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Free keywords:
low-quality DNA; formaldehyde; SNP genotyping; interspecific hybridization; species-specific SNPs
Abstract:
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.
