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MBE Advance Access originally published online on July 7, 2004
Molecular Biology and Evolution 2004 21(10):1813-1819; doi:10.1093/molbev/msh203
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Molecular Biology and Evolution vol. 21 no. 10 © Society for Molecular Biology and Evolution 2004; all rights reserved.

Research Article

Chloroplast Phylogeny Indicates that Bryophytes Are Monophyletic

Tomoaki Nishiyama*, Paul G. Wolf{dagger}, Masanori Kugita1,{ddagger}, Robert B. Sinclair1,§, Mamoru Sugita1,||, Chika Sugiura1,||, Tatsuya Wakasugi,1, Kyoji Yamada,1, Koichi Yoshinaga{ddagger},1, Kazuo Yamaguchi#, Kunihiko Ueda** and Mitsuyasu Hasebe*,{dagger}{dagger}

* National Institute for Basic Biology, Okazaki, Japan; {dagger} Department of Biology, Utah State University; {ddagger} Faculty of Science, Shizuoka University, Shizuoka, Japan; § The Jackson Laboratory, Bar Harbour, Maine; || Center for Gene Research, Nagoya University, Nagoya, Japan; Department of Biology, Faculty of Science, Toyama University, Toyama, Japan; # Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa, Japan; ** Division of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan; and {dagger}{dagger} Department of Molecular Biomechanics, Sokendai, Okazaki, Japan

E-mail: mhasebe{at}nibb.ac.jp.

Opinions on the basal relationship of land plants vary considerably and no phylogenetic tree with significant statistical support has been obtained. Here, we report phylogenetic analyses using 51 genes from the entire chloroplast genome sequences of 20 representative green plant species. The analyses, using translated amino acid sequences, indicated that extant bryophytes (mosses, liverworts, and hornworts) form a monophyletic group with high statistical confidence and that extant bryophytes are likely sisters to extant vascular plants, although the support for monophyletic vascular plants was not strong. Analyses at the nucleotide level could not resolve the basal relationship with statistical confidence. Bryophyte monophyly inferred using amino acid sequences has a good statistical foundation and is not rejected statistically by other data sets. We propose bryophyte monophyly as the currently best hypothesis.

Key Words: land plants • bryophytes • codon usage • nucleotide composition • LogDet


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