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Empirical assessment of software efficiency and accuracy to detect introgression under variable stocking scenarios in brook charr (Salvelinus fontinalis)

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Abstract

Stocking wild populations with domesticated fish is a common practice that promotes variable levels of introgression depending on the stocking intensity. The detection of hybridization and introgression has recently benefited from the application of Bayesian techniques implemented in various software. However, few studies have assessed their efficiency under various scenarios of stocking in the wild. The objective of this study is to assess quantitatively the effects of using two of the most widely distributed software, Structure and NewHybrids, on the level of introgression detected in wild brook charr (Salvelinus fontinalis) subjected to variable stocking intensities. We first found differences in the efficiency of software assignments based on simulated individuals, with Structure performing better than NewHybrids. However, NewHybrids showed higher assignments accuracy than Structure for the same sets of individuals. Thus, our results suggest that these software should be used in combination to assess the effects of stocking. Indeed, Structure is particularly relevant to evaluate the presence of hybrids in wild populations, whereas NewHybrids might be preferred to accurately assess the number of hybrids present in a sample. When applied to wild populations, Structure assigned more individuals than NewHybrids to the wild category. Moreover, the proportions of assigned domestic and hybrid individuals were higher in more intensively stocked lakes, whereas the opposite trend was observed for wild individuals.

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Acknowledgments

We are grateful to Fabien Lamaze, Bruno Mayot, Marc-André Poulin, Andréanne Lessard and Mélissa Lieutenant-Gosselin for their help with field sampling and laboratory analyses. We also thank Associate editor Michael Schwartz and two anonymous reviewers for their helpful comments on a previous version of the manuscript. We acknowledge the important contributions of the Ministère des Ressources Naturelles et de la Faune du Québec (MRNF), the Société des Établissement de Plein-Air du Québec (SÉPAQ) and the Réseau Aquaculture Québec (RAQ) to the project. This research was financially supported by a strategic project grant from the Natural Sciences and Engineering Research Council (NSERC) of Canada to LB and DG.

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Authors and Affiliations

  1. Département de biologie, Université Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada

    A. D. Marie & D. Garant

  2. IBIS (Institut de Biologie Intégrative et des Systèmes), Pavillon Charles-Eugène-Marchand, Université Laval, Québec, QC, G1V 0A6, Canada

    L. Bernatchez

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  1. A. D. Marie
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  2. L. Bernatchez
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  3. D. Garant
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Correspondence to D. Garant.

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Marie, A.D., Bernatchez, L. & Garant, D. Empirical assessment of software efficiency and accuracy to detect introgression under variable stocking scenarios in brook charr (Salvelinus fontinalis). Conserv Genet 12, 1215–1227 (2011). https://doi.org/10.1007/s10592-011-0224-y

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