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  with a modified version of SNAP . Error bars indicated approximate 95% confidence intervals (± s.e. ∞ 1.96).
Arenas and Posada BMC Bioinformatics 2007 8:458 doi:10.1186/1471-2105-8-458