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MBE Advance Access published online on June 8, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi191
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Published by Oxford University Press 2005.
Accepted May 27, 2005

Research Article

Identifying the Basal Angiosperm Node in Chloroplast Genome Phylogenies: Sampling One's Way Out of the Felsenstein Zone

Jim Leebens-Mack 1*, Linda A. Raubeson 2, Liying Cui 1, Jennifer V. Kuehl 3, Matthew H. Fourcade 3, Timothy W. Chumley 4, Jeffrey L. Boore 5, Robert K. Jansen 4, and Claude W. dePamphilis 1

1 Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA 16802
2 Department of Biological Sciences, Central Washington University, Ellensburg, WA 98926
3 DOE Joint Genome Institute, Walnut Creek, CA 94598
4 Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin TX 78712
5 DOE Joint Genome Institute, Walnut Creek, CA 94598; Department of Integrative Biology, University of California, Berkeley CA 94720

* To whom correspondence should be addressed.
Jim Leebens-Mack, E-mail: jleebensmack{at}psu.edu


  Abstract

While there has been strong support for Amborella and Nymphaeales (water lilies) as branching from basal-most nodes in the angiosperm phylogeny, this hypothesis has recently been challenged by phylogenetic analyses of 61 protein-coding genes extracted from the chloroplast genome sequences of Amborella, Nymphaea and 12 other available land plant chloroplast genomes. These character-rich analyses placed the monocots, represented by three grasses (Poaceae), as sister to all other extant angiosperm lineages. We have extracted protein-coding regions from draft sequences for six additional chloroplast genomes to test whether this surprising result could be an artifact of long-branch attraction due to limited taxon sampling. The added taxa include three monocots (Acorus, Yucca and Typha), a water lily (Nuphar), a ranunculid (Ranunculus), and a gymnosperm (Ginkgo). Phylogenetic analyses of the expanded DNA and protein datasets together with microstructural characters (indels) provided unambiguous support for Amborella and the Nymphaeales as branching from the basal-most nodes in the angiosperm phylogeny. However, their relative positions proved to be dependent on method of analysis, with parsimony favoring Amborella as sister to all other angiosperms, and maximum likelihood and neighborjoining methods favoring an Amborella + Nympheales clade as sister. The maximum likelihood phylogeny supported the later hypothesis, but the likelihood for the former hypothesis was not significantly different. Parametric bootstrap analysis, single gene phylogenies, estimated divergence dates and conflicting indel characters all help to illuminate the nature of the conflict in resolution of the most basal nodes in the angiosperm phylogeny. Molecular dating analyses provided median age estimates of 161 mya for the most recent common ancestor of all extant angiosperms and 145 mya for the most recent common ancestor of monocots, magnoliids and eudicots. Whereas long sequences reduce variance in branch lengths and molecular dating estimates, the impact of improved taxon sampling on the rooting of the angiosperm phylogeny together with the results of parametric bootstrap analyses demonstrate how long-branch attraction can mislead genome-scale phylogenetic analyses.

Keywords: Angiosperm phylogeny; phylogenomics; parametric bootstrap.
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