Reconstructing the Tree of Life —— Taxonomy and Systematics of Species Rich Taxa

----- 重建生命之树

ISBN: 9780367389581 出版年：2006 页码：374 CRC Press

Introduction to the Systematics of Species Rich Groups, T.R. Hodkinson and J.A.N. Parnell Introduction What is a Species Rich Group? Reconstructing and Using the Tree of Life Taxonomy of Species Rich Groups Conclusions: Blame Evolution and Politicians References Taxonomy/Systematics in the Twenty-First Century, F.R. Schram Historical Wailings Using Technology Institutional Issues Human Capital The Biodiversity Crisis What to Do? Concluding Remarks Acknowledgements References Assembling the Tree of Life: Magnitude, Shortcuts and Pitfalls, O. Seberg and G. Petersen Introduction The Scale of the Problem Shortcuts in Systematics: DNA Taxonomy The Identification Problem Instability of Linnaean Names Taxonomic Bias The 'Taxonomic Impediment' Inadequacy of Taxonomic Data and Standards in Existing Databases Conclusion Acknowledgements References Evolutionary History of Prokaryotes: Tree or No Tree? J.O. McInerney, D.E. Pisani, M.J. O'Connell, D.A. Fitzpatrick, and C.J. Creevey A Brief History of Prokaryotic Systematics The Ribosomal RNA Revolution Conflicting Trees Methodological Developments An Emerging Consensus? The Prokaryotic Influence on the Eukaryote Conclusions, Future Directions and Open Questions Acknowledgements References Supertree Methods for Building the Tree of Life: Divide-and-Conquer Approaches to Large Phylogenetic Problems, M. Wilkinson and J.A. Cotton Introduction Divide-and-conquer Methods Effective Overlap Fast Quartet-based Supertree Construction Conclusion References Taxon Sampling versus Computational Complexity and Their Impact on Obtaining the Tree of Life, O.R.P. Bininda-Emonds and A. Stamatakis Introduction Materials and Methods Results Discussion Conclusions Acknowledgements References Tools to Construct and Study Big Trees: A Mathematical Perspective, M. Steel Trees (and networks) of Life Constructing Supertrees and Supernetworks An Application for Large Trees: Phylogenetic Diversity Concluding Comments Acknowledgments References The Analysis of Molecular Sequences in Large Data Sets: Where Should We Put Our Effort? W.C. Wheeler The Problem Presented by Unaligned Sequence Data Cladogram Search Heuristics Homology Determination Heuristics Example Data Comparisons What is Happening in Large Data Sets? Acknowledgments References Species-Level Phylogenetics of Large Genera: Prospects of Studying Coevolution and Polyploidy, N. Ronsted, E. Yektaei-Karin, K. Turk, J. J. Clarkson and M. W. Chase Introduction: Prospects of Studying Large Genera Coevolution of Figs and their Pollinating Wasps Low Levels of Variation in Standard Markers Low Copy Nuclear Markers: The Ideal Tools Using AFLP and other Fingerprinting Techniques Double Dating of Fig and Wasp Lineages: Evidence for Codivergence Incongruence in Phylogenetic Trees: Effects of Polyploids and Hybrids Conclusions Acknowledgments References The Diversification of Flowering Plants through Time and Space: Key Innovations, Climate and Chance, T.J. Davies and T.G. Barraclough Introduction Measuring Diversification Rates Key Innovations Evolutionary Rates and the Latitudinal Gradient in Species Richness Traits x Environment: Diversification of Irises in the Cape of South Africa Conclusions Acknowledgments References Skewed Distribution of Species Number in Grass Genera: Is It a Taxonomic Artefact? K. W. Hilu Introduction The Grass Family (Poaceae) Materials and Methods Results and Discussion Conclusion Acknowledgments References Reconstructing Animal Phylogeny in the Light of Evolutionary Developmental Biology, A. Minelli, E. Negrisolo, and G. Fusco Development, Phylogeny and the Historical Roots of Evo-Devo Morphology to Molecules to Morphology Evo-Devo Insights into Evolutionary Change Dealing with Characters from an Evo-Devo Perspective Conclusion Acknowledgments References Insect Biodiversity and Industrialising the Taxonomic Process: The Plant Bug Case Study (Insecta: Heteroptera: Miridae), G. Cassis, M.A. Wall, and R. Schuh Introduction Estimates and Drivers of Insect Diversity Dealing with Diversity: From the Cottage to the Factory Plant Bug Diversity, Biology and Classification Plant Bugs as a Cottage Industry Taxonomic, Collections and Classification Impediments Plant Bugs in the Twentyfirst Century: Industrial Cyber-Taxonomy Conclusion Acknowledgments References Cichlid Fish Diversity and Speciation, J.R. Stauffer, Jr., K. Black, M. Geerts, A. F. Konings, and K. R. McKaye Introduction Cichlid Phylogeny Cichlid Distribution Cichlid Diversity and Speciation Cichlid Adaptive Radiation Future Directions References Fungal DiversITY, A.M.C. Tang, B.D. Shenoy, and K.D. Hyde Introduction to the Fungi Problems in Estimating Fungal Diversity Global Fungal Diversity Estimate: Described and Undescribed Examples of Fungal Diversity from Selected Hosts Species Rich Genera of Fungi An Era of Genomics and Molecular Biology Concluding Remarks References Matters of Scale: Dealing with One of the Largest Genera of Angiosperms, J.A.N. Parnell, L.A. Craven, and E. Biffin Introduction Taxonomic History Current Research Future Prospects Acknowledgments References Supersizing: Progress in Documenting and Understanding Grass Species Richness, T.R. Hodkinson, Y. Bouchenak-Khelladi, M. S. Kinney, V. Savolainen, S.W.L. Jacobs, and N. Salamin Introduction Taxonomy and Classification of the Grasses Phylogenetics of the Grasses Future Perspectives Conclusion Acknowledgments References Collecting Strategies for Large and Taxonomically Challenging Taxa: Where Do We Go from Here, and How Often? T.M.A. Utteridge and R.P.J. de Kok Introduction Methods Results Discussion Conclusions Acknowledgments References Large and Species Rich Taxa: Diatoms, Geography and Taxonomy, D.M. Williams and G. Reid Introduction There are Taxa, and Then There are Taxa There are Numbers, and Then There are Numbers There are Names, and Then There are Names There is Biogeography, and Then There is Biogeography Summary References Systematics of the Species Rich Algae: Red Algal Classification, Phylogeny and Speciation, J. Brodie and G. C. Zuccarello Introduction The Red Algae Conclusions References