Straina 1247 PittDD Rd* RM7033 RM7271 RM7429 RM6181 1181 R2846* 375 432 R2866* 22.4-21* 1124 22.1-21* Eagan PittHH* PittAA* 1207 1209 1233 PittII* RM6169 PittEE* 176 477 3655* 1008 PittGG* 1158 RM6158 1159 PittBB R3021* 86028NP* nt nt d d d d e nt nt nt nt nt nt nt nt b nt nt nt nt nt nt e nt nt nt nt nt nt nt e nt nt nt nt OM OM N P RI unk. B OM OM OM OM M HN OM HN M OM OM OM OM OM OM A OM OM OM OM OM O OM unk. OM OM HN OM Uptake 8.361022 7.061021 1.6 1.761023 5.461022 6.961022 2.761023 9.461023 1.761023 4.561021 8.661023 1.761021 1.361023 6.061022 6.661023 5.461023 3.061023 9.061023 3.261022 8.161023 6.761023 5.661022 1.161021 3.161023 6.361023 4.561022 1.861022 1.061022 5.461022 2.161023 1.061022 3.561023 3.761022 4.261023 TF 1.761025 5.361023 1.061022 5.961028 1.261023 3.961023 5.561028 1.261026 1.761027 1.461022 2.361027 1.361024 1.861027 1.461023 2.261026 5.461023 2.861028 8.961023 5.061024 6.061024 3.661024 2.7661026 7.261025 2.161027 6.661027 2.661028 8.661026 2.761024 1.261026 1.161028 4.961026 1.761028 2.161027 5.561026 13.80 13.80 13.80 13.80 13.80 13.80 16.30 16.40 17.10 17.22 17.22 17.27 17.28 17.35 17.42 17.63 17.81 18.04 18.52 18.52 18.52 18.62 18.67 19.60 20.03 20.05 20.46 21.46 21.46 22.00 22.29 22.38 26.83 30.47 44.44 Phylogeny of Competence magnitude. The goal of this paper is to place this variation into the context of the evolutionary relationships of these strains, to determine the extent to which loss and gain events have contributed to the present distribution of competence. Previous work has been unable to establish the evolutionary relationships of H. influenzae strains; analysis using seven concat- enated Multi-Locus Sequence Typing (MLST) loci resulted in tree topologies that did not provide strong support for most clades [17,18]. The lack of resolution in the topologies from these studies may have had several causes: insufficient variation in the 3 kb of sequence used for the MLST analysis, the inability of parsimony reconstruction methods to accurately resolve the relationships of strains, and/or population processes that interfere with phyloge- netic reconstruction, such as recombination between strains or changes in effective population size [19–21]. To infer the evolutionary relationships of the H. influenzae strains used in our Table 1. H. influenzae strains and their characteristics. Sero-type Isolated fromb Instability (MLST)c,d Instability (Gen)c,d Instability (Comp)c,d Uptake data and transformation frequencies (TF) are from ref. [16]. Strains are sorted by their instability in the MLST dataset. aStrains with genome sequence data available indicated by *. bM: meningitis. N: nasopharynx; OM: otitis media; HN: Healthy nasopharynx; O: Otorrhea; P: Pneumonia; RI: Respiratory infection; B: Bronchitis; A: Asthma; Unk.: no information available. cn/a: data not available. I = Instability. doi:10.1371/journal.pone.0005854.t001 PLoS ONE | www.plosone.org 2 June 2009 | Volume 4 | Issue 6 | e5854 1144.92 1263.95 1176.09 1255.80 1201.15 1264.19 1266.07 1113.88 1257.59 1214.35 1371.98 1355.62 1321.30 160.74 202.12 178.06 177.39 172.83 162.62 157.07 145.03 163.42 166.26 185.45 194.65 185.74