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MBE Advance Access originally published online on October 20, 2004
Molecular Biology and Evolution 2005 22(2):317-332; doi:10.1093/molbev/msi019
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Molecular Biology and Evolution vol. 22 no. 2 © Society for Molecular Biology and Evolution 2005; all rights reserved.

Research Article

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

Cornelia Löhne and Thomas Borsch

Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany

E-mail: c.loehne{at}uni-bonn.de.

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 three 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. Nonpairing stretches (loops, bulges, and interhelical nucleotides) were considerably more variable in both substitutions and indels than in helical elements. Differences among the domains are basically a function of their structural composition. After the exclusion of four mutational hotspots accounting for less than 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 are substitutions. In showing Amborella first branching and providing support for a magnoliid clade through a synapomorphic indel, the petD data set 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.

Key Words: chloroplast noncoding DNA • group II intron • petD • phylogeny • microstructural changes • basal angiosperms


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