Moreover, although the unrooted ML tree indicated that there were no distinct haplotype groups with high bootstrap support, the results of our phylogeographic analysis revealed that there were high levels of genetic differentiation among populations, and that the genetic pattern of this species was mainly constituted by multiple unrelated founding events.
MP bootstrap analysis of the mt16S partition indicated a number of interior nodes with <60% bootstrap support (similar result using NJ), with a mean bootstrap value across all internal nodes of 77.4% (73.2% for NJ).
▪ Consensus by bootstrap support: The result with the highest bootstrap value was chosen.
All computations were performed with a cutoff level of 50% bootstrap for including a polychromatic quartet in the analysis, but qualitatively similar results were obtained for other bootstrap values, and even without taking bootstrap support into consideration (results not shown).
Deeper nodes were not well supported in the MP bootstrap analysis, with average internal node bootstrap support only 52%; results were comparable for NJ bootstrap.
The bootstrap support for the results of the phylogenetic analysis was based on 500 replicates.
Bootstrap support for the results of the NJ and MP analyses was based on 1,000 pseudoreplicate data sets generated from the original multiple nucleotide sequence alignment.
When focusing on specific types of diseases, represented by smaller numbers of OTUs for three categories (URI, GAS and HEM), bootstrap support impacted the results.
The tree topology of this node resembles that for the species phylogeny: Mesorhizobium, Rhizobium and Sinorhizobium cluster together with a high level of bootstrap support (100%); these results suggest that these DGCs of these species are probably derived from a single ancestral gene that subsequently underwent rearrangements, gene duplications and losses after species and strain differentiation.
Whereas single gene phylogenies that rely on EST sequences have limited bootstrap support as the result of limited sequence information, concatenated alignments result in phylogenetic trees with strong bootstrap support for already established relationships.
