Table Of Content

Population Genetics vdxiaovd Population Genetics A Concise Guide John H.vvvspie THEJ OHNSH OPKINS UNIVERSITPYR ESS Baltimore and London ._./,.,.I.,.,_,_,,.,,... ...l,.,ll.”_.~....,. ,.,., ,.*..I .....I ....,.. .. ,..I .......,..,’ . , , ’ 0 1998 The JohnsH opkine University Press All rights reserved. Published 1998 Printed in the United Stateofs America on acid-free paper 9 8 7 6 5 4 3 The JohnsH opkins University Press 2715 North Charles Street Baltimore, Maryland 21218-4363 www.press.jhu.edu Library of Congress Cataloging-in-Publication Data will be'found at the endo f this book. A catalog record for this book is available from the British Library. ISBN 0-8018-5764-6 ISBN 0-8018-5755-(4p bk.) To Robin Gordon Contents List of Figures ix Preface xi 1 The Hardy-Weinberg Law 1 . . . . . . . . . . . . . . . . . . . . 1.1 DNA variatioinn Drosophila 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.2 Loci and alleles 5 . . . . . . . . . . . . . . . . . . . 1.3 Genotypea nd allele frequencies 9 . . . . . . . . . . . . . . . . . . . . 1.4 Randomly matingp opulations 11 . . . . . . . . . . . . . . . . . . . . . . . . . 1.5 Answers to problems 17 2 Genetic Drift 19 . . . . . . . . . . . . . . . . . . . . . . . . 2.1 A computers imulation 20 . . . . . . . . . . . . . . . . . . . . . 2.2 The decay of heterozygosity 22 . . . . . . . . . . . . . . . . . . . . . . . . . . 2.3 Mutationa nd drift 27 . . . . . . . . . . . . . . . . . . . . . . . . . . 2.4 Then eutralt heory 32 . . . . . . . . . . . . . . . . . . . . . . . 2.5 Effective population size 35 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.6 The coalescent 38 . . . . . . . . . . . . . . . . . . . . . . . . . . 2.7 Binomial sampling 42 . . . . . . . . . . . . . . . . . . . . . . . . . 2.8 Answers to problems 47 Selection 3 Natural 49 . . . . . . . . . . . . . . . . . . . . . . . 3.1 The fundamental model 51 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.2 Relative fitness 52 . . . . . . . . . . . . . . . . . . . . . . . 3.3 Three kinds of selection 55 3.4 Mutation-selectiobn a lance . . . . . . . . . . . . . . . . . . . . . 60 . . . . . . . . . . . . . . . . . . 3.5 The heterozygous effects of alleles 62 . . . . . . . . . . . . . . . . . . . . . . . 3.6 Changineg n vironments 71 . . . . . . . . . . . . . . . . . . . . . . . . . . 3.7 Selection and drift 77 . . . . . . . . . . . . . . . . 3.8 Derivation of the fixationp robability 80 . . . . . . . . . . . . . . . . . . . . . . . . . 3.9 Answers to problems 83 vii .....I\ ~,~-lI.,-_,.YI,IXOI*",.IIIY,'~I-,~"~.~....'.'.,.~..~..,.~..I. ....................................... x ............................. ... Vlll Contents 4 Nonrandom Mating 85 . . . . . . . . . . . . . . . . . . . . 4.1 Generalized Hardy-Weinberg 86 . . . . . . . . . . . . . . . . . . . . . . . . . . 4.2 Identity by descent 87 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4.3 Inbreeding 90 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4.4 Subdivision 96 4.5A nswers to problems . . . . . . . . . . . . . . . . . . . . . . . . . 101 5 Quantitative Genetics 103 5.1C orrelation between relatives . . . . . . . . . . . . . . . . . . . . 103 . . . . . . . . . . . . . . . . . . . . . . . . . 5.2 Response to selection 114 . . . . . . . . . . . . . . . . . 5.3 Evolutionaryq uantitative genetics 118 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5.4 Dominance 124 . . . . . . . . . . . . . . . . . . . . . . 5.5 The intensity of selection 130 . . . . . . . . . . . . . . . . . . . . . . . . . 5.6A nswers to problems 131 6 The Evolutionary Advantage of Sex 133 . . . . . . . . . . . . . . . . . . . . . . . . . . 6.1 Genetic segregation 134 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6.2 Crossing-over 137 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6.3 Muller’s ratchet 141 . . . . . . . . . . . . . . . . . . . . . . . . . 6.4 Kondrashov’s hatchet 145 . . . . . . . . . . . . . . . . . . . . . . . . . 6.5 Answers to problems 149 Appendix A Mathematical Necessities 151 Appendix B Probability 155 Bibliography 167 Index 171 List of Figures . . . . . . . . . . . . . . . . . . . . . . 1.1 The ADH coding sequence 3 . . . . . . . . . . . . . . . . . . . . . . . . . . 1.2 Two ADH sequences 6 . . . . . . . . . . . . . . . . . . . . . . 1.3 Differences between alleles 8 . . . . . . . . . . . . . . . . . . . . . . . 1.4 Proteihn e terozygosities 16 . . . . . . . . . . . . . . . . . . . . . . 2.1 Simulation of geneticd rift 21 . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.2 Driftw ith N = 1 22 2.3 The derivation of g' . . . . . . . . . . . . . . . . . . . . . . . . . 24 . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.4 Neutrael v olution 31 . . . . . . . . . . . . . . . . . . . . . . . . 2.5 Hemoglobin evolution 33 . . . . . . . . . . . . . . . . . . . . . 2.6 The effective population size 36 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.7 A coalescent 39 . . . . . . . . . . . . . . . . . . . . . 2.8 Simulation of heterozygosity 43 . . . . . . . . . . . . . . . . . . 2.9 Distributions of allele frequencies 45 . . . . . . . . . . . . . . . . . . 3.1 The rnedionigm allele in Paneda 50 3.2 A simple lifce y cle . . . . . . . . . . . . . . . . . . . . . . . . . . 51 . . . . . . . . . . . . . . . . . . . . . . . . . 3.3 Directional selection 54 . . . . . . . . . . . . . . . . . . . . . . . . . . 3.4 Balancing selection 57 . . . . . . . . . . . . . . . . . . . . . . . 3.5 Hiddenv ariation crosses 63 . . . . . . . . . . . . . . . . . . . . . . . . . 3.6 Drosophila viability 65 . . . . . . . . . . . . . . . . 3.7 At ypicalG reenberg and Crow locus 67 . . . . . . . . . . . . . . . . . . . . . . . . 3.8 A model of dominance 69 ..................... 3.9 Spatial variationi n selection 73 . . . . . . . . . . . . . . . . . . . . . . . . . 4.1 Coefficient of kinship 87 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4.2 Shared alleles 88 . . . . . . . . . . . . . . . . . . . . . . . . . 4.3 Effects of inbreeding 90 . . . . . . . . . . . . . . . . . . . . . . . . . . 4.4 Evolution of selfing 94 . . . . . . . . . . . . . . . . . . . . . . . . . . . 4.5 The island model 99 . . . . . . . . . . . . . . . . . . 5.1 The height of evolution students 104 . . . . . . . . . . . . . . . . . . . . . 5.2 Quantitative genetics model 105 . . . . . . . . . . . . . . . . . . . . . . . . 5.3 Regression of Y on X 112 5.4 A selective breedinge xperiment . . . . . . . . . . . . . . . . . . .1 14 ix ..........- . .. . . . . . . . . . . . . . . . X List of Figures . . . . . . . . . . . . . . . . . . . . . . 5.5 The response to selection 116 5.6 The selection intensity . . . . . . . . . . . . . . . . . . . . . . . . 117 . . . . . . . . . . . . . . . . . . . 5.7 Selection of different intensities 119 . . . . . . . . . . . . . . . . . . . 5.8 Additive and dominance effects 125 . . . . . . . . . . . . . . . . . . . . . . 6.1 Sex versus parthenogenesis 134 . . . . . . . . . . . . . . . . . . . . . . 6.2 Evolution in parthenogens 135 . . . . . . . . . . . . . . . . . . . . . 6.3. Asexual directional selection 137 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6.4 Two loci 138 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6.5 Muller’s ratchet 142 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6.6 Recombination 145 . . . . . . . . . . . . . . . . . . . . . . . . . 6.7 Synergistic epistasis 146 . . . . . . . . . . . . . . . . . . . . 6.8 Asexual mutation distribution 147 Preface At various times I have taught population genetics in two- to five-week chunks. This is precious little time in which to teach a subject, like population genetics, that stands quite apafrrto m the rest of biology in the way that itm akes scientific progress. As there are no textbooks short enough for these chunks, I wrote a Minimalist's Guide to Population Genetics. In this 21-page guide I attempted to distill population genetics down to itse ssence. This guide was, for me, a central canon of the theoretical side of the field. The minimalist approach of the guide has been retained in this, its expanded incarnation. My goal has been to focus on that part of population genetics that is central and incontrovertible. I feel strongly that a student who understands well the core of population genetics is much better equipped to understand evolution than is one who understands less well each of a greater number of topics. If this book is mastered, then the rest of population genetics should be approachable. Population genetics is concerned with the genetic basis of evolution. It differs from much of biology in that its importanti nsights are theoretical rather than observational or experimental. It could hardly be otherwise. The objects of study are primarily the frequencies and fitnesses of genotypes in natural populations. Evolution is the change in the frequencies of genotypes through time, perhaps due to their differences in fitness. While genotype frequencies are easily measured,t heir change is not. The time scale of change of most naturally occurring genetic variants is very long, probably on the order of tens of thousands to millions of years. Changes this slow are impossible to observe directly. Fitness differences between genotypes,. which may be responsible for some of the frequency changes, are so extraordinarily small, probably less than 0.01 percent, that they too areim possible to measure directly. Although we can observe the state of a population, there really is no way to explore directly the evolution of a population. Rather, progress is made in population genetics by constructing mathematical models of evolution, studying their behavior, and then checking whether the states of populations are compatible with this behavior. Early in the history of population genetics, certain models exhibited dynamics that were of such obvi- ous universal importance that thef act that they could not be directly verified in a natural setting seemed unimportant. There is no better example than genetic drift, the small random changes in genotype frequencies caused by variation in offspring number between individuals and, in diploids, genetic segregation. Ge- xi