Supplemental Figure Legends
S.Figure 1. Frequency distribution plots of number of loci of a given depth for the RAD library before (blue) and after (orange) filtering by read depth.
S.Figure 2. Example allele plots for score 1-4 loci. Boundaries are indicated for each genotype category corresponding to octoploid genotypes (white: allele ratios shared with tetraploid genotypes; grey: allele ratios exclusive to octoploid genotypes; red: regions of indeterminate ratio recorded as missing).
S.Figure 3. Boxplot of percent Mendelian incompatibilities between true sire and offspring for those offspring correctly assigned to that sire (BLF-0021) by Colony2, or assigned to a missing father (*1).
S.Figure 4. Relationship between ploidy estimation confidence, heterozygosity, and sequencing coverage. Ploidy estimation confidence (minimum alternative likelihood ratio) versus reads corresponding to target loci. Color scale represents percent heterozygous genotypes. Inset graph shows lower left quadrant in detail.
S.Figure 5. Boxplot of individual inbreeding (Weir) by locality for select localities with N>7 individuals.