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Evolutionary Genomics and Proteomics
Edited by Mark Pagel, University of Reading, and Andrew Pomiankowski, University College London
Nov. 21, 2007
295 pages, 90 illustrations
About This Title
Evolutionary Genomics and Proteomics is the first major review of developments in the rapidly advancing areas of genomics and proteomics, with particular emphasis on placing these fields in an evolutionary context. With a growing understanding of genes, their diversity and regulation, and how their products work together in networks of interacting elements, a new era of biology is emerging. The genome is coming to be seen not just as a collection of genes, but as a complex set of instructions for making a phenotype, written in digital form. The challenge for evolutionary biologists is to use this information to understand how phenotypic novelty, complexity, robustness, and evolvability emerge—as well as how these forces sculpt the genome—and to link genomic and phenotypic diversity within populations.
Evolutionary Genomics and Proteomics highlights new research in all these areas with thirteen chapters from leading scientists on topics including systems biology, the origin of genes and lateral gene transfer, gene regulation and gene dispensability, proteome complexity, genomic immune systems, sex-biased genomic expression, sex chromosome evolution, gene and protein network evolution, adaptive genome evolution, and human evolutionary genomics. The chapters are richly illustrated and written for students and researchers in the life sciences.
Reviews and Commentary
“I highly recommend this volume to anyone interested in the exciting new field of evolutionary population genomics. It is very nicely formatted with many attractive color graphs that schematically illustrate the text. The book will also be suitable as a teaching volume at the graduate level.”
—Nico M. van Straalen, The Quarterly Review of Biology
“Evolutionary Genomics and Proteomics can truly be regarded as an opening salvo for a new phase in genomics (and all follow-up -omics), where the evolutionary approach will become key to the identification of the function of individual genes and gene networks. It will certainly be of great use as both a basic textbook and compilation of in-depth reviews for graduate students and molecular biologists that either enter the genomics field or would like to apply novel conceptional thinking in comparative genomics.”
—Evgeni Sokurenko, Microbe
“Evolutionary Genomics and Proteomics superbly highlights the new research problems that have arisen from a genome-wide perspective on evolution, and sets out the looming challenges faced by evolutionary biologists wishing to understand how phenotypic diversity, complexity, robustness, and evolvability emerge. A must-have book for anyone interested in these exciting new fields.”
—Andrew G. Clark, Cornell University
Table of Contents
1. The Organismal Prospect
Mark Pagel and Andrew Pomiankowski
- Evolutionary Genetics in the Time of Genomics
- The Organism in the Genome
- Complexity and Regulation
- The Origins of Novelty
- Robustness and Evolvability
- Genome Immunity
- Identifying Selective Change
- What If Evolutionary Genomic and Proteomic Scientists Succeed?
2. Evolutionary Systems Biology
Eugene Koonin and Yuri Wolf
- Systems Biology: The New Big Science of “Omes”
- Systems Biology in the Light of Evolution: The Quest for the Link between Genomic and Phenotypic Evolution
- Correlations between Variables Characterizing Genome Evolution and Functioning
- The Multidimensional Space of Omics
- Glimpses of Biology behind the Correlations
- Some Generalizations: Evolutionary Systems Biology—A Nascent Field in Turmoil
3. The Origin of New Genes
Chuanzhu Fan, J. J. Emerson, and Manyuan Long
- Recent Discoveries of New Genes
- Mechanisms to Generate New Genes
- Evolutionary Forces for New Gene Retention
- The Location and Movement of New Genes
- Inferring the Functionality of New Genes
- General Methods to Detect New Genes
- Comparative Genomic Hybridization to Detect New Genes
- Outlooks and Perspectives
4. Lateral Gene Transfer
W. Ford Doolittle, Camilla L. Nesbř, Eric Bapteste, and Olga Zhaxybayeva
- A Very Brief History of Lateral Genomics
- Methods of Lateral Gene Transfer
- Detecting LGT
- Ever-Present Alternatives
- Quantifying LGT
- An LGT-Resistant Core
- LGT and Microevolution
- LGT and Macroevolution
- Eukaryotes, the Other Iceberg
- Reuniting Process and Pattern
5. Evolution of Genomic Expression
Bernardo Lemos, Christian R. Landry, Pierre Fontanillas, Susan C. P. Renn, Rob Kulathinal, Kyle M. Brown, and Daniel L. Hartl
- The Complex Regulation of Genomic Expression
- Classical Transcription Regulation in Cis and Trans
- Epigenetic Regulation and Chromatin Modifications
- Post-Transcriptional Regulation
- Measuring Attributes of Genomic Expression with Experimental and Computational Tools
- The Evolution of Genomic Expression: What Do We Know?
- Gene Regulatory Networks, Subnetworks, and Modules
6. The Evolution of Proteome Complexity and Diversity
Laszló Patthy
- Evolution of Protein Complexity
- Evolution of Proteome Complexity
- Multidomain Proteome Complexity
- Proteome Interaction Networks
- Multidomain Proteins and Organismic Complexity
- Factors Favoring the Formation of Multidomain Proteins
7. Genomic Redundancy and Dispensability
Laurence D. Hurst and Csaba Pál
- Are “Dispensable” Genes Really Dispensable?
- By What Mechanisms are Nontrivially Dispensable Genes Dispensable?
- Why Did Dispensability Evolve?
8. Genome Defense
Christopher B. Schaefer, Mary Grace Goll, and Timothy H. Bestor
- Mechanisms of Genome Defense
- Cytosine Methylation
- Editing as a Form of Defensive Mutagenesis
9. Sex-Biased Genomic Expression
Brian Oliver
- One Species, Two Optimal Genomes
- Y Chromosomes
- X Chromosomes
- Comparing Mammalian, Drosophila, and C. elegans X Chromosomes
- Moving Forward
10. Sex Chromosome Origins and Evolution
D. Charlesworth
- The Diversity of Sex Chromosomes
- The Origins of Sex-Determining Loci and Recombination Suppression around the Sex-Determining Locus Region
- Evolution in Young and Proto–Sex Chromosomes: Sexually Antagonistic Genes
- Determining the Age of Sex Chromosomes
- Degeneration and Loss of Adaptation of Genes on the Nonrecombining Sex Chromosome
- Do Y Chromosomes Always Degenerate, and What Determines Which Genes Are Retained?
- How is Recombination Suppressed?
- Further Chromosome Rearrangements
- Neo–Sex Chromosome Formation
- Evolution and Adaptation of Ancient Sex Chromosomes: Evolution of Dosage Compensation and of Changed Gene Content
- Adaptation of Sex Chromosomes
11. Molecular Signatures of Adaptive Evolution
Alan Filipski, Sonja Prohaska, and Sudhir Kumar
- Codon Usage Bias and the Estimates of Selection Ratio (ω)
- Hypermutability of CpG Dinucleotides and the Estimates of Selection Ratio
- Using Pseudogenes to Estimate Nonsynonymous Mutation Rates
- Rate of Intron Divergence as a Proxy for Nonsynonymous Mutation Rates
- Direct Estimates of Mutation Rates in the Laboratory
12. Gene Networks and Natural Selection
Andreas Wagner
- Is There a Network Biology?
- Natural Selection and Network Parts
- Natural Selection and Small-Scale, Local Network Features
- Natural Selection and Global Network Structure
13. Human Evolutionary Genomics
Ines Hellmann and Rasmus Nielsen
- Mutations—The Sources of Genome Variability
- Recombination
- Transposable Elements
- Evolution through Gene Duplication
- Analyses of Protein-Coding Regions
- Human-Specific Genetic Adaptations
- Selection on Noncoding Sequences
- Expression Data
- Amount of Selection Affecting the Human Genome and the Genetic Load of Humans
Pricing and Options
| Titles | Product Code | Price (USD) | ||
|---|---|---|---|---|
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Evolutionary Genomics and Proteomics (paper) | 978-0-87893-654-0 | $59.95 | Purchase | Request Exam Copy |
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Evolutionary Genomics and Proteomics (casebound) | 978-0-87893-655-7 | $84.95 | Purchase | |
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