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The intra-generic relationships of the Australian genus Calotis, with various chromosome base numbers from x = 8 to x = 4, were examined by the comparison of nucleotide sequences of the complete ITS region of nuclear rDNA and of the matK gene of chloroplast DNA. Within a monophyletic Calotis, four lineages were identified. Reconstruction of ancestral states suggests that the chromosome base number for Calotis is x = 8. Dysploidal reductions in chromosome base number from x = 8 to x = 7 and from x = 8 to x = 5 or 4 have occurred independently at least three times. Lower base numbers of x = 7, 5, and 4 are found predominantly in the arid and semi-arid zone species of Central and Western Australia. Total karyotypic length (genome size) is greater in perennials than in annuals within the genus Calotis. The elaborated pappus and surface structures of cypsela, and life form of species seem to be homoplasous with multiple origins in the evolutionary history of the lineage.