Next Generation Systematics

doi:10.1017/CBO9781139236355

We live in an age of ubiquitous genomics. Next generation sequencing (NGS) technology, both widely adopted and advancing at pace, has transformed the data landscape, opening up an enormous source of heritable characters to the comparative biologist. Its impact on systematics, like many other fields of biology, has been felt throughout its breadth: from defining species boundaries to estimating their evolutionary histories. This volume examines the broad range of ways in which NGS data are being used in systematics and in the fields that it underpins, from biodiversity prospecting to evo-devo. Experts in their fields draw on contemporary case studies to demonstrate state-of-the-art applications of NGS data. These, along with novel analyses, comprehensive reviews and lively perspectives, are combined to produce an authoritative account of contemporary issues in systematics that have been impacted by the adoption of NGS.

'… the book provides a very good overview of how the field of systematics is being shaped by the impact of a promising technology. In focusing on the major achievements and the challenges ahead it conveys a realistic vision for the future. One that has the potential to motivate many readers to embrace these approaches or to focus on solving the mentioned challenges.'

Toni Gabaldón Source: The Quarterly Review of Biology

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Contents

Frontmatter
pp i-vi
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Contents
pp vii-viii
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List of contributors
pp ix-x
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Introduction: studying diversity in an era of ubiquitous genomics
pp 1-10
- By James A. Cotton, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK, Peter D. Olson, The Natural History Museum, London, UK
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Part I - Next Generation Phylogenetics
pp 11-12
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1 - Perspective: Challenges in assembling the ‘next generation’ Tree of Life
pp 13-27
- By Michael J. Sanderson, University of Arizona, Tucson, USA
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2 - The role of next generation sequencing technologies in shaping the future of insect molecular systematics
pp 28-61
- By Joseph Hughes, MRC–University of Glasgow Centre for Virus Research, Glasgow, UK, Stuart Longhorn, Oxford Museum of Natural History, Oxford, UK
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3 - Phylogenomics of Nematoda
pp 62-83
- By Mark Blaxter, University of Edinburgh, UK, Georgios Koutsovoulos, University of Edinburgh, UK, Martin Jones, University of Edinburgh, UK, Sujai Kumar, University of Edinburgh, UK, Ben Elsworth, University of Edinburgh, UK
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4 - High-throughput multiplexed mitogenomics for Metazoa: prospects and limitations
pp 84-100
- By Peter G. Foster, The Natural History Museum, London, UK, Maria A. Stalteri, The Natural History Museum, London, UK, Andrea Waeschenbach, The Natural History Museum, London, UK, D. Timothy J. Littlewood, The Natural History Museum, London, UK
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5 - Investigating bacterial microevolution through next generation sequencing
pp 101-120
- By Josephine M. Bryant, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK, Simon R. Harris, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
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Part II - Next Generation Biodiversity Science
pp 121-122
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6 - Perspective: Après le déluge: ubiquitous field barcoding should drive 21st century taxonomy
pp 123-153
- By Richard M. Bateman, Jodrell Laboratory, Royal Botanic Gardens, Kew, UK
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7 - Perspective: Biodiversity and the (data) beast
pp 154-174
- By Holly M. Bik, University of California Davis Genome Center, USA, W. Kelley Thomas, University of New Hampshire, USA
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8 - Next generation biodiversity analysis
pp 175-194
- By Mehrdad Hajibabaei, University of Guelph, Ontario, Canada, Ian King, University of Guelph, Ontario, Canada
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9 - Protist systematics, ecology and next generation sequencing
pp 195-216
- By David Bass, Sciences, The Natural History Museum, London, UK, Thomas Bell, Imperial College London, Silwood Park Campus, Ascot, UK
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Part III - Next Generation Challenges and Questions
pp 217-218
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10 - Perspective: Systematics in the age of genomics
pp 219-228
- By Antonis Rokas, Vanderbilt University, Nashville, Tennessee, USA
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11 - Perspective: The role of next generation sequencing for integrative approaches in evolutionary biology
pp 229-236
- By Ralf J. Sommer, Max-Planck Institute for Developmental Biology, Tübingen, Germany
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12 - Next generation apomorphy: the ubiquity of taxonomically restricted genes
pp 237-263
- By Paul A. Nelson, Biola University, La Mirada, California, USA, Richard J. A. Buggs, Queen Mary University of London, UK
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13 - Utilizing next generation sequencing for evo-devo study of plant traits
pp 264-281
- By Rachel H. Walker, University of Cambridge, UK, Paula J. Rudall, Royal Botanic Gardens, Kew, UK, Beverley J. Glover, University of Cambridge, UK
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14 - An NGS approach to archaeobotanical museum specimens as genetic resources in systematics research
pp 282-304
- By Oliver Smith, University of Warwick, Coventry, UK, Sarah A. Palmer, University of Warwick, Coventry, UK, Rafal Gutaker, University of Warwick, Coventry, UK, Robin G. Allaby, University of Warwick, Coventry, UK
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15 - From sequence reads to evolutionary inferences
pp 305-335
- By James A. Cotton, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
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Index
pp 336-347
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Systematics Association Special Volumes
pp 348-352
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Plate section
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Next Generation Systematics

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Contents

Frontmatter
pp i-vi

Contents
pp vii-viii

List of contributors
pp ix-x

Introduction: studying diversity in an era of ubiquitous genomics
pp 1-10

Part I - Next Generation Phylogenetics
pp 11-12

1 - Perspective: Challenges in assembling the ‘next generation’ Tree of Life
pp 13-27

2 - The role of next generation sequencing technologies in shaping the future of insect molecular systematics
pp 28-61

3 - Phylogenomics of Nematoda
pp 62-83

4 - High-throughput multiplexed mitogenomics for Metazoa: prospects and limitations
pp 84-100

5 - Investigating bacterial microevolution through next generation sequencing
pp 101-120

Part II - Next Generation Biodiversity Science
pp 121-122

6 - Perspective: Après le déluge: ubiquitous field barcoding should drive 21st century taxonomy
pp 123-153

7 - Perspective: Biodiversity and the (data) beast
pp 154-174

8 - Next generation biodiversity analysis
pp 175-194

9 - Protist systematics, ecology and next generation sequencing
pp 195-216

Part III - Next Generation Challenges and Questions
pp 217-218

10 - Perspective: Systematics in the age of genomics
pp 219-228

11 - Perspective: The role of next generation sequencing for integrative approaches in evolutionary biology
pp 229-236

12 - Next generation apomorphy: the ubiquity of taxonomically restricted genes
pp 237-263

13 - Utilizing next generation sequencing for evo-devo study of plant traits
pp 264-281

14 - An NGS approach to archaeobotanical museum specimens as genetic resources in systematics research
pp 282-304

15 - From sequence reads to evolutionary inferences
pp 305-335

Index
pp 336-347

Systematics Association Special Volumes
pp 348-352

Plate section

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Next Generation Systematics

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