Long‐term evaluation of fitness and demographic effects of a Chinook Salmon supplementation program

Janowitz‐Koch, Ilana; Rabe, Craig; Kinzer, Ryan; Nelson, Doug D.; Hess, Maureen A.; Narum, Shawn R.

doi:10.1111/eva.12725

Cited by 45 publications

(121 citation statements)

References 80 publications

(151 reference statements)

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“…Flow cytometry analysis of 100 individuals produced using this method demonstrated that all 100 were triploid (P. Branigan, unpublished data). GT‐seq was used to genotype these samples for a panel of 298 SNPs (Janowitz‐Koch et al, ). The loci in this panel have median and mean ± SD mean read depths around 140 and 225 ± 270 reads per individual, respectively.…”

Section: Methodsmentioning

confidence: 99%

Differentiating diploid and triploid individuals using single nucleotide polymorphisms genotyped by amplicon sequencing

Delomas

2019

Molecular Ecology Resources

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Triploidy can occur naturally or be induced in fish and shellfish during artificial propagation in order to produce sterile individuals. Fisheries managers often stock these sterile triploids as a means of improving angling opportunities without risking unwanted reproduction of the stocked fish. Additionally, the rearing of all‐triploid individuals has been suggested as a means to reduce the possibility of escaped aquaculture fish interbreeding with wild populations. Efficient means of determining if an individual is triploid or diploid are therefore needed both to monitor the efficacy of triploidy‐inducing treatments and, when sampling fish from a body of water that has a mixture of diploids and triploids, to determine the ploidy of a fish prior to further analyses. Currently, ploidy is regularly measured through flow cytometry, but this technique typically utilizes a fresh blood sample. This study presents an alternative, cost‐effective method of determining ploidy by analysing amplicon‐sequencing data for biallelic single‐nucleotide polymorphisms (SNPs). For each sample, heterozygous genotypes are identified and the likelihoods of diploidy and triploidy are calculated based on the read counts for each allele. The accuracy of this method is demonstrated using triploid and diploid brook trout (Salvelinus fontinalis) genotyped with a panel of 234 SNPs and Chinook salmon (Oncorhynchus tshawytscha) genotyped with a panel of 298 SNPs following the GT‐seq methodology of amplicon sequencing.

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Section: Methodsmentioning

confidence: 99%

Differentiating diploid and triploid individuals using single nucleotide polymorphisms genotyped by amplicon sequencing

Delomas

2019

Molecular Ecology Resources

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“…; Janowitz‐Koch et al. ). In the Pacific Northwest, supplementation is a principal strategy that is intended to mitigate the effects on Pacific Salmon Onchorynchus spp.…”

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confidence: 99%

In‐Stream Egg Incubators Produce Hatchery Chinook Salmon with Similarities to and Differences from Natural Juveniles

Conley

Ebel

Hargrove

et al. 2020

N American J Fish Manag

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Supplementing fish populations at the egg stage is a low‐cost alternative to hatchery rearing that is presumed to improve adaptation to local natural conditions. The Shoshone‐Bannock Tribes began supplementing Chinook Salmon Onchorynchus tschwytscha in Panther Creek, Idaho, at the eyed egg stage in 2014. The Chinook Salmon eggs were artificially fertilized and reared to eye‐up in the hatchery and then planted in custom‐made in‐stream incubators (egg boxes) for volitional release and natural rearing. Using data from three brood years, we evaluated the efficacy of this supplementation program solely in terms of juvenile production. We related juvenile production to the placement and retrieval of the egg boxes, assessed the relative contributions of offspring (parr and emigrants) from the egg boxes (HOR) to overall juvenile abundance, and compared the performance (length, condition, dispersal distance, and survival) of HOR versus natural‐origin (NOR) juveniles. Brood year and box placement within the stream (distance upstream) were the best predictors of whether or not an egg box was retrieved from its original location. Meanwhile, the condition of the box (i.e., intact, damaged, or missing) was the best single predictor of juvenile production. Supplemented eggs represented an estimated 42, 50, and 42% of the total egg deposition in Panther Creek in brood years 2014, 2015, and 2016, respectively. A parentage analysis revealed that the egg boxes accounted for 6, 22, and 35%, respectively, of the parr production for the respective brood years when the data were normalized to the estimated egg deposition—less than the egg‐to‐parr production that was estimated for natural redds. As fall parr, the HOR fish differed from the NOR fish in terms of their length and dispersal behavior, but they were of similar length and condition at their emigration from Panther Creek and exhibited no significant difference in downstream survival through the Federal Columbia River Power System (FCRPS). Collectively, our results provide useful insights to fisheries managers who are interested in initiating or refining egg supplementation programs.

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“…Adopting such an approach for the Hunder trout would be beneficial for quantifying past and future impact of stocking on genetic variation. It could also aid in developing strategies for enhancing stocking practices to minimise negative genetic and demographic impacts (Araki & Schmid 2010) and for weighing different stocking practices against compensatory mitigation measures (Johnston et al 2018, Arlinghaus et al 2002, Janowitz-Koch et al 2018.…”

Section: Discussionmentioning

confidence: 99%

A future without stocking? The importance of harvest and river regulation for long-term population viability of migratory salmonids

Stubberud¹,

Langangen²,

Rustadbakken³

et al. 2019

Preprint

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1. Humans are influencing animal and plant populations both directly (e.g.through harvest) and indirectly by altering environments. For many exploitedspecies, stocking with captive-bred individuals is a common strategy tomitigate negative human impacts and sustain populations over time. However,accumulating knowledge of negative side effects of stocking calls for quantificationof consequences and exploration of sustainable alternatives.2. Evaluating alternative management strategies using quantitative models iscentral to conservation. Here, we investigate the effects of several managementstrategies on a population of landlocked, migratory brown trout (Salmotrutta) inhabiting a large lake and spawning in a dammed river. We assess thepopulation level consequences of terminating a long-term stocking programmeand evaluate whether the loss of artificial recruitment may be compensatedby changes in harvest regulations and/or river habitat improvement.3. We build an integral projection model (IPM) classifying individuals bybody size, life history stage, and location relative to the hydropower damand parameterised it with 50 years of individual-based data supplementedwith literature values. We first analyse the model to assess size, structure,and relative importance of different mortality components across life stagesand locations in trout populations with and without stocking. We theninvestigate potential responses of an unstocked population to managementactions involving different sets of harvest rules, reductions in dam passagemortality, and improvements of spawning habitat below the dam.4. Our model predicts a strong population decline of 12–21% per year in theabsence of stocking. This decline is largely attributed to high harvest mortality,and drastic reductions in fishing pressure thus necessary to ensure populationviability without stocking. Reducing mortality associated with passage of thehydropower dam and restoring spawning areas has only small positive effectson population growth. Nonetheless, these mitigation measures can contributeto population viability when combined with changes in harvest regulations.5. Intensely harvested populations may rely heavily on the addition of captive-bredindividuals, and our results indicate that premature termination of stockingprogrammes can be detrimental without compensatory mitigation measuressuch as harvest reductions and habitat improvements. It is therefore crucialto collect necessary data and assess the impacts of alternative managementstrategies using quantitative models prior to making decisions.

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Long‐term evaluation of fitness and demographic effects of a Chinook Salmon supplementation program

Cited by 45 publications

References 80 publications

Differentiating diploid and triploid individuals using single nucleotide polymorphisms genotyped by amplicon sequencing

Differentiating diploid and triploid individuals using single nucleotide polymorphisms genotyped by amplicon sequencing

In‐Stream Egg Incubators Produce Hatchery Chinook Salmon with Similarities to and Differences from Natural Juveniles

A future without stocking? The importance of harvest and river regulation for long-term population viability of migratory salmonids

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