Results of Shimodaira-Hasegawa test of alternative tree topologies for housekeeping and vacA genesa

TopologyLikelihood score for data set
Core genesvacA
Core gene tree9,773.96−14,725.85*
vacA tree−10,156.12*14,247.38
  • a Data set denotes the alignment of the concatenated core genes and the vacA gene. Topology denotes the maximum-likelihood trees shown in Fig. S3 in the supplemental material. The likelihood scores (−lnL) are shown in the table and are based on comparing each data set across its own ML tree topology and the alternative topology. The lowest (best) likelihood scores are indicated in boldface for each data set. Significance of the likelihood differences from the comparisons of a common data set across different topologies was measured using a bootstrap approach with RELL sampling and full optimization for 1,000 replicates. For example, the score from the comparison of the core genes data set against the core gene topology (−9773.96) is significantly better than the score from the alternative comparison of the core genes data set against the vacA gene topology (−10156.12). *, P < 0.001.