9780198599630

Modern Developments in Theoretical Population Genetics The Legacy of Gustave Malecot

by ;
  • ISBN13:

    9780198599630

  • ISBN10:

    0198599633

  • Format: Paperback
  • Copyright: 2002-11-07
  • Publisher: Oxford University Press

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Summary

This book contains chapters by leading population genetics that summarize many of the recent developments in population genetics theory and its application to genetic data. The book was inspired by a meeting in honour of the late French population geneticist, Gustave Malecot, held at the Ecole Normale Superieure in Paris, France, in the summer of 1999. Malecot was, along with R.A. Fisher, J.B.S. Haldane, and S. Wright, among the founders of theoretical population genetics. The meeting demonstrated both the great interest in Malecot's work and its relevance to the recent development of the theory of coalescents and the application of that theory to genetic variation observed at the level of DNA sequence. The introductory papers in the book review Malecot's life and his contributions to the theory of population genetics. Later chapters present recent developments in population genetics with particular emphasis on the theory of coalescents. They include discussions of methods for inferring past changes in population size and patterns of genetic exchange, for inferring the ages of individual mutations, and for analysing the relationships among closely linked genes.

Table of Contents

Contributors ix
Introduction: the Malecot lineage in population genetics
1(6)
Michel Veuille
Montgomery Slatkin
Gustave Malecot
1(1)
Theory and Population genetics
1(1)
Malecot and population genetics theory
2(1)
From `descent with modification' to the `coalescent'
3(2)
From Malecot to modern developments in population genetics theory
5(2)
The scientific work of Gustave Malecot (1911-1998): our common heritage
7(13)
Michel Gillois
Family, formation, and career
7(1)
French scientific climate from 1900 to 1940
7(1)
Continuity and unity of Malecot's works
8(5)
Some comments about Malecot's works
13(3)
Gustave Malecot facing evolution
16(1)
The man
16(4)
Applications and extensions of Malecot's work in human genetics
20(17)
Newton E. Morton
Introduction
20(1)
Population structure
21(3)
Forensic DNA
24(3)
Linkage disequilibrium (LD)
27(6)
Envoi
33(4)
Usefulness of the identity coefficients for assessing evolutionary forces
37(15)
Tomoko Ohta
Concerted evolution of gene families
37(2)
Generation of genetic diversity
39(4)
Linkage disequilibrium between nucleotide sites
43(2)
Evolution of new genes
45(3)
Discussion
48(4)
Pre-speciation coalescence and the effective size of ancestral populations
52(20)
Naoyuki Takahata
Yoko Satta
Introduction
52(1)
Theory and application
53(6)
Intragenic recombination, rate heterogeneity, and simulation
59(8)
Discussion and conclusion
67(5)
Recent applications of diffusion theory to population genetics
72(22)
Wolfgang Stephan
Yuseob Kim
Introduction
72(1)
The speed of Muller's ratchet in a haploid asexual population
73(5)
The effect of background selection on weakly selected, partially linked polymorphisms
78(8)
Effect of genetic hitch-hiking on neutral, partially linked polymorphisms
86(3)
Concluding remarks
89(5)
Ancestral inference from gene trees
94(24)
R.C. Griffiths
Coalescent trees and gene trees
94(5)
Probabilities of gene trees
99(2)
The likelihood of a gene tree
101(3)
Ages of mutations
104(6)
Subdivided populations
110(2)
genetree software
112(2)
The frequency of single mutations
114(1)
Ages of single mutations
114(4)
Contrasts for a within-species comparative method
118(12)
Joseph Felsenstein
Introduction
118(1)
The model
119(1)
The expectations of the phenotypes
119(1)
Covariances of means between populations
120(1)
Statistical tasks
120(1)
Spectrum of the migration matrix
121(1)
The spectrum of the means
122(1)
The spectrum of the covariances
123(1)
Fitting models to the means
124(1)
An example
125(2)
Future directions
127(1)
Conclusion
128(2)
The relationship between coalescence times and population divergence times
130(35)
Noath A. Rosenberg
Marcus W. Feldman
Introduction
130(1)
Definitions
131(5)
Methods of inference
136(3)
Relationship between coalescence times and divergence times
139(16)
Studies of human populations
155(3)
Extensions to three or more populations: gene trees and species trees
158(1)
Conclusions
159(6)
Spatio-temporal properties of gene genealogies in geographically structured populations
165(18)
Bryan K. Epperson
Introduction
165(2)
Assumed features of general systems of populations
167(2)
Definition of space-time probabilities of identity by descent
169(1)
Relationship of temporal lag one space-time probabilities of IBD to the purely spatial probabilities of IBD
169(2)
Recursive relationships among temporal orders of space-time probabilities of IBD
171(1)
General results for isotropic systems at equilibrium
171(1)
General isotropic migration patterns in equilibrium systems existing in one spatial dimension
172(3)
Space-time coalescence probabilities
175(3)
Numerical examples
178(2)
Conclusions
180(3)
Linkage analysis and coalescents
183(11)
Warren Ewens
Norman Kaplan
Introduction
183(1)
Prospective and retrospective processes
184(2)
Linkage analysis
186(1)
Aspects of the coalescent process
187(3)
Association-based fine mapping for disease genes
190(4)
Seperation of time scales and convergence to the coalescent in structured populations
194(39)
Magnus Nordborg
Stephen M. Krone
Introduction
194(3)
Basic example
197(16)
Further examples
213(9)
Conclusion
222(2)
Appendix: proof of weak convergence to the coalescent in the case of full collapse
224(9)
The age of alleles
233(28)
Montgomery Slatkin
Introduction
233(1)
General considerations
234(1)
Diffusion theory for a population of constant size
235(1)
Coalescent theory for neutral alleles
236(3)
Birth--death approximation for low frequency alleles
239(3)
Importance sampling
242(2)
Comparison of different methods
244(3)
Intra-allelic coalescent
247(3)
Applications
250(7)
Conclusion
257(4)
Index 261

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