Phylogenetic analysis of co-expression modules. (A) Mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) were used to measure the tree-wide and tip-level clustering of each module, respectively. The two small panels on the left show that -2 is a significant threshold (with p=0.01) for both MPD and MNTD z scores. In the right panel, modules (red dots) are displayed in 4 quadrants. Modules in the 2nd and 3rd quadrants have significant low MPD values (< -2), indicating that their genes display tree-wide clustering. Modules in the 4th quadrant have significantly low MNTD (<-2) but not significant MPD values, indicating that their genes exhibit tip-level clustering. (B) Phylogenetic profiles showing the distribution of the member genes of the salmon and yellowgreen modules shown here as examples. The dendrogram on the top of the module profile is the phylogenetic tree based on 16 s rRNA of 236 species selected in an unbiased fashion (see methods). The solid vertical red line corresponds to C. crescentus.