Figure 3

Distribution of Fis values of: diploid SNPs (brown), de novo SNPs (pink) and HomeoSplitter SNPs (green). Fis values were calculated as the heterozygosity deficit relative to panmixia. Allelic frequencies were estimated from the called genotypes with high confidence values (see text). Negative Fis values suggest fixed divergence between homeologous/paralogous copies. Fis around 0 indicate possible mixture of homeology and intra genome polymorphism. Fis values close to 1 sign a priori intra genome polymorphic sites. See Figure 1 for the pipeline leading to the detection of these three SNP sets