ABSTRACT
Although reticulate evolution has been a frequent occurrence during the history of plants, determining how it has contributed to plant evolution will require analyzing many nuclear loci and developing effective analytical methods. The objective of this study was to make progress toward meeting these requirements in the evolutionarily complex subtribe Machaerantherinae. The 5S ribosomal RNA (rRNA) spacer was investigated to characterize its structure and variation. Analysis of the spacer supported relationships that were mostly the same as those supported by ITS and ETS sequence data. Two methods were used to estimate support for 11 occurrences of incongruence between 5S/ITS/ETS and cpDNA data sets. The five best-supported incongruences were proposed to have had reticulate evolutionary histories. For Arida blepharophylla, Xanthisma rhizomatum, and Pyrrocoma, 5S and ITS/ETS evidence supported the same or similar relationships, indicating that these two regions of the nuclear genome were descended from the same ancestor or from two closely related ancestors, with cpDNA coming from a more distantly related ancestor. The 5S and ITS/ETS evidence disagreed on the relationships of Arida riparia, suggesting that its ITS/ETS region came from one ancestor and its 5S region and cpDNA from a different ancestor.