Defining Loci in Restriction-Based Reduced Representation Genomic Data from Nonmodel Species: Sources of Bias and Diagnostics for Optimal Clustering

Figure 2

Potentially confounding duplication across all possible 100 bp fragments in three genomes. At this scale of comparison most loci are single-copy in each genome (copy class 1) and do not present a paralog clustering problem when trying to de novo assemble alleles. Paralogous loci from copy class 2 have the potential to be clustered together and if each paralog is homozygous, the cluster will be incorrectly interpreted as a diploid heterozygous locus even after a ploidy-informed filter. In principle, a ploidy-informed filter should be able to identify and remove most clusters derived from loci in the 3+ copy class.