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Bootstrap values for the clusters of West Yunnan and Southeast China are 74% and 86%, respectively.
The bootstrap values for the studied sequences were plotted at the midpoint of each window.
Node bootstrap values for the tree constructed using cytb sequences were determined in PAUP* v4.0beta10 using both Maximum Likelihood (ML; 1000 "fast" stepwise-addition replicates) and Distance (1000 full heuristic replicates) algorithms.
Another explanation may be that fewer reads have been confidently classified as phylum Bacteroidetes in samples A and B; the average genus bootstrap values for the two most numerous phyla were found to be 93% for Bacteroidetes and 71% for Firmicutes.
Using the mouse TNF promoter sequence as the outgroup, we performed phylogenetic analyses and obtained very strong bootstrap values for the nodes of divergence of the genera using neighbor joining methods based on genetic distances (Kimura 2-parameter model) as well as maximum parsimony (Figure 3).
Bootstrap values for the nodes were determined by analyzing 500 replicates.
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The very low bootstrap values for this part of the supermatrix tree (results not shown) indicate a surprising lack of signal within and/or a high degree of conflict among the sequence data.
Both the ML and Bayesian trees (Fig. 3A) maintained the split between the SoxB1s and SoxB2s, which was confirmed by the branch supports calculated with the approximate likelihood ratio test and the SH-like test, although the bootstrap value for the ML tree was less than 50%.
Similarly, the bootstrap value for the cluster of Solan and Panipat populations was 56%%.
The ompA phylogeny has a low bootstrap value for the branching of Rickettsia sp. PoTiRb169.
Indeed, Hashiguchi and Nishida (2006) indicated that the supporting bootstrap value for the monophyly of subfamily 6 was just 51.
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