Evolutionary dynamics: the mathematics of genes and traits
Gespeichert in:
| 1. Verfasser: | |
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| Format: | Buch |
| Sprache: | English |
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Bristol, UK
IOP Publishing
[2015]
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| Schriftenreihe: | IOP expanding physics
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| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis Klappentext |
| Beschreibung: | 1 Band (verschiedene Seitenzählungen) |
| ISBN: | 9780750310956 |
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Datensatz im Suchindex
| _version_ | 1804177676498370560 |
|---|---|
| adam_text | Contents
A
Preface xiii
Acknowledgements xviii
1 Introduction 1-1
1.1 Of snails and snakes 1-4
1.2 The three key elements 1-8
1.2.1 Heritability 1-8
1.2.2 Selective pressure 1-12
1.2.3 Variation 1-13
1.3 Stochastic! ty 1-15
1.4 Towards a mathematics of evolution 1-17
1.4.1 A top-down concept of fitness 1-18
1.4.2 Trait fitness 1-21
1.5 Organization of this book 1 -24
Suggested courses 1-24
Bibliography 1-25
Further reading 1-25
2 Cell biology and molecular genetics 2-1
2.1 Cellular architecture and proliferation 2-1
2.1.1 Genetics and cell division 2-3
2.2 DNA, RNA and proteins 2-9
2.2.1 Transcription and translation 2-9
2.2.2 Coding DNA, non-coding DNA and genes 2-15
2.3 Metabolism 2-18
Further reading 2-22
Exercises 2-22
3 Phylogeny and development 3-1
3.1 Phylogénie trees 3-2
3.1.1 Tree theory 3-3
3.1.2 In-groups and out-groups 3-4
3.1.3 Classification 3-5
3.1.4 Rooted and unrooted trees 3-7
3.1.5 Constructing trees 3-8
vii
Evolutionary Dynamics
3.1.6 The distance matrix 3-10
3.1.7 Constructing an unrooted tree 3-11
3.2 Development 3-14
3.2.1 Developmental pathways in differentiation 3-14
3.2.2 ‘Recapitulation of phytogeny’ versus ‘bottleneck’ 3-14
3.2.3 Modification of modular development 3-17
3.2.4 Patterning and cell fate commitment 3-22
3.2.5 Genetic innovation in evolving development 3-28
Bibliography 3-32
Further reading 3-32
Exercises 3-32
4 Elementary evolutionary dynamics 4-1
4.1 Conceptual challenges and the standard assumption 4-2
4.2 Haploids 4-3
4.2.1 Two genomic variants 4-3
4.2.2 Multiple genomic variants 4-10
4.2.3 Bilinear frequency dependence 4-12
4.3 Diploids 4-19
4.3.1 Two gametotypes 4-19
4.3.2 Multiple gametotypes 4-25
4.4 Projection onto tightly linked clusters of loci 4-27
4.4.1 Decay of linkage 4-27
4.4.2 Averaged fitness: a closure problem 4-29
4.4.3 Dynamics of entire gametotypes 4-31
4.5 Drift and fixation 4-32
4.5.1 A simple model of genetic drift 4-33
4.5.2 Connected demes 4-37
4.5.3 A genetic model of latent neutral variation 4-40
Further reading 4-43
Exercises 4-43
5 Probability and measurement 5-1
5.1 Fundamental laws of probability 5-1
5.2 Random variables and their distributions 5-3
5.2.1 Sampling from a given distribution function 5-5
5.2.2 Mixed distributions 5-5
5.2.3 The survivor 5-6
vin
Evolutionary Dynamics
5.3 Expectation and variance 5-7
5.4 Common distributions and their properties 5-11
5.4.1 The exponential and geometric distributions 5-11
5.4.2 Common discrete distributions 5-12
5.4.3 The normal distribution and its ilk 5-15
5.5 Measurement scales 5-19
Further reading 5-21
Exercises 5-21
6 Statistical inference and estimation 6-1
6.1 The essential ideas 6-1
6.1.1 Dinosaur eggs: which species? 6-1
6.1.2 The concept of likelihood 6-3
6.1.3 The P-value 6-4
6.1.4 Dinosaur eggs: are the mean clutch sizes different? 6-5
6.2 Justifying the likelihood ratio principle 6-8
6.2.1 The Neyman—Pearson lemma 6-9
6.2.2 The generalized likelihood ratio principle 6-10
6.3 Linking alleles to traits 6-11
6.3.1 Nominal traits 6-12
6.3.2 Ordinal traits 6-16
6.3.3 Quantitative traits 6-18
6.4 Microarrays: the stepping down procedure 6-27
6.5 Analysis of bivariate data 6-28
6.5.1 The correlation coefficient 6-29
6.5.2 A non-parametric test and a parametric test 6-30
6.5.3 Conditional statistics 6-31
Bibliography 6-32
Further reading 6-32
Exercises 6-32
7 Sequence, structure and function 7-1
7.1 Principles of dynamic programming 7-2
7.2 Sequence phylogenies 7-5
7.2.1 Maximum-likelihood assignment of ancestral states 7-6
7.2.2 Maximum-likelihood tree topology 7-7
ix
Evolutionary Dynamics
7.3 Sequence alignment 7-8
7.3.1 Alignment patterns 7-9
7.3.2 Scoring: matches and penalties 7-10
7.3.3 The alignment cursor 7-12
7.4 Deep structure 7-14
7.4.1 Hidden Markov chains 7-16
7.4.2 Reconstruction of the state sequence 7-17
7.5 From sequence to function 7-18
7.5.1 Cylinder sets 7-19
7.5.2 Correlation functions 7-20
Bibliography 7-27
Further reading 7-27
Exercises 7-27
8 Analysis of quantitative trait loci 8-1
8.1 Recombinant distributions 8-2
8.1.1 Dynamics of inbreeding 8-2
8.1.2 One locus 8-6
8.1.3 Two loci 8-7
8.1.4 More than two loci 8-14
8.2 Genetic markers and mapping 8-15
8.2.1 The marker framework 8-17
8.2.2 Generalization of the likelihood function 8-18
8.2.3 Marker framework maps 8-20
8.2.4 Applications 8-25
8.2.5 Expression QTL 8-26
8.3 The number of quantitative trait loci 8-28
8.3.1 A statistical quandary 8-29
8.3.2 Justification of the normal distribution 8-29
Bibliography 8-31
Further reading 8-31
Exercises 8-31
9 Evolutionary dynamics of QTL 9-1
9.1 Heritability 9-1
9.1.1 Breeding success, breeding failure 9-2
9.1.2 The rate of evolution 9-6
x
Evolutionary Dynamics
9.2 Dynamics of the additive genetic component 9-10
9.2.1 The next-generation map 9-10
9.2.2 Transfer kernel models 9-13
9.2.3 Dynamics of fully linked traits 9-17
9.2.4 Dynamics of completely unlinked traits 9-20
9.3 The persistence of sex 9-21
9.3.1 Persistence of polymorphy 9-23
9.3.2 Asexual advantage 9-27
9.3.3 The origins of sex 9-37
Bibliography 9-39
Further reading 9-39
Exercises 9-40
10 Adaptive dynamics and spéciation 10-1
10.1 Adaptive dynamics 10-2
10.1.1 Invasion fitness 10-2
10.1.2 Stabilizing selection 10-4
10.1.3 Disruptive selection and spéciation 10-7
10.1.4 Protected polymorphisms 10-9
10.2 Fisher’s law for adaptive dynamics 10-10
10.3 Adaptive radiations and mass extinctions 10-14
10.3.1 A simple stochastic model of adaptive radiation 10-15
10.3.2 The quasi-stationary distribution 10-16
10.3.3 Persistence and extinction 10-19
Bibliography 10-23
Further reading 10-23
Exercises 10-23
11 Traits as objects of selection 11-1
11.1 Regimenting traits 11 -2
11.1.1 The trouble with traits 11-3
11.1.2 Trait probes 11 -7
11.1.3 Fitness for regimented traits 11-12
11.1.4 Specifications of the trait mapping 11-13
11.2 Scope and limitations of the additive genetic model 11-16
11.2.1 Estimation of the additive coefficients 11-18
11.2.2 Higher-order interactions 11-20
11.2.3 The generalized additive genetic model 11-23
xi
Evolutionary Dynamics
Bibliography 11 -26
Further reading 11-26
Exercises 11 -26
12 Fitness and optimality 12-1
12.1 Evolution of protandry in butterflies 12-4
12.1.1 Virgins governing reproductive success 12-8
12.2 Evolution of juvenility 12-13
12.3 Evolution of homeostasis 12-17
12.3.1 Control diagrams in engineering and in living systems 12-18
12.3.2 The objective functional 12-21
12.4 Fitness probes 12-25
12.4.1 Construction of the fitness probe 12-26
12.4.2 General application of the fitness probe 12-31
12.4.3 Fitness probes for regimented traits and genotypes 12-36
12.4.4 A variational principle 12-40
Bibliography 12-44
Further reading 12-44
Exercises 12-44
Appendices
A A Species, spéciation and systematics A-l
B Dangerous ideas B-l
C Dynamics C-l
D Constrained optimization D-l
E Thermal physics E-l
xii
lOP Expanding Physics
Evolutionary Dynamics
The mathematics of genes and traits
Hugo van den Berg
This beautifully illustrated and stimulating book develops an understanding of the gene-to-trait
problem in the context of evolutionary dynamics, from the modem perspective of integrative
biology. This gene-to-trait problem lies at the heart of a great many questions in biology,
evolutionary or otherwise. The author presents both elementary and advanced material in a way
that brings out how the gene-to-trait problem is related to both bio informatics and mathematical
models of biological systems.
Key ideas and techniques that underlie some of the most widely-used bioinformatics methods
are discussed in this integrative context. A range of examples of biomathematical models is
developed in an evolutionary framework. The book covers the standard theories of evolutionary
genetics and adaptive dynamics. Bioinformatics techniques are discussed from the perspective
of sequence analysis (alignment, hidden-Markov models, tree inference, and sequence-to-
function mapping) and quantitative trait analysis. The two strands of evolutionary dynamics
and bioinformatics are then brought together in a chapter on the evolutionary dynamics of
quantitative traits, which leads to a number of insights that become the basis for a general
definition of fitness, discussed in the context of the question whether it is valid to argue from
optimality criteria in an evolutionary context.
Written for researchers and postgraduate students with a background in physics or applied
mathematics and a desire to apply their skills to problems in the life sciences, the book includes
a number of introductory chapters on genetics and cell biology, phylogeny and development,
mathematical probability, and inferential statistics. In addition, appendices summarise
background material on spéciation and systematics, controversies surrounding evolutionary
thinking, dynamical systems, optimality arguments, as well as statistical and thermal physics.
About Expanding Physics
Expanding Physics™ publishes high-quality texts from leading voices across the research
landscape on key areas in physics and related subject areas.
ISBN
□ “75D3“lQ*15-b
90 0 00
9 780750 310956
iopscience.org/books
О юр ebooks
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| spelling | Berg, Hugo van den 1968- Verfasser (DE-588)143085387 aut Evolutionary dynamics the mathematics of genes and traits Hugo van den Berg Bristol, UK IOP Publishing [2015] 1 Band (verschiedene Seitenzählungen) txt rdacontent n rdamedia nc rdacarrier IOP expanding physics Literaturangaben Mathematische Modellierung (DE-588)7651795-0 gnd rswk-swf Evolutionsbiologie (DE-588)4153283-1 gnd rswk-swf Mathematisches Modell (DE-588)4114528-8 gnd rswk-swf Evolutionsbiologie (DE-588)4153283-1 s Mathematisches Modell (DE-588)4114528-8 s DE-604 Mathematische Modellierung (DE-588)7651795-0 s 1\p DE-604 Erscheint auch als Online-Ausgabe, mobi 978-0-7503-1125-0 Erscheint auch als Online-Ausgabe 978-0-7503-1094-9 Digitalisierung UB Bayreuth - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029799745&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis Digitalisierung UB Bayreuth - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029799745&sequence=000002&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA Klappentext 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Berg, Hugo van den 1968- Evolutionary dynamics the mathematics of genes and traits Literaturangaben Mathematische Modellierung (DE-588)7651795-0 gnd Evolutionsbiologie (DE-588)4153283-1 gnd Mathematisches Modell (DE-588)4114528-8 gnd |
| subject_GND | (DE-588)7651795-0 (DE-588)4153283-1 (DE-588)4114528-8 |
| title | Evolutionary dynamics the mathematics of genes and traits |
| title_auth | Evolutionary dynamics the mathematics of genes and traits |
| title_exact_search | Evolutionary dynamics the mathematics of genes and traits |
| title_full | Evolutionary dynamics the mathematics of genes and traits Hugo van den Berg |
| title_fullStr | Evolutionary dynamics the mathematics of genes and traits Hugo van den Berg |
| title_full_unstemmed | Evolutionary dynamics the mathematics of genes and traits Hugo van den Berg |
| title_short | Evolutionary dynamics |
| title_sort | evolutionary dynamics the mathematics of genes and traits |
| title_sub | the mathematics of genes and traits |
| topic | Mathematische Modellierung (DE-588)7651795-0 gnd Evolutionsbiologie (DE-588)4153283-1 gnd Mathematisches Modell (DE-588)4114528-8 gnd |
| topic_facet | Mathematische Modellierung Evolutionsbiologie Mathematisches Modell |
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