Fig. 5

Neighbour-joining analysis of the tfs3 variable gene subset. The phylogenetic tree was calculated from concatenated sequence of four tfs3 variable subset genes comprising in order, t3_V24, t3_C3, t3_C2 and t3_V25 from 76 genomes. All positions in the initial sequence alignment containing gaps and missing data were eliminated prior to analysis. The four-digit number codes correspond to different alleles of each gene determined from previous phylogenetic analysis of individual genes (Additional file 3: Figure S5c, d). Two principal clades correspond to sequences from strains of hpAfrica1/hpEurope (clade 1) and hpEAsia (clade 2) lineages. The two remaining clades demonstrate characteristic high divergence of hspAmerind sequences but notably also include sequences from other H. pylori phylogeographic groups. A diversity of other unclustered allelic profiles arising from the inter-population exchange of variable subset tfs3 genes or gene fragments are also apparent. Coloured circles representing gene sequences are coloured according to phylogeographic lineage of the originating strain as indicated. u; unassigned (phylogeny could not be determined due to substantially admixed sequence). Uncoloured circles indicate sequences from strains which could not be definitively assigned to a particular phylogeographic population