Evolutionary Biology from Concept to Application (eBook)

Preface 5
Contents 7
Contributors 9
I Modelization of Evolution 12
Rate of Adaptation of Large Populations 13
1.1 Background and Introduction 13
1.2 Two Models 18
1.2.1 Strong Selection Model 19
1.2.2 Weak Selection Model 21
1.3 Strong Selection: Asymptotic Adaptation Rate 24
1.4 Weak Selection: Girsanov Calculations 27
1.4.1 The Girsanov Transform 27
1.4.2 Moments of the Neutral Process 30
1.4.3 Representation Using the Neutral Process 32
1.5 Open Problems 35
References 36
A Phylogenetic Mixture Model for Heterotachy 38
2.1 Introduction 38
2.2 Branch Length Sets Mixture Model 40
2.3 Model Testing 41
2.6 Application to Published Data Sets 43
2.7 Results 2.7.1 Four –Taxon Simulation 44
2.7.2 Seventy-Taxon Simulation 45
2.7.3 Application to Real Data 45
2.8 Discussion 46
References 49
II Concepts in Evolutionary Biology 51
Accelerated Evolution of Genes of Recent Origin 52
3.1 Introduction 52
3.2 Results 3.2.1 De . nition of Groups of Genes of Different Age 55
3.2.2 Evolutionary Rate of Genes of Different Age 55
3.2.3 Length of Genes of Different Age 58
3.2.4 Functions of Primate Genes of Different Age 58
3.2.5 Estimation of the Age of Genes 60
3.3 Discussion 3.3.1 Differences between Genes of Different Age 61
3.3.2 Properties of Novel Genes 62
3.3.3 Hypotheses to Explain the Origin of Novel Genes 63
3.4 Conclusion 64
References 65
Life-Cycle Features of Tumour Cells 67
4.1 Introduction 67
4.2 From Embryonal to Stem Cell Theories of Cancer 68
4.3 Cancer Testes Antigens: Expression in Tumour and Germ Cells 69
4.4 From Mitosis to Polyploidy and Life Cycles 69
4.5 Endomitosis: The Earliest Evolutionary Analogue of Meiosis 71
4.6 Endomitotic Tumour Cells Express Meiotic Kinases 71
4.7 Genetic Consequences of Reproductive Polyploidy in Tumour Microevolution 71
4.8 Do Tumour Cells Display Life-Cycle Behaviour Similar to that of Unicellular Protozoans? 72
4.9 Role of p53 74
4.10 Adaptive Paleogenesis in Tumours 74
4.11 Conclusion 75
References 75
General Evolutionary Regularities of Organic and Social Life 78
5.1 Introduction 78
5.2 Processes of Polymerization in Foraminiferal Development 82
5.3 Processes of Differentiation in Foraminiferal Development 84
5.4 Processes of Integration in Foraminiferal Development 86
5.5 Aromorphoses in Foraminiferal Evolutionary Development 89
5.6 General Character of the Main Evolutionary Regularities 5.6.1 Different Levels of the Organization of Matter 90
5.6.2 Processes of Polymerization, Differentiation, and Integration in the Development of Human Society 91
5.6.3 Processes of Polymerization, Differentiation, and Aromorphoses in the Development of the Material Objects of Social Integrative Systems 94
5.7 Conclusions 95
References 96
Old and New Concepts in EvoDevo 100
6.1 Introduction 100
6.2 Two Different Approaches to Development and Evolution 101
6.3 Homology, Modularity, Developmental Networks 103
6.4 Can NeoDarwinism Provide a Theory of EvoDevo? 105
6.5 EvoDevo Beyond NeoDarwinism 106
6.6 EvoDevo and the Traditional Taxonomy of Protochordates: Current Achievements and Historical Roots 110
6.7 An Alternative View on the Phylogeny of Protochordates and the Origin of Vertebrates 114
References 115
III Knowledge 120
Overturning the Prejudices about Hydra and Metazoan Evolution 121
7.1 Diffusion: Potentially an Ideal Mechanism for Material Transport in Primitive Metazoans 7.1.1 A Theoretical Consideration 121
7.1.2 Problems of the Diffusion Paradigm” 122
7.1.3 Is Diffusion Powerful Enough for Circulation in Hydra? 124
7.1.4 Is Diffusion Powerful enough for Digestion in Hydra? 126
7.2 Does the Diffuse Nerve Net Have a Function in Hydra? 7.2.1 Common Knowledge 128
7.2.2 Problems Emerging 128
7.2.3 Diffuse Nerve Net as an Enteric Nervous System 128
7.3 Body Plan of Hydra: Closed Sac or a Tube as in Higher Metazoans? 7.3.1 Common Knowledge 130
7.3.2 Problems Emerging 131
7.3.3 Experimental Analysis 132
7.4 Discussion 135
References 136
The Search for the Origin of Cnidarian Nematocysts in Dino . agellates 139
8.1 Background 139
8.1.1 A Stinging Cell Type in Cnidarians 140
8.1.2 Polykrikos and the Extrusive Organelles 142
8.2 Comparison of Nematocysts between Hydra and Polykrikos 8.2.1 Similarities in the Structure of Nematocysts between Hydra and Polykrikos 143
8.2.2 The Strategy to Capture Prey 146
8.3 Nematocyst-Related Genes 148
8.3.1 Common Cytoskeletal Genes of Nematocysts 149
8.3.2 Nematocyst-Speci.c Genes in Hydra are not found in other Metazoans 150
8.3.3 Do Hydra and Polykrikos Share Homologous Protein in Making Nematocysts? 151
8.4 Evolution of Nematocysts? 152
8.4.1 Gene Loss or Lateral Gene Transfer? 152
References 154
IV Applied Evolutionary Biology 157
A Possible Relationship Between the Phylogenetic Branch Lengths and the Chaetognath rRNA Paralog Gene Functionalities: Ubiquitous, Tissue- Speci .c or Pseudogenes 158
9.1 Introduction 158
9.2 Materials and Methods 159
9.3 Results 9.3.1 18S rRNA Hybridizations 159
9.3.2 28S rRNA Hybridizations 160
9.3.3 Molecular Phylogenies 161
9.4 Discussion 163
9.5 Conclusion 165
References 165
Mode and Tempo of matK: Gene Evolution and Phylogenetic Implications 168
10.1 Introduction 168
10.2 Gene Structure 170
10.3 Evolution of matK 172
10.4 matK Role in Plant Phylogenetics 172
10.5 Why Is matK So Signal Rich? 174
10.6 Support for Function 176
10.6.1 Evolutionary Evidence 177
10.6.2 Evidence from Bioinformatics 177
10.6.3 Molecular Evidence 178
10.7 Conclusions 179
References 180
Phylogeography and Conservation of the Rare South African Fruit Chafer Ichnestoma stobbiai ( Coleoptera: Scarabaeidae) 183
11.1 Introduction 183
11.2 Materials and Methods 11.2.1 Data Production 185
11.2.2 Data Analyses 187
11.3 Results 188
11.4 Discussion 193
11.5 Conclusion 196
References 196
Nothing in Medicine Makes Sense Except in the Light of Evolution: A Review 199
12.1 Introduction 200
12.2 Illness, a Threshold on a Reaction Norm 200
12.3 The Central Mechanism at the Base of Evolutionary Medicine 202
12.3.1 Infections and Susceptibility to Autoimmune and Allergic Diseases 203
12.3.2 Obesity, Type 2 Diabetes, Arterial Hypertension and the Thrifty Gene Hypothesis 204
12.3.3 The Multiple Medical Consequences of Global Warming 205
12.4 Medical Applications, Carcinogenesis 207
References 208
An Overview of Evolutionary Biology Concepts for Functional Annotation: Advances and Challenges 210
13.1 Improving Functional Annotation Using Evolutionary Biology 210
13.2 Considering the Evolutionary Shift 211
13.3 Evolutionary Biology Concepts in the Genomic Era 213
13.3.1 Comparative Genomic Approach 214
13.3.2 Towards a Functional Annotation on the Community Scale 214
13.4 Conclusion 214
References 215
Index 217