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New possibilities arise for studies of hybridization: SNP-based markers for the multi-species Daphnia longispina complex derived from transcriptome data

Rusek, Jakub ; Ayan, Gökce B. ; Turko, Patrick ; Tellenbach, Christoph ; Giessler, Sabine ; Spaak, Piet ; Wolinska, Justyna

In: Journal of Plankton Research, 2015, vol. 37, no. 3, p. 626-635

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    Titre
    • New possibilities arise for studies of hybridization: SNP-based markers for the multi-species Daphnia longispina complex derived from transcriptome data
    Auteur
    • Rusek, Jakub. Department of Biology II, Ludwig Maximilians University, Grosshaderner Strasse 2, Planegg-Martinsried 82512, Germany
    • Ayan, Gökce B.. Department of Biology II, Ludwig Maximilians University, Grosshaderner Strasse 2, Planegg-Martinsried 82512, Germany
    • Turko, Patrick. Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf 8600, Switzerland
    • Tellenbach, Christoph. Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf 8600, Switzerland
    • Giessler, Sabine. Department of Biology II, Ludwig Maximilians University, Grosshaderner Strasse 2, Planegg-Martinsried 82512, Germany
    • Spaak, Piet. Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf 8600, Switzerland
    • Wolinska, Justyna. Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin 12587, Germany
    Type de document
    • Postprint
    Langue
    • Anglais
    Publié dans
    • Journal of Plankton Research, 2015, vol. 37, no. 3, p. 626-635. Oxford University Press
    Autre version électronique
    Identifiant OAI-PMH
    • oai:doc.rero.ch:303952
    Summary
    In order to trace community dynamics and reticulate evolution in hybrid species complexes, long-term comparative studies of natural populations are necessary. Such studies require the development of tools for fine-scale genetic analyses. In the present study, we developed species-diagnostic SNP-based markers for hybridizing freshwater crustaceans: the multispecies Daphnia longispina complex. Specifically, we took advantage of transcriptome data from a key species of this hybrid complex, the annotated genome of a related Daphnia species and well-defined reference genotypes from three parental species. Altogether eleven nuclear loci with several species-specific SNP sites were identified in sequence alignments of these reference genotypes from three parental species and their interspecific hybrids. A PCR-RFLP assay was developed for cost-efficient large population screening by SNP-based genotyping. Taxon assignment by RFLP patterns was nearly perfectly concordant with microsatellite genotyping across several screened populations from Europe. Finally, we were able to amplify two short regions of these loci in formaldehyde-preserved samples dating back to the year 1960. The species-specific SNP-based markers developed here provide valuable tools to study hybridization over time, including the long-term impact of various environmental factors on hybridization and biodiversity changes. SNP-based genotyping will finally allow eco-evolutionary dynamics to be revealed at different time scales