ABSTRACT
Our understanding of angiosperm phylogeny has undergone a revolution over the last three decades, largely due to two spectacular advances in the science of systematic botany (Judd et al. 2007). With the advent of polymerase chain reaction (PCR) technology (Saiki et al. 1988), direct comparison of the nucleotide sequences of organismal DNA became possible. Second, phylogenetic analysis (cladistics) has become the standard methodology for testing hypotheses of phylogeny among organisms in systematic biology (Wiley 1981; Felsenstein 2004) based upon principles formally enumerated by Hennig (1966). The main principle of cladistics de‹nes any inclusive group of organisms (a clade), regardless of taxonomic rank, by the presence of one or more shared, derived character states (synapomorphies). Such a group is described as being monophyletic. To accept a taxonomic grouping based on shared primitive character states (symplesiomorphies) is not acceptable, and results in polyphyletic (taxonomic groups with multiple evolutionary origins) or paraphyletic groups (groups from which one or more members of common descent are excluded). Clades in a phylogenetic tree that share immediate common ancestry are often referred to as “sister” groups. A further principle of parsimony, still the most widely used approach in cladistics, states that the shortest possible phylogenetic tree (or cladogram), that is, the one that requires the least number of steps (character state changes), is the most accurate. One or more outgroups outside of the taxa of immediate interest (the ingroup) are included to polarize the character state changes (base substitutions in the instance of DNA sequences) at the outset of the cladistic analysis. Several con‹dence tests of a particular phylogenetic resolution are employed by systematists, the most widely used being the bootstrap* (Felsenstein 1985, 1988; Sanderson 1989; Hillis and Bull 1993). A high bootstrap value for a particular clade is a sign of robustness; a low value means that the clade is not well supported. Two other approaches used in phylogenetic reconstruction are maximum likelihood (Huelsenbeck and Crandall 1997) and Bayesian analysis (Beaumont 2010). The combination of phylogenetic analysis with DNA sequence data, or the ‹eld of molecular systematics, has in many
I. Introduction ............................................................................................................................. 17 II. Overview of Current Angiosperm Phylogeny ......................................................................... 18 III. Monocot Phylogeny ................................................................................................................. 19
A. New Phylogeny of the Lilioid Monocotyledons ............................................................... 19 1. Asparagales .................................................................................................................20 2. Liliales ......................................................................................................................... 33
B. Cannaceae, Costaceae, and Zingiberaceae ....................................................................... 39 C. Araceae .............................................................................................................................40
