Identifying best practices for sibship inference with tetrasomic single nucleotide polymorphisms

Sibship inference is commonly performed for conservation and management purposes in polyploid taxa like sturgeons. While no program has been developed for compatibility with polyploid genetic markers, the program Colony can effectively analyze polyploid genotypes converted to pseudo-diploid dominant format (PDDF). This approach has largely been applied to microsatellites and was also demonstrated to be effective with the novel GTseq panel of tetrasomic SNPs developed for the white sturgeon (Acipenser transmontanus). These two polyploid marker types have not been directly compared with respect to sibship inference accuracy. Additionally, the biallelic nature of SNPs enables their conversion to pseudo-diploid codominant format (PDCF), which has not been tested for sibship inference. Utilizing the white sturgeon microsatellite and GTseq SNP panels, we tested these three converted marker classes (microsatellite PDDF, SNP PDDF, and SNP PDCF) for sibship inference in a captive-spawned offspring group of known sibship structure and further tested the two classes of converted SNPs in a second such offspring group. Broadly, we found that both microsatellites and SNPs in PDDF could produce complete accuracy, although the latter performed less accurately in one of the offspring groups. Inputting inflated mistyping rates was necessary to maximize accuracy for these two converted marker classes. In both groups, SNPs in PDCF yielded poor accuracy. Our results demonstrate how to employ tetrasomic SNPs for sibship inference most effectively and are applicable to polyploid taxa with tetrasomic loci more broadly.