A molecular systematic study of Scrophulariaceae sensu lato using DNA sequences of three plastid genes (rbcL, ndhF, and rps2) revealed at least five distinct monophyletic groups. Thirty‐nine genera representing 24 tribes of the Scrophulariaceae s.l. (sensu lato) were analyzed along with representatives of 15 other families of Lamiales. The Scrophulariaceae s.s. (sensu stricto) include part or all of tribes Aptosimeae, Hemimerideae, Leucophylleae, Manuleae, Selagineae, and Verbasceae (= Scrophularieae) and the conventional families Buddlejaceae and Myoporaceae. Veronicaceae includes all or part of tribes Angelonieae, Antirrhineae, Cheloneae, Digitaleae, and Gratioleae and the conventional families Callitrichaceae, Globulariaceae, Hippuridaceae, and Plantaginaceae. The Orobanchaceae include tribes Buchnereae, Rhinantheae, and the conventional Orobanchaceae. All sampled members of Orobanchaceae are parasitic, except Lindenbergia, which is sister to the rest of the family. Family Calceolariaceae Olmstead is newly erected herein to recognize the phylogenetic distinctiveness of tribe Calceolarieae. The Calceolariaceae are close to the base of the Lamiales. The Stilbaceae are expanded by the inclusion of Halleria. Mimulus does not belong in any of these five groups.

Microstructural changes in several very slowly evolving chloroplast introns and intergenic spacers were characterized across a broad range of angiosperms, including most of the major basal lineages. Insertion/deletion events (indels) in the surveyed noncoding regions of the large inverted repeat (IR) region were shown to be rarer than nucleotide substitutions and thus constitute one of the slowest and least homoplastic types of data available to plant systematists. In our study we scored 180 indels in noncoding regions, of which 36 were parsimony informative within the angiosperms. Because they are relatively few in number, their general utility is currently limited. However, they provide support for specific major taxa, including the angiosperms as a whole, the water lilies, and Illiciaceae and relatives. Support for the basalmost angiosperm split is largely inconclusive, but a single indel supported a basal placement of the water lilies, not Amborella. We estimate that roughly double or triple the current amount (ca. 2.2 kb) of noncoding IR DNA would be required to obtain indel support for most of the deepest branches at the base of the angiosperms. A variety of molecular processes appear to be responsible for the observed indels. Indels are more frequently associated with tandem repeat sequences than not. Insertions are significantly more frequently associated with tandem repeats than are deletions. The latter finding may be, in part, a function of an ascertainment bias for insertions versus deletions. Single‐base indels were the most common size class, but there was an unexplained deficit of some other small indel size classes. Coding indels can be problematical, particularly when they overlap among taxa in an alignment. We favor one simple scheme for coding overlapping indels but argue that no existing scheme for coding overlapping indels for phylogenetic analysis, or dealing with them in alignment, is ideal. Several small inversions were observed. These included the most homoplastic microstructural character in the current study. Each inversion was associated with short flanking inverted repeats.

We estimate phylogenetic relationships and the biogeographic and pollination history of Costus subgenus Costus (Costaceae) using sequence data from the internal and external transcribed spacer (ITS and ETS) regions of 18S–26S nuclear ribosomal DNA. The African members of the subgenus form a series of lineages basal to a monophyletic neotropical species radiation. The neotropical species have large, showy flowers visited by either euglossine bees or hummingbirds. The hummingbird pollination syndrome is supported as a derived character state from the bee pollination syndrome, and we estimate that it has evolved independently seven or more times in the neotropics. A molecular clock approach suggests that diversification of the neotropical clade has been recent and rapid and that it coincides with dramatic climatic and geologic changes, Andean orogeny, and the closing of the Panama isthmus that occurred in the Pliocene and Pleistocene epochs. We propose a scenario for the diversification of Costus, in which rapid floral adaptation in geographic isolation and range shifts in response to environmental changes contribute to reproductive isolation among close relatives. We suggest that these processes may be common in other recently diversified plant lineages centered in Central America or the Northern Andean phytogeographic region.

In many plant species, exposure to a prolonged period of cold during the winter promotes flowering in the spring, a process termed vernalization. In Arabidopsis thaliana, the vernalization requirement of winter-annual ecotypes is caused by the MADS-box gene FLOWERING LOCUS C (FLC), which is a repressor of flowering. During the vernalization process, FLC is downregulated by alteration of its chromatin structure, thereby permitting flowering to occur. In wheat, a vernalization requirement is imposed by a different repressor of flowering, suggesting that some components of the regulatory network controlling the vernalization response differ between monocots and dicots. The extent to which the molecular mechanisms underlying vernalization have been conserved during the diversification of the angiosperms is not well understood. Using phylogenetic analysis, we identified homologs of FLC in species representing the three major eudicot lineages. FLC homologs have not previously been documented outside the plant family Brassicaceae. We show that the sugar beet FLC homolog BvFL1 functions as a repressor of flowering in transgenic Arabidopsis and is downregulated in response to cold in sugar beet. Cold-induced downregulation of an FLC-like floral repressor may be a central feature of the vernalization response in at least half of eudicot species.