Preface to the Second Edition |
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xiii | |
Preface to the First Edition |
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xv | |
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1 | (22) |
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Phylogenetic Propositions |
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3 | (3) |
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6 | (1) |
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7 | (9) |
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8 | (1) |
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Organisms and Grouping of Organisms |
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9 | (2) |
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Phylogenetic History and Evolution |
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11 | (2) |
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13 | (2) |
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15 | (1) |
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Philosophy and Systematics |
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16 | (5) |
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The Form of Phylogenetic Hypotheses |
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19 | (2) |
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21 | (2) |
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Chapter 2 Species and Speciation |
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23 | (43) |
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What Is It to Be a Species? |
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24 | (3) |
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24 | (2) |
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26 | (1) |
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27 | (1) |
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27 | (12) |
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29 | (1) |
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The Evolutionary Species Concept |
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30 | (2) |
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Justifications for the ESC |
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32 | (1) |
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33 | (1) |
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Process-Based Concepts Emphasizing Reproductive Isolation |
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34 | (2) |
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Phylogenetic Species Concepts |
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36 | (1) |
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Some Additional Species Concepts |
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37 | (1) |
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Sorting through Species Concepts |
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38 | (1) |
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Speciation: Modes and Patterns |
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39 | (11) |
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41 | (1) |
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Allopartic Mode I: Vicariance |
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42 | (2) |
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Allopatric Speciation, Mode II Peripatric Speciation |
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44 | (1) |
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Distinguishing between Allopatric Modes of Speciation |
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44 | (5) |
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49 | (1) |
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49 | (1) |
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Identifying Modes of Speciation in the Fossil Record |
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50 | (4) |
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The Evolutionary Species Concept, Speciation, and Ecology |
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54 | (1) |
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Empirical Methods for Determining Species Limits |
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54 | (11) |
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55 | (6) |
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61 | (4) |
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65 | (1) |
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Chapter 3 Supraspecific Taxa |
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66 | (19) |
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Concepts of Naturalness and Supraspecific Taxa |
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67 | (1) |
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68 | (2) |
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Monophyly, Paraphyly and Polyphyly |
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70 | (2) |
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Hennig's Concepts Placed in History |
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72 | (1) |
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Natural Higher Taxa as Monophyletic Groups sensu Hennig (1966) |
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73 | (1) |
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Logical Consistency: The Hallmark of Proposed Natural Classifications |
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74 | (6) |
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Paraphyletic Groups Misrepresent Character Evolution |
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80 | (1) |
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Paraphyly and Polyphyly: Two Forms of Nonmonophyly |
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81 | (2) |
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Node-Based and Stem-Based Monophyly: Same Concept Different Graphs |
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83 | (1) |
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83 | (2) |
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85 | (22) |
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87 | (4) |
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Stem-Based Phylogenetic Trees |
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87 | (2) |
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Node-Based Phylogenetic Trees |
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89 | (2) |
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91 | (1) |
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92 | (7) |
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Nelson Trees in Phylogenetics |
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92 | (1) |
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From Nelson Trees to Phylogenetic Trees |
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93 | (6) |
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99 | (1) |
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Individuals versus Sets of Individuals Used in an Analysis |
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99 | (1) |
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Representing Character Evolution on Trees |
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100 | (1) |
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Unrooted Trees and Their Relationship to Phylogenetic Trees |
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101 | (1) |
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102 | (1) |
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Other Kinds of Tree Terminology |
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103 | (1) |
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Concepts of Monophyly and Trees |
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104 | (2) |
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106 | (1) |
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Chapter 5 Characters and Homology |
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107 | (45) |
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107 | (2) |
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Character States as Properties |
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109 | (1) |
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110 | (1) |
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Historical Character States as Properties |
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111 | (1) |
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Ahistorical Kind Properties |
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112 | (1) |
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Historical Groups and Natural Kinds |
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113 | (1) |
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114 | (8) |
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Haszprunar's Homology Synthesis |
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115 | (2) |
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Concepts of Homology in Systematics |
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117 | (1) |
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Phylogenetic Characters and Phylogenetic Homology: An Overview |
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118 | (1) |
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Taxic Homologies as Properties of Monophyletic Groups |
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119 | (2) |
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Transformational Homology: Linking Different Hypotheses of Qualitative Identity in a Transformation Series |
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121 | (1) |
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Discovering and Testing Homology |
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122 | (10) |
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124 | (1) |
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Similarity and Remane's Criteria |
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124 | (1) |
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Similarity in Position: Morphology |
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124 | (1) |
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Similarity in Position: Molecular Characters |
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125 | (4) |
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Special or Intrinsic Similarity |
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129 | (2) |
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Stacking Transformations: Intermediate Forms |
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131 | (1) |
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132 | (4) |
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Phylogenetic Homology (Forging Congruence between Hennig's and Patterson's Views) |
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136 | (1) |
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Avoiding Circularity: How Congruence Works |
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136 | (1) |
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137 | (13) |
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Qualitative versus Quantitative Characters: Avoiding Vague Characters |
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139 | (1) |
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Morphometrics and Phylogenetics |
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140 | (4) |
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Characters, Transformation Series, and Coding |
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144 | (3) |
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Complex Characters or Separate Characters? |
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147 | (1) |
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147 | (2) |
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Homology and "Presence-Absence" Coding |
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149 | (1) |
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150 | (2) |
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Chapter 6 Parsimony and Parsimony Analysis |
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152 | (51) |
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152 | (2) |
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Parsimony: Basic Principles |
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153 | (1) |
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154 | (1) |
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Classic Hennigian Argumentation |
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154 | (12) |
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156 | (6) |
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Example 1 The Phylogenetic Relationships of Leysera |
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162 | (4) |
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A Posteriori Character Argumentation |
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166 | (1) |
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Algorithmic versus Optimality Approaches |
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166 | (2) |
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Optimality-Driven Parsimony |
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168 | (1) |
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169 | (2) |
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171 | (5) |
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172 | (1) |
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Rearranging Tree Topologies |
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173 | (2) |
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175 | (1) |
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176 | (1) |
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Optimizing Characters on Trees |
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176 | (3) |
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177 | (1) |
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178 | (1) |
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179 | (9) |
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Example 2 Olenelloid Trilobites |
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184 | (4) |
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188 | (5) |
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Using Consensus Techniques to Compare Trees |
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193 | (2) |
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Statistical Comparisons of Trees |
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195 | (1) |
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Weighting Characters in Parsimony |
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196 | (3) |
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196 | (2) |
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198 | (1) |
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Weighting by Character Elimination |
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199 | (1) |
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Weighting: Concluding Remarks |
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199 | (1) |
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Phylogenetics Without Transformation? |
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199 | (3) |
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202 | (1) |
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Chapter 7 Parametric Phylogenetics |
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203 | (26) |
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Maximum Likelihood Techniques |
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205 | (14) |
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209 | (1) |
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Likelihood in Phylogenetics: An Intuitive Introduction |
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210 | (2) |
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Likelihood in Phylogenetics: A More Formal Introduction |
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212 | (6) |
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218 | (1) |
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219 | (7) |
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Interpreting Models in a Phylogenetic Context |
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226 | (1) |
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227 | (2) |
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Chapter 8 Phylogenetic Classification |
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229 | (31) |
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Classificaitons: Some General Types |
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230 | (3) |
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Classification of Natural Kinds |
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230 | (1) |
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Historical Classifications (Systematizations) |
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231 | (2) |
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Convenience Classifications |
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233 | (1) |
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Biological Classifications |
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233 | (1) |
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Constituents and Grouping in Phylogenetic Classifications |
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233 | (1) |
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234 | (11) |
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Definition of Linnean Higher Categories |
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235 | (1) |
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Conventions for Annotated Linnean Classifications |
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236 | (5) |
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Ancestors in Phylogenetic Classification |
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241 | (3) |
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Species and Higher Taxa of Hybrid Origin |
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244 | (1) |
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Alternative Methods of Classifying in the Phylogenetics Community |
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245 | (3) |
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248 | (7) |
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250 | (3) |
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Stability of Names Relative to Clade Content |
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253 | (2) |
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255 | (2) |
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The Future of Linnean Nomenclature |
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257 | (1) |
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Alternative "Schools" and Logical Consistency |
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258 | (1) |
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258 | (2) |
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Chapter 9 Historical Biogeography |
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260 | (56) |
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The Distinction between Ecological and Phylogenetic Biogeography and the Importance of Congruence |
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261 | (3) |
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Hierarchies of Climate and Geological Change and Their Relationship to Phylogenetic Biogeographic Patterns and Processes |
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264 | (1) |
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The Importance of Vicariance in the Context of Evolutionary Theory |
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265 | (1) |
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The Importance of "Dispersal" in Phylogenetic Biogeography |
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265 | (6) |
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Geodispersal: Not Dispersal |
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266 | (4) |
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Historical Perspective on Geodispersal and the Cyclical Nature of Oscillations between Vicariance and Geodispersal |
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270 | (1) |
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271 | (7) |
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"Area" as It Relates to Phylogenetic Biogeographic Analysis |
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274 | (3) |
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The Boundaries of Biotic Areas and Comparing the Geographic Ranges of Taxa |
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277 | (1) |
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278 | (1) |
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Analytical Methods in Phylogenetic Biogeography |
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278 | (2) |
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Historical Biogeography Using Modified Brooks Parsimony Analysis |
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280 | (13) |
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282 | (3) |
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Steps 1 and 2 Fitch Optimization of Area States on a Phylogeny |
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285 | (3) |
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288 | (1) |
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Step 3.1 The Vicariance Matrix |
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288 | (1) |
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Step 3.2 The Dispersal Matrix |
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289 | (1) |
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Steps 4 and 5 MBPA Analyses and Comparison |
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290 | (3) |
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Alternative Biogeographic Methods |
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293 | (4) |
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How Extinction Affects Our Ability to Study Biogeographic Patterns in the Extant Biota |
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297 | (4) |
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Statistical Approaches to Biogeographic Analysis |
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301 | (4) |
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Tracking Biogeographic Change within a Single Clade |
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305 | (2) |
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Phylogeography: Within Species Biogeography |
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307 | (1) |
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The Biogeography of Biodiversity Crises |
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308 | (2) |
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A Brief History of the Events Influencing Our Present Concepts of Historical Biogeography |
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310 | (1) |
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Fundamental Divisions in Biogeography, a Pre-Evolutionary Context, or What Causes Biogeographic Patterns, Vicariance or Dispersal? |
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310 | (2) |
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The Growing Evolutionary Perspective and the Continued Debate About Vicariance and Dispersal |
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312 | (2) |
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314 | (2) |
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Chapter 10 Specimens and Curation |
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316 | (15) |
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Specimens, Vouchers, and Samples |
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316 | (3) |
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The Need for Voucher Specimens |
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317 | (1) |
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318 | (1) |
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318 | (1) |
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318 | (1) |
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Access to Specimens in the Age of the Internet |
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318 | (1) |
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Collecting and Collection Information |
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319 | (3) |
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321 | (1) |
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The Systematics Collection |
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322 | (4) |
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322 | (1) |
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323 | (1) |
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Receipt of Specimens, Accessing the Collections, and Initial Sorting |
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323 | (1) |
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324 | (1) |
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324 | (1) |
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324 | (1) |
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Arrangements of Collections |
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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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The Responsibility of Curators |
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326 | (1) |
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The Importance of Museum Collections |
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326 | (1) |
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Integrating Biodiversity and Ecological Data |
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327 | (2) |
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A Simple Example: Range Predictions |
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328 | (1) |
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Predicting Species Invasions |
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329 | (1) |
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329 | (1) |
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329 | (2) |
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Chapter 11 Publication and Rules of Nomenclature |
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331 | (18) |
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Kinds of Systematic Literature |
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331 | (3) |
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Descriptions of New Species |
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331 | (1) |
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332 | (1) |
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332 | (1) |
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Faunistic and Floristic Works |
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332 | (1) |
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333 | (1) |
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333 | (1) |
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333 | (1) |
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Handbooks and Field Guides |
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334 | (1) |
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334 | (1) |
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334 | (1) |
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334 | (3) |
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334 | (1) |
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335 | (2) |
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Publication of Systematic Studies |
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337 | (8) |
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Major Features of the Formal Taxonomic Work |
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338 | (1) |
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338 | (1) |
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339 | (1) |
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340 | (1) |
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340 | (1) |
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341 | (1) |
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Illustrations and Graphics |
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341 | (1) |
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Comparisons and Discussion |
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342 | (1) |
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342 | (1) |
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343 | (1) |
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343 | (1) |
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344 | (1) |
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344 | (1) |
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The Rules of Nomenclature |
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345 | (3) |
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Basic Nomenclatural Concepts |
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346 | (1) |
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346 | (1) |
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Correct Name and Valid Name |
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346 | (1) |
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347 | (1) |
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347 | (1) |
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Conserved Names (Nomen conservadum) |
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347 | (1) |
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347 | (1) |
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347 | (1) |
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347 | (1) |
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348 | (1) |
Literature Cited |
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349 | (41) |
Index |
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390 | |