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(American Journal of Botany. 2008;95:626-641.) doi: 10.3732/ajb.2007308 © 2008 Botanical Society of America, Inc.

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Phylogeny of marattioid ferns (Marattiaceae): inferring a root in the absence of a closely related outgroup¹

Department of Integrative Biology, University of California, Berkeley, 1001 Valley Life Sciences Bldg., California 94720-2465 USA

ABSTRACT

Closely related outgroups are optimal for rooting phylogenetic trees; however, such ideal outgroups are not always available. A phylogeny of the marattioid ferns (Marattiaceae), an ancient lineage with no close relatives, was reconstructed using nucleotide sequences of multiple chloroplast regions (rps4 + rps4–trnS spacer, trnS–trnG spacer + trnG intron, rbcL, atpB), from 88 collections, selected to cover the broadest possible range of morphologies and geographic distributions within the extant taxa. Because marattioid ferns are phylogenetically isolated from other lineages, and internal branches are relatively short, rooting was problematic. Root placement was strongly affected by long-branch attraction under maximum parsimony and by model choice under maximum likelihood. A multifaceted approach to rooting was employed to isolate the sources of bias and produce a consensus root position. In a statistical comparison of all possible root positions with three different outgroups, most root positions were not significantly less optimal than the maximum likelihood root position, including the consensus root position. This phylogeny has several important taxonomic implications for marattioid ferns: Marattia in the broad sense is paraphyletic; the Hawaiian endemic Marattia douglasii is most closely related to tropical American taxa; and Angiopteris is monophyletic only if Archangiopteris and Macroglossum are included.

Key Words: Angiopteris • Christensenia • Danaea • long-branch attraction • Marattia • Marattiaceae • rooting

Received for publication 1 January 2007. Accepted for publication 14 February 2008.

FOOTNOTES

¹ The author thanks B. Mishler, A. Smith, K. Will, T. Carlson, and others for manuscript comments and plant material: M. Frantz, J. Strother, S. Lin, M. Lehnert, J. Game, the Mishler and Baldwin laboratories, D. Kelch, K. Pryer, E. Schuettpelz, H. Schneider, J. Metzgar, M. Windham, N. Nagalingum, P. Korall, A. Grusz, G. Theseira, Forest Research Institute Malaysia, D. Palmer, P. Bily and the Nature Conservancy (Maui), M. Christenhusz, D. Lorence and N.T.B.G., S. Stroud and the Ascension Island Conservation Centre, M. A. H. Mohamed and University of Malaya, R.B.G. Kew, R.B.G. Edinburgh, D. Walker, B. Weigle, R. Whitehead, K. Roux and S.A.N.B.I., Xishuangbana Botanic Garden, University of California Botanical Garden, T. Ranker, S. Graham, H. Rai, T. Motley, and D. Barrington. This research was a portion of the author’s doctoral dissertation research, which was supported by NSF Doctoral Dissertation Improvement Grant (DEB-0608497), NSF ATOL Grant (DEB-0228729), University of California Pacific Rim Foundation, Polynesia Education and Research Laboratories Research Fellowship, and the University of California, Berkeley Department of Integrative Biology Summer Research and Hansen Travel Grants.

² E-mail: murdock{at}berkeley.edu

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