SNP panels for differentiating advanced-generation hybrid classes in recently diverged stocks: A sensitivity analysis to inform monitoring of sockeye salmon re-stocking programs

Elliott, Lucas D.; Russello, Michael A.

doi:10.1016/j.fishres.2018.09.001

Cited by 10 publications

(11 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Biological data (length and sex) and tissue samples (operculum punches preserved in ethanol) were collected from all sampled fish. Moreover, the 2016 and 2017 samples were previously genetically assigned to pure-stock or F 1 hybrid using a panel of 32 TaqMan® SNP assays and subjected to otolith microchemistry analysis 36 to determine fish migratory history and investigate maternal migratory signatures that are passed transgenerationally to offspring 41 .…”

Section: Methodsmentioning

confidence: 99%

“…Due to the salmonid whole genome duplication event, we filtered out suspected homeologs by removing any locus with a negative F is or H obs > 0.5 that occurred in both reference populations 44 . The resulting SNP dataset was then filtered for quality using VCFtools 45 to remove SNPs not in Hardy–Weinberg equilibrium and to calculate Weir and Cockerham (1984)’s θ , an unbiased estimate of F st 46 , between Skaha Lake kokanee and Okanagan River sockeye salmon following 36 . We removed loci with insufficient flanking sequence required for primer design by retaining loci with the SNP positioned between the 40th and 70th base pairs of the RAD tag sequences and selected the top 650 loci exhibiting the highest F st .…”

Section: Methodsmentioning

confidence: 99%

“…In that regard, traditional markers may not have the statistical power to identify advanced hybrid classes 34 , with an estimated minimum of 70 markers required to discriminate between pure parental species and advanced backcrosses 35 . A previous simulation-based sensitivity analysis found that a panel comprised of 300 highly differentiated SNPs has the resolution needed to detect advanced hybrid classes between sockeye salmon and kokanee in Skaha Lake 36 . With this in mind, advancements in massively parallel sequencing can be leveraged to improve the identification of hybridization in systems by pooling barcoded amplicons to increase the power of genetic panels for classification 37 ; Genotyping-in-Thousands by sequencing (GT-seq) is a particularly useful approach in cases where large sample sizes need to be cost-effectively genotyped 38 .…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Genotyping-in-Thousands by sequencing panel development and application for high-resolution monitoring of introgressive hybridization within sockeye salmon

Chang

Ward

Elliott

et al. 2022

Sci Rep

Self Cite

View full text Add to dashboard Cite

Stocking programs have been widely implemented to re-establish extirpated fish species to their historical ranges; when employed in species with complex life histories, such management activities should include careful consideration of resulting hybridization dynamics with resident stocks and corresponding outcomes on recovery initiatives. Genetic monitoring can be instrumental for quantifying the extent of introgression over time, however conventional markers typically have limited power for the identification of advanced hybrid classes, especially at the intra-specific level. Here, we demonstrate a workflow for developing, evaluating and deploying a Genotyping-in-Thousands by Sequencing (GT-seq) SNP panel with the power to detect advanced hybrid classes to assess the extent and trajectory of intra-specific hybridization, using the sockeye salmon (Oncorhynchus nerka) stocking program in Skaha Lake, British Columbia as a case study. Previous analyses detected significant levels of hybridization between the anadromous (sockeye) and freshwater resident (kokanee) forms of O. nerka, but were restricted to assigning individuals to pure-stock or “hybrid”. Simulation analyses indicated our GT-seq panel had high accuracy, efficiency and power (> 94.5%) of assignment to pure-stock sockeye salmon/kokanee, F1, F2, and B2 backcross-sockeye/kokanee. Re-analysis of 2016/2017 spawners previously analyzed using TaqMan® assays and otolith microchemistry revealed shifts in assignment of some hybrids to adjacent pure-stock or B2 backcross classes, while new assignment of 2019 spawners revealed hybrids comprised 31% of the population, ~ 74% of which were B2 backcross or F2. Overall, the GT-seq panel development workflow presented here could be applied to virtually any system where genetic stock identification and intra-specific hybridization are important management parameters.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genotyping-in-Thousands by sequencing panel development and application for high-resolution monitoring of introgressive hybridization within sockeye salmon

Chang

Ward

Elliott

et al. 2022

Sci Rep

Self Cite

View full text Add to dashboard Cite

show abstract

“…The hybrid test was conducted using 300 fixed SNPs from the GBS dataset and 68 SNPs in MassARRAY assays, respectively. We trimmed our GBS datasets to 300 unlinked diagnostic SNPs because analyses failed to run with more markers due to an underflow issue (Elliott and Russello 2018). Three independent analyses were conducted with different random subsets of 300 for assignment evaluation.…”

Section: Hybridization Analysesmentioning

confidence: 99%

SNP analyses highlight a unique, imperiled southern walleye (Sander vitreus) in the Mobile River Basin

Zhao

Silliman

Lewis

et al. 2020

Can. J. Fish. Aquat. Sci.

View full text Add to dashboard Cite

Walleye (Sander vitreus) is a popular sportfish threatened by overexploitation, habitat destruction, and loss of genetic integrity due to non-native walleye stocking. Previous studies have identified a genetically distinct lineage of walleye in the Mobile River Basin, but further work is needed to assess population structure and introgression among this southern lineage and northern populations. Here we generated 2782 genome-wide single nucleotide polymorphisms (SNPs) to characterize the genetic uniqueness of southern walleye. We also found strong evidence for a historical declining population trend with reduced genetic diversity and effective population size in a southern walleye population of conservation importance. A 68-SNP panel was developed for rapid identification of genetic integrity and hybrid classification among northern and southern walleye, enabling us to identify an anthropogenic hybrid zone resulting from the previous introduction of northern walleye into the Black Warrior River drainage, Alabama. Our results highlight the need for conservation management of southern walleye in the Mobile River Basin, with our 68-SNP assay already being implemented in ongoing stream survey and captive breeding programs.

show abstract

“…The suite of microsatellite markers used in this study is currently the best tool for identifying pure Pallid Sturgeon but is not sufficient to resolve among multiple backcross categories, a problem that will likely require significantly more independent markers (Elliott and Russello ). One of us (E.J.H.)…”

Section: Discussionmentioning

confidence: 99%

Morphological Identification Overestimates the Number of Pallid Sturgeon in the Lower Mississippi River due to Extensive Introgressive Hybridization

et al. 2019

View full text Add to dashboard Cite

Pallid Sturgeon Scaphirhynchus albus and Shovelnose Sturgeon S. platorynchus are congeners occupying overlapping habitats within the Missouri and Mississippi River basins. The Pallid Sturgeon is listed as federally endangered under the Endangered Species Act in the United States, whereas the Shovelnose Sturgeon is not. Observational data across the range of both species include specimens that appear to be phenotypically and genotypically intermediate between Pallid Sturgeon and Shovelnose Sturgeon, though these occurrences are most frequent in the Mississippi River. Based on both morphological and genetic data, the variability and overlap within Scaphirhynchus spp. phenotypes has resulted in debate about the accuracy of existing identification methods of Pallid Sturgeon within the Mississippi River portion of its range (i.e., distinguishing Pallid, Shovelnose, and hybrid sturgeons). As a result, increasing questions have surfaced relative to species identification, implications of purported hybridization, the accuracy of local demographic estimations, and how those effect management actions. This project is the first comprehensive analysis to compare genotypic, phenotypic, and field identification data in order to evaluate the accuracy of existing field identification of the two congener Scaphirhynchus spp. and their purported hybrids in the lower Mississippi River. Our results indicate current field identification methods are not reliable for identifying Pallid Sturgeon in the lower Mississippi River, likely due to introgressive hybridization between Pallid and Shovelnose sturgeons and the resulting continuum of morphotypes and genotypes in hybridized individuals. We conclude that reliance on current morphological‐based field identification methods to quantify Pallid Sturgeon may lead to inaccurate assessments that could negatively impact the conservation and management of this endangered species, including the use of hybrid broodstock for conservation stocking and erroneous estimates of stock and recruitment.

show abstract

SNP panels for differentiating advanced-generation hybrid classes in recently diverged stocks: A sensitivity analysis to inform monitoring of sockeye salmon re-stocking programs

Cited by 10 publications

References 27 publications

Genotyping-in-Thousands by sequencing panel development and application for high-resolution monitoring of introgressive hybridization within sockeye salmon

Genotyping-in-Thousands by sequencing panel development and application for high-resolution monitoring of introgressive hybridization within sockeye salmon

SNP analyses highlight a unique, imperiled southern walleye (Sander vitreus) in the Mobile River Basin

Morphological Identification Overestimates the Number of Pallid Sturgeon in the Lower Mississippi River due to Extensive Introgressive Hybridization

Contact Info

Product

Resources

About