دانلود کتاب Evolutionary Analysis

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Cover ... 1 Title Page ... 2 Copyright Page ... 3 Contents ... 5 Preface ... 10 Acknowledgments ... 14 PART 1 INTRODUCTION ... 16 CHAPTER 1 A Case for Evolutionary Thinking: Understanding HIV ... 16 1.1 The Natural History of the HIV Epidemic ... 17 1.2 Why Does HIV Therapy Using Just One Drug Ultimately Fail? ... 24 1.3 Are Human Populations Evolving as a Result of the HIV Pandemic? ... 30 1.4 Where Did HIV Come From? ... 33 1.5 Why Is HIV Lethal? ... 38 Computing Consequences 1.1 When did HIV move from chimpanzees to humans? ... 39 Summary ... 46 Questions ... 46 Exploring the Literature ... 47 Citations ... 48 CHAPTER 2 The Pattern of Evolution ... 52 2.1 Evidence of Microevolution: Change through Time ... 54 2.2 Evidence of Speciation: New Lineages from Old ... 59 2.3 Evidence of Macroevolution: New Forms from Old ... 64 2.4 Evidence of Common Ancestry: All Life-Forms Are Related ... 70 2.5 The Age of Earth ... 77 Computing Consequences 2.1 A closer look at radiometric dating ... 80 Summary ... 81 Questions ... 82 Exploring the Literature ... 83 Citations ... 84 CHAPTER 3 Evolution by Natural Selection ... 88 3.1 Artificial Selection: Domestic Animals and Plants ... 89 3.2 Evolution by Natural Selection ... 92 3.3 The Evolution of Flower Color in an Experimental Snapdragon Population ... 94 3.4 The Evolution of Beak Shape in Galápagos Finches ... 96 Computing Consequences 3.1 Estimating heritabilities despite complications ... 99 3.5 The Nature of Natural Selection ... 105 3.6 The Evolution of Evolutionary Biology ... 109 3.7 Intelligent Design Creationism ... 112 Summary ... 119 Questions ... 120 Exploring the Literature ... 121 Citations ... 121 CHAPTER 4 Estimating Evolutionary Trees ... 124 4.1 How to Read an Evolutionary Tree ... 125 4.2 The Logic of Inferring Evolutionary Trees ... 129 4.3 Molecular Phylogeny Inference and the Origin of Whales ... 138 Computing Consequences 4.1 Calculating the likelihood of an evolutionary tree ... 144 Computing Consequences 4.2 Neighbor joining: A distance matrix method ... 145 4.4 Using Phylogenies to Answer Questions ... 152 Summary ... 156 Questions ... 156 Exploring the Literature ... 158 Citations ... 158 PART 2 MECHANISMS OF EVOLUTIONARY CHANGE ... 162 CHAPTER 5 Variation Among Individuals ... 162 5.1 Three Kinds of Variation ... 163 Computing Consequences 5.1 Epigenetic inheritance and evolution ... 169 5.2 Where New Alleles Come From ... 172 5.3 Where New Genes Come From ... 176 Computing Consequences 5.2 Measuring genetic variation in natural populations ... 177 5.4 Chromosome Mutations ... 181 5.5 Rates and Fitness Effects of Mutations ... 184 Summary ... 189 Questions ... 190 Exploring the Literature ... 191 Citations ... 191 CHAPTER 6 Mendelian Genetics in Populations I: Selection and Mutation ... 194 6.1 Mendelian Genetics in Populations: Hardy–Weinberg Equilibrium ... 195 Computing Consequences 6.1 Combining probabilities ... 200 Computing Consequences 6.2 The Hardy– Weinberg equilibrium principle with more than two alleles ... 204 6.2 Selection ... 206 Computing Consequences 6.3 A general treatment of selection ... 209 Computing Consequences 6.4 Statistical analysis of allele and genotype frequencies using the X[sup(2)](chi-square) test ... 213 Computing Consequences 6.5 Predicting the frequency of the CCR5-?32 allele in future generations ... 216 6.3 Patterns of Selection: Testing Predictions of Population Genetics Theory ... 216 Computing Consequences 6.6 An algebraic treatment of selection on recessive and dominant alleles ... 219 Computing Consequences 6.7 Stable equilibria with heterozygote superiority and unstable equilibria with heterozygote inferiority ... 223 6.4 Mutation ... 231 Computing Consequences 6.8 A mathematical treatment of mutation as an evolutionary mechanism ... 233 Computing Consequences 6.9 Allele frequencies under mutation–selection balance ... 235 Computing Consequences 6.10 Estimating mutation rates for recessive alleles ... 237 6.5 An Engineering Test of Population Genetics Theory ... 239 Computing Consequences 6.11 Predicting the frequency of Medea across generations ... 241 Summary ... 242 Questions ... 242 Exploring the Literature ... 244 Citations ... 246 CHAPTER 7 Mendelian Genetics in Populations II: Migration, Drift, and Nonrandom Mating ... 248 7.1 Migration ... 249 Computing Consequences 7.1 An algebraic treatment of migration as an evolutionary process ... 251 Computing Consequences 7.2 Selection and migration in Lake Erie water snakes ... 253 7.2 Genetic Drift ... 255 Computing Consequences 7.3 The probability that a given allele will be the one that drifts to fixation ... 263 Computing Consequences 7.4 Effective population size ... 266 Computing Consequences 7.5 The rate of evolutionary substitution under genetic drift ... 271 7.3 Genetic Drift and Molecular Evolution ... 275 7.4 Nonrandom Mating ... 290 Computing Consequences 7.6 Genotype frequencies in an inbred population ... 294 7.5 Conservation Genetics of the Florida Panther ... 298 Summary ... 300 Questions ... 300 Exploring the Literature ... 302 Citations ... 303 CHAPTER 8 Evolution at Multiple Loci: Linkage and Sex ... 306 8.1 Evolution at Two Loci: Linkage Equilibrium and Linkage Disequilibrium ... 307 Computing Consequences 8.1 The coefficient of linkage disequilibrium ... 310 Computing Consequences 8.2 Hardy– Weinberg analysis for two loci ... 311 Computing Consequences 8.3 Sexual reproduction reduces linkage disequilibrium ... 316 8.2 Practical Reasons to Study Linkage Disequilibrium ... 322 Computing Consequences 8.4 Estimating the age of the GBA–84GG mutation ... 324 8.3 The Adaptive Significance of Sex ... 329 Computing Consequences 8.5 A demographic model of the maintenance of males in the nematode Caenorhabditis elegans ... 332 Summary ... 339 Questions ... 340 Exploring the Literature ... 341 Citations ... 342 CHAPTER 9 Evolution at Multiple Loci: Quantitative Genetics ... 344 9.1 The Nature of Quantitative Traits ... 345 9.2 Identifying Loci That Contribute to Quantitative Traits ... 349 Computing Consequences 9.1 Genetic mapping and LOD scores ... 353 9.3 Measuring Heritable Variation ... 358 Computing Consequences 9.2 Additive genetic variation versus dominance genetic variation ... 360 9.4 Measuring Differences in Survival and Reproductive Success ... 363 Computing Consequences 9.3 The selection gradient and the selection differential ... 364 9.5 Predicting the Evolutionary Response to Selection ... 365 9.6 Modes of Selection and the Maintenance of Genetic Variation ... 371 9.7 The Bell-Curve Fallacy and Other Misinterpretations of Heritability ... 375 Summary ... 380 Questions ... 380 Exploring the Literature ... 382 Citations ... 382 PART 3 ADAPTATION ... 384 CHAPTER 10 Studying Adaptation: Evolutionary Analysis of Form and Function ... 384 10.1 All Hypotheses Must Be Tested: Oxpeckers Reconsidered ... 385 10.2 Experiments ... 388 Computing Consequences 10.1 A primer on statistical testing ... 392 10.3 Observational Studies ... 393 10.4 The Comparative Method ... 397 Computing Consequences 10.2 Calculating phylogenetically independent contrasts ... 399 10.5 Phenotypic Plasticity ... 402 10.6 Trade-Offs and Constraints ... 404 10.7 Selection Operates on Different Levels ... 412 10.8 Strategies for Asking Interesting Questions ... 416 Summary ... 417 Questions ... 417 Exploring the Literature ... 419 Citations ... 420 CHAPTER 11 Sexual Selection ... 422 11.1 Sexual Dimorphism and Sex ... 423 11.2 Sexual Selection on Males: Competition ... 432 11.3 Sexual Selection on Males: Female Choice ... 438 Computing Consequences 11.1 Runaway sexual selection ... 445 11.4 Sexual Selection on Females ... 453 11.5 Sexual Selection in Plants ... 456 11.6 Sexual Dimorphism in Humans ... 459 Summary ... 463 Questions ... 463 Exploring the Literature ... 465 Citations ... 466 CHAPTER 12 The Evolution of Social Behavior ... 470 12.1 Four Kinds of Social Behavior ... 471 12.2 Kin Selection and Costly Behavior ... 474 Computing Consequences 12.1 Calculating relatedness as the probability of identity by descent ... 476 12.3 Multilevel Selection and Cooperation ... 486 Computing Consequences 12.2 Different perspectives on the same evolutionary process ... 488 12.4 Cooperation and Conflict ... 492 12.5 The Evolution of Eusociality ... 498 Summary ... 501 Questions ... 502 Exploring the Literature ... 503 Citations ... 504 CHAPTER 13 Aging and Other Life-History Characters ... 506 13.1 Basic Issues in Life-History Analysis ... 508 13.2 Why Do Organisms Age and Die? ... 510 Computing Consequences 13.1 Late-acting deleterious mutations are weakly selected ... 516 Computing Consequences 13.2 Alleles conferring early benefits and late costs can be adaptive ... 519 13.3 How Many Offspring Should an Individual Produce in a Given Year? ... 528 13.4 How Big Should Each Offspring Be? ... 532 13.5 Conflicts of Interest between Life Histories ... 537 13.6 Life Histories in a Broader Evolutionary Context ... 540 Summary ... 545 Questions ... 545 Exploring the Literature ... 547 Citations ... 547 CHAPTER 14 Evolution and Human Health ... 550 14.1 Evolving Pathogens: Evasion of the Host’s Immune Response ... 552 14.2 Evolving Pathogens: Antibiotic Resistance ... 560 14.3 Evolving Pathogens: Virulence ... 563 14.4 Tissues as Evolving Populations of Cells ... 568 14.5 Selection Thinking Applied to Humans ... 571 14.6 Adaptation and Medical Physiology: Fever ... 579 14.7 Adaptation and Human Behavior: Parenting ... 582 Computing Consequences 14.1 Is cultural evolution Darwinian? ... 584 Summary ... 590 Questions ... 590 Exploring the Literature ... 592 Citations ... 592 CHAPTER 15 Genome Evolution and the Molecular Basis of Adaptation ... 596 15.1 Diversity among Genomes ... 597 15.2 Mobile Genetic Elements ... 601 15.3 The Evolution of Mutation Rates ... 606 15.4 Gene Duplication and Gene Families ... 609 15.5 The Locus of Adaptation in Natural Populations ... 616 Summary ... 621 Questions ... 621 Exploring the Literature ... 622 Citations ... 623 PART 4 THE HISTORY OF LIFE ... 624 CHAPTER 16 Mechanisms of Speciation ... 624 16.1 Species Concepts ... 625 16.2 Mechanisms of Isolation ... 631 16.3 Mechanisms of Divergence ... 638 16.4 Hybridization and Gene Flow between Species ... 644 16.5 What Drives Diversification? ... 652 Summary ... 655 Questions ... 656 Exploring the Literature ... 657 Citations ... 658 CHAPTER 17 The Origins of Life and Precambrian Evolution ... 660 17.1 What Was the First Living Thing? ... 662 17.2 Where Did the First Living Thing Come From? ... 670 17.3 What Was the Last Common Ancestor of All Extant Organisms and What Is the Shape of the Tree of Life? ... 678 17.4 How Did LUCA’s Descendants Evolve into Today’s Organisms? ... 693 Summary ... 698 Questions ... 699 Exploring the Literature ... 701 Citations ... 701 CHAPTER 18 Evolution and the Fossil Record ... 706 18.1 The Nature of the Fossil Record ... 707 18.2 Evolution in the Fossil Record ... 711 Computing Consequences 18.1 Evolutionary trends ... 721 18.3 Taxonomic and Morphological Diversity over Time ... 722 18.4 Mass and Background Extinctions ... 724 18.5 Macroevolution ... 734 18.6 Fossil and Molecular Divergence Timing ... 742 Summary ... 745 Questions ... 746 Exploring the Literature ... 747 Citations ... 747 CHAPTER 19 Development and Evolution ... 750 19.1 The Divorce and Reconciliation of Development and Evolution ... 751 19.2 Hox Genes and the Birth of Evo-Devo ... 753 19.3 Post Hox: Evo-Devo 2.0 ... 759 19.4 Hox Redux: Homology or Homoplasy? ... 778 19.5 The Future of Evo-Devo ... 779 Summary ... 780 Questions ... 781 Exploring the Literature ... 781 Citations ... 782 CHAPTER 20 Human Evolution ... 784 20.1 Relationships among Humans and Extant Apes ... 785 20.2 The Recent Ancestry of Humans ... 795 20.3 Origin of the Species Homo sapiens ... 805 Computing Consequences 20.1 Using allele frequencies and linkage disequilibrium to date the modern human expansion from Africa ... 812 20.4 The Evolution of Distinctive Human Traits ... 817 Summary ... 822 Questions ... 822 Exploring the Literature ... 824 Citations ... 825 Glossary ... 830 A ... 830 B ... 830 C ... 830 D ... 831 E ... 831 F ... 832 G ... 832 H ... 832 I ... 833 K ... 833 L ... 833 M ... 833 N ... 834 O ... 834 P ... 834 Q ... 835 R ... 835 S ... 835 T ... 836 U ... 836 V ... 836 W ... 836 Credits ... 837 Index ... 845 A ... 845 B ... 846 C ... 847 D ... 849 E ... 850 F ... 851 G ... 852 H ... 853 I ... 855 J ... 855 K ... 855 L ... 856 M ... 856 N ... 858 O ... 859 P ... 859 Q ... 861 R ... 861 S ... 862 T ... 864 U ... 865 V ... 865 W ... 865 X ... 865 Y ... 865 Z ... 865