Complementarity and discriminatory power of genotype and otolith shape in describing the fine-scale population structure of an exploited fish, the common sole of the Eastern English Channel

Date 2020
Author(s) Randon MarineORCID1, 2, Le Pape Olivier1, Ernande BrunoORCID3, 4, Mahe KeligORCID3, Volckaert Filip5, Petit Eric1, Lassalle Gilles1, Le Berre Thomas1, Reveillac Elodie1, 6
Affiliation(s) 1 : ESE, Ecologie et Santé des Ecosystèmes, Agrocampus Ouest, INRAE, 65 rue de Saint-Brieuc, F-35042 Rennes Cedex, France
2 : Statistical and Actuarial Science Department, Simon Fraser University, 8888 University Drive, V5A2L6 Burnaby, BC, Canada
3 : Ifremer, Laboratory of Fisheries – Sclerochronology Centre, 150 quai Gambetta, BP 699, F-62321 Boulogne-sur-Mer, France.
4 : IIASA, Evolution and Ecology Program, Schlossplatz 1, A-2361 Laxenburg, Austria
5 : Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
6 : UMR 7266 LIENSs, Littoral, Environnement et Sociétés, La Rochelle University, 2 rue Olympe de Gouges, F-17000 La Rochelle, France
DOI 10.17882/74421
Publisher SEANOE
Keyword(s) Integration, Marine connectivity, Metapopulation, Flatfish, Otolith, SNP markers
Abstract

Marine organisms show population structure at a relatively fine spatial scale, even in open habitats. The tools commonly used to assess subtle patterns of connectivity have diverse levels of resolution. We have assessed the discriminatory power of genetic markers and otolith shape to reveal the population structure of the common sole (Solea solea), living in the Eastern English Channel stock off France and the UK. The aims were to (i) inform the short and long-term population structure by comparing genetic and otolith shape approaches, and (ii) combine the tracers in a single analysis to assess the interest of a combined approach. First, we applied Single Nucleotide Polymorphisms to assess population structure at an evolutionary scale. Then, we tested for spatial segregation of the subpopulations using otolith shape as an integrative tracer of life history. Finally, we combined the genotypes and otolith phenotypes in a supervised machine learning framework to probabilistically assign adults to subpopulations. Genetic assignments and otolith shape analyses provided congruent results suggestive of a metapopulation structure for the common sole of the Eastern English Channel. Despite congruent results from genetics and otolith shape, the combined analysis did not provide realistic reallocation probabilities. Our findings support the idea that independent analyses of tracers provide fruitful insights and that a combined approach should be preferred when a large and balanced number of fish is available for each tracer analyzed.

Licence CC-BY-ND
Data
File Size Format Processing Access
SNP markers data and Fourier and otolith shape indices of common sole of the Eastern English Channel 5 MB .csv and .gen Raw data Open access
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How to cite 

Randon Marine, Le Pape Olivier, Ernande Bruno, Mahe Kelig, Volckaert Filip, Petit Eric, Lassalle Gilles, Le Berre Thomas, Reveillac Elodie (2020). Complementarity and discriminatory power of genotype and otolith shape in describing the fine-scale population structure of an exploited fish, the common sole of the Eastern English Channel. SEANOE. https://doi.org/10.17882/74421


In addition to properly cite this dataset, it would be appreciated that the following work(s) be cited too, when using this dataset in a publication :


Randon Marine, Le Pape Olivier, Ernande Bruno, Mahé Kelig, Volckaert Filip A. M., Petit Eric, Lassalle Gilles, Le Berre Thomas, Réveillac Elodie (2020). Complementarity and discriminatory power of genotype and otolith shape in describing the fine-scale population structure of an exploited fish, the common sole of the Eastern English Channel. Plos One, 15(11), e0241429 (20p.). Publisher's official version : https://doi.org/10.1371/journal.pone.0241429 , Open Access version : https://archimer.ifremer.fr/doc/00658/77009/