Preface ix Chapter 1: Mathematical Modeling in Biology 1 1.1 Introduction 1 1.2 HIV 2 1.3 Models of HIV/AIDS 5 1.4 Concluding Message 14 Chapter 2: How to Construct a Model 17 2.1 Introduction 17 2.2 Formulate the Question 19 2.3 Determine the Basic Ingredients 19 2.4 Qualitatively Describe the Biological System 26 2.5 Quantitatively Describe the Biological System 33 2.6 Analyze the Equations 39 2.7 Checks and Balances 47 2.8 Relate the Results Back to the Question 50 2.9 Concluding Message 51 Chapter 3: Deriving Classic Models in Ecology and Evolutionary Biology 54 3.1 Introduction 54 3.2 Exponential and Logistic Models of Population Growth 54 3.3 Haploid and Diploid Models of Natural Selection 62 3.4 Models of Interactions among Species 72 3.5 Epidemiological Models of Disease Spread 77 3.6 Working Backward--Interpreting Equations in Terms of the Biology 79 3.7 Concluding Message 82 Primer 1: Functions and Approximations 89 P1.1 Functions and Their Forms 89 P1.2 Linear Approximations 96 P1.3 The Taylor Series 100 Chapter 4: Numerical and Graphical Techniques--Developing a Feeling for Your Model 110 4.1 Introduction 110 4.2 Plots of Variables Over Time 111 4.3 Plots of Variables as a Function of the Variables Themselves 124 4.4 Multiple Variables and Phase-Plane Diagrams 133 4.5 Concluding Message 145 Chapter 5: Equilibria and Stability Analyses--One-Variable Models 151 5.1 Introduction 151 5.2 Finding an Equilibrium 152 5.3 Determining Stability 163 5.4 Approximations 176 5.5 Concluding Message 184 Chapter 6: General Solutions and Transformations--One-Variable Models 191 6.1 Introduction 191 6.2 Transformations 192 6.3 Linear Models in Discrete Time 193 6.4 Nonlinear Models in Discrete Time 195 6.5 Linear Models in Continuous Time 198 6.6 Nonlinear Models in Continuous Time 202 6.7 Concluding Message 207 Primer 2: Linear Algebra 214 P2.1 An Introduction to Vectors and Matrices 214 P2.2 Vector and Matrix Addition 219 P2.3 Multiplication by a Scalar 222 P2.4 Multiplication of Vectors and Matrices 224 P2.5 The Trace and Determinant of a Square Matrix 228 P2.6 The Inverse 233 P2.7 Solving Systems of Equations 235 P2.8 The Eigenvalues of a Matrix 237 P2.9 The Eigenvectors of a Matrix 243 Chapter 7: Equilibria and Stability Analyses--Linear Models with Multiple Variables 254 7.1 Introduction 254 7.2 Models with More than One Dynamic Variable 255 7.3 Linear Multivariable Models 260 7.4 Equilibria and Stability for Linear Discrete-Time Models 279 7.5 Concluding Message 289 Chapter 8: Equilibria and Stability Analyses--Nonlinear Models with Multiple Variables 294 8.1 Introduction 294 8.2 Nonlinear Multiple-Variable Models 294 8.3 Equilibria and Stability for Nonlinear Discrete-Time Models 316 8.4 Perturbation Techniques for Approximating Eigenvalues 330 8.5 Concluding Message 337 Chapter 9: General Solutions and Tranformations--Models with Multiple Variables 347 9.1 Introduction 347 9.2 Linear Models Involving Multiple Variables 347 9.3 Nonlinear Models Involving Multiple Variables 365 9.4 Concluding Message 381 Chapter 10: Dynamics of Class-Structured Populations 386 10.1 Introduction 386 10.2 Constructing Class-Structured Models 388 10.3 Analyzing Class-Structured Models 393 10.4 Reproductive Value and Left Eigenvectors 398 10.5 The Effect of Parameters on the Long-Term Growth Rate 400 10.6 Age-Structured Models--The Leslie Matrix 403 10.7 Concluding Message 418 Chapter 11: Techniques for Analyzing Models with Periodic Behavior 423 11.1 Introduction 423 11.2 What Are Periodic Dynamics? 423 11.3 Composite Mappings 425 11.4 Hopf Bifurcations 428 11.5 Constants of Motion 436 11.6 Concluding Message 449 Chapter 12: Evolutionary Invasion Analysis 454 12.1 Introduction 454 12.2 Two Introductory Examples 455 12.3 The General Technique of Evolutionary Invasion Analysis 465 12.4 Determining How the ESS Changes as a Function of Parameters 478 12.5 Evolutionary Invasion Analyses in Class-Structured Populations 485 12.6 Concluding Message 502 Primer 3: Probability Theory 513 P3.1 An Introduction to Probability 513 P3.2 Conditional Probabilities and Bayes' Theorem 518 P3.3 Discrete Probability Distributions 521 P3.4 Continuous Probability Distributions 536 P3.5 The (Insert Your Name Here) Distribution 553 Chapter 13: Probabilistic Models 567 13.1 Introduction 567 13.2 Models of Population Growth 568 13.3 Birth-Death Models 573 13.4 Wright-Fisher Model of Allele Frequency Change 576 13.5 Moran Model of Allele Frequency Change 581 13.6 Cancer Development 584 13.7 Cellular Automata--A Model of Extinction and Recolonization 591 13.8 Looking Backward in Time--Coalescent Theory 594 13.9 Concluding Message 602 Chapter 14: Analyzing Discrete Stochastic Models 608 14.1 Introduction 608 14.2 Two-State Markov Models 608 14.3 Multistate Markov Models 614 14.4 Birth-Death Models 631 14.5 Branching Processes 639 14.6 Concluding Message 644 Chapter 15: Analyzing Continuous Stochastic Models--Diffusion in Time and Space 649 15.1 Introduction 649 15.2 Constructing Diffusion Models 649 15.3 Analyzing the Diffusion Equation with Drift 664 15.4 Modeling Populations in Space Using the Diffusion Equation 684 15.5 Concluding Message 687 Epilogue: The Art of Mathematical Modeling in Biology 692 Appendix 1: Commonly Used Mathematical Rules 695 A1.1 Rules for Algebraic Functions 695 A1.2 Rules for Logarithmic and Exponential Functions 695 A1.3 Some Important Sums 696 A1.4 Some Important Products 696 A1.5 Inequalities 697 Appendix 2: Some Important Rules from Calculus 699 A2.1 Concepts 699 A2.2 Derivatives 701 A2.3 Integrals 703 A2.4 Limits 704 Appendix 3: The Perron-Frobenius Theorem 709 A3.1: Definitions 709 A3.2: The Perron-Frobenius Theorem 710 Appendix 4: Finding Maxima and Minima of Functions 713 A4.1 Functions with One Variable 713 A4.2 Functions with Multiple Variables 714 Appendix 5: Moment-Generating Functions 717 Index of Definitions, Recipes, and Rules 725 General Index 727

Sarah P. Otto is Professor of Zoology at the University of British Columbia. Troy Day is Associate Professor of Mathematics and Biology at Queen's University