0.0025 0.3965 20.0448 0.0198 0.0073 20.0689 0.03 20.0137 0.0008 0.0239 20.0003 20.0017 0.0571 20.0086 20.001 20.0219 20.0091 20.017 0.5707 20.001 20.0009 20.0055 0.0036 20.0021 0.1172 20.0069 1.487 20.0029 0.0985 20.0087 20.0183 0.0117 0.0271 0.0014 0.345 20.0256 0.0105 0.001 0.0029 0.0345 20.0092 20.0009 0.0231 20.0011 20.0025 0.0407 20.0089 20.0004 20.0174 20.0027 20.0012 0.5556 20.0004 20.0072 20.0062 0.0033 20.0032 0.2228 0.0157 1.499 20.005 0.0971 20.0101 20.0175 0.0122 0.0277 Genome 20.0124 20.0078 20.0043 20.0015 20.0106 20.0045 0.009 20.0028 0.1226 0.0218 1.579 Comp. 20.0118 20.0049 20.0035 20.0048 20.0125 20.0032 0.0131 20.0069 0.1267 0.0286 1.577 361027 0.0141 2661025 2161026 2161025 561024 2861027 361026 2861026 561024 661024 361024 2461026 2261026 2461027 2261025 0.0053 2561027 0.0044 2361027 261024 2361025 2961026 2261027 161024 2461026 0.01 2261027 761025 2861027 2161025 861024 0.0035 MLST CF 2661028 0.014 2761027 2961027 2461025 0.0011 2161026 361026 2761026 561024 661024 361024 2761026 2261026 2861028 2361025 0.0053 2461027 0.0046 2561028 261024 2461025 2961026 2561027 161024 2461026 0.01 2361027 761025 2161026 2161025 861024 0.0035 Table 5. Change in DNA uptake and transformation during divergence of each strain from its most recent ancestor. DNA uptake* MLST BUCKy MLST CF Transformation frequency MLST BUCKy Strain 176 375 432 477 1008 1124 1158 1159 1181 1207 1209 1233 1247 3655 22.1-21 22.4-21 86028NP Eagan PittAA PittBB PittDD PittEE PittGG PittHH PittII R2846 R2866 R3021 Rd RM6158 RM6169 RM6181 RM7033 RM7271 RM7429 Phylogeny of Competence Genome 2361026 2561026 2261026 2661027 261024 2261026 2861026 2661027 161024 2461026 0.01 Comp. 2661026 2961027 261026 2361026 261024 2161026 2961026 2261027 161024 2261026 0.01 Bold font indicates a decrease. *The percent radio-labeled DNA taken up per optical density unit. doi:10.1371/journal.pone.0005854.t005 established variation in resources [37], and many DNA repair pathways appear to be largely uniform across a wide range of niches, consistent with the ubiquity of endogenous damaging agents, we lack systematic data. Materials and Methods Datasets MLST dataset. The aligned sequences of adk, atpG, frdB, fucK, mdh, pgi, and recA from all of the 35 strains listed in Table 1 were downloaded from http://haemophilus.mlst.net/. Genome dataset. Genome sequences available for H. influenzae strains were downloaded from NCBI in Nov 2007. The genomes of strains 22.1-21, 22.4-21, PittAA, PittHH, PittII, R2846, R2866, and R3021 had not been completely assembled and so were only available as multiple contigs. Because no annotation was available we were unable to identify orthologs for these genomes. Genomes were aligned using mauveAligner (Mauve version 2.1.1) [38,39] with default parameters, which resulted in alignments of 116 genome segments. Ten segments were excluded from phylogenetic analyses after visual examination of each alignment because it was obvious that one or more sequences were not homologous. An PLoS ONE | www.plosone.org 10 June 2009 | Volume 4 | Issue 6 | e5854