Evolutionary Dynamics: Mathematics available in Hardcover, eBook
- ISBN-10:
- 0750310952
- ISBN-13:
- 9780750310956
- Pub. Date:
- 10/19/2015
- Publisher:
- Iop Publishing Ltd
- ISBN-10:
- 0750310952
- ISBN-13:
- 9780750310956
- Pub. Date:
- 10/19/2015
- Publisher:
- Iop Publishing Ltd
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Product Details
ISBN-13: | 9780750310956 |
---|---|
Publisher: | Iop Publishing Ltd |
Publication date: | 10/19/2015 |
Pages: | 538 |
Product dimensions: | 7.00(w) x 10.10(h) x 1.20(d) |
Table of Contents
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 Stochasticity 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 Phylogenic 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
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 phylogeny' 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
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 prograniming 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
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
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 speciation 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 speciation 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
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, speciation and systematics A-1
B Dangerous ideas B-1
C Dynamics C-1
D Constrained optimization D-1
E Thermal physics E-1