Comparison of the rDNA loci from natural populations with computer simulated loci generated by simple crossover models of concerted evolution.

<p>(A) The empirical data determined for rDNA loci from the natural populations in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003179#pgen-1003179-g002" target="_blank">Figure 2</a> are re-plotted to show the distributions of rDNA locus size (left panel), total R2 number per locus (middle panel), and the number of R2 copies duplicated by crossovers (right panel). The R2 duplication frequency was derived from the approach used in ref. 20 to count the total number of R2 copies in 18 rDNA loci. (B) Simulation data based on the modeling approach described in ref. 17 in which the crossover events are uniformly distributed throughout the rDNA locus. The following parameters were used. Population size = 4000; generations = 10000; replicates = 60; number of uninserted rDNA units required for peak fitness = 100; maximum fecundity = 6; SCE rate = 0.3; ICE rate = 0.0001; crossover offset = 1–8 rDNA units; R2 retrotransposition rate = 0.009 for all loci containing R2 elements; loop deletion rate = 0.00005; deletion size = 1–15 rDNA units. See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003179#s4" target="_blank">Materials and Methods</a> for a description of these parameters. How these parameters influence the size of the rDNA locus and number of inserted units can be found in ref. 17. The three panels showing the distributions of locus size, number of R2, and R2 duplication state are shown below the corresponding data from the natural populations. (C) Simulation data based on the transcription domain model for the regulation of R2 elements in a population. The following parameters were used (also described in the <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003179#s4" target="_blank">Materials and Methods</a>). Population size = 5000; generations = 50000; replicates = 60; transcription domain size = 40; number of uninserted rDNA units in the domain required for peak fitness = 34; maximum fecundity = 6; SCE rate = 0.2 and clustered near the transcription domain with s = 0.05; ICE rate = 0.0001, s = 0.05; crossover offset = 1–11 rDNA units; R2 retrotransposition rate = 0.18 times a square root function of the number of full-length R2 copies in the domain, s = 0.4; loop deletion rate = 0.00007 times the size of the rDNA locus; element induced deletion rate = 0.0065 times the number of full-length R2 copies in the domain; deletion size = 1–30 rDNA units, s = 0.2. The panels containing the distributions of locus size, the number of R2, and R2 duplication state are again shown below the corresponding data from the natural populations.