics, Cowlitz Formation, and Toutle Formation from the early to middle Miocene Columbia River Basalt Group. Based on lithology, geochemistry, stratigraphic relationships, and magnetic polarity, 6 individual Columbia River Basalt flows have been mapped in this study. The three lower Grande Ronde flows are of normal polarity and Ortley low MgO chemical composition. The lowermost flow (N2 Ortley #1) is absent in the Columbia Heights area, low MgO, about 10 meters thick and consists of pillow-palagonite sequences in the upper quarry on Mt. Solo. Aphyric N2 Ortley flow #2 is over 35 meters thick with well-developed upper and lower colonnade, and of intermediate MgO. N2 Ortley flow #3 is pillow-palagonite in the Storedahl Quarry and low MgO. A -4-meter thick tuffaceous overbank siltstone and basalt conglomeratic channel interbed separates the three low MgO Ortley flows from the overlying high MgO N2 Grande Ronde Sentinel Bluffs flow. A single exposure of well-developed large colonnade with sparse 1 cm labradorite laths, and reddish oxidized soil, defines the N Sand Hollow flow of the Frenchman Springs Member of the Wanapum Formation. The overlying Pomona Member is mapped based on previous work by other authors. Pliocene gravels and arkosic sand of the Troutdale Formation form upland terrace deposits up to 100 meters thick in southern parts of the study area, and represent the uplifted paleo-thalweg and overbank flood deposits of the downcutting, antecedent ancestral Columbia River. Well-rounded clasts are a mixture of extrabasinal granitic and metamorphic quartzite, and intrabasinal porphyritic basaltic andesite, dacite, and basalt from the western Cascades and Columbia River Basalts. Troutdale terrace gravels grade northward into contemporaneous volcanic pebble and cobble gravel terrace deposits produced along the ancestral Cowlitz River that are dominantly composed of porphyritic andesite gravel and volcanic sand from the western Cascades. Lower terraces along the Cowlitz River were deposited by the late Pleistocene Missoula Floods. All of these unconsolidated to semiconsolidated gravels and sands are prone to landslides, and the Aldercrest-Banyon landslide, the second worst landslide disaster in American history, occurred in the Troutdale Formation gravels. After eruption of the Grays River Volcanics and deposition of the Cowlitz Formation, the forearc underwent a period of transtension in the late-middle Eocene related to magmatic upwelling and reorganization of the subducting Farallon Plate. This event produced a northwest-trending set of oblique slip normal faults, along which Grays River dikes intruded. Starting in the early Miocene the region underwent a transpressional event, reactivating many of the northwest-trending faults, and producing the Columbia Heights Anticline, Hazel Dell Syncline, the Coal Creek Fault, and the Kelso Fault Zone. The paleotopography resulting from this event was stream eroded to a nearly flat plain before emplacement of the Columbia River Basalts, which are nearly horizontal today. Continued offset along the northwest-trending fault set has also offset the Columbia River Basalts. Continued oblique slip post-Miocene broad arching of the Coast Range and downcutting by the Columbia and Cowlitz Rivers has resulted in Pliocene and Pleistocene terraces, and produced an east-west fault set that offsets all earlier structural features.
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254. [Article] Willamette BiOp - Genetic Diversity of Willamette River Spring Chinook Salmon Populations
Abstract -- In this study, we used multilocus microsatellite genotype data from 813 spring Chinook salmon Oncorhynchus tshawytscha to investigate patterns of genetic diversity within and among wild and ...Citation Citation
- Title:
- Willamette BiOp - Genetic Diversity of Willamette River Spring Chinook Salmon Populations
Abstract -- In this study, we used multilocus microsatellite genotype data from 813 spring Chinook salmon Oncorhynchus tshawytscha to investigate patterns of genetic diversity within and among wild and hatchery populations from the Willamette River and Catherine Creek (Grande Ronde River, Oregon). We found that hatchery populations from the Willamette River presented higher heterozygosities than local wild populations, though no pattern was found for allelic richness. An analysis of genetic divergence (?) revealed little or no differentiation between hatchery and local wild populations within Willamette River subbasins. However, we observed weak but statistically significant structure among most Willamette River subbasins. Phylogenetic analyses of Willamette River populations further indicated that hatchery populations are most similar to local wild populations, though no inference could be made for wild Middle Fork Willamette Chinook due to an inadequate sample size. Genetic population structure did not closely reflect geographic structure of the Willamette River, as North Santiam River populations clustered with McKenzie River populations and South Santiam River populations formed a clade with hatchery Chinook from the Middle Fork Willamette River. Structure was particularly weak among populations from the Middle Fork Willamette and South Santiam rivers. We evaluated the accuracy of genetic stock identification for Willamette River spring Chinook, based on 13 GAPS (Genetic Analysis of Pacific Salmon) microsatellite markers. We found that with the GAPS baseline, individuals could be assigned to their population of origin (subbasin) with 43% - 64% accuracy. We estimated 100% assignment accuracy to the Catherine Creek Hatchery population, reflecting the distinctiveness of Willamette River Chinook relative to that population. We observed no measurable increase in assignment accuracy by adding four gene-linked markers to the GAPS baseline. We tested for signals of positive selection on both GAPS microsatellites and four gene-linked markers by examining inter-locus patterns of genetic differentiation. Although we found no evidence for locus-specific selection among Willamette River populations, one GAPS microsatellite and an immune-relevant marker presented aberrantly large genetic diversity index (FST) values between Willamette River populations and the Catherine Creek population. This result suggests that these loci may be linked to genes under positive selection that has generated markedly different allele frequencies in Catherine Creek and Willamette River spring Chinook. Lastly we used our empirical genotypic data from the McKenzie River hatchery and wild populations to perform forward-time simulations, modeling changes in ?, mean heterozygosity and total allele count over 30 generations. We use the term “migration” to describe the interaction of hatchery and wild fish in these simulations; namely the proportion of natural-origin fish spawned in the hatchery as broodstock and the proportion of hatchery fish present on natural spawning grounds. Our findings indicated that migration rates of at least 5% resulted in <2% decline in heterozygosity and an asymptotic FST value of 0.005 or less. No migration from one or both populations resulted in markedly higher rates of population divergence, loss of heterozygosity and reduction in alleles present. The mean number of alleles present (per locus) in the hatchery and wild populations was more sensitive to differences in migration rate than heterozygosity, whereby low levels of hatchery straying and natural-origin broodstock integration best conserved genetic diversity.