Discussion of Phylogenetic Relationships
Although many aspects of core Caryophyllales have been thoroughly investigated during the past several decades (e.g., chemistry by Mabry and colleagues, pollen by Nowicke and colleagues, wood anatomy by Carlquist and colleagues), revised views on the phylogenetic relationships of Caryophyllales require renewed efforts to identify synapomorphies and to reconstruct patterns of morphological, chemical, and anatomical evolution. Furthermore, the poly- and paraphyly of several important families of core Caryophyllales demonstrate that additional phylogenetic studies with increased taxon sampling are needed to resolve relationships and develop a truly phylogenetic classification.
The most comprehensive phylogenetic study of Caryophyllales to date is that of Cuénoud et al. (2002), in which 127 taxa of Caryophyllales representing all 29 families were sampled for matK sequence analysis. A subset of this matrix was combined with sequences from rbcL, atpB, and 18S rDNA to provide a four-gene matrix for 26 genera of Caryophyllales. This combination of analyses strongly supported the monophyly of the expanded Caryophyllales sensu APG II. Within Caryophyllales are two large clades (core and noncore Caryophyllales, which Judd et al. 2002 referred to as Caryophyllales and Polygonales, respectively), with Rhabdodendron (of the monogeneric Rhabdodendraceae) and Simmondsia (of the monospecific Simmondsiaceae) unplaced.
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