An introduction to molecular evolution and phylogenetics:
Gespeichert in:
| Vorheriger Titel: | Bromham, Lindell Reading the story in DNA |
|---|---|
| 1. Verfasser: | |
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Oxford
Oxford University Press
[2016]
|
| Ausgabe: | Second edition |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | Preface: "The first edition of this book was titled 'Reading the Story in DNA: a beginner's guide to molecular evolution'. This new edition contains some of the same material, but has been considerably expanded, updated, and remodelled" |
| Beschreibung: | xv, 514 Seiten Illustrationen, Diagramme |
| ISBN: | 9780198736363 |
Internformat
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| 245 | 1 | 0 | |a An introduction to molecular evolution and phylogenetics |c Lindell Bromham |
| 250 | |a Second edition | ||
| 264 | 1 | |a Oxford |b Oxford University Press |c [2016] | |
| 300 | |a xv, 514 Seiten |b Illustrationen, Diagramme | ||
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| 500 | |a Preface: "The first edition of this book was titled 'Reading the Story in DNA: a beginner's guide to molecular evolution'. This new edition contains some of the same material, but has been considerably expanded, updated, and remodelled" | ||
| 650 | 4 | |a Molecular evolution | |
| 650 | 4 | |a Phylogeny | |
| 650 | 0 | 7 | |a Phylogenetik |0 (DE-588)4174591-7 |2 gnd |9 rswk-swf |
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Datensatz im Suchindex
| _version_ | 1804175779185033216 |
|---|---|
| adam_text | Dedication V
Preface vi
Acknowledgements ix
List of Tech Boxes xvi
List of Case Studies xvii
1 Introduction
The story in DNA
pagel
Reading the story in DNA 2
Individuals, families, and populations 3
Uncovering the evolutionary past 5
Tracing ancestors 5
About this book 10
What is this book for? 10
Who is this book for? 11
How the book is structured 12
How to use this book 13
0 Conclusion 15
© Points to remember 16
© Ideas for discussion 16
G Examples used in this chapter 17
Heroes of the Genetic Revolution 1: Fred Sanger 18
TechBox 1.1: GenBank 19
TechBox 1.2: BLAST 23
Case Study 1.1: Identification: solving
the mystery of the Chilean blob 25
Case Study 1.2: Forensics: using DNA to trace
trade in whale meat 28
Introduction
Jf
2 DNA
The immortal germline
page 31
Material basis of heredity 32
Principles of heredity 33
Discovery of the gene 36
Structure of DNA 38
The central dogma 41
DNA extraction 42
Ubiquity of DNA 42
Extracting DNA 42
© Conclusion 43
0 Points to remember 44
© Ideas for discussion 45
© Sequences used in this chapter 45
G Examples used in this chapter 45
Heroes of the Genetic Revolution 2:
August Weismann 46
TechBox 2.1: DNA structure 47
TechBox 2.2: DNA extraction 52
Case Study 2.1: Environmental DNA: tracking
changes in Arctic vegetation over time 54
Case Study 2.2: Ancient DNA: cataloguing
diversity of extinct giant birds 57
3 Mutation
We are all mutants
page 61
Mutation
Point mutations 62
Single nucleotide polymorphisms (SNPs) 65
Identifying individuals using SNPs 65
Using SNPs to track inherited traits 67
Estimating the mutation rate 68
Mutation rates are a compromise 72
Is mutation random? 73
© Conclusion 75
© Points to remember 75
© Ideas for discussion 76
G Examples used in this chapter 76
Heroes of the Genetic Revolution 3: James Crow 78
TechBox 3.1: Single nucleotide
polymorphisms (SNPs) 79
Contents
TechBox 3,2: Biobanking 84
Case Study 3.1: SNPs: genetic resources for crop
development in a non-model species 88
Case Study 3.2: Mutation rate: mutation
accumulation in a laboratory population 91
Repfication
4 Replication .........« it
Endless copies
page 95 Z~Z, ^
DNA replication 96
Template reproduction 97
Replication 98
DNA amplification 102
Polymerase chain reaction (PCR) 103
Contamination 106
Copy errors create hierarchies 106
Sequence evolution 107
Hierarchies reveal history 110
© Conclusion 113
© Points to remember 114
0 Ideas for discussion 115
© Sequences used in this chapter 116
Q Examples used in this chapter 116
Heroes of the Genetic Revolution 4:
Rosalind Franklin 117
TechBox 4.1: DNA replication 118
TechBox 4.2: DNA amplification 121
Case Study 4.1: Replication: taller plants have
lower rates of molecular evolution 124
Case Study 4.2: Hierarchies: genes and language
track human settlement of Oceania 127
5 Genome Genome
Accident and design l|f Sj
page 131 Bv
Genome size 132
The paradox of genome size 133
Doubling and dividing: genome replication 134
Recombination 136
Chromosomal rearrangement 138
Repeat sequences 139
Comparing repeat sequences 141
Transposable elements 145
LINEs, SINEs, and retroviruses 146
The genomic record of transposition 147
© Conclusion 149
© Points to remember 150
0 Ideas for discussion 150
© Sequences used in this chapter 151
Q Examples used in this chapter 151
Heroes of the Genetic Revolution 5:
Barbara McClintock 152
TechBox 5.1: Sanger sequencing 153
TechBox 5.2: High-throughput sequencing 157
Case Study 5.1: Duplication: gene copies and
microsatellites help aphids tolerate nicotine 161
Case Study 5.2: Genome: a leukaemia virus
becoming part of the koala genome 164
6 Gene
Making an organism
page 167
Genes
Gene structure and expression
Transcription and translation
Regulation of gene expression
Sequence evolution
Divided genes: exons and introns
Identifying genes
Regulatory sequences
0 Conclusion
© Points to remember
© Ideas for discussion
0 Sequences used in this chapter
O Examples used in this chapter
Heroes of the Genetic Revolution 6:
Francis Crick
TechBox 6.1: Genetic code
TechBox 6.2: Primers and probes
170
171
173
175
175
178
181
182
183
184
184
184
185
186
189
Case Study 6.1: Gene families: duplication
and loss of taste receptor genes 191
Case Study 6.2: Genetic code: multiple proteins
from a single human gene 194
Contents
7 Selection
Descent with modification
page 197
Variation
Substitution
Natural selection
The power of selection
Fitness
Genetic background
Linkage
Are humans still evolving?
© Conclusion
© Points to remember
© Ideas for discussion
© Sequences used in this chapter
0 Examples used in this chapter
201
202
205
206
208
209
214
214
215
215
215
Heroes of the Genetic Revolution 7: J. B. S. Haldane 216
TechBox 7.1: Fitness 217
TechBox 7.2: Detecting selection 220
Case Study 7.1: Selection: tracking insecticide
resistance over time using museum specimens 222
Case Study 7.2: Variation: experiments on
evolutionary rescue under environmental change 225
8 Drift
Chance and necessity
page 229
Neutral theory
Genetic load
Genetic drift
Neutrality
Population size
Heroes of the Genetic Revolution 8: Tomoko
Ohta CfcffiJK?) 248
TechBox 8.1: Neutral theory 249
TechBox 8.2: Population size 252
Case Study 8.1: Substitution: mutation
accumulation in asexual walking stick insects 255
Case Study 8.2: Population size: inbreeding
depression in an endangered species 258
9 Species
Origin of species
page 262
Taxonomy
Classification
Relatedness
Divergence
Speciation
Hybrid incompatibility
Species
Defining species
DNA taxonomy
© Conclusion
© Points to remember
© Ideas for discussion
0 Examples used in this chapter
Heroes of the Genetic Revolution 9:
Rosemary Gillespie
TechBox 9.1: Phylogeography
TechBox 9.2: Barcoding
Case Study 9.1: Speciation: evolution of
novel flower colour through reinforcement
Case Study 9.2: Barcoding: cataloguing
weevil diversity in New Guinea
266
267
267
268
269
272
274
275
276
277
277
278
279
284
288
291
Alignment
Inbreeding 238 10 Alignment ^
Patterns of substitution 239 Same but different
Chance and complexity 242 page 295
® Conclusion 244 _____
© Points to remember 245
© Ideas for discussion 246 Homology 296
© Sequences used in this chapter 247 Systematic hierarchy 297
0 Examples used in this chapter 247 Shared by descent 300
Contents
DNA can reveal homology 301
Alignment establishes homology 302
Alignment 302
Alignment gaps 303
Homologous sites 304
Manual alignment 305
Automated alignment 306
How to make the best alignment 308
© Conclusion 310
© Points to remember 310
® Ideas for discussion 311
© Sequences used in this chapter 311
Q Examples used in this chapter 311
Heroes of the Genetic Revolution 10:
Margaret Oakley Dayhoff 312
TechBox 10.1: De-extinction 313
TechBox 10.2: Multiple sequence alignment 317
Case Study 10.1: Alignment: identifying insertions
and deletions in endosymbiont genomes 321
Case Study 10.2: Horizontal gene transfer:
genes in parasitic plants derived from their hosts 325
11 Phylogeny
Tree of life
page 329
History
Life as a tree
Molecular phylogenetics
Phylogeny reconstruction
Splits
Similarity
Distance methods
Conflict
330
332
335
340
342
345
345
347
Case Study 11.1: Networks: bobtail squid and
their symbiotic bioluminescent bacteria 362
Case Study 11.2: Distance: tracing the origins
and evolution of the domesticated apple 365
12 Hypotheses
Seeing the wood for the trees
page 369
Comparing trees 370
Possible histories 371
Evaluating alternative trees 372
Multiple hits 374
Statistical inference of phylogeny 376
Models of molecular evolution 377
Likelihood 378
Testing phylogenetic hypotheses 379
Phylogenetic support 380
Which phylogenetic method should I choose? 384
© Conclusion 385
© Points to remember 386
© Ideas for discussion 387
© Examples used in this chapter 387
Heroes of the Genetic Revolution 12:
Hélène Morion 388
TechBox 12.1: Maximum likelihood 389
TechBox 12.2: Bootstrap 392
Case Study 22.1: Epidemiology: using
ancient DNA to identify the origins of a plague 396
Case Study 12.2: Prediction: relating
ethnobotanical resources across different
cultures 400
Ratw
Networks 349 13 Rates . ... r?
Tempo and mode
0 Conclusion 350
page 403 ......
© Points to remember 350
® Ideas for discussion 351
O Examples used in this chapter 352 ------
Heroes of the Genetic Revolution 11: Rate of evolutionary change 404
Joseph Felsenstein 353 Variation in the rate of evolution 405
TechBox 11.1: Distance methods 354 Estimating branch lengths 406
TechBox 11.2: Phylogenetic networks 358 Variation in rates across sites 408
Contents
Comparing rates 409
Mutation rate variation 409
Accounting for descent 411
Generation time effect 413
Lineage-specific rates 415
Comparing substitution rates 415
Testing for rate variation 418
0 Conclusion 419
® Points to remember 420
© Ideas for discussion 421
0 Sequences used in this chapter 421
O Examples used in this chapter 422
Heroes of the Genetic Revolution 13:
Xia Hua (mK) 423
TechBox 13.1: Substitution models 424
TechBox 13.2: Bayesian phylogenetics 428
Case Study 13.1: Rates: flightless insects
have faster substitution rates 432
Case Study 13.2: Diversification: mutation
rates are linked to species richness in plants 434
Divergence 443
Divergence dates 444
Estimating number of substitutions 447
Accuracy and precision 450
Dating with confidence 453
Molecular dating 455
Modelling rate change 456
Challenging assumptions 457
© Conclusion 460
© Points to remember 461
© Ideas for discussion 461
0 Sequences used in this chapter 462
G Examples used in this chapter 462
Heroes of the Genetic Revolution 14:
Andrew Rambaut 464
TechBox 14.1: Calibration 465
TechBox 14.2: Molecular dating 471
Case Study 14.1: Calibration: did kauri survive
the Oligocène drowning of New Zealand? 476
Case Study 14.2: Dates: using phylogenies
to trace the source of disease outbreaks 480
14 Dates
Telling the time
page 438
Confidence 439
Fossilization: a chance at immortality 441
Alternative hypotheses 442
Coda: You are a scientist
What do I do now?
page 484
Glossary
Index
|
| any_adam_object | 1 |
| author | Bromham, Lindell |
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| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.838 |
| dewey-search | 572.838 |
| dewey-sort | 3572.838 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| edition | Second edition |
| format | Book |
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| spelling | Bromham, Lindell Verfasser (DE-588)1186181311 aut An introduction to molecular evolution and phylogenetics Lindell Bromham Second edition Oxford Oxford University Press [2016] xv, 514 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Preface: "The first edition of this book was titled 'Reading the Story in DNA: a beginner's guide to molecular evolution'. This new edition contains some of the same material, but has been considerably expanded, updated, and remodelled" Molecular evolution Phylogeny Phylogenetik (DE-588)4174591-7 gnd rswk-swf Molekulare Evolution (DE-588)4812902-1 gnd rswk-swf Molekulare Evolution (DE-588)4812902-1 s Phylogenetik (DE-588)4174591-7 s b DE-604 Vorangegangen ist Bromham, Lindell Reading the story in DNA Oxford : Oxford Univ. Press, 2008 978-0-19-929091-8 (DE-604)BV023261363 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028681368&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Bromham, Lindell An introduction to molecular evolution and phylogenetics Molecular evolution Phylogeny Phylogenetik (DE-588)4174591-7 gnd Molekulare Evolution (DE-588)4812902-1 gnd |
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| title | An introduction to molecular evolution and phylogenetics |
| title_auth | An introduction to molecular evolution and phylogenetics |
| title_exact_search | An introduction to molecular evolution and phylogenetics |
| title_full | An introduction to molecular evolution and phylogenetics Lindell Bromham |
| title_fullStr | An introduction to molecular evolution and phylogenetics Lindell Bromham |
| title_full_unstemmed | An introduction to molecular evolution and phylogenetics Lindell Bromham |
| title_old | Bromham, Lindell Reading the story in DNA |
| title_short | An introduction to molecular evolution and phylogenetics |
| title_sort | an introduction to molecular evolution and phylogenetics |
| topic | Molecular evolution Phylogeny Phylogenetik (DE-588)4174591-7 gnd Molekulare Evolution (DE-588)4812902-1 gnd |
| topic_facet | Molecular evolution Phylogeny Phylogenetik Molekulare Evolution |
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