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Description

To document the world’s diversity of species and reconstruct the tree of life we need to undertake some simple but mountainous tasks. Most importantly, we need to tackle species rich groups. We need to collect, name, and classify them, and then position them on the tree of life. We need to do this systematically across all groups of organisms and because of the biodiversity crisis we need to do it quickly. With contributions from key systematic and taxonomic researchers, Reconstructing the Tree of Life: Taxonomy and Systematics of Species Rich Taxa outlines the core of the problem and explores strategies that bring us closer to its solution.

The editors split the book into three parts: introduction and general concepts, reconstructing and using the tree of life, and taxonomy and systematics of species rich groups (case studies). They introduce, with examples, the concept of species rich groups and discuss their importance in reconstructing the tree of life as well as their conservation and sustainable utilization in general. The book highlights how phylogenetic trees are becoming “supersized” to handle species rich groups and the methods that are being developed to deal with the computational complexity of such trees. It discusses factors that have lead some groups to speciate to a staggering degree and also provides case studies that highlight the problems and prospects of dealing with species rich groups in taxonomy.

To understand species rich taxa, evolution has set scientists a difficult, but not unattainable, challenge that requires the meshing together of phylogenetics and taxonomy, considerable advances in informatics, improved and increased collecting, training of taxonomists, and significant financial support. This book provides the tools and methods needed to meet that challenge.

Reviews

”…a true gem…brings together the remarkable efforts of an international community of taxonomists and systematists with expertise spanning a wide range of organisms…. I strongly recommend this book to all professional systematists with an interest in large-scale phylogenies and related issues [and] intermediate and advanced students…..

—Marcello Ruta, University of Bristol, UK, writing in the Systematist 2007 No. 29

"The book is an excellent source of information for studying methods and tools for assembling the tree of life that includes all known organisms."

— Grzegorz Marszalkowski, Department of Plant Physiology, Warsaw Agricultural University, Poland in Acta Physiol, Volume 30, 2008

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

Name: Reconstructing the Tree of Life: Taxonomy and Systematics of Species Rich Taxa (Hardback)CRC Press 
Description: Edited by Trevor R. Hodkinson, John A.N. ParnellSeries Editor: Alan WarrenContributors: Frederick R. Schram, Alessandro Minelli, Ward C. Wheeler, Juliet Brodie, Ole Seberg, J.O. McInerney, M. Wilkinson, O.R.P. Bininda-Emonds, M. Steel, N. Ronsted, T.J. Davies, Khidir W. Hilu, Gerasimos Cassis, J.R. Stauffer, Jr., Timothy Utteridge, A.M.C. Tang, T.G. Barraclough, Lyn Craven, David M. Williams, Mark W. Chase, Vincent Savolainen, Kevin D. Hyde, Giuseppe Fusco, Gitte Petersen, Davide Pisani, Mary J. O'Connell, Christopher J. Creevey, James A. Cotton, Alexandros Stamatakis, E. Yektaei-Karin, Katherine Turk, J.J. Clarkson, Enrico Negrisolo, Michael A. Wall, Randall Schuh, Ad Konings, Kristin E. Black, Martin Geerts, Kenneth R. McKaye, Belle Damodara Shenoy, Ed Biffin, Surrey W.L. Jacobs, Nicolas Salamin, Rogier P.J. de Kok, Geraldine Reid, Giuseppe C. Zuccarello, David Fitzpatrick, Yanis Bouchenak-Khelladi, Michael S. Kinney. To document the world’s diversity of species and reconstruct the tree of life we need to undertake some simple but mountainous tasks. Most importantly, we need to tackle species rich groups. We need to collect, name, and classify them, and then...
Categories: Natural History, Botany, Statistics for the Biological Sciences