Mixed‐stock analysis using Rapture genotyping to evaluate stock‐specific exploitation of a walleye population despite weak genetic structure

Euclide, Peter T.; MacDougall, Tom; Robinson, Jason M.; Faust, Matthew D.; Wilson, Chris C.; Chen, Kuan‐Yu; Marschall, Elizabeth A.; Larson, Wesley A.; Ludsin, Stuart A.

doi:10.1111/eva.13209

Cited by 22 publications

(19 citation statements)

References 111 publications

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“…This relatively stronger differentiation between the Canadian lakes used here and the waterbody in Kansas was similar in magnitude to differentiation observed between walleye in Minnesota and Wisconsin (USA), differences which were attributed to Pleistocene lineages (Bootsma et al, 2021). Walleye population differentiation between Lake Winnipeg and Lake Manitoba was consistent with certain other walleye populations within watersheds (e.g., Grand River, Ontario, Canada vs other Lake Erie stocks in Euclide et al, 2021; Sarah Lake vs. Lake Koronis, Minnesota, USA in Bootsma et al, 2021). Retreating glacial refugia dispersed walleye into different watersheds approximately 7,000-10,000 years ago (Bootsma et al, 2021;Stepien et al, 2009).…”

Section: Moderate Differentiation Between Two Connected Lakessupporting

confidence: 78%

A chromosomal inversion may facilitate adaptation despite periodic gene flow in a freshwater fish

Thorstensen

Euclide

Jeffrey

et al. 2022

Ecology and Evolution

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Differences in genomic architecture between populations, such as chromosomal inversions, may play an important role in facilitating adaptation despite opportunities for gene flow. One system where chromosomal inversions may be important for ecoevolutionary dynamics is in freshwater fishes, which often live in heterogenous environments characterized by varying levels of connectivity and varying opportunities for gene flow. In the present study, reduced representation sequencing was used to study possible adaptation in n = 345 walleye (Sander vitreus) from three North American waterbodies: Cedar Bluff Reservoir (Kansas, USA), Lake Manitoba (Manitoba, Canada), and Lake Winnipeg (Manitoba, Canada). Haplotype and outlier-based tests revealed a putative chromosomal inversion that contained three expressed genes and was nearly fixed in walleye assigned to Lake Winnipeg. These patterns exist despite the potential for high gene flow between these proximate Canadian lakes, suggesting that the inversion may be important for facilitating adaptive divergence between the two lakes despite gene flow. However, a specific adaptive role for the putative inversion could not be tested with the present data. Our study illuminates the importance of genomic architecture consistent with local adaptation in freshwater fishes. Furthermore, our results provide additional evidence that inversions may facilitate local adaptation in many organisms that inhabit connected but heterogenous environments.

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Section: Moderate Differentiation Between Two Connected Lakessupporting

confidence: 78%

A chromosomal inversion may facilitate adaptation despite periodic gene flow in a freshwater fish

Thorstensen

Euclide

Jeffrey

et al. 2022

Ecology and Evolution

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“…Given widespread stocking and potamodromous movements in walleye, it may be surprising that the species showed as much population differentiation as has been observed between waterbodies in multiple watersheds (Bootsma et al, 2020; Euclide et al, 2021; Munaweera Arachchilage et al, 2021; Raby et al, 2018; Turner et al, 2021). While stocking has led to extensive homogenization in some walleye populations, the lack of gene flow from stocking in the present data and among other waterbodies implicates potential mechanisms by which gene flow is prevented (Bootsma et al, 2020).…”

Section: Discussionmentioning

confidence: 97%

“…RAD-seq library preparation was performed with the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, Massachusetts, USA) with the PstI restriction enzyme. BestRAD libraries were baited using protocols outlined in Euclide et al, (2021) using a RAD-Capture panel for a different walleye research project in the Laurentian Great Lakes that was still ongoing at the time of publication (Ali et al, 2016). The panel includes a single bait for 99,636 SNP loci identified from a preliminary PSTI RAD-sequencing survey of 48 walleye collected in the Great Lakes ( n = 9 – 10 from each of Lakes Superior, Huron, Michigan, Erie, and Ontario; USA) designed by Arbor Biosciences (Ann Arbor, Michigan, USA).…”

Section: Methodsmentioning

confidence: 99%

A chromosomal inversion may facilitate adaptation despite periodic gene flow in a freshwater fish

Thorstensen

Euclide

Jeffrey

et al. 2021

Preprint

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Genomic architecture, such as chromosomal inversions, may play an important role in facilitating adaptation despite opportunities for gene flow. One system where chromosomal inversions may be important for eco-evolutionary dynamics are in freshwater fish, which often live in heterogenous environments characterized by varying levels of connectivity and varying opportunities for gene flow. In the present study, reduced representation sequencing was used to study possible adaptation in n=345 walleye (Sander vitreus) from three North American waterbodies: Cedar Bluff Reservoir (Kansas, USA), Lake Manitoba (Manitoba, Canada), and Lake Winnipeg (Manitoba, Canada). Haplotype and outlier-based tests revealed a putative chromosomal inversion that contained three expressed genes and was nearly fixed for alternate genotypes in each Canadian lake. These patterns exist despite several opportunities for gene flow between these proximate Canadian lakes, suggesting that the inversion may be important for facilitating adaptative divergence between the two lakes despite gene flow. Our study illuminates the importance of genomic architecture for facilitating local adaptation in freshwater fish and provides additional evidence that inversions may facilitate local adaptation in many organisms that inhabit connected but heterogenous environments.

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“…Successful management measures require that reproductively isolated populations are governed as independent stocks (Reiss et al, 2009). However, it is frequently assumed, without well-grounded scientific evidence, that the exploited species form single panmictic populations (Euclide et al, 2021). Management measures have consequently been inappropriate and in many cases led to unintentional overexploitation of local populations (Hutchinson, 2008;Li et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Lack of panmixia of Bothnian Bay vendace - Implications for fisheries management

López

Nord²,

Kaljuste³

et al. 2022

Front. Mar. Sci.

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Overexploitation of fisheries is recognized as a major environmental and socioeconomic problem that threats biodiversity and ecosystem functioning. Inappropriate management policies of fish stocks have been applied as a consequence of inadequate characterization of subtle genetic structure in many fish species. In this study, we aim to assess the extent of genetic differentiation and structure of vendace (Coregonus albula) collected from eight locations in the Bothnian Bay, the northernmost part of the Baltic Sea. Specifically, we test if this species forms a single panmictic population or is divided into several genetically distinct units. We used restriction site-associated DNA sequencing (RAD-seq) to identify 21,792 SNPs based on 266 individuals. We identified a clear pattern of genetic differentiation between River Kalix and the other sampling locations, and a weak structuring between samples from Swedish and Finnish coast. Outlier analysis detected 41 SNPs putatively under divergent selection, mainly reflecting the divergence between River Kalix and the other samples. The outlier SNPs were located within or near 25 genes, including voltage-dependent calcium channel subunit alpha-2 (CACNA2D2), cadherin 26 (CDH26) and carbonic anhydrase 4-like (CA4) that have earlier been associated with salt-tolerance and salinity stress. Our study provides the first genome-wide perspective on genetic structuring of Baltic Sea vendace and rejects the hypothesis of panmixia in the Bothnian Bay. As such, our work demonstrates the power of RAD-sequencing to detect low but significant genetic structuring relevant for fisheries management.

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Mixed‐stock analysis using Rapture genotyping to evaluate stock‐specific exploitation of a walleye population despite weak genetic structure

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 22 publications

References 111 publications

A chromosomal inversion may facilitate adaptation despite periodic gene flow in a freshwater fish

A chromosomal inversion may facilitate adaptation despite periodic gene flow in a freshwater fish

A chromosomal inversion may facilitate adaptation despite periodic gene flow in a freshwater fish

Lack of panmixia of Bothnian Bay vendace - Implications for fisheries management

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