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.
Author(s): Olaf R. P. Bininda-Emonds (auth.), Olaf R. P. Bininda-Emonds (eds.)
Series: Computational Biology 4
Edition: 1
Publisher: Springer Netherlands
Year: 2004
Language: English
Pages: 550
Tags: Evolutionary Biology; Discrete Mathematics in Computer Science; Mathematical and Computational Biology; Mathematical Logic and Foundations
Front Matter....Pages i-xiv
Front Matter....Pages 1-1
New uses for old phylogenies....Pages 3-14
Front Matter....Pages 15-15
The MRP Method....Pages 17-34
An Assessment of Matrix Representation with Compatibility in Supertree Construction....Pages 35-63
MRF Supertrees....Pages 65-85
Everything You always wanted to Know about the Average Consensus, and More....Pages 87-105
Tangled Tales from Multiple Markers....Pages 107-125
Front Matter....Pages 127-127
Supertree Methods for Ancestral Divergence Dates and other Applications....Pages 129-150
Supertree Algorithms for Nested Taxa....Pages 151-171
Quartet Supertrees....Pages 173-191
Bayesian Supertrees....Pages 193-224
Front Matter....Pages 225-225
Some Desiderata for Liberal Supertrees....Pages 227-246
Taxonomy, Supertrees, and the Tree of Life....Pages 247-265
Garbage in, Garbage out....Pages 267-280
Reconstructing Divergence Times for Supertrees....Pages 281-299
Performance of Supertree Methods on Various Data Set Decompositions....Pages 301-328
Front Matter....Pages 329-329
Unrooted Supertrees....Pages 331-351
The Cladistics of Matrix Representation with Parsimony Analysis....Pages 353-368
A Critique of Matrix Representation with Parsimony Supertrees....Pages 369-388
Supertrees, Components and Three-Item Data....Pages 389-408
Front Matter....Pages 409-409
A Molecular Supertree of the Artiodactyla....Pages 411-437
Front Matter....Pages 409-409
Supertrees....Pages 439-460
Using Supertrees to Investigate Species Richness in Grasses and Flowering Plants....Pages 461-486
Detecting Diversification Rate Variation in Supertrees....Pages 487-533
Back Matter....Pages 535-550
