A Biologist's Guide to Mathematical Modeling in Ecology and Evolution

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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

A wonderfully pedagogical introduction to mathematical modeling in population biology: an ideal first course for biologists. -- Simon A. Levin, Princeton University This book is an amazing teaching resource for developing a comprehensive understanding of the methods and importance of biological modeling. But more than that, this book should be read by every student of evolutionary biology and ecology so that they can come to a deeper appreciation of the fundamental ideas and models that underlie these fields. -- Patrick C. Phillips, University of Oregon There is an increasing use of mathematics throughout the biological sciences, yet the training of most biologists still woefully lacks crucial mathematical tools. Sally Otto and Troy Day are themselves two masters at the deft use of theoretical models to crystallize conceptual insights about ecological and evolutionary problems, and in this wonderful book they make accessible to a broad audience the essential mathematical tool kit biologists need, both to read the literature and to craft and analyze models themselves. -- Robert D. Holt, University of Florida I am often asked by biologists to recommend a book on mathematical modeling, but I must tell them that there is no single good book that will guide them through the difficult first stages of learning to make models. Otto and Day's book fills the gap. The quality is high throughout, the scholarship is sound, the book is comprehensive. The authors are both first-rate scientists. I think this will be a classic. -- Steven A. Frank, author of "Immunology and Evolution of Infectious Disease" This book provides a general introduction to mathematical modeling--in particular, to population modeling--in the biological sciences. This past year I taught a 400-level course in mathematical modeling of biological systems, and I had to do so without a textbook because no adequate text existed. Otto and Day's book would have met my needs beautifully. This book is an important addition to the field. -- Carl Bergstrom, University of Washington This book has the ambitious and worthy goal of teaching biologists enough about modeling and about mathematical methods to be both intelligent consumers of models and competent creators of their own models. Its concentration on the process of building rather than analyzing models is its strongest point. -- Frederick R. Adler, author of "Modeling the Dynamics of Life: Calculus and Probability for Life Scientists"

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

Honorable Mention for the 2007 Best Professional/Scholarly Book in Biological Sciences, Association of American Publishers "A gentle but thorough introduction to the mathematical techniques employed in ecological and evolutionary theory. Readers who ... finish this well-written book will be prepared to read and understand a sizeable fraction of the current literature."--Donald L. DeAngelis, Quarterly Review of Biology "At long last, Sally Otto and Troy Day have provided relief for biologists and epidemiologists in search of an easily read, practical, and thorough starting point from which to learn mathematical modeling... We would recommend this book over shorter texts that are labeled as 'introductory'... The depth and detail that Otto and Day have included in this text arc appealing rather than intimidating, and the structure of the text is empowering rather than didactic or formulaic."--Sanjay Basu and Alison P. Galvani, Siam Review "[T]he great value of the Otto/Day book is that it attempts pedagogical soundness, and so is useful for teaching. Besides being perfectly readable, it engages and impresses the reader quickly not only with the subject matter, but also with the quality of printing and layout which have to be seen to be believed. These praises may sound lavish by many a reader of these columns but first see the book or better still buy the volume and you will see our passion and rage for going all out in praise of this volume."--Current Engineering Practice "I highly recommend this book for every university biology department because it provides both a unique, and often uplifting, introduction and a comprehensive reference of techniques for building and analysing mathematical models."--Volker Grimm, Basic and Applied Ecology

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