The ghosts of propagation past: haplotype information clarifies the relative influence of stocking history and phylogeographic processes on contemporary population structure of walleye (<i>Sander vitreus</i>)

Bootsma, Matthew; Miller, Loren M.; Sass, Greg G.; Euclide, Peter T.; Larson, Wesley A.

doi:10.1111/eva.13186

Cited by 21 publications

(27 citation statements)

References 143 publications

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“…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 ; Sarah Lake vs Lake Koronis, Minnesota, USA & in Bootsma et al, 2020). Retreating glacial refugia dispersed walleye into different watersheds approximately 7,000-10,000 years ago (Bootsma et al, 2020;Stepien et al, 2009). Therefore, the population structure identified in the present study represents differentiation following geologically recent changes to the overall landscape.…”

Section: Population Geneticssupporting

confidence: 74%

“…As a haplotype-based test, XP-EHH provided evidence that this region was selected for not in Lake Manitoba, but in Lake Winnipeg instead (Sabeti et al, 2007). In a different study on walleye in Wisconsin and Minnesota (USA) (Bootsma et al, 2020), this chromosome 8 region was also a consistent outlier with F ST and BAYESCAN analyses (Foll & Gaggiotti, 2008). However, SNP data were too sparse to interrogate the genomic architecture of this outlier region.…”

Section: Putative Chromosomal Inversionmentioning

confidence: 99%

“…Last, walleye fry were opportunistically stocked in Lake Winnipeg from Lake Manitoba (Manitoba, Canada) between 1917-2002 (Manitoba Government, 2020). While intensive stocking complicated analyses of walleye ancestry in walleye of Minnesota and Wisconsin (USA) (Bootsma et al, 2020), stocking of walleye fry, which likely experience significant mortality, had little to no effect in South Dakota and Missouri (USA) (Fielder, 1992; Koppelman et al, 1992). Therefore, the genetic impacts of fry stocking in this system are likely minimal.…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Population Geneticssupporting

confidence: 74%

Section: Putative Chromosomal Inversionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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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“…A haplotype approach maximizes the biological information encoded by each marker-single SNPs can only describe two alleles present in the metapopulation, while haplotypes can describe several alleles. This increase in information content by markers often allows for an increase in resolution both when identifying differentiation between populations and when assigning individuals to a population (Leitwein et al 2020;Bootsma et al 2021).…”

Section: Haplotype-based Population Structurementioning

confidence: 99%

Population genomics analysis with RAD, reprised: Stacks 2

Rivera‐Colón

Catchen

2021

Preprint

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Restriction enzymes have been one of the primary tools in the population genetics toolkit for fifty years, being coupled with each new generation of technology to provide a more detailed view into the genetics of natural populations. Restriction site-Associated DNA protocols, which joined enzymes with short-read sequencing technology have democratized the field of population genomics, providing a means to assay the underlying alleles in scores of populations. More than ten years on, the technique has been widely applied across the tree of life and served as the basis for many different analysis techniques. Here, we provide a detailed protocol to conduct a RAD analysis from experimental design to de novo analysis – including parameter optimization – as well as reference-based analysis, all in Stacks version 2, which is designed to work with paired-end reads to assemble RAD loci up to 1000 nucleotides in length. The protocol focuses on major points of friction in the molecular approaches and downstream analysis, with special attention given to validating experimental analyses. Finally, the protocol provides several points of departure for further analysis.

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“…2017; Bootsma et al. 2021). These two processes in conjunction may have served to homogenize the regional gene pool or otherwise obscure Brook Trout population structure to levels undetectable by this study.…”

Section: Discussionmentioning

confidence: 99%

Broadscale Population Structure and Hatchery Introgression of Midwestern Brook Trout

et al. 2021

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Brook Trout Salvelinus fontinalis have faced significant declines throughout their native range and have been stocked in Midwestern waters since the late 1800s to offset such losses. Several studies have investigated the genetic effects of these stockings, but these efforts have been confined to relatively small spatial scales. In this study, we compiled 8,454 Brook Trout microsatellite genotypes from 188 wild Midwestern populations and 26 hatchery strains to provide novel insights of broadscale population structure, regional patterns of genetic diversity, and estimates of hatchery introgression for inland Wisconsin populations. Our results indicate high levels of differentiation among our study populations, a lack of hydrological population structuring, lower estimates of genetic diversity in the Driftless Area, and that hatchery introgression has been largely confined to regions of inland Wisconsin that have been heavily affected by anthropogenic disturbances (i.e., the Driftless Area). We also provide evidence that populations may be able to purge hatchery‐derived alleles, discuss possible mechanisms behind this phenomenon, and consider their relevance to accurate estimation of hatchery introgression. Collectively, these results summarize the genetic effects of over a century of anthropogenic disturbance on native Brook Trout populations and emphasize the importance of integrating historical data into contemporary genetic research of intensively managed species.

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The ghosts of propagation past: haplotype information clarifies the relative influence of stocking history and phylogeographic processes on contemporary population structure of walleye (Sander vitreus)

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 21 publications

References 143 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

Population genomics analysis with RAD, reprised: Stacks 2

Broadscale Population Structure and Hatchery Introgression of Midwestern Brook Trout

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