Modern developments in theoretical population genetics : the legacy of Gustave Malécot / edited by Montgomery Slatkin and Michel Veuille.

Format:

Book

Contributor:

Slatkin, Montgomery.

Veuille, Michel.

Language:

English

Subjects (All):

Population genetics.

Genetics--Statistical methods.

Genetics.

Genetics--Mathematical models.

Genetics--statistics & numerical data.

Genetics, Population--methods.

Medical Subjects:

Genetics--statistics & numerical data.

Genetics, Population--methods.

Physical Description:

x, 264 pages : illustrations ; 25 cm

Place of Publication:

Oxford ; New York : Oxford University Press, [2002]

Summary:

Slatkin and Veuille invite leading population geneticists to summarise many of the recent developments in population genetics theory and its application to genetic data. The book has been assembled in honour of the late Gustave Malecot, one of the pioneers of theoretical population genetics. Whilst early chapters summarise Malecot's life and scientific contributions, the rest of the book is devoted to topics that trace their origin in Malecot's work. Several of the contributions describe recent developments in the coalescent theory, which can be viewed as a generalisation of Malecot's method for analysing identity by descent. Other chapters discuss recent developments in the study of geographic variation, genetic linkage, and allele age. The diversity of topics and the effectiveness with which various theoretical methods can be applied to DNA sequence data illustrates both the increasing relevance of theoretical population genetics and the depth of Malecot's insight into fundamental genetic processes. This exciting work will be of interest to population and statistical geneticists as well as a wider audience of evolutionary biologists.

Contents:

1 Introduction: the Malecot lineage in population genetics / Michel Veuille, Montgomery Slatkin 1

1.1 Gustave Malecot 1

1.2 Theory and population genetics 1

1.3 Malecot and population genetics theory 2

1.4 From 'descent with modification' to the 'coalescent' 3

1.5 From Malecot to modern developments in population genetics theory 5

2 The scientific work of Gustave Malecot (1911-1998): our common heritage / Michel Gillois 7

2.1 Family, formation, and career 7

2.2 French scientific climate from 1900 to 1940 7

2.3 Continuity and unity of Malecot's works 8

2.4 Some comments about Malecot's works 13

2.5 Gustave Malecot facing evolution 16

2.6 The man 16

3 Applications and extensions of Malecot's work in human genetics / Newton E. Morton 20

3.2 Population structure 21

3.3 Forensic DNA 24

3.4 Linkage disequilibrium (LD) 27

3.5 Envoi 33

4 Usefulness of the identity coefficients for assessing evolutionary forces / Tomoko Ohta 37

4.1 Concerted evolution of gene families 37

4.2 Generation of genetic diversity 39

4.3 Linkage disequilibrium between nucleotide sites 43

4.4 Evolution of new genes 45

5 Pre-speciation coalescence and the effective size of ancestral populations / Naoyuki Takahata, Yoko Satta 52

5.2 Theory and application 53

5.3 Intragenic recombination, rate heterogeneity, and simulation 59

6 Recent applications of diffusion theory to population genetics / Wolfgang Stephan, Yuseob Kim 72

6.2 The speed of Muller's ratchet in a haploid asexual population 73

6.3 The effect of background selection on weakly selected, partially linked polymorphisms 78

6.4 Effect of genetic hitch-hiking on neutral, partially linked polymorphisms 86

7 Ancestral inference from gene trees / R. C. Griffiths 94

7.1 Coalescent trees and gene trees 94

7.2 Probabilities of gene trees 99

7.3 The likelihood of a gene tree 101

7.4 Ages of mutations 104

7.5 Subdivided populations 110

7.6 Genetree software 112

7.7 The frequency of single mutations 114

7.8 Ages of single mutations 114

8 Contrasts for a within-species comparative method / Joseph Felsenstein 118

8.2 The model 119

8.3 The expectations of the phenotypes 119

8.4 Covariances of means between populations 120

8.5 Statistical tasks 120

8.6 Spectrum of the migration matrix 121

8.7 The spectrum of the means 122

8.8 The spectrum of the covariances 123

8.9 Fitting models to the means 124

8.10 An example 125

8.11 Future directions 127

9 The relationship between coalescence times and population divergence times / Noah A. Rosenberg, Marcus W. Feldman 130

9.3 Methods of inference 136

9.4 Relationship between coalescence times and divergence times 139

9.5 Studies of human populations 155

9.6 Extensions to three or more populations: gene trees and species trees 158

10 Spatio-temporal properties of gene genealogies in geographically structured populations / Bryan K. Epperson 165

10.2 Assumed features of general systems of populations 167

10.3 Definition of space-time probabilities of identity by descent 169

10.4 Relationship of temporal lag one space-time probabilities of IBD to the purely spatial probabilities of IBD 169

10.5 Recursive relationships among temporal orders of space-time probabilities of IBD 171

10.6 General results for isotropic systems at equilibrium 171

10.7 General isotropic migration patterns in equilibrium systems existing in one spatial dimension 172

10.8 Space-time coalescence probabilities 175

10.9 Numerical examples 178

11 Linkage analysis and coalescents / Warren Ewens, Norman Kaplan 183

11.2 Prospective and retrospective processes 184

11.3 Linkage analysis 186

11.4 Aspects of the coalescent process 187

11.5 Association-based fine mapping for disease genes 190

12 Separation of time scales and convergence to the coalescent in structured populations / Magnus Nordborg, Stephen M. Krone 194

12.2 Basic example 197

12.3 Further examples 213

12.5 Appendix: proof of weak convergence to the coalescent in the case of full collapse 224

13 The age of alleles / Montgomery Slatkin 233

13.2 General considerations 234

13.3 Diffusion theory for a population of constant size 235

13.4 Coalescent theory for neutral alleles 236

13.5 Birth-death approximation for low frequency alleles 239

13.6 Importance sampling 242

13.7 Comparison of different methods 244

13.8 Intra-allelic coalescent 247

13.9 Applications 250.

Notes:

Includes bibliographical references and index.

ISBN:

0198599625

0198599633

OCLC:

49844409