Corvallis, OR, United States
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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.


Johnson M.A.,Corvallis Research Laboratory | Friesen T.A.,Corvallis Research Laboratory
North American Journal of Fisheries Management | Year: 2013

We used data from 17 brood years of coded-wire-tagged hatchery spring Chinook Salmon Oncorhynchus tshawytscha from the upper Willamette River to test for changes in mean age at maturity, fork length, and sex ratio. We found only limited evidence for any trend in age at maturity or sex ratio. However, Chinook Salmon sampled from tangle nets, recreational fisheries, spawning grounds, and hatcheries all presented trends of decline in mean fork length. Rates of change in fork length ranged from 0 to 5 mm per year in most sample collections, though fork length declined more rapidly for samples from tangle nets. We also observed a positive relationship between adult fork lengths and the median monthly Pacific Decadal Oscillation index in the year prior to juvenile liberation (the brood year). We suggest that future research should investigate the potential cause(s) for the decline in size of hatchery spring Chinook Salmon from the upper Willamette River, with attention to harvest, broad-scale environmental conditions, and hatchery spawning and rearing practices. © American Fisheries Society 2013.


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.


Monzyk F.R.,Corvallis Research Laboratory | Friesen T.A.,Corvallis Research Laboratory | Romer J.D.,Corvallis Research Laboratory
Transactions of the American Fisheries Society | Year: 2015

Abstract: We assessed infection prevalence and intensity by the ectoparasitic copepod Salmincola californiensis among salmonid species rearing in reservoirs and streams upstream of reservoirs in the Willamette River basin, Oregon, during 2012 and 2013. Infection levels of juvenile Chinook Salmon Oncorhynchus tshawytscha, Rainbow Trout O. mykiss, and Cutthroat Trout O. clarkii were greater in reservoirs than in streams and increased with the age and size of fish. Copepods were more likely to be attached within the brachial cavity of reservoir fish (79%), whereas fins were the most common attachment site on stream fish (71%). Chinook Salmon in reservoirs were more vulnerable to infection than other species. Age-0 Chinook Salmon in reservoirs showed increasing infection prevalence throughout the year, reaching 84% by fall (compared with 11% in streams). Infection intensity was greater for age-0 Chinook Salmon in reservoirs than for those in streams. Infection prevalence for reservoir-rearing Rainbow Trout was < 1% at age 0, 22% at age 1, 36% at age 2, and 38% at age 3. Intensity was low for age-1 Rainbow Trout and increased for age-2 and age-3 fish. Infection prevalence for reservoir-rearing Cutthroat Trout collected in spring (39%) was greater than for those rearing in streams (4.5%). Juvenile kokanee O. nerka were only present in reservoirs and were rarely infected with copepods. The lack of water current in reservoirs may increase the likelihood of infection in the brachial cavity. Greater infection levels observed for juvenile Chinook Salmon compared with the other species in reservoirs may be a function of behavioral, physiological, and habitat differences. We concluded that copepod infection in reservoirs reached levels that could decrease the fitness and survival of Chinook Salmon smolts, potentially hampering conservation and recovery efforts. Received December 23, 2014; accepted May 10, 2015 © 2015, © American Fisheries Society.


Kirk Schroeder R.,Corvallis Research Laboratory | Whitman L.D.,Corvallis Research Laboratory | Cannon B.,Corvallis Research Laboratory | Olmsted P.,Corvallis Research Laboratory
Canadian Journal of Fisheries and Aquatic Sciences | Year: 2016

Migratory and rearing pathways of juvenile spring Chinook salmon (Oncorhynchus tshawytscha) were documented in the Willamette River basin to identify life histories and estimate their contribution to smolt production and population stability. We identified six primary life histories that included two phenotypes for early migratory tactics: fry that migrated up to 140-200 km shortly after emergence (movers) and fish that reared for 8-16 months in natal areas (stayers). Peak emigration of juvenile salmon from the Willamette River was in June-July (subyearling smolts), March-May (yearling smolts), and November-December (considered as “autumn smolts”). Alternative migratory behaviors of juvenile salmon were associated with extensive use of diverse habitats that eventually encompassed up to 400 rkm of the basin, including tributaries in natal areas and large rivers. Juvenile salmon that reared in natal reaches and migrated as yearlings were the most prevalent life history and had the lowest temporal variability. However, the total productivity of the basin was increased by the contribution of fish with dispersive life histories, which represented over 50% of the total smolt production. Life-history diversity reduced the variability in the total smolt population by 35% over the weighted mean of individual life histories, providing evidence of a considerable portfolio effect through the asynchronous contributions of life histories. Protecting and restoring a diverse suite of connected habitats in the Willamette River basin will promote the development and expression of juvenile life histories, thereby providing stability and resilience to native salmon populations. © 2016, National Research Council of Canada. All Rights Reserved.


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.


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.


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.


Clements S.,U.S. Geological Survey | Clements S.,Corvallis Research Laboratory | Stahl T.,U.S. Geological Survey | Stahl T.,Corvallis Research Laboratory | Schreck C.B.,U.S. Geological Survey
Aquaculture | Year: 2012

We used radio and acoustic telemetry to study the behavior and survival of wild steelhead trout (Oncorhynchus mykiss) and hatchery coho salmon (Oncorhynchus kisutch) and steelhead outmigrants in a small coastal estuary during two years. Survival was generally low for hatchery fish but more variable, both within and between years, for wild steelhead. The rate of downstream movement in the river varied both within and between species and was generally not correlated with flow. Both hatchery and wild steelhead tended to spend less than a day in the estuary, and tended to move downstream on outgoing tides. In contrast, hatchery coho salmon spent a longer period of time in the estuary (~. 8. d). On several occasions, coho salmon were observed moving both upstream and downstream between the upper (freshwater) and lower (saline) zones of the estuary. We also documented a high incidence of predation by avian and mammalian predators on coho outmigrants. © 2011 Elsevier B.V.


Johnson M.A.,Corvallis Research Laboratory | Friesen T.A.,Corvallis Research Laboratory
North American Journal of Fisheries Management | Year: 2014

Effective management of Pacific salmon requires an accurate understanding of both population genetic diversity and structure. Spring Chinook Salmon Oncorhynchus tshawytscha from the upper Willamette River (UWR), Oregon, are listed as threatened under the U.S. Endangered Species Act, and although this evolutionarily significant unit is recognized to be distinct from other Columbia River stocks, genetic relationships among its constituent hatchery and wild populations remain obscure. We used genotypic data from 13 microsatellite loci to test whether hatchery populations of UWR spring Chinook Salmon are most similar to wild populations within the same subbasin, or whether hatchery populations from different subbasins are more similar to each other than to local wild populations. We also tested for differences between the genetic diversities of hatchery and wild populations, as measured through heterozygosity and allelic richness. Our results suggest that populations are weakly structured among subbasins and, in all cases, hatchery populations are genetically most similar to local wild populations. We also found heterozygosity to be higher (P = 0.009) in hatchery populations (median, 81.5%) than in wild populations (median, 75.2%), but observed no significant difference with respect to allelic richness (P = 0.406). We conclude that hatchery-origin UWR spring Chinook Salmon represent genetically appropriate founder populations for ongoing reintroduction programs and recommend that the conservation and recovery of this stock proceed through management actions developed specifically for each subbasin. We further recommend that current restrictions on hatchery stock transfers among UWR subbasins be continued to preserve extant population genetic structure.Received January 8, 2014; accepted April 29, 2014. © 2014 © American Fisheries Society.

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