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Shawn R Narum - One of the best experts on this subject based on the ideXlab platform.
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Physiological and genomic signatures of evolutionary thermal adaptation in redband trout from extreme climates.
Evolutionary Applications, 2018Co-Authors: Zhongqi Chen, Anthony P. Farrell, Amanda Matala, Nicholas Hoffman, Shawn R NarumAbstract:: Temperature is a master environmental factor that limits the geographical distribution of species, especially in ectotherms. To address challenges in biodiversity conservation under ongoing climate change, it is essential to characterize relevant functional limitations and adaptive genomic content at population and species levels. Here, we present evidence for adaptive divergence in cardiac function and genomic regions in redband trout (Oncorhynchus Mykiss Gairdneri) populations from desert and montane streams. Cardiac phenotypes of individual fish were measured in the field with a custom-built electrocardiogram apparatus. Maximum heart rate and its rate limiting temperature during acute warming were significantly higher in fish that have evolved in the extreme of a desert climate compared to a montane climate. Association mapping with 526,301 single nucleotide polymorphisms (SNPs) across the genome revealed signatures of thermal selection both within and among ecotypes. Among desert and montane populations, 435 SNPs were identified as putative outliers under natural selection and 20 of these loci showed significant association with average summer water temperatures among populations. Phenotypes for cardiac performance were variable within each ecotype, and 207 genomic regions were strongly associated with either maximum heart rate or rate limiting temperatures among individuals. Annotation of significant loci provided candidate genes that underlie thermal adaptation, including pathways associated with cardiac function (IRX5, CASQ1, CAC1D, and TITIN), neuroendocrine system (GPR17 and NOS), and stress response (SERPH). By integrating comparative physiology and population genomics, results here advance our knowledge on evolutionary processes of thermal adaptation in aquatic ectotherms.
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Mechanisms of thermal adaptation and evolutionary potential of conspecific populations to changing environments
Molecular Ecology, 2018Co-Authors: Zhongqi Chen, Anthony P. Farrell, Amanda Matala, Shawn R NarumAbstract:: Heterogeneous and ever-changing thermal environments drive the evolution of populations and species, especially when extreme conditions increase selection pressure for traits influencing fitness. However, projections of biological diversity under scenarios of climate change rarely consider evolutionary adaptive potential of natural species. In this study, we tested for mechanistic evidence of evolutionary thermal adaptation among ecologically divergent redband trout populations (Oncorhynchus Mykiss Gairdneri) in cardiorespiratory function, cellular response and genomic variation. In a common garden environment, fish from an extreme desert climate had significantly higher critical thermal maximum (p 3°C) than fish from cooler montane climate. In addition, the desert population had the highest maximum heart rate during warming (20% greater than montane populations), indicating improved capacity to deliver oxygen to internal tissues. In response to acute heat stress, distinct sets of cardiac genes were induced among ecotypes, which helps to explain the differences in cardiorespiratory function. Candidate genomic markers and genes underlying these physiological adaptations were also pinpointed, such as genes involved in stress response and metabolic activity (hsp40, ldh-b and camkk2). These markers were developed into a multivariate model that not only accurately predicted critical thermal maxima, but also evolutionary limit of thermal adaptation in these specific redband trout populations relative to the expected limit for the species. This study demonstrates mechanisms and limitations of an aquatic species to evolve under changing environments that can be incorporated into advanced models to predict ecological consequences of climate change for natural organisms.
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differential expression of genes that control respiration contribute to thermal adaptation in redband trout Oncorhynchus Mykiss Gairdneri
Genome Biology and Evolution, 2015Co-Authors: Michael R Garvin, Gary H Thorgaard, Shawn R NarumAbstract:Organisms can adapt to local environmental conditions as a plastic response or become adapted through natural selection on genetic variation. The ability to adapt to increased water temperatures will be of paramount importance for many fish species as the climate continues to warm and water resources become limited. Because increased water temperatures will reduce the dissolved oxygen available for fish, we hypothesized that adaptation to low oxygen environments would involve improved respiration through oxidative phosphorylation (OXPHOS). To test this hypothesis, we subjected individuals from two ecologically divergent populations of inland (redband) rainbow trout (Oncorhynchus Mykiss Gairdneri) with historically different temperature regimes (desert and montane) and their F1 progeny to diel cycles of temperature stress and then examined gene expression data for 80 nuclear- and mitochondrial-encoded OXPHOS subunits that participate in respiration. Of the 80 transcripts, 7 showed ≥ 2-fold difference in expression levels in gill tissue from desert fish under heat stress whereas the montane fish had none and the F1 only had one differentially expressed gene. A structural analysis of the proteins encoded by those genes suggests that the response could coordinate the formation of supercomplexes and oligomers. Supercomplexes may increase the efficiency of respiration because complexes I, III, and IV are brought into close proximity and oligomerization of complex V alters the macrostructure of mitochondria to improve respiration. Significant differences in gene expression patterns in response to heat stress in a common environment indicate that the response was not due to plasticity but had a genetic basis.
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Transcriptomic response to heat stress among ecologically divergent populations of redband trout
BMC Genomics, 2015Co-Authors: Shawn R Narum, Nathan R. CampbellAbstract:Background As ectothermic organisms have evolved to differing aquatic climates, the molecular basis of thermal adaptation is a key area of research. In this study, we tested for differential transcriptional response of ecologically divergent populations of redband trout ( Oncorhynchus Mykiss Gairdneri ) that have evolved in desert and montane climates. Each pure strain and their F1 cross were reared in a common garden environment and exposed over four weeks to diel water temperatures that were similar to those experienced in desert climates within the species’ range. Gill tissues were collected from the three strains of fish (desert, montane, F1 crosses) at the peak of heat stress and tested for mRNA expression differences across the transcriptome with RNA-seq. Results Strong differences in transcriptomic response to heat stress were observed across strains confirming that fish from desert environments have evolved diverse mechanisms to cope with stressful environments. As expected, a large number of total transcripts (12,814) were differentially expressed in the study (FDR ≤ 0.05) with 2310 transcripts in common for all three strains, but the desert strain had a larger number of unique differentially expressed transcripts (2875) than the montane (1982) or the F1 (2355) strain. Strongly differentiated genes (>4 fold change and FDR ≤ 0.05) were particularly abundant in the desert strain (824 unique contigs) relative to the other two strains (montane = 58; F1 = 192). Conclusions This study demonstrated patterns of acclimation (i.e., phenotypic plasticity) within strains and evolutionary adaptation among strains in numerous genes throughout the transcriptome. Key stress response genes such as molecular chaperones (i.e., heat shock proteins) had adaptive patterns of gene expression among strains, but also a much higher number of metabolic and cellular process genes were differentially expressed in the desert strain demonstrating these biological pathways are critical for thermal adaptation to warm aquatic climates. The results of this study further elucidate the molecular basis for thermal adaptation in aquatic ecosystems and extend the potential for identifying genes that may be critical for adaptation to changing climates.
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Transcriptomic response to heat stress among ecologically divergent populations of redband trout
BMC Genomics, 2015Co-Authors: Shawn R Narum, Nathan R. CampbellAbstract:As ectothermic organisms have evolved to differing aquatic climates, the molecular basis of thermal adaptation is a key area of research. In this study, we tested for differential transcriptional response of ecologically divergent populations of redband trout (Oncorhynchus Mykiss Gairdneri) that have evolved in desert and montane climates. Each pure strain and their F1 cross were reared in a common garden environment and exposed over four weeks to diel water temperatures that were similar to those experienced in desert climates within the species’ range. Gill tissues were collected from the three strains of fish (desert, montane, F1 crosses) at the peak of heat stress and tested for mRNA expression differences across the transcriptome with RNA-seq. Strong differences in transcriptomic response to heat stress were observed across strains confirming that fish from desert environments have evolved diverse mechanisms to cope with stressful environments. As expected, a large number of total transcripts (12,814) were differentially expressed in the study (FDR ≤ 0.05) with 2310 transcripts in common for all three strains, but the desert strain had a larger number of unique differentially expressed transcripts (2875) than the montane (1982) or the F1 (2355) strain. Strongly differentiated genes (>4 fold change and FDR ≤ 0.05) were particularly abundant in the desert strain (824 unique contigs) relative to the other two strains (montane = 58; F1 = 192). This study demonstrated patterns of acclimation (i.e., phenotypic plasticity) within strains and evolutionary adaptation among strains in numerous genes throughout the transcriptome. Key stress response genes such as molecular chaperones (i.e., heat shock proteins) had adaptive patterns of gene expression among strains, but also a much higher number of metabolic and cellular process genes were differentially expressed in the desert strain demonstrating these biological pathways are critical for thermal adaptation to warm aquatic climates. The results of this study further elucidate the molecular basis for thermal adaptation in aquatic ecosystems and extend the potential for identifying genes that may be critical for adaptation to changing climates.
Clint C. Muhlfeld - One of the best experts on this subject based on the ideXlab platform.
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Genetic Structure of Columbia River Redband Trout Populations in the Kootenai River Drainage, Montana, Revealed by Microsatellite and Allozyme Loci
Transactions of The American Fisheries Society, 2002Co-Authors: Kathy L. Knudsen, Clint C. Muhlfeld, George K. Sage, Robb F. LearyAbstract:Abstract We describe the genetic divergence among 10 populations of redband trout Oncorhynchus Mykiss Gairdneri from the upper Columbia River drainage. Resident redband trout from two watersheds in the Kootenai River drainage and hatchery stocks of migratory Kamloops redband trout from Kootenay Lake, British Columbia, were analyzed using allele frequency data from microsatellite and allozyme loci. The Kamloops populations have significantly different allele frequencies from those of the Kootenai River drainage. Of the total genetic variation detected in the resident redband trout, 40.7% (microsatellites) and 15.5% (allozymes) were due to differences between populations from the two Kootenai River watersheds. The divergence among populations within each watershed, however, was less than 3.5% with both techniques. Our data indicate that watershed-specific broodstocks of redband trout are needed by fisheries managers for reintroduction or the supplementation of populations at risk of extinction.
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Spawning Characteristics of Redband Trout in a Headwater Stream in Montana
North American Journal of Fisheries Management, 2002Co-Authors: Clint C. MuhlfeldAbstract:Abstract I investigated the spawning characteristics of redband trout Oncorhynchus Mykiss Gairdneri (a rainbow trout subspecies) during the spring of 1998 in Basin Creek, a third-order headwater stream located in the Kootenai River drainage in northwestern Montana. I examined the timing of spawning as related to discharge and water temperature and analyzed microhabitat selection of 30 completed redds in a low-gradient (0.5–1.5%) reach. Redband trout spawned as flow declined after peak runoff and as mean daily water temperature exceeded 6.0°C and maximum daily temperature exceeded 7.0°C. Redband trout began spawning on 6 June (mean daily discharge = 2.1 m3/s), 10 d after the peak discharge (8.7 m3/s) occurred. The last redd was completed on 24 June, when discharge was 1.5 m3/s. The mean total redd length was 53 cm (SD = 14; range = 31–91 cm), and the mean total area was 51 cm2 (SD = 8; range = 46–76 cm2). Eighty percent of the redds were located in pool tailouts, 13% in runs, and 7% in riffles. Spawning re...
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Summer Habitat Use by Columbia River Redband Trout in the Kootenai River Drainage, Montana
North American Journal of Fisheries Management, 2001Co-Authors: Clint C. Muhlfeld, David H. Bennett, Brian MarotzAbstract:Abstract The reported decline in the abundance, distribution, and genetic diversity of Columbia River redband trout Oncorhynchus Mykiss Gairdneri (a rainbow trout subspecies) has prompted fisheries managers to investigate their habitat requirements, identify critical habitat, and develop effective conservation and recovery programs. We analyzed the microhabitat, mesohabitat, and macrohabitat use and distribution of Columbia River redband trout by means of snorkel surveys in two watersheds in the Kootenai River drainage, Montana and Idaho, during the summers of 1997 and 1998. Juvenile (36–125 mm total length, TL) and adult (≥126 mm TL) fish preferred deep microhabitats (≥0.4 m) with low to moderate velocities (≤0.5 m/s) adjacent to the thalweg. Conversely, age-0 (≤35 mm) fish selected slow water (≤0.1 m/s) and shallow depths (≤0.2 m) located in lateral areas of the channel. Age-0, juvenile, and adult fish strongly selected pool mesohabitats and avoided riffles; juveniles and adults generally used runs in p...
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Fall and Winter Habitat Use and Movement by Columbia River Redband Trout in a Small Stream in Montana
North American Journal of Fisheries Management, 2001Co-Authors: Clint C. Muhlfeld, David H. Bennett, Brian MarotzAbstract:Abstract We used radiotelemetry to quantify the movements and habitat use of resident adult Columbia River redband trout Oncorhynchus Mykiss Gairdneri (hereafter, redband trout) from October to December 1997 in South Fork Callahan Creek, a third-order tributary to Callahan Creek in the Kootenai River drainage in northwestern Montana. All redband trout (N = 23) were consistently relocated in a stream reach with moderate gradient (2.3%) near the site of original capture. Some fish (N = 13) displayed sedentary behavior, whereas others were mobile (N = 10). The mean total distance moved during the study for all fish combined was 64 m (SD = 105 m; range, 0–362 m), and the mean home range from October through December was 67 m (SD = 99 m; range, 5–377 m). Thirteen redband trout made short upstream and downstream movements (mean total movement = 134 m; range, 8–362 m) that were related to habitat use. Mobile fish commonly migrated to complex pools that spanned the entire channel width (primary pools). Eight of 1...
Nathan R. Campbell - One of the best experts on this subject based on the ideXlab platform.
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Transcriptomic response to heat stress among ecologically divergent populations of redband trout
BMC Genomics, 2015Co-Authors: Shawn R Narum, Nathan R. CampbellAbstract:Background As ectothermic organisms have evolved to differing aquatic climates, the molecular basis of thermal adaptation is a key area of research. In this study, we tested for differential transcriptional response of ecologically divergent populations of redband trout ( Oncorhynchus Mykiss Gairdneri ) that have evolved in desert and montane climates. Each pure strain and their F1 cross were reared in a common garden environment and exposed over four weeks to diel water temperatures that were similar to those experienced in desert climates within the species’ range. Gill tissues were collected from the three strains of fish (desert, montane, F1 crosses) at the peak of heat stress and tested for mRNA expression differences across the transcriptome with RNA-seq. Results Strong differences in transcriptomic response to heat stress were observed across strains confirming that fish from desert environments have evolved diverse mechanisms to cope with stressful environments. As expected, a large number of total transcripts (12,814) were differentially expressed in the study (FDR ≤ 0.05) with 2310 transcripts in common for all three strains, but the desert strain had a larger number of unique differentially expressed transcripts (2875) than the montane (1982) or the F1 (2355) strain. Strongly differentiated genes (>4 fold change and FDR ≤ 0.05) were particularly abundant in the desert strain (824 unique contigs) relative to the other two strains (montane = 58; F1 = 192). Conclusions This study demonstrated patterns of acclimation (i.e., phenotypic plasticity) within strains and evolutionary adaptation among strains in numerous genes throughout the transcriptome. Key stress response genes such as molecular chaperones (i.e., heat shock proteins) had adaptive patterns of gene expression among strains, but also a much higher number of metabolic and cellular process genes were differentially expressed in the desert strain demonstrating these biological pathways are critical for thermal adaptation to warm aquatic climates. The results of this study further elucidate the molecular basis for thermal adaptation in aquatic ecosystems and extend the potential for identifying genes that may be critical for adaptation to changing climates.
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Transcriptomic response to heat stress among ecologically divergent populations of redband trout
BMC Genomics, 2015Co-Authors: Shawn R Narum, Nathan R. CampbellAbstract:As ectothermic organisms have evolved to differing aquatic climates, the molecular basis of thermal adaptation is a key area of research. In this study, we tested for differential transcriptional response of ecologically divergent populations of redband trout (Oncorhynchus Mykiss Gairdneri) that have evolved in desert and montane climates. Each pure strain and their F1 cross were reared in a common garden environment and exposed over four weeks to diel water temperatures that were similar to those experienced in desert climates within the species’ range. Gill tissues were collected from the three strains of fish (desert, montane, F1 crosses) at the peak of heat stress and tested for mRNA expression differences across the transcriptome with RNA-seq. Strong differences in transcriptomic response to heat stress were observed across strains confirming that fish from desert environments have evolved diverse mechanisms to cope with stressful environments. As expected, a large number of total transcripts (12,814) were differentially expressed in the study (FDR ≤ 0.05) with 2310 transcripts in common for all three strains, but the desert strain had a larger number of unique differentially expressed transcripts (2875) than the montane (1982) or the F1 (2355) strain. Strongly differentiated genes (>4 fold change and FDR ≤ 0.05) were particularly abundant in the desert strain (824 unique contigs) relative to the other two strains (montane = 58; F1 = 192). This study demonstrated patterns of acclimation (i.e., phenotypic plasticity) within strains and evolutionary adaptation among strains in numerous genes throughout the transcriptome. Key stress response genes such as molecular chaperones (i.e., heat shock proteins) had adaptive patterns of gene expression among strains, but also a much higher number of metabolic and cellular process genes were differentially expressed in the desert strain demonstrating these biological pathways are critical for thermal adaptation to warm aquatic climates. The results of this study further elucidate the molecular basis for thermal adaptation in aquatic ecosystems and extend the potential for identifying genes that may be critical for adaptation to changing climates.
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Thermal adaptation and acclimation of ectotherms from differing aquatic climates
Molecular Ecology, 2013Co-Authors: Shawn R Narum, Kevin A. Meyer, Nathan R. Campbell, Michael R. Miller, Ronald W. HardyAbstract: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 shortterm 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.
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Adaptation of redband trout in desert and montane environments
Molecular Ecology, 2010Co-Authors: Shawn R Narum, Christine C. Kozfkay, Nathan R. Campbell, Kevin A. MeyerAbstract: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.
Brian Marotz - One of the best experts on this subject based on the ideXlab platform.
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Summer Habitat Use by Columbia River Redband Trout in the Kootenai River Drainage, Montana
North American Journal of Fisheries Management, 2001Co-Authors: Clint C. Muhlfeld, David H. Bennett, Brian MarotzAbstract:Abstract The reported decline in the abundance, distribution, and genetic diversity of Columbia River redband trout Oncorhynchus Mykiss Gairdneri (a rainbow trout subspecies) has prompted fisheries managers to investigate their habitat requirements, identify critical habitat, and develop effective conservation and recovery programs. We analyzed the microhabitat, mesohabitat, and macrohabitat use and distribution of Columbia River redband trout by means of snorkel surveys in two watersheds in the Kootenai River drainage, Montana and Idaho, during the summers of 1997 and 1998. Juvenile (36–125 mm total length, TL) and adult (≥126 mm TL) fish preferred deep microhabitats (≥0.4 m) with low to moderate velocities (≤0.5 m/s) adjacent to the thalweg. Conversely, age-0 (≤35 mm) fish selected slow water (≤0.1 m/s) and shallow depths (≤0.2 m) located in lateral areas of the channel. Age-0, juvenile, and adult fish strongly selected pool mesohabitats and avoided riffles; juveniles and adults generally used runs in p...
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Fall and Winter Habitat Use and Movement by Columbia River Redband Trout in a Small Stream in Montana
North American Journal of Fisheries Management, 2001Co-Authors: Clint C. Muhlfeld, David H. Bennett, Brian MarotzAbstract:Abstract We used radiotelemetry to quantify the movements and habitat use of resident adult Columbia River redband trout Oncorhynchus Mykiss Gairdneri (hereafter, redband trout) from October to December 1997 in South Fork Callahan Creek, a third-order tributary to Callahan Creek in the Kootenai River drainage in northwestern Montana. All redband trout (N = 23) were consistently relocated in a stream reach with moderate gradient (2.3%) near the site of original capture. Some fish (N = 13) displayed sedentary behavior, whereas others were mobile (N = 10). The mean total distance moved during the study for all fish combined was 64 m (SD = 105 m; range, 0–362 m), and the mean home range from October through December was 67 m (SD = 99 m; range, 5–377 m). Thirteen redband trout made short upstream and downstream movements (mean total movement = 134 m; range, 8–362 m) that were related to habitat use. Mobile fish commonly migrated to complex pools that spanned the entire channel width (primary pools). Eight of 1...
Ted G. Wise - One of the best experts on this subject based on the ideXlab platform.
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A genetically distinct wild redband trout (Oncorhynchus Mykiss Gairdneri) population in Crane Prairie Reservoir, Oregon, persists despite extensive stocking of hatchery rainbow trout (O. m. irideus)
Conservation Genetics, 2008Co-Authors: Andrew P. Matala, Steven Marx, Ted G. WiseAbstract:Crane Prairie Reservoir in the upper Deschutes River Basin has historically supported a wild population of migratory Deschutes River redband trout. Owing to its status as a premier destination for recreational angling in Oregon, the reservoir has been stocked with domesticated hatchery rainbow trout since 1955. In recent years the wild redband trout population has experienced a substantial decline. Effects on productivity related to genetic interaction with naturally spawning hatchery-origin fish (fitness risks) have not been determined. The species Oncorhynchus Mykiss has been characterized with substantial genetic diversity throughout the Deschutes River Basin that further heightens the challenge of identifying specific conservation needs of wild populations. A conservation plan for Crane Prairie wild redband trout requires a better understanding of the natural reproductive success of out-of-basin hatchery trout in the reservoir tributaries, and the similarity between Crane Prairie redband trout with other extant redband trout populations in the basin. Using a suite of 17 microsatellite nuclear DNA markers, we evaluated the genetic structure among Crane Prairie Reservoir redband trout, hatchery rainbow trout, and two adjacent populations of redband trout from within the Upper Deschutes River Basin. We observed significant heterogeneity between the hatchery and wild Crane Prairie populations that may reflect differences in life histories, differential productivity and assortative mating. The genetic distinctions observed among the three redband trout populations suggest restricted gene flow and genetic drift within the upper basin. Temporally stratified sampling and larger numbers of samples will be necessary to confirm these conclusions.
