scholarly journals Genotyping-in-Thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0261966
Author(s):  
Sarah L. Chang ◽  
Hillary G. M. Ward ◽  
Michael A. Russello
Keyword(s):  
Fisheries Management ◽  
Sockeye Salmon ◽  
Multiple Scales ◽  
Survey Methods ◽  
Oncorhynchus Nerka ◽  
Nucleotide Polymorphisms ◽  
Kokanee Salmon ◽  
High Concordance ◽  
Migratory Form ◽  
Mixed Stock

The ability to differentiate life history variants is vital for estimating fisheries management parameters, yet traditional survey methods can be inaccurate in mixed-stock fisheries. Such is the case for kokanee, the freshwater resident form of sockeye salmon (Oncorhynchus nerka), which exhibits various reproductive ecotypes (stream-, shore-, deep-spawning) that co-occur with each other and/or anadromous O. nerka in some systems across their pan-Pacific distribution. Here, we developed a multi-purpose Genotyping-in-Thousands by sequencing (GT-seq) panel of 288 targeted single nucleotide polymorphisms (SNPs) to enable accurate kokanee stock identification by geographic basin, migratory form, and reproductive ecotype across British Columbia, Canada. The GT-seq panel exhibited high self-assignment accuracy (93.3%) and perfect assignment of individuals not included in the baseline to their geographic basin, migratory form, and reproductive ecotype of origin. The GT-seq panel was subsequently applied to Wood Lake, a valuable mixed-stock fishery, revealing high concordance (>98%) with previous assignments to ecotype using microsatellites and TaqMan® SNP genotyping assays, while improving resolution, extending a long-term time-series, and demonstrating the scalability of this approach for this system and others.

scholarly journals Importance of sample size for estimating prevalence: A case example of infectious hematopoietic necrosis viral RNA detection in mixed-stock Fraser River Sockeye salmon (Oncorhynchus nerka), British Columbia, Canada.

2020 ◽  
Author(s):  
Emilie Laurin ◽  
Julia Bradshaw ◽  
Laura Hawley ◽  
Ian A. Gardner ◽  
Kyle A Garver ◽  
...  
Keyword(s):  
British Columbia ◽  
Sample Size ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Small Sample ◽  
Viral Rna ◽  
Sample Sizes ◽  
Apparent Prevalence ◽  
Infectious Hematopoietic Necrosis ◽  
Mixed Stock

Proper sample size must be considered when designing infectious-agent prevalence studies for mixed-stock fisheries, because bias and uncertainty complicate interpretation of apparent (test)-prevalence estimates. Sample size varies between stocks, often smaller than expected during wild-salmonid surveys. Our case example of 2010-2016 survey data of Sockeye salmon (Oncorhynchus nerka) from different stocks of origin in British Columbia, Canada, illustrated the effect of sample size on apparent-prevalence interpretation. Molecular testing (viral RNA RT-qPCR) for infectious hematopoietic necrosis virus (IHNv) revealed large differences in apparent-prevalence across wild salmon stocks (much higher from Chilko Lake) and sampling location (freshwater or marine), indicating differences in both stock and host life-stage effects. Ten of the 13 marine non-Chilko stock-years with IHNv-positive results had small sample sizes (< 30 samples per stock-year) which, with imperfect diagnostic tests (particularly lower diagnostic sensitivity), could lead to inaccurate apparent-prevalence estimation. When calculating sample size for expected apparent prevalence using different approaches, smaller sample sizes often led to decreased confidence in apparent-prevalence results and decreased power to detect a true difference from a reference value.

A comparison of polymorphism of genetic markers and population sample sizes required for mixed-stock analysis of sockeye salmon (Oncorhynchus nerka) in British Columbia

2011 ◽  
Vol 68 (3) ◽  
pp. 550-562 ◽  
Author(s):  
Terry D. Beacham ◽  
B. McIntosh ◽  
C. G. Wallace
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Population Sample ◽  
Identification Accuracy ◽  
Stock Identification ◽  
Nucleotide Polymorphisms ◽  
Sample Sizes ◽  
Genetic Stock ◽  
Baseline Sample

We evaluated two questions: (i) do microsatellites require larger population baseline sample sizes than single nucleotide polymorphisms (SNPs) to allow the accuracy provided by the microsatellites in genetic stock identification (GSI) applications to be expressed, and (ii) do less genetically distinct populations require larger population baseline sample sizes than more distinct populations to improve population-specific accuracy in GSI applications? Forty-six SNP loci were surveyed in 40 populations of sockeye salmon ( Oncorhynchus nerka ) over 16 regions from southern and central British Columbia and were split into two groups: the top 23 SNPs evaluated for stock identification for British Columbia sockeye salmon and the poorest 23 nuclear SNPs. Fourteen microsatellites were surveyed and split into two groups, with loci from the top 7 loci for stock identification accuracy assembled in one group, and the remaining 7 microsatellites assigned to a second group. SNPs and microsatellites with lower stock identification power required larger population sample sizes to allow expression of stock identification potential. To achieve the same level of population-specific accuracy, SNPs required fewer individuals to be sampled in a population than did microsatellites. Less genetically distinct populations required larger population sample sizes to achieve a given level of accuracy in estimated stock compositions.

Experimental Harvest Policies for a Mixed-Stock Fishery: Fraser River Sockeye Salmon, Oncorhynchus nerka

1990 ◽  
Vol 47 (1) ◽  
pp. 145-155 ◽  
Author(s):  
Jeremy S. Collie ◽  
Randall M. Peterman ◽  
Carl J. Walters
Keyword(s):  
Regression Model ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Maximum Sustainable Yield ◽  
Sustainable Yield ◽  
Fraser River ◽  
Harvest Rate ◽  
Ricker Model ◽  
Exploitation Rate ◽  
Mixed Stock

We investigated harvest strategies aimed at rebuilding the less abundant stocks of Fraser River sockeye salmon, Oncorhynchus nerka. Monte Carlo simulations were run to estimate catch under four different harvest policy designs and three alternative parameterizations of the Ricker model. A pooled regression model was fit to 34 yr of spawner–recruit data from the 10 major stocks of Fraser sockeye. Compared with estimating separate parameters for each stock, the pooled regression model resulted in a more precise estimate of the Ricker a parameter (productivity at low stock sizes). Exploitation rate for maximum sustainable yield depends only on the a parameter and is thus well defined by the pooled regression even though the corresponding optimal escapement levels remain uncertain. A reduction in harvest rates to 70% from the current average 80% increased the simulated 40-yr catch by 31%. More extreme harvest-rate reductions, involving 50% exploitation rates on some stocks for four generations, allowed faster rebuilding and further increases in catch. Extreme harvest-rate reductions were necessary to obtain a 0.5 or greater probability of correctly detecting increased escapements, should the less-abundant runs increase as expected.

scholarly journals Genomic changes associated with reproductive and migratory ecotypes in sockeye salmon (Oncorhynchus nerka)

2017 ◽  
Author(s):  
Andrew J Veale ◽  
Michael A Russello
Keyword(s):  
Life History ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Multiple Comparisons ◽  
Nucleotide Polymorphisms ◽  
Life History Variation ◽  
Genomic Changes ◽  
Outlier Loci ◽  
Patterns And Processes ◽  
Genomic Regions

AbstractMechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here we used paired migratory [anadromous vs. resident (kokanee)] and reproductive [shore- vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence. Restriction-site associated DNA sequencing was used to genotype this sampling at 7,347 single nucleotide polymorphisms (SNPs), 334 of which were identified as outlier loci and candidates for divergent selection within at least one ecotype comparison. Eighty-six of these outliers were present in multiple comparisons, with thirty-three detected across multiple catchments. Of particular note, one locus was detected as the most significant outlier between shore and stream-spawning ecotypes in multiple comparisons and across catchments (Columbia, Fraser and Snake). We also detected several islands of divergence, some shared among comparisons, potentially showing linked signals of differential selection. The SNPs and genomic regions identified in our study offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.

Otolith mass as a predictor of age in kokanee salmon (Oncorhynchus nerka) from four Colorado reservoirs

2012 ◽  
Vol 69 (10) ◽  
pp. 1569-1575 ◽  
Author(s):  
Jesse M. Lepak ◽  
C. Nathan Cathcart ◽  
Mevin B. Hooten
Keyword(s):  
Machine Learning ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Age Determination ◽  
Fish Populations ◽  
Financial Resources ◽  
Machine Learning Technique ◽  
Kokanee Salmon ◽  
Extensive Training ◽  
Learning Technique

Estimating ages of individuals in fish populations is crucial for determining characteristics necessary to effectively manage sport fisheries. Currently, the most accepted approach for fish age determination is using thin sectioned otoliths for interpretation. This method is labor-intensive, requires extensive training, and subjectively determines age. Several studies have shown that otolith mass increases with age, yet use of otolith mass to determine fish age is relatively underutilized. However, determining fish age using otolith mass requires relatively little training, is relatively nonsubjective, and is faster compared with other aging techniques. We collected kokanee salmon (i.e., landlocked sockeye salmon, Oncorhynchus nerka ) in 2004 from four reservoirs and from 2000 to 2009 in one reservoir to evaluate the efficacy of using otolith mass to determine fish ages. We used a machine learning technique to predict kokanee salmon ages using otolith mass and various other covariates. Our findings suggest this method has potential to substantially reduce time and financial resources required to age fish. We conclude that using otolith mass to determine fish age may represent an efficient and accurate approach for some species.

Missing the target: uncertainties in achieving management goals in fisheries on Fraser River, British Columbia, sockeye salmon (Oncorhynchus nerka)

2006 ◽  
Vol 63 (12) ◽  
pp. 2722-2733 ◽  
Author(s):  
Carrie A Holt ◽  
Randall M Peterman
Keyword(s):  
British Columbia ◽  
Fisheries Management ◽  
Return Migration ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Simulation Models ◽  
Mortality Rates ◽  
Fraser River ◽  
Management Options ◽  
Fishing Regulations

In sockeye salmon (Oncorhynchus nerka) fisheries, management targets are rarely achieved exactly, thereby creating uncertainties about outcomes from implementing fishing regulations. Although this type of uncertainty may be large, it is seldom incorporated into simulation models that evaluate management options. One objective of this study was to quantify the deviations that occur between realized and target mortality rates (i.e., the target fraction of adult recruits that die each year during return migration, mostly due to harvesting) in fisheries for sockeye salmon from the Fraser River, British Columbia. We found that for some sockeye stocks, realized mortality rates were higher than targets when recruitment was low (resulting in conservation concerns) and lower than targets when recruitment was high (resulting in foregone catch). Scientists and managers can at least partially account for effects of such deviations between realized and target mortality rates (outcome uncertainties) by choosing target harvest rules that reflect typical patterns in those deviations. We derived a method to permit modelers to incorporate those patterns into analyses of management options.

Institutional Learning and Spawning Channels for Sockeye Salmon (Oncorhynchus nerka)

1992 ◽  
Vol 49 (6) ◽  
pp. 1126-1136 ◽  
Author(s):  
Ray Hilborn
Keyword(s):  
British Columbia ◽  
Fisheries Management ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Decision Makers ◽  
The Other ◽  
Institutional Learning ◽  
1960S And 1970S ◽  
The 1960S ◽  
Design Construction

In the 1960s and 1970s, six artificial spawning channels for sockeye salmon (Oncorhynchus nerka) were constructed in British Columbia. I use the evaluation of these facilities and the response to the evaluation to test the hypothesis that fisheries management agencies can learn from experience. One of the facilities was almost immediately determined to be successful, but it took approximately 20 yr for the agency to evaluate the success of the other five. The evaluation was ambiguous for three of these. Only when facilities were overwhelmingly successful or total failures did clear answers emerge. The Canadian Department of Fisheries and Oceans (DFO) has experimented, evaluated, and learned about design, construction, and operation of spawning channels. DFO appears to be less successful at using the evaluation of adult production resulting from spawning channels. Learning appears to work best when goals are well defined, experiments can be conducted and evaluated rapidly, and there is a close organizational connection between decision makers, evaluators, and operators.

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