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Theoretical Evolutionary Genetics Joseph Felsenstein

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Theoretical Evolutionary Genetics Joseph Felsenstein THEORETICAL EVOLUTIONARY GENETICS JOSEPH FELSENSTEIN Theoretical Evolutionary Genetics GENOME 562 Joseph Felsenstein Department of Genome Sciences and Department of Biology University of Washington Box 357730 Seattle, Washington 98195-7730 March, 2005 Copyright (c) 1978, 1983, 1988, 1991, 1992, 1994, 1995, 1997, 1999, 2001, 2003, 2005 by Joseph Felsenstein. All rights reserved. Not to be reproduced without author's permission. Contents PREFACE xiii 1 RANDOM MATING POPULATIONS 1 I.1 Asexual inheritance. 1 I.2 Haploid inheritance . 3 I.3 Diploids with two alleles: Hardy-Weinberg laws. 4 I.4 Multiple alleles. 7 I.5 Overlapping generations. 9 I.6 Different Gene Frequencies in the Two Sexes . 11 I.7 Sex linkage. 13 I.8 Linkage. 17 I.9 Estimating Gene Frequencies . 20 Maximum likelihood . 21 Confidence intervals . 22 Gene counting (EM algorithm) . 24 I.10 Testing Hypotheses about Frequencies . 25 Exercises . 28 Complements/Problems . 30 2 NATURAL SELECTION 35 II.1 Introduction . 35 II.2 Selection in Asexuals - Discrete Generations . 36 Fitness and population density . 37 Selection coefficients . 40 Change of genotype (or gene) frequency . 40 Haploids . 41 History . 41 II.3 Selection in Asexuals - Continuous Reproduction . 41 II.4 Selection in Diploids . 43 Multiplicative (geometric) fitnesses . 45 Additive fitnesses . 46 A recessive gene . 47 A dominant gene . 48 Overdominance and underdominance . 48 II.5 Rates of Change of Gene Frequency . 49 v Asexuals and haploids . 49 Asexuals and haploids - continuous generations . 51 Multiplicative fitnesses . 53 Additive fitnesses . 53 An approximation . 54 The recessive case . 55 The dominant case . 57 Dominance, recessiveness, and change under natural selection . 57 History . 59 II.6 Overdominance and Underdominance . 61 Overdominance . 62 Analyzing stability . 63 Stability of overdominant equilibria . 65 Underdominance . 65 Protected polymorphism . 66 History . 68 II.7 Selection and Fitness . 68 Asexuals and haploids . 69 Diploidy { two alleles . 70 Fitness optimization . 71 Segregational load . 73 II.8 Selection and Fitness : Multiple Alleles . 75 Effect of selection . 75 Equilibrium . 76 Stability and mean fitness . 77 II.9 Selection Dependent on Population Density . 79 Asexuals and haploids . 79 Diploids . 81 Oscillations and chaos . 83 Some particular growth laws . 83 Additional work . 84 II.10 Temporal Variation in Fitnesses . 85 Asexuals and haploids . 85 Diploids . 86 Fitnesses varying within a generation . 88 References . 88 II.11 Frequency-Dependent Fitnesses . 89 Asexuals and haploids . 90 Diploids . 92 References . 93 II.12 Kin selection: a specific case of frequency - dependence . 94 Kin and group selection . 95 A model of pairwise interaction . 95 Pitfalls . 98 References . 99 Exercises . 99 Complements/Problems . 102 3 MUTATION 105 III.1 Introduction . 105 III.2 Effect of Mutation on Gene Frequencies . 106 Two alleles . 106 Approach to equilibrium . 107 III.3 Mutation with Multiple Alleles . 109 Multiple alleles . 109 A distinction . 110 III.4 Mutation versus Selection: Haploids . 110 III.5 Mutation vs. Selection: Effects of Dominance . 112 Recessive mutants . 113 Dominance . 115 Polyploidy . 118 III.6 Mutational Load. 119 A heuristic approach . 120 Weak selection and mutational load.
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