Defining Loci in Restriction-Based Reduced Representation Genomic Data from Nonmodel Species: Sources of Bias and Diagnostics for Optimal Clustering
Figure 1
Pairwise divergence distribution for simulated allelic loci (green) and polyploidy duplicated loci (blue) in soybean (a), and pairwise divergence distribution of stickleback (pink), soybean (green), and C. savignyi (orange) simulated alleles (b). The shaded region in (a) between 0.02 and 0.08 pairwise divergence represents the “confounding duplication” region in which alleles and paralogs are indistinguishable during de novo assembly. The divergence of polyploidy duplicated paralogs in (a) is derived from [8]. Dashed vertical lines in (b) indicate distribution means. Different ranges are used for the - and -axis values in (a) and (b).
