Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach

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Date
2018
Authors
Jacobs, A.
De Noia, M.
Praebel, K.
Kanstad-Hanssen, O.
Paterno, M.
Jackson, D.
McGinnity, Philip
Sturm, A.
Elmer, K. R.
Llewellyn, M. S.
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Nature Publishing Group:
Published Version
10.1038/s41598-018-19323-z
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Abstract
Caligid sea lice represent a significant threat to salmonid aquaculture worldwide. Population genetic analyses have consistently shown minimal population genetic structure in North Atlantic Lepeophtheirus salmonis, frustrating efforts to track louse populations and improve targeted control measures. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations. We identified 1286 robustly supported SNPs among four L. salmonis populations from Ireland, Scotland and Northern Norway. Only weak global structure was observed based on the full SNP dataset. The application of a random forest machine-learning algorithm identified 98 discriminatory SNPs that dramatically improved population assignment, increased global genetic structure and resulted in significant genetic population differentiation. A large proportion of SNPs found to be under directional selection were also identified to be highly discriminatory. Our data suggest that it is possible to discriminate between nearby L. salmonis populations given suitable marker selection approaches, and that such differences might have an adaptive basis. We discuss these data in light of sea lice adaption to anthropogenic and environmental pressures as well as novel approaches to track and predict sea louse dispersal.
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Keywords
Eel , Anguilla-rostrata , Sea Lice , Life-history , Wild , Differentiation , Resistance , Salinity , Ireland , Markers , Coasts
Citation
Jacobs, A., De Noia, M., Praebel, K., Kanstad-Hanssen, Ø., Paterno, M., Jackson, D., McGinnity, P., Sturm, A., Elmer, K. R. and Llewellyn, M. S. (2018) 'Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach', Scientific Reports, 8, 1203 (9pp). doi: 10.1038/s41598-018-19323-z
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https://www.nature.com/articles/s41598-018-19323-z
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https://hdl.handle.net/10468/5489
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Biological, Earth and Environmental Sciences - Journal Articles
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© 2018, the Authors. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.