The inference of phylogenetic relationships among the main lineages of terrestrial plants, with emphasis on the positions of the major bryophyte groups, using small-subunit ribosomal RNA gene sequences

Small-subunit ribosomal RNA gene sequences were used to infer a molecular phylogeny of all major groups of land plants and contribute to the understanding of the evolutionary events underlying the transition from algal ancestors to land flora. Emphasis was placed on the phylogenetics of lower plants, with a special focus on bryophyte phylogeny. A well-constructed set of rDNA sequences from representative green plant taxa was accomplished through filling out gaps in the available data by sequencing rDNA in five additional taxa from a range of lower plants. Only sequences which are relatively error free and at least 93% complete were included. The alignment of the nuclear-encoded rRNA sequences was achieved using secondary structure information. The aligned sequences were subjected to both character and distance based methods of phylogenetic analysis. The results of this study suggest that 18S rDNA sequence data do not contain sufficient phylogenetic signal to resolve the relationship of the bryophytes amongst themselves or to other lower plants. A well constructed set of representative taxa from most major plant groups coupled with complete 18S rDNA sequence, the most appropriate alignment, and exhaustive phylogenetic analyses fail still to provide clusters with reasonable confidence as measured by bootstrap or decay analysis. Evidence for the lack of phylogenetic signal to resolve deep phylogenetic branches among lower plants is demonstrated by low confidence values in the phylogenetic trees regardless of the method employed. Further support for this contention is provided with analysis using random tree-length distribution and by phylogenetic analyses with different categories of sites classified according to substitution rate calculations. The graphical display of relative substitution rate variabilities using the lower plant 18S rRNA variability model displays the extent of conservation of the 18S rRNA gene sequence among the lower plants. (Abstract shortened by UMI.)...