Phylogeny of Competence Figure 4. BUCKy trees for each of the three datasets. Numbers next to branching points indicate the concordance factors, which are indicators of the number of alignment blocks supporting the clade, out of 7, 101, and 30 for the MLST, Genome, and Uptake/Transformation dataset respectively. doi:10.1371/journal.pone.0005854.g004 normal DNA uptake and 300-fold reduced transformation [35], but this strain has higher uptake and transformation than its closest relatives. Pseudogene alleles were also identified in two other strains, R3021 (comD) and PittAA (ligA). However these genes’ roles in uptake and transformation are unknown, and ancestral phenotypes could not be inferred because R3021 was placed differently in the different trees (Table 5) and PittAA’s closest relative was strain 3665, whose uptake and transformation have not been measured. None of the other competence genes in these and other sequenced genomes had obvious defects, indicating that changes in competence phenotypes are due to single nucleotide polymorphisms. Figure 5. SplitsTree networks for each of the three datasets. doi:10.1371/journal.pone.0005854.g005 PLoS ONE | www.plosone.org 8 June 2009 | Volume 4 | Issue 6 | e5854