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To resolve the relationships of taxa within the Beaufortia suballiance (Myrtaceae), 72 ingroup taxa were analysed by parsimony methods and nrDNA sequence data from the 5S and ITS-1 ribosomal DNA spacer regions.

Although basal nodes in the consensus tree (combined data set) are not supported by bootstrap or jackknife values, a number of clades are well supported, showing that Melaleuca is polyphyletic. Monophyletic groups include: endemic species of Melaleuca from New Caledonia (including species of Callistemon recently transferred to Melaleuca); the tropical Melaleuca leucadendra group; Australian species of Callistemon, which relate to species of Melaleuca predominantly from the South-East; and a group of south-western and eastern Australian melaleucas that relate to a clade of three south-western genera, Eremaea, Conothamnus and Phymatocarpus. Calothamnus, Regelia and Beaufortia may also relate to this latter group. Lamarchea is possibly related to northern melaleucas. The results have implications for generic revisions of the large genus Melaleuca.

Biogeographic subtree analysis, based only on supported nodes of the taxon cladogram, showed New Caledonia, New Guinea, Eastern Queensland and the Northern Desert unresolved at the base of the area cladogram. The position of some of these areas is likely to be artifactual, but New Caledonia is interpreted as in the correct position. At a higher node, the monsoonal northern areas of Australia (Kimberley, Arnhem and Cape York), Atherton, the Pilbara and Western Desert relate to the southern regions, which form a group. The South-West of Australia is related to Eyre and Adelaide (designated area ’south’) and Tasmania is related to the South-East and MacPherson-Macleay. The vicariance between northern and southern regions in Australia possibly relates to an early major climatic change (from the Early Tertiary). The biogeographic analysis helped illuminate taxon relationships.