Molecular Phylogenetic Analysis by Maximum Likelihood for all Isolated, Culturable Strains of Bacteria Isolated from Fish Intestines.

<p>The evolutionary history was inferred by using the Maximum Likelihood method based on the Kimura 2-parameter model. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035398#pone.0035398-Kimura1" target="_blank">[48]</a> The bootstrap consensus tree inferred from 2000 replicates is taken to represent the evolutionary history of the taxa analyzed. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035398#pone.0035398-Felsenstein1" target="_blank">[49]</a> Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (2000 replicates) are shown next to the branches. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035398#pone.0035398-Felsenstein1" target="_blank">[49]</a> Initial tree(s) for the heuristic search were obtained automatically as follows. When the number of common sites was <100 or less than one fourth of the total number of sites, the maximum parsimony method was used; otherwise BIONJ method with MCL distance matrix was used. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+<i>G</i>, parameter = 0.4869)). The rate variation model allowed for some sites to be evolutionarily invariable ([+<i>I</i>], 38.9340% sites). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 53 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 1244 positions in the final dataset. Evolutionary analyses were conducted in MEGA5. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035398#pone.0035398-Tamura1" target="_blank">[30]</a> Strains identified as psychrophilic bacteria in NCBI denoted with blue diamonds. Strains whose closest published NCBI relatives are uncultured clones denoted with open triangles.