Molecular and genome evolution:
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| Main Author: | |
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| Format: | Book |
| Language: | English |
| Published: |
Sunderland, Massachusetts
Sinauer Associates, Inc
[2016]
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| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | xvii, 612, 54, 34 Seiten Illustrationen, Diagramme 30 cm |
| ISBN: | 1605354694 9781605354699 |
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MARC
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| 245 | 1 | 0 | |a Molecular and genome evolution |c Dan Graur, University of Houston |
| 264 | 1 | |a Sunderland, Massachusetts |b Sinauer Associates, Inc |c [2016] | |
| 300 | |a xvii, 612, 54, 34 Seiten |b Illustrationen, Diagramme |c 30 cm | ||
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| adam_text | Titel: Molecular and genome evolution
Autor: Graur, Dan
Jahr: 2016
Table of Contents
Introduction 1
CHAPTER 1 /The Molecular
Nucleotide Sequences 5
Genomes 7
Genome constituents 7
Somatic genome processing 7
DNA Replication 8
Transcription and Posttranscriptional
Modifications of RNA 9
Genes 11
Protein-coding genes 12
RNA-specifying genes 14
Nontranscribed genes 15
Pseudogenes 16
Amino Acids 16
Basis of Biology and Evolution 5
Proteins 19
Translation and Genetic Codes 20
Information Flow among DNA, RNA, and
Proteins 24
Mutation 24
Classification of mutations 25
Point Mutations 26
Segmental Mutations 30
Recombination 30
Deletions and insertions 31
Inversions 34
Spatial distribution of mutations 34
Are Mutations Random? 34
CHAPTER 2/Allele Dynamics in Populations 35
Standing Genetic Variation 35
Gene diversity 36
Nucleotide diversity 37
Structural variation 38
What Is Evolution? 38
Changes in Allele Frequencies 39
Selection 40
Codominance 42
Dominance and recessiveness 43
Overdominance and underdominance 44
Random Genetic Drift 47
Census Population Size and Effective
Population Size 49
Short-term effective population size 50
Coalescence and long-term effective population size 51
Factors conspiring to reduce the effective population
size relative to the census population size 54
Gene Substitution 55
Fixation probability 55
Fixation time 56
Rate of gene substitution 58
Mutational meltdown: The double jeopardy of small
populations 58
Nearly neutral mutations 58
Second-Order Selection 60
The evolution of mutation rates 60
The evolution of mutational robustness 62
Violations of Mendel s Laws of Inheritance 63
Transmission Ratio Distortion 63
Segregation distortion 64
Postsegregation distortion 65
Converting elements 65
Sex allocation distortion 66
Autonomous replicating elements 66
Linkage Equilibrium and Disequilibrium 66
Hitchhiking and Selective Sweep 67
Molecular signatures of selective sweeps 68
The evolution of lactase persistence in Africa and
Europe 70
Background Selection 71
Epistasis 71 A test of neutrality based on genetic polymorphism 75
The Driving Forces in Evolution 72 Consequences of Explosive Population
The neo-Darwinian theory and the neutral mutation Growth: Single-Nucleotide Variation in
hypothesis 72 Humans 76
The distribution of fitness effects 74
CHAPTER 3/DNA and Amino Acid Sequence Evolution 79
Nucleotide Substitution in a DNA
Sequence 79
Jukes and Cantor s one-parameter model 80
Kimura s two-parameter model 82
Number of Nucleotide Substitutions between
Two DNA Sequences 83
Number of substitutions between two noncoding
sequences 84
Substitution schemes with more than two
parameters 86
Violation of assumptions 87
Saturation 88
Number of Substitutions between Two
Protein-Coding Genes 88
Number of Amino Acid Replacements
between Two Proteins 93
Alignment of Nucleotide and Amino Acid
Sequences 93
Pairwise alignment 94
Manual alignment 95
The dot matrix method 95
Scoring matrices and gap penalties 97
Alignment algorithms 100
Multiple-sequence alignment 101
Quality of alignments 104
Alignment of Genomic Sequences 106
CHAPTER 4 / Rates and Patterns
Rates of Point Mutation 107
Rates of Segmental Mutations 110
Rates of Nucleotide Substitution 111
Rates of substitution in protein-coding sequences 111
Rates of substitution in noncoding regions 115
Causes of Variation in Substitution Rates 116
The concept of functional constraint 116
Quantifying the degree of protein tolerance toward
amino acid replacements 116
Synonymous versus nonsynonymous rates 117
Variation among different gene regions 117
Variation among genes 119
Variables associated with protein evolutionary rates 120
Evolutionary conservation and disease 121
Relaxation of selection 122
Selective intolerance toward indels 123
Identifying positive and purifying selection 123
Estimating the intensity of purifying selection 124
Are slowly evolving regions always important? 125
Male-Driven Evolution: Mutational Input and
Slow-X Evolution 126
Rates of Evolution under Positive
Selection 128
Prevalence of positive selection 129
of Molecular Evolution 107
Fast-X evolution 130
Rates of Evolution under Balancing
Selection 130
Patterns of Substitution and
Replacement 130
Patterns of spontaneous mutation 131
Patterns of mutation and strand asymmetry 134
Clustered multinucleotide substitutions: Positive
selection or nonrandomness of mutation? 135
Patterns of amino acid replacement 137
What protein properties are conserved in protein
evolution? 138
Heterotachy 139
Nonrandom Usage of Synonymous
Codons 139
Measures of codon usage bias 140
Species-specific and universal patterns of codon
usage 141
Determinants of Codon Usage 142
Interspecific variation in codon usage and amino acid
usage 142
Intragenomic variation in codon usage 142
Translational efficiency and translation accuracy 143
The tRNA adaptation index 145
Intragenic variation in codon usage 147
Indirect selection on codon usage 148
Why do only some organisms have biased codon
usages? 148
Codon usage in unicellular and multicellular
organisms 148
Codon usage and population size 149
Molecular Clocks 149
Relative Rate Tests 151
Local Clocks 154
Nearly equal rates in mice and rats 154
Lower rates in humans than in monkeys 154
Higher rates in rodents than in other mammals 155
Evaluation of the molecular clock hypothesis 156
Primitive versus advanced : A question of rates 157
Causes of Variation in Substitution Rates
among Evolutionary Lineages 157
The DNA repair hypothesis 158
The generation-time effect hypothesis
The metabolic rate hypothesis 159
The varying-selection hypothesis 159
Are Living Fossils Molecular Fossils Too? 160
Phyletic Gradualism, Punctuated Equilibria,
and Episodic Molecular Evolution 160
Rates of Substitution in Organelle DNA 161
Mitochondrial rates of evolution 161
Plastid rates of evolution 162
Substitution and rearrangement rates 162
Rates of Substitution in Viruses 163
Human immunodeficiency viruses 163
CHAPTER 5 / Molecular Phytogen
Impacts of Molecular Data on Phylogenetic
Studies 165
Advantages of Molecular Data in Phylogenetic
Studies 167
Species and Speciation 167
The species concept 167
Speciation 168
Terminology 170
Phylogenetic Trees 170
Rooted and unrooted trees 171
Scaled and unsealed trees 172
The Newick format 173
Number of possible phylogenetic trees 174
Tree balance 175
True and inferred trees 177
Gene trees and species trees 177
Taxa and clades 178
Types of Molecular Homology 179
Types of Data 180
Character data 180
Assumptions about character evolution 181
Polarity and taxonomic distribution of character
states 182
Distance data 183
Methods of Tree Reconstruction 184
Distance Matrix Methods 184
Unweighted pair-group method with arithmetic means
(UPGMA) 184
Sattath and Tversky s neighbors-relation method 186
Saitou and Nei s neighbor-joining method 187
:ics and Phylogenetic Trees 165
Maximum Parsimony Methods 187
Weighted and unweighted parsimony 191
Searching for the maximum parsimony tree 191
Maximum Likelihood Methods 194
Bayesian Phylogenetics 197
Topological Comparisons 198
Topological distance 199
Consensus trees 199
Supertrees 200
Rooting Unrooted Trees 201
Outgroup rooting 202
Midpoint rooting 202
Estimating Branch Lengths 204
Calibrating Phylogenetic Trees and Estimating
Divergence Times 205
Assessing Tree Reliability 207
The bootstrap 208
Tests for two competing trees 209
Problems Associated with Phylogenetic
Reconstruction 211
Strengths and weaknesses of different methods 211
Minimizing error in phylogenetic analysis 212
Genome Trees 214
Genome trees based on shared gene content 214
Genome trees from BLASTology 214
Molecular Phylogenetic Examples 214
Phylogeny of apes 215
The utility of polarized character states: Cetartiodactyla
and SINE phylogeny 220
Molecular Phylogenese Archeology 222
The disextinction of the quagga 224
The dusky seaside sparrow: A lesson in conservation
biology 225
Molecular Phylogenetics and the Law 227
At the Limits of the Tree Metaphor: The
Phytogeny of Eukaryotes and the Origin of
Organelles 228
The phylogeny of eukaryotes 228
CHAPTER 6/ Reticulate Evolution
Networks 237
Phylogenese and Phylogenomic
Networks 238
The median network method 239
The conditioned-reconstruction method 240
Inferred reticulations: Are they real? 243
Examples of Real-Life Phylogenetic
Networks 243
Reticulate evolution by recombination: A resurrected
blood-group allele in humans 244
Speciation by hybridization: The reticulate evolution of
woodferns 246
The Tree of Life Hypothesis 247
The Vertical and Horizontal Components of
Prokaryote Evolution 249
Prokaryote taxonomy and the meaning of species in
prokaryotes 250
The Phylogeny of Everything 253
The eukaryote-prokaryote divide and the taxonomic
validity of Procaryota 253
Origin of organelles 230
Phylogenetic Trees as a Means to an End 232
Parallelism and convergence as signifiers of positive
selection 232
Detecting amino acid sites under positive selection 233
Reconstructing ancestral proteins and inferring
paleoenvironments 234
Mapping nonmolecular characters onto molecular trees
234
and Phylogenetic Networks 237
The Eubacteria-Archaebacteria divide 253
The tripartite tree of life and its inadequacy 255
The Origin of Eukaryotes 257
The gradual origin hypothesis 258
The fateful encounter hypothesis 259
Eukaryotes as an organizational upgrade 262
The nonrandom origin of operational and informational
genes in eukaryotes 263
Why genes in pieces? The origin of the nuclear
membrane 264
All complex life is eukaryotic: The energetics of gene
expression 266
The eukaryotic cell as a one-off innovation and a
possible solution to the Fermi paradox 268
Archaebacterial Systematics: Clade-Specific
Archaebacterial Genes and Clade-Specific
Horizontal Gene Imports from Eubacteria
269
The Two Primary Domains of Life 271
The Public Goods Hypothesis 271
CHAPTER 7/Evolution by DNA Duplication 273
Types of DNA Duplication 274
Mechanisms of DNA Duplication 274
Dating Duplications 275
Gene Duplication and Gene Families 276
The Prevalence of Gene Duplication 278
Modes of Evolution of Multigene Families 278
Divergent Evolution of Duplicated Genes 279
Nonfunctionalization and gene loss 280
Nonfunctionalization time 281
Retention of original function following gene
duplication 283
Evolution of rRNA-specifying genes 284
Neofunctionalization 285
Multifunctionality and subfunctionalization 287
Neosubfunctionalization 294
Rates of Evolution in Duplicated Genes 295
Rates and patterns of expression divergence between
duplicated genes 295
Human Globins 297
Concerted Evolution 299
Unequal crossing over 301
Gene conversion 302
Examples of gene conversion 304
The relative roles of gene conversion and unequal
crossing over 306
Factors Affecting Concerted Evolution 308
Number of repeats 308
Arrangement of repeats 308
Structure of the repeat unit 308
Functional requirements and selection 309
Population size 310
Evolutionary Implications of Concerted
Evolution 310
Spread of advantageous mutations 311
Retardation of paralogous gene divergence 311
Generation of genie variation 311
Methodological pitfalls due to concerted evolution 311
Positive selection or biased gene conversion? The curi-
ous histories of HAR1 and FXY 312
Birth-and-Death Evolution 314
Expansion and contraction of gene families 314
Examples of birth-and-death evolution 315
The death of gene families 325
Mixed Concerted Evolution and Birth-and-
Death Evolution 325
Polysomy 326
Polyploidy 326
Diploidization 330
Distinguishing between gene duplication and genome
duplication 331
CHAPTER 8/ Evolution by Molecular Tinkering 339
Protein Domains 339
Internal Gene Duplication 340
Properties and prevalence of internal gene
duplication 343
Exon-Domain Correspondence 348
Mosaic Proteins 349
Exon Shuffling 351
Phase limitations on exon shuffling 352
Prevalence of domain shuffling and the evolutionary
mobility of protein domains 353
Domain shuffling and protein-protein interaction
networks 356
Gene Fusion and Fission 356
Domain Accretion 360
Strategies of Multidomain Gene
Assembly 361
Evolution by Exonization and
Pseudoexonization 362
Evolution of Overlapping Genes 364
Alternative Splicing 368
Sex determination and alternative splicing 369
Evolution of alternative splicing 370
Increasing proteome diversity: Alternative splicing or
gene duplication? 372
De Novo Origination of Genes 373
Nested and Interleaved Genes 375
Gene Loss and Unitary Pseudogenes: A
Molecular Revisiting of the Law of Use and
Disuse 376
Functional Convergence 382
Origin and Evolution of Spliceosomal
Introns 383
A Grand View of Molecular Tinkering:
Suboptimality and Gratuitous
Complexity 385
Tinkering in action: The patchwork approach to the
evolution of novel metabolic pathways 386
Irremediable complexity by constructive neutral
evolution 388
CHAPTER 9 / Mobile Elements in Evolution 391
Mobile Elements, Transposable Elements, and DNA-Mediated Transposable Elements 395
Transposition 391
Classification of Transposable Elements 393
Conservative and replicative transposition 393
DNA- and RNA-mediated transposition 394
Enzymatic classification of transposable elements 394
Autonomous and nonautonomous transposable
elements 394
Active and fossil transposable elements 394
Taxonomic, developmental, and target-site specificity of
transposition 394
Insertion sequences 395
Transposons 396
Nonautonomous DNA-mediated transposable
elements 397
Retroelements 398
Retrons 398
TERT genes 399
Mitochondrial retroplasmids 399
Group II introns and twintrons 400
Retrotransposons 400
Retroviruses 401
Pararetroviruses 402
Evolutionary origin of retroelements 402
Nonautonomous and fossil retrotransposable
elements 403
LINEs and SINEs 405
SINEs derived from 7SL RNA 405
SINEs derived from tRNAs and SINEs containing 5S
rRNA 407
SINEs containing snRNA 408
Mosaic SINEs 408
Where there s a SINE, there s a LINE 408
Rate of SINEs evolution 410
Retrosequences 410
Retrogenes 411
Semiprocessed retrogenes 413
Retropseudogenes 413
Endogenous non-retroviral fossils 416
The Ecology of Transposable Elements 417
Transposable elements and the host genome: An evolu-
tionary tug-of-war 417
Transposable elements and segregation distortion 418
Evolutionary dynamics of transposable-element copy
number 419
Genetic and Evolutionary Effects of
Transposition 420
Transposable elements as mutagens 420
Transposable elements and somatic mosaicism 424
CHAPTER 10/Prokaryotic Genon
Genome Size in Prokaryotes 452
The pangenome, the core genome, and the accessory
genome 453
Increases and decreases in prokaryotic genome sizes 455
Genome Miniaturization 457
Genome size reduction in intracellular symbionts and
parasites 457
The miniaturization of organelle genomes 459
The evolution of mitochondrial genome sizes 460
The evolution of plastid genome sizes 462
The Minimal Genome 463
The comparative genomics approach: Identifying the
core genome of all life forms 464
Probabilistic reconstruction of gene content in the last
universal ancestor of life 466
The experimental gene inactivation approach: Gene
essentiality 466
The molecular domestication of transposable
elements 424
Transposition and Speciation 430
Horizontal Gene Transfer 431
Telltale signs of horizontal gene transfer 431
Mechanisms of horizontal gene transfer among
prokaryotes 432
Prevalence and limitations of horizontal gene transfer
in prokaryotes 435
Genomic consequences of gene transfer among
prokaryotes 437
Clinical consequences of gene transfer among
prokaryotes 437
Horizontal Gene Transfer Involving
Eukaryotes 438
Horizontal gene transfer from eukaryotes to
prokaryotes 438
Horizontal gene transfer from prokaryotes to
eukaryotes 438
Horizontal transfer among eukaryotes 440
Horizontal gene transfer among plants 441
Horizontal transfer of a functional gene from fungi
to aphids 441
Horizontal transfer of transposable elements among
animals 442
Promiscuous DNA 446
Transfer of intact functional genes to the nucleus 447
Transfer of nonfunctional DNA segments from
organelles to the nucleus: numts and nupts 447
Rates and evolutionary impacts of norgDNA
insertion 448
Evolution 451
GC Content in Prokaryotes 467
Possible explanations for variation in GC content 468
Chargaff s parity rules 470
GC Skew and Gene-Density Asymmetries Are
Related to DNA Replication Biases 471
Replichores and chirochores 471
The location of genes in leading and lagging
strands 474
Chromosomal Evolution in Prokaryotes 477
Evolution of chromosome number in prokaryotes 478
Estimating the number of gene order rearrangement
events 480
Gene order evolution 483
Operon evolution 483
The Emergence of Alternative Genetic
Codes 486
CHAPTER 11 / Eukaryotic Genome
Functionality and nonfunctionality in
eukaryotic genomes 492
What is function in an evolutionary context? 492
What do genomes do? An evolutionary classification of
genomic function 494
Changes in functional affiliation 496
Detecting functionality at the genome level 496
Phenotypic validation of positive
selection 499
What proportion of the human genome is
functional? 503
How much garbage DNA is in the human genome? 503
Genome Size, DNA Content, and C Value 505
Genome size variation and genomic content in
eukaryotes 505
Intraspecific variation in genome size 507
Mutations That Increase or Decrease Genome
Size 507
The contribution of genome duplication to genome
size 508
The contribution of transposable elements to genome
size 509
Deletions and genome size 510
Genomic Paradoxes in Eukaryotes 511
The C-value paradox 511
Possible solutions to the C-value paradox 513
Why so much of the genome is transcribed—or is
it? 516
Life History and Cellular Correlates of
Genome Size 517
The nucleocytoplasmic ratio 518
The coincidence hypothesis 519
Nucleotypic hypotheses 519
The nucleoskeletal hypothesis 520
Is small genome size an adaptation to flight? 521
The C-Value Paradox: The Neutralist
Hypothesis 522
Selfish DNA 523
The mutational hazard hypothesis 524
Is it junk DNA or is it indifferent DNA? 526
Trends in Genome Size Evolution 527
Is there an upper limit to genome size? 527
Genome miniaturization in eukaryotes 528
Evolution 491
Protein-Coding Gene Number Variation and
the G-Value Paradox 532
Possible solutions to the G-value paradox 534
The I value 535
Gene Number Evolution 536
Methodologies for Studying Gene Repertoire
Evolution 537
Gene-family cluster analysis 538
Functional clustering of proteins 539
Supervised machine learning and the subcellular
localization of proteins 541
Gene ontology 542
Chromosome Number and Structure 544
Chromosome number variation 544
Chromosome morphology and chromosome types 545
Chromosome size variation 546
Euchromatin and heterochromatin 547
Chromosomal Evolution 548
Chromosome number evolution 548
Chromosomal rearrangements 551
Evolutionary patterns of chromosomal
rearrangements 555
Is gene order conserved? 555
Gene Distribution Between and Within
Chromosomes 556
Gene density 556
Do genes cluster by function? 557
The Repetitive Structure of the Eukaryotic
Genome 558
Tandemly repeated sequences 560
Mutational processes affecting repeat-unit number in
tandemly repeated DNA 562
The contribution of tandem repeats to genome size 564
Do tandemly repeated DNA sequences have a
function? 564
Centromeres as examples of indifferent DNA 565
Genome Compositional Architecture 565
Segmentation algorithms and compositional
domains 568
Compositional architectures of mammalian nuclear
genomes 570
The origin and evolution of compositional domains 572
CHAPTER 12/The Evolution of Gene Regulation 575
Pretranscriptional Regulation 576
Regulation by covalent modifications of histones 576
DNA methylation 576
Regulation at the Transcriptional Level 577
Promoters 577
Promoter evolution 580
Divergent transcription 581
Enhancers 582
Shadow enhancers 585
Insulators 591
Posttranscriptional Regulation 592
RNA interference 593
Patterns of evolution of miRNAs 594
Do miRNAs have a deep evolutionary history? 595
Does translational regulation contribute to phenotypic
evolution? 595
CHAPTER 13/Experimental Molecular Evolution 597
What Is Experimental Evolution? 598
The basic design of evolutionary experiments 599
How to measure fitness and changes in fitness in
evolutionary experiments 600
The Contribution of Experimental Evolution to
Evolutionary Biology 601
Population divergence and the adaptive landscape
metaphor 602
Historical contingency 604
Epistasis 607
Mutation Dynamics 608
Neutral mutation rates 608
Non-neutral mutation rates 608
Targets of Selection 610
Literature Cited LC-1
Index 1-1
|
| any_adam_object | 1 |
| author | Graur, Dan 1953- |
| author_GND | (DE-588)172103940 |
| author_facet | Graur, Dan 1953- |
| author_role | aut |
| author_sort | Graur, Dan 1953- |
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| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.8/38 |
| dewey-search | 572.8/38 |
| dewey-sort | 3572.8 238 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| format | Book |
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| id | DE-604.BV043359842 |
| illustrated | Illustrated |
| indexdate | 2024-07-10T07:23:55Z |
| institution | BVB |
| isbn | 1605354694 9781605354699 |
| language | English |
| lccn | 2015040070 |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-028779096 |
| oclc_num | 936344370 |
| open_access_boolean | |
| owner | DE-20 DE-19 DE-BY-UBM |
| owner_facet | DE-20 DE-19 DE-BY-UBM |
| physical | xvii, 612, 54, 34 Seiten Illustrationen, Diagramme 30 cm |
| publishDate | 2016 |
| publishDateSearch | 2016 |
| publishDateSort | 2016 |
| publisher | Sinauer Associates, Inc |
| record_format | marc |
| spelling | Graur, Dan 1953- Verfasser (DE-588)172103940 aut Molecular and genome evolution Dan Graur, University of Houston Sunderland, Massachusetts Sinauer Associates, Inc [2016] xvii, 612, 54, 34 Seiten Illustrationen, Diagramme 30 cm txt rdacontent n rdamedia nc rdacarrier Genom (DE-588)4156640-3 gnd rswk-swf Molekulare Evolution (DE-588)4812902-1 gnd rswk-swf Molekulare Evolution (DE-588)4812902-1 s Genom (DE-588)4156640-3 s DE-604 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028779096&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Graur, Dan 1953- Molecular and genome evolution Genom (DE-588)4156640-3 gnd Molekulare Evolution (DE-588)4812902-1 gnd |
| subject_GND | (DE-588)4156640-3 (DE-588)4812902-1 |
| title | Molecular and genome evolution |
| title_auth | Molecular and genome evolution |
| title_exact_search | Molecular and genome evolution |
| title_full | Molecular and genome evolution Dan Graur, University of Houston |
| title_fullStr | Molecular and genome evolution Dan Graur, University of Houston |
| title_full_unstemmed | Molecular and genome evolution Dan Graur, University of Houston |
| title_short | Molecular and genome evolution |
| title_sort | molecular and genome evolution |
| topic | Genom (DE-588)4156640-3 gnd Molekulare Evolution (DE-588)4812902-1 gnd |
| topic_facet | Genom Molekulare Evolution |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028779096&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT graurdan molecularandgenomeevolution |