Olaf R. P. Bininda-Emonds (ed.)
(2004年刊行,Kluwer Academic Publishers[Computational Biology Series Volume 4], Dordrecht, xiv+550 pp., ISBN:1402023294 [paperback] / ISBN:1402023286 [hardcover])
【目次】
List of contributers viii
Preface and acknowledgements xii
Introduction 1
Olaf R. P. Bininda-Emonds
New uses for old phylogenies: an introduction to the volume 3
1. Reviews of existing methods 15
Bernard R. Baum and Mark A. Ragan
The MRP method 17
Howard A. Ross and Allen G. Rodrigo
An assessment of matrix representation with compatibility in supertree construction 35
J. Gordon Burleigh, Oliver Eulenstein, David Fernandez-Baca, and Michael J. Sanderson
MRF supertrees 65
Francois-Joseph Lapointe and Claudine Levasseur
Everything you always wanted to know about average consensus, and more 87
James Cotton and Roderic R. M. Page
Tangled trees from multiple markers: reconciling conflict between phylogenies to build molecular supertrees 107
2. New supertree methods 127
David Bryant, Charles Semple, and Mike Steel
Supertree methods for ancestral divergence dates and other applications 129
Philip Daniel and Charles Semple
Supertree algorithms for nested taxa 151
Raul Piaggio-Talice, J. Gordon Burleigh, and Oliver Eulenstein
Quartet supertrees 173
Frederik Ronquist, John Huelsenbeck, and Tom Britton
Bayesian supertrees 193
3. Methodological considerations 225
Mark Wilkinson, Joseph L. Thorley, Davide Pisami, Francois-Joseph Lapointe, and James O. McInerney
Some desiderata for liberal supertrees 227
Roderic R. M. Page
Taxonomy, supertrees, and the tree of life 247
Olaf R. P. Bininda-Emonds, Kate E. Jones, Samantha A. Price, Marcel Cardillo, Richard Grenyer, and Andy Purvis
Garbage in, garbage out: data issues in supertree construction 267
Rutgers Vos and Arne O. Mooers
Reconstructing divergence times for supertrees: a molecular approach 281
Usman Roshan, Bernard M. E. Moret, Tiffani L. Williams, and Tandy Warnow
Performance of supertree methods on various data set decompositions 301
4. A critical look at supertrees 329
Sebastion Boecker
Unrooted supertrees: limitations, traps, and phylogenetic patchworks 331
Harold N. Bryant
The cladistics of matrix representation with parsimony analysis 353
John Gatesy and Mark S. Springer
A critique of matrix representation with parsimony supertrees 369
David M. Williams
Supertrees, components and three-item data 389
5. Supertrees and their applications 409
Annette S. Mahon
A molecular supertree of the Artiodactyla 411
John L. Gittleman, Kate E. Jones, and Samantha A. Price
Supertrees: using complete phylogenies in coparative biology 439
Nicolas Salamin and T. Jonathan Davies
Using supertrees to investigate species richness in grasses and flowering plants 461
Brian R. Moore, Kai M. A. Chan, and Michael J. Donoghue
Detecting diversification rate variation in supertrees 487
Taxon index 535
Subject index 537