Modern Developments in Theoretical Population Genetics The Legacy of Gustave Malécot

by Slatkin, Montgomery; Veuille, Michel

• ISBN13: 9780198599623
• ISBN10: 0198599625
• Edition: 1st
• Format: Hardcover
• Copyright: 2002-11-07
• Publisher: Oxford University Press

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)
Noah 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)
Separation 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