Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life

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.

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)

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)

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.

List of contributors. Preface and acknowledgements. Introduction. New uses for old phylogenies: an introduction to the volume; O.R.P. Bininda-Emonds. 1: Reviews of existing methods. The MRP method; B.R. Baum, M.A. Ragan. An assessment of matrix representation with compatibility in supertree construction; H.A. Ross, A.G. Rodrigo. MRF supertrees; J.G. Burleigh, O.Eulenstein, D. Fernández-Baca, M. J. Sanderson l. Everything you always wanted to know about average consensus and more; F.-J. Lapointe, C. Levasseur. Tangled trees from multiple markers: reconciling conflict between phylogenies to build molecular supertrees; J. Cotton, R.R.M. Page. 2: New supertree methods. Supertree methods for ancestral divergence dates and other applications; D. Bryant, C. Semple, M. Steel Supertree algorithms for nested taxa; P. Daniel, C. Semple. Quartet supertrees; R. Piaggio-Talice, J.G. Burleigh, O. Eulenstein Bayesian supertrees; F. Ronquist, J. Huelsenbeck, T. Britton 3: Methodological considerations. Some desiderata for liberal supertrees; M. Wilkinson, J.L. Thorley, D. Pisani, F.-J. Lapointe, J.O. McInerney Taxonomy, supertrees and the Tree of Life; R.R.M. Page. Garbage in, garbage out: data issues in supertree construction; O.R.P. Bininda-Emonds, K.E> Jones, S.A. Price, M. Cardillo, A. Purvis Reconstucting divergence times for supertrees: a molecular approach; R. Vos, A. Mooers. Performance of supertree methods on various data set decompositions; U. Roshan, B.M.E. Moret, T.L. Williams, T. Warnow 4: A critical look at supertrees. Unrooted supertrees: Limitations, traps and phylogenic patchworks; S. Böcker. The cladistics of matrix representation with parsimony analysis; H.N. Bryant. A critique of matrix representation with parsimony supertrees; J. Gatesby, M. Springer. Supertrees, components and three-item data; D.M. Williams. 5: Supertrees and their applications. A molecular supertree of the Artiodactyla; A.S. Mahon. Supertrees: using complete phylogenies in comparative biology; J.L. Gittleman, et al. Using supertrees to investigate species richness in grasses and flowering plants; N. Salamin, T.J. Davies. Detecting diversification rate variation in supertrees; B.R. Moore, K.M.A. Chan, M.J. Donothue Taxon index. Subject index.