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PART I The C-value Enigma |
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Genome Size Evolution in Animals |
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Why Should Anyone Care about Genome Size? |
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4 | (1) |
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Genome Size in Animals: A Historical Perspective |
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5 | (5) |
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5 | (1) |
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``A Remarkable Constancy'' and the Origin of the ``C-value'' |
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6 | (1) |
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7 | (2) |
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The Modern View: From Paradox to Puzzle |
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9 | (1) |
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The State of Knowledge of Animal Genome Size |
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10 | (2) |
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The Animal Genome Size Database |
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10 | (2) |
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12 | (12) |
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Vertebrates (and Nonvertebrate Chordates) |
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12 | (4) |
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16 | (8) |
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Intraspecific Variation in Animals |
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24 | (3) |
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Mechanisms of Genome Size Change |
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27 | (13) |
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``Selfish DNA'' and the Spread of Transposable Elements |
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27 | (2) |
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``Junk DNA'' and the Accumulation of Pseudogenes |
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29 | (2) |
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31 | (1) |
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31 | (1) |
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Polyploidy, C-value, and Genome Size |
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32 | (2) |
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Sentinel Sequences and Global Forces |
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34 | (1) |
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Insertion--Deletion Biases |
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35 | (4) |
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Genome Size and G+C Content |
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39 | (1) |
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Assessing the Directionality of Animal Genome Size Evolution |
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40 | (1) |
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Genome Size and Cell Size |
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41 | (11) |
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Explaining the Correlation |
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48 | (4) |
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Genome Size and Organismal Phenotypes |
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52 | (15) |
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53 | (1) |
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54 | (6) |
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60 | (2) |
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62 | (2) |
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64 | (2) |
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66 | (1) |
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Measuring Animal Genome Sizes |
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67 | (4) |
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67 | (1) |
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Feulgen Microdensitometry |
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68 | (1) |
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Feulgen Image Analysis Densitometry |
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69 | (1) |
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What about Genome Sequencing? |
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69 | (2) |
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Concluding Remarks and Future Prospects |
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71 | (19) |
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Genome Size Evolution in Plants |
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A Brief History of Genome Size Study in Plants |
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90 | (4) |
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The First Estimates of DNA Amounts |
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90 | (2) |
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The Main Areas of Focus of Early Genome Size Studies |
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92 | (1) |
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Impact of the Molecular Revolution on Genome Size Research |
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93 | (1) |
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Genome Size Studies in the Post-Genomic Era |
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94 | (1) |
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The State of Knowledge Regarding Plant Genome Sizes |
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94 | (4) |
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C-values in Cyberspace: Development of the Plant DNA C-values Database |
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95 | (1) |
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Uses and Users of the Plant DNA C-values Database |
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96 | (2) |
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Patterns in Plant Genome Size Evolution |
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98 | (5) |
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The Extent of Variation across Plant Taxa |
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98 | (1) |
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Genome Size in a Phylogenetic Context |
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99 | (4) |
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How Do Plant Genome Sizes Evolve? |
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103 | (11) |
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Sequences Responsible for the Range of Genome Sizes Encountered in Plants |
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105 | (1) |
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What Triggers the Spread of Transposable Elements? |
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106 | (3) |
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109 | (1) |
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Genome Size Increase by Polyploidy |
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109 | (3) |
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Mechanisms of Genome Size Decrease |
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112 | (2) |
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Key Correlates of Genome Size across Plant Species |
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114 | (15) |
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Early Work on the Phenotypic Consequences of Genome Size Variation in Plants |
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114 | (2) |
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116 | (2) |
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118 | (1) |
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118 | (1) |
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119 | (2) |
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Causation at the Cellular Level: The Nucleotype Concept |
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121 | (1) |
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122 | (2) |
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Minimum Generation Time and Developmental Lifestyle |
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124 | (4) |
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Physiology and Climate Response |
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128 | (1) |
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Ecological and Evolutionary Implications of Genome Size Variation |
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129 | (5) |
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Geographical Distribution and the Large Genome Constraint Hypothesis |
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130 | (2) |
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Genome Size and Plant Response to Human Environmental Change |
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132 | (2) |
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Intraspecific Variation in Genome Size |
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134 | (7) |
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Overview of Intraspecific Variation |
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134 | (2) |
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Genuine Intraspecific Variation in Angiosperms |
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136 | (1) |
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The Special Case of Maize |
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137 | (1) |
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Genuine Intraspecific Variation in Nonangiosperms |
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138 | (1) |
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Intraspecific Variation and Speciation |
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139 | (1) |
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The Mystery of DNA Constancy |
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140 | (1) |
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Methodology for Estimating Genome Size in Plants |
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141 | (8) |
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Chemical Extraction and Reassociation Kinetics |
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141 | (1) |
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Feulgen Microdensitometry |
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142 | (2) |
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Feulgen Image Analysis Densitometry |
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144 | (1) |
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145 | (2) |
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Complete Genome Sequencing |
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147 | (1) |
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Some Comments on Plant Genome Size Standards |
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148 | (1) |
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Concluding Remarks and Future Prospects |
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149 | (16) |
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Expansion of the Plant Genome Size Dataset |
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150 | (1) |
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151 | (1) |
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Ecological and Environmental Questions |
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151 | (1) |
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151 | (14) |
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PART II The Evolution of Genomic Parasites |
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A Brief History of the Study of Transposable Elements |
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165 | (5) |
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The Discovery of Transposable Elements |
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166 | (1) |
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Early TE Studies in Bacteria |
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167 | (1) |
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Early TE Studies in Fungi |
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167 | (1) |
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Early TE Studies in Plants |
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168 | (1) |
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Early TE Studies in Animals |
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168 | (1) |
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A Recent Explosion of New Information from DNA Sequencing |
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169 | (1) |
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Who Cares about Transposable Elements? |
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170 | (1) |
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170 | (10) |
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Autonomous and Nonautonomous Elements |
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170 | (1) |
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Classification Based on Mode of Transposition |
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171 | (8) |
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The Relationship Between Class I and II Elements |
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179 | (1) |
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Hallmarks of TE Sequences |
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180 | (2) |
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Dispersed Multigene Families |
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180 | (1) |
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180 | (1) |
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180 | (1) |
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Coding Regions and Motifs |
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181 | (1) |
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Fixed and Segregating Insertion Sites |
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182 | (1) |
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Methods Used in the Identification and Study of TEs |
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182 | (4) |
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Genetic Analysis of Naturally Occurring Unstable Mutations |
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182 | (1) |
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Methods of Molecular Analysis |
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183 | (1) |
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Data from Genome Sequencing Projects |
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184 | (1) |
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Reconstruction of Ancestral TEs from Incomplete Contemporary Copies |
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185 | (1) |
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Databases for Repetitive DNA Sequences |
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185 | (1) |
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185 | (1) |
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Applications of TEs to Other Areas of Biology |
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186 | (2) |
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Transformation Systems Based on Transposable Elements |
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186 | (1) |
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Transposable Element Mutagenesis and Gene Tagging |
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186 | (1) |
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Transposable Elements as Markers in Evolutionary Studies |
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187 | (1) |
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The Use of Mobile Introns for Targeted Gene Manipulation |
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188 | (1) |
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The Prevalence of TEs in Eukaryotic Genomes |
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188 | (5) |
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188 | (1) |
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189 | (1) |
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Examples of Common TEs in Familiar Organisms |
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189 | (4) |
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The Distribution of TEs Within Genomes |
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193 | (4) |
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Selection as a Mechanism for Reducing TE Copy Number |
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193 | (1) |
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The Role of Recombination in Determining TE Distributions |
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194 | (1) |
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TE Frequencies in Euchromatin and Heterochromatin |
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195 | (1) |
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Inter- and Intrachromosomal Variation in TE Density |
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195 | (1) |
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TE Target Site Specificities |
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196 | (1) |
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The Dynamics of TE Evolution |
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197 | (4) |
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Long-Term Evolution and TE Life Cycles |
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197 | (1) |
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Mechanisms of Spread and Loss |
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198 | (3) |
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Regulation of TE Activity |
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201 | (4) |
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Element-Mediated Regulation |
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201 | (1) |
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Host-Mediated Regulation of TE Activity |
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202 | (1) |
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Repeat-Induced Gene Silencing |
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203 | (1) |
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Disruption of TE Regulation by Environmental Stresses |
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204 | (1) |
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A Continuum of TE-Host Interactions from Parasitism to Mutualism |
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205 | (1) |
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TEs as Mutagens and Sources of Genomic Variation |
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205 | (8) |
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Coding Sequences and the Evolution of Novel Host Genes |
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205 | (2) |
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207 | (1) |
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207 | (1) |
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Gene Regulatory Sequences |
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207 | (1) |
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208 | (1) |
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209 | (1) |
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210 | (1) |
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211 | (1) |
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212 | (1) |
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Concluding Remarks and Future Prospects |
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213 | (11) |
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A Brief History of the Study of B Chromosomes |
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224 | (3) |
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224 | (1) |
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What is a ``B Chromosome''? |
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225 | (1) |
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B Chromosomes as Genomic Parasites |
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225 | (2) |
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The Frequency of B Chromosome Infection |
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227 | (6) |
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How Widely Distributed Are B Chromosomes? |
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227 | (3) |
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The Likelihood of Infection |
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230 | (1) |
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Variation in the Intensity of Infection |
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230 | (3) |
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The Biology of B Chromosomes |
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233 | (13) |
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233 | (1) |
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234 | (1) |
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234 | (6) |
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240 | (2) |
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242 | (3) |
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245 | (1) |
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The Origin(s) of B Chromosomes |
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246 | (6) |
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Derivation from A Chromosomes |
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247 | (1) |
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248 | (1) |
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249 | (1) |
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249 | (1) |
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Accumulation of Transposable Elements |
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250 | (1) |
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Similarities to Sex Chromosomes: Analogy or Homology? |
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251 | (1) |
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252 | (1) |
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Interactions with the Host Genome |
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252 | (9) |
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Effects on Gene Expression |
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253 | (1) |
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Recombination in A Chromosomes |
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253 | (3) |
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256 | (2) |
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258 | (2) |
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260 | (1) |
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Interactions with the Host Organism |
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261 | (4) |
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Impacts on the Cellular and Organismal Phenotypes |
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261 | (2) |
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B Chromosomes and Host Reproductive Mode |
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263 | (1) |
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264 | (1) |
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264 | (1) |
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The Dynamics of B Chromosome Evolution |
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265 | (8) |
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The B Chromosome Life Cycle |
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265 | (3) |
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The Life Spans of B Chromosomes |
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268 | (2) |
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Can B Chromosomes Become Beneficial? |
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270 | (1) |
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Can B Chromosomes Integrate into the Standard Genome? |
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271 | (2) |
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Concluding Remarks and Future Prospects |
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273 | (17) |
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PART III Duplications, Duplications... |
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Small-Scale Gene Duplications |
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The Long Pedigree of Gene Duplication Research |
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290 | (8) |
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Early Chromosomal Studies |
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290 | (4) |
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Studies at the Protein Level: Evidence for Gene Duplication and Divergence from Isozymes |
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294 | (1) |
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The Advent of PCR and DNA Sequencing |
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294 | (2) |
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Gene Duplications in the Post-Genomic Era |
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296 | (2) |
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Mechanisms of Gene Duplication |
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298 | (3) |
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298 | (1) |
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Duplicative Transposition |
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298 | (2) |
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300 | (1) |
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The Life and Death of Gene Duplicates in the Genome |
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301 | (5) |
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The Birth and Death of Gene Duplicates |
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301 | (1) |
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The Evolution of Gene Families |
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302 | (3) |
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The Contribution of Gene Duplication to Genome Structure |
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305 | (1) |
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What Happens to Duplicated Genes? |
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306 | (10) |
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306 | (1) |
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306 | (2) |
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308 | (2) |
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Changes in Expression Patterns |
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310 | (2) |
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312 | (2) |
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314 | (2) |
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316 | (1) |
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Hox Gene Duplication and the Evolution of Animal Development |
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316 | (3) |
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The General Evolutionary Importance of Gene Duplications |
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319 | (1) |
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Concluding Remarks and Future Prospects |
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320 | (10) |
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Large-Scale Gene and Ancient Genome Duplications |
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Historical Perspectives on the Importance of Large-Scale Duplications |
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330 | (1) |
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Mechanisms of Large-Scale Duplication |
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331 | (3) |
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331 | (1) |
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332 | (1) |
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333 | (1) |
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334 | (1) |
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334 | (1) |
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How Large-Scale Gene Duplications Are Studied |
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334 | (10) |
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Identification of Block Duplications |
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334 | (1) |
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335 | (5) |
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Hidden Duplications, Ghost Duplications, and Multiplicons |
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340 | (3) |
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Genomic Profiles: An Extension to the Map-Based Approach |
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343 | (1) |
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Dating Duplication Events |
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344 | (3) |
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Absolute Dating Based on Synonymous Substitutions |
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345 | (1) |
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345 | (1) |
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Dating by Phylogenetic Means |
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346 | (1) |
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Putting Theory into Practice: Evidence for Large-Scale Gene Duplication Events |
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347 | (9) |
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1R/2R: Genome Duplications in Vertebrates |
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348 | (2) |
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3R: An Additional Round of Genome Duplication in Teleost Fishes |
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350 | (4) |
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Ancient Genome Duplications in Plants |
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354 | (2) |
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Large-Scale Duplications in the Evolutionary Process |
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356 | (7) |
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The Maintenance of Duplicated Genes |
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356 | (2) |
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Which Genes Are Maintained, and Why? |
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358 | (1) |
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The Maintenance of Duplicated Genomes |
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359 | (2) |
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Speciation and Divergent Resolution |
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361 | (2) |
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Concluding Remarks and Future Prospects |
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363 | (9) |
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PART IV ...And More Duplications |
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History of the Study of Polyploidy in Plants |
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372 | (1) |
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373 | (6) |
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379 | (5) |
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How Common Is Polyploidy in Plants? |
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379 | (4) |
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The Frequency of Allopolyploidy versus Autopolyploidy |
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383 | (1) |
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Polyploid Formation and Establishment |
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384 | (6) |
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Mechanisms and Chances of Formation |
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384 | (4) |
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Likelihood of Establishment |
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388 | (2) |
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Multiple Origins of Polyploid Species |
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390 | (6) |
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The Rule, Not the Exception |
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390 | (4) |
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Genotypic and Phenotypic Consequences of Multiple Origins |
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394 | (1) |
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A Case of Particular Interest: The Arctic Flora |
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395 | (1) |
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Impacts of Polyploidization at the Cellular and Organismal Levels |
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396 | (8) |
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397 | (1) |
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398 | (2) |
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Physiology and Development |
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400 | (1) |
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401 | (1) |
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Plant-Animal Interactions |
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402 | (2) |
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Impacts of Polyploidization at the Genome Level |
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404 | (10) |
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405 | (2) |
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Genomic Downsizing and ``Diploidization'' |
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407 | (1) |
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The Fates of Plant Genes Duplicated by Polyploidy |
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408 | (5) |
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413 | (1) |
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Nuclear-Cytoplasmic Interactions |
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413 | (1) |
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Concluding Remarks and Future Prospects |
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414 | (14) |
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The Origins and Classification of Polyploid Animals |
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428 | (1) |
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Autopolyploidy and Allopolyploidy |
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428 | (1) |
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429 | (4) |
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Chromosome Number and Nuclear DNA Content |
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429 | (1) |
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430 | (1) |
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Meiotic Chromosome Behavior |
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430 | (2) |
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432 | (1) |
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Why Is Polyploidy Less Common in Animals than in Plants? |
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433 | (7) |
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Disruption of Sex Determination |
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434 | (2) |
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Degenerate Sex Chromosomes and Dosage Compensation |
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436 | (1) |
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Impediments to Meiotic Disjunction |
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437 | (1) |
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Interploidy Crosses and Triploid Sterility |
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438 | (1) |
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Disruption of Development |
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438 | (1) |
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Not Enough Hybridization . . . or Maybe Too Much? |
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439 | (1) |
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440 | (1) |
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Polyploidy and Unisexuality |
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440 | (4) |
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441 | (1) |
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Why Are Polyploidy and Unisexuality Linked? |
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442 | (2) |
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Polyploidy in Vertebrates |
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444 | (1) |
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444 | (1) |
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445 | (1) |
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445 | (1) |
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446 | (1) |
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447 | (14) |
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An Entire Family of Polyploids: Salmonidae |
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448 | (3) |
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Another Entirely Polyploid Family: Catostomidae |
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451 | (1) |
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Several Species of Polyploids: Cyprinidae |
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452 | (4) |
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Special Cases: Poeciliidae |
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456 | (3) |
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Miscellaneous Polyploid Fishes |
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459 | (2) |
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461 | (11) |
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Diploid-Polyploid Species Pairs in Frogs |
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462 | (7) |
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Polyploidy in Salamanders: Ambystomatidae |
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469 | (2) |
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A Polyploid Family of Salamanders (?): Sirenidae |
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471 | (1) |
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472 | (1) |
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472 | (3) |
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473 | (2) |
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475 | (1) |
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475 | (2) |
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Vertebrate Polyploids: A Summary |
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477 | (1) |
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Polyploidy in Invertebrates |
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478 | (1) |
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478 | (2) |
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Water Fleas (Order Cladocera) |
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479 | (1) |
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Brine Shrimp (Order Anostraca) |
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480 | (1) |
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480 | (6) |
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486 | (4) |
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487 | (1) |
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488 | (2) |
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490 | (3) |
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493 | (1) |
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Miscellaneous Invertebrates |
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494 | (2) |
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494 | (1) |
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495 | (1) |
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495 | (1) |
|
|
|
496 | (1) |
|
Polyploidy and Geographic Distribution in Invertebrates |
|
|
496 | (4) |
|
|
|
497 | (1) |
|
|
|
498 | (1) |
|
Physiology, Development, and Ecology |
|
|
499 | (1) |
|
|
|
499 | (1) |
|
The Evolutionary Fate of Polyploids |
|
|
500 | (1) |
|
Concluding Remarks and Future Prospects |
|
|
501 | (21) |
|
PART V Sequence and Structure |
|
|
|
Comparative Genomics in Eukaryotes |
|
|
|
|
|
|
|
The Early History of Comparative Eukaryotic Genomics |
|
|
522 | (11) |
|
The Basics of Eukaryotic Chromosome Structure |
|
|
522 | (2) |
|
Karyotyping: The Beginning of Comparative Genomics |
|
|
524 | (7) |
|
|
|
531 | (2) |
|
Working with Eukaryotic Genomes |
|
|
533 | (3) |
|
Mapping: Genetic and Physical |
|
|
534 | (1) |
|
Sequencing: The Holy Grail of Comparative Genomics |
|
|
534 | (1) |
|
Annotation: Making Biological Sense of the Letters |
|
|
535 | (1) |
|
The Genesis of Large-Scale Sequencing Projects for Eukaryotes |
|
|
536 | (5) |
|
Sequencing the Human Genome: The Most Ambitious Idea |
|
|
536 | (1) |
|
Private versus Public Efforts |
|
|
537 | (4) |
|
Genome Sequencing in Fungi |
|
|
541 | (3) |
|
Saccharomyces cerevisiae: The First Eukaryote to Be Sequenced |
|
|
541 | (1) |
|
Other Fungal Sequencing Projects |
|
|
542 | (2) |
|
Caenorhabditis elegans and Drosophila melanogaster: The First Animal Genomes to Be Sequenced |
|
|
544 | (2) |
|
|
|
544 | (2) |
|
|
|
546 | (1) |
|
|
|
546 | (9) |
|
Genome Variation in Human Populations |
|
|
552 | (2) |
|
|
|
554 | (1) |
|
The Mouse and Rat Genomes: The Rise of Modern Mammalian Comparative Genomics |
|
|
555 | (4) |
|
Genome Sequencing in Plants and Their Pathogens |
|
|
559 | (3) |
|
Comparative Genomics of Arabidopsis |
|
|
559 | (1) |
|
|
|
560 | (2) |
|
The Rice Blast Fungus: Magnaporthe grisea |
|
|
562 | (1) |
|
Other Invertebrate Animal Genomes |
|
|
562 | (2) |
|
|
|
562 | (1) |
|
The Sea Squirt: A Primitive Chordate |
|
|
563 | (1) |
|
Genomewide Duplications in Vertebrates? |
|
|
564 | (1) |
|
|
|
564 | (2) |
|
Encephalitozoon cuniculi: A Parasitic Eukaryote with a Tiny Genome |
|
|
564 | (1) |
|
Plasmodium: The Malaria Pathogen |
|
|
565 | (1) |
|
Dictyostelium: The ``Slime Mold'' |
|
|
566 | (1) |
|
Comparative Genomics and Phylogenetics in Eukaryotes |
|
|
566 | (3) |
|
Concluding Remarks and Future Prospects |
|
|
569 | (17) |
|
Complete Genome Sequencing |
|
|
569 | (3) |
|
Partial-Genome Comparisons |
|
|
572 | (1) |
|
|
|
573 | (1) |
|
|
|
574 | (12) |
|
Comparative Genomics in Prokaryotes |
|
|
|
|
|
|
|
|
|
586 | (4) |
|
Classifying Prokaryotes the Old-Fashioned Way |
|
|
586 | (3) |
|
The Deepest Split of All? |
|
|
589 | (1) |
|
The Rise of Complete Prokaryotic Genome Sequencing |
|
|
590 | (3) |
|
|
|
590 | (2) |
|
The Prokaryote Genome Sequencing Explosion |
|
|
592 | (1) |
|
General Insights about Prokaryote Genomes |
|
|
593 | (13) |
|
Genome Organization: Assumptions and Exceptions |
|
|
594 | (2) |
|
Structure of Prokaryotic Chromosomal DNA |
|
|
596 | (1) |
|
DNA Replication in Prokaryotes |
|
|
597 | (1) |
|
|
|
597 | (4) |
|
Gene Order: Plasticity and Stability |
|
|
601 | (2) |
|
|
|
603 | (3) |
|
|
|
606 | (1) |
|
Horizontal Transfer of Genetic Material |
|
|
606 | (10) |
|
Identifying and Characterizing Horizontal Transfers |
|
|
607 | (1) |
|
Transfer from Viruses to Bacteria: Prophages in Bacterial Genomes |
|
|
608 | (2) |
|
|
|
610 | (2) |
|
|
|
612 | (3) |
|
Implications for Prokaryote Evolution and the Study Thereof |
|
|
615 | (1) |
|
Highlights from Specific Prokaryote Genome Sequencing Projects |
|
|
616 | (15) |
|
Haemophilus influenzae (1995) |
|
|
617 | (1) |
|
Methanocaldococcus jannaschii (1996) |
|
|
618 | (1) |
|
|
|
619 | (2) |
|
Mycobacterium tuberculosis (1998) |
|
|
621 | (1) |
|
Drinococcus radiodurans (1999) |
|
|
622 | (1) |
|
|
|
623 | (1) |
|
Streptococcus spp. (2001) |
|
|
624 | (3) |
|
Streptomyces coelicolor (2002) |
|
|
627 | (1) |
|
Bacillus anthracis (2003) |
|
|
628 | (2) |
|
|
|
630 | (1) |
|
The Evolution of Genome Size in Prokaryotes |
|
|
631 | (10) |
|
Factors that Limit Prokaryote Genome Size |
|
|
634 | (2) |
|
Mechanisms of Genome Size Increase |
|
|
636 | (1) |
|
Genome Reductions in Obligate Parasites and Endosymbionts |
|
|
637 | (3) |
|
Bacteria, Organelles, or Something in Between? |
|
|
640 | (1) |
|
The Minimal Genome Concept |
|
|
641 | (4) |
|
|
|
642 | (2) |
|
|
|
644 | (1) |
|
Genomic Insights into Prokaryotic Abundance and Diversity |
|
|
645 | (6) |
|
What Is a Prokaryotic Species? |
|
|
645 | (1) |
|
Genetic Delineation of Species |
|
|
646 | (1) |
|
Genomic Perspectives on Prokaryote Diversity |
|
|
647 | (2) |
|
Shotgun First, Ask Questions Later |
|
|
649 | (2) |
|
Applications of Prokaryote Genomics |
|
|
651 | (5) |
|
|
|
651 | (3) |
|
Industry and the Environment |
|
|
654 | (1) |
|
Agriculture and Food Production |
|
|
655 | (1) |
|
|
|
655 | (1) |
|
Concluding Remarks and Future Prospects |
|
|
656 | (24) |
|
Which Prokaryotes Can (or Cannot) Be Sequenced? |
|
|
657 | (1) |
|
Policy Issues: From Sequence Completeness to Bioterrorism |
|
|
658 | (2) |
|
Prokaryote Genomics: The End of the Beginning |
|
|
660 | (20) |
|
PART VI The Genome in Evolution |
|
|
|
Macroevolution and the Genome |
|
|
|
|
|
Part One---Macroevolutionary Theory and Genome Evolution |
|
|
680 | (1) |
|
A Brief History of Evolutionary Theory |
|
|
680 | (4) |
|
From Darwin to Neo-Darwinism |
|
|
680 | (2) |
|
Genomes, Fossils, and Theoretical Inertia |
|
|
682 | (2) |
|
Is a Theory of Macroevolution Necessary? |
|
|
684 | (9) |
|
Microevolution, Macroevolution, and Extrapolationism |
|
|
684 | (2) |
|
Critiques of Strict Extrapolationism |
|
|
686 | (6) |
|
Reductionism in the Post-Genomic Era |
|
|
692 | (1) |
|
The Structure of Macroevolutionary Theory |
|
|
693 | (5) |
|
|
|
694 | (1) |
|
Species Selection: Concepts and Challenges |
|
|
694 | (1) |
|
Aggregate versus Emergent Characters |
|
|
695 | (1) |
|
|
|
696 | (1) |
|
Bottom-up Processes: The Effect Hypothesis versus Emergent Fitness |
|
|
696 | (1) |
|
Top-down Processes: Context-dependent Sorting |
|
|
697 | (1) |
|
Macroevolutionary Theory: A Summary |
|
|
698 | (1) |
|
A Macroevolutionary Look at the Genome |
|
|
698 | (10) |
|
Did the Genome Originate by Group Selection? |
|
|
698 | (2) |
|
Genomic Parasites Require a Hierarchical Interpretation |
|
|
700 | (4) |
|
Genome Size, Emergent Fitness, and an Upside-down Acid Test |
|
|
704 | (2) |
|
Context-dependent Sorting of Genes and Nongenes |
|
|
706 | (1) |
|
Genomes in the Evolutionary Hierarchy |
|
|
707 | (1) |
|
Part Two---``Nonstandard'' Genomic Processes and Major Evolutionary Transitions |
|
|
708 | (1) |
|
The Origin of Genomes and Cells |
|
|
709 | (1) |
|
|
|
709 | (1) |
|
|
|
710 | (2) |
|
|
|
710 | (1) |
|
Increased Genetic Complexity |
|
|
711 | (1) |
|
The Origin of Multicellularity and the Emergence of Complex Metazoa |
|
|
712 | (2) |
|
Transposable Elements and Gene Regulation |
|
|
712 | (1) |
|
Spliceosomal Introns and Exon Shuffling |
|
|
712 | (1) |
|
Gene Duplication and Developmental Complexity |
|
|
713 | (1) |
|
The Evolution of Immunity |
|
|
714 | (1) |
|
The Origin of Vertebrates |
|
|
715 | (1) |
|
|
|
715 | (1) |
|
Silencing and/or Splicing |
|
|
716 | (1) |
|
|
|
716 | (4) |
|
Diversity in Gene Expression |
|
|
717 | (1) |
|
|
|
717 | (2) |
|
Gene Duplication and Back Again |
|
|
719 | (1) |
|
Nonstandard Genomic Processes: A Summary |
|
|
719 | (1) |
|
Concluding Remarks and Future Prospects |
|
|
720 | (11) |
|
From Reductionism to Integrationism |
|
|
720 | (1) |
|
A Post-Genomic Evolutionary Synthesis |
|
|
721 | (1) |
|
Genomes and the Future of Biology |
|
|
722 | (9) |
| Index |
|
731 | |