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| Contributors | |
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| Introduction: the Malecot lineage in population genetics | |
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| Gustave Malecot | |
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| Theory and population genetics | |
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| Malecot and population genetics theory | |
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| From 'descent with modification' to the 'coalescent' | |
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| From Malecot to modern developments in population genetics theory | |
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| The scientific work of Gustave Malecot (1911-1998): our common heritage | |
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| Family, formation, and career | |
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| French scientific climate from 1900 to 1940 | |
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| Continuity and unity of Malecot's works | |
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| Some comments about Malecot's works | |
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| Gustave Malecot facing evolution | |
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| The man | |
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| Applications and extensions of Malecot's work in human genetics | |
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| Introduction | |
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| Population structure | |
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| Forensic DNA | |
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| Linkage disequilibrium (LD) | |
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| Envoi | |
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| Usefulness of the identity coefficients for assessing evolutionary forces | |
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| Concerted evolution of gene families | |
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| Generation of genetic diversity | |
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| Linkage disequilibrium between nucleotide sites | |
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| Evolution of new genes | |
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| Discussion | |
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| Pre-speciation coalescence and the effective size of ancestral populations | |
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| Introduction | |
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| Theory and application | |
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| Intragenic recombination, rate heterogeneity, and simulation | |
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| Discussion and conclusion | |
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| Recent applications of diffusion theory to population genetics | |
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| Introduction | |
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| The speed of Muller's ratchet in a haploid asexual population | |
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| The effect of background selection on weakly selected, partially linked polymorphisms | |
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| Effect of genetic hitch-hiking on neutral, partially linked polymorphisms | |
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| Concluding remarks | |
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| Ancestral inference from gene trees | |
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| Coalescent trees and gene trees | |
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| Probabilities of gene trees | |
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| The likelihood of a gene tree | |
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| Ages of mutations | |
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| Subdivided populations | |
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| Genetree software | |
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| The frequency of single mutations | |
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| Ages of single mutations | |
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| Contrasts for a within-species comparative method | |
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| Introduction | |
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| The model | |
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| The expectations of the phenotypes | |
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| Covariances of means between populations | |
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| Statistical tasks | |
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| Spectrum of the migration matrix | |
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| The spectrum of the means | |
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| The spectrum of the covariances | |
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| Fitting models to the means | |
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| An example | |
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| Future directions | |
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| Conclusion | |
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| The relationship between coalescence times and population divergence times | |
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| Introduction | |
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| Definitions | |
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| Methods of inference | |
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| Relationship between coalescence times and divergence times | |
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| Studies of human populations | |
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| Extensions to three or more populations: gene trees and species trees | |
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| Conclusions | |
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| Spatio-temporal properties of gene genealogies in geographically structured populations | |
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| Introduction | |
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| Assumed features of general systems of populations | |
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| Definition of space-time probabilities of identity by descent | |
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| Relationship of temporal lag one space-time probabilities of IBD to the purely spatial probabilities of IBD | |
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| Recursive relationships among temporal orders of space-time probabilities of IBD | |
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| General results for isotropic systems at equilibrium | |
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| General isotropic migration patterns in equilibrium systems existing in one spatial dimension | |
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| Space-time coalescence probabilities | |
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| Numerical examples | |
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| Conclusions | |
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| Linkage analysis and coalescents | |
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| Introduction | |
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| Prospective and retrospective processes | |
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| Linkage analysis | |
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| Aspects of the coalescent process | |
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| Association-based fine mapping for disease genes | |
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| Separation of time scales and convergence to the coalescent in structured populations | |
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| Introduction | |
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| Basic example | |
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| Further examples | |
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| Conclusion | |
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| Appendix: proof of weak convergence to the coalescent in the case of full collapse | |
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| The age of alleles | |
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| Introduction | |
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| General considerations | |
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| Diffusion theory for a population of constant size | |
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| Coalescent theory for neutral alleles | |
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| Birth-death approximation for low frequency alleles | |
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| Importance sampling | |
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| Comparison of different methods | |
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| Intra-allelic coalescent | |
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| Applications | |
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| Conclusion | |
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| Index | |