Preface |
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xi | |
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1 | (106) |
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A Case for Evolutionary Thinking: Understanding HIV |
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3 | (32) |
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The Natural History of the HIV/AIDS Epidemic |
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4 | (6) |
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Why Does AZT Work in the Short Run, But Fail in the Long Run? |
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10 | (7) |
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Box 1.1 Can understanding how resistance evolves help researchers design better treatments? |
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14 | (3) |
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17 | (5) |
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Why Are Some People Resistant to Infection by HIV? |
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22 | (2) |
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24 | (11) |
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Box 1.2 When did HIV move from chimpanzees to humans? |
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28 | (1) |
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29 | (1) |
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30 | (1) |
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31 | (1) |
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31 | (4) |
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The Evidence for Evolution |
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35 | (34) |
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Evidence of Change through Time |
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36 | (11) |
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Box 2.1 A brief history of ideas on evolution |
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37 | (10) |
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Evidence of Common Ancestry |
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47 | (10) |
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Box 2.2 Homology and model organisms |
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56 | (1) |
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57 | (5) |
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Box 2.3 A closer look at radiometric dating |
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61 | (1) |
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Is There Necessarily a Conflict between Evolutionary Biology and Religion? |
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62 | (7) |
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64 | (1) |
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65 | (1) |
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66 | (1) |
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67 | (2) |
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Darwinian Natural Selection |
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69 | (38) |
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Artificial Selection: Domestic Animals and Plants |
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70 | (2) |
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Evolution by Natural Selection |
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72 | (2) |
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The Evolution of Flower Color in an Experimental Snapdragon Population |
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74 | (2) |
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The Evolution of Beak Shape in Galapagos Finches |
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76 | (11) |
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Box 3.1 Issues that complicate how heritabilities are estimated |
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82 | (5) |
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The Nature of Natural Selection |
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87 | (5) |
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The Evolution of Darwinism |
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92 | (3) |
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The Debate over ``Scientific Creationism'' and Intelligent Design Theory |
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95 | (12) |
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104 | (1) |
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104 | (1) |
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105 | (1) |
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105 | (2) |
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PART 2 MECHANISMS OF EVOLUTIONARY CHANGE |
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107 | (222) |
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Mutation and Genetic Variation |
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109 | (32) |
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Where New Alleles Come From |
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109 | (11) |
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Where New Genes Come From |
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120 | (3) |
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123 | (4) |
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Measuring Genetic Variation in Natural Populations |
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127 | (14) |
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Box 4.1 Gel electrophoresis |
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132 | (5) |
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137 | (1) |
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137 | (1) |
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138 | (1) |
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139 | (2) |
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Mendelian Genetics in Populations I: Selection and Mutation as Mechanisms of Evolution |
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141 | (54) |
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Mendelian Genetics in Populations: The Hardy--Weinberg Equilibrium Principle |
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142 | (12) |
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Box 5.1 Combining probabilities |
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147 | (5) |
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Box 5.2 The Hardy--Weinberg equilibrium principle with more than two alleles |
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152 | (2) |
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154 | (41) |
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Box 5.3 A general treatment of selection |
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159 | (3) |
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Box 5.4 Hardy--Weinberg equilibrium among different mutant alleles that cause a recessive genetic disease |
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162 | (2) |
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Box 5.5 Statistical analysis of allele and genotype frequencies using the X2 (chi-square) test |
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164 | (2) |
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Box 5.6 Predicting the frequency of the CCR5-Δ32 allele in future generations |
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166 | (1) |
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Patterns of Selection: Testing Predictions of Population Genetic Theory |
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166 | (4) |
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Box 5.7 An algebraic treatment of selection on recessive and dominant alleles |
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170 | (4) |
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Box 5.8 Stable equilibria with heterozygote superiority and unstable equilibria with heterozygote inferiority |
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174 | (8) |
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182 | (2) |
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Box 5.9 A mathematical treatment of mutation as an evolutionary force |
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184 | (3) |
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Box 5.10 Allele frequencies under mutation-selection balance |
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187 | (1) |
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Box 5.11 Estimating mutation rates for recessive alleles |
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188 | (2) |
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190 | (1) |
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191 | (1) |
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192 | (1) |
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193 | (2) |
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Mendelian Genetics in Populations II: Migration, Genetic Drift, and Nonrandom Mating |
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195 | (58) |
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197 | (7) |
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Box 6.1 An algebraic treatment of migration as an evolutionary force |
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199 | (2) |
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Box 6.2 Selection and migration in Lake Erie water snakes |
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201 | (3) |
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204 | (19) |
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Box 6.3 The probability that a given allele will be the one that drifts to fixation |
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213 | (4) |
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Box 6.4 Effective population size |
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217 | (5) |
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Box 6.5 The rate of evolutionary substitution under genetic drift |
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222 | (1) |
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Genetic Drift and Molecular Evolution |
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223 | (13) |
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236 | (9) |
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Box 6.6 Genotype frequencies under genetic drift |
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241 | (4) |
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Conservation Genetics of the Illinois Greater Prairie Chicken |
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245 | (8) |
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248 | (1) |
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248 | (2) |
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250 | (1) |
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251 | (2) |
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Evolution at Multiple Loci: Linkage and Sex |
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253 | (36) |
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Evolution at Two Loci: Linkage Equilibrium and Linkage Disequilibrium |
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254 | (13) |
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Box 7.1 The coefficient of linkage disequilibrium |
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257 | (1) |
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Box 7.2 Hardy--Weinberg analysis for two loci |
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258 | (4) |
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Box 7.3 Sexual reproduction reduces linkage disequilibrium |
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262 | (5) |
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Practical Reasons for Measuring Linkage Disequilibrium |
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267 | (7) |
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Box 7.4 Estimating the age of the CCR5-Δ32 mutation |
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269 | (5) |
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The Adaptive Significance of Sex |
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274 | (15) |
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285 | (1) |
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286 | (1) |
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287 | (1) |
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288 | (1) |
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Evolution at Multiple Loci: Quantitative Genetics |
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289 | (40) |
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The Nature of Quantitative Traits |
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289 | (5) |
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Identifying Loci That Contribute to Quantitative Traits |
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294 | (9) |
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300 | (3) |
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Measuring Heritable Variation |
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303 | (5) |
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Box 8.2 Additive genetic variation versus dominance genetic variation |
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306 | (2) |
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Measuring Differences in Survival and Reproductive Success |
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308 | (5) |
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Box 8.3 The selection gradient and the selection differential |
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310 | (1) |
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Box 8.4 Selection on multiple traits and correlated characters |
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311 | (2) |
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Predicting the Evolutionary Response to Selection |
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313 | (4) |
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Modes of Selection and the Maintenance of Genetic Variation |
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317 | (4) |
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The Bell-Curve Fallacy and Other Misinterpretations of Heritability |
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321 | (8) |
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325 | (1) |
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326 | (1) |
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327 | (1) |
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328 | (1) |
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329 | (218) |
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Studying Adaptation: Evolutionary Analysis of Form and Function |
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331 | (42) |
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All Hypotheses Must Be Tested: The Giraffe's Neck Reconsidered |
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332 | (3) |
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335 | (5) |
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Box 9.1 A primer on statistical testing |
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340 | (1) |
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340 | (5) |
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345 | (5) |
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Box 9.2 Calculating phylogenetically independent contrasts |
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348 | (2) |
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350 | (1) |
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Trade-Offs and Constraints |
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351 | (7) |
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Selection Operates on Different Levels |
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358 | (10) |
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Box 9.3 Categories of transposable elements |
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362 | (6) |
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Strategies for Asking Interesting Questions |
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368 | (5) |
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368 | (1) |
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369 | (1) |
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370 | (1) |
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371 | (2) |
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373 | (46) |
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Sexual Dimorphism and Sex |
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374 | (7) |
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Male--Male Competition: Intrasexual Selection |
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381 | (7) |
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Box 10.1 Alternative male mating strategies |
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385 | (3) |
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388 | (16) |
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Box 10.2 Extra-pair copulations and multiple mating |
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392 | (9) |
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Box 10.3 Runaway sexual selection in stalk-eyed flies? |
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401 | (3) |
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404 | (2) |
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Sexual Selection in Plants |
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406 | (4) |
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Sexual Dimorphism in Body Size in Humans |
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410 | (9) |
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412 | (1) |
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413 | (2) |
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415 | (1) |
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416 | (3) |
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Kin Selection and Social Behavior |
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419 | (36) |
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Kin Selection and the Evolution of Altruism |
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420 | (11) |
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Box 11.1 Calculating coefficients of relatedness |
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421 | (5) |
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426 | (5) |
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431 | (8) |
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Box 11.3 The evolution of the sex ratio |
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434 | (5) |
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Parent--Offspring Conflict |
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439 | (4) |
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443 | (12) |
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Box 11.4 Prisoner's dilemma: Analyzing cooperation and conflict using game theory |
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445 | (4) |
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449 | (1) |
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450 | (1) |
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451 | (1) |
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452 | (3) |
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Aging and Other Life History Characters |
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455 | (46) |
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Basic Issues in Life History Analysis |
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457 | (2) |
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Why Do Organisms Age and Die? |
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459 | (15) |
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Box 12.1 A trade-off between cancer risk and aging |
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464 | (11) |
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Box 12.2 Is there an evolutionary explanation for menopause? |
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475 | |
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How Many Offspring Should an Individual Produce in a Given Year? |
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474 | (7) |
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How Big Should Each Offspring Be? |
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481 | (6) |
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Conflicts of Interest between Life Histories |
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487 | (3) |
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Life Histories in a Broader Evolutionary Context |
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490 | (11) |
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496 | (1) |
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496 | (1) |
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497 | (1) |
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498 | (3) |
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Evolution and Human Health |
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501 | (46) |
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Evolving Pathogens: Evasion of the Host's Immune Response |
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503 | (6) |
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Evolving Pathogens: Antibiotic Resistance |
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509 | (4) |
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Evolving Pathogens: Virulence |
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513 | (4) |
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Tissues as Evolving Populations of Cells |
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517 | (4) |
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Box 13.1 Genetic sleuthing solves a medical mystery |
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518 | (3) |
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The Adaptationist Program Applied to Humans |
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521 | (7) |
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Adaptation and Medical Physiology: Fever |
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528 | (5) |
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Adaptation and Human Behavior: Parenting |
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533 | (14) |
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Box 13.2 Is cultural evolution Darwinian? |
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534 | (8) |
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542 | (1) |
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542 | (1) |
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543 | (1) |
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544 | (3) |
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PART 4 THE HISTORY OF LIFE |
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547 | (224) |
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Reconstructing Evolutionary Trees |
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549 | (34) |
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The Logic of Phylogeny Inference |
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550 | (5) |
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555 | (12) |
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Box 14.1 Alternatives to parsimony: Maximum liklihood and genetic distances |
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562 | (5) |
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Using Phylogenies to Answer Questions |
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567 | (16) |
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578 | (1) |
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578 | (3) |
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581 | (1) |
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581 | (2) |
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583 | (32) |
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583 | (6) |
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Box 15.1 What about bacteria and archaea? |
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585 | (4) |
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Mechanisms of Genetic Isolation |
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589 | (7) |
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596 | (7) |
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603 | (5) |
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The Genetics of Speciation |
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608 | (7) |
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611 | (1) |
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612 | (1) |
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613 | (1) |
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613 | (2) |
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The Origins of Life and Precambrian Evolution |
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615 | (48) |
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What Was the First Living Thing? |
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616 | (10) |
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Where Did the First Living Thing Come From? |
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626 | (10) |
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Box 16.1 The Panspermia Hypothesis |
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628 | (8) |
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What Was the Last Common Ancestor of All Extant Organisms and What Is the Shape of the Tree of Life? |
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636 | (15) |
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Box 16.2 Horizontal gene transfer in bacteria |
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647 | (4) |
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How Did the Last Common Ancestor's Descendants Evolve into Today's Organisms? |
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651 | (12) |
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656 | (1) |
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657 | (1) |
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658 | (1) |
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659 | (4) |
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The Cambrian Explosion and Beyond |
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663 | (38) |
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The Nature of the Fossil Record |
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664 | (3) |
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667 | (10) |
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Macroevolutionary Patterns |
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677 | (7) |
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684 | (17) |
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697 | (1) |
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697 | (1) |
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698 | (1) |
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699 | (2) |
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Development and Evolution |
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701 | (26) |
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Homeotic Genes, Pattern Formation, and Diversification |
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702 | (7) |
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The Genetics of Homology: Limbs |
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709 | (7) |
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716 | (5) |
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Lessons from Evo-Devo Research |
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721 | (6) |
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723 | (1) |
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724 | (1) |
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724 | (1) |
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725 | (2) |
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727 | (44) |
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Relationships among Humans and the Extant Apes |
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728 | (7) |
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Box 19.1 Genetic differences between humans, chimpanzees, and gorillas |
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736 | |
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The Recent Ancestry of Humans |
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735 | (11) |
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The Origin of the Species Homo sapiens |
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746 | (13) |
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Box 19.2 Genetic diversity among living humans |
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749 | (9) |
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Box 19.3 Using linkage disequilibrium to date the divergence between African and non-African populations |
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758 | (1) |
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The Evolution of Uniquely Human Traits |
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759 | (12) |
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765 | (1) |
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766 | (1) |
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767 | (1) |
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767 | (4) |
Glossary |
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771 | (7) |
Illustration Credits |
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778 | (6) |
Index |
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784 | |