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This book's aim is to obtain and organize knowledge about the diversity of living things. Their epistomological and methodological fundamentals are explained in the framework of the biology of evolution. The methods of construction and use of phylogenetic trees are presented as well as the classification and description of taxa with the nomenclature rules.
This book's aim is to obtain and organize knowledge about the diversity of living things. Their epistomological and methodological fundamentals are explained in the framework of the biology of evolution. The methods of construction and use of phylogenetic trees are presented as well as the classification and description of taxa with the nomenclature rules.
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Introduction xi Philippe GRANDCOLAS and Marie-Christine MAUREL Chapter 1 Symmetry of Shapes in Biology: from D'Arcy Thompson to Morphometrics 1 Sylvain GERBER and Yoland SAVRIAMA 1.1 Introduction 1 1.2 D'Arcy Thompson, symmetry and morphometrics 2 1.3 Isometries and symmetry groups 4 1.4 Biological asymmetries 5 1.5 Principles of geometric morphometrics 6 1.6 The treatment of symmetry in morphometrics 8 1.7 Some examples of applications 12 1.8 Conclusion 13 1.9 References 14 Chapter 2 Impact of a Point Mutation in a Protein Structure 17 Mathilde CARPENTIER and Jacques CHOMILIER 2.1 Composition 17 2.2 Folding 18 2.3 Substitution(s) in protein structures 20 2.4 Effect on overall structure and function 20 2.5 Effect on stability 22 2.6 Effect on the peptide backbone 23 2.7 Conclusion 28 2.8 References 28 Chapter 3 The Role of Taxonomy and Natural History in the Study of the Evolution of Eneopterinae Crickets 33 Tony ROBILLARD 3.1 Introduction 33 3.2 Taxonomy in modern comparative approaches 35 3.3 A model group 37 3.4 Contribution of taxonomy for phylogenetic reconstructions and classification 40 3.5 Contribution of taxonomy to biogeography 44 3.6 Taxonomic exploration and evolution of species traits 48 3.7 Conclusion 52 3.8 Acknowledgments 54 3.9 References 54 Chapter 4 Systematics in the (Post)genomic Era: A Look at the Drosophila Model 61 Amir YASSIN 4.1 Drosophila: a star of genetics but a systematic nebula 61 4.2 Subspecies: identification of "genomic islands of divergence"? 63 4.3 Species complexes: congruence between species trees and gene trees 67 4.4 Supraspecific ranks: phylogeny, genome and morphome 70 4.5 Conclusion 73 4.6 Acknowledgments 74 4.7 References 74 Chapter 5 Dealing with Multiple Environments: The Challenges of the Trypanosome Lifecycle 79 Estefanía CALVO ALVAREZ and Philippe BASTIN 5.1 Human African trypanosomiasis, the disease 79 5.2 Cell biology of Trypanosoma brucei 80 5.3 Survival and maturation of T brucei in the tsetse vector 84 5.4 Adaptations of T brucei to the mammalian host 92 5.5 Conclusion 99 5.6 References 99 Chapter 6 Challenges Inherent in the Systematics and Taxonomy of Genera that have Recently Experienced Explosive Radiation: The Case of Orchids of the Genus Ophrys 113 Joris BERTRAND, Michel BAGUETTE, Nina JOFFARD and Bertrand SCHATZ 6.1 Introduction 114 6.2 Speciation in Ophrys: an evolutionary divergence seen as a reticulated continuum 115 6.3 Current state of knowledge on Ophrys systematics 121 6.4 Integrative genomics and taxonomy: perspectives and issues 125 6.5 Conclusion 129 6.6 Acknowledgments 130 6.7 References 130 Chapter 7 Exploration and Origins of Biodiversity in Madagascar: The Message of Ferns 135 Germinal ROUHAN and Myriam GAUDEUL 7.1 Introduction 135 7.2 Madagascar: a complex biogeographical context 136 7.3 Ferns and lycophytes: an ideal model for the biogeography of Madagascar 140 7.4 Origins of the lineages of ferns in Madagascar 140 7.5 The example of Rumohra: dispersions to Madagascar and around the world 142 7.6 Conclusion 144 7.7 References 144 Chapter 8 Mediterranean and Atlantic Algae, a Fraternal Relationship? 147 Line LE GALL, Delphine GEY and Florence ROUSSEAU 8.1 Introduction 148 8.2 Materials and methods 152 8.3 Results 159 8.4 Discussion 163 8.5 Acknowledgments 164 8.6 References 165 Chapter 9 Ontogeny and Evolution of the Hyperorgan of Delphinieae 171 Florian JABBOUR, Julie ZALKO, Antoine MOREL, Samuel FRACHON and Isabelle BOUCHART-DUFAY 9.1 Introduction 171 9.2 Synorganization: a concept, definitions 172 9.3 Ontogeny and evolution of the hyperorgan of Delphinieae 174 9.4 The study of synorganization in evolutionary biology 178 9.5 Conclusion 181 9.6 Acknowledgments 181 9.7 References 182 Chapter 10 Identification of Interspecific Chromosomal Homologies: Chromosomal Microdissection and Chromosomal Painting in Antarctic Teleosts Nototheniidae 185 Juliette AUVINET, Agnès DETTAÏ, Olivier CORITON, Catherine OZOUF-COSTAZ and Dominique HIGUET 10.1 Introduction 185 10.2 Materials and methods 191 10.3 Results 195 10.4 Discussion 199 10.5 Conclusion 204 10.6 References 205 List of Authors 215 Index 221
Introduction xi Philippe GRANDCOLAS and Marie-Christine MAUREL Chapter 1 Symmetry of Shapes in Biology: from D'Arcy Thompson to Morphometrics 1 Sylvain GERBER and Yoland SAVRIAMA 1.1 Introduction 1 1.2 D'Arcy Thompson, symmetry and morphometrics 2 1.3 Isometries and symmetry groups 4 1.4 Biological asymmetries 5 1.5 Principles of geometric morphometrics 6 1.6 The treatment of symmetry in morphometrics 8 1.7 Some examples of applications 12 1.8 Conclusion 13 1.9 References 14 Chapter 2 Impact of a Point Mutation in a Protein Structure 17 Mathilde CARPENTIER and Jacques CHOMILIER 2.1 Composition 17 2.2 Folding 18 2.3 Substitution(s) in protein structures 20 2.4 Effect on overall structure and function 20 2.5 Effect on stability 22 2.6 Effect on the peptide backbone 23 2.7 Conclusion 28 2.8 References 28 Chapter 3 The Role of Taxonomy and Natural History in the Study of the Evolution of Eneopterinae Crickets 33 Tony ROBILLARD 3.1 Introduction 33 3.2 Taxonomy in modern comparative approaches 35 3.3 A model group 37 3.4 Contribution of taxonomy for phylogenetic reconstructions and classification 40 3.5 Contribution of taxonomy to biogeography 44 3.6 Taxonomic exploration and evolution of species traits 48 3.7 Conclusion 52 3.8 Acknowledgments 54 3.9 References 54 Chapter 4 Systematics in the (Post)genomic Era: A Look at the Drosophila Model 61 Amir YASSIN 4.1 Drosophila: a star of genetics but a systematic nebula 61 4.2 Subspecies: identification of "genomic islands of divergence"? 63 4.3 Species complexes: congruence between species trees and gene trees 67 4.4 Supraspecific ranks: phylogeny, genome and morphome 70 4.5 Conclusion 73 4.6 Acknowledgments 74 4.7 References 74 Chapter 5 Dealing with Multiple Environments: The Challenges of the Trypanosome Lifecycle 79 Estefanía CALVO ALVAREZ and Philippe BASTIN 5.1 Human African trypanosomiasis, the disease 79 5.2 Cell biology of Trypanosoma brucei 80 5.3 Survival and maturation of T brucei in the tsetse vector 84 5.4 Adaptations of T brucei to the mammalian host 92 5.5 Conclusion 99 5.6 References 99 Chapter 6 Challenges Inherent in the Systematics and Taxonomy of Genera that have Recently Experienced Explosive Radiation: The Case of Orchids of the Genus Ophrys 113 Joris BERTRAND, Michel BAGUETTE, Nina JOFFARD and Bertrand SCHATZ 6.1 Introduction 114 6.2 Speciation in Ophrys: an evolutionary divergence seen as a reticulated continuum 115 6.3 Current state of knowledge on Ophrys systematics 121 6.4 Integrative genomics and taxonomy: perspectives and issues 125 6.5 Conclusion 129 6.6 Acknowledgments 130 6.7 References 130 Chapter 7 Exploration and Origins of Biodiversity in Madagascar: The Message of Ferns 135 Germinal ROUHAN and Myriam GAUDEUL 7.1 Introduction 135 7.2 Madagascar: a complex biogeographical context 136 7.3 Ferns and lycophytes: an ideal model for the biogeography of Madagascar 140 7.4 Origins of the lineages of ferns in Madagascar 140 7.5 The example of Rumohra: dispersions to Madagascar and around the world 142 7.6 Conclusion 144 7.7 References 144 Chapter 8 Mediterranean and Atlantic Algae, a Fraternal Relationship? 147 Line LE GALL, Delphine GEY and Florence ROUSSEAU 8.1 Introduction 148 8.2 Materials and methods 152 8.3 Results 159 8.4 Discussion 163 8.5 Acknowledgments 164 8.6 References 165 Chapter 9 Ontogeny and Evolution of the Hyperorgan of Delphinieae 171 Florian JABBOUR, Julie ZALKO, Antoine MOREL, Samuel FRACHON and Isabelle BOUCHART-DUFAY 9.1 Introduction 171 9.2 Synorganization: a concept, definitions 172 9.3 Ontogeny and evolution of the hyperorgan of Delphinieae 174 9.4 The study of synorganization in evolutionary biology 178 9.5 Conclusion 181 9.6 Acknowledgments 181 9.7 References 182 Chapter 10 Identification of Interspecific Chromosomal Homologies: Chromosomal Microdissection and Chromosomal Painting in Antarctic Teleosts Nototheniidae 185 Juliette AUVINET, Agnès DETTAÏ, Olivier CORITON, Catherine OZOUF-COSTAZ and Dominique HIGUET 10.1 Introduction 185 10.2 Materials and methods 191 10.3 Results 195 10.4 Discussion 199 10.5 Conclusion 204 10.6 References 205 List of Authors 215 Index 221
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