A PHYLOGENETIC STRUCTURE FOR THE MONOCOTYLEDONS, AS INFERRED FROM CHLOROPLAST DNA RESTRICTION SITE VARIATION, AND A COMPARISON OF MEASURES OF CLADE SUPPORT

Phylogenetic relationships within the monocots were analyzed by cladis tic analysis of restriction site and length variation in the inverted repeat region of the chloroplast genomes of 52 taxa. Nine equally most parsimonious trees were identified and 38 clades were resolved by the strict consensus tree. A clade consisting of Acorus and Gymnostachys (traditionally included in Araceae) was resolved as the sister group o f all other monocots. Among the remaining monocots a dichotomy was res olved between a clade that includes Alismatanae and Aranae (i.e., Arac eae sens. strict.), and another that includes all remaining monocots. Within the latter group, Lilianae, including Pandananae, Cyclanthanae, and Velloziales, constitute a paraphyletic group, within which is nes ted a clade in which Arecanae are resolved as the sister group of a Br omelianae-Commelinanae-Zingiberanae complex. Bootstrap analysis, Breme r support (i.e., ''decay'') analysis, and successive character removal were conducted to generate three measures of clade stability. Despite overall concordance between the three measures, several clades had re latively strong support as assessed by one method and weak support as assessed by another. Three procedures were employed for Bremer support analysis, including the ''subparsimonious search procedure'' that is employed most frequently. Each of the other two procedures involves a series of subanalyses, each targeting a single clade resolved in all e qually most parsimonious trees. The ''clade deresolution procedure'' e stimates Bremer Support for a target clade by determining lengths of c ladograms that differ from equally most parsimonious cladograms only b y the lack of resolution of that clade. The ''constrained inconsistenc y search procedure'' estimates Bremer Support for a target clade by a series of constrained cladistic analyses, each with monophyly forced f or a clade that is inconsistent with the target clade. The subparsimon ious search procedure was the most successful of the three by one meas ure, the number of clades for which it provided the most accurate (i.e ., lowest) estimate of Bremer support. However, for some clades for wh ich this procedure did not produce the most accurate estimate, its est imates were several steps higher than those of the other two methods.