Plant molecular systematics has been transformed during the past 15 years through the combined application of molecular techniques and phylogenetic methodology. During this brief window in time, molecular data have become increasingly sophisticated and increasingly easy to obtain. The ease with which molecular data are currently generated provides both opportunities and challenges for molecular systematics. These include (1) choices of DNA regions for analysis, including the development of nuclear genes appropriate for phylogeny reconstruction at a number of hierarchical levels and whole-genome comparisons, particularly of the chloroplast genome; (2) data handling, including the development and refinement of phylogenetic methodologies for analysis of many samples and methods for storage and retrieval of both data sets and trees; (3) integration of molecular and other types of data; (4) use of molecular-based phylogenetic trees for analyses of morphological, biochemical, and molecular characters; and (5) extension of phylogenetic/historical methodologies not only for analysis of population dynamics but also for analysis of gene histories, both across taxa and within gene families.

Key words: analysis, character evolution, DNA, genomes, phylogeny