The origins of genome architecture:
Gespeichert in:
| Beteilige Person: | |
|---|---|
| Format: | Buch |
| Sprache: | Englisch |
| Veröffentlicht: |
Sunderland, Mass.
Sinauer Associates
2007
|
| Schlagwörter: | |
| Links: | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016237459&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| Beschreibung: | Literaturverz. S. [401] - 470 |
| Umfang: | XVI, 494 S. Ill., graph. Darst. |
| ISBN: | 9780878934843 0878934847 |
Internformat
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Datensatz im Suchindex
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|---|---|
| adam_text | THE ORIGINS
OF GENOME
ARCHITECTURE
Michael Lynch
Indiana University
Sinauer Associates, Inc Publishers
Sunderland, Massachusetts
Contents
Preface xiii
1The Origin of Eukaryotes 1
Entry into the DNA World 4
A viral origin of DNA? B
Membranes early or late? 7
The Three Domains of Cellular Life 9
Tree, ring, or web of life? 13
Eukaryotic gene acquisition from endosymbionts 14
The unity of the eukaryotes 15
The Stem Eukaryote 16
The Eukaryotic Radiation 18
The unikonts and bikonts 21
A eukaryotic big bang? 22
Genome Repatterning and the Eukaryotic Radiation 23
A Synopsis of the First 2 Billion Years of Biology 26
CONTENTS vii
2 Genome Size and Organismal Complexity 29
Genome Size and Complexity 30
The Selfish-DNA and Bulk-DNA Hypotheses 32
The Metabolic Cost of DNA 34
Directional Mutation Pressures on Genome Size 35
Population Size and the Mutational Hazard of Excess DNA 39
3 The Human Genome 43
Gene Number 43
Introns and Exons 49
Regulatory DNA 51
Mobile Genetic Elements 56
LINEs and SINEs 57
LTR elements 59
Transposons BO
Pseudogenes 60
The Unique Trajectory of Human Evolution 63
4 Why Population Sjze Matters 69
Random Genetic Drift at a Neutral Locus 70
The Effects of Selection 74
The Importance of Linkage 76
The theory of genetic draft 78
Empirical considerations 81
The Three Genomic Perils of Evolving Large Body Size 83
Smaller population size 84
Higher mutation rates 84
Reduced recombination in large genomes 86
viii CONTENTS
The Global Effective Population Sizes of Species 90
Sources of bias 92
Resolution of the paradox of variation 95
Mutation as a Weak Selective Force 97
5Three Keys to Chromosomal Integrity 101
Origins of Replication 102
ORI specification 104
Evolutionary consequences 105
Centromeres 107
The centromeric-drive hypothesis 109
Centromere positioning 112
Centromere definition 113
Telomeres 116
6 The IMucleotide Composition Landscape 121
The Molecular Spectrum of Mutational Effects 122
Biased Gene Conversion 127
Evolutionary Consequences of Replication 133
Isochores 136
The Nonadaptive Basis of Genome-Wide Nucleotide
Composition Variation 139
Codon Usage Bias 141
Prokaryotes 144
Eukaryotes 146
Unsolved problems 149
7Mobile Genetic Elements 151
Non-LTR Retrotransposons 153
The IR system of hybrid dysgenesis 157
CONTENTS ix
LTR Retrotransposons 159
The gypsy element 163
Transposons 164
The P element 166
Rates of Insertion and Fitness Effects 167
Regulation of Mobile Element Activity 169
The opportunity for self-regulation 170
Host-encoded mechanisms for mobile element
containment 172
The Population Biology of Mobile Elements 174
Conditions for establishment 174
Conditions for element number stabilization 179
Insights from population surveys 181
Mobile elements and species extinction 185
Positive Effects of Mobile Element Insertions 189
8Genomic Expansion by Gene Duplication 193
The Evolutionary Demography of Duplicate Genes 194
Origins of segmental duplications 199
Whole genome duplication 202
Mechanisms for the Preservation of Duplicate Genes 209
Neofunctionalization 209
The masking effect of duplicate genes 213
Subfunctionalization 215
The Fates of Duplicated Protein Sequences 219
Patterns of molecular evolution 220
The Case for Subfunctionalization 225
Speciation via the Divergent Resolution of Duplicate Genes 228
9 Genes in Pieces 237
The Spliceosome(s) 238
The Introns Early-lntrons Late Debate 242
X CONTENTS
A Group II Origin? 244
Mechanisms of Origin and Loss 247
The Intrinsic Cost of Introns 251
Introns and Population Size 253
Rates of Intron Gain and Loss 256
Adaptive Exploitation of Introns 262
Modifiers of the recombination rate 262
Alternative splicing 263
Messenger RNA surveillance 265
10 Transcript Production 271
Transcription and Translation Initiation 272
The Premature Translation Initiation Problem 276
Transcription Termination 282
The Deployment of trans Splicing 287
Evolution of Modular Gene Organization 292
The passive emergence of modularity 294
The demise of operons 297
11Expansion and Contractionof Organelle Genomes 303
Establishment and Stabilization of Organelles 305
The early stages of mitochondrial evolution 305
Intergenomic transfer 308
The origins of plastids 310
Genome Content and Organization 312
The Population Genetic Environment 316
Mutation 317
Transmission and recombination 321
Effective population size 323
CONTENTS xi
Mutation Pressure and the Diversification
of Organelle Genomes 326
The proliferation of noncoding DNA 327
Modifications of the genetic code 330
Messenger RNA editing 333
Muller s Ratchet and the Mitochondrion 336
Insights from More Recent Endosymbioses 342
12 Sex Chromosomes 347
The Origins of Sex Chromosomes 349
The Population Genetic Environment 351
Degeneration of the Y Chromosome 354
Retailoring the X Chromosome 358
13 Genomfart 363
The Origins of Modern Evolutionary Theory 364
Evolution as a Science in the Post-Darwinian World 366
Nothing in Evolution Makes Sense Except in the Light
of Population Genetics 370
The Passive Emergence of Genomic Complexity
by Nonadaptive Processes 372
Do the Roots of Organismal Complexity Also Reside
in Nonadaptive Processes? 377
An Entree to Understanding the Origins of Genomic Determinants
of Organismal Complexity 380
Evolvability 386
Closing Comments 389
Glossary 391
Literature Cited 401
Author Index 471
Subject Index 483
|
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| id | DE-604.BV023033653 |
| illustrated | Illustrated |
| indexdate | 2024-12-20T13:07:05Z |
| institution | BVB |
| isbn | 9780878934843 0878934847 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016237459 |
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| owner_facet | DE-19 DE-BY-UBM DE-20 |
| physical | XVI, 494 S. Ill., graph. Darst. |
| publishDate | 2007 |
| publishDateSearch | 2007 |
| publishDateSort | 2007 |
| publisher | Sinauer Associates |
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| spellingShingle | Lynch, Michael 1951- The origins of genome architecture Genomes Genomics Molekulare Evolution (DE-588)4812902-1 gnd Genom (DE-588)4156640-3 gnd |
| subject_GND | (DE-588)4812902-1 (DE-588)4156640-3 |
| title | The origins of genome architecture |
| title_auth | The origins of genome architecture |
| title_exact_search | The origins of genome architecture |
| title_full | The origins of genome architecture Michael Lynch |
| title_fullStr | The origins of genome architecture Michael Lynch |
| title_full_unstemmed | The origins of genome architecture Michael Lynch |
| title_short | The origins of genome architecture |
| title_sort | the origins of genome architecture |
| topic | Genomes Genomics Molekulare Evolution (DE-588)4812902-1 gnd Genom (DE-588)4156640-3 gnd |
| topic_facet | Genomes Genomics Molekulare Evolution Genom |
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