Comparison of D_r/D_c between pairs of bacterial species.

(a) Dr/Dc is significantly higher in endosymbionts (pair A) than in related free-living bacteria (pair B). For these comparisons, the value of [(Dr/Dc, pair A)/(Dr/Dc, pair B)] (or, the ‘elevation index’ described in the text) exceeds one, as does the lower bound of the 99% confidence interval of this index. In addition, the elevation of Dr/Dc is highly significant by the sign test and Wilcoxon test. (b) By contrast, differences in Dr/Dc within free-living groups or within endosymbionts were more subtle. While Buchnera showed a higher Dr/Dc ratio than Blochmannia, this is only marginally significant (p<0.017) by the sign test and has a relatively low ChiSquare value in the Wilcoxon test. Dr and Dcvalues were estimated under the classification scheme of Miyata et al. [56]. aFor each comparison between two genome pairs, the ratio of the two Dr/Dc values is the ‘elevation index’ described in the text and represented in Figures 3 and 4. The index was calculated for each of the 256 orthologs and then the subsequent calculations (of median, mean, and confidence intervals) were performed. bSignificance of the sign test was evaluated using (a) an exact one-sided binomial test for comparisons between endosymbionts vs. free-living bacteria to test the null hypothesis that Dr/Dc is not higher in the endosymbiont pair, and (b) using a two-way test for comparisons within endosymbionts or within free-living groups. cSignificance of the Wilcoxon test was evaluated using a ChiSquare approximation.