Molecular Biology and Evolution, Vol 16, 1774-1784, Copyright © 1999 by Society for Molecular Biology and Evolution
PS Soltis, DE Soltis, PG Wolf, DL Nickrent, SM Chaw and RL Chapman
Previous studies of the phylogeny of land plants based on analysis of 18S
ribosomal DNA (rDNA) sequences have generally found weak support for the
relationships recovered and at least some obviously spurious relationships,
resulting in equivocal inferences of land plant phylogeny. We hypothesized
that greater sampling of both characters and taxa would improve inferences
of land plant phylogeny based on 18S rDNA sequences. We therefore conducted
a phylogenetic analysis of complete (or nearly complete) 18S rDNA sequences
for 93 species of land plants and 7 green algal relatives. Parsimony
analyses with equal weighting of characters and characters state changes
and parsimony analyses weighting (1) stem bases half as much as loop bases
and (2) transitions half as much as transversions did not produce
substantially different topologies. Although the general structure of the
shortest trees is consistent with most hypotheses of land plant phylogeny,
several relationships, particularly among major groups of land plants,
appear spurious. Increased character and taxon sampling did not
substantially improve the performance of 18S rDNA in phylogenetic analyses
of land plants, nor did analyses designed to accommodate variation in
evolutionary rates among sites. The rate and pattern of 18S rDNA evolution
across land plants may limit the usefulness of this gene for phylogeny
reconstruction at deep levels of plant phylogeny. We conclude that the
mosaic structure of 18S rDNA, consisting of highly conserved and highly
variable regions, may contain historical signal at two levels. Rapidly
evolving regions are informative for relatively recent divergences (e.g.,
within angiosperms, seed plants, and ferns), but homoplasy at these sites
makes it difficult to resolve relationships among these groups. At deeper
levels, changes in the highly conserved regions of small-subunit rDNAs
provide signal across all of life. Because constraints imposed by the
secondary structure of the rRNA may affect the phylogenetic information
content of 18S rDNA, we suggest that 18S rDNA sequences be combined with
other data and that methods of analysis be employed to accommodate these
differences in evolutionary patterns, particularly across deep divergences
in the tree of life.
ORIGINAL ARTICLE
The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal?
Department of Botany, Washington State University, Pullman 99164-4238, USA. psoltis@wsu.edu
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