Figure Legends
Figure 1. Conformance of white sturgeon SNP loci to expectations of tetrasomy. Top panel) Box plot of ranked conformance to a mixture model (Delomas et al. submitted) of tetraploidy (4N) vs. allele plot scores. Bottom Panel) Box plot of percent Mendelian incompatibilities by locus in known parent-offspring trios vs. allele plot scores.
Figure 2. Signal for parentage detection in white sturgeon SNPs. Top Panel) Percent Mendelian incompatibilities between parent-offspring and non-parent offspring trios from hatchery white sturgeon. Bottom Panel) Log odds scores for single parent assignment in Polygene when both, one, or neither parents are included for 326 offspring from the same hatchery cross.
Figure 3. Box plot of the Huang et al. (2015) maximum likelihood estimate of relatedness for 326 offspring from a partial 5x6 hatchery cross of white sturgeon. Full, full siblings; Half, half siblings.
Figure 4. Relationship between ploidy estimation confidence, heterozygosity, genotype completeness, and sequencing coverage. Top Panel) Ploidy estimation confidence (minimum alternative likelihood ratio) versus reads corresponding to target loci. Color scale represents percent genotype completeness. Inset graph shows lower left quadrant in detail. Bottom Panel) Percent genotype completeness versus reads corresponding to target loci. Color scale represents percent heterozygous genotypes. Dotted line corresponds to sequencing coverage generally achieving 90% genotype completeness (100k reads).
Figure 5. Minor allele frequency (MAF) of white sturgeon SNP loci in sampled populations, ordered by mean MAF (black line). “Minor allele” status was chosen based on mean allele frequency, though in some populations the minor allele is more common. Only populations with greater than seven individuals are shown. Orange, Columbia River Basin localities; green, outside Columbia Basin.
Figure 6. Statistics of genetic association for each white sturgeon SNP locus in populations with >50 individuals versus allele plot ratings. Top Panel) Number of statistically significant linkage associations. Bottom Panel) Number of statistically significant departures from Hardy-Weinberg equilibrium.