Molecular phylogenetic analysis of the <i>acr1</i>-<i>vcr147</i>-<i>acaDC</i>-<i>acr2</i> locus by Maximum Likelihood method.

<p>The evolutionary history was inferred by using the Maximum Likelihood method based on the Kimura 2-parameter model <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004714#pgen.1004714-Kimura1" target="_blank">[61]</a>. The tree with the highest log likelihood (−5461.6977) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.6567)). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 45 nucleotide sequences (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004714#pgen.1004714.s006" target="_blank">Table S2</a>). Codon positions included were 1st+2nd+3rd+Noncoding. There were a total of 2469 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004714#pgen.1004714-Tamura1" target="_blank">[58]</a>. The background color of each leaf indicates the original host species from which each plasmid was isolated. Insertions (Ω), deletion (Δ) and frameshift (Ψ) mutations are indicated where appropriate. *, Although pYT3 shares sequence identity with the IncA/C plasmids, it lacks an IncA/C-specific replication initiation gene (<i>repA</i>) and contains an IncFIB replicon instead (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004714#pgen.1004714.s001" target="_blank">Figure S1</a>) <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004714#pgen.1004714-Tamamura1" target="_blank">[62]</a>.