A CHLOROPLAST DNA PHYLOGENY OF THE CARYOPHYLLALES BASED ON STRUCTURAL AND INVERTED REPEAT RESTRICTION SITE VARIATION

Phylogenetic relationships among 25 representatives of the Caryophyllales and three outgroup taxa from Polygonaceae and Plumbaginaceae were assessed using structural variation in the chloroplast genome and restriction site variation in the highly conserved inverted repeat region of the chloroplast genome. In addition to the previously reported loss of the chloroplast rpl2 intron in the common ancestor of the Caryophyllales, observed structural mutations include: 1) the loss of the rpl16 intron in the chloroplast genome of Limonium (Plumbaginaceae); 2) three large, phylogenetically informative deletions within the gene ORF2280, and 3) parallel, 6-kb inversions in the large single-copy region of the chloroplast genomes in Pereskia (Cactaceae) and in Atriplex and Chenopodium (Chenopodiaceae). Sixty-two of the 161 restriction sites scored were phylogenetically informative. Parsimony analyses of the structural and restriction site characters indicate that: 1) the Caryophyllales consist of two major clades, one comprising Amaranthaceae and Chenopodiaceae, and the other all remaining families; 2) two families, Phytolaccaceae and Portulacaceae (Portulaca and Claytonia), are polyphyletic, with elements of the former (Phytolacca and Rivina) strongly linked with Nyctaginaceae; 3) Pereskia (the only examined representative of Cactaceae) is, surprisingly, strongly linked to Portulaca, and 4) Caryophyllaceae and Molluginaceae, the only anthocyanin-producing taxa in the order, occur in the same portion of the trees and are not basal to the group. Relationships among several families are poorly resolved.