Natural Systems

Dr Markus Eichhorn, School of Biology, University of Nottingham, UK.

Preface xv

0.0.1 To students xvi

0.0.2 To instructors xvii

Acknowledgments xxi

Abbreviations xxiii

1 Introduction: Defining nature 1

1.1 How little we know 1

1.2 Pressing questions 2

1.3 The hierarchy of nature 3

1.4 Biodiversity 5

1.5 Myths to bust 7

1.6 Further reading 8

1.6.1 Recommended reading 8

PART I SPECIES

2 What is a species? 3

2.1 The big question 3

2.2 Species concepts 6

2.2.1 Nominalistic species concepts 6

2.2.2 Morphological species concepts 7

2.2.3 Biological species concepts 8

2.2.4 Phylogenetic species concepts 10

2.2.5 Genetic species concepts 11

2.3 Solving the riddle 15

2.4 Coda: Species richness 16

2.5 Conclusions 16

2.5.1 Recommended reading 17

2.5.2 Questions for the future 17

3 The history of life 21

3.1 The big question 21

3.2 Sources of evidence 21

3.2.1 The fossil record 21

3.2.2 Molecular evidence 22

3.3 A brief history of diversity 23

3.4 Uneven diversity 29

3.5 Conclusions 31

3.5.1 Recommended reading 32

3.5.2 Questions for the future 32

4 How many species are there? 35

4.1 The big question 35

4.2 How can we not know? 36

4.3 Discovery rates 37

4.4 Scaling 40

4.5 Sampling-based methods 41

4.6 Other organisms 47

4.7 Wrapping up 48

4.8 Conclusions 50

4.8.1 Recommended reading 50

4.8.2 Questions for the future 50

PART II DIVERSITY

5 Measuring diversity 57

5.1 The big question 57

5.2 Scales of diversity 58

5.3 Species richness 58

5.4 Believing in estimates 63

5.5 A SAD story 65

5.6 Diversity of species 67

5.7 Other measures of diversity 71

5.8 diversity 75

5.9 Case study: the Binatang project 76

5.10 Conclusions 80

5.10.1 Recommended reading 80

5.10.2 Questions for the future 80

6 Niches 85

6.1 The big question 85

6.2 Historical background 86

6.3 Back to basics 89

6.4 Birth and death rates 90

6.5 The ZNGI 95

6.6 Impact vectors 98

6.7 Supply points 98

6.8 Coexistence 98

6.9 The evidence 106

6.10 Implications 112

6.11 Conclusions 116

6.11.1 Recommended reading 117

6.11.2 Questions for the future 117

7 Patterns in species richness 121

7.1 The big question 121

7.2 Area 121

7.3 Local and regional species richness 124

7.4 Local patterns in species richness 131

7.5 Congruence 137

7.6 Assembling a model 139

7.7 Conclusions 139

7.7.1 Recommended reading 140

7.7.2 Questions for the future 141

8 Drivers of diversity 147

8.1 The big question 147

8.2 Coexistence or co-occurrence? 148

8.3 Energy and resources 148

8.4 Diversity begets diversity 154

8.4.1 Heterogeneity in space 154

8.4.2 Heterogeneity in time 158

8.5 Disturbance 160

8.6 Top-down control 162

8.7 Expanding our model 168

8.8 Conclusions 169

8.8.1 Recommended reading 169

8.8.2 Questions for the future 169

9 Does diversity matter? 175

9.1 The big question 175

9.2 Ecosystems 176

9.3 What shape is the relationship? 178

9.4 Field experiments 181

9.5 A problem with peas 185

9.6 Other measures of diversity 186

9.7 Multifunctionality 188

9.8 The real world 189

9.9 The link between species richness and productivity 194

9.10 Conclusions 194

9.10.1 Recommended reading 195

9.10.2 Questions for the future 196

PART III COMMUNITIES

10 Organisation at the community scale 203

10.1 The big question 203

10.2 Definitions 204

10.3 Communities in the field 205

10.4 Quantitative approaches 206

10.5 Community structure 210

10.6 Food chains 213

10.7 Food webs 216

10.8 Complexity and stability 221

10.9 Trophic cascades 222

10.10 SAD again 225

10.11 Complex systems 228

10.12 Unified Neutral Theory 231

10.13 Metabolic Theory of Ecology 234

10.14 Conclusions 236

10.14.1 Recommended reading 237

10.14.2 Questions for the future 237

11 Stability 245

11.1 The big question 245

11.2 Stable states 245

11.3 Changing environments 249

11.4 Hysteresis 253

11.5 Predicting changes 256

11.6 Coral reefs 257

11.7 Shifting baselines 259

11.8 Conclusions 263

11.8.1 Recommended reading 264

11.8.2 Questions for the future 265

11.9 Coda: the seduction of Gaia 265

12 Changes through time 273

12.1 The big question 273

12.2 Succession 274

12.3 Succession and niche theory 275

12.4 Examples of succession 279

12.5 Disturbance 281

12.6 Modelling succession 283

12.7 Regeneration 286

12.8 Plants and animals 287

12.9 Case study: Mpala, Kenya 288

12.10 Conclusions 290

12.10.1 Recommended reading 291

12.10.2 Questions for the future 291

13 Changes through space 295

13.1 The big question 295

13.2 Community assembly 296

13.2.1 Competitive exclusion 297

13.2.2 Historical processes 300

13.2.3 Habitat checkerboards 302

13.2.4 Chance & contingency 302

13.3 Metacommunities 304

13.4 Dispersal limitation 313

13.5 Combining environment and dispersal 318

13.6 Conclusions 322

13.6.1 Recommended reading 322

13.6.2 Questions for the future 323

PART IV BIOGEOGRAPHY

14 Global patterns of life 331

14.1 The big question 331

14.2 Biogeography 331

14.3 Phytogeography 336

14.4 Ecoregions 340

14.5 Empirical approaches 341

14.6 The oceans 345

14.7 Fresh water 349

14.8 Conclusions 349

14.8.1 Recommended reading 350

14.8.2 Questions for the future 350

15 Regional species richness 355

15.1 The big question 355

15.2 Climate and productivity 357

15.3 Other processes 360

15.4 Scale and productivity 362

15.5 Latitudinal gradients 367

15.6 Centres of origin 369

15.7 Regional Species-Area Relationships 370

15.8 Confounding effects 371

15.9 Conclusions 373

15.9.1 Recommended reading 373

15.9.2 Questions for the future 374

16 Latitudinal gradients 381

16.1 The big question 381

16.2 Hypotheses 382

16.3 Geographic Area 382

16.4 Climatic stability 385

16.5 Productivity 386

16.6 Niche size 387

16.7 Evolutionary speed 390

16.8 Out of the tropics 393

16.9 Conclusions 398

16.9.1 Recommended reading 399

16.9.2 Questions for the future 399

17 Earth history 407

17.1 The big question 407

17.2 Geological history 408

17.3 Continental drift 409

17.4 Echoes of Pangæa 412

17.5 Climatic effects 416

17.6 Ice Ages 419

17.7 Sea level 424

17.8 Extinctions 425

17.9 Conclusions 429

17.9.1 Recommended reading 431

17.9.2 Questions for the future 431

18 Dispersal 437

18.1 The big question 437

18.2 Range expansion 438

18.3 Mechanisms of dispersal 440

18.4 Barriers 442

18.5 Case studies 445

18.5.1 New Zealand 445

18.5.2 Madagascar 448

18.6 Conclusions 454

18.6.1 Recommended reading 455

18.6.2 Questions for the future 455

19 Life on islands 461

19.1 The big question 461

19.2 Types of island 462

19.3 Island biotas 464

19.4 Evolution of endemics 465

19.5 Size changes 467

19.6 Reproduction and dispersal 470

19.7 Super-generalists 474

19.8 Endemic communities 475

19.9 Disharmony 475

19.10 Assembly rules 477

19.11 Island species richness 478

19.12 The Equilibrim Model of Island Biogeography 481

19.13 Testing the theory 485

19.14 Conclusions 486

19.14.1 Recommended reading 487

19.14.2 Questions for the future 487

20 Reinventing islands 493

20.1 The big question 493

20.2 A critique of EMIB 494

20.3 Rival hypotheses 497

20.4 Disturbance 498

20.5 Relaxation 502

20.6 Extinctions 504

20.7 Invasions 505

20.8 A new theory? 506

20.9 Evolution 508

20.10 Conclusions 515

20.10.1 Recommended reading 515

20.10.2 Questions for the future 516

21 What is a natural system? 521

21.1 The big question 521

21.2 Lessons learnt 523

21.2.1 Ecological processes are scale-dependent 523

21.2.2 All interactions are nested 523

21.2.3 There is no such thing as the balance of nature 524

21.2.4 Everything is contingent 524

21.3 Processes not systems 525

A Diversity analysis case study: Butterfly conservation in the Rocky Mountains 527

A.1 Software resources 528

A.2 Calculations 529

A.3 Synthesis 536

A.4 Conclusions 537

Glossary 541

Index 547