Data from: Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing

Caviar-producing sturgeons belonging to the genus Acipenser are considered
to be one of the most endangered species groups in the world. Continued
overfishing in spite of increasing legislation, zero catch quotas and
extensive aquaculture production have led to the collapse of wild stocks
across Europe and Asia. The evolutionary relationships among Adriatic,
Russian, Persian and Siberian sturgeons are complex because of past
introgression events and remain poorly understood. Conservation
management, traceability and enforcement suffer a lack of appropriate DNA
markers for the genetic identification of sturgeon at the species,
population and individual level. This study employed RAD sequencing to
discover and characterize single nucleotide polymorphism (SNP) DNA markers
for use in sturgeon conservation in these four tetraploid species over
three biological levels, using a single sequencing lane. Four population
meta-samples and eight individual samples from one family were barcoded
separately before sequencing. Analysis of 14.4 Gb of paired-end RAD data
focused on the identification of SNPs in the paired-end contig, with
subsequent in silico and empirical validation of candidate markers.
Thousands of putatively informative markers were identified including, for
the first time, SNPs that show population-wide differentiation between
Russian and Persian sturgeons, representing an important advance in our
ability to manage these cryptic species. The results highlight the
challenges of genotyping-by-sequencing in polyploid taxa, while
establishing the potential genetic resources for developing a new range of
caviar traceability and enforcement tools.