Phylogenetic Supertrees

1. Front Matter

   Pages i-xiv

   PDF

2. Introduction

   1. Front Matter

      Pages 1-1

      PDF

   2. New uses for old phylogenies

      • Olaf R. P. Bininda-Emonds

      Pages 3-14

3. Reviews of existing methods

   1. Front Matter

      Pages 15-15

      PDF

   2. The MRP Method

      • Bernard R. Baum, Mark A. Ragan

      Pages 17-34

   3. An Assessment of Matrix Representation with Compatibility in Supertree Construction

      • Howard A. Ross, Allen G. Rodrigo

      Pages 35-63

   4. MRF Supertrees

      • J. Gordon Burleigh, Oliver Eulenstein, David Fernández-Baca, Michael J. Sanderson

      Pages 65-85

   5. Everything You always wanted to Know about the Average Consensus, and More

      • François-Joseph Lapointe, Claudine Levasseur

      Pages 87-105

   6. Tangled Tales from Multiple Markers

      • James A. Cotton, Roderic D. M. Page

      Pages 107-125

4. New supertree methods

   1. Front Matter

      Pages 127-127

      PDF

   2. Supertree Methods for Ancestral Divergence Dates and other Applications

      • David Bryant, Charles Semple, Mike Steel

      Pages 129-150

   3. Supertree Algorithms for Nested Taxa

      • Philip Daniel, Charles Semple

      Pages 151-171

   4. Quartet Supertrees

      • Raul Piaggio-Talice, J. Gordon Burleigh, Oliver Eulenstein

      Pages 173-191

   5. Bayesian Supertrees

      • Fredrik Ronquist, John P. Huelsenbeck, Tom Britton

      Pages 193-224

5. Methodological considerations

   1. Front Matter

      Pages 225-225

      PDF

   2. Some Desiderata for Liberal Supertrees

      • Mark Wilkinson, Joseph L. Thorley, Davide Pisani, François-Joseph Lapointe, James O. McInerney

      Pages 227-246

   3. Taxonomy, Supertrees, and the Tree of Life

      • Roderic D. M. Page

      Pages 247-265

   4. Garbage in, Garbage out

      • Olaf R. P. Bininda-Emonds, Kate E. Jones, Samantha A. Price, Marcel Cardillo, Richard Grenyer, Andy Purvis

      Pages 267-280

   5. Reconstructing Divergence Times for Supertrees

      • Rutger A. Vos, Arne Ø. Mooers

      Pages 281-299

   6. Performance of Supertree Methods on Various Data Set Decompositions

      • Usman Roshan, Bernard M. E. Moret, Tiffani L. Williams, Tandy Warnow

      Pages 301-328

This is the first book on "phylogenetic supertrees", a recent, but controversial development for inferring evolutionary trees. Rather than analyze the combined primary character data directly, supertree construction proceeds by combining the tree topologies derived from those data. This difference in strategy has allowed for the exciting possibility of larger, more complete phylogenies than are otherwise currently possible, with the potential to revolutionize evolutionarily-based research. This book provides a comprehensive look at supertrees, ranging from the methods used to build supertrees to the significance of supertrees to bioinformatic and biological research. Reviews of many the major supertree methods are provided and four new techniques, including a Bayesian implementation of supertrees, are described for the first time. The far-reaching impact of supertrees on biological research is highlighted both in general terms and through specific examples from diverse clades such as flowering plants, even-toed ungulates, and primates. The book also critically examines the many outstanding challenges and problem areas for this relatively new field, showing the way for supertree construction in the age of genomics. Interdisciplinary contributions from the majority of the leading authorities on supertree construction in all areas of the bioinformatic community (biology, computer sciences, and mathematics) will ensure that this book is a valuable reference with wide appeal to anyone interested in phylogenetic inference.

• Cladistics
• Phylogenie
• Ringe
• Topologie
• algorithms
• computer
• computer science
• evolution
• genome

From the reviews:

"It provides a very worthwhile introduction to a topic that is receiving a lot of attention among phylogeneticists in the new millennium: how to combine the information contained in multiple phylogenetic trees with partially overlapping sets of taxa. … this book achieves what it sets out to achieve, which is to provide an overview and evaluation of possible approaches to the construction of supertrees. … This book does a good job of explaining the arithmetic and the mathematics of supertrees … ." (David A. Morrison, Systematic Biology, Vol. 55 (3), 2006)

• Lehrstuhl für Tierzucht, Technische Universität München, Freising- Weihenstephan, Germany

  Olaf R. P. Bininda-Emonds

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