yzPhylogenetic Supertrees: Combining Information to Reveal the Tree of Life
yҎҁzOlaf R. P. Bininda-Emonds
yoŁzKluwer Academic Publishers, Dordrecht
ypzComputational Biology Series, Volume 4
yŐzxiv+550 pp.
y艿zUS$ 39.00 [paperback]
yISBNz1-4020-2329-4 [paperback] / 1-4020-2328-6 [hardcover]

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