A Rapid, Ethanol‐Free Fish Tissue Collection Method for Molecular Genetic Analyses

LaHood, Eric S.; Miller, Jason J.; Apland, Chase; Ford, Michael J.

doi:10.1577/t07-181.1

Cited by 30 publications

(27 citation statements)

References 3 publications

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“…A 1‐cm 2 clip from the caudal fin of each broodfish was stored on Whatman chromatography paper (LaHood et al. ). The eggs were collected and fertilized from Pahsimeroi's segregated broodstock program (i.e., crosses between hatchery‐origin individuals), using a 1:1 or 2:1 male : female sex ratio.…”

Section: Methodsmentioning

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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Section: Methodsmentioning

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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“…Before releasing them, we retained upper caudal fin clips (on chromatography paper; LaHood et al . ) of up to 10 specimens captured at each site, but made no attempt to identify sculpins in the field because most species cannot be easily distinguished, and we sometimes handled hundreds of individuals at each site. We captured sculpins in 187 streams and analysed 1–5 fish (generally 2) from 119 streams (and at two sites on five of these streams).…”

Section: Methodsmentioning

confidence: 99%

DNA barcoding at riverscape scales: assessing biodiversity among fishes of the genus Cottus (Teleostei) in northern Rocky Mountain streams

Young

McKelvey

Pilgrim

et al. 2013

Molecular Ecology Resources

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There is growing interest in broad-scale biodiversity assessments that can serve as benchmarks for identifying ecological change. Genetic tools have been used for such assessments for decades, but spatial sampling considerations have largely been ignored. Here, we demonstrate how intensive sampling efforts across a large geographical scale can influence identification of taxonomic units. We used sequences of mtDNA cytochrome c oxidase subunit 1 and cytochrome b, analysed with maximum parsimony networks, maximum-likelihood trees and genetic distance thresholds, as indicators of biodiversity and species identity among the taxonomically challenging fishes of the genus Cottus in the northern Rocky Mountains, USA. Analyses of concatenated sequences from fish collected in all major watersheds of this area revealed eight groups with species-level differences that were also geographically circumscribed. Only two of these groups, however, were assigned to recognized species, and these two assignments resulted in intraspecific genetic variation (>2.0%) regarded as atypical for individual species. An incomplete inventory of individuals from throughout the geographical ranges of many species represented in public databases, as well as sample misidentification and a poorly developed taxonomy, may have hampered species assignment and discovery. We suspect that genetic assessments based on spatially robust sampling designs will reveal previously unrecognized biodiversity in many other taxa.

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“…PBT sampling in the Columbia River basin has since transitioned to an alternative dry storage method that uses absorptive paper to preserve and store samples (LaHood et al 2008). Storing tissue in ethanol-filled vials can be relied upon to ensure high-quality DNA, even when stored for long periods of time and evaporation is limited.…”

Section: Sampling Broodstockmentioning

confidence: 99%

Parentage‐Based Tagging: Reviewing the Implementation of a New Tool for an Old Problem

et al. 2019

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Parentage‐based tagging (PBT), an innovative and large‐scale application of genetic parentage assignments, is transforming how fisheries managers determine the age and origin of sampled fish. PBT is an efficient alternative for mass tagging and has been widely implemented in the Pacific Northwest. While still an emerging technology, PBT is being used to provide information to managers in state, federal, and tribal agencies on the harvest, research, and conservation of Chinook Salmon Oncorhynchus tshawytscha and steelhead O. mykiss in this region. We review the development of PBT in the Pacific Northwest focusing on the technical and logistical challenges for implementing a regional PBT program. We also showcase recent results and review management efforts that made use of PBT‐derived data.

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A Rapid, Ethanol‐Free Fish Tissue Collection Method for Molecular Genetic Analyses

Cited by 30 publications

References 3 publications

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

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

DNA barcoding at riverscape scales: assessing biodiversity among fishes of the genus Cottus (Teleostei) in northern Rocky Mountain streams

Parentage‐Based Tagging: Reviewing the Implementation of a New Tool for an Old Problem

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