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Nampa, ID, United States

Narum S.R.,Columbia River Inter Tribal Fish Commission | Campbell N.R.,Columbia River Inter Tribal Fish Commission | Kozfkay C.C.,Eagle Fish Genetics Laboratory | Meyer K.A.,414 East Locust Lane
Molecular Ecology | Year: 2010

Natural populations that evolve under extreme climates are likely to diverge because of selection in local environments. To explore whether local adaptation has occurred in redband trout (Oncorhynchus mykiss gairdneri) occupying differing climate regimes, we used a limited genome scan approach to test for candidate markers under selection in populations occurring in desert and montane streams. An environmental approach to identifying outlier loci, spatial analysis method and linear regression of minor allele frequency with environmental variables revealed six candidate markers (P < 0.01). Putatively neutral markers identified high genetic differentiation among desert populations relative to montane sites, likely due to intermittent flows in desert streams. Additionally, populations exhibited a highly significant pattern of isolation by temperature (P < 0.0001) and those adapted to the same environment had similar allele frequencies across candidate markers, indicating selection for differing climates. These results imply that many genes are involved in the adaptation of redband trout to differing environments, and selection acts to reinforce localization. The potential to predict genetic adaptability of individuals and populations to changing environmental conditions may have profound implications for species that face extensive anthropogenic disturbances. © 2010 Blackwell Publishing Ltd. Source


Narum S.R.,Columbia River Inter Tribal Fish Commission | Narum S.R.,University of Idaho | Campbell N.R.,Columbia River Inter Tribal Fish Commission | Meyer K.A.,414 East Locust Lane | And 2 more authors.
Molecular Ecology | Year: 2013

To elucidate the mechanisms of thermal adaptation and acclimation in ectothermic aquatic organisms from differing climates, we used a common-garden experiment for thermal stress to investigate the heat shock response of redband trout (Oncorhynchus mykiss gairdneri) from desert and montane populations. Evidence for adaptation was observed as expression of heat shock genes in fish from the desert population was more similar to control (unstressed) fish and significantly different (P ≤ 0.05) from those from the montane population, while F1 crosses were intermediate. High induction of heat shock proteins (Hsps) in the montane strain appeared to improve short-term survival during first exposure to high water temperatures, but high physiological costs of Hsp production may have led to lower long-term survival. In contrast, the desert strain had significantly lower heat shock response than the montane fish and F1 crosses, suggesting that these desert fish have evolved alternative mechanisms to deal with thermal stress that provide better balance of physiological costs. Genomewide tests of greater than 10 000 SNPs found multiple SNPs that were significantly associated with survival under thermal stress, including Hsp47 which consistently appeared as a strong candidate gene for adaption to desert climates. Candidate SNPs identified in this study are prime targets to screen more broadly across this species' range to predict the potential for adaptation under scenarios of climate change. These results demonstrate that aquatic species can evolve adaptive responses to thermal stress and provide insight for understanding how climate change may impact ectotherms. © 2013 John Wiley & Sons Ltd. Source


McCormick J.L.,University of Idaho | Quist M.C.,U.S. Geological Survey | Schill D.J.,414 East Locust Lane
North American Journal of Fisheries Management | Year: 2012

Roving-roving and roving-access creel surveys are the primary techniques used to obtain information on harvest of Chinook salmon Oncorhynchus tshawytscha in Idaho sport fisheries. Once interviews are conducted using roving-roving or roving-access survey designs, mean catch rate can be estimated with the ratio-of-means (ROM) estimator, the mean-of-ratios (MOR) estimator, or the MOR estimator with exclusion of short-duration (≤0.5 h) trips. Our objective was to examine the relative bias and precision of total catch estimates obtained from use of the two survey designs and three catch rate estimators for Idaho Chinook salmon fisheries. Information on angling populations was obtained by direct visual observation of portions of Chinook salmon fisheries in three Idaho river systems over an 18-d period. Based on data from the angling populations, Monte Carlo simulations were performed to evaluate the properties of the catch rate estimators and survey designs. Among the three estimators, the ROM estimator provided the most accurate and precise estimates of mean catch rate and total catch for both roving-roving and roving-access surveys. On average, the root mean square error of simulated total catch estimates was 1.42 times greater and relative bias was 160.13 times greater for roving-roving surveys than for roving-access surveys. Length-of-stay bias and nonstationary catch rates in roving-roving surveys both appeared to affect catch rate and total catch estimates. Our results suggest that use of the ROM estimator in combination with an estimate of angler effort provided the least biased and most precise estimates of total catch for both survey designs. However, roving-access surveys were more accurate than roving-roving surveys for Chinook salmon fisheries in Idaho. © American Fisheries Society 2012. Source


Thorson J.T.,National Oceanic and Atmospheric Administration | Scheuerell M.D.,National Oceanic and Atmospheric Administration | Buhle E.R.,National Oceanic and Atmospheric Administration | Copeland T.,414 East Locust Lane
Journal of Animal Ecology | Year: 2014

Spatial, phenotypic and genetic diversity at relatively small scales can buffer species against large-scale processes such as climate change that tend to synchronize populations and increase temporal variability in overall abundance or production. This portfolio effect generally results in improved biological and economic outcomes for managed species. Previous evidence for the portfolio effect in salmonids has arisen from examinations of time series of adult abundance, but we lack evidence of spatial buffering of temporal variability in demographic rates such as survival of juveniles during their first year of life. We therefore use density-dependent population models with multiple random effects to represent synchronous (similar among populations) and asynchronous (different among populations) temporal variability as well as spatial variability in survival. These are fitted to 25 years of survey data for breeding adults and surviving juveniles from 15 demographically distinct populations of Chinook salmon (Oncorhynchus tshawytscha) within a single metapopulation in the Snake River in Idaho, USA. Model selection identifies the most support for the model that included both synchronous and asynchronous temporal variability, in addition to spatial variability. Asynchronous variability (log-SD = 0·55) is approximately equal in magnitude to synchronous temporal variability (log-SD = 0·67), but much lower than spatial variability (log-SD = 1·11). We also show that the pairwise correlation coefficient, a common measure of population synchrony, is approximated by the estimated ratio of shared and total variance, where both approaches yield a synchrony estimate of 0·59. We therefore find evidence for spatial buffering of temporal variability in early juvenile survival, although between-population variability that persists over time is also large. We conclude that spatial variation decreases interannual changes in overall juvenile production, which suggests that conservation and restoration of spatial diversity will improve population persistence for this metapopulation. However, the exact magnitude of spatial buffering depends upon demographic parameters such as adult survival that may vary among populations and is proposed as an area of future research using hierarchical life cycle models. We recommend that future sampling of this metapopulation employ a repeated-measure sampling design to improve estimation of early juvenile carrying capacity. © 2013 British Ecological Society. Source


Copeland T.,414 East Locust Lane | Meyer K.A.,414 East Locust Lane
Transactions of the American Fisheries Society | Year: 2011

The abundance of lotic salmonids varies substantially through time, but the extent to which several sympatric species respond coherently to large-scale bioclimatic conditions has rarely been investigated for freshwater fishes. We compared correlations in salmonid density in central Idaho and examined the relationships between changes in salmonid density and the variation in large-scale bioclimatic conditions as indexed by stream flow, air temperature, drought, coastal upwelling, and the number of Chinook salmon Oncorhynchus tshawytscha redds (a surrogate for nutrient influx and therefore increased stream productivity). The average densities of six stream-dwelling salmonid fishes were highly synchronous, with declines from the mid-1980s to the mid-1990s followed by a rebound through 2003. All pairwise correlations were positive and 8 of 15 were statistically significant. Stream flow and Chinook salmon redds were correlated with fish densities as a group, but the importance of bioclimatic indices differed by species and varied by the lag times applied. Stream flow 3 and 4 years previous was most important for brook trout Salvelinus fontinalis and bull trout S. confluentus. The presence of Chinook salmon redds from the previous year was most important for Chinook salmon. The coastal upwelling index 4 years previous was most important for mountain whitefish Prosopium williamsoni and steelhead O. mykiss. No variable captured much of the variation in the density of westslope cutthroat trout O. clarkii lewisi. Models based on data from 1985 to 2003 correctly predicted the synchronous declines in fish density observed for all species from 2004 to 2009, suggesting that the bioclimatic indices we chose were useful surrogates for large-scale factors influencing the temporal changes in salmonid densities in central Idaho. For fishery managers, interspecies synchrony may allow a more powerful multispecies approach to monitoring and reveal the tractability of large systems tomanagement control. However, causal mechanisms are hard to infer and require further research (e.g., the effects of ocean conditions). Our study provides a basis for such work. © American Fisheries Society 2011. Source

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