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Hagerman, ID, United States

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).

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.

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.

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.

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