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