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Analysis of Acorus calamus Chloroplast Genome and Its Phylogenetic Implications

Citation

Goremykin, V and Holland, BR and Hirsch-Ernst, KI and Hellwig, FH, Analysis of Acorus calamus Chloroplast Genome and Its Phylogenetic Implications, Molecular Biology and Evolution, 22, (9) pp. 1813-1822. ISSN 0737-4038 (2005) [Refereed Article]


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The definitive publisher-authenticated version is available online at: www.oxfordjournals.org

DOI: doi:10.1093/molbev/msi173

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) grade is basal within angiosperms, studies of complete chloroplast genome sequences also suggested 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. We generated a concatenated alignment (89,436 positions for 15 taxa), encompassing 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 self-evident explanation for this failure appears to be a long-branch attraction (LBA) between the clade of grasses and the out-group. However, this LBA cannot explain the discrepancies observed between tree topology recovered using the maximum likelihood (ML) method and the topologies recovered using the parsimony and distance-based methods when grasses are deleted. Furthermore, the fact that neither maximum parsimony nor distance methods consistently recover the ML tree, when according to the simulations they would be expected to, when the out-group (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 ML 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.

Item Details

Item Type:Refereed Article
Keywords:Acorus calamus • chloroplast genomes • angiosperms • gymnosperms • molecular evolution • systematic phylogenetic error
Research Division:Biological Sciences
Research Group:Evolutionary Biology
Research Field:Phylogeny and Comparative Analysis
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Biological Sciences
Author:Holland, BR (Associate Professor Barbara Holland)
ID Code:62969
Year Published:2005
Web of Science® Times Cited:103
Deposited By:Mathematics
Deposited On:2010-03-31
Last Modified:2010-04-30
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