Preface xv
Acknowledgements xix
Abbreviations xxi
1 Introduction: defining nature 1
1.1 How little we know 1
1.2 Pressing questions 2
1.3 The hierarchy of nature 2
1.4 Biodiversity 4
1.5 Myths to bust 4
1.6 Further information 5
1.6.1 Recommended reading 5
References 5
Part I: Species
2 What is a species? 9
2.1 The big question 9
2.2 Species concepts 10
2.2.1 Nominalistic 10
2.2.2 Morphological 11
2.2.3 Biological 12
2.2.4 Phylogenetic 13
2.2.5 Genetic 14
2.3 Solving the riddle 16
2.4 Coda: Species richness 17
2.5 Conclusions 17
2.5.1 Recommended reading 17
2.5.2 Questions for the future 17
References 17
3 The history of life 19
3.1 The big question 19
3.2 Sources of evidence 19
3.2.1 The fossil record 19
3.2.2 Molecular evidence 20
3.3 A brief history of diversity 20
3.4 Uneven diversity 24
3.5 Conclusions 25
3.5.1 Recommended reading 26
3.5.2 Questions for the future 26
References 26
4 How many species are there? 29
4.1 The big question 29
4.2 How can we not know? 29
4.3 Discovery rates 30
4.4 Scaling 32
4.5 Sampling-based methods 33
4.6 Other organisms 36
4.7 Wrapping up 36
4.8 Conclusions 37
4.8.1 Recommended reading 38
4.8.2 Questions for the future 38
References 38
Part II: Diversity
5 Measuring diversity 43
5.1 The big question 43
5.2 Scales of diversity 43
5.3 Species richness 43
5.4 Believing in estimates 46
5.5 A SAD story 47
5.6 Diversity of species 49
5.7 Other measures of diversity 51
5.8 diversity 53
5.9 Case study: The Binatang project 54
5.10 Conclusions 57
5.10.1 Recommended reading 57
5.10.2 Questions for the future 57
References 57
6 Niches 61
6.1 The big question 61
6.2 Historical background 61
6.3 Back to basics 63
6.4 Birth and death rates 63
6.5 The ZNGI 66
6.6 Impact vectors 67
6.7 Supply points 67
6.8 Coexistence 68
6.9 The evidence 71
6.10 Implications 73
6.11 Conclusions 76
6.11.1 Recommended reading 77
6.11.2 Questions for the future 77
References 77
7 Patterns in species richness 79
7.1 The big question 79
7.2 Area 79
7.3 Local and regional species richness 81
7.4 Local patterns in species richness 85
7.4.1 Elevation 85
7.4.2 Depth 88
7.4.3 Peninsulas and Bays 88
7.4.4 Isolation 89
7.4.5 Mid-Domain Effects 89
7.5 Congruence 89
7.6 Assembling a model 90
7.7 Conclusions 91
7.7.1 Recommended reading 91
7.7.2 Questions for the future 92
References 92
8 Drivers of diversity 95
8.1 The big question 95
8.2 Coexistence or co-occurrence? 95
8.3 Energy and resources 95
8.4 Diversity begets diversity 101
8.4.1 Heterogeneity in space 101
8.4.2 Heterogeneity in time 103
8.5 Disturbance 104
8.6 Top-down control 105
8.7 Expanding our model 109
8.8 Conclusions 110
8.8.1 Recommended reading 110
8.8.2 Questions for the future 111
References 111
9 Does diversity matter? 113
9.1 The big question 113
9.2 Ecosystems 113
9.3 What shape is the relationship? 115
9.4 Field experiments 117
9.5 Other measures of diversity 121
9.6 Multifunctionality 122
9.7 The real world 125
9.8 Species richness and productivity 126
9.9 Conclusions 127
9.9.1 Recommended reading 127
9.9.2 Questions for the future 128
References 128
Part III: Communities
10 Organisation at the community scale 133
10.1 The big question 133
10.2 Definitions 133
10.3 Communities in the field 134
10.4 Quantitative approaches 135
10.5 Community structure 137
10.6 Food chains 140
10.7 Food webs 142
10.8 Complexity and stability 145
10.9 Trophic cascades 147
10.10 SAD again 148
10.11 Complex systems 151
10.12 Unified neutral theory 153
10.13 Metabolic theory of ecology 155
10.14 Conclusions 156
10.14.1 Recommended reading 157
10.14.2 Questions for the future 157
References 157
11 Stability 161
11.1 The big question 161
11.2 Stable states 161
11.3 Changing environments 164
11.4 Hysteresis 165
11.5 Predicting changes 167
11.6 Coral reefs 169
11.7 Shifting baselines 170
11.8 Conclusions 173
11.8.1 Recommended reading 174
11.8.2 Questions for the future 175
11.9 Coda: the seduction of Gaia 175
References 176
12 Changes through time 179
12.1 The big question 179
12.2 Succession 179
12.3 Succession and niche theory 180
12.4 Examples of succession 182
12.5 Disturbance 184
12.6 Modelling succession 185
12.7 Regeneration 187
12.8 Plants and animals 188
12.9 Case study: Mpala, Kenya 188
12.10 Conclusions 190
12.10.1 Recommended reading 190
12.10.2 Questions for the future 190
References 191
13 Changes through space 193
13.1 The big question 193
13.2 Community assembly 193
13.2.1 Competitive exclusion 194
13.2.2 Historical processes 196
13.2.3 Habitat checkerboards 197
13.2.4 Chance and contingency 198
13.3 Metacommunities 199
13.4 Dispersal limitation 204
13.5 Combining environment and dispersal 208
13.6 Conclusions 210
13.6.1 Recommended reading 210
13.6.2 Questions for the future 210
References 210
Part IV: Biogeography
14 Global patterns of life 215
14.1 The big question 215
14.2 Biogeography 215
14.3 Phytogeography 217
14.4 Ecoregions 222
14.5 Empirical approaches 223
14.6 The oceans 225
14.7 Fresh water 228
14.8 Conclusions 228
14.8.1 Recommended reading 229
14.8.2 Questions for the future 229
References 229
15 Regional species richness 233
15.1 The big question 233
15.2 Climate and productivity 234
15.3 Other processes 236
15.4 Scale and productivity 238
15.5 Latitudinal gradients 240
15.6 Centres of origin 243
15.7 Regional species-area relationships 244
15.8 Confounding effects 244
15.9 Conclusions 245
15.9.1 Recommended reading 246
15.9.2 Questions for the future 246
References 246
16 Latitudinal gradients 249
16.1 The big question 249
16.2 Hypotheses 249
16.3 Geographic area 249
16.4 Climatic stability 251
16.5 Productivity 252
16.6 Niche size 253
16.7 Evolutionary speed 254
16.8 Out of the tropics 257
16.9 Conclusions 261
16.9.1 Recommended reading 262
16.9.2 Questions for the future 262
References 262
17 Earth history 265
17.1 The big question 265
17.2 Geological history 265
17.3 Continental drift 266
17.4 Echoes of Pangaea 269
17.5 Climatic effects 272
17.6 Ice ages 274
17.7 Sea level 278
17.8 Extinctions 278
17.9 Conclusions 281
17.9.1 Recommended reading 283
17.9.2 Questions for the future 283
References 283
18 Dispersal 287
18.1 The big question 287
18.2 Range expansion 287
18.3 Mechanisms of dispersal 289
18.4 Barriers 290
18.5 Case studies 292
18.5.1 New Zealand 292
18.5.2 Madagascar 295
18.6 Conclusions 299
18.6.1 Recommended reading 300
18.6.2 Questions for the future 300
References 300
19 Life on islands 303
19.1 The big question 303
19.2 Types of island 303
19.3 Island biotas 305
19.4 Evolution of endemics 305
19.5 Size changes 307
19.6 Reproduction and dispersal 310
19.7 Super-generalists 311
19.8 Endemic communities 312
19.9 Disharmony 312
19.10 Assembly rules 314
19.11 Island species richness 314
19.12 The equilibrium model of island biogeography 317
19.13 Testing the theory 319
19.14 Conclusions 320
19.14.1 Recommended reading 320
19.14.2 Questions for the future 320
References 320
20 Reinventing islands 323
20.1 The big question 323
20.2 A critique of EMIB 323
20.3 Rival hypotheses 326
20.4 Disturbance 326
20.5 Relaxation 329
20.6 Extinctions 331
20.7 Invasions 331
20.8 A new theory? 332
20.9 Evolution 333
20.10 Conclusions 338
20.10.1 Recommended reading 338
20.10.2 Questions for the future 338
References 338
21 What is a natural system? 341
21.1 The big question 341
21.2 Lessons learnt 342
21.2.1 Ecological processes are scale dependent 342
21.2.2 All interactions are nested 342
21.2.3 There is no such thing as the balance of nature 342
21.2.4 Everything is contingent 343
21.3 Processes not systems 343
References 344
Appendix A Diversity analysis case study: Butterfly conservation in the Rocky Mountains 345
A.1 Software resources 345
A.2 Calculations 346
A.3 Synthesis 350
A.4 Conclusions 351
References 352
Glossary 353
Index 359
