Figure 1From: Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demographyEffect of population structure on the estimation of synonymous and nonsynonymous divergence. Nine different scenarios were simulated, combining three migration rates (m = 0.0002, 0.01 and ∞ (= one deme)) and three dN/dS ratios (dashed line = 0.1, solid line = 1, dotted line = 10). For each scenario, 500 alignments with 10 sequences 333 codons long, were simulated. In all cases, the mutation rate was 5.4 ∞ 10-5, the transition/transversion ratio was 1.0, and the effective population size was 1000. Mean synonymous divergence per synonymous site (dS), nonsynonymous divergence per nonsynonymous site (dN), and their ratio (dN/dS) were estimated according to Nei and Gojobori [32] with a modified version of SNAP [33]. Error bars indicated approximate 95% confidence intervals (± s.e. ∞ 1.96).Back to article page