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MBE Advance Access published online on October 20, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi019
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted October 4, 2004

Research Article

Molecular Evolution and Phylogenetic Utility of the petD Group II Intron: a Case Study in Basal Angiosperms

Cornelia Löhne 1* and Thomas Borsch 1

1 Nees Institute for Biodiversity of Plants, University of Bonn, Meckenheimer Allee 170, 53115 Bonn, Germany

* To whom correspondence should be addressed.
Cornelia Löhne, E-mail: c.loehne{at}uni-bonn.de


  Abstract

Sequences of spacers and group I introns in plant chloroplast genomes have recently been shown to be very effective in phylogenetic reconstruction at higher taxonomic levels and not only for inferring relationships among species. Group II introns, being more frequent in those genomes than group I introns, may be further promising markers. Because group II introns are structurally constrained, we assumed that sequences of a group II intron should be alignable across seed plants. We designed universal amplification primers for the petD intron and sequenced this intron in a representative selection of 47 angiosperms and gymnosperms. Our sampling of taxa is the most representative of major seed plant lineages to date for group II introns. Through differential analysis of structural partitions we studied patterns of molecular evolution and their contribution to phylogenetic signal. Non-pairing stretches (loops, bulges, interhelical nucleotides) were considerably more variable in both substitutions and indels than helical elements. Differences among the domains are basically a function of their structural composition. After the exclusion of two mutational hotspots accounting for <18 % of sequence length, which are located in loops of domains I and IV, all sequences could be aligned unambiguously across seed plants. Microstructural changes predominantly occurred in loop regions and are mostly simple sequence repeats. An indel matrix comprising 241 characters revealed microstructural changes to be of lower homoplasy than substitutions. In showing Amborella first branching and providing support for a magnoliid clade through a synapomorphic indel, the petD dataset proved effective in testing between alternative hypotheses on the basal nodes of the angiosperm tree. Within angiosperms, group II introns offer phylogenetic signal that is intermediate in information content between that of spacers and group I introns on the one hand, and coding sequences on the other.

Keywords: chloroplast noncoding DNA; group II intron; petD; phylogeny; microstructural changes; basal angiosperms.
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