Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

Table 4 Shimodaira-Hasegawa test results.

P. krempfiitopologies	P. albicaulis, P. lambertianaN, P. parvifloratopologies	P-value
Figure 2 vs. 3A	2 vs. 3A	0.011*
Figure 2 vs. 2	2 vs. 3A	0.153
Figure 2 vs. 3A	2 vs. 2	0.024*
Figure 2 vs. 3B	2 vs. 3B	0.351
Figure 2 vs. 3A	2 vs. 3B	0.063
Figure 2 vs. 3A	2 vs. 2	0.063
Figure 2 vs. 3C	2 vs. 3C	0.005*
Figure 2 vs. 2	2 vs. 3C	0.050
Figure 2 vs. 3C	2 vs. 2	0.024*

Results of significance testing for topology comparisons of the full alignment (Figure 2) versus the three other largest data partitions (Figure 3). For each set of comparisons, the first row represents comparison of unmodified maximum likelihood topologies. In the second and third rows the positions of P. krempfii and P. albicaulis - P. lambertiana N - P. parviflora were modified as indicated. Topologies that differ within a comparison are indicated in bold. Significant topological differences at P < 0.05 are indicated with an asterisk.

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