128 representative Neisseria meningitidis genomes from the 20th and 21st Century. The relationships between meningococcal isolates are represented by two datasets in which (a.) 1605 core meningococcal loci (cgMLST) or (b.) 53 ribosomal protein genes (rMLST), a subset of the 1605 core loci, are used. In both trees major phylogenetic groups are noted A-D. For cross-compatible identification, and where there are 2 or more strains per lineage are present, the major MLST derived clonal complexes (cc) are identified by colour: red – ST-1 cc, purple – ST-5 cc, pink – ST-4 cc, teal – ST-37 cc, yellow – ST-11 cc, orange – ST-8 cc, green – ST-41/44 cc, blue – ST-32 cc, grey – ST-269 cc, olive – ST-18 cc. Capsular types other than A, B, or C are noted in parentheses, accept for Lineage 11 which are labelled (cps B and cps C). Unlabelled nodes are undefined lineages and currently do not have a clonal complex association; a full list of lineage and associated clonal complex nomenclature can be found in Table 4.