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Genomic population structure of Grass Pickerel (Esox americanus vermiculatus) in Canada: management guidance for an at-risk fish at its northern range limit

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Abstract

Eighty nine (42%) of Canada’s 215 freshwater fish species have been assessed as at risk by the Committee on the Status of Endangered Wildlife in Canada. This study examines genomic population structure of the at-risk Grass Pickerel (Esox americanus vermiculatus), a small (≤ 33 cm) predatory fish that in Canada has a range spanning approximately 114,000 km2 of southern Ontario. Within this range it occupies approximately ten sites that are mostly shallow, weedy, and slow-flowing. Its populations and habitat are declining. This study defines population clusters and quantifies genomic diversity within and between populations based on > 5500 loci and > 950 SNPs from genomes of 66 individuals representing the subspecies’ entire Canadian range. Ordination and STRUCTURE analyses revealed four major geographic/genomic clusters centered in the Georgian Bay-Severn River, southeastern shore of Lake Huron, Niagara Peninsula, and upper St. Lawrence River. Major clusters were distinguished by relatively high Hudson Fst values (0.205–0.480), with Georgian Bay-Severn River being consistently most distinct. The Niagara Peninsula major cluster contained an additional three discernable sub-clusters differentiated by Fst values as great or greater than major clusters, despite spanning only ca. 200 km2. Genomically distinct Niagara sub-clusters occurred in Abino Drain, Big Forks Creek, and Tea Creek. Samples from sites between both major and minor clusters exhibited admixture from adjacent clusters. Despite current management of Grass Pickerel under a single designatable unit throughout its Canadian range, we map considerable geographic population structure that should help guide the designation of additional conservation units.

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Acknowledgements

We thank Fisheries and Oceans Canada for supporting this research financially and by providing tissue samples, and the Natural Sciences and Engineering Research Council of Canada for funding (NSERC Discovery Grants: RGPIN-2014-05226 to NEM, RGPIN-2016-06221 to NRL, RGPIN-2016-06538 to JTW; NSERC Discovery Accelerator Grant 492890 to JTW). Computations were performed on the Niagara supercomputer at the SciNet High Performance Computing Consortium, funded by the University of Toronto, the Canadian Foundation for Innovation, the Government of Ontario, and Ontario Research Fund – Research Excellence.

Funding

Research was supported by Fisheries and Oceans Canada, the Natural Sciences and Engineering Research Council of Canada (NSERC Discovery Grants: RGPIN-2014-05226 to NEM, RGPIN-2016-06221 to NRL, RGPIN-2016-06538 to JTW; NSERC Discovery Accelerator Grant 492890 to JTW), the University of Toronto, the Canadian Foundation for Innovation, the Government of Ontario, and Ontario Research Fund – Research Excellence.

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Author notes

  1. Nathan K. Lujan

    Present address: Department of Natural History, Royal Ontario Museum, Toronto, ON, M5S 2C6, Canada

Authors and Affiliations

  1. Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada

    Nathan K. Lujan, Jason T. Weir, Fielding A. Montgomery, Nathan R. Lovejoy & Nicholas E. Mandrak

  2. Department of Biological Sciences, University of Mississippi, Oxford, MS, 38677, USA

    Nathan K. Lujan & Brice P. Noonan

  3. Fisheries and Oceans Canada, 867 Lakeshore Road, Burlington, ON, L7S 1A1, Canada

    Julia E. Colm

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Contributions

NKL, NEM, and NRL conceptualized the study, JEC collected samples, NKL and BPN collected data, NKL and JTW analyzed data, FAM prepared maps, NKL, JEC, and NEM drafted the manuscript with input from all authors.

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Correspondence to Nathan K. Lujan.

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Collections, handling, and subsampling of fish for this study was approved by the Fisheries and Oceans Canada institutional review board.

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10592_2022_1450_MOESM1_ESM.png

Supplemental Fig. S1. Evanno’s delta K (Evanno et al., 2005) distribution from a Structure Harvester (Earl and von Holdt, 2012) analysis of output from a STRUCTURE (Pritchard et al., 2000) analysis of SNPs from 43 Grass Pickerel (Esox americanus vermiculatus) individuals distributed across southern Ontario and southwestern Quebec (excluding only individuals from the Georgian Bay-Severn River drainage). Supplementary file1 (PNG 20 kb)

10592_2022_1450_MOESM2_ESM.png

Supplemental Fig. S2. Evanno’s delta K (Evanno et al., 2005) distribution from a Structure Harvester (Earl and von Holdt, 2012) analysis of output from a STRUCTURE (Pritchard et al., 2000) analysis of SNPs from 26 Grass Pickerel (Esox americanus vermiculatus) individuals distributed across the Niagara Peninsula and north shore of Lake Erie. Supplementary file2 (PNG 21 kb)

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Lujan, N.K., Colm, J.E., Weir, J.T. et al. Genomic population structure of Grass Pickerel (Esox americanus vermiculatus) in Canada: management guidance for an at-risk fish at its northern range limit. Conserv Genet 23, 713–725 (2022). https://doi.org/10.1007/s10592-022-01450-w

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