Conclusions
We described here the combination of techniques which will make genetic data for polyploids more accessible and facilitate population genetic and evolutionary studies of polysomic species. Together, these methods address some of the standing challenges to developing genetic resources for polyploids, including the identification of homeolog-specific genetic variants, inference of ploidy-aware genotypes, and estimation of parentage and other population genetic statistics. We demonstrate the efficacy of these techniques for white sturgeon, a polysomic and ploidy variable species of strong conservation concern in the Pacific Northwest. The molecular markers we present will greatly facilitate the conservation management of imperiled populations. These markers, along with our updated genotyping-by-thousands pipeline, allow the efficient generation of genetic data and estimation of ploidy for large numbers of samples from diverse tissue collections. These data will help researchers address a number of outstanding questions, including the efficiency and effects of alternative conservation schemes including hatchery spawning, repatriation, and translocation of white sturgeon in the Columbia River Basin. Although questions remain about the segregation of chromosomes and individual loci in white sturgeon, our examinations suggest the loci described here are reliably tetrasomic for putatively octoploid individuals.