Hagerman, ID, United States
Hagerman, ID, United States

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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.

Hecht B.C.,University of Idaho | Hecht B.C.,Columbia River Inter Tribal Fish Commission | Campbell N.R.,Columbia River Inter Tribal Fish Commission | Holecek D.E.,University of Idaho | Narum S.R.,Columbia River Inter Tribal Fish Commission
Molecular Ecology | Year: 2013

Little is known of the genetic basis of migration despite the ecological benefits migratory species provide to their communities and their rapid global decline due to anthropogenic disturbances in recent years. Using next-generation sequencing of restriction-site-associated DNA (RAD) tags, we genotyped thousands of single nucleotide polymorphisms (SNPs) in two wild populations of migratory steelhead and resident rainbow trout (Oncorhynchus mykiss) from the Pacific Northwest of the United States. One population maintains a connection to the sea, whereas the other population has been sequestered from its access to the ocean for more than 50 years by a hydropower dam. Here we performed a genome-wide association study to identify 504 RAD SNP markers from several genetic regions that were associated with the propensity to migrate both within and between the populations. Our results corroborate those in previous quantitative trait loci studies and provide evidence for additional loci associated with this complex migratory life history. Our results suggest a complex multi-genic basis with several loci of small effect distributed throughout the genome contributing to migration in this species. We also determined that despite being sequestered for decades, the landlocked population continues to harbour genetic variation associated with a migratory life history and ATPase activity. Furthermore, we demonstrate the utility of genotyping-by-sequencing and how RAD-tag SNP data can be readily compared between studies to investigate migration within this species. © 2012 John Wiley & Sons Ltd.

Hess J.E.,Columbia River Inter Tribal Fish Commission | Campbell N.R.,Columbia River Inter Tribal Fish Commission | Close D.A.,University of British Columbia | Docker M.F.,University of Manitoba | Narum S.R.,Columbia River Inter Tribal Fish Commission
Molecular Ecology | Year: 2013

Unlike most anadromous fishes that have evolved strict homing behaviour, Pacific lamprey (Entosphenus tridentatus) seem to lack philopatry as evidenced by minimal population structure across the species range. Yet unexplained findings of within-region population genetic heterogeneity coupled with the morphological and behavioural diversity described for the species suggest that adaptive genetic variation underlying fitness traits may be responsible. We employed restriction site-associated DNA sequencing to genotype 4439 quality filtered single nucleotide polymorphism (SNP) loci for 518 individuals collected across a broad geographical area including British Columbia, Washington, Oregon and California. A subset of putatively neutral markers (N = 4068) identified a significant amount of variation among three broad populations: northern British Columbia, Columbia River/southern coast and 'dwarf' adults (FCT = 0.02, P ≪ 0.001). Additionally, 162 SNPs were identified as adaptive through outlier tests, and inclusion of these markers revealed a signal of adaptive variation related to geography and life history. The majority of the 162 adaptive SNPs were not independent and formed four groups of linked loci. Analyses with matsam software found that 42 of these outlier SNPs were significantly associated with geography, run timing and dwarf life history, and 27 of these 42 SNPs aligned with known genes or highly conserved genomic regions using the genome browser available for sea lamprey. This study provides both neutral and adaptive context for observed genetic divergence among collections and thus reconciles previous findings of population genetic heterogeneity within a species that displays extensive gene flow. © 2012 John Wiley & Sons Ltd.

Narum S.R.,Columbia River Inter Tribal Fish Commission | Hess J.E.,Columbia River Inter Tribal Fish Commission
Molecular Ecology Resources | Year: 2011

Genome scans with many genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under selection. In particular, SNPs are dense throughout the genome of most organisms and are commonly observed in functional genes making them ideal markers to study adaptive molecular variation. This approach has become commonly employed in ecological and population genetics studies to detect outlier loci that are putatively under selection. However, there are several challenges to address with outlier approaches including genotyping errors, underlying population structure and false positives, variation in mutation rate and limited sensitivity (false negatives). In this study, we evaluated multiple outlier tests and their type I (false positive) and type II (false negative) error rates in a series of simulated data sets. Comparisons included simulation procedures (FDIST2, arlequin v.3.5 and BAYESCAN) as well as more conventional tools such as global FST histograms. Of the three simulation methods, FDIST2 and BAYESCAN typically had the lowest type II error, BAYESCAN had the least type I error and Arlequin had highest type I and II error. High error rates in Arlequin with a hierarchical approach were partially because of confounding scenarios where patterns of adaptive variation were contrary to neutral structure; however, Arlequin consistently had highest type I and type II error in all four simulation scenarios tested in this study. Given the results provided here, it is important that outlier loci are interpreted cautiously and error rates of various methods are taken into consideration in studies of adaptive molecular variation, especially when hierarchical structure is included. © 2011 Blackwell Publishing Ltd.

Hess J.E.,Columbia River Inter Tribal Fish Commission | Matala A.P.,Columbia River Inter Tribal Fish Commission | Narum S.R.,Columbia River Inter Tribal Fish Commission
Molecular Ecology Resources | Year: 2011

Genetic stock identification (GSI) is an important tool in fisheries management. Microsatellites (μSATs) have been the dominant genetic marker for GSI; however, increasing availability and numerous advantages of single-nucleotide polymorphism (SNP) markers make them an appealing alternative. We tested performance of 13 μSAT vs. 92 SNP loci in a fine-scale application of GSI, using a new baseline for Chinook salmon consisting of 49 collections (n=4014) distributed across the Columbia River Basin. In GSI, baseline genotypes for both marker sets were used independently to analyse a real fishery mixture (n=2731) representing the total run of Chinook salmon passing Bonneville Dam in the Columbia River. Marker sets were evaluated using three criteria: (i) ability to differentiate reporting groups, (ii) proportion of correct assignment in mixture simulation tests and baseline leave-one-out analyses and (iii) individual assignment and confidence intervals around estimated stock proportions of a real fishery mixture. The μSATs outperformed the SNPs in resolving fine-scale relationships, but all 105 markers combined provided greatest power for GSI. SNPs were ranked by relative information content based on both an iterative procedure that optimized correct assignment to the baseline and ranking by minor allele frequency. For both methods, we identified a subset of the top 50 ranked loci, which were similar in assignment accuracy, and both reached maximum available power of the total 92 SNP loci (correct assignment=73%). Our estimates indicate that between 100 and 200 highly informative SNP loci are required to meet management standards (correct assignment>90%) for resolving stocks in finer-scale GSI applications. © 2011 Blackwell Publishing Ltd.

Campbell N.R.,Columbia River Inter Tribal Fish Commission | Narum S.R.,Columbia River Inter Tribal Fish Commission
Molecular Ecology Resources | Year: 2011

Single-nucleotide polymorphisms (SNPs) have potential for broad application in population and conservation genetics, but availability of these markers is limited in many nonmodel species. In this study, genomic and expressed sequence tagged (EST) sequences from closely related salmonids (Chinook salmon and rainbow trout) were used to design primers for amplification and sequencing of sockeye (Oncorhynchus nerka) and coho (Oncorhynchus kisutch) salmon DNA for SNP discovery. One hundred and six primer sets were designed and tested for amplification in each species. An ascertainment panel of 32 diverse individuals from each species was used as template for PCR amplification and Sanger sequencing. In total, 21647 bases of consensus sequence were screened in sockeye salmon and 20784 bases in coho salmon with 93 and 149 SNP sites identified, respectively. Sixty-four SNP sites were chosen for assay development, and 54 of the assays were validated by comparison with genotype and sequence data (O. nerka=23; O. kisutch=31). These validated SNP assays along with 142 other available SNP assays [O. nerka=103 (126 total); O. kisutch=30 (61 total)] were used to genotype collections of O. nerka (N=5) and O. kisutch (N=4) from various sites in the Columbia River to evaluate the utility of these markers in this region. Results from factorial correspondence analysis indicate that these SNP markers are capable of distinguishing O. nerka populations, but O. kisutch collections were less distinct because of their common ancestry. © 2011 Blackwell Publishing Ltd.

Graves D.,Columbia River Inter Tribal Fish Commission | Maule A.,U.S. Geological Survey
Climatic Change | Year: 2014

The goal of this study was to support an assessment of the potential effects of climate change on select natural, social, and economic resources in the Yakima River Basin. A workshop with local stakeholders highlighted the usefulness of projecting climate change impacts on anadromous steelhead (Oncorhynchus mykiss), a fish species of importance to local tribes, fisherman, and conservationists. Stream temperature is an important environmental variable for the freshwater stages of steelhead. For this study, we developed water temperature models for the Satus and Toppenish watersheds, two of the key stronghold areas for steelhead in the Yakima River Basin. We constructed the models with the Stream Network Temperature Model (SNTEMP), a mechanistic approach to simulate water temperature in a stream network. The models were calibrated over the April 15, 2008 to September 30, 2008 period and validated over the April 15, 2009 to September 30, 2009 period using historic measurements of stream temperature and discharge provided by the Yakama Nation Fisheries Resource Management Program. Once validated, the models were run to simulate conditions during the spring and summer seasons over a baseline period (1981-2005) and two future climate scenarios with increased air temperature of 1 °C and 2 °C. The models simulated daily mean and maximum water temperatures at sites throughout the two watersheds under the baseline and future climate scenarios. © 2012 Springer Science+Business Media Dordrecht.

Dittmer K.,Columbia River Inter Tribal Fish Commission
Climatic Change | Year: 2013

Over the last 100 years, linear trends of tributary streamflow have changed on Columbia River Basin tribal reservations and historical lands ceded by tribes in treaties with the United States. Analysis of independent flow measures (Seasonal Flow Fraction, Center Timing, Spring Flow Onset, High Flow, Low Flow) using the Student t test and Mann-Kendall trend test suggests evidence for climate change trends for many of the 32 study basins. The trends exist despite interannual climate variability driven by the El Niño-Southern Oscillation and Pacific Decadal Oscillation. The average April-July flow volume declined by 16 %. The median runoff volume date has moved earlier by 5.8 days. The Spring Flow Onset date has shifted earlier by 5.7 days. The trend of the flow standard deviation (i.e., weather variability) increased 3 % to 11 %. The 100-year November floods increased 49 %. The mid-Columbia 7Q10 low flows have decreased by 5 % to 38 %. Continuation of these climatic and hydrological trends may seriously challenge the future of salmon, their critical habitats, and the tribal peoples who depend upon these resources for their traditional livelihood, subsistence, and ceremonial purposes. © 2013 The Author(s).

Hess J.E.,Columbia River Inter Tribal Fish Commission | Narum S.R.,Columbia River Inter Tribal Fish Commission
Transactions of the American Fisheries Society | Year: 2011

Run timing in Chinook salmon Oncorhynchus tshawytscha is a life history trait that varies among populations throughout the Columbia River basin and has a demonstrated genetic basis. In this study, we used 92 singlenucleotide polymorphic (SNP) markers linked to at least 75 different functional genes (including OtsClock1a) to test for correlations with run timing. We obtained samples of adult Chinook salmon on a weekly basis as they passed a fixed point (Bonneville Dam) on the lower Columbia River main stem during the majority of the migratory run from April to October for three sequential years from 2007 to 2009 (n = 2,731, 3,479, and 2,960, respectively). Since these fish represented unknown mixtures of the three major genetic lineages in the Columbia River basin, we used genetic stock identification to assign individuals to their likely stock of origin. We then determined whether allelic variation at the SNP loci was correlated with the date of passage of fish in the context of stock of origin. Nine SNP loci were identified as candidates based on significant correlations with date of passage using the spatial analysis method. A multivariate analysis was then used to rank these eight candidate loci according to the proportion of genetic variation that day of passage explained relative to two other predictor variables: population structure and temperature. The three top-ranked loci were Ots_TAPBP, Ots_97077-179R, and Ots_myoD-364, which have known involvement in immunological functioning and muscle differentiation. Future work will test candidate SNPs using run-timing information from fish of known origin within particular Columbia River subbasins to help validate the role of these genetic linkage groups in this important life history trait. © American Fisheries Society 2011.

Narum S.R.,Columbia River Inter Tribal Fish Commission | Campbell N.R.,Columbia River Inter Tribal Fish Commission
Journal of Heredity | Year: 2010

Heat shock proteins (Hsps) are induced in response to high temperatures and other stressors, and sequence variation plays a role in regulation of expression of these genes. In this study, we investigated the sequence variation in the 3 major classes of Hsps (Hsp90, Hsp70, and low-molecular weight Hsp) within and among 3 cold-water fish species of Oncorhynchus (Oncorhynchus clarki, Oncorhynchus mykiss, and Oncorhynchus tshawytscha) with variable life history and thermal tolerance characteristics. Sequences collectively totaled 4556 bp across 9 gene fragments and 198 single nucleotide polymorphisms and 43 indel sites were observed among species. Within species, sequence variation was much lower for O. clarki than the other 2 species. Sequence variation within and among species was high in cis-regulatory regions that are potentially involved in transcription of Hsps under variable stressors. Our results indicate that Hsp genes may be locally adapted in O. clarki, whereas higher Hsp polymorphism is necessary for O. mykiss and O. tshawytscha and variation at the sequence level may have important evolutionary consequences for these species. Further studies are needed to determine the association of observed sequence variation with the regulation of Hsps and performance of fish under stress. © 2009 The American Genetic Association.

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