Preface -- Contents -- Basic Models -- ATGCs of life -- Wright-Fisher model -- The coalescent -- Shape of the genealogical tree -- Infinite alleles model -- Hoppe's urn, Ewens' sampling formula -- Chinese restaurants and sufficient statistics -- Branching process viewpoint -- Infinite sites model -- Segregating sites -- Nucleotide diversity -- Pairwise differences -- Folded site frequency spectrum -- Moran model -- Fixation probability and time -- Site frequency spectrum mean -- Estimation and Hypothesis Testing -- Site frequency spectrum covariance -- Estimates of -- Hypothesis testing overview -- Difference statistics -- Tajima's D -- Fu and Li's D -- Fay and Wu's H -- Conditioning on Sn -- The HKA test -- McDonald-Kreitman test -- Recombination -- Two loci -- Sample of size 2 -- Sample of size n -- m loci -- Samples of size 2 -- Samples of size n -- Pairwise differences -- Linkage disequilibrium -- Ancestral recombination graph -- Simulation -- Two approximate algorithms -- Counting recombinations -- Estimating recombination rates -- Equations for the two-locus sampling distribution -- Simulation methods -- Composite likelihood estimation of -- Haplotypes and hot spots -- Population Complications -- Large family sizes -- Population growth -- Exponential growth -- Sudden population expansion -- Founding effects and bottlenecks -- Effective population size -- Matrix migration models -- Strobeck's theorem -- Fast migration limit -- Symmetric island model -- Identity by descent -- Mean and variance of coalescence times -- Effective population sizes -- Large n limit -- Fixation indices -- Stepping Stone Model -- d = 1, Exact results -- d = 1 and 2, Fourier methods -- d = 2, Coalescence times -- Random walk results -- Samples of size 2 -- Fixation indices FST -- d = 2, Genealogies -- Simulation results -- d = 1, Continuous models.

d = 2, Continuous models -- Natural Selection -- Directional selection -- Fixation probability -- Time to fixation -- Three phases of the fixation process -- Ancestral selection graph -- Balancing selection -- Background selection -- Muller's ratchet -- Evolutionary advantages of recombination -- Sex, epistasis, and Kondrashov -- Hitchhiking -- Better approximations -- Recurrent sweeps -- Nucleotide diversity -- Genealogies -- Segregating sites -- Diffusion Processes -- Infinitesimal mean and variance -- Examples of diffusions -- Transition probabilities -- Hitting probabilities -- Stationary measures -- Occupation times -- Green's functions -- Examples -- Conditioned processes -- Boundary behavior -- Site frequency spectrum -- Poisson random field model -- Fluctuating selection -- Multidimensional Diffusions -- K allele model -- Fixation probabilities and time -- Stationary distributions -- Recombination -- A clever change of variables -- Time-dependent behavior -- Equilibrium when there is mutation -- Hill-Robertson interference -- Gene duplication -- Watterson's double recessive null model -- Subfunctionalization -- Genome Rearrangement -- Inversions -- Breakpoint graph -- Hurdles -- When is parsimony reliable? -- Phase transition -- Bayesian approach -- Nadeau and Taylor's analysis -- Genomic distance -- Graph distance -- Bayesian estimation -- Midpoint problem -- Genome duplication -- Yeast -- Maize -- Arabidopsis thaliana -- References -- Index.