Nampa, ID, United States
Nampa, ID, United States

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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.

Schill D.J.,University of Idaho | LaBar G.W.,University of Idaho | Mamer E.R.J.M.,414 East Locust Lane | Meyer K.A.,414 East Locust Lane
North American Journal of Fisheries Management | Year: 2010

Factors affecting length at maturity and other important reproductive characteristics have not been investigated for Idaho redband trout Oncorhynchus mykiss gairdneri residing in desert streams. Prespawning redband trout were collected from nine streams, and estimates of length at sexual maturity, median age at maturity, sex ratio, and fecundity were developed along with models predicting length at maturity from physical stream conditions. Males first matured 1-2 years prior to females in seven of nine streams, while in the remaining two populations a few fish of both sexes first matured at the same age. Total length (TL) was strongly related (P < 0.0004; n = 49) to fecundity (F) via the curvilinear function F = 0.0002TL2.5989. Redband trout residing in Idaho desert streams appeared to be less fecund than several other stream-dwelling populations of Pacific salmon Oncorhynchus spp. The best estimate of sex ratio for all fish, including immature fish, was 1:1. The best two-variable logit model for predicting length at maturity in males included stream order and conductivity, whereas the best model for females included drainage area above the sample site and stream gradient. These models can be used by fishery managers to estimate the total number of mature redband trout present in Idaho streams and, in combination with other data, can be used to approximate effective population sizes across southwestern Idaho desert stocks. © The American Fisheries Society 2010.

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.

Steven Elle F.,414 East Locust Lane | Koenig M.K.,414 East Locust Lane | Meyer K.A.,414 East Locust Lane
North American Journal of Fisheries Management | Year: 2010

Mass marks are useful for evaluating releases of hatchery fishes for management and research purposes. Calcein is a chemical that shows potential for producing a cost-effective batch mark that can be easily applied to large numbers of small fish and can be detected externally by nonlethal means. However, calcein shows some drawbacks related to mark deterioration when exposed to direct sunlight. We evaluated calcein mark retention over time in rainbow trout Oncorhynchus mykiss by using both external (head, fins) and internal structures (otoliths), and we compared mark retention between fish reared in normal outdoor raceways under ambient light conditions and those reared indoors in shaded circular tanks. Calcein marks on rainbow trout that were marked as fry and reared in outdoor raceways deteriorated significantly within 8 d of marking and remained at low or undetectable levels throughout the study. Mark quality was much better for rainbow trout reared indoors but still degraded over the 7-month evaluation period. Calcein marks were visible over the entire study period for otoliths of fish reared both indoors and outdoors, with better results being obtained for fish reared indoors. While calcein shows potential for generating a successful nonlethal batch mark, it may have limited use in situations where fish are exposed to sunlight, which can degrade the external mark. Marks in otoliths were retained well but required time-consuming processing and lethal sampling. For use of otolith marks, we recommend combining calcein with some other external mark (e.g., adipose fin clip) to aid in identifying chemically marked individuals. © Copyright by the American Fisheries Society 2010.

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.

Sullivan C.L.,414 East Locust Lane | Meyer K.A.,414 East Locust Lane | Schill D.J.,414 East Locust Lane
North American Journal of Fisheries Management | Year: 2013

Circle hooks are becoming commonplace in recreational fisheries because they often reduce deep hooking, but there has been little evaluation of their effectiveness in trout fisheries. To compare the occurrence of deep hooking and angling success rates for stream-dwelling trout, we used three baited hook types (i.e., inline circle hooks, inline J hooks, and 4°-offset J hooks) fished with two angling methods (i.e., active fishing, using a traditional bait fishing hook set; and passive fishing, with no sharp hook set). Of the 583 wild trout caught by anglers, 20% were deep hooked. The deep hooking rate varied by hook type and angling method, but the interaction term hook type × angling method was statistically significant, indicating that the effect of hook type could not be interpreted separately from fishing method. Accordingly, the occurrence of deep hooking was significantly greater for offset J hooks fished passively (28 ± 9% [95% CI about the mean]) and inline J hooks fished actively (27 ± 9%) than for offset J hooks fished actively (9 ± 6%) and inline circle hooks fished actively (10 ± 6%). Fish length affected deep-hooking rates, such that trout smaller than 250 mm were less likely to be deeply hooked than trout 250-350 mm in length. Hooking success (i.e., successful hook-ups divided by strikes) was greatest for actively fished inline J hooks (75 ± 7%), lowest for passively fished inline circle hooks (45 ± 6%) and passively fished offset J hooks (48 ± 8%), and always greater for actively fished hooks than for passively fished hooks of the same type. We found deep hooking was nearly twice as likely for inline circle hooks when fished according to manufacturers' recommendations (i.e., passively) than when fished actively. These results and those of others suggest that fishing circle hooks actively when bait fishing for stream-dwelling trout will result in less deep hooking than fishing circle hooks passively. © 2013 Copyright Taylor and Francis Group, LLC.

Koenig M.K.,414 East Locust Lane | Meyer K.A.,414 East Locust Lane
North American Journal of Fisheries Management | Year: 2011

Idaho Department of Fish and Game hatcheries stock predominantly sterile triploid (3n) rainbow trout Oncorhynchus mykiss to provide sportfishing opportunities while minimizing the genetic risks to wild stocks. Triploid catchable-sized rainbow trout are stocked in over 500 water bodies across Idaho annually, but there remains some uncertainty regarding the performance of triploid rainbow trout relative to their diploid (2n) counterparts. We examined the relative survival, growth, and returns of diploid and triploid all-female catchable rainbow trout across 13 lakes and reservoirs. Most reservoirs showed higher returns of 2n rainbow trout to anglers. In 2008, 3n rainbow trout returned on average at only 72% and 81% of the rates of 2n trout in gill nets and snout collection boxes, respectively, and the difference for both methods was statistically significant. Carryover of marked rainbow trout from 2008 was low or zero in most reservoirs. Where there was carryover, snout collection boxes suggested that 3n rainbow trout returned to anglers at 71% of the rate of 2n rainbow trout in the second year after planting, but the difference was not statistically significant. Triploid rainbow trout did not show any growth advantages over 2n rainbow trout but were similar in length, weight, and dressed weight. The disparity in returns between 2n and 3n trout varied across reservoirs but was more pronounced in locations subjected to greater drawdown and with greater species diversity. While 2n rainbow trout may grow and survive better in reservoirs subject to low water levels, triploid rainbow trout may perform equally well under good habitat conditions while not having genetic impacts on native stocks. These findings are rather fortuitous for fisheries managers, as triploids probably perform better in higher-quality habitats where native trout often exist, whereas diploids are better suited to reservoirs with degraded habitats where native stocks have usually been extirpated. © American Fisheries Society 2011.

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.

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.

Kozfkay C.C.,800 Trout Road | Campbell M.R.,800 Trout Road | Meyer K.A.,414 East Locust Lane | Schill D.J.,414 East Locust Lane
Transactions of the American Fisheries Society | Year: 2011

The genetic structure of redband trout Oncorhynchus mykiss gairdnerii in the upper Snake River basin was investigated at various scales using 13 microsatellite loci. The majority of the genetic variation was partitioned between streams, although differentiation among watersheds was significant. This diversity was probably historically partitioned at the watershed scale when steelhead O. mykiss (anadromous rainbow trout) were present, with the exception of small, isolated, headwater streams where there may have been only resident trout. Genetic structure appears to have been altered by a combination of factors, including habitat fragmentation and hybridization with hatchery trout. Redband trout populations in the desert and montane environments both experienced reduced gene flow, but the desert populations displayed higher degrees of genetic differentiation. There was also a significant inverse relationship between the degree of genetic differentiation and the level of allelic diversity. Interspecific hybrids with cutthroat trout O. clarkii were detected within 9% of the sampled sites, but they made up only 2% of fish and were mostly confined to one sample location. In contrast, intraspecific hybrids with coastal rainbow trout O. m. irideus were detected within 31% of the samples sites and were more than twice as likely to be found where historical records indicated that stocking of hatchery rainbow trout occurred. The inclusion of intraspecific hybridized populations altered genetic structure by creating an artificial shared ancestry among populations from different drainages and led to higher levels of genetic variation in each of the populations. The threats of fragmentation and hybridization will need to be considered in developing conservation and management policies for redband trout in Idaho. © American Fisheries Society 2011.

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