فهرست مطالب کتاب ژنتیک جمعیت با برنامه R: مقدمه ای برای علوم زیستی:

Acknowledgements v
Chapter 1: Learning through Programming 1
1.1 Introduction 1
1.2 Organization 5
Chapter 2: Downloading and Installing R 7
2.1 Introduction to R 8
2.2 Working directories and saving 12
Chapter 3: Basic Commands in R 15
3.1 Input and calculations 15
3.2 Assigning objects to variables 18
3.3 Parts of a function 19
3.4 Classes of objects 22
3.5 Matrices 27
Chapter 4: Allele and Genotype Frequencies 35
4.1 Introduction to population genetics 35
4.2 Simulating genotypes 46
4.3 Calculating allele frequencies from datasets 56
Chapter 5: Statistical Tests and Algorithms 65
5.1 Deviation from expectations 65
5.2 Extending to more than two alleles 73
5.3 Blood types and allele frequencies 83
5.4 Expectation Maximization algorithm 87
Chapter 6: Genetic Variation 93
6.1 Genetic drift and evolutionary sampling 93
6.2 Variation over time 109
6.3 Quantifying variation 116
6.4 Equilibrium heterozygosity and effective population size 121
6.5 Overlapping generations 123
Chapter 7: Adaptation and Natural Selection 125
7.1 Positive selection 125
7.2 Adaptation, diploidy and dominance 133
Chapter 8: Population Differences 155
8.1 Quantifying divergence 155
8.2 Relative likelihood of the population of origin 159
8.3 DNA fingerprinting 167
Chapter 9: Pointing the Way to Additional Topics 171
9.1 The coalescent 172
9.2 Tests of neutrality 182
9.3 Linkage disequilibrium 185
9.4 Deleterious alleles 189
9.5 Fixation probability under selection and drift 190
9.6 Selfish genes 193
9.7 Broadening the models 195
9.8 R packages 196
References 201
Index 205