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MBE Advance Access published online on June 1, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi173
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org
Accepted May 17, 2005

Research Article

Analysis of Acorus calamus Chloroplast Genome and its Phylogenetic Implications

Vadim V. Goremykin 1*, Barbara Holland 2, Karen I. Hirsch-Ernst 3, and Frank H. Hellwig 1

1 Institut für Spezielle Botanik, Universität Jena, Philosophenweg 16, D-07743 Jena, Germany
2 Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, New Zealand
3 Zentrum Pharmakologie und Toxikologie, Universität Göttingen, Robert-Koch-Str. 40, D-37075 Göttingen, Germany

* To whom correspondence should be addressed.
Vadim V. Goremykin, E-mail: Vadim.Goremykin{at}uni-jena.de


  Abstract

Determining the phylogenetic relationships among the major lines of angiosperms is a long standing problem, yet the uncertainty as to the phylogenetic affinity of these lines persists. While a number of studies have suggested that the ANITA (Amborella-Nymphaeales-Illiciales-Trimeniales-Aristolochiales) clade is basal within angiosperms, studies of complete chloroplast genome sequences also suggest an alternative tree, wherein the line leading to the grasses branches first among the angiosperms. To improve taxon sampling in the existing chloroplast genome data we sequenced the chloroplast genome of the monocot Acorus calamus. The concatenated alignment (89,436 positions for 15 taxa) encompasses almost all sequences usable for phylogeny reconstruction within spermatophytes. The data still contain support for both the ANITA-basal and grasses-basal hypotheses. Using simulations we can show that were the ANITA-basal hypothesis true, parsimony (and distance based methods with many models) would be expected to fail to recover it. The straightforward explanation for this failure appears to be a long branch attraction between the clade of grasses and the outgroup. However, this long branch attraction cannot explain the discrepancies observed between tree topology recovered by maximum likelihood method and the topologies recovered using parsimony and distance based methods when grasses are deleted. Furthermore, the fact that neither maximum parsimony nor distance methods consistently recover the maximum likelihood tree, when according to the simulations they would be expected to, when the outgroup (Pinus) is deleted, suggests that either the generating tree is not correct or the best symmetric model is misspecified (or both). We demonstrate that the tree recovered under maximum likelihood is extremely sensitive to model specification, and that the best symmetric model is misspecified. Hence, we remain agnostic regarding phylogenetic relationships among basal angiosperm lineages.

Keywords: Acorus calamus; chloroplast genomes; angiosperms; gymnosperms; molecular evolution; systematic phylogenetic error.
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