Trevor R. Hodkinson and John A.N. Parnell (eds.)
（2006年12月26日刊行，Systematics Association Special Volume Series 72, CRC Press, Boca Raton, xvi+351 pp.，ISBN:0849395798 [hbk] → 版元ページ）
前半は巨大データとかスーパーツリーの話とか．後半はケーススタディ．
【目次】
Preface v
The Editors vii
Contributors ix
Section A: Introduction and General Context
1. Introduction to the Systematics of Species Rich Groups (T.R. Hodkinson and J.A.N. Parnell) 3
Introduction
What is a Species Rich Group?
Reconstructing and Using the Tree of Life
Taxonomy of Species Rich Groups
Conclusions: Blame Evolution and Politicians
References2. Taxonomy/Systematics in the Twenty-First Century (F.R. Schram) 21
Historical Wailings
Using Technology
Institutional Issues
Human Capital
The Biodiversity Crisis
What to Do?
Concluding Remarks
Acknowledgements
References3. Assembling the Tree of Life: Magnitude, Shortcuts and Pitfalls (O. Seberg and G. Petersen) 33
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
ReferencesSection B: Reconstructing and Using the Tree of Life
4. 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) 49
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
References5. Supertree Methods for Building the Tree of Life: Divide-and-Conquer Approaches to Large Phylogenetic Problems (M. Wilkinson and J.A. Cotton) 61
Introduction
Divide-and-conquer Methods
Effective Overlap
Fast Quartet-based Supertree Construction
Conclusion
References6. Taxon Sampling versus Computational Complexity and Their Impact on Obtaining the Tree of Life (O.R.P. Bininda-Emonds and A. Stamatakis) 77
Introduction
Materials and Methods
Results
Discussion
Conclusions
Acknowledgements
References7. Tools to Construct and Study Big Trees: A Mathematical Perspective (M. Steel) 97
Trees (and networks) of Life
Constructing Supertrees and Supernetworks
An Application for Large Trees: Phylogenetic Diversity
Concluding Comments
Acknowledgments
References8. The Analysis of Molecular Sequences in Large Data Sets: Where Should We Put Our Effort? (W.C. Wheeler) 113
The Problem Presented by Unaligned Sequence Data
Cladogram Search Heuristics
Homology Determination Heuristics
Example Data
Comparisons
What is Happening in Large Data Sets?
Acknowledgments
References9. Species-Level Phylogenetics of Large Genera: Prospects of Studying Coevolution and Polyploidy (N. R?nsted, E. Yektaei-Karin, K. Turk, J. J. Clarkson and M. W. Chase) 129
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
References10. The Diversification of Flowering Plants through Time and Space: Key Innovations, Climate and Chance (T.J. Davies and T.G. Barraclough) 149
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
References11. Skewed Distribution of Species Number in Grass Genera: Is It a Taxonomic Artefact? (K. W. Hilu) 165
Introduction
The Grass Family (Poaceae)
Materials and Methods
Results and Discussion
Conclusion
Acknowledgments
References12. Reconstructing Animal Phylogeny in the Light of Evolutionary Developmental Biology (A. Minelli, E. Negrisolo, and G. Fusco) 177
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
ReferencesSection C: Taxonomy and Systematics of Species Rich Groups (Case Studies)
13. Insect Biodiversity and Industrialising the Taxonomic Process: The Plant Bug Case Study (Insecta: Heteroptera: Miridae). (G. Cassis, M.A. Wall, and R. Schuh) 193
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
References14. Cichlid Fish Diversity and Speciation (J.R. Stauffer, Jr., K. Black, M. Geerts, A. F. Konings, and K. R. McKaye) 213
Introduction
Cichlid Phylogeny
Cichlid Distribution
Cichlid Diversity and Speciation
Cichlid Adaptive Radiation
Future Directions
References15. Fungal Diversity (A.M.C. Tang, B.D. Shenoy, and K.D. Hyde) 227
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
References16. Matters of Scale: Dealing with One of the Largest Genera of Angiosperms (J.A.N. Parnell, L.A. Craven, and E. Biffin) 251
Introduction
Taxonomic History
Current Research
Future Prospects
Acknowledgments
References17. 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) 275
Introduction
Taxonomy and Classification of the Grasses
Phylogenetics of the Grasses
Future Perspectives
Conclusion
Acknowledgments
References18. 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) 297
Introduction
Methods
Results
Discussion
Conclusions
Acknowledgments
References19. Large and Species Rich Taxa: Diatoms, Geography and Taxonomy (D.M. Williams and G. Reid) 305
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
References20. Systematics of the Species Rich Algae: Red Algal Classification, Phylogeny and Speciation (J. Brodie and G. C. Zuccarello) 323
Introduction
The Red Algae
Conclusions
References
Index 337
