Phylogenetic Supertrees: Combining information to reveal the Tree of Life (Computational Biology, 4)

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. New Uses For Old Phylogenies : An Introduction To The Volume / Olaf R.p. Bininda-emonds -- The Mrp Method / Bernard R. Baum And Mark A. Ragan -- An Assessment Of Matrix Representation With Compatibility In Supertree Construction / Howard A. Ross And Allen G. Rodrigo -- Mrf Supertrees / G. Gordon Burleigh ... [et Al.] -- Everything You Always Wanted To Know About Average Consensus, And More / François-joseph Lapointe And Claudine Levasseur -- Tangled Trees From Multiple Markers : Reconciling Conflict Between Phylogenies To Build Molecular Supertrees / James Cotton And Roderic R.m. Page -- Supertree Methods For Ancestral Divergence Dates And Other Applications / David Bryant, Charles Semple And Mike Steel -- Supertree Algorithms For Nested Taxa / Philip Daniel And Charles Semple -- Quartet Supertrees / Raul Piaggio-talice, J. Gordon Burleigh And Oliver Eulenstein -- Bayesian Supertrees / Fredrik Ronquist, John Huelsenbeck And Tom Britton --^ Some Desiderata For Liberal Supertrees / Mark Wilkinson ... [et Al.] -- Taxonomy, Supertrees, And The Tree Of Life / Roderic D.m. Page -- Garbage In, Garbage Out : Data Issues In Supertree Construction / Olaf R.p. Bininda-emonds ... [et Al.] -- Reconstructing Divergence Times For Supertrees : A Molecular Approach / Rutger Vos And Arne Ø. Mooers -- Performance Of Supertree Methods On Various Data Set Decompositions / Usman Roshan ... [et Al.] -- Unrooted Supertrees : Limitations, Traps, And Phylogenetic Patchworks / Sebastian Böcker -- The Cladistics Of Matrix Representation With Parsimony Analysis / Harold N. Bryant -- A Critique Of Matrix Representation With Parsimony Supertrees / John Gatesy And Mark S. Springer -- Supertrees, Components And Three-item Data / David M. Williams -- A Molecular Supertree Of The Artiodactyla / Annette S. Mahon -- Supertrees : Using Complete Phylogenies In Comparative Biology / John L. Gittleman, Kate E. Jones And Samantha A. Price --^ Using Supertrees To Investigate Species Richness In Grasses And Flowering Plants / Nicolas Salamin And T. Jonathan Davies -- Detecting Diversification Rate Variation In Supertrees / Brian R. Moore, Kai M.a. Chan And Michael J. Donoghue. Edited By Olaf R.p. Bininda-emonds. Includes Bibliographical References And Indexes. 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 "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 trees 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."--BOOK JACKET