Figure 4.

Multigene analysis of synonymous and nonsynonymous sequence divergence. Shown are the dS (left) and dN (right) trees resulting from a codon-based likelihood analysis of a combined data set of five mitochondrial genes (atp1, cob, cox1, cox2, and cox3). Branch lengths are in units of synonymous substitutions per synonymous site for the dS tree and nonsynonymous substitutions per nonsynonymous site for the dN tree; note the 10-fold difference in scaling between the two trees. Topological constraints were enforced during the analysis (see methods). Sequences for two to five of the genes analyzed were available for any one plant [see Supp. Table 5 in Additional file 2]. S. = Silene; P. = Plantago.

Mower et al. BMC Evolutionary Biology 2007 7:135   doi:10.1186/1471-2148-7-135
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