Simulated region recovery and optimal per-individual read investment demonstrate marker set flexibility.

A single set of reagents coupled with appropriate digest (and sizing) conditions can be used to tune the number of recovered fragments over two orders of magnitude in most species (see text). Parameters for ddRADseq recovery simulations: “wide” automated size selection (300 bp±36 bp simulated with mean = 300 bp, SD = 18 bp; see Figure 4) with different RE combinations. The values in each cell report: the approximate number of fragments expected (in thousands), the fraction of the diploid genome that would be sampled in a 100 bp, paired end read (200 bp total), and the expected number of reads (in thousands) required to saturate the regions at >7× coverage.