Phylogeny of Competence Figure 3. Factors resulting in the lack of resolution in consensus trees. (A) Two topologies from individual aligned blocks in the genome dataset. The two aligned blocks are of similar length (15,320 bp and 15,693 bp) but result in very different topologies. (B) The number of nodes resolved as a function of the aligned block length. Aligned block length explains a significant portion of the variation in the number of nodes resolved. doi:10.1371/journal.pone.0005854.g003 transformation did not change in the same direction, suggesting that selective pressures may act independent of DNA uptake to increase or decrease the amount of incoming DNA that is recombined. One interpretation is that the costs and benefits of recombining DNA can be separate from the costs and benefits of taking it up. However, this could also be due to pleiotropic effects of selection for changes in recombinational repair or nuclease activity. The sequence differences our previous study identified in some genes required for DNA uptake and transformation do not account for the phenotypic differences [16]. For example, strain 22.1-21’s frameshift mutation in pilD inactivates a peptidase required for the assembly of uptake machinery in other bacteria, but this strain takes up significant amounts of DNA and routinely produces hundreds of transformants [4]. Equally perplexing is the comM frameshift in strain R2866. A comM mutant of strain Rd has PLoS ONE | www.plosone.org 6 June 2009 | Volume 4 | Issue 6 | e5854