Evolutionary Genomics and Systems Biology E-Book

Gustavo Caetano-Anollés

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 1185

Veröffentlichungsjahr: 2011

Beschreibung

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.

Leseprobe

Contents

Preface

Contributors

Part I Evolution of Life

1. Evolutionary Genomics Leads the WayDavid Penny and Lesley J. Collins

1.1 Introduction

1.2 Evolution and the Power of Genomes

1.3 The Problem of Deep Phylogeny and “The Tree”

1.4 Fred, the Last Common Ancestor of Modern Eukaryotes

1.5 Eukaryote Origins: Continuity from the RNA World?

1.6 Minimal Genomes and Reductive Evolution

1.7 Evolutionary Genomics for the Future

References

2. Current Approaches to Phylogenomic ReconstructionDenis Baurain and Hervé Philippe

2.1 Phylogenomics and Supermatrices

2.2 Phylogenetic Signal Versus Nonphylogenetic Signal

2.3 Probabilistic Models and Nonphylogenetic Signal

2.4 Reduction of Nonphylogenetic Signal Under Fixed Models

2.5 CAT Model

2.6 Case Study: Cambrian Explosion

2.7 Conclusion

References

3. The Universal Tree of Life and the Last Universal Cellular Ancestor: Revolution and CounterrevolutionsPatrick Forterre

3.1 Introduction

3.2 The Woesian Revolution

3.3 A Rampant “Prokaryotic” Counterrevolution

3.4 How to Polarize Characters Without a Robust Root?

3.5 The Hidden Root: When the Weather Became Cloudy

3.6 LUCA and Its Companions

3.7 The Problem of Horizontal Gene Transfer and Ancient Phylogenies: Trees Versus Gene Webs

3.8 The Nature of the RNA World

3.9 The DNA Replication Paradox and the Nature of LUCA

3.10 When Viruses Find Their Way into the Universal Tree of Life

3.11 Future Directions

References

4. Eukaryote Evolution: The Importance of the Stem GroupAnthony M. Poole

4.1 Introduction

4.2 Interpreting Trees

4.3 Moving Beyond the Deep Roots of Eukaryotes

4.4 Concluding Remarks

References

5. The Role of Information in Evolutionary Genomics of BacteriaAntoine Danchin and Agnieszka Sekowska

5.1 Introduction

5.2 Revisiting Information

5.3 Ubiquitous Functions for Life

5.4 The Cenome and the Paleome

5.5 Functions Corresponding to Nonessential Persistent Genes

5.6 A Ubiquitous Information-Gaining Process: Making a Young Organism from an Aged One

5.7 Provisional Conclusion

Acknowledgments

References

6. Evolutionary Genomics of YeastsBernard Dujon

6.1 Introduction

6.2 A Brief History of Hemiascomycetous Yeast Genomics

6.3 The Scientific Attractiveness of S. cerevisiae

6.4 Evolutionary Genomics of Hemiascomycetes

6.5 Surprises

6.6 What Next?

Acknowledgments

Epilogue

References

Part II Evolution of Molecular Repertoires

7. Genotypes and Phenotypes in the Evolution of MoleculesPeter Schuster

7.1 The Landscape Paradigm

7.2 Molecular Phenotypes

7.3 The RNA Model

7.4 Conclusions and Outlook

Acknowledgments

References

8. Genome Evolution Studied Through Protein StructurePhilip E. Bourne, Kristine Briedis, Christopher Dupont, Ruben Valas, and Song Yang

8.1 Introduction

8.2 Structural Granularity and Its Implications

8.3 Protein Domains in the Study of Genome Rearrangements

8.4 Protein Domain Gain and Loss

8.5 And in the Beginning

8.6 But Let Us Not Forget the Influence of the Environment

8.7 Conclusions

References

9. Chromosomal Rearrangements in EvolutionHao Zhao and Guillaume Bourque

9.1 Introduction

9.2 Genome Representation

9.3 Constructing Genome Permutations from Sequence Data

9.4 Genomic Distances

9.5 Reconstruction of Ancestors and Evolutionary Scenarios

9.6 Recent Applications on Large Genomes

9.7 Challenges and Promising New Approaches

Acknowledgment

References

10. Molecular Structure and Evolution of GenomesTodd A. Castoe, A. P. Jason de Koning, and David D. Pollock

10.1 Introduction

10.2 Overview of Considerations in Studying Protein Evolution

10.3 Function and Evolutionary Genomics

10.4 Integrating Inferences to Detect and Interpret Adaptation: An Example with Snake Metabolic Proteins

10.5 Conclusion

References

11. The Evolution of Protein Material CostsJason G. Bragg and Andreas Wagner

11.1 Introduction

11.2 Protein Material Costs

11.3 An Example: Proteomic Sulfur Sparing

11.4 Episodic Nutrient Scarcity Can Shape Protein Material Costs

11.5 Highly Expressed Gene Products Often Exhibit Reduced Material Costs

11.6 Material Costs and the Evolution of Genomes

11.7 Material Costs and Other Costs of Making Proteins

11.8 Conclusions

Acknowledgments

References

12. Protein Domains as Evolutionary UnitsAndrew D. Moore and Erich Bornberg-Bauer

12.1 Modular Protein Evolution

12.2 Domain-Based Homology Identification

12.3 Domains in Genomics and Proteomics

12.4 The Coverage Problem

12.5 Conclusion

References

13. Domain Family Analyses to Understand Protein Function EvolutionAdam James Reid, Sarah Addou, Robert Rentzsch, Juan Ranea, and Christine Orengo

13.1 Introduction

13.2 Universal Domain Structure Families Identified in the Last Universal Common Ancestor

13.3 Some Domain Families Recur More Frequently and Are Structurally Very Diverse

13.4 Correlation of Structural Diversity in Superfamilies with Functional Diversity

13.5 To What Extent Does Function Vary Between Homologous?

13.6 How Safely Can Function Be Inherited Between Homologues?

13.7 How Are Domain Families Distributed in Protein Complexes?

References

14. Noncoding RNAAlexander Donath, Sven Findeib, Jana Hertel, Manja Marz, Wolfgang Otto, Christine Schulz, Peter F. Stadler, and Stefan Wirth

14.1 Introduction

14.2 Ancient RNAs

14.3 Domain-Specific RNAs

14.4 Conserved ncRNAs with Limited Distribution

14.5 ncRNAs from Repeats and Pseudogenes

14.6 mRNA-like ncRNAs

14.7 RNAs with Dual Functions

14.8 Concluding Remarks

Acknowledgments

References

15. Evolutionary Genomics of microRNAs and Their RelativesAndrea Tanzer, Markus Riester, Jana Hertel, Clara Isabel Bermudez-Santana, Jan Gorodkin, Ivo L. Hofacker, and Peter F. Stadler

15.1 Introduction

15.2 The Small RNA Zoo

15.3 Small RNA Biogenesis

15.4 Computational microRNA Prediction

15.5 microRNA Targets

15.6 Evolution of microRNAs

15.7 Origin(s) of microRNA Families

15.8 Genomic Organization

15.9 Summary and Outlook

References

16. Phylogenetic Utility of RNA Structure: Evolution’s Arrow and Emergence of Early Biochemistry and Diversified LifeFeng-Jie Sun, Ajith Harish, and Gustavo Caetano-Anollés

16.1 Introduction

16.2 Structural Characters and Derived Phylogenetic Trees

16.3 Applications

16.4 Conclusions

Acknowledgments

References

Part III Evolution of Biological Networks

17. A Hitchhiker’s Guide to Evolving NetworksCharles G. Kurland and Otto G. Berg

17.1 Introduction

17.2 Phylogenetic Continuities, Biological Coherence

17.3 Nested Structural Networks

17.4 Optimal Networks

17.5 The Emperor’s BLAST Search Revisited

17.6 Will the Real Missing Link Please Stand Up?

17.7 All’s Well

Acknowledgments

References

18. Evolution of Metabolic NetworksEivind Almaas

18.1 Introduction

18.2 Metabolic Network Properties

18.3 Network Models For Metabolic Evolution

18.4 Dynamic Models Of Genome-Level Metabolic Function References

19. Single-Gene and Whole-Genome Duplications and the Evolution of Protein–Protein Interaction NetworksGrigoris Amoutzias and Yves Van de Peer

19.1 Introduction

19.2 Evolution of PINs

19.3 Single-Gene Duplications

19.4 Whole-Genome Duplications

19.5 Diploidization Phase

19.6 Dosage Balance Hypothesis

19.7 Types of Interactions

19.8 WGDs, Transient Interactions, and Organismal Complexity

19.9 Studies on PPIs of Ohnologues

19.10 Concerns About the Methods of Analysis and the Quality of the Data

19.11 The Importance of Medium-Scale Studies: the Case of Dimerization

19.12 Evolution of Dimerization Networks

19.13 Conclusions

Acknowledgment

References

20. Modularity and Dissipation in Evolution of Macromolecular Structures, Functions, and NetworksGustavo Caetano-Anollés, Liudmila Yafremava, and Jay E. Mittenthal

20.1 Introduction

20.2 Biological Structure as an Emergent Property of Dissipative Systems

20.3 Information and Its Dissipation

20.4 Time, Thermodynamic Irreversibility, and Growth of Order in the Universe

20.5 Information Dissipation and Modularity Pervade Structure in Biology

20.6 Modularity and Dissipation in Protein Evolution

20.7 Conclusions

Acknowledgments

References

Index

Copyright © 2010 by Wiley-Blackwell. All rights reserved

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Library of Congress Cataloging-in-Publication Data:

Evolutionary genomics and systems biology / [edited by] Gustavo

Caetano-Anollés.

p.; cm.Includes bibliographical references and index.ISBN 978-0-470-19514-7 (cloth)1. Evolutionary genetics. 2. Molecular evolution. I. Caetano-Anollés, Gustavo, 1955-[DNLM: 1. Evolution, Molecular. 2. Genome–genetics. 3. Systems Biology. QU 475 E9566 2010]QH390.E985 2010

572.8'38–dc222009025383

PREFACE

“The hardest thing to see is what is in front of our eyes.”

Johan Wolfgang von Goethe

Change, the process of becoming different, is at the heart of biology. Without it, nothing makes sense. Understanding and describing change is a fundamental endeavor in mathematics and the natural sciences. Change embraces evolutionary thought but is particularly difficult to define in complex dynamical systems, such as those encountered in life. The intricate arrangement of parts in these systems is responsible for unique relationships that must be established and emergent properties that must be explored.

What makes something in biology unique? Closely related individuals in a population may differ little in terms of their genetic makeup. Yet they can exhibit marked phenotypic differences, beginning with appearance and behavior. They can react differently when exposed to mutation or stress. Their progeny can even inherit genetic or learned features differently. As taxonomical distance widens, what is unique widens to the extreme. For example, there is only 1.2% difference in the genomic makeup of chimp and human at the nucleotide level1, yet phenotypic differences are huge. We may be tempted to explain uniqueness by citing critical differences (e.g., unique proteins, gene copy variants, or regulatory mechanisms) or general patterns (e.g., differential regulation of a large number of genes). We can claim that the repertoire of proteins or noncoding RNA, or the way the expression or functioning of these molecules is regulated are the ones responsible, or that the explanation lies in the integration of the thousands of component parts that make up biological systems. The genomic revolution now provides millions of protein sequences with which to dissect what is different, yet we are far away from understanding the complexities of life.

In face of so much diversity, we could frame the question differently. What makes something in biology common? Again, we find ourselves amazed by unabated similarities in everything from molecules, molecular structures, and cellular machinery, to body plans, behavior, and language. Why homogeneity amid so much heterogeneity? The answer I believe lies in the patterns and processes that are responsible for evolutionary change and the complexity and embedded simplicity of our evolving world. Modern phylogenetics and evolutionary bioinformatics have a lot to say about how to approach these questions, especially within the molecular realm. Similarly, the emerging field of evolutionary genomics attempts to address the complexity of entire repertoires of component parts acquired by the genomic revolution by reconciling what is common and what is unique at different levels of organization and along taxonomical transects. Approaches link pragmatism with theoretical discourse, the bench with the computer, and statistical inference with the hypothetico-deductive method in a more modern framework for scientific and philosophical advance. Concepts are borrowed from unlikely disciplines, such as graph theory and networks from applied mathematics and social sciences, and biologists brush comfortably with algorithms and simulations. This is probably where frontiers in science live.

These past several months have been exciting because of what they represent. This is why this book is particularly timely. The birth of Darwin, 200 years ago, and the publication of his famous book2 50 years later are clearly of profound importance. Darwin catalyzed everlasting change in science and society, revolutionizing biology and prompting the search for deeper understanding of the fundamentals of biological change. His views took more relevance in the synthesis that ensued, and their significance was later (though slowly) embraced by molecular biology. The report of the first crystallographic structure (Protein Data Bank entry 1MBN)3 50 years ago also marks a fundamental milestone in the exploration of the atomic makeup of the molecules of life. About 50,000 molecules later, we have better understanding of the molecular machinery of the cell as we try to reconcile models of structure with biological function. The beginning of this year also marks the acquisition of the sequences of the first 1000 organisms, which now span superkingdoms Archaea, Bacteria, and Eukarya, showing that the genomic revolution is indeed full fledged and unstoppable. Postgenomic science has changed the face of biology forever. The reductionist view of understanding the living world by atomizing systems and examining their parts is slowly caving in to more integrative approaches that impinge on the power of synthesis and the integration of knowledge. Physics enters the realm of biology and vice versa, but so do computer science, statistics, mathematics, and philosophy. A marvelous time for science!

The confluence of technological feats, such as “nextgen” sequencing, with informatics and exponential increases in our biological knowledge base prompted the consideration of advances in two seemingly distinct but emerging fields of endeavor, Evolutionary Genomics and Systems Biology. This book represents an attempt to bring timely problems and insights from a selected group of researchers to the table. The treatment of advances and challenges is therefore by no means exhaustive. In fact, the purpose was to entice thought rather than to seek exhaustive coverage. Following that spirit, the book has been organized in three sections, treating aspects of evolutionary genomics and systems biology that are crucial for the “new biology”. In Part I, “Evolution of Life,” six chapters cover the impact that evolutionary genomics has had on our understanding of life, from the general to the specific, exploring current challenges, controversial but central issues, and the relevance of model systems in biology. In Part II, “Evolution of Molecular Repertoires,” 10 chapters discuss how levels of organization map to each other, how structure and function impinge on genomic repertoires, the centrality of evolutionary models, and the hidden world of RNA molecules that pervades biology. Finally, in Part III, “Evolution of Biological Networks,” four chapters explore the complexity of the cellular makeup and wiring diagram of an organism, the dynamics and emerging properties of networks, and the role of fundamental evolutionary processes in the integration of component parts in systems. I hope the readers will find each and every chapter exciting and thought provoking.

This book could have not been possible without the patience and wholehearted cooperation of its contributors, which made this project feasible. I also wish to thank those who generously took time out of their busy schedules to provide valuable comments. Their input is highly appreciated. I would also like to thank Jay E. Mittenthal for his friendship and encouragement, Derek Caetano-Anolleés for artwork, and Karen Chambers and her team at Wiley for being so understanding in all issues related to the production of this book. Finally, I wish to recognize the National Science Foundation for continued and enabling support and my research team for making all things possible. From a personal point of view, I am particularly grateful to my wife, Gloria, for her patience, encouragement, and understanding, but fundamentally, for the sacrifices she bore when I embarked in the pursuit of science. Without her, none of this would have been possible.

GUSTAVO CAETANO-ANOLLÉS

Urbana, IllinoisJanuary 2010

1The Chimpanzee Sequencing Analysis Consortium, 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69–87.

2Darwin, C.R., 1859. On the Origin of Species by Means of Natural Selection. Murray, London.

3Kendrew, J.C., Bodo, G., Dintzis, H.M., Parrish, R.G., Wycoff, H.W., and Phillips, D.C., 1958. A three-dimensional model of the myoglobin molecule obtained by X-ray analysis. Nature 181:662–666

Contributors

Sarah Addou, Department of Structural & Molecular Biology, University College, London, England

Eivind Almaas, Professor of Systems Biology, Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway

Grigoris Amoutzias, VIB Department of Plant Systems Biology, Ghent University, Belgium, Brussels

Denis Baurain, Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Li ege, Li ege, Belgium

Otto G. Berg, Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden

Clara Isabel Bermudez-Santana, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany; Department of Biology, National University of Colombia, Bogot a, Colombia

Erich Bornberg-Bauer, IEB, University of Muenster, Muenster, Germany

Philip E. Bourne, Skaag School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, California

Guillaume Bourque, Computational & Mathematical Biology, Genome Institute of Singapore, Singapore

Jason G. Bragg, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts

Kristine Briedis, Skaag School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, California

Gustavo Caetano-Anollés, Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois

Todd A. Castoe, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado

Lesley J Collins, Allan Wilson Center for Molecular Ecology and Evolution, Institute for Molecular BioSciences, Massey University, Palmerston North, New Zealand Antoine Danchin, Genetics of Bacterial Genomes/CNRS Institute Pasteur, Paris, France A. P. Jason de Koning, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado

Alexander Donath, Bioinformatics Group, Department of Computer Science and Inter-disciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

Bernard Dujon, Molecular Genetic Unit of Levures, Institute Pasteur, Paris, France

Christopher Dupont, Skaag School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, California

Sven Findeiβ, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

Patrick Forterre, Institute Pasteur and Institute of Genetics and Microbiology, University of South, Paris, France

Jan Gorodkin, Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Frederiksberg, Denmark

Ajith Harish, Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois

Jana Hertel, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

Ivo L. Hofacker, Institute for Theoretical Chemistry, University of Vienna, Wien, Austria Charles G. Kurland, Department of Microbial Ecology, Lund University, Lund, Sweden

Manja Marz, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

Jay E. Mittenthal, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois

Andrew D. Moore, IEB, University of Muenster, Muenster, Germany

Christine Orengo, Department of Structural & Molecular Biology, University College, London, England

Wolfgang Otto, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

David Penny, Allan Wilson Center for Molecular Ecology and Evolution, Institute for Molecular BioSciences, Massey University, Palmerston North, New Zealand

Herv e Philippe, Department of Biochemistry, Robert-Cedergren Center, University of Montr eal, Montr eal, Qu ebec, Canada

David D. Pollock, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado

Anthony M. Poole, Department of Molecular Biology and Functional Genomics, Stock-holm University, Stockholm, Sweden, and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand

Juan Ranea, Department of Structural & Molecular Biology, University College, London, England

Adam James Reid, Department of Structural & Molecular Biology, University College, London, England

Robert Rentzsch, Department of Structural & Molecular Biology, University College, London, England

Markus Riester, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

Christine Schulz, Fraunhoffer Institute for Cell Therapy and Immunology, Leipzig, Germany

Peter Schuster, Institute for Theorectical Chemistry, Wien University, Wien, Austria; Santa Fe Institute, Santa Fe, New Mexico

Agnieszka Sekowska, Genetics of Bacterial Genomes/CNRS, Institut Pasteur, Paris, France

Peter F. Stadler, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Wien, Austria; Fraunhoffer Institute for Cell Therapy and Immunology, Leipzig, Germany; Santa Fe Institute, Santa Fe, New Mexico

Feng-Jie Sun, W. M. Keck Center for Comparative and Functional Genomics, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois

Andrea Tanzer, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Wien, Austria

Ruben Valas, Skaag School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, California

Yves Van de Peer, VIB Department of Plant Systems Biology, Ghent University, Belgium

Andreas Wagner, Department of Biochemistry, University of Zurich and Zurich, Switzerland; Santa Fe Institute, Santa Fe, New Mexico

Stefan Wirth, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

Liudmila S. Yafremava, Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois

Song Yang, Skaag School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, California

Hao Zhao, Computational & Mathematical Biology, Genome Institute of Singapore, Singapore

Part I

Evolution of Life

Chapter 1

Evolutionary Genomics Leads the Way

David Penny and Lesley J. Collins

1.1 INTRODUCTION

1.2 EVOLUTION AND THE POWER OF GENOMES

1.3 THE PROBLEM OF DEEP PHYLOGENY AND “THE TREE”

1.4 FRED, THE LAST COMMON ANCESTOR OF MODERN EUKARYOTES

1.5 EUKARYOTE ORIGINS: CONTINUITY FROM THE RNA WORLD?

1.6 MINIMAL GENOMES AND REDUCTIVE EVOLUTION

1.7 EVOLUTIONARY GENOMICS FOR THE FUTURE

REFERENCES

1.1 INTRODUCTION

When the older of our authors was an undergraduate (we won’t tell you how long ago, but it was certainly way back in the last millennium), there were considered three “Great Scientific Problems.” All three were questions about origins that might (in principle) have genuine scientific answers, but at that time they were thought to be so complex that we might never find them—the questions might just be too big to ever find a scientific solution. The questions were

1. the origin of humans,

2. the origin of life, and

3. the origin of the universe.

It is brilliant that in a single working life the first is answered and the second is crumbling away. The third (the origin of the universe) we recognized even “way back then” as a question of a different kind in that, in principle, could lead to an infinite regress. That is, solve the question about the origin of our universe (say, hypothesis A) and it immediately opens up another question, namely, what explains hypothesis A. So the third question is best left to the physicists or philosophers! As we show below, analyzing genomics datasets allows us to address such major questions where solutions were not possible even 5–10 years ago.

1.2 EVOLUTION AND THE POWER OF GENOMES

The first step is showing how access to information about complete genomes allowed the first of the above three questions to be answered; so in this section, we will only refer to the comparison of the chimpanzee and human genomes. The practical point is how these two genomes can be used as a test of the question whether microevolutionary processes are sufficient for macroevolution (Penny and Phillips, 2004). Can the origin of the human genome be understood solely in terms of the normal microevolutionary processes that occur in natural populations? This is a major scientific question—perhaps “the” major question.

The genetic processes in populations (that we know about) include point mutations (SNPs, single nucleotide polymorphisms), small insertions and deletions (indels, from a single nucleotide to larger indels), variations in copy number (of a gene or other fragment of DNA, CNVs; Redon et al., 2006), inversions and translocations of sections of chromosome and also chromosome fusions, and activated retrotransposable elements. These are precisely the differences we see between the human and chimpanzee genomes, and the classes of differences are outlined in Table 1.1 (see Li and Saunders (2005) and Levy and Strausberg (2008)).

Thus, the conclusion is that the human genome arises strictly from the natural processes that occur in plant and animal populations—we can find nothing different or unexpected about the genetic processes leading to humans. The conclusion is extremely powerful and should be reiterated continually by biologists talking to members of the public, especially in more religious countries. In principle, other possibilities exist for the origin of the human genome. Although we make jokes about it, saying that perhaps a Kindly Creator, or a Group of Itinerant Space Travellers (the GIST model), might have inserted into the human genome a whole lot of genes for both wisdom and intelligence. Just think of that, we tell our students, many, many genes in the human genome for wisdom and intelligence. After the appropriate pause, we continue—all we have to do now is to find how to turn those genes on!

All right,so on the surface the story is a joke,but the story has a very serious purpose and carries a much deeper significance. As far as we can tell, the human genome arose from an ape-like genomic ancestor through 100% normal microevolutionary processes—processes that occur within populationsorbetween sibling species.Soyes, inprinciple, therewere other alternatives. If normal microevolutionary processes are to lead to humans, then that is a very powerful conclusion about the sufficiency of microevolutionary processes.