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Ward E.J.,National Oceanic and Atmospheric Administration | Pess G.R.,National Oceanic and Atmospheric Administration | Anlauf-Dunn K.,Corvallis Research Laboratory | Jordan C.E.,National Oceanic and Atmospheric Administration
Canadian Journal of Fisheries and Aquatic Sciences | Year: 2012

Trend analyses are common in the analysis of fisheries data, yet the majority of them ignore either observation error or spatial correlation. In this analysis, we applied a novel hierarchical Bayesian state-space time series model with spatial correlation to a 12-year data set of habitat variables related to coho salmon (Oncorhynchus kisutch) in coastal Oregon, USA. This model allowed us to estimate the degree of spatial correlation separately for each habitat variable and the importance of observation error relative to environmental stochasticity. This framework allows us to identify variables that would benefit from additional sampling and variables where sampling could be reduced. Of the eight variables included in our analysis, we found three metrics related to habitat quality correlated at large spatial scales (gradient, fine sediment, shade cover). Variables with higher observation error (pools, active channel width, fine sediment) could be made more precise with more repeat visits. Our spatio-temporal model is flexible and extendable to virtually any spatially explicit monitoring data set, even with large amounts of missing data and no repeated observations. Potential extensions include fisheries catch data, abiotic indicators, invasive species, or species of conservation concern. Source


Anlauf K.J.,University of Idaho | Anlauf K.J.,Corvallis Research Laboratory | Moffitt C.M.,University of Idaho
Freshwater Biology | Year: 2010

Aggregations of fine sediments are a suitable proxy for the presence and abundance of Tubifex tubifex, one of the obligate hosts in the parasitic life cycle that causes salmonid whirling disease (. Myxobolus cerebralis). To determine and evaluate practical approaches to predict fine sediments (<2 mm diameter) that could support Tubifex spp. aggregations, we measured habitat features in a catchment with field measures and metrics derived from digital data sets and geospatial tools at three different spatial extents (m2) within a hierarchical structure. We used linear mixed models to test plausible candidate models that best explained the presence of fine sediments measured in stream surveys with metrics from several spatial extents. The percent slow water habitat measured at the finest extent provided the best model to predict the likely presence of fine sediments. The most influential models to predict fine sediments using landscape metrics measured at broader extents included variables that measure the percentage land cover in conifer or agriculture, specifically, decreases in conifer cover and increases in agriculture. The overall best-fitting model of the presence of fine sediments in a stream reach combined variables measured and operating at different spatial extents. Landscape features modelled within a hierarchical framework may be useful tools to evaluate and prioritise areas with fine sediments that may be at risk of infection by Myxobolus cerebralis. © 2010 Blackwell Publishing Ltd. Source


Sharpe C.S.,Corvallis Research Laboratory
Transactions of the American Fisheries Society | Year: 2014

Due to the challenges associated with monitoring in riverine environments, unbiased and precise spawner abundance estimates are often lacking for populations of Pacific salmon Oncorhynchus spp. listed under the Federal Endangered Species Act. We investigated genetic approaches to estimate the 2009 spawner abundance for a population of Columbia River Chinook Salmon Oncorhynchus tshawytscha via genetic mark-recapture and rarefaction curves. The marks were the genotyped carcasses collected from the spawning area during the first sampling event. The second sampling event consisted of a collection of juveniles from a downstream migrant trap located below the spawning area. The parents that assigned to the juveniles through parentage analysis were considered the recaptures, which was a subset of the genotypes captured in the second sample. Using the Petersen estimator, the genetic mark-recapture spawner abundance estimates based on the binomial and hypergeometric models were 910 and 945 Chinook Salmon, respectively. These results were in agreement with independently derived spawner abundance estimates based on redd counts, area-under-the-curve methods, and carcass tagging based on the Jolly-Seber model. Using a rarefaction curve approach, which required only the juvenile offspring sample, our estimate of successful breeders was 781 fish. Our genetic-based approaches provide new alternatives to estimate adult Pacific salmon abundance in challenging environmental conditions or for populations with poor or unknown estimates of precision. Received December 7, 2012; accepted July 17, 2013. © 2014 Copyright Taylor and Francis Group, LLC. Source


Anlauf-Dunn K.J.,Corvallis Research Laboratory | Ward E.J.,National Oceanic and Atmospheric Administration | Strickland M.,Corvallis Research Laboratory | Jones K.,Corvallis Research Laboratory
Canadian Journal of Fisheries and Aquatic Sciences | Year: 2014

The distribution, quality, and connectivity of instream habitat can influence adult salmon occupancy and abundance patterns and alter population dynamics. In this study, we evaluated the relationships between adult coho salmon (Oncorhynchus kisutch) occupancy and abundance with instream habitat conditions, including measures of spawning gravel, habitat complexity, and juvenile rearing habitat. We used corresponding adult salmon spawning and instream habitat data collected within coastal Oregon watersheds as part of a long-term monitoring program. We modeled two processes as a function of habitat characteristics: the number of coho salmon when they were present and the occupancy probabilities of coho salmon. The results from both submodels were then combined into an estimate of total abundance at each site. Adult coho salmon occupancy was best predicted by the capacity of the habitat to support parr during the winter, complex pools, percent bedrock, and site distance to the ocean. Although lacking the predictive capacity of the occupancy model, increases in adult coho counts at sites were also influenced by the site distance to the ocean, and there is evidence that both percent gravel and complex pools may also be valuable predictors. By taking advantage of long-term datasets with broad spatial range, using an integrative approach across coho salmon life stages, and utilizing innovative Bayesian modeling techniques, this study is a unique approach to understanding a complicated ecological narrative. Combined, our results indicate the spatial distribution and proximity of spawning and rearing habitats may maximize productivity for coho salmon in coastal Oregon watersheds. © 2014, National Research Council of Canada. All rights received. Source


Pearse D.E.,Southwest Fisheries Science Center | Gunckel S.L.,Corvallis Research Laboratory | Jacobs S.E.,Corvallis Research Laboratory
Transactions of the American Fisheries Society | Year: 2011

Freshwater-resident coastal rainbow trout Oncorhynchus mykiss irideus and the anadromous form of the subspecies, coastal steelhead (summer and winter runs), are present throughout the lower Klamath River-Trinity River system. Although coastal steelhead and other anadromous salmonids historically migrated into the Upper Klamath Basin (which encompasses the upper Klamath River and Upper Klamath Lake) and associated tributaries, the construction of Copco Dam in 1918 and Iron Gate Dam in 1962 stopped all upstream migration of fish past these barriers. In the Upper Klamath Lake basin, native Upper Klamath Lake redband trout O. mykiss newberrii are found along with coastal rainbow trout that were trapped above the dams or stocked from hatchery sources. However, relatively little is known about the genetic relationships among the O. mykiss populations within the Upper Klamath Basin. A population genetic analysis based on data from 17 variable microsatellite loci was conducted for samples collected in the Upper Klamath Basin, including rainbow trout and Upper Klamath Lake redband trout (presumably representative of the ancestral coastal and inland lineages) as well as samples of O. mykiss from neighboring inland lake basins. In addition, the Upper Klamath Basin samples were compared with data from O. mykiss populations below Iron Gate Dam. Results demonstrate the presence of distinct inland and coastal genetic lineages as well as divergent lineages represented by samples from the inland lake basins; these results have significant implications for future restoration of O. mykiss in the greater Klamath River-Trinity River system. © American Fisheries Society 2011. Source

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