Phylogenetic tree of 44 <i>B</i>. <i>goodwinii</i> strains based on a concatenated sequence of 7 housekeeping gene fragments (abc, dnaJ, dnaN, gyrB, infB, nusA, rpoB).

<p>The evolutionary history was inferred by using the Maximum Likelihood method based on the Hasegawa-Kishino-Yano model (HKY+G+I) <i>with</i> estimated transition/transversion bias value. The tree with the highest log likelihood (-13387.9427) is shown. Initial tree for the heuristic search was obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood approach, and then selecting the topology with superior log likelihood value. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The numbers at the nodes represent the relative distance between the strains with bootstrap support from 1000 resampled datasets. Individual Sequence Type (ST) numbers are indicated. Different colour nodes show the four corresponding clusters estimated by the Discriminant Analysis of Principal Components (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178390#pone.0178390.g004" target="_blank">Fig 4</a>). Blue and orange colour branches indicate a separation into 2 clusters of STs within the population, whereas green colour branch indicate the recombinant genotype as estimated by STRUCTURE analysis (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178390#pone.0178390.g005" target="_blank">Fig 5</a>). <i>Gibbsiella quercinecans</i> type strain FRB97 (Brady <i>et al</i>., 2010) was used as the outgroup (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178390#pone.0178390.s001" target="_blank">S1 Fig</a>).