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Rusek, Jakub; Ayan, Gokce; Turko, Patrick; Tellenbach, Christoph; Giessler, Sabine; Spaak, Piet; Wolinska, Justyna (2014): New possibilities arise for studies of hybridization: SNP-based markers for the multi-species Daphnia longispina complex derived from transcriptome data [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.836026

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Abstract:
In order to trace population community dynamics and reticulate evolution in hybrid species complexes, long-term comparative studies of natural populations are necessary and thus, tools for fine-scale genetic analyses are needed. In the present study, we developed species-diagnostic SNP 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 22 individuals of three parental species and their hybrids. A PCR-RFLP assay was developed for cost-efficient large population screening by SNP-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 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 for revealing eco-evolutionary dynamics at different time scales.
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Rusek, Jakub; Ayan, Gokce; Turko, Patrick; Tellenbach, Christoph; Giessler, Sabine; Spaak, Piet; Wolinska, Justyna (2015): New possibilities arise for studies of hybridization: SNP-based markers for the multi-species Daphnia longispina complex derived from transcriptome data. data submission http://issues.pangaea.de/browse/PDI-8400, Journal of Plankton Research, 37(3), 626-635, https://doi.org/10.1093/plankt/fbv028
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