Evolutionary Biology (eBook)

184822_1_En_FM1_OnlinePDF 2
Outline placeholder 1
Preface 5
Preface 5
Meeting Report: 12th Evolutionary Biology Meeting in Marseille 6
Meeting Report: 12th Evolutionary Biology Meeting in Marseille 5
Contents 6
Contents 5
Contributors 6
Contributors 5
184822_1_En_1_Chapter_OnlinePDF 20
Chapter Chapter 1: Spontaneous Generation Revisited at the Molecular Level 21
1.1Introduction 21
1.2From HCN to Nucleotides 22
1.2.1From Formamide to Nucleic Bases 22
1.2.2From Nucleic Bases to Acyclo-Nucleosides 23
1.2.3From Nucleosides to Nucleotides 24
1.2.4Formamide 25
1.2.5Water 25
1.3Stability 26
1.3.1Stability of the Relevant Bonds 26
1.3.2pH and Sequence Context 28
1.3.3Minerals and Protection 31
1.4Polymerization 32
1.4.1Nonenzymatic Syntheses in Water 32
1.4.2Ligation of Oligomers as a Way-Out from the Futile Cycle of Syntheses/Degradations 33
1.5Conclusion 37
References 38
184822_1_En_2_Chapter_OnlinePDF 41
Chapter Chapter 2: Minimal Cell Model to Understand Origin of Life and Evolution 41
2.1Introduction 41
2.2Spontaneous Movement of Amphiphilic Self-assemblies 42
2.2.1Self-winding Helix of Oleic Acid 43
2.2.2Self-propelled Oil Droplets 46
2.2.2.1Self-propelled Oil Droplets from Lipophilic Precursor of Surfactant (Oleic Acid-Oleate) 46
2.2.2.2Self-propelled Oil Droplets Consuming Surfactant as Fuel 47
2.3Dynamics of Self-reproduction Exhibited by Giant Vesicles 49
2.3.1Self-reproducing Vesicular System of the Nutrient-Containing Type 51
2.3.2Robustly Reproducing Giant Vesicular System 52
2.4Population Analysis of Self-reproducing Giant Vesicles by Flow Cytometry 54
2.4.1Protocol of Flow Cytometric Analysis 54
2.4.2Population Analysis of Self-reproducing Vesicles 55
2.4.3Self-reproducing Vesicles as a Molecular Model of Evolution 57
2.5Self-replication of Informational Substances in a Giant Vesicle 58
2.5.1Enzymatic Reaction in Vesicle 58
2.5.2Performance of Polymerase Chain Reaction in GV 58
2.5.3Flow Cytometric Analysis of PCR in Vesicles 60
2.5.4Meaning of Encapsulation in Enzymatic Reactions 61
2.6Coupling between Self-reproduction of GV and Self-replication of DNA 63
2.6.1Design and Preparation of DNA-cholesterol Conjugate 63
2.6.2Replication of DNA Inside GV Carrying DNA-Cholesterol Conjugate 64
2.6.3Partition Mechanism in Cell Division of Escherichia coli 65
2.7Evolution Towards Artificial Cell 66
References 67
184822_1_En_3_Chapter_OnlinePDF 69
Chapter Chapter 3: New Fossils and New Hope for the Origin of Angiosperms* 69
3.1Introduction 69
3.2Definition of Flower and Angiosperm 70
3.3Acquisition of the Features 73
3.4Examples of Early Angiosperms 74
3.4.1Chaoyangia 74
3.4.1.1Brief History 74
3.4.1.2Discussion 74
3.4.1.3Diagnosis 75
3.4.1.4Description 75
3.4.2Callianthus 77
3.4.2.1Brief History 77
3.4.2.2Discussion 77
3.4.2.3Diagnosis 77
3.4.2.4Description 78
3.4.3Xingxueanthus 79
3.4.3.1Brief History 79
3.4.3.2Discussion 79
3.4.3.3Diagnosis 80
3.4.3.4Description 80
3.4.4Schmeissneria 81
3.4.4.1Brief History 81
3.4.4.2Discussion 82
3.4.4.3Diagnosis 82
3.4.4.4Description 83
3.5Conclusion 84
References 86
184822_1_En_4_Chapter_OnlinePDF 89
Chapter Chapter 4: Vertebrate Evolution: The Strange Case of Gymnophionan Amphibians 89
4.1Introduction 89
4.2Morphological Data 90
4.2.1General Anatomy 90
4.2.2Integument 91
4.2.3Skeleton 91
4.2.4Brain 92
4.2.5Sense Organs 92
4.2.6Digestive Tract 93
4.2.7Respiratory System 94
4.2.8Heart 94
4.2.9Immune System 94
4.2.10Excretion System 94
4.2.11Endocrine Organs 95
4.2.12Male Genital Tract 95
4.2.13Female Genital Tract 96
4.2.14Development and Metamorphosis 96
4.3Biogeography 97
4.4Fossils 97
4.4.1Molecular Data 97
4.5Systematic Position 97
4.5.1Internal Classification 98
4.5.2Position of Gymnophiona Among Vertebrates 98
4.6Conclusion 100
References 101
184822_1_En_5_Chapter_OnlinePDF 108
Chapter Chapter 5: The Evolution of Morphogenetic Signalling in Social Amoebae 108
5.1Introduction 108
5.2The Life Cycle of D. discoideum 110
5.2.1Cell Differentiation and Morphogenesis 110
5.2.2Signals that Control D. discoideum Development 111
5.3Phenotypic Evolution in the Social Amoebae 115
5.4The Evolution of cAMP Signalling 117
5.4.1Extracellular cAMP 117
5.4.2Intracellular cAMP 119
5.5Conclusions 121
References 122
184822_1_En_6_Chapter_OnlinePDF 125
Chapter Chapter 6: On the Surprising Weakness of Pancreatic Beta-Cell Antioxidant Defences: An Evolutionary Perspective 125
6.1Introduction 126
6.1.1Beta-Cellsbeta-cells and Glucose Homeostasisglucosehomeostasis 126
6.1.2Reactive Oxygen Speciesreactive oxygen species: Effects on Beta-Cells 128
6.1.3Antioxidantantioxidant Defences in Beta-Cells Versus Other Cell Types 129
6.1.4Beta-Cell Antioxidant Defences: Gender Differences 130
6.2Concepts from an Evolutionary Hypothesis 130
6.3Robustnessrobustness, Homeostasishomeostasis and Allostasisglucoseallostasis 134
6.4Clinical Implications and Future Directions 135
References 137
184822_1_En_7_Chapter_OnlinePDF 142
Chapter Chapter 7: The Importance of Transpositions and Recombination to Genome Instability According hobo-Element Distribution 142
7.1Introduction 143
7.2Material and Methods 144
7.3Results and Discussion 144
7.3.1The Hobo Sequences with Preserved Activity Are More Conserved than the Inactive Sequences 144
7.3.2The Hobo Elements from Different Chromosomes Display Less Similarity than the Neighboring Hobos 146
7.3.3Analysis of the Number of Hypothetical Hobo Insertion Sites Confirms the Suggestion on a Recent Invasion of Hobo in 148
7.3.4The New Hobo Sequences Are Evenly Distributed in the Genome, Whereas the Old Hobo Sequences Tend for Pericentromeri 149
References 152
184822_1_En_8_Chapter_OnlinePDF 154
Chapter Chapter 8: Long-Term Evolution of Histone Families: Old Notions and New Insights into Their Mechanisms of Diversificati 154
8.1Introduction 155
8.2Histone Genes Display Highly Heterogeneous Organization Patterns Across Eukaryotic Genomes 156
8.2.1Prokaryotic Chromatin and the Origin of Histones 156
8.2.2The Transition Toward the Eukaryotic Cell and the Appearance of Pluricellularity in Light of Histone Diversificatio 158
8.3Histone Variants Impart Specific Functions to Nucleosomes 160
8.3.1Linker Histones 160
8.3.2Core Histones 161
8.4Eukaryotic Histones Arose from Archaeal Histones Following a Recurrent Gene Duplication Process 163
8.5The Long-Term Evolution of Histone Genes Is Guidedby a Birth-and-Death Process That PromotesGenetic Diversity 165
8.6Replication-Dependent Histone Variants Are Derived from a Common Replication- Independent Ancestor 168
8.7Conclusions 171
References 172
184822_1_En_9_Chapter_OnlinePDF 178
Chapter Chapter 9: Masculinization Events and Doubly Uniparental Inheritance of Mitochondrial DNA: A Model for Understanding th 178
9.1Doubly Uniparental Inheritance of Mitochondrial DNA in Bivalves - An Overview 179
9.2Details of DUI and Variations on the Basic Model 179
9.3Phylogenetic Patterns 180
9.4Functional Studies of M Type Polymorphisms in Mytilus 182
9.5A (Primarily) Deterministic Model for Periodic Replacement of SM Types by RM Types 184
9.6Future Research Opportunities 186
References 186
184822_1_En_10_Chapter_OnlinePDF 189
Chapter Chapter 10: Missing the Subcellular Target: A Mechanism of Eukaryotic Gene Evolution 189
10.1Introduction 189
10.2Protein Subcellular Relocations (PSR): A Mechanism for the Evolution of New Genes and Gene Functions 191
10.2.1Protein Subcellular Localization through the N-Terminal Peptide 191
10.2.2PSR is Widespread in Gene Families 193
10.2.3Changes in Subcellular Location Can Alter Protein Function 194
10.3Conclusion 195
References 196
184822_1_En_11_Chapter_OnlinePDF 198
Chapter Chapter 11: The Evolution of Functional Gene Clusters in Eukaryote Genomes 198
11.1Physically and Functionally Linked Gene Clusters 198
11.1.1Operons: Typical Gene Clusters in Prokaryote Genomes 198
11.1.2Gene Clusters in Eukaryote Genomes 199
11.2Leaky Gene Expression 200
11.3Tandemly Duplicated Genes 201
11.4Interacting Gene Clusters 201
11.5Evolution of Functional Gene Clusters 203
11.5.1Evolution of Bidirectional Promoters in Eukaryote Genomes 203
11.5.2Evolution of Co-expressed Gene Clusters 203
11.5.3Evolution of Interacting Gene Clusters 204
11.6Concluding Remarks 204
References 205
184822_1_En_12_Chapter_OnlinePDF 208
Chapter Chapter 12: Knowledge Standardization in Evolutionary Biology: The Comparative Data Analysis Ontology 208
12.1Introduction 209
12.1.1Knowledge Representation as a Positive Heuristic in Biomedicine 209
12.1.2Ontologies in the Petabyte Era of Biological Research 210
12.1.3The Central Role of Evolutionary Biology 212
12.1.4Current Biomedical Ontologies 213
12.2The Comparative Data Analysis Ontology 214
12.2.1History of CDAO Development 214
12.2.2CDAO: Some Evaluation Considerations 214
12.2.3CDAO Version 2.0 216
12.3Conceptual Revolutions in Evolutionary Biology and Historical Analysis of CDAO Concepts 217
12.3.1Conceptual Reformulations in Evolutionary Biology Since Darwin 217
12.3.2History of CDAO Concepts: The Taxonomic Unit 218
12.3.2.1TU@CDAO 219
12.3.3History of CDAO Concepts: The Character and the Character-State Data Matrix 219
12.3.3.1Character@CDAO 220
12.3.4History of CDAO Concepts: The Tree 221
12.3.4.1Tree@CDAO 222
12.4Conclusions 223
12.5Future Developments 224
References 225
184822_1_En_13_Chapter_OnlinePDF 228
Chapter Chapter 13: Large-Scale Analyses of Positive Selection Using Codon Models 229
13.1Introduction 229
13.1.1Positive Selection as a Mechanism of Adaptation 229
13.1.2Functional Categories of Genes 230
13.1.3The Case of Duplicated Genes 230
13.2Which Codon Model for Which Problem? 231
13.2.1Pairwise Estimate of dN/dS 232
13.2.2Branch Models 232
13.2.3Site Models 233
13.2.4Branch-Site Models 233
13.3Issues in Deep and Large-Scale Analysis 235
13.3.1Sampling 235
13.3.2Alignment Quality 235
13.3.3Saturation of dS 235
13.3.4False Discovery Rate 237
13.4Large-Scale Studies 237
13.4.1General Scans for Positive Selection 237
13.4.2From Human-Chimpanzee Comparisons to a Study of Vertebrates 238
13.4.3What is the Effect of Genome Duplication on the Incidence of Positive Selection? 240
13.5Selectome, A Database of Branch-Site Positive Selection 243
13.6Conclusion 244
References 245
184822_1_En_14_Chapter_OnlinePDF 248
Chapter Chapter 14: Molecular Coevolution and the Three-Dimensionality of Natural Selection 248
14.1Natural Selection and the Neutral Theory of Molecular Evolution 249
14.2Measuring the Intensity of Selection 250
14.2.1Heterogeneous Selective Constraints Throughout Time and Sequence Space 251
14.3Structural Constraints and Molecular Coevolution 253
14.3.1Methods to Measure Correlated Variation in Proteins 254
14.3.2Molecular Adaptive Coevolution and Epistasis 257
References 259
184822_1_En_15_Chapter_OnlinePDF 263
Chapter Chapter 15: The Evolutionary Constraints in Mutational Replacements 263
15.1Introduction 263
15.2Methods 265
15.3Results 267
15.3.1Dinucleotide Replacements 267
15.3.2Trinucleotide Replacements 272
15.3.3Codon-Codon Replacements 273
15.4Discussion 275
References 276
184822_1_En_16_Chapter_OnlinePDF 278
Chapter Chapter 16: Why Phylogenetic Trees are Often Quite Robust Against Lateral Transfers 278
16.1Introduction 278
16.2Effect of Lateral Transfer on the Order of the Branches in a Tree 279
16.3Effect of Lateral Transfer on the Reconstructed Tree with the Neighbor-Joining Algorithm (NJ) 282
16.4Representing Phylogenetic Information in Case of Lateral Transfers 283
16.5How to Detect Lateral Transfers 286
16.6Examples with Real Data 288
16.6.1Whole Genome Phylogenies 288
16.6.2Deep Branches in SSU rRNA Phylogenies of Archaea 290
16.7Conclusions 290
References 291
184822_1_En_17_Chapter_OnlinePDF 293
Chapter Chapter 17: The Genome Sequence of Meloidogyne incognita Unveils Mechanisms of Adaptation to Plant-Parasitism in Metazo 294
17.1Introduction 294
17.2M. incognita Genome Organization and Comparison to Other Nematode Genomes 297
17.3The Gene Content of Plant-Parasitic Nematodes 298
17.4Genes Potentially Involved in Plant-Parasitism 299
17.5Other Singularities Potentially Reflecting Adaptation to a Plant-Parasitic Lifestyle 302
17.6Is the C. elegans Genome Representative of Nematode Diversity? 303
17.7RNAi and Development of New Antiparasitic Drug Targets 305
17.8Conclusion 305
References 307
184822_1_En_18_Chapter_OnlinePDF 310
Chapter Chapter 18: Ecological Genomics of Nematode Community Interactions: Model and Non-model Approaches 310
18.1Introduction 311
18.1.1Global Environmental Change 311
18.1.2The Ecological Genomic Approach 311
18.2Evolutionary Framework for Ecological Genomic Studies 312
18.3Nematode Ecological Genomics: Model and Non-model Approaches 313
18.3.1Global Environmental Change and the Grassland Ecosystemgrassland ecosystem 313
18.3.2The Importance of Nematode Ecologynematode ecology 313
18.3.3The Nematode Ecological Genomic Approach 314
18.3.4C. elegans as a Model Nematode 314
18.3.5Non-model Approaches 315
18.3.5.1Grassland Nematode Community Responses 315
18.3.5.2Differential Nematode Response 315
18.3.5.3Microbial CommunityMicrobial community Response to NitrogenAddition and Burning 317
18.3.6Model Approaches 318
18.3.6.1Use of C. elegans to Model Ecological Interactions 318
18.3.6.2C. elegansC. elegans Genes Involved in Response to Changes in Bacterial Environment 318
18.3.6.3Specificity of the C. elegans Functional Response 320
18.3.6.4Do Nematodes ``Know´´ What Is Good for Them? 323
18.4Conclusions 323
References 326
184822_1_En_19_Chapter_OnlinePDF 329
Chapter Chapter 19: Comparative Evolutionary Histories of Fungal Chitinases 329
19.1Introduction 329
19.2The Fungal Chitinase Gene Family 331
19.2.1Phylogeny and Nomenclature of Fungal Chitinases 331
19.2.2Structure of Fungal Chitinases 333
19.2.3Functions of Fungal Chitinases 333
19.3Chitinase Gene Family Evolution 334
19.3.1Analysis of Gene Gain and Loss 334
19.3.2Expansions and Contractions of Chitinases 336
19.4Correlations Between Gene Family Evolution and Fungal Lifestyles 338
19.4.1Chitinase Expansions in Filamentous Ascomycetes 338
19.4.2Methodological Assumptions with Implications for Data Interpretation 340
19.5Conclusions 340
References 341
184822_1_En_20_Chapter_OnlinePDF 344
Chapter Chapter 20: Aging: Evolutionary Theory Meets Genomic Approaches 344
20.1Introduction 344
20.2The Evolution of Aging: Why Not Immortality? 346
20.3Measuring and Interpreting Life Span Phenotypes 347
20.4Conservation of Longevity Control 349
20.4.1IIS Promotes Aging 350
20.4.2Sirtuins: Playing Both Sides? 351
20.4.3Reduced TOR Signaling Provides Consistent Life Span Extension 352
20.4.4DR and the Search for a Mechanism 352
20.5Aging Genomics 353
20.5.1Microarrays Uncover Age-Associated Gene Expression Patterns 354
20.5.2Genome-Scale Life Span Screens Identify a Large Number of Longevity Genes 355
20.6The Search for Conserved Longevity Determinants: The Genome-Wide Multi-organism Approach 356
20.7Uncovering the Mechanisms Behind Conserved Longevity Factors: A Central Role for Translation? 357
20.8Conclusion 358
References 359
184822_1_En_21_Chapter_OnlinePDF 366
Chapter Chapter 21: Galaxies and Cladistics 367
21.1Introduction 367
21.2The astrocladisticsAstrocladistics Project 370
21.2.1Aphylogenetic Phylogenetic Framework for the Galaxies 370
21.2.2Transmission with Modification Among Galaxies 372
21.3Applying Cladistics to Galaxies 374
21.4The First Extragalactic Trees 375
21.5Some Open Questions 379
21.6Conclusion 380
References 381
184822_1_En_22_Chapter_OnlinePDF 383
Chapter Chapter 22: Economics Pursuing the Mold of Evolutionary Biology: ``Accident´´ and ``Necessity´´ in the Quest to make E 383
22.1Introduction 383
22.2The ``Nomothetic Paradox´´ in Economics 384
22.3Possible Model in Biology 386
22.4The Parallel Provided by ``Accident´´ and ``Necessity´´ 389
22.5Arthur and Monod 391
22.6The Flaw in the Analogy 393
References 395
184822_1_En_BM2_OnlinePDF 397
: Index 397