Instead, the strains branched deeply within the Proteobacteria as shown in a phylogenetic tree created by maximum likelihood [19], Figure 3. Very similar tree topologies were found by neighbor-joining, maximum parsimony or minimum evolution methods using MEGA3 [20](data not shown).
In case of FAFLP data, the trees were constructed using the binary data by minimum evolution method with topology validated through an interior branch test, a t-test, which is computed using the bootstrap procedure.
A minimum evolution tree for L. casei MLST data was reconstructed by using MEGA based on the numbers of parsimoniously informative sites and the results of a bootstrapping test of strain phylogeny (Kumar et al. 2004).
For 15,011 16s RNAs, RAxML 7.2.5's parsimony and FastTree's minimum evolution phase take about the same time (data not shown).
HW performed the Phylogenetic tree construction with Minimum Evolution and Maximum Parsimony methods and aided in data analysis.
In this analysis, the distance matrices for rDNA data sets were generated using the minimum evolution objective function (ME; [ 58, 59]) under the general time-reversible model of nucleotide substitution (GTR; [ 60- 62]) using PAUP* 4.0d105 [ 55].
For the CaM data set (340 bp), we used the minimum evolution (ME) method with HKY85 distances.
Data retrieved for neighborhood joining were compared with minimum evolution and maximum parsimony methods.
Phylogenetic trees were generated by the minimum evolution method and the interior branch method; 1,000 resamplings of the data were used to calculate percentage of the branches obtained.
Analyses of the concatenation of the nine nuclear genes, as well as a full data set of 24 genes, were carried out using minimum evolution, maximum parsimony, maximum likelihood, and Bayesian inference.
