Preface |
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xv | |
Website Support Materials |
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xvii | |
Acknowledgements |
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xix | |
About the Author |
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xxi | |
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SECTION ONE AN INTRODUCTION TO EVOLUTION |
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1 | (36) |
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3 | (6) |
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4 | (1) |
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Evolutionary research today |
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5 | (2) |
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7 | (1) |
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8 | (1) |
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8 | (1) |
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2 A Potted History of Evolutionary Science |
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9 | (6) |
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9 | (1) |
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10 | (1) |
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The era of evolutionary genetics |
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11 | (1) |
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12 | (2) |
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14 | (1) |
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14 | (1) |
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15 | (10) |
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16 | (2) |
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18 | (2) |
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Four billion years of life |
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20 | (1) |
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20 | (1) |
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20 | (1) |
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20 | (3) |
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23 | (1) |
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23 | (2) |
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4 Life Today: Species, Diversity, and Classification |
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25 | (12) |
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The diversity of life today |
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26 | (1) |
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27 | (2) |
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Variation within a species |
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29 | (1) |
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The numbers of species today |
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30 | (1) |
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Taxonomies: Organising diversity |
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31 | (4) |
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Phytogenies and evolutionary history |
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35 | (1) |
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36 | (1) |
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36 | (1) |
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36 | (1) |
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SECTION TWO THE EVIDENCE FOR EVOLUTION |
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37 | (54) |
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5 Analysing Evolutionary Change |
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39 | (12) |
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Descent with modification is the identifier for evolution |
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39 | (5) |
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Cladistic links organisms by anatomical inheritance |
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44 | (1) |
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Linnaean and cladistic taxonomies are different |
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45 | (1) |
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45 | (1) |
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46 | (1) |
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46 | (1) |
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47 | (1) |
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The broader importance of Darwin's ideas |
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48 | (1) |
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49 | (1) |
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49 | (1) |
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49 | (2) |
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6 The Anatomical Evidence for Evolutionary Change |
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51 | (14) |
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The evolution of the pentadactyl limb |
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52 | (4) |
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The evolution of the mammalian skull |
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56 | (1) |
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The evolution of middle-ear bones and the reorganization of the jaw |
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57 | (2) |
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The evolution of the zygomatic arch |
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59 | (1) |
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The evolution of the secondary palate |
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60 | (1) |
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The evolution of mammalian teeth |
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61 | (1) |
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The evolution of the equidae |
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61 | (3) |
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64 | (1) |
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64 | (1) |
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64 | (1) |
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65 | (12) |
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Phylograms and cladograms are subtly different |
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66 | (2) |
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Constructing sequence-based phylogenetic trees |
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68 | (1) |
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69 | (1) |
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Choosing sequences for phylogenetic analysis |
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69 | (2) |
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Three examples of molecular phytogenies |
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71 | (1) |
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The evolutionary status of the Amphillim 1/5 Gene |
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71 | (1) |
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Phylogenetic relationships among a group of anemone fish |
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72 | (1) |
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Phylogenetic relationships across the family of hox genes |
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72 | (1) |
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Gene trees, species trees, and phylogenomics |
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73 | (1) |
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Adding timings to phylograms |
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74 | (1) |
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Molecular phylogenetics today |
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75 | (1) |
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75 | (1) |
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76 | (1) |
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76 | (1) |
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77 | (14) |
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The molecular basis of evo-devo homologies |
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78 | (1) |
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Signal and receptor homologies |
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78 | (1) |
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Transcription factor homologies |
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79 | (7) |
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Protein network homologies |
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86 | (2) |
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Implications of protein homologies |
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88 | (1) |
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89 | (1) |
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90 | (1) |
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90 | (1) |
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SECTION THREE THE HISTORY OF LIFE |
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91 | (138) |
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9 The First Two Billion Years |
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93 | (16) |
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94 | (2) |
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FUCA, the first universal common ancestor |
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96 | (1) |
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LUCA, the last universal common ancestor |
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97 | (1) |
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The prokaryotic seas: Eubacteria and Archaebacteria |
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98 | (1) |
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99 | (1) |
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100 | (1) |
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FECA, the first eukaryote common ancestor |
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101 | (2) |
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LECA, the last eukaryote common ancestor |
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103 | (1) |
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104 | (1) |
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Membranes and cytoskeleton |
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105 | (1) |
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105 | (1) |
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106 | (1) |
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107 | (1) |
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107 | (2) |
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10 The Roots of the Eukaryotic Tree of Life |
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109 | (16) |
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The diversification of the leca |
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112 | (1) |
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Flagella, centrioles, and basal bodies |
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112 | (1) |
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113 | (1) |
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Sexual reproduction and diploidy |
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114 | (1) |
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115 | (1) |
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115 | (2) |
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The origins of social behaviour |
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117 | (1) |
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The acquisition of multicellularity |
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117 | (2) |
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119 | (4) |
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123 | (1) |
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123 | (1) |
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123 | (1) |
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123 | (2) |
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11 The Evolution of Algae and Plants |
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125 | (16) |
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126 | (2) |
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128 | (1) |
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128 | (2) |
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130 | (2) |
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132 | (4) |
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136 | (2) |
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138 | (1) |
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139 | (1) |
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139 | (2) |
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12 The Ediacaran Period and the Early Evolution of the Metazoa |
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141 | (12) |
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142 | (3) |
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The evolution of diploblastic and triploblastic embryos |
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145 | (1) |
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146 | (1) |
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147 | (1) |
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The evolution of Urbilateria |
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147 | (3) |
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150 | (1) |
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151 | (1) |
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151 | (2) |
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13 The Cambrian Explosion and the Evolution of Protostomes |
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153 | (18) |
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The Cambrian fossil record |
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154 | (2) |
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156 | (1) |
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156 | (1) |
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156 | (2) |
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The Bilateria and protostome diversity |
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158 | (2) |
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160 | (1) |
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The major protostome phyla |
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161 | (1) |
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162 | (2) |
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164 | (5) |
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169 | (1) |
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170 | (1) |
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170 | (1) |
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14 Deuterostome Evolution: From the Beginnings to the Amphibians |
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171 | (20) |
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Modern deuterostome anamniotes |
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172 | (2) |
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174 | (1) |
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The minor chordate clades |
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174 | (1) |
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175 | (2) |
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The early deuterostome fossil record |
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177 | (1) |
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178 | (3) |
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181 | (4) |
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185 | (1) |
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186 | (1) |
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187 | (1) |
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187 | (1) |
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188 | (1) |
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189 | (1) |
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189 | (1) |
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190 | (1) |
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15 Vertebrate Evolution: Stem Mammals, Reptiles, and Birds |
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191 | (18) |
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Anatomical innovations in stem amniotes |
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193 | (1) |
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The evolution of the amniote egg |
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193 | (2) |
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The evolution of the early amniote skeleton |
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195 | (3) |
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The fossil record of Mesozoic reptiles |
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198 | (1) |
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199 | (1) |
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The Mesozoic Era (252-66 Mya) |
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200 | (4) |
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The K-T extinction and the beginnings of the Cenozoic Era (66 Mya) |
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204 | (1) |
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204 | (1) |
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204 | (1) |
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205 | (2) |
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207 | (1) |
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208 | (1) |
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208 | (1) |
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16 Vertebrate Evolution: Mammals |
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209 | (20) |
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The mammalian fossil record from the Mesozoic |
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212 | (3) |
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The evolution of some key mammalian features |
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215 | (1) |
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216 | (1) |
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216 | (5) |
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The evolution of the Cetacea |
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221 | (2) |
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223 | (1) |
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Probosces with a second function |
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223 | (1) |
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223 | (1) |
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Back to the sea and the evolution of whales |
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224 | (3) |
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227 | (1) |
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227 | (1) |
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227 | (2) |
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SECTION FOUR THE MECHANISMS OF EVOLUTION |
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229 | (106) |
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17 Variation 1: Mutations and Phenotypes |
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233 | (18) |
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234 | (1) |
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Unusual variation: Sports and anomalies |
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235 | (1) |
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Variation leading to human disease |
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236 | (2) |
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238 | (1) |
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239 | (1) |
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239 | (2) |
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The effects of mutation on the genotype |
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241 | (1) |
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The effect of mutation on individual genes |
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242 | (1) |
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Larger-scale genomic changes |
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243 | (1) |
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244 | (1) |
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The role of the environment in generating variation |
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245 | (1) |
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Transgenerational epigenetic inheritance (TEI) |
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245 | (3) |
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248 | (1) |
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248 | (1) |
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249 | (1) |
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249 | (2) |
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18 Variation 2: Evolutionary Change |
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251 | (18) |
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Some origins of anatomical change |
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252 | (1) |
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253 | (1) |
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253 | (1) |
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254 | (3) |
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Other evolutionary variants |
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257 | (3) |
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The effect of mutation on signaling and network systems |
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260 | (1) |
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Signals, receptors, and transcription factors |
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260 | (1) |
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261 | (2) |
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Developmental constraints on variation |
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263 | (3) |
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The mutational basis of trait change--The broader view |
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266 | (1) |
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266 | (1) |
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267 | (1) |
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267 | (2) |
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19 Adaptation, Symbionts, and Holobionts |
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269 | (16) |
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271 | (1) |
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271 | (2) |
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273 | (1) |
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273 | (1) |
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274 | (1) |
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Facilitating reproduction |
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275 | (1) |
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Increasing offspring numbers |
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276 | (1) |
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276 | (2) |
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278 | (3) |
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Developmental plasticity and adaptive change |
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281 | (1) |
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282 | (1) |
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283 | (1) |
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283 | (2) |
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285 | (16) |
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286 | (2) |
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The evolution of the camera eye under selection |
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288 | (2) |
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290 | (1) |
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The advantages and disadvantages of sexual reproduction |
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290 | (1) |
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291 | (1) |
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292 | (1) |
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Kin selection and altruism |
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292 | (4) |
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The speed of change under selection |
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296 | (1) |
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297 | (1) |
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297 | (1) |
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Generating anatomical novelties |
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297 | (2) |
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Selection pressures imposed by humans |
|
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299 | (1) |
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300 | (1) |
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300 | (1) |
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300 | (1) |
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21 Evolutionary Population Genetics |
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301 | (18) |
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Classical population genetics |
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303 | (1) |
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303 | (1) |
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304 | (1) |
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304 | (1) |
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305 | (1) |
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306 | (2) |
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308 | (1) |
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Neutral theory versus selection |
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309 | (1) |
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Small populations and founder groups |
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310 | (1) |
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Quantitative and complex traits |
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311 | (1) |
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311 | (1) |
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312 | (1) |
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313 | (2) |
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315 | (1) |
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316 | (1) |
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316 | (1) |
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|
317 | (2) |
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319 | (16) |
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320 | (1) |
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321 | (1) |
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The morphological criterion |
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321 | (1) |
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321 | (1) |
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321 | (1) |
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322 | (1) |
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|
322 | (2) |
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Modes of reproductive isolation |
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324 | (1) |
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324 | (1) |
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325 | (1) |
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325 | (1) |
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326 | (1) |
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326 | (1) |
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327 | (1) |
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Speciation speeds under allopatric conditions |
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328 | (1) |
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329 | (2) |
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331 | (1) |
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The genetics of speciation |
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332 | (1) |
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The key role of chromosomes |
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333 | (1) |
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334 | (1) |
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334 | (1) |
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334 | (1) |
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SECTION FIVE HUMAN EVOLUTION |
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335 | (58) |
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23 Human Evolution 1: The Fossil Evidence |
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337 | (14) |
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340 | (2) |
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342 | (1) |
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Possible early hominins (7-4.5 Mya) |
|
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342 | (1) |
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Archaic hominins (4.5-2.5 Mya) |
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342 | (1) |
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Megadont archaic hominins (2.5-1 Mya) |
|
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343 | (1) |
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Transitional hominins (-2.5-1.4 Mya) |
|
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343 | (1) |
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Pre-modern Homo (1.9 Mya-30Kya) |
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|
343 | (4) |
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Anatomically modern Homo (from 0.2 Mya onwards) |
|
|
347 | (1) |
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|
347 | (1) |
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|
348 | (1) |
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349 | (1) |
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|
349 | (2) |
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24 Human Evolution 2: Genes and Migrations |
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351 | (12) |
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Information from chimpanzee genomes |
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352 | (1) |
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353 | (2) |
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Contemporary human genomes |
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355 | (1) |
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355 | (1) |
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356 | (1) |
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|
357 | (3) |
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360 | (1) |
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361 | (1) |
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362 | (1) |
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|
362 | (1) |
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25 Human Evolution 3: The Origins of Modern Humans |
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363 | (18) |
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364 | (1) |
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364 | (1) |
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|
365 | (2) |
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367 | (1) |
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367 | (1) |
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368 | (3) |
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|
371 | (1) |
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The origins of human differences |
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|
371 | (2) |
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|
373 | (3) |
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|
376 | (1) |
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|
377 | (1) |
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|
377 | (1) |
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Are humans still evolving? |
|
|
378 | (1) |
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|
379 | (1) |
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|
380 | (1) |
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|
380 | (1) |
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|
381 | (12) |
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The achievements of evolutionary science |
|
|
382 | (1) |
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|
382 | (1) |
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|
383 | (1) |
|
The mechanisms of speciation |
|
|
384 | (1) |
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|
385 | (1) |
|
The speed of evolutionary change and noncanonical heritability |
|
|
385 | (2) |
|
The origins of novel phenotypes |
|
|
387 | (1) |
|
Neurobiology and behaviour |
|
|
387 | (1) |
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|
387 | (1) |
|
The evolutionary future of Homo sapiens |
|
|
388 | (1) |
|
Is the human species still evolving |
|
|
388 | (1) |
|
The effect of humans on the planet |
|
|
389 | (1) |
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|
390 | (1) |
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|
391 | (2) |
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|
393 | (67) |
|
Appendix 1 Systems Biology |
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|
395 | (8) |
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|
396 | (1) |
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|
397 | (1) |
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Events within each level are complex |
|
|
398 | (1) |
|
There are interactions between levels |
|
|
398 | (1) |
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|
398 | (1) |
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A note on systems terminology |
|
|
399 | (2) |
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|
401 | (1) |
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|
401 | (2) |
|
Appendix 2 A History of Evolutionary Thought |
|
|
403 | (16) |
|
|
404 | (1) |
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The move to evolutionary thinking |
|
|
405 | (1) |
|
|
406 | (1) |
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Lamarck: The first evolutionary scientist |
|
|
407 | (2) |
|
|
409 | (2) |
|
The 19th century after Darwin |
|
|
411 | (2) |
|
|
413 | (2) |
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|
415 | (1) |
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416 | (1) |
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416 | (1) |
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417 | (1) |
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|
417 | (1) |
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|
417 | (1) |
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|
418 | (1) |
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Appendix 3 A Brief History of the World |
|
|
419 | (2) |
|
Appendix 4 Rocks, Dates, and Fossils |
|
|
421 | (6) |
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|
421 | (1) |
|
Ageing rocks (geochronology) |
|
|
422 | (1) |
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|
423 | (1) |
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|
424 | (2) |
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|
426 | (1) |
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|
426 | (1) |
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|
426 | (1) |
|
Appendix 5 Constructing Molecular Phytogenies |
|
|
427 | (6) |
|
Phylogenies based on shared/absent sequences |
|
|
427 | (1) |
|
Phylogenies based on distance matrices |
|
|
428 | (1) |
|
Phylogenies based on tree-searching methods |
|
|
429 | (1) |
|
|
429 | (1) |
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|
429 | (1) |
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|
430 | (1) |
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|
431 | (1) |
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|
431 | (1) |
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|
431 | (2) |
|
Appendix 6 Three Key Model Organisms: Mouse, Drosophila, and H. sapiens |
|
|
433 | (8) |
|
|
434 | (2) |
|
|
436 | (1) |
|
Similarities and differences |
|
|
437 | (1) |
|
|
438 | (1) |
|
|
438 | (1) |
|
|
438 | (3) |
|
Appendix 7 Some Principles of Animal Developmental Biology |
|
|
441 | (10) |
|
Driving developmental change |
|
|
444 | (1) |
|
|
445 | (1) |
|
|
446 | (2) |
|
The origins of anatomical differences |
|
|
448 | (1) |
|
The role of the genome in development |
|
|
449 | (1) |
|
|
450 | (1) |
|
|
450 | (1) |
|
|
450 | (1) |
|
Appendix 8 Evolution and Creationism |
|
|
451 | (9) |
|
|
452 | (1) |
|
|
452 | (1) |
|
Evolutionary criticisms of creationism |
|
|
453 | (3) |
|
|
456 | (1) |
|
|
456 | (1) |
|
The creationists' criticisms of evolution |
|
|
457 | (3) |
Conclusions |
|
460 | (1) |
Websites |
|
461 | (2) |
Glossary |
|
463 | (8) |
References |
|
471 | (26) |
Index |
|
497 | |