SNP-based markers for the multi-species Daphnia longispina complex derived from transcriptome data

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.