Cramer Fish science

Auburn, CA, United States

Cramer Fish science

Auburn, CA, United States
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Teply M.,Cramer Fish science
Western Journal of Applied Forestry | Year: 2013

Uneven-aged stands with multistory, diverse canopies are common throughout the forests of the Inland Northwest, and both current regulations and prescriptions under consideration often promote further diversification. Understanding the potential effects of alternative riparian management prescriptions on stream shade is important, and effects may vary with even-aged versus uneven-aged conditions. For a range of riparian stand conditions in Central Idaho, in this article, we compare shade predictions from two approaches using a widely used model introduced by Chen et al. in 1998, one that accounts for multiple canopies ("canopy-explicit approach") and another that accounts for a single-layer canopy ("canopy-average approach"). We found slight improvements using the canopy-explicit approach when there were distinct overstory and understory canopies. However, we found that both approaches underpredicted shade levels observed in the field. The underestimate is influenced by the Forest Vegetation Simulator (FVS) canopy cover metric that we used to inform the model; this metric underestimates vertical nonoverlapping cover, an important input to the shade model. We used the canopy-explicit approach to evaluate effects of the Idaho Forestry Program (IFP), a major conservation agreement that the State of Idaho is currently pursing with federal agencies, on stream shade. For this evaluation, we compared shade predicted to occur through implementation of the IFP with that from passive (no harvest) management. For the IFP, we found that shade reduction would be approximately 5%, on average, largely because of the effect of the 25-ft stream-adjacent no-harvest zone that this alternative requires. We also compared shade produced under the IFP with shade targets developed by the Idaho Department of Environmental Quality. Predicted IFP shade levels were lower than target levels, in large part because of the effect of the FVS cover metric. Overall, these comparisons highlight the usefulness of the approach in comparing the effects of different management alternatives on shade, despite the bias introduced by using the FVS cover metric and problems inherent in comparing results developed through simulation to targets based on different methods. Copyright © 2013 by the Society of American Foresters.

Courter I.I.,Cramer Fish science | Child D.B.,DC Consulting LLC | Hobbs J.A.,University of California at Davis | Garrison T.M.,Cramer Fish science | And 2 more authors.
Canadian Journal of Fisheries and Aquatic Sciences | Year: 2013

Rainbow trout (Oncorhynchus mykiss) have diverse life histories, including both freshwater-resident and anadromous "steelhead" life-history forms. Here, we demonstrate that female resident rainbow trout produce anadromous offspring that survive and return to spawn as adult steelhead. This study represents the first successful attempt to quantify steelhead production rates from female resident rainbow trout across a large watershed. Otolith microchemistry (8786) techniques were used to determine the maternal life history (resident or anadromous) of 498 emigrating steelhead kelts in the Yakima Basin, Washington. Five geochemically distinct freshwater rearing regions were identified within the basin. All five regions were predicted to produce steelhead with resident maternal life histories. Basin-wide, 20% and 7% of steelhead collected in 2010 and 2011, respectively, had resident maternal life histories. Cross-life-history form production may be critical to persistence of anadromous life histories within partially anadromous salmonid populations, particularly in areas where anadromous fish abundance is low due to natural or anthropogenic influences.

Del Real S.C.,East Bay Municipal Utility District | Workman M.,U.S. Fish and Wildlife Service | Merz J.,Cramer Fish science
Environmental Biology of Fishes | Year: 2012

The lower Mokelumne River (LMR), located in the California Central Valley, supports a population of natural-origin Oncorhynchus mykiss. In addition, the Mokelumne River Fish Hatchery (Hatchery) contributes hatchery produced O. mykiss to the system annually. We conducted a 3 year acoustic tagging study to evaluate the migratory characteristics of LMR hatchery and natural-origin O. mykiss to the Pacific Ocean. Specifically, we analyzed downstream movement and migration rates, routes, and success of acoustically tagged O. mykiss of hatchery and natural origin under variable release locations in non-tidal and tidal habitats. Results from our study suggest there are significant differences in the proportion of hatchery and natural O. mykiss that demonstrate downstream movement. Fish origin, size, and release location all had a significant effect on whether an individual demonstrated downstream movement. Mokelumne origin O. mykiss that initiated downstream movement utilized numerous migration routes throughout the Delta during their migration towards the Pacific Ocean. We identified four primary migration pathways from the lower Mokelumne River through the Sacramento-San Joaquin Delta while the Delta Cross Channel was closed. However, several other pathways were utilized. Origin had a significant effect on O. mykiss success in reaching key points in the Delta and through the Estuary. Fish size had a significant effect on whether an individual reached the marine environment. Of the 467 O. mykiss tagged, 34 successfully reached the Pacific Ocean (Golden Gate Bridge), and of these, 33 were hatchery-origin and 1 was natural-origin. A higher proportion of hatchery-origin fish (10% of tagged) migrated to the ocean compared to natural-origin fish (<1%). Our study provides valuable information on the differences between hatchery and natural-origin O. mykiss migration characteristics as well as unique insight into the migratory behavior of little studied non-Sacramento River origin salmonids. © 2011 Springer Science+Business Media B.V.

Cavallo B.,Cramer Fish science | Merz J.,University of California at Santa Cruz | Setka J.,East Bay Municipal Utility District
Environmental Biology of Fishes | Year: 2013

We evaluated the effects of non-native, piscivorous fish removal and artificial flow manipulation on survival and migration speed of juvenile Chinook salmon, Oncorhynchus tshawytscha, emigrating through the eastern Sacramento-San Joaquin Delta of California (Delta) using a Before-After-Control-Impact study design. Acoustically-tagged salmon survival increased significantly after the first predator reduction in the impact reach. However, survival estimates returned to pre-impact levels after the second predator removal. When an upstream control gate opened (increasing flow and decreasing tidal effect) juvenile salmon emigration time decreased and survival increased significantly through the impact reach. Though a short-term, single season experiment, our results demonstrate that predator control and habitat manipulation in the Delta tidal transition zone can be effective management strategies to enhance salmon survival in this highly altered system. © 2012 Springer Science+Business Media B.V.

Miller J.A.,Oregon State University | Gray A.,Cramer Fish science | Merz J.,University of California at Santa Cruz
Marine Ecology Progress Series | Year: 2010

Chinook salmon is an anadromous species that varies in size at freshwater emigration, which is hypothesized to increase population resiliency under variable environmental regimes. In California's Central Valley (USA), the majority of naturally spawned juveniles emigrate in 2 pulses: small juveniles (referred to as fry), typically ≤55 mm fork length (FL), emigrate from natal streams in February-March, whereas larger juveniles (smolts), typically >75 mm FL, emigrate in mid-April-May. In some river systems, there is a smaller pulse of emigrants of intermediate size (parr), typically 56 to 75 mm FL. Although the relative contribution of these migratory phenotypes to the adult population is unknown, management activities focus on survival of larger emigrants and most artificially produced fish (98%) are released from hatcheries at parr and smolt sizes. We reconstructed individual length at freshwater emigration for a sample of adult Central Valley Chinook salmon from 2 emigration years using chemical (Sr:Ca and Ba:Ca) and structural otolith analyses. The adult sample was comprised of individuals that emigrated as parr (mean ≤ 48%), followed by smolts (32%) and fry (20%). Fry-sized emigrants likely represent natural production because fish ≤55 mm FL comprise<2% of the hatchery production. The distribution of migratory phenotypes represented in the adult sample was similar in both years despite apparent interannual variation in juvenile production, providing evidence for the contribution of diverse migratory phenotypes to the adult population. The contribution of all 3 migratory phenotypes to the adult population indicates that management and recovery efforts should focus on maintenance of life-history variation rather than the promotion of a particular phenotype. © Inter-Research 2010 ·

Zeug S.C.,Cramer Fish science | Cavallo B.J.,Cramer Fish science
Ecology of Freshwater Fish | Year: 2013

Chinook salmon (Oncorhynchus tschawytscha) populations within the highly modified San Francisco Estuary, California, have seen precipitous declines in recent years. To better understand this decline, a decade of coded-wire tag release and recovery data for juvenile salmon was combined with physicochemical data to construct models that represented alternative hypotheses of estuarine conditions that influence tag recovery rate in the ocean. An information theoretic approach was used to evaluate the weight of evidence for each hypothesis and model averaging was performed to determine the level of support for variables that represented individual hypotheses. A single best model was identified for salmon released into the Sacramento River side of the estuary, whereas two competitive models were selected for salmon released into the San Joaquin River side of the estuary. Model averaging found that recovery rates were greatest for San Joaquin River releases when estuary water temperatures were lower, and salmon were released at larger sizes. Recovery rate of Sacramento releases was greatest during years with better water quality. There was little evidence that large-scale water exports or inflows influenced recovery rates in the ocean during this time period. These results suggest that conceptual models of salmon ecology in estuaries should be quantitatively evaluated prior to implementation of recovery actions to maximise the effectiveness of management and facilitate the recovery of depressed Chinook populations. © 2012 John Wiley & Sons A/S.

Cordell J.R.,University of Washington | Toft J.D.,University of Washington | Gray A.,Cramer Fish science | Ruggerone G.T.,Natural Resources Consultants Inc. | Cooksey M.,University of Washington
Ecological Engineering | Year: 2011

The Duwamish estuary is an industrialized waterway located in Seattle, WA, USA. Despite a history of habitat loss, naturally produced juvenile Chinook salmon use the estuary. In addition to experiencing degraded habitat in the estuary, wild salmon growth may be affected by competition with more than three million hatchery fish released yearly into the river. Restoring habitat to benefit salmon in the Duwamish River is a priority for trustees of public resources, and a number of wetland restoration sites have been created there. We tested the function of restored sites in the Duwamish estuary for juvenile Chinook salmon by comparing fish densities from enclosure nets or beach seines at three paired restored/un-restored sites and by applying environmental and diet data to a bioenergetics model. We also examined temporal and diet overlap of wild juvenile Chinook salmon with other salmon species and with hatchery-reared Chinook salmon using non-metric multidimensional scaling (NMDS). At a brackish upstream site with a relatively large opening to the river, we found higher densities of juvenile Chinook salmon at the restored site. NMDS results indicated that juvenile Chinook salmon fed on different taxa at the restored sites than at the reference sites. However, modeled growth was similar at restored and reference sites. Co-occurring juvenile chum and Chinook salmon fed differently, with chum eating smaller prey, and Chinook salmon eating larger prey. Co-occurring hatchery and wild juvenile Chinook salmon had similar diets, indicating that they may compete for prey. However, modeled growth was positive and did not differ between hatchery and wild fish, suggesting that food was not limiting. Bioenergetics models indicated that overall juvenile Chinook salmon growth potential at the brackish water site was consistently higher than at more saline sites. Our results suggest that restoration sites in the Duwamish estuary that have larger access openings and are located in brackish water may have increased function over other configurations. © 2010 Elsevier B.V.

Teply M.,Cramer Fish science | Cramer S.P.,Cramer Fish science | Poletika N.N.,Dow AgroSciences
Integrated Environmental Assessment and Management | Year: 2012

In this paper, we present a novel approach for determining the probable co-occurrence of juvenile salmon or steelhead with agricultural pesticides and apply it to spring Chinook (Oncorhynchus tshawytscha) salmon in the Willamette Basin, Oregon. We adapted a published exposure analysis framework by explicitly considering fish migration among habitat units and assuming that habitat use is proportional to habitat quality. Temporal variability in habitat use was accounted for via biweekly time steps over the entire period when asingle brood was expected to spawn until the last juvenile migrated to sea. Spatial variability was accounted for at the watershed and reach scale. Exposure to 6 acetylcholinesterase-inhibiting insecticides at any life stage was expressed in terms of the future adults (adult-equivalents; AEQ). Several datasets were available to inform our framework with input values on extent of spring Chinook fish use, habitat quality preferred by juvenile spring Chinook, choice of juvenile lifehistory pathways, timing of emergence, and timing of migration either in-stream or to sea. We used insecticide concentration profiles constructed from available monitoring data to demonstrate the effect of accounting for variation in space and time on predicted exposure to chemical residues. In contrast to the assumption commonly used in screening-level risk assessments that the entire population in a watershed is exposed, available data applied to our model framework indicate that a small fraction of AEQ juveniles in the Willamette Basin would co-occur with detectable concentrations of the 6 insecticides. Overall, our results indicated that the use of a spatially and temporally explicit framework yields a better understanding of the proportion of organisms potentially impacted by agricultural pesticides. Integr Environ Assess Manag 2012;8:271-284. © 2011 SETAC.

Rook B.J.,Cramer Fish science | Hansen M.J.,U.S. Geological Survey | Gorman O.T.,U.S. Geological Survey
North American Journal of Fisheries Management | Year: 2012

The cisco Coregonus artedi was once the most abundant fish species in the Great Lakes, but currently cisco populations are greatly reduced and management agencies are attempting to restore the species throughout the basin. To increase understanding of the spatial scale at which density-independent and density-dependent factors influence cisco recruitment dynamics in the Great Lakes, we used a Ricker stock-recruitment model to identify and quantify the appropriate spatial scale for modeling age-1 cisco recruitment dynamics in Lake Superior. We found that the recruitment variation of ciscoes in Lake Superior was best described by a five-parameter regional model with separate stock-recruitment relationships for the western, southern, eastern, and northern regions. The spatial scale for modeling was about 260 km (range = 230-290 km). We also found that the density-independent recruitment rate and the rate of compensatory density dependence varied among regions at different rates. The density-independent recruitment rate was constant among regions (3.6 age-1 recruits/spawner), whereas the rate of compensatory density dependence varied 16-fold among regions (range =-0.2 to -2.9/spawner). Finally, we found that peak recruitment and the spawning stock size that produced peak recruitment varied among regions. Both peak recruitment (0.5-7.1 age-1 recruits/ha) and the spawning stock size that produced peak recruitment (0.3-5.3 spawners/ha) varied 16-fold among regions. Our findings support the hypothesis that the factors driving cisco recruitment operate within four different regions of Lake Superior, suggest that large-scale abiotic factors are more important than small-scale biotic factors in influencing cisco recruitment, and suggest that fishery managers throughout Lake Superior and the entire Great Lakes basin should address cisco restoration and management efforts on a regional scale in each lake. © American Fisheries Society 2012.

Diversion of freshwater can cause significant changes in hydrologic dynamics and this can have negative consequences for fish populations. Additionally, fishes can be directly entrained into diversion infrastructure (e.g. canals, reservoirs, pumps) where they may become lost to the population. However, the effect of diversion losses on fish population dynamics remains unclear. We used 15 years of release and recovery data from coded-wire-tagged juvenile Chinook Salmon (Oncorhynchus tshawytscha) to model the physical, hydrological and biological predictors of salvage at two large water diversions in the San Francisco Estuary. Additionally, entrainment rates were combined with estimates of mortality during migration to quantify the proportion of total mortality that could be attributed to diversions. Statistical modeling revealed a strong positive relationship between diversion rate and fish entrainment at both diversions and all release locations. Other significant relationships were specific to the rivers where the fish were released, and the specific diversion facility. Although significant relationships were identified in statistical models, entrainment loss and the mean contribution of entrainment to total migration mortality were low. The greatest entrainment mortality occurred for fish released along routes that passed closest to the diversions and certain runs of Chinook Salmon released in the Sacramento River suffered greater mortality but only at the highest diversion rates observed during the study. These results suggest losses at diversions should be put into a population context in order to best inform effective management of Chinook Salmon populations. © 2014 Zeug, Cavallo.

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