The study of plant phylogeny using amino acid sequences of Ribulose-1,5-Bisphosphate Carboxylase.  II.  The analysis of small subunit data to form phylognetic trees.

Martin, PG; Dowd, JM; Stone, Sheridan

doi:10.1071/bt9830411

Cited by 17 publications

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“…One might therefore expect high levels of homoplasy in neutral molecular characters given a sufficient amount of time. Archie (1989b) has shown that the consistency indices of two plant nucleotide data sets (derived by Bremer, 1988, from the amino acid studies of Martin et al, 1983Martin et al, , 1985 do not differ from those expected in randomly generated data, perhaps indicating near saturation with homoplastic multiple hits.…”

Section: Homoplasy and Selectionmentioning

confidence: 98%

The Suitability of Molecular and Morphological Evidence in Reconstructing Plant Phylogeny

Donoghue¹,

Sanderson²

1992

Molecular Systematics of Plants

176

118

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Renewed interest in phylogenies over the last few decades coincides with a growing sense that it will actually be possible to obtain an accurate picture of evolutionary history. Indeed, the prospects of retrieving phylogeny now seem better than ever, owing to basic theoretical advance (due mainly to Hennig, 1966), the availability of computer programs that can handle large data sets, and the accessibility of new sources of evidence, especially molecular characters.It is our impression that methods of phylogenetic inference-their assumption and reliability-have received more attention than the data upon which phylogenies are based. However, the rapidly increasing use of molecular techniques has focused attention on the pros and cons of molecular versus morphological evidence. Hillis (1987) and Patterson (1987) have reviewed the main arguments, and a summary of results for a number of major groups is available in the proceedings of the recent Nobel symposium (Fernholm et al., 1989). Regarding plant phylogeny in particular, only Sytsma (1990) has attempted a general survey and comparison of molecular and morphological studies. However, reviews of the use of particular molecules (e.g., Palmer et al., 1988, on chloroplast DNA) include useful discussion of molecular versus morphological results, and comparisons have been made within several angiosperm families (e.g., see in this volume, Chapter 10 by Doyle et al. on Fabaceae, Chapter 11 by Jansen et al. on Asteraceae, and Chapter 13 by Sytsma and Smith on Onagraceae).This chapter is not a general review. Few generalizations seem possible at present, because there are too few careful morphological and molecular cladisticWe are grateful to all those who generously shared their unpublished research and/or commented on the manuscript:

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Section: Homoplasy and Selectionmentioning

confidence: 98%

The Suitability of Molecular and Morphological Evidence in Reconstructing Plant Phylogeny

Donoghue¹,

Sanderson²

1992

Molecular Systematics of Plants

176

118

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“…If these data are reliable, a much needed general framework of angiosperm phylogeny could be generated. Most protein sequence data used in phylogenetic reconstruction come from the small subunit of ribulose biphosphate carboxylase (RBC-SSU; Martin et al, 1983;Martin and Dowd, 1984a, 1984b, 1984c, p1astocyanin (Boulter et al, 1979), and cytochrome c (Boulter et al, 1972). Sometimes the phylogenetic trees generated from sequences in these different proteins are inconsistent, and there is uncertainty about the stability of the data.…”

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confidence: 99%

“…A major problem is that the number of variable amino acid positions currently available in a single protein (15-30) is generally too small for a well supported hypothesis about the interrelationships of the taxa investigated (Peacock, 1981). The combination of data from several species into familial sequences (Martin et al, 1983) and the subsequent combination offamilial sequences from several proteins (Martin et al, 1985) yield data sets with a larger number of informative amino acid positions. Such data sets may become large enough to say something about the interrelationships of the angiosperm families included.…”

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confidence: 99%

“…The methods differed and were much constrained by the algorithms and computer power available at the time (Boulter et aI., 1972(Boulter et aI., , 1979Martin et aI., 1983Martin et aI., , 1985Martin and Dowd, 1986a). Essentially, I use the same parsimony analysis as Martin et al (1983Martin et al ( , 1985; based on the algorithm of Hendy and Penny [1982]), but in addition to constructing cladograms, I seek to determine the extent of homoplasy in the amino acid sequences, how many cladograms are possible, and what reliable phylogenetic information is actually present in those cladograms.…”

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The Limits of Amino Acid Sequence Data in Angiosperm Phylogenetic Reconstruction

Bremer¹

1988

Evolution

1,500

962

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Amino acid sequence data are available for ribulose biphosphate carboxylase, plastocyanin, cytochrome c, and ferredoxin for a number of angiosperm families. Cladistic analysis of the data, including evaluation of all equally or almost equally parsimonious cladograms, shows that much homoplasy (parallelisms and reversals) is present and that few or no well supported monophyletic groups offamilies can be demonstrated. In one analysis ofnine angiosperm families and 40 variable amino acid positions from three proteins, the most parsimonious cladograms were 151 steps long and contained 63 parallelisms and reversals (consistency index = 0.583). In another analysis of six families and 53 variable amino acid positions from four proteins, the most parsimonious cladogram was 161 steps long and contained 50 parallelisms and reversals (consistency index = 0.689). Single changes in both data matrices could yield most parsimonious cladograms with quite different topologies and without common monophyletic groups. Presently, amino acid sequence data are not comprehensive enough for phylogenetic reconstruction among angiosperms. More informative positions are needed, either from sequencing longer parts ofthe proteins or from sequencing more proteins from the same taxa.

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“…One might therefore expect high levels of homoplasy in neutral molecular characters given a sufficient amount of time. Archie (1989b) has shown that the consistency indices of two plant nucleotide data sets (derived by , from the amino acid studies of Martin et al, 1983Martin et al, , 1985 do not differ from those expected in randomly generated data, perhaps indicating near saturation with homoplastic multiple hits.…”

Section: Homoplasy and Selectionmentioning

confidence: 97%

Molecular Systematics of Plants

Soltis¹,

Soltis²,

Doyle³

1992

201

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F Of more intormation contact:AlI rights reserved. No part ofthis book covered by the copyright hereon may be reproduced Of used in any form or by any means--graphic, electronic. Of mechanical, inc1uding photocopying. recording. taping, Of intonnation storage and retrieval systems--without the written pennission of the publisher.2 3 4 5 6 7 8 9 XXX OI 00 99 98 97 96 Library of Congress Cataloging-ill-Publicatioll DataMolocular systematics ofplaots / edited by Pamela S. Sollis. Douglas E. Sollis, and Jelt' J. Doyle. p. em. lncludes bibliographical references and index.

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The study of plant phylogeny using amino acid sequences of Ribulose-1,5-Bisphosphate Carboxylase. II. The analysis of small subunit data to form phylognetic trees.

Cited by 17 publications

References 0 publications

The Suitability of Molecular and Morphological Evidence in Reconstructing Plant Phylogeny

The Suitability of Molecular and Morphological Evidence in Reconstructing Plant Phylogeny

The Limits of Amino Acid Sequence Data in Angiosperm Phylogenetic Reconstruction

Molecular Systematics of Plants

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