A comprehensive, authoritative look at an emergent area in
post-genomic science, Evolutionary genomics is an up-and-coming,
complex field that attempts to explain the biocomplexity of the
living world. Evolutionary Genomics and Systems Biology is
the first full-length book to blend established and emerging
concepts in bioinformatics, evolution, genomics, and structural
biology, with the integrative views of network and systems biology.
Three key aspects of evolutionary genomics and systems biology
are covered in clear detail: the study of genomic history, i.e.,
understanding organismal evolution at the genomic level; the study
of macromolecular complements, which encompasses the evolution of
the protein and RNA machinery that propels life; and the
evolutionary and dynamic study of wiring
diagrams--macromolecular components in interaction--in
the context of genomic complements. The book also features:
* A solid, comprehensive treatment of phylogenomics, the
evolution of genomes, and the evolution of biological networks,
within the framework of systems biology
* A special section on RNA biology--translation, evolution
of structure, and micro RNA and regulation of gene expression
* Chapters on the mapping of genotypes to phenotypes, the role of
information in biology, protein architecture and biological
function, chromosomal rearrangements, and biological networks and
disease
* Contributions by leading authorities on each topic
Evolutionary Genomics and Systems Biology is an ideal
book for students and professionals in genomics, bioinformatics,
evolution, structural biology, complexity, origins of life,
systematic biology, and organismal diversity, as well as those
individuals interested in aspects of biological sciences as they
interface with chemistry, physics, and computer science and
engineering.
Autorentext
Gustavo Caetano-Anollés, PhD, is Professor in the Department of Crop Sciences at the University of Illinois in Urbana-Champaign, Illinois. He has more than 150 well-cited original research publications in areas related to DNA technology and genomics, and holds half a dozen US patents in various areas of DNA science and biotechnology. His successful book, DNA Markers: Protocols, Applications, and Overviews, was published by Wiley in 1997.
Zusammenfassung
A comprehensive, authoritative look at an emergent area in post-genomic science, Evolutionary genomics is an up-and-coming, complex field that attempts to explain the biocomplexity of the living world. Evolutionary Genomics and Systems Biology is the first full-length book to blend established and emerging concepts in bioinformatics, evolution, genomics, and structural biology, with the integrative views of network and systems biology.
Three key aspects of evolutionary genomics and systems biology are covered in clear detail: the study of genomic history, i.e., understanding organismal evolution at the genomic level; the study of macromolecular complements, which encompasses the evolution of the protein and RNA machinery that propels life; and the evolutionary and dynamic study of wiring diagramsmacromolecular components in interactionin the context of genomic complements. The book also features:
- A solid, comprehensive treatment of phylogenomics, the evolution of genomes, and the evolution of biological networks, within the framework of systems biology
- A special section on RNA biologytranslation, evolution of structure, and micro RNA and regulation of gene expression
- Chapters on the mapping of genotypes to phenotypes, the role of information in biology, protein architecture and biological function, chromosomal rearrangements, and biological networks and disease
- Contributions by leading authorities on each topic
Evolutionary Genomics and Systems Biology is an ideal book for students and professionals in genomics, bioinformatics, evolution, structural biology, complexity, origins of life, systematic biology, and organismal diversity, as well as those individuals interested in aspects of biological sciences as they interface with chemistry, physics, and computer science and engineering.
Inhalt
Preface xiii
Contributors xvii
Part I Evolution of Life.
1. Evolutionary Genomics Leads the Way 3
David Penny and Lesley J. Collins
1.1 Introduction 3
1.2 Evolution and the Power of Genomes 4
1.3 The Problem of Deep Phylogeny and "The Tree" 5
1.4 Fred, the Last Common Ancestor of Modern Eukaryotes 7
1.5 Eukaryote Origins: Continuity from the RNAWorld? 10
1.6 Minimal Genomes and Reductive Evolution 12
1.7 Evolutionary Genomics for the Future 13
2. Current Approaches to Phylogenomic Reconstruction 17
Denis Baurain and Herve Philippe
2.1 Phylogenomics and Supermatrices 17
2.2 Phylogenetic Signal Versus Nonphylogenetic Signal 19
2.3 Probabilistic Models and Nonphylogenetic Signal 22
2.4 Reduction of Nonphylogenetic Signal Under Fixed Models 28
2.5 CAT Model 31
2.6 Case Study: Cambrian Explosion 33
2.7 Conclusion 35
3. The Universal Tree of Life and the Last Universal Cellular Ancestor: Revolution and Counterrevolutions 43
Patrick Forterre
3.1 Introduction 43
3.2 The Woesian Revolution 45
3.3 A Rampant "Prokaryotic" Counterrevolution 47
3.4 How to Polarize Characters Without a Robust Root? 50
3.5 The Hidden Root: When the Weather Became Cloudy 51
3.6 LUCA and Its Companions 54
3.7 The Problem of Horizontal Gene Transfer and Ancient Phylogenies: Trees Versus Gene Webs 54
3.8 The Nature of the RNAWorld 55
3.9 The DNA Replication Paradox and the Nature of LUCA 56
3.10 When Viruses Find Their Way into the Universal Tree of Life 58
3.11 Future Directions 59
4. Eukaryote Evolution: The Importance of the Stem Group 63
Anthony M. Poole
4.1 Introduction 63
4.2 Interpreting Trees 68
4.3 Moving Beyond the Deep Roots of Eukaryotes 70
4.4 Concluding Remarks 76
5. The Role of Information in Evolutionary Genomics of Bacteria 81
Antoine Danchin and Agnieszka Sekowska
5.1 Introduction 81
5.2 Revisiting Information 83
5.3 Ubiquitous Functions for Life 84
5.4 The Cenome and the Paleome 87
5.5 Functions Corresponding to Nonessential Persistent Genes 89
5.6 A Ubiquitous Information-Gaining Process: Making a Young Organism from an Aged One 89
5.7 Provisional Conclusion 91
6. Evolutionary Genomics of Yeasts 95
Bernard Dujon
6.1 Introduction 95
6.2 A Brief History of Hemiascomycetous Yeast Genomics 96
6.3 The Scientific Attractiveness of S. cerevisiae 98
6.4 Evolutionary Genomics of Hemiascomycetes 104
6.5 Surprises 111
6.6 What Next? 113
Part II Evolution of Molecular Repertoires.
7. Genotypes and Phenotypes in the Evolution of Molecules 123
Peter Schuster
7.1 The Landscape Paradigm 123
7.2 Molecular Phenotypes 125
7.3 The RNA Model 132
7.4 Conclusions and Outlook 148
8. Genome Evolution Studied Through Protein Structure 153
Philip E. Bourne, Kristine Briedis, Christopher Dupont, Ruben Valas, and Song Yang
8.1 Introduction 153
8.2 Structural Granularity and Its Implications 156
8.3 Protein Domains in the Study of Genome Rearrangements 158
8.4 Protein Domain Gain and Loss 160
8.5 And in the Beginning . . . 161
8.6…