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The Origins of Genome Architecture
Michael Lynch
2007
389 pages, 96 illustrations
casebound
About the Book
With official genomic blueprints now available for hundreds of species, and thousands more expected in the near future, the field of biology has been forever transformed. Such readily accessible data have encouraged the proliferation of adaptive arguments for the evolution of gene and genomic features, often with little or no attention being given to simpler and more powerful alternative explanations. By integrating the central observations from molecular biology and population genetics relevant to comparative genomics, Lynch shows why the details matter.
Presented in a nontechnical fashion, at both the population-genetic and molecular-genetic levels, this book offers a unifying explanatory framework for how the peculiar architectural diversity of eukaryotic genomes and genes came to arise. Under Lynch’s hypothesis, the genome-wide repatterning of eukaryotic gene structure, which resulted primarily from nonadaptive processes, provided an entirely novel resource from which natural selection could secondarily build new forms of organismal complexity.
About the Author
Michael Lynch is a Distinguished Professor in the Department of Biology at Indiana University. He received his B.S. in Biology from St. Bonaventure University, and his Ph.D. in Ecology from the University of Minnesota. Dr. Lynch is a former President of the Society for the Study of Evolution, current President of the American Genetics Association, council member of the Society for Molecular Biology and Evolution, and fellow of the American Academy of Arts and Sciences. In 1998, he and Bruce Walsh coauthored Genetics and Analysis of Quantitative Traits. His research is focused on the mechanisms of evolution at the molecular, genomic, and phenotypic levels, and makes use of equations and several model systems (Daphnia, Caenorhabditis, Paramecium, and Saccharomyces).
Reviews and Commentary
“This book is a must-read for every genome researcher … It is the best, most up-to-date and thorough summary of genome evolution published. … Almost every page introduces interesting, unanswered problems, making it a gold mine for graduate students in search of a thesis topic.”
—Axel Meyer, Nature
“If you want a good summary of what genomics has revealed about genome architecture over the last two decades, merged with a nontechnical exposition of the relevant principles of population genetics, this is the book to get.”
—Daniel Hartl, Nature Genetics
“… the book's first 12 chapters are a must-read for anyone interested in the evolution of genomes. This Origins represents a serious, valiant, and highly scholarly attempt at making sense of the new data provided by the genomic revolution. To that aim, Lynch deploys the full array of conceptual tools that make up the modern synthesis paradigm in evolutionary biology.”
—Massimo Pigliucci, Science
“This volume would be an excellent foundation for an upper-level undergraduate course or a graduate seminar. It has become increasingly clear that a blind reliance on the explanatory power of natural selection has led to a lot of ‘sloppy thinking’ and this book is a start toward clearing up some of this problem.”
—Richard J. Mural, The Quarterly Review of Biology
“This is a truly remarkable book, which will forever change your view of evolutionary biology. Anyone with even tangential interest in evolution needs to read the preface, epilogue, and especially the fourth chapter on population size. Lynch takes a detailed knowledge of molecular genetics and genomics, combined with a refined fluency in population genetics, to create sound sweeping descriptions and predictions about evolution. … Read Lynch's book, have your students read it, and let's revise our views of evolution.”
—Root Gorelick, Plant Science Bulletin
“Lynch presents a synthesis of molecular genetics and evolutionary biology with a goal of driving new interdisciplinary research and understanding. He succeeds admirably. This extremely interesting book presents genomic evolution in a comprehensive manner and with different perspectives. … What makes this volume so useful is that each chapter presents not only what and how, but also why (and why it matters). This book will appeal to everyone interested in genetics, molecular biology, and evolution. Highly recommended.”
—D. Carroll, Choice
Table of Contents
1. The Origin of Eukaryotes
- Entry into the DNA World
- A viral origin of DNA?
- Membranes early or late?
- The Three Domains of Cellular Life
- Tree, ring, or web of life?
- Eukaryotic gene acquisition from endosymbionts
- The unity of the eukaryotes
- The Stem Eukaryote
- The Eukaryotic Radiation
- The unikonts and bikonts
- A eukaryotic big bang?
- Genome Repatterning and the Eukaryotic Radiation
- A Synopsis of the First 2 Billion Years of Biology
2. Genome Size and Organismal Complexity
- Genome Size and Complexity
- The Selfish-DNA and Bulk-DNA Hypotheses
- The Metabolic Cost of DNA
- Directional Mutation Pressures on Genome Size
- Population Size and the Mutational Hazard of Excess DNA
3. The Human Genome
- Gene Number
- Introns and Exons
- Regulatory DNA
- Mobile Genetic Elements
- LINEs and SINEs
- LTR elements
- Transposons
- Pseudogenes
- The Unique Trajectory of Human Evolution
4. Why Population Size Matters
- Random Genetic Drift at a Neutral Locus
- The Effects of Selection
- The Importance of Linkage
- The theory of genetic draft
- Empirical considerations
- The Three Genomic Perils of Evolving Large Body Size
- Smaller population size
- Higher mutation rates
- Reduced recombination in large genomes
- The Global Effective Population Sizes of Species
- Sources of bias
- Resolution of the “paradox of variation”
- Mutation as a Weak Selective Force
5. Three Keys to Chromosomal Integrity
- Origins of Replication
- ORI specification
- Evolutionary consequences
- Centromeres
- The centromeric-drive hypothesis
- Centromere positioning
- Centromere definition
- Telomeres
6. The Nucleotide Composition Landscape
- The Molecular Spectrum of Mutational Effects
- Biased Gene Conversion
- Evolutionary Consequences of Replication
- Isochores
- The Nonadaptive Basis of Genome-Wide Nucleotide Composition Variation
- Codon Usage Bias
- Prokaryotes
- Eukaryotes
- Unsolved problems
7. Mobile Genetic Elements
- Non-LTR Retrotransposons
- The IR system of hybrid dysgenesis
- LTR Retrotransposons
- The gypsy element
- Transposons
- The P element
- Rates of Insertion and Fitness Effects
- Regulation of Mobile Element Activity
- The opportunity for self-regulation
- Host-encoded mechanisms for mobile element containment
- The Population Biology of Mobile Elements
- Conditions for establishment
- Conditions for element number stabilization
- Insights from population surveys
- Mobile elements and species extinction
- Positive Effects of Mobile Element Insertions
8. Genomic Expansion by Gene Duplication
- The Evolutionary Demography of Duplicate Genes
- Origins of segmental duplications
- Whole genome duplication
- Mechanisms for the Preservation of Duplicate Genes
- Neofunctionalization
- The masking effect of duplicate genes
- Subfunctionalization
- The Fates of Duplicated Protein Sequences
- Patterns of molecular evolution
- The Case for Subfunctionalization
- Speciation via the Divergent Resolution of Duplicate Genes
9. Genes in Pieces
- The Spliceosome(s)
- The Introns Early–Introns Late Debate
- A Group II Origin?
- Mechanisms of Origin and Loss
- The Intrinsic Cost of Introns
- Introns and Population Size
- Rates of Intron Gain and Loss
- Adaptive Exploitation of Introns
- Modifiers of the recombination rate
- Alternative splicing
- Messenger RNA surveillance
10. Transcript Production
- Transcription and Translation Initiation
- The Premature Translation Initiation Problem
- Transcription Termination
- The Deployment of trans Splicing
- Evolution of Modular Gene Organization
- The passive emergence of modularity
- The demise of operons
11. Expansion and Contraction of Organelle Genomes
- Establishment and Stabilization of Organelles
- The early stages of mitochondrial evolution
- Intergenomic transfer
- The origins of plastids
- Genome Content and Organization
- The Population Genetic Environment
- Mutation
- Transmission and recombination
- Effective population size
- Mutation Pressure and the Diversification of Organelle Genomes
- The proliferation of noncoding DNA
- Modifications of the genetic code
- Messenger RNA editing
- Muller’s Ratchet and the Mitochondrion
- Insights from More Recent Endosymbioses
12. Sex Chromosomes
- The Origins of Sex Chromosomes
- The Population Genetic Environment
- Degeneration of the Y Chromosome
- Retailoring the X Chromosome
13. Genomfart
- The Origins of Modern Evolutionary Theory
- Evolution as a Science in the Post-Darwinian World
- Nothing in Evolution Makes Sense Except in the Light of Population Genetics
- The Passive Emergence of Genomic Complexity by Nonadaptive Processes
- Do the Roots of Organismal Complexity Also Reside in Nonadaptive Processes?
- An Entrée to Understanding the Origins of Genomic Determinants of Organismal Complexity
- Evolvability
- Closing Comments
Glossary
Literature Cited
Author Index
Subject Index
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