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
Source/Fonte
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 [SIC]
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
SOURCE/FONTE
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Destaquei em itálico alguns títulos de Lynch. Só pra provocar o leitor a comprar e ler o livro dele. Nota: Lynch é evolucionista convicto, e não faz parte do grupo de teóricos do Design Inteligente.
