Table of Contents

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. Rønsted, 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