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| Preface | |
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| Basic Models | |
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| ATGCs of life | |
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| Wright-Fisher model | |
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| The coalescent | |
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| Shape of the genealogical tree | |
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| Infinite alleles model | |
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| Hoppe's urn, Ewens' sampling formula | |
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| Chinese restaurants and sufficient statistics | |
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| Branching process viewpoint | |
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| Infinite sites model | |
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| Segregating sites | |
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| Nucleotide diversity | |
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| Pairwise differences | |
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| Folded site frequency spectrum | |
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| Moran model | |
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| Fixation probability and time | |
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| Site frequency spectrum mean | |
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| Estimation and Hypothesis Testing | |
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| Site frequency spectrum covariance | |
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| Estimates of [theta] | |
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| Hypothesis testing overview | |
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| Difference statistics | |
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| Tajima's D | |
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| Fu and Li's D | |
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| Fay and Wu's H | |
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| Conditioning on S[subscript n] | |
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| The HKA test | |
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| McDonald-Kreitman test | |
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| Recombination | |
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| Two loci | |
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| Sample of size 2 | |
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| Sample of size n | |
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| m loci | |
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| Samples of size 2 | |
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| Samples of size n | |
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| Pairwise differences | |
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| Linkage disequilibrium | |
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| Ancestral recombination graph | |
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| Simulation | |
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| Two approximate algorithms | |
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| Counting recombinations | |
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| Estimating recombination rates | |
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| Equations for the two-locus sampling distribution | |
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| Simulation methods | |
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| Composite likelihood estimation of [rho] | |
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| Haplotypes and hot spots | |
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| Population Complications | |
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| Large family sizes | |
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| Population growth | |
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| Exponential growth | |
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| Sudden population expansion | |
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| Founding effects and bottlenecks | |
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| Effective population size | |
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| Matrix migration models | |
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| Strobeck's theorem | |
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| Fast migration limit | |
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| Symmetric island model | |
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| Identity by descent | |
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| Mean and variance of coalescence times | |
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| Effective population sizes | |
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| Large n limit | |
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| Fixation indices | |
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| Stepping Stone Model | |
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| d = 1, Exact results | |
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| d = 1 and 2, Fourier methods | |
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| d = 2, Coalescence times | |
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| Random walk results | |
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| Samples of size 2 | |
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| Fixation indices F[subscript ST] | |
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| d = 2, Genealogies | |
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| Simulation results | |
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| d = 1, Continuous models | |
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| d = 2, Continuous models | |
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| Natural Selection | |
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| Directional selection | |
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| Fixation probability | |
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| Time to fixation | |
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| Three phases of the fixation process | |
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| Ancestral selection graph | |
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| Balancing selection | |
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| Background selection | |
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| Muller's ratchet | |
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| Evolutionary advantages of recombination | |
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| Sex, epistasis, and Kondrashov | |
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| Hitchhiking | |
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| Better approximations | |
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| Recurrent sweeps | |
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| Nucleotide diversity | |
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| Genealogies | |
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| Segregating sites | |
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| Diffusion Processes | |
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| Infinitesimal mean and variance | |
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| Examples of diffusions | |
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| Transition probabilities | |
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| Hitting probabilities | |
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| Stationary measures | |
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| Occupation times | |
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| Green's functions | |
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| Examples | |
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| Conditioned processes | |
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| Boundary behavior | |
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| Site frequency spectrum | |
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| Poisson random field model | |
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| Fluctuating selection | |
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| Multidimensional Diffusions | |
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| K allele model | |
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| Fixation probabilities and time | |
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| Stationary distributions | |
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| Recombination | |
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| A clever change of variables | |
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| Time-dependent behavior | |
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| Equilibrium when there is mutation | |
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| Hill-Robertson interference | |
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| Gene duplication | |
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| Watterson's double recessive null model | |
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| Subfunctionalization | |
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| Genome Rearrangement | |
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| Inversions | |
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| Breakpoint graph | |
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| Hurdles | |
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| When is parsimony reliable? | |
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| Phase transition | |
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| Bayesian approach | |
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| Nadeau and Taylor's analysis | |
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| Genomic distance | |
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| Graph distance | |
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| Bayesian estimation | |
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| Midpoint problem | |
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| Genome duplication | |
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| Yeast | |
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| Maize | |
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| Arabidopsis thaliana | |
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| References | |
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| Index | |