Figure 1
**Effect 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).