The phylogeny of three groups of arid Australian acacias – the Acacia victoriae, A. murrayana and A. pyrifolia groups – was constructed based on parsimony analysis of sequence data from the internal and external transcribed spacers (ITS and ETS) of the nuclear ribosomal DNA. Forty ingroup taxa were sequenced, including multiple accessions for some taxa and two species (A. platycarpa and A. longispinea) that had been identified in other analyses as relatives of these acacias. Acacia anthochaera was used as the functional outgroup.
The ITS and ETS regions proved to be sufficiently variable to resolve relationships at both the specific and intra-specific level. Two main clades were resolved. One clade confirmed the monophyly of the Acacia murrayana group, and relationships of species were strongly supported. All taxa in this clade have a similar pattern of seedling leaf development. In the second clade, the A. pyrifolia group is nested within the A. victoriae group and all taxa have spinose stipules. Acacia platycarpa and A. longispinea are related to this clade. Phyllode nerve number (uninerved or plurinerved) proved to be homoplasious.
Acacia victoriae is a widespread and very variable species. The molecular data identified two major groups: a group of populations occurring across northern Australia and a group of populations from the Western, Central and Eastern deserts. Further analysis of population variation is required to assess the taxonomic status of various forms in this species complex.
The geographic distributions of sister taxa suggest predominantly allopatric speciation. The degree of molecular divergence and position of the clades within subgenus Phyllodineae suggest that the lineages are not of recent origin, but have a history that relates to increased aridity in the Australian Eremean region during the Cenozoic.