Schematic illustration of simulation to generate input data. Panel A illustrates a simulation output, which will become an input data to be fed into various neutrality tests. It consists of n sequences sampled from a population, and each sequence is composed of an SV locus flanked by S SNP sites. (In this example, n = 8 and S = 10.) B. Flanking SNPs are simulated according to the infinite-site model, which guarantees that each SNP site underwent only one mutation (yellow lightening bolt) along the sequence genealogy. The panel shows the mutation at the SNP site on the immediate left of the SV locus (colored cyan and magenta). C. The SV locus is simulated according to the two-state model of recurrent mutations. The character “a“denotes the wild-type (or ancestral) state (here a one-copy state represented by a thick black arrow), and the character “A“denotes the mutant (or derived) state (here a two-copy state represented by two thick red arrows). The forward and backward mutation rates per generation are denoted by μ and v, respectively. D. The SV states in this example were generated by two forward mutations (red lightening bolts) and a backward mutation (blue lightening bolt) along the genealogy, resulting in m = 3 sampled mutants (red ID numbers).
Ezawa et al. BMC Genetics 2013 14:37 doi:10.1186/1471-2156-14-37