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Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks

Authors

  • PHILINE G. D. FEULNER,

    1. Institute for Evolution and Biodiversity, Evolutionary Bioinformatics, Westfaelische Wilhelms University, Huefferstr. 1, 48149 Muenster, Germany
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    • These authors contributed equally to this work.

  • FRÉDÉRIC J. J. CHAIN,

    1. Max Planck Institute for Evolutionary Biology, Department of Evolutionary Ecology, August-Thienemann-Str. 2, 24306 Ploen, Germany
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    • These authors contributed equally to this work.

  • MAHESH PANCHAL,

    1. Max Planck Institute for Evolutionary Biology, Department of Evolutionary Ecology, August-Thienemann-Str. 2, 24306 Ploen, Germany
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    • These authors contributed equally to this work.

  • CHRISTOPHE EIZAGUIRRE,

    1. Max Planck Institute for Evolutionary Biology, Department of Evolutionary Ecology, August-Thienemann-Str. 2, 24306 Ploen, Germany
    2. Helmholtz Center for Ocean Research (GEOMAR), Evolutionary Ecology of Marine Fishes, Duesternbrooker Weg 20, 24105 Kiel, Germany
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  • MARTIN KALBE,

    1. Max Planck Institute for Evolutionary Biology, Department of Evolutionary Ecology, August-Thienemann-Str. 2, 24306 Ploen, Germany
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  • TOBIAS L. LENZ,

    1. Max Planck Institute for Evolutionary Biology, Department of Evolutionary Ecology, August-Thienemann-Str. 2, 24306 Ploen, Germany
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    • Present address: Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, 77 Ave. Louis Pasteur, Boston, MA 02115, USA.

  • MARVIN MUNDRY,

    1. Institute for Evolution and Biodiversity, Evolutionary Bioinformatics, Westfaelische Wilhelms University, Huefferstr. 1, 48149 Muenster, Germany
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  • IRENE E. SAMONTE,

    1. Max Planck Institute for Evolutionary Biology, Department of Evolutionary Ecology, August-Thienemann-Str. 2, 24306 Ploen, Germany
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  • MONIKA STOLL,

    1. Genetic Epidemiology of Vascular Disorders, Leibniz-Institute for Arteriosclerosis Research, Domagkstr. 3, 48149 Muenster, Germany
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  • MANFRED MILINSKI,

    1. Max Planck Institute for Evolutionary Biology, Department of Evolutionary Ecology, August-Thienemann-Str. 2, 24306 Ploen, Germany
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    • Shared senior authorship.

  • THORSTEN B. H. REUSCH,

    1. Helmholtz Center for Ocean Research (GEOMAR), Evolutionary Ecology of Marine Fishes, Duesternbrooker Weg 20, 24105 Kiel, Germany
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    • Shared senior authorship.

  • ERICH BORNBERG-BAUER

    1. Institute for Evolution and Biodiversity, Evolutionary Bioinformatics, Westfaelische Wilhelms University, Huefferstr. 1, 48149 Muenster, Germany
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    • Shared senior authorship.


Philine G. D. Feulner, Fax: +49 251 83 24668; E-mail: p.feulner@uni-muenster.de

Abstract

Since the end of the Pleistocene, the three-spined stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to various freshwater habitats probably originating from ancestral marine populations. Standing genetic variation and the underlying genomic architecture both have been speculated to contribute to recent adaptive radiations of sticklebacks. Here, we expand on the current genomic resources of this fish by providing extensive genome-wide variation data from six individuals from a marine (North Sea) stickleback population. Using next-generation sequencing and a combination of paired-end and mate-pair libraries, we detected a wide size range of genetic variation. Among the six individuals, we found more than 7% of the genome is polymorphic, consisting of 2 599 111 SNPs, 233 464 indels and structural variation (SV) (>50 bp) such as 1054 copy-number variable regions (deletions and duplications) and 48 inversions. Many of these polymorphisms affect gene and coding sequences. Based on SNP diversity, we determined outlier regions concordant with signatures expected under adaptive evolution. As some of these outliers overlap with pronounced regions of copy-number variation, we propose the consideration of such SV when analysing SNP data from re-sequencing approaches. We further discuss the value of this resource on genome-wide variation for further investigation upon the relative contribution of standing variation on the parallel evolution of sticklebacks and the importance of the genomic architecture in adaptive radiation.

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