Comparative Utility of Chloroplast DNA Restriction Site and DNA Sequence Data for Phylogenetic Studies in Plants

Abstract

Restriction enzyme comparisons of plant genomes have been used widely to address systematic and evolutionary questions during the past 15 years. Most studies have examined variation in chloroplast DNA (cpDNA) or nuclear ribosomal DNA (rDNA) to estimate phylogenetic relationships among species, genera, and in a few cases families of plants (e.g., Jorgensen and Cluster, 1988; Palmer et al., 1988; Olmstead and Palmer, 1994). The restriction site approach also has been used to examine intraspecific variation and genetic diversity among populations (e.g., Neale et al., 1986; Soltis et al., 1989, 1991a, 1997; Whittemore and Schaal, 1991; Fenster and Ritland, 1992; Kim et al., 1992a; Hong et al., 1993; Petit et al., 1993; Byrne and Moran, 1994; Dong and Wagner, 1994; McCauley, 1994; Mason-Gamer et al., 1995; Bain and Jansen, 1996). Restriction site and DNA sequence data have three characteristics that make them especially useful for phylogenetic analyses (Holsinger and Jansen, 1993). First, discrete character states can be scored unambiguously. Second, a large number of characters potentially can be obtained for each taxon. Third, both types of data provide valuable information on the extent and nature of divergence between sequences. None of these features are present in earlier DNA methods, such as DNA—DNA hybridization.