HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Submit a response Alert me when this article is cited Alert me when eLetters are posted Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in ISI Web of Science Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via ISI Web of Science (63) Citing Articles via Google Scholar Google Scholar Articles by Burleigh, J. G. Articles by Mathews, S. Search for Related Content PubMed Articles by Burleigh, J. G. Articles by Mathews, S. Agricola Articles by Burleigh, J. G. Articles by Mathews, S.

Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life¹

²Section of Evolution and Ecology, University of California, Davis, California 95616 USA; ³Arnold Arboretum of Harvard University, Cambridge, Massachusetts 02138 USA

Effects of taxonomic sampling and conflicting signal on the inference of seed plant trees supported in previous molecular analyses were explored using 13 single-locus data sets. Changing the number of taxa in single-locus analyses had limited effects on log likelihood differences between the gnepine (Gnetales plus Pinaceae) and gnetifer (Gnetales plus conifers) trees. Distinguishing among these trees also was little affected by the use of different substitution parameters. The 13-locus combined data set was partitioned into nine classes based on substitution rates. Sites evolving at intermediate rates had the best likelihood and parsimony scores on gnepine trees, and those evolving at the fastest rates had the best parsimony scores on Gnetales-sister trees (Gnetales plus other seed plants). When the fastest evolving sites were excluded from parsimony analyses, well-supported gnepine trees were inferred from the combined data and from each genomic partition. When all sites were included, Gnetales-sister trees were inferred from the combined data, whereas a different tree was inferred from each genomic partition. Maximum likelihood trees from the combined data and from each genomic partition were well-supported gnepine trees. A preliminary stratigraphic test highlights the poor fit of Gnetales-sister trees to the fossil data.

Key Words: Gnetales • multilocus analyses • phylogenetic signal • rate class • seed plant phylogeny • taxonomic sampling

This article has been cited by other articles:

				A. G. Murdock Phylogeny of marattioid ferns (Marattiaceae): inferring a root in the absence of a closely related outgroup Am. J. Botany, May 1, 2008; 95(5): 626 - 641. [Abstract] [Full Text] [PDF]

				C.-S. Wu, Y.-N. Wang, S.-M. Liu, and S.-M. Chaw Chloroplast Genome (cpDNA) of Cycas taitungensis and 56 cp Protein-Coding Genes of Gnetum parvifolium: Insights into cpDNA Evolution and Phylogeny of Extant Seed Plants Mol. Biol. Evol., June 1, 2007; 24(6): 1366 - 1379. [Abstract] [Full Text] [PDF]

				J. S. Sperry, U. G. Hacke, and J. Pittermann Size and function in conifer tracheids and angiosperm vessels Am. J. Botany, October 1, 2006; 93(10): 1490 - 1500. [Abstract] [Full Text] [PDF]

				R. M. Bateman, J. Hilton, and P. J. Rudall Morphological and molecular phylogenetic context of the angiosperms: contrasting the 'top-down' and 'bottom-up' approaches used to infer the likely characteristics of the first flowers J. Exp. Bot., October 1, 2006; 57(13): 3471 - 3503. [Abstract] [Full Text] [PDF]

				E. A. Kellogg Progress and challenges in studies of the evolution of development J. Exp. Bot., October 1, 2006; 57(13): 3505 - 3516. [Abstract] [Full Text] [PDF]

				D. W. Taylor, H. Li, J. Dahl, F. J. Fago, D. Zinniker, and J. M. Moldowan Biogeochemical evidence for the presence of the angiosperm molecular fossil oleanane in Paleozoic and Mesozoic non-angiospermous fossils Paleobiology, March 1, 2006; 32(2): 179 - 190. [Abstract] [Full Text] [PDF]

				A. T. Moles, D. D. Ackerly, C. O. Webb, J. C. Tweddle, J. B. Dickie, and M. Westoby A Brief History of Seed Size Science, January 28, 2005; 307(5709): 576 - 580. [Abstract] [Full Text] [PDF]

				J. D. Palmer, D. E. Soltis, and M. W. Chase The plant tree of life: an overview and some points of view Am. J. Botany, October 1, 2004; 91(10): 1437 - 1445. [Abstract] [Full Text] [PDF]

				P. S. Soltis and D. E. Soltis The origin and diversification of angiosperms Am. J. Botany, October 1, 2004; 91(10): 1614 - 1626. [Abstract] [Full Text] [PDF]

				P. R. Crane, P. Herendeen, and E. M. Friis Fossils and plant phylogeny Am. J. Botany, October 1, 2004; 91(10): 1683 - 1699. [Abstract] [Full Text] [PDF]

				W. E. Friedman, R. C. Moore, and M. D. Purugganan The evolution of plant development Am. J. Botany, October 1, 2004; 91(10): 1726 - 1741. [Abstract] [Full Text] [PDF]

				K. M. Pryer, E. Schuettpelz, P. G. Wolf, H. Schneider, A. R. Smith, and R. Cranfill Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences Am. J. Botany, September 1, 2004; 91(10): 1582 - 1598. [Abstract] [Full Text] [PDF]