The evolution of the genome:
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Amsterdam [u.a.]
Elsevier Acad. Pr.
2005
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XXVI, 740 S. Ill., graph. Darst. |
| ISBN: | 0123014638 |
Internformat
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| 245 | 1 | 0 | |a The evolution of the genome |c ed. by T. Ryan Gregory |
| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier Acad. Pr. |c 2005 | |
| 300 | |a XXVI, 740 S. |b Ill., graph. Darst. | ||
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Datensatz im Suchindex
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|---|---|
| adam_text | CONTENTS
PART I
The C alue Enigma
1 Genome Size Evolution in Animals
T Ryan Gregory
Why Should Anyone Care about Genome Size? 4
Genome Size in Animals: A Historical Perspective 5
The Discovery of DNA 5
A Remarkable Constancy and the Origin of the C value 6
The C value Paradox 7
The Modem View: From Paradox to Puzzle 9
The State of Knowledge of Animal Genome Size 10
The Animal Genome Size Database 10
Patterns of Variation 12
Vertebrates (and Nonvertebrate Chordates) 12
Invertebrates 16
Intraspecific Variation in Animals 24
Mechanisms of Genome Size Change 27
Selfish DNA and the Spread of Transposable Elements 27
Junk DNA and the Accumulation of Pseudogenes 29
Introns 31
Chromosome Level Events 31
Polyploidy, C value, and Genome Size 32
Sentinel Sequences and Global Forces 34
Insertion Deletion Biases 35
Genome Size and G+C Content 39
xiv Contents
Assessing the Directionality of Animal Genome Size Evolution 40
Genome Size and Cell Size 41
Explaining the Correlation 48
Genome Size and Organismal Phenotypes 52
Body Size 53
Metabolism 54
Developmental Rate 60
Developmental Complexity 62
Organ Complexity 64
Longevity 66
Measuring Animal Genome Sizes 67
Flow Cytometry 67
Feulgen Microdensitometry 68
Feulgen Image Analysis Densitometry 69
What about Genome Sequencing? 69
Concluding Remarks and Future Prospects 71
2 Genome Size Evolution in Plants
Michael D. Bennett and Ilia}. Leitch
A Brief History of Genome Size Study in Plants 90
The First Estimates of DNA Amounts 90
The Main Areas of Focus of Early Genome Size Studies 92
Impact of the Molecular Revolution on Genome Size Research 93
Genome Size Studies in the POst Genomic Era 94
The State of Knowledge Regarding Plant Genome Sizes 94
C values in Cyberspace: Development of the Plant DNA C values Database 95
Uses and Users of the Plant DNA C values Database 96
Patterns in Plant Genome Size Evolution 98
The Extent of Variation across Plant Taxa 98
Genome Size in a Phylogenetic Context 99
How Do Plant Genome Sizes Evolve? 103
Sequences Responsible for the Range of Genome Sizes Encountered
in Plants 105
What Triggers the Spread of Transposable Elements? 106
Satellite DNA 109
Genome Size Increase by Polyploidy 109
Mechanisms of Genome Size Decrease 112
Key Correlates of Genome Size across Plant Species 114
Early Work on the Phenotypic Consequences of Genome Size
Variation in Plants 114
Chromosome Size 116
Contents XV
Nucleus Size 118
Cell Size 118
Cell Division Rate 119
Causation at the Cellular Level: The Nucleotype Concept 121
Pollen and Seeds 122
Minimum Generation Time and Developmental Lifestyle 124
Physiology and Climate Response 128
Ecological and Evolutionary Implications of Genome Size Variation 129
Geographical Distribution and the Large Genome Constraint
Hypothesis 130
Genome Size and Plant Response to Human Environmental Change 132
Intraspecific Variation in Genome Size 134
Overview of Intraspecific Variation 134
Genuine Intraspecific Variation in Angiosperms 136
The Special Case of Maize 137
Genuine Intraspecific Variation in Nonangiosperms 138
Intraspecific Variation and Speciation 139
The Mystery of DNA Constancy 140
Methodology for Estimating Genome Size in Plants 141
Chemical Extraction and Reassociation Kinetics 141
Feulgen Microdensitometry 142
Feulgen Image Analysis Densitometry 144
Flow Cytometry 145
Complete Genome Sequencing 147
Some Comments on Plant Genome Size Standards 148
Concluding Remarks and Future Prospects 149
Expansion of the Plant Genome Size Dataset 150
Mechanistic Questions 151
Ecological and Environmental Questions 151
Evolutionary Questions 151
PART II
The Evolution of Genomic Parasites
3 Transposable Elements
Margaret G. Kidwell
A Brief History of the Study of Transposable Elements 165
The Discovery of Transposable Elements 166
Early TE Studies in Bacteria 167
I
Xvi Contents
Early TE Studies in Fungi 167
Early TE Studies in Plants 168
Early TE Studies in Animals 168
A Recent Explosion of New Information from DNA Sequencing 169
Who Cares about Transposable Elements? 170
How Are TEs Classified? 170
Autonomous and Nonautonomous Elements 170
Classification Based on Mode of Transposition 171
The Relationship Between Class 1 and II Elements 179
Hallmarks of TE Sequences 180
Dispersed Multigene Families 180
Target Site Duplications 180
Terminal Repeats 180
Coding Regions and Motifs 181
Fixed and Segregating Insertion Sites 182
Methods Used in the Identification and Study of TEs 182
Genetic Analysis of Naturally Occurring Unstable Mutations 182
Methods of Molecular Analysis 183
Data from Genome Sequencing Projects 184
Reconstruction of Ancestral TEs from Incomplete Contemporary
Copies 185
Databases for Repetitive DNA Sequences 185
Phylogenetic Analysis 185
Applications of TEs to Other Areas of Biology 186
Transformation Systems Based on Transposable Elements 186
Transposable Element Mutagenesis and Gene Tagging 186
Transposable Elements as Markers in Evolutionary Studies 187
The Use of Mobile Introns for Targeted Gene Manipulation 188
The Prevalence of TEs in Eukaryotic Genomes 188
Ancient Origins 188
Present Day Prevalence 189
Examples of Common TEs in Familiar Organisms 189
The Distribution of TEs Within Genomes 193
Selection as a Mechanism for Reducing TE Copy Number 193
The Role of Recombination in Determining TE Distributions 194
TE Frequencies in Euchromatin and Heterochromatin 195
Inter and Intrachromosomal Variation in TE Density 195
TE Target Site Specificities 196
The Dynamics of TE Evolution 197
Long Term Evolution and TE Life Cycles 197
Mechanisms of Spread and Loss 198
Contents XVli
Regulation of TE Activity 201
Element Mediated Regulation 201
Host Mediated Regulation of TE Activity 202
Repeat Induced Gene Silencing 203
Disruption of TE Regulation by Environmental Stresses 204
A Continuum of TE Host Interactions from Parasitism
to Mutualism 205
TEs as Mutagens and Sources of Genomic Variation 205
Coding Sequences and the Evolution of Novel Host Genes 205
Introns 207
Alternative Splicing 207
Gene Regulatory Sequences 207
Telomeres 208
Centromeres 209
Transduction 210
Genome Size 211
Host Genome Structure 212
Concluding Remarks and Future Prospects 213
4 B Chromosomes
Juan Pedro M. Camacho
A Brief History of the Study of B Chromosomes 224
The Name Game 224
What is a B Chromosome ? 225
B Chromosomes as Genomic Parasites 225
The Frequency of B Chromosome Infection 227
How Widely Distributed Are B Chromosomes? 227
The Likelihood of Infection 230
Variation in the Intensity of Infection 230
The Biology of B Chromosomes 233
Size 233
Structure 234
Composition 234
Meiotic Behavior 240
Mechanisms of Drive 242
Centromeric Drive 245
The Origin(s) of B Chromosomes 246
Derivation from A Chromosomes 247
From Which Species? 248
From Which Population? 249
XviU Contents
From Which Chromosome? 249
Accumulation of Transposable Elements 250
Similarities to Sex Chromosomes: Analogy or Homology? 251
Drive to Survive! 252
Interactions with the Host Genome 252
Effects on Gene Expression 253
Recombination in A Chromosomes 253
The Odd Even Effect 256
Host Resistance 258
Host Tolerance 260
Interactions with the Host Organism 261
Impacts on the Cellular and Organismal Phenotypes 261
B Chromosomes and Host Reproductive Mode 263
Population Dynamics 264
Parasite Prudence 264
The Dynamics of B Chromosome Evolution 265
The B Chromosome life Cycle 265
The life Spans of B Chromosomes 268
Can B Chromosomes Become Beneficial? 270
Can B Chromosomes Integrate into the Standard Genome? 271
Concluding Remarks and Future Prospects 273
PART III
Duplications, Duplications...
5 Small Scale Gene Duplications
John S. Taylor andjeroen Raes
The Long Pedigree of Gene Duplication Research 290
Early Chromosomal Studies 290
Studies at the Protein Level: Evidence for Gene Duplication
and Divergence from Isozymes 294
The Advent of PCR and DNA Sequencing 294
Gene Duplications in the Post Genomic Era 296
Mechanisms of Gene Duplication 298
Aneuploidy 298
Duplicative Transposition 298
Local Tandem Duplication 300
The Life and Death of Gene Duplicates in the Genome 301
The Birth and Death of Gene Duplicates 301
Contents xix
The Evolution of Gene Families 302
The Contribution of Gene Duplication to Genome Structure 305
What Happens to Duplicated Genes? 306
Nonfunctionalization 306
Those That Beat the Odds 306
Sequence Divergence 308
Changes in Expression Patterns 310
Neofunctionalization 312
Subfunctionalization 314
Reversion 316
Hox Gene Duplication and the Evolution of Animal
Development 316
The General Evolutionary Importance of Gene Duplications 319
Concluding Remarks and Future Prospects 320
6 Large Scale Gene and Ancient Genome Duplications
Yxes Van de Peer and Axel Meyer
Historical Perspectives on the Importance of Large Scale
Duplications 330
Mechanisms of Large Scale Duplication 331
Autopolyploidy 331
Allopolyploidy 332
Aneuploidy 333
Block Duplications 334
Tandem Duplications 334
How Large Scale Gene Duplications Are Studied 334
Identification of Block Duplications 334
The Map Based Approach 335
Hidden Duplications, Ghost Duplications, and Multiplicons 340
Genomic Profiles: An Extension to the Map Based Approach 343
Dating Duplication Events 344
Absolute Dating Based on Synonymous Substitutions 345
Protein Based Distances 345
Dating by Phylogenetic Means 346
Putting Theory into Practice: Evidence for Large Scale
Gene Duplication Events 347
1R/2R: Genome Duplications in Vertebrates 348
3R: An Additional Round of Genome Duplication in Teleost Fishes 350
Ancient Genome Duplications in Plants 354
Large Scale Duplications in the Evolutionary Process 356
The Maintenance of Duplicated Genes 356
XX Contents
Which Genes Are Maintained, and Why? 358
The Maintenance of Duplicated Genomes 359
Speciation and Divergent Resolution 361
Concluding Remarks and Future Prospects 363
PART IV
...And More Duplications
7 Polyploidy in Plants
Jennifer A. late, Douglas E. Soltis, and Pamela S. Soltis
History of the Study of Polyploidy in Plants 372
Types of Polyploids 373
Frequency of Polyploids 379
How Common Is Polyploidy in Plants? 379
The Frequency of Allopolyploidy versus Autopolyploidy 383
Polyploid Formation and Establishment 384
Mechanisms and Chances of Formation 384
Likelihood of Establishment 388
Multiple Origins of Polyploid Species 390
The Rule, Not the Exception 390
Genotypic and Phenotypic Consequences of Multiple Origins 394
A Case of Particular Interest: The Arctic Flora 395
Impacts of Polyploidization at the Cellular and Organismal Levels 396
Cell Size 397
Reproductive Biology 398
Physiology and Development 400
Geographic Distribution 401
Plant Animal Interactions 402
Impacts of Polyploidization at the Genome Level 404
Genomic Rearrangements 405
Genomic Downsizing and Diploidization 407
The Fates of Plant Genes Duplicated by Polyploidy 408
Transposable Elements 413
Nuclear Cytoplasmic Interactions 413
Concluding Remarks and Future Prospects 414
8 Polyploidy in Animals
T Ryan Gregory and Barbara K Mable
The Origins and Classification of Polyploid Animals 428
Autopolyploidy and Allopolyploidy 428
Contents XXI
Identifying Polyploids 429
Chromosome Number and Nuclear DNA Content 429
Cell and Nucleus Size 430
Meiotic Chromosome Behavior 430
Protein Electrophoresis 432
Why Is Polyploidy Less Common in Animals than
in Plants? 433
Disruption of Sex Determination 434
Degenerate Sex Chromosomes and Dosage Compensation 436
Impediments to Meiotic Disjunction 437
Interploidy Crosses and Triploid Sterility 438
Disruption of Development 438
Not Enough Hybridization ... or Maybe Too Much? 439
Nucleotypic Constraints 440
Polyploidy and Unisexuality 440
Definitions 441
Why Are Polyploidy and Unisexuality Linked? 442
Polyploidy in Vertebrates 444
Jawless Fishes 444
Cartilaginous Fishes 445
Lungfishes 445
Chondrosteans 446
Teleosts 447
An Entire Family of Polyploids: Salmonidae 448
Another Entirely Polyploid Family: Catostomidae 451
Several Species of Polyploids: Cyprinidae 452
Special Cases: Poeciliidae 456
Miscellaneous Polyploid Fishes 459
Amphibians 461
Diploid Polyploid Species Pairs in Frogs 462
Polyploidy in Salamanders: Ambystomatidae 469
A Polyploid Family of Salamanders (?): Sirenidae 471
Rare Triploidy in Newts 472
Reptiles 472
The Genus Cnemidophorus 473
Other Polyploid Reptiles 475
Mammals and Birds 475
Vertebrate Polyploids: A Summary 477
Polyploidy in Invertebrates 478
Crustaceans 478
V ter Fleas (Order Cladocera) 479
Brine Shrimp (Order Anostraca) 480
XXU Contents
Insects 480
Molluscs 486
Bivalves 487
Gastropods 488
Annelids 490
Flatworms 493
Miscellaneous Invertebrates 494
Nematodes 494
Rotifers 495
Tardigrades 495
Arachnids 496
Polyploidy and Geographic Distribution in Invertebrates 496
Unisexuality 497
Genetic Factors 498
Physiology, Development, and Ecology 499
History 499
The Evolutionary Fate of Polyploids 500
Concluding Remarks and Future Prospects 501
partV
Sequence and Structure
9 Comparative Genomics in Eukaryotes
Alan Filipski and Sudhir Kumar
The Early History of Comparative Eukaryotic Genomics 522
The Basics of Eukaryotic Chromosome Structure 522
Karyoryping: The Beginning of Comparative Genomics 524
Genome Architecture 531
Working with Eukaryotic Genomes 533
Mapping: Genetic and Physical 534
Sequencing: The Holy Grail of Comparative Genomics 534
Annotation: Making Biological Sense of the Letters 535
The Genesis of Large Scale Sequencing Projects for Eukaryotes 536
Sequencing the Human Genome: The Most Ambitious Idea 536
Private versus Public Efforts 537
Genome Sequencing in Fungi 541
Saccharomyces cerevisiae: The First Eukaryote to Be Sequenced 541
Other Fungal Sequencing Projects 542
Contents XXUi
Caenorhabditis elegans and Drosophila melanogaster: The First Animal
Genomes to Be Sequenced 544
The Worm Project 544
The Fruit Fly Project 546
The Human Genome Project 546
Genome Variation in Human Populations 552
Pufferfish Synergy 554
The Mouse and Rat Genomes: The Rise of Modem Mammalian
Comparative Genomics 555
Genome Sequencing in Plants and Their Pathogens 559
Comparative Genomics of Arabidopsis 559
The Rice Genome 560
The Rice Blast Fungus: Magnaporthe grisea 562
Other Invertebrate Animal Genomes 562
The Mosquito Genome 562
The Sea Squirt: A Primitive Chordate 563
Genomewide Duplications in Vertebrates? 564
Protist Genomes 564
Encephalitozoon cuniculi: A Parasitic Eukaryote with a Tiny Genome 564
Plasmodium: The Malaria Pathogen 565
Dictyostdium: The Slime Mold 566
Comparative Genomics and Phylogenetics in Eukaryotes 566
Concluding Remarks and Future Prospects 569
Complete Genome Sequencing 569
Partial Genome Comparisons 572
The Tree of life 573
The Charter of Genomics 574
10 Comparative Genomics in Prokaryotes
T Ryan Gregory and Rob DeSalle
What Is a Prokaryote? 586
Classifying Prokaryotes the Old Fashioned Way 586
The Deepest Split of All? 589
The Rise of Complete Prokaryotic Genome Sequencing 590
From Viruses to Venter 590
The Prokaryote Genome Sequencing Explosion 592
General Insights about Prokaryote Genomes 593
Genome Organization: Assumptions and Exceptions 594
Structure of Prokaryotic Chromosomal DNA 596
DNA Replication in Prokaryotes 597
XXIV Contents
Gene Content 597
Gene Order: Plasticity and Stability 601
Base Pair Composition 603
Repeat Content 606
Horizontal Transfer of Genetic Material 606
Identifying and Characterizing Horizontal Transfers 607
Transfer from Viruses to Bacteria: Prophages in Bacterial Genomes 608
Transfer among Bacteria 610
Transfer across Domains 612
Implications for Prokaryote Evolution and the Study Thereof 615
Highlights from Specific Prokaryote Genome Sequencing Projects 616
Haemophilus infiuenzae (1995) 617
Methanocaldococcus jannaschii (1996) 618
Escherichia coli (1997) 619
Mycobacterium tuberculosis (1998) 621
Deinococcus radiodurans (1999) 622
Vibrio choterae (2000) 623
Streptococcus spp. (2001) 624
Streptotnyces coelicolor (2002) 627
Bacillus anthracis (2003) 628
Wolbachia pipiens (2004) 630
The Evolution of Genome Size in Prokaryotes 631
Factors that Limit Prokaryote Genome Size 634
Mechanisms of Genome Size Increase 636
Genome Reductions in Obligate Parasites and Endosymbionts 637
Bacteria, Organelles, or Something in Between? 640
The Minimal Genome Concept 641
Breaking it Down 642
Building it Up 644
Genomic Insights into Prokaryotic Abundance and Diversity 645
What Is a Prokaryotic Species? 645
Genetic Delineation of Species 646
Genomic Perspectives on Prokaryote Diversity 647
Shotgun First, Ask Questions Later 649
Applications of Prokaryote Genomics 651
Medicine 651
Industry and the Environment 654
Agriculture and Food Production 655
Evolutionary Biology 655
Concluding Remarks and Future Prospects 656
Which Prokaryotes Can (or Cannot) Be Sequenced? 657
Policy Issues: From Sequence Completeness to Bioterrorism 658
Prokaryote Genomics: The End of the Beginning 660
Contents XXV
PART VI
The Genome in Evolution
11 Macroevolution and the Genome
X Ryan Gregory
Part One—Macroevolutionary Theory and Genome Evolution 680
A Brief History of Evolutionary Theory 680
From Darwin to Neo Darwinism 680
Genomes, Fossils, and Theoretical Inertia 682
Is a Theory of Macroevolution Necessary? 684
Microevolution, Macroevolution, and Extrapolationism 684
Critiques of Strict Extrapolationism 686
Reductionism in the Post Genomic Era 692
The Structure of Macroevolutionary Theory 693
Group Selection 694
Species Selection: Concepts and Challenges 694
Aggregate versus Emergent Characters 695
Selection versus Sorting 696
Bottom up Processes: The Effect Hypothesis versus
Emergent Fitness 696
Top down Processes: Context dependent Sorting 697
Macroevolutionary Theory: A Summary 698
A Macroevolutionary Look at the Genome 698
Did the Genome Originate by Group Selection? 698
Genomic Parasites Require a Hierarchical Interpretation 700
Genome Size, Emergent Fitness, and an Upside down Acid Test 704
Context dependent Sorting of Genes and Nongenes 706
Genomes in the Evolutionary Hierarchy 707
Part Two— Nonstandard Genomic Processes and
Major Evolutionary Transitions 708
The Origin of Genomes and Cells 709
The Evolution of Sex 709
The Origin of Eukaryotes 710
Linear Chromosomes 710
Increased Genetic Complexity 711
The Origin of Multicellularity and the Emergence of
Complex Metazoa 712
Transposable Elements and Gene Regulation 712
Spliceosomal Introns and Exon Shuffling 712
Gene Duplication and Developmental Complexity 713
The Evolution of Immunity 714
I
XXVi Contents
The Origin of Vertebrates 715
Gen(om)e Duplication 715
Silencing and/or Splicing 716
Human Uniqueness 716
Diversity in Gene Expression 717
The Role of Alu Elements 717
Gene Duplication and Back Again 719
Nonstandard Genomic Processes: A Summary 719
Concluding Remarks and Future Prospects 720
From Reductionism to Integrationism 720
A Post Genomic Evolutionary Synthesis 721
Genomes and the Future of Biology 722
Index 731
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| id | DE-604.BV019700606 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T20:04:08Z |
| institution | BVB |
| isbn | 0123014638 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-013028173 |
| oclc_num | 60740017 |
| open_access_boolean | |
| owner | DE-M49 DE-BY-TUM DE-20 DE-29T DE-91G DE-BY-TUM DE-526 DE-11 DE-19 DE-BY-UBM |
| owner_facet | DE-M49 DE-BY-TUM DE-20 DE-29T DE-91G DE-BY-TUM DE-526 DE-11 DE-19 DE-BY-UBM |
| physical | XXVI, 740 S. Ill., graph. Darst. |
| publishDate | 2005 |
| publishDateSearch | 2005 |
| publishDateSort | 2005 |
| publisher | Elsevier Acad. Pr. |
| record_format | marc |
| spelling | The evolution of the genome ed. by T. Ryan Gregory Amsterdam [u.a.] Elsevier Acad. Pr. 2005 XXVI, 740 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Genoom gtt Génomes Polyploïdie Genomes Genom (DE-588)4156640-3 gnd rswk-swf Evolution (DE-588)4071050-6 gnd rswk-swf Pflanzen (DE-588)4045539-7 gnd rswk-swf Tiere (DE-588)4060087-7 gnd rswk-swf Genom (DE-588)4156640-3 s Evolution (DE-588)4071050-6 s DE-604 Tiere (DE-588)4060087-7 s Pflanzen (DE-588)4045539-7 s b DE-604 Gregory, T. Ryan Sonstige oth HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=013028173&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | The evolution of the genome Genoom gtt Génomes Polyploïdie Genomes Genom (DE-588)4156640-3 gnd Evolution (DE-588)4071050-6 gnd Pflanzen (DE-588)4045539-7 gnd Tiere (DE-588)4060087-7 gnd |
| subject_GND | (DE-588)4156640-3 (DE-588)4071050-6 (DE-588)4045539-7 (DE-588)4060087-7 |
| title | The evolution of the genome |
| title_auth | The evolution of the genome |
| title_exact_search | The evolution of the genome |
| title_full | The evolution of the genome ed. by T. Ryan Gregory |
| title_fullStr | The evolution of the genome ed. by T. Ryan Gregory |
| title_full_unstemmed | The evolution of the genome ed. by T. Ryan Gregory |
| title_short | The evolution of the genome |
| title_sort | the evolution of the genome |
| topic | Genoom gtt Génomes Polyploïdie Genomes Genom (DE-588)4156640-3 gnd Evolution (DE-588)4071050-6 gnd Pflanzen (DE-588)4045539-7 gnd Tiere (DE-588)4060087-7 gnd |
| topic_facet | Genoom Génomes Polyploïdie Genomes Genom Evolution Pflanzen Tiere |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=013028173&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT gregorytryan theevolutionofthegenome |