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 Lynchs 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.
Table of Contents
1. The Origin of Eukaryotes
* Entry into the DNA World
o A viral origin of DNA?
o Membranes early or late?
* The Three Domains of Cellular Life
o Tree, ring, or web of life?
o Eukaryotic gene acquisition from endosymbionts
o The unity of the eukaryotes
* The Stem Eukaryote
* The Eukaryotic Radiation
o The unikonts and bikonts
o 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
o LINEs and SINEs
o LTR elements
o 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
o The theory of genetic draft
o Empirical considerations
* The Three Genomic Perils of Evolving Large Body Size
o Smaller population size
o Higher mutation rates
o Reduced recombination in large genomes
* The Global Effective Population Sizes of Species
o Sources of bias
o Resolution of the paradox of variation
* Mutation as a Weak Selective Force
5. Three Keys to Chromosomal Integrity
* Origins of Replication
o ORI specification
o Evolutionary consequences
* Centromeres
o The centromeric-drive hypothesis
o Centromere positioning
o 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
o Prokaryotes
o Eukaryotes
o Unsolved problems
7. Mobile Genetic Elements
* Non-LTR Retrotransposons
o The IR system of hybrid dysgenesis
* LTR Retrotransposons
o The gypsy element
* Transposons
o The P element
* Rates of Insertion and Fitness Effects
* Regulation of Mobile Element Activity
o The opportunity for self-regulation
o Host-encoded mechanisms for mobile element containment
* The Population Biology of Mobile Elements
o Conditions for establishment
o Conditions for element number stabilization
o Insights from population surveys
o Mobile elements and species extinction
* Positive Effects of Mobile Element Insertions
8. Genomic Expansion by Gene Duplication
* The Evolutionary Demography of Duplicate Genes
o Origins of segmental duplications
o Whole genome duplication
* Mechanisms for the Preservation of Duplicate Genes
o Neofunctionalization
o The masking effect of duplicate genes
o Subfunctionalization
* The Fates of Duplicated Protein Sequences
o 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 EarlyIntrons 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
o Modifiers of the recombination rate
o Alternative splicing
o 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
o The passive emergence of modularity
o The demise of operons
11. Expansion and Contraction of Organelle Genomes
* Establishment and Stabilization of Organelles
o The early stages of mitochondrial evolution
o Intergenomic transfer
o The origins of plastids
* Genome Content and Organization
* The Population Genetic Environment
o Mutation
o Transmission and recombination
o Effective population size
* Mutation Pressure and the Diversification of Organelle Genomes
o The proliferation of noncoding DNA
o Modifications of the genetic code
o Messenger RNA editing
* Mullers 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