Quantifying the Evolution of Early Life (eBook)

Dedication 6
Foreword 10
Preface 12
Contents 16
Contributors 18
Part I Numerical Methods 22
Chapter 1: Ordination Methods and the Evaluation of Ediacaran Communities 23
1.1 Introduction 24
1.2 Dataset Summary 25
1.3 Data Standardization 26
1.4 Ordination Methods 26
1.4.1 Principal Components Analysis (PCA) 26
1.4.2 Correspondence and Detrended Correspondence Analysis (CA/DCA) 30
1.4.3 Non-Metric Multidimensional Scaling (NMDS) 33
1.5 Comparison and Interpretation of Results 36
1.6 Conclusion 39
References 40
Chapter 2: Exploratory Multivariate Techniques and Their Utility for Understanding Ancient Ecosystems 42
2.1 Introduction 43
2.2 Characterization of Data 45
2.3 Common Multivariate Ordinations 47
2.3.1 Principal Components Analysis 47
2.3.2 Principal Coordinates Analysis 53
2.3.3 Non-Metric Multidimensional Scaling 54
2.3.4 Detrended Correspondence Analysis 59
2.3.5 Discriminant Analysis and Canonical Variate Analysis 61
2.4 Conclusions 64
Acknowledgments 64
References 64
Chapter 3: Morphometrics in the Study of Ediacaran Fossil Forms 68
3.1 Introduction 69
3.2 Definitions and Terminology 70
3.2.1 Size, Shape, and Form 71
3.2.2 Isometry and Allometry 72
3.2.3 Discrete, Categorical, and Continuous Variables 72
3.3 Scale of Morphometric Studies 73
3.3.1 Assemblage-Level 73
3.3.2 Taxon-Level 74
3.3.3 Species-Level 74
3.4 Morphometric Datasets 74
3.4.1 Traditional Morphometric Dataset: Charniodiscus 75
3.4.1.1 Traditional Morphometric Data Analysis 75
3.4.1.2 Principal Components Analysis (PCA) 76
3.4.1.3 Principal Coordinates Analysis (PCO) 79
3.4.1.4 Loading Plots 79
3.4.1.5 Non-Metric Multidimensional Scaling (nMDS) 80
3.4.1.6 How to Pick Which Analysis to Use? 81
3.4.2 Geometric Morphometric Dataset: Charnia 81
3.4.2.1 Geometric Morphometric Data Analysis 81
3.4.2.2 Landmark Data Collection and Superposition Methods 83
3.4.2.3 Charnia Modularity 85
3.5 Conclusions 87
References 89
Chapter 4: Analyzing Predation from the Dawn of the Phanerozoic 91
4.1 Introduction 92
4.1.1 Predation and the Cambrian Explosion 92
4.1.2 A Brief Review of Cambrian Predation 93
4.2 Measuring Predation 99
4.2.1 Traces in Sediment of Predatory Behavior 100
4.2.2 Traces of Predation on the Prey Skeleton 101
4.2.3 Crushing Traces 106
4.2.4 Drilling Traces 107
4.2.5 Stereotypy 107
4.3 Data and Statistics 109
4.3.1 Organizing the Data 109
4.3.2 Statistical Tests 111
4.3.3 Predation Traces as Landmarks 115
4.3.4 Predation Frequencies 118
4.4 Cambrian Considerations 121
References 123
Chapter 5: Ecospace Utilization During the Ediacaran Radiation and the Cambrian Eco-explosion 128
5.1 Introduction 129
5.2 Theoretical Ecospace 130
5.3 Paleoecology of Ediacaran Animals 132
5.4 Ecospace Occupation During the Ediacaran 133
5.5 Comparing Diversification in Ecology, Taxonomy, and Morphology During the Ediacaran Period 136
5.6 Trends in Ecospace Utilization from the Ediacaran to the Phanerozoic 137
5.6.1 Quantitative Tests 141
5.6.2 Ecological Change in the Cambrian Explosion: Tiering, Motility, Feeding 143
5.6.3 A Comment on Ediacaran-Phanerozoic Trends 144
5.7 Future Work 144
5.8 Conclusions 145
References 146
Chapter 6: Quantifying Bioturbation in Ediacaran and Cambrian Rocks 151
6.1 Introduction 152
6.2 Semi-Quantitative Methods 153
6.2.1 Ichnofabric Indices (Droser and Bottjer 1986) 154
6.2.2 Bioturbation Index (Taylor and Goldring 1993 Modified After Reineck 1963)156
6.2.3 Bedding Plane Bioturbation Indices(Miller and Smail 1997) 157
6.3 Quantitative Methods 158
6.3.1 Grid-Based Estimation of Percentage Area 158
6.3.1.1 Bedding Plane Analysis: 10 × 10.cm Grids (Heard and Pickering 2008) 159
6.3.1.2 Analysis of Cores: 10 × 6 cm Grids (Heard et al. 2008) 160
6.3.1.3 Intersection Grid Method for Bedding Planes(Marenco and Bottjer 2010) 160
6.3.2 Image Analysis 164
6.3.2.1 Thin Section Image Analysis or the H Method (Francus 2001) 164
6.3.2.2 Automated Image Analysis of X-Radiographs(Löwemark 2003) 166
6.3.3 Imaging Techniques (X-Radiography, CT, MRI) 167
6.3.3.1 Calculating Burrow Volume Using CT (Dufour et al. 2005) 168
6.4 Summary 171
References 172
Chapter 7: Assessing the Role of Skeletons in Early Paleozoic Carbonate Production: Insights from Cambro-Ordovician Strata, Western Newfoundland 177
7.1 Introduction 178
7.2 Skeletons and the Early Radiation of Life 180
7.3 Methods 180
7.4 Biases in Thin Section Analysis 186
7.5 Geological Setting of Strata in Newfoundland 187
7.6 Analysis of Point Counting Abundance 188
7.6.1 Series 3 to Furongian (Cambrian) and Tremadocian (Lower Ordovician) Results 188
7.6.2 Floian (Lower Ordovician) to Dapingian (Middle Ordovician) Results 193
7.7 Secular Trends in Cambro-Ordovician Skeletal Abundance, Western Newfoundland 194
7.8 Future Work 195
7.9 Conclusions 196
References 197
Chapter 8: Exploring the Ecological Dynamics of Extinction 200
8.1 Introduction 201
8.2 Taxonomic Signals – How to Identify Extinction Intervals 203
8.2.1 Extinction Rates 204
8.3 Ecological Signals 205
8.3.1 Exploring Patterns of Extinction Among Taxa 205
8.3.2 Exploring Paleoecological Data 206
8.3.2.1 Collecting Paleoecological Data 207
8.3.2.2 Ordinations 213
8.3.2.3 Evenness 214
8.3.2.4 Rank–Abundance Curves (RACs) 214
8.4 Examples 218
8.4.1 Extinction Rates 219
8.4.1.1 Results 219
8.4.1.2 Interpretation 219
8.4.2 Ordination 221
8.4.2.1 Results 221
8.4.2.2 Interpretation 221
8.4.3 Community Structure 222
8.4.3.1 Results 222
8.4.3.2 Interpretation 223
8.5 Implications for Future Work 226
8.6 Summary 226
Appendixes 227
Appendix 8.1 Diversity and Evolutionary Rates for Early Cambrian Taxa 227
Appendix 8.2 Community Data for Early Cambrian Assemblages 229
References 232
Part II Technological Approaches 236
Chapter 9: Fossils with Little Relief: Using Lasers to Conserve, Image, and Analyze the Ediacara Biota 237
9.1 Introduction 238
9.2 History of Imaging the Ediacara Biota 239
9.3 The Application of Lasers to the Ediacara Biota 241
9.3.1 Serially Lit Photograph Sets 242
9.3.2 High Resolution Laser Scanning and Composite Master Drawings 243
9.4 Other Recent Applications of Lasers to Paleontology 246
9.4.1 Scanning of Whole Large Skeletons for Biomechanics Studies 249
9.4.2 Scanning Large Bedding Planes, e.g. Vertebrate Track-Ways 249
9.4.3 Scanning Cliffs to Map Erosion at Important Fossil Sites 250
9.4.4 High Resolution Scanning of Taxonomically Relevant Characters to Aid Classification and Analysis of Detailed Morphology 250
9.5 Concluding Remarks 251
References 252
Chapter 10: Confocal Laser Scanning Microscopy and Raman (and Fluorescence) Spectroscopic Imagery of Permineralized Cambrian and Neoproterozoic Fossils 255
10.1 Introduction 256
10.1.1 Statement of the Problem 257
10.1.2 Focus of This Study 258
10.2 CLSM and Raman Imagery 259
10.2.1 Overview 259
10.2.2 Confocal Laser Scanning Microscopy 259
10.2.3 Raman (and Fluorescence) Spectroscopy and Imagery 260
10.3 Materials and Methods 261
10.3.1 Materials 261
10.3.2 Optical Microscopy 262
10.3.3 Confocal Laser Scanning Microscopy 262
10.3.4 Raman (and Fluorescence) Spectroscopy 262
10.4 Paleontological Uses and Limitations of CLSM and Raman Imagery 264
10.4.1 Applicability of the Two Techniques 264
10.4.2 Limitations of the Two Techniques 264
10.4.3 Comparative Strengths and Weaknesses of the Two Techniques 265
10.4.4 Use of CLSM and Raman, Combined 266
10.5 CLSM and Raman (and Fluorescence) Spectroscopic Imagery of Early Cambrian and Neoproterozoic Fossils 266
10.5.1 Early Cambrian Ctenophore Embryo 266
10.5.2 Late Neoproterozoic Scale Fossils 269
10.5.3 Late Neoproterozoic Filamentous Cyanobacteria 272
10.5.4 Late Neoproterozoic Spheroidal Acritarchs and Cyanobacteria 275
10.6 Geochemical Maturity of the Fossil-Comprising Kerogen 278
10.6.1 Raman Spectra and the Raman Index of Preservation 278
10.6.2 Geochemical Maturity of the Analyzed Kerogens 280
10.7 Conclusions 280
References 282
Chapter 11: X-Ray Microanalysis of Burgess Shale and Similarly Preserved Fossils 285
11.1 Introduction 286
11.2 Preservation of Burgess Shale Fossils 288
11.3 Instrumentation 291
11.3.1 ‘High Vacuum’ and ‘Variable Pressure’ SEMs 291
11.3.2 Specimen Charging 291
11.3.3 Alternative SEM Systems 292
11.4 Simulation of Electron Beam-Sample Interactions 292
11.5 Size and Shape of the Interaction Volume 293
11.6 Selection and Preparation of Samples for X-Ray Analysis 293
11.6.1 Destructive Preparation Techniques 293
11.6.2 Selection and Preparation of Paleontological Specimens for VP-SEM 294
11.7 X-Ray Imaging and Microanalysis 295
11.7.1 Principles of X-Ray Generation 295
11.7.2 Structure of the ED Spectrum 297
11.8 Element, or X-Ray, Mapping 299
11.8.1 Contribution of the Continuum to X-Ray Maps 300
11.8.2 Importance of the Detector Window 300
11.8.3 Operator-Controlled Variables 300
11.8.4 Resolution of X-Ray Maps 301
11.8.5 X-Ray Analysis of ‘Layered Substrates’ 302
11.8.6 Elemental Mapping at Low Accelerating Voltages 304
11.8.7 Specimen Topography 305
11.8.8 Interpretation of Element Abundance from X-Ray Maps 307
11.9 Determining Composition Under VP Conditions: The Beam Skirt Effect 309
11.10 Selection of ED Detectors 309
11.11 Quantitative Analysis of the Composition of Mineral Phases Using X-Rays 310
11.12 Summary 310
References 311
Chapter 12: Ultrastructural Approaches to the Microfossil Record: Assessing Biological Affinities by Use of Transmission Electron Microscopy 314
12.1 Introduction 315
12.2 The Transmission Electron Microscope 315
12.3 Preparation for TEM 317
12.3.1 Primary Fixation 318
12.3.2 Secondary Fixation 318
12.3.3 Dehydration 318
12.3.4 Infiltration and Embedding 319
12.3.5 A Modified Preparation Technique for Small Specimens 319
12.3.6 Sectioning the Sample (Microtoming) 321
12.3.7 Support Grid 321
12.3.8 Staining 321
12.4 How to Interpret TEM Structures 322
12.4.1 Strengths of the Technique 322
12.5 TEM in Geobiology 323
12.5.1 Current Research in Geobiology Using TEM 324
12.6 Discussion 329
12.7 Conclusions 330
References 331
Chapter 13: Paleobiological Applications of Focused Ion Beam Electron Microscopy (FIB-EM): An Ultrastructural Approach to the (Micro)Fossil Record 334
13.1 A Brief History of the Focused Ion Beam Electron Microscope 335
13.2 FIB-EM Systems 339
13.2.1 Technical Description and Operational Capabilities 339
13.2.2 Principal Uses 341
13.2.3 Overview of the FIB-EM “Lift-Out” Method for Preparation of Electron-Transparent Ultrathin Foils 343
13.2.4 Overview of the FIB-EM Nanotomography Method: A Three-Dimensional View of Microstructure 345
13.3 FIB-EM Methods in the Paleobiological Literature 347
13.4 FIB-EM Nanotomography: An Acritarch-Based Case Study 351
13.4.1 Examining Acritarch Ultrastructure: A Brief Introduction 351
13.4.2 Sample Description and Preparation 352
13.4.3 FIB-EM Nanotomography of Shuiyougou Acritarchs 353
13.4.4 Case Study Results 353
13.4.4.1 FIB-EM Nanotomography of Dictyosphaera delicata 353
13.4.4.2 FIB-EM Nanotomography of Shuiyousphaeridium macroreticulatum 354
13.4.5 Case Study Discussion 360
13.5 Strengths of FIB-EM Instrument and Final Remarks 362
References 363
Chapter 14: Reconstructing Deep-Time Biology with Molecular Fossils 368
14.1 Introduction 369
14.1.1 Deep Time Phylogeny 369
14.1.2 Sedimentary Organic Matter 371
14.1.2.1 Organic Matter Preservation 371
14.1.2.2 Kerogen Formation 374
14.1.2.3 Bitumen Expulsion 374
14.1.2.4 Fluid Inclusions 375
14.2 Sampling Strategies 375
14.2.1 Precambrian Sedimentary Basins 375
14.2.2 Outcrop and Core 376
14.2.3 Interregional Approaches 377
14.3 Preparative Methods 378
14.3.1 Materials 378
14.3.2 Preparation of Rock Samples 379
14.3.3 Extraction 380
14.3.3.1 Free Bitumen (Bitumen 1) 380
14.3.3.2 Mineral-Occluded Bitumen (Bitumen 2) 380
14.3.3.3 Elemental Sulfur 381
14.3.3.4 Internal Standards 382
14.3.4 Sample Fractionation by Liquid Chromatography 382
14.3.4.1 Open Column Chromatography 382
Medium and Large Columns 383
Small Columns 384
Argentation Chromatography 384
14.3.4.2 Molecular Sieve Separations 385
14.4 Analytical Methods 386
14.4.1 Gas Chromatography (GC) 386
14.4.1.1 GC Injection 386
14.4.1.2 GC Column and Oven Program Selection 388
14.4.2 GC – Flame Ionization Detector (FID) 389
14.4.3 Mass Spectrometry (MS) 389
14.4.4 Pyrolysis 394
14.4.5 High Performance Liquid Chromatography (HPLC) 395
14.4.6 Stable Isotope Analysis 395
14.5 Guidelines to Interpretation 397
14.5.1 Typical Bitumen Composition 397
14.5.2 Compound Identification 398
14.5.3 Contamination 399
14.5.3.1 Branched Alkanes with Quaternary Carbon Atoms (BAQCs) 399
14.5.3.2 Patterns of n-Alkane Hydrocarbons 400
14.5.3.3 Thermal Maturity Parameters and Their Use 401
14.5.3.4 Age-Sensitive Biomarker Distributions 404
14.5.3.5 Early or Late Eukaryotes? 407
14.5.4 Blanks 408
14.6 Concluding Remarks and Future Directions 409
References 409
Chapter 15: Carbon and Sulfur Stable Isotopic Systems and Their Application in Paleoenvironmental Analysis 415
15.1 Introduction 416
15.2 Introduction to Stable Isotopes 417
15.2.1 Basic Principles and Reference Standards 417
15.2.2 Isotopic Fractionation and the Fractionation Factor 419
15.3 The Carbon Cycle and Isotopic System 421
15.3.1 Carbon Fractionation and the Vital Affect 422
15.3.2 Carbon Reservoirs 423
15.4 The Sulfur Cycle and Isotopic System 425
15.4.1 Sulfur Fractionation 426
15.4.2 Sulfur Reservoirs 427
15.5 Stable Isotopes Mass Spectrometryand Sampling Techniques 429
15.5.1 Isotope Ratio Mass Spectrometry 429
15.5.2 Gases Used in Carbon and Sulfur Isotopic Extraction 430
15.5.3 Common Preparation Techniques and Quality Control 431
15.6 Diagenetic Alteration of Stable Isotopes 434
15.6.1 Diagenetic Alteration of Carbon Isotopes 435
15.6.2 Diagenetic Alteration of Sulfur Isotopes 437
15.7 Mass Balance, Mechanisms, and Secular Trends Through Geologic Time 438
15.7.1 Carbon 438
15.7.2 Sulfur 443
15.8 Case Study: The Terminal NeoproterozoicShuram Anomaly 445
15.8.1 Characteristics and Correlation of the Shuram Anomaly 446
15.8.2 Mechanisms for the Shuram Anomaly 448
15.9 Summary 450
References 451
Index 463