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Research Article

Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny

Todd J. Barkman, Gordon Chenery, Joel R. McNeal, James Lyons-Weiler, Wayne J. Ellisens, Gerry Moore, Andrea D. Wolfe, and Claude W. dePamphilis
PNAS November 21, 2000 97 (24) 13166-13171; https://doi.org/10.1073/pnas.220427497
Todd J. Barkman
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Gordon Chenery
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Joel R. McNeal
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James Lyons-Weiler
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Wayne J. Ellisens
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Gerry Moore
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Andrea D. Wolfe
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Claude W. dePamphilis
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  1. Communicated by Masatoshi Nei, Pennsylvania State University, University Park, PA (received for review June 9, 2000)

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Abstract

Plant phylogenetic estimates are most likely to be reliable when congruent evidence is obtained independently from the mitochondrial, plastid, and nuclear genomes with all methods of analysis. Here, results are presented from separate and combined genomic analyses of new and previously published data, including six and nine genes (8,911 bp and 12,010 bp, respectively) for different subsets of taxa that suggest Amborella + Nymphaeales (water lilies) are the first-branching angiosperm lineage. Before and after tree-independent noise reduction, most individual genomic compartments and methods of analysis estimated the Amborella + Nymphaeales basal topology with high support. Previous phylogenetic estimates placing Amborella alone as the first extant angiosperm branch may have been misled because of a series of specific problems with paralogy, suboptimal outgroups, long-branch taxa, and method dependence. Ancestral character state reconstructions differ between the two topologies and affect inferences about the features of early angiosperms.

Footnotes

    • ↵‡ Present address: Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008.

    • ↵§ To whom reprint requests may be addressed. E-mail: cwd3{at}psu.edu or todd.barkman{at}wmich.edu.

    • See commentary on page 12939.

    • Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. AY009406–AY009456).

    • Article published online before print: Proc. Natl. Acad. Sci. USA, 10.1073/pnas.220427497.

    • Article and publication date are at www.pnas.org/cgi/doi/10.1073/pnas.220427497

  • Abbreviations

    pt,
    plastid;
    mt,
    mitochondrial;
    nuc,
    nuclear;
    BP,
    bootstrap proportion;
    NJ,
    neighbor joining;
    ML,
    maximum likelihood;
    RASA,
    Relative Apparent Synapomorphy Analysis;
    tRASA,
    test statistic for phylogenetic signal;
    UW,
    unweighted parsimony;
    T,
    transversion parsimony;
    NJ-P,
    neighbor joining with p distance;
    HKY,
    Hasegawa–Kishino–Yano;
    GTR,
    general-time-reversible
    • Received June 9, 2000.
    • Accepted September 6, 2000.
    • Copyright © 2000, The National Academy of Sciences
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    Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny
    Todd J. Barkman, Gordon Chenery, Joel R. McNeal, James Lyons-Weiler, Wayne J. Ellisens, Gerry Moore, Andrea D. Wolfe, Claude W. dePamphilis
    Proceedings of the National Academy of Sciences Nov 2000, 97 (24) 13166-13171; DOI: 10.1073/pnas.220427497

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    Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny
    Todd J. Barkman, Gordon Chenery, Joel R. McNeal, James Lyons-Weiler, Wayne J. Ellisens, Gerry Moore, Andrea D. Wolfe, Claude W. dePamphilis
    Proceedings of the National Academy of Sciences Nov 2000, 97 (24) 13166-13171; DOI: 10.1073/pnas.220427497
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