A COMPARISON OF ANGIOSPERM PHYLOGENIES FROM NUCLEAR 18S RDNA AND RBCL SEQUENCES

To investigate the phylogenetic utility of entire, nuclear-encoded small subunit (18S) ribosomal DNA sequences, we compared the rate of evolution and phylogenetic resolution of entire 18S sequences with those for the chloroplast gene rbcL using a suite of 59 angiosperms and 3 gymnosperms (Gnetum, Ephedra, and Zamia) as outgroups. For rbcL, 482 (33.6%) of the 1431 base positions were phylogenetically informative, whereas for 18S rDNA 341 (18.4%) of the 1853 positions were informative. Pairwise comparisons within the angiosperms show that rbcL is generally about three times more variable than 18S rDNA. However, because the 18S region is approximately 400 base pairs longer than rbcL, the ratio of the number of phylogenetically informative sites per molecule is only about 1.4 times greater for rbcL compared to 18S rDNA. Not only are sites more variable in rbcL than in 18S rDNA, but this variability is more evenly distributed over the length of rbcL. In contrast, 18S rDNA shows highly variable regions interspersed with regions of extreme conservation. Minimum-length Fitch trees were constructed for each matrix, and the results were compared to a tree derived from a previous global analysis of rbcL sequences based on 499 seed plants. Parsimony analyses showed that several clades are strongly supported by both data sets, such as Gnetales, monocots, paleoherbs, Santalales, and various clades within Rosidae s.l. and Asteridae s.l. Some clades (e.g., Santalales) have higher base substitution rates for 18S rDNA, permitting the assessment of inter- and intrafamilial relationships. This comparative study indicates that 18S rDNA sequences contain sufficient information to conduct phylogenetic studies at higher taxonomic levels (family and above) within angiosperms, rDNA sequences are best applied to such deep divergences, but the amount of variation differs significantly among taxonomic groups.