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MBE Advance Access published online on June 27, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg163
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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Accepted May 5, 2003
© 2003 Society for Molecular Biology and Evolution

Original Articles

Molecular Evolution of Insertions and Deletion in the Chloroplast Genome of Silene

Pär K. Ingvarsson 1*, Sarah Ribstein 1, and Douglas R. Taylor 1

1 Department of Biology, Gilmer Hall, University of Virginia, PO Box 400328, Charlottesville, VA 22904-4328, USA

* To whom correspondence should be addressed. E-mail: pelle{at}eg.umu.se.


  Abstract

Insertions, deletions and inversions in the chloroplast genome of higher plants have been shown to be extremely useful for resolving phylogenetic relationships between both closely related taxa and among more basal lineages. Introns and intergenic spacers from the chloroplast genome are now increasingly used for phylogenetic and population genetic studies of populations from a single species and it is therefore interesting to know whether indels can provide useful data and hence increase the power of intraspecific studies. Here we show that indels in three cpDNA intergenic spacers and one cpDNA intron for two species of Silene evolve at slightly higher rates than base pair substitutions. Repeat indels appear to have the highest rate of evolution and are thus more prone to homoplasy. We show that coded indel data have high information content for phylogenetic analysis and indels thus provide useful information to infer phylogenetic relationships at the intraspecific level.

Key Words: insertions, deletions, chloroplast, Silene


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