Phylogeny of Competence Figure 7. DNA uptake (A) and transformation frequencies (B) mapped onto the tree obtained from ClonalFrame. Light grey indicates low uptake (or transformation) and increasing intensity of grey indicates increasing uptake (or transformation). The numbers on the scale for DNA uptake and transformation correspond to the percent of radio-labeled DNA taken up per optical density unit and the transformation frequency, respectively [16]. doi:10.1371/journal.pone.0005854.g007 additional 5 were excluded because they were short (,50 nt) and had no polymorphism. The lengths of the remaining 101 segments ranged from 150 to 108,151 nt, with a median of 7,901 nt and a mean of 14,700 nt. Gaps were removed from aligned blocks before phylogenetic inference in MrBayes (see below). Uptake/transformation gene dataset. A list of H. influenzae Rd genes whose products regulate competence, contribute to DNA uptake machinery, or interact with incoming DNA has been previously compiled for the 13 strains with sequences available (Table 2; [40]). Briefly, competence gene sequences from strain Rd were used as queries in BLAST searches against the 13 strains with complete genome sequences available. Competence gene sequences were aligned manually or in CLUSTALW. PLoS ONE | www.plosone.org 11 June 2009 | Volume 4 | Issue 6 | e5854