plosone-phylo
pone.0018441.g003.png
Comparison of strain clustering based on mCGH and MLST.
A) Neighbor-net representation of gene distances based on the distribution of genes from the accessory genome. Strain names as well as the defining splits having a bootstrap support of greater than 85% are printed in the same colors as in Figure 2. Clustering based on gene content distance and maximum parsimony results in the same eight genome groups. Serogroup B and C strains as well as the two cnl strains are separated from the other four serogroups based on gene content, and the cycles within the serogroup B/C subgraph indicate a high rate of gene transfer among these strains. Strains from the same CC always reside on common splits. B) Neighbor-net representation based on the concatenated alignments of the seven housekeeping gene fragments form the meningococcal core genome used for MLST comprising 383 parsimony informative sites. A MLSA-based clustering of strains results in the separation of strains from the same serogroup or belonging to the same GGs. The large number of cycles in the graph indicates a high rate of homologous recombination among the genes used for MLST and that a MLSA-based reconstruction of the deep phylogeny of these strains is not possible.
pone.0018441.g003.png
Comparison of strain clustering based on mCGH and MLST.
A) Neighbor-net representation of gene distances based on the distribution of genes from the accessory genome. Strain names as well as the defining splits having a bootstrap support of greater than 85% are printed in the same colors as in Figure 2. Clustering based on gene content distance and maximum parsimony results in the same eight genome groups. Serogroup B and C strains as well as the two cnl strains are separated from the other four serogroups based on gene content, and the cycles within the serogroup B/C subgraph indicate a high rate of gene transfer among these strains. Strains from the same CC always reside on common splits. B) Neighbor-net representation based on the concatenated alignments of the seven housekeeping gene fragments form the meningococcal core genome used for MLST comprising 383 parsimony informative sites. A MLSA-based clustering of strains results in the separation of strains from the same serogroup or belonging to the same GGs. The large number of cycles in the graph indicates a high rate of homologous recombination among the genes used for MLST and that a MLSA-based reconstruction of the deep phylogeny of these strains is not possible.