Phylogenetics (eBook, PDF)
Theory and Practice of Phylogenetic Systematics
Phylogenetics (eBook, PDF)
Theory and Practice of Phylogenetic Systematics
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The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as the first, with many exciting developments yet to come. This new…mehr
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- Produktdetails
- Verlag: John Wiley & Sons
- Seitenzahl: 432
- Erscheinungstermin: 22. September 2011
- Englisch
- ISBN-13: 9781118017869
- Artikelnr.: 38230890
- Verlag: John Wiley & Sons
- Seitenzahl: 432
- Erscheinungstermin: 22. September 2011
- Englisch
- ISBN-13: 9781118017869
- Artikelnr.: 38230890
Introduction. Phylogenetic Propositions. Topics Covered. Terms and
Concepts. Disciplines. Organisms and Grouping of Organisms. Phylogenetic
History and Evolution. Attributes of Organisms. Classification. Philosophy
and Systematics. The Form of Phylogenetic Hypotheses. Chapter Summary.
Chapter 2. Species and Speciation. What Is It to Be a Species? Species as
Kinds. Species as Sets. Species as Individuals. Species Concepts.
Process-Based Concepts. The Evolutionary Species Concept. Justifications
for the ESC. Variations on the ESC. Process-Based Concepts Emphasizing
Reproductive Isolation. Phylogenetic Species Concepts. Some Additional
Species Concepts. Sorting through Species Concepts. Speciation: Modes and
Patterns. Allopartic Speciation. Allopartic Mode I: Vicariance. Allopatric
Speciation, Mode II Peripatric Speciation. Distinguishing between
Allopatric Modes of Speciation. Parapatric Speciation. Sympatric
Speciation. Identifying Modes of Speciation in the Fossil Record. The
Evolutionary Species Concept, Speciation, and Ecology. Empirical Methods
for Determining Species Limits. Nontree-Based Methods. Tree-Based Methods.
Chapter Summary. Chapter 3. Supraspecific Taxa. Concepts of Naturalness and
Supraspecific Taxa. The Natural Taxon. Monophyly, Paraphyly and Polyphyly.
Hennig's Concepts Placed in History. Natural Higher Taxa as Monophyletic
Groups sensu Hennig (1966). Logical Consistency: The Hallmark of Proposed
Natural Classifi cations. Paraphyletic Groups Misrepresent Character
Evolution. Paraphyly and Polyphyly: Two Forms of Nonmonophyly. Node-Based
and Stem-Based Monophyly: Same Concept Different Graphs. Chapter Summary.
Chapter 4. Tree Graphs. Phylogenetic Trees. Stem-Based Phylogenetic Trees.
Node-Based Phylogenetic Trees. Cyclic Graphs. Cladograms. Nelson Trees in
Phylogenetics. From Nelson Trees to Phylogenetic Trees. Gene Trees.
Individuals versus Sets of Individuals Used in an Analysis. Representing
Character Evolution on Trees. Unrooted Trees and Their Relationship to
Phylogenetic Trees. Node Rotation. Other Kinds of Tree Terminology.
Concepts of Monophyly and Trees. Chapter Summary. Chapter 5. Characters and
Homology. A Concept of Character. Character States as Properties. Shared
Character States. Historical Character States as Properties. Ahistorical
Kind Properties. Historical Groups and Natural Kinds. Homology.
Haszprunar's Homology Synthesis. Concepts of Homology in Systematics.
Phylogenetic Characters and Phylogenetic Homology: An Overview. Taxic
Homologies as Properties of Monophyletic Groups. Transformational Homology:
Linking Different Hypotheses of Qualitative Identity in a Transformation
Series. Discovering and Testing Homology. Patterson's Tests. Similarity and
Remane's Criteria. Similarity in Position: Morphology. Similarity in
Position: Molecular Characters. Special or Intrinsic Similarity. Stacking
Transformations: Intermediate Forms. Conjunction. Phylogenetic Homology
(Forging Congruence between Hennig's and Patterson's Views). Avoiding
Circularity: How Congruence Works. Working with Characters. Qualitative
versus Quantitative Characters: Avoiding Vague Characters. Morphometrics
and Phylogenetics. Characters, Transformation Series, and Coding. Complex
Characters or Separate Characters? Missing Data. Homology and
"Presence-Absence" Coding. Chapter Summary. Chapter 6. Parsimony and
Parsimony Analysis. Parsimony. Parsimony: Basic Principles. Kinds of
Parsimony. Classic Hennigian Argumentation. Polarization. Example 1. The
Phylogenetic Relationships of Leysera. A Posteriori Character
Argumentation. Algorithmic versus Optimality Approaches. Optimality-Driven
Parsimony. Determining Tree Length. Finding Trees. Random Addition
Searches. Rearranging Tree Topologies. The Parsimony Ratchet. Simulated
Annealing. Optimizing Characters on Trees. ACCTRAN Optimization. DELTRAN
Optimization. Summary Tree Measures. Example 2: Olenelloid Trilobites.
Evaluating Support. Using Consensus Techniques to Compare Trees.
Statistical Comparisons of Trees. Weighting Characters in Parsimony. A
Priori Weighting. Weighting by Performance. Weighting by Character
Elimination. Weighting: Concluding Remarks. Phylogenetics Without
Transformation? Chapter Summary. Chapter 7. Parametric Phylogenetics.
Maximum Likelihood Techniques. Simplicity. Likelihood in Phylogenetics: An
Intuitive Introduction. Likelihood in Phylogenetics: A More Formal
Introduction. Selecting Models. Bayesian Analysis. Interpreting Models in a
Phylogenetic Context. Chapter Summary. Chapter 8. Phylogenetic Classifi
cation. Classifications: Some General Types. Classification of Natural
Kinds. Historical Classifications (Systematizations). Convenience
Classifications. Biological Classifications. Constituents and Grouping in
Phylogenetic Classifications. The Linnean Hierarchy. Definition of Linnean
Higher Categories. Conventions for Annotated Linnean Classifications.
Ancestors in Phylogenetic Classification. Species and Higher Taxa of Hybrid
Origin. Alternative Methods of Classifying in the Phylogenetics Community.
The PhyloCode. PhyloCode Controversies. Stability of Names Relative to
Clade Content. Proper Names of Taxa. The Future of Linnean Nomenclature.
Alternative "Schools" and Logical Consistency. Chapter Summary. Chapter 9.
Historical Biogeography. The Distinction between Ecological and
Phylogenetic Biogeography and the Importance of Congruence. Hierarchies of
Climate and Geological Change and Their Relationship to Phylogenetic
Biogeographic Patterns and Processes. The Importance of Vicariance in the
Context of Evolutionary Theory. The Importance of "Dispersal" in
Phylogenetic Biogeography. Geodispersal: Not Dispersal. Historical
Perspective on Geodispersal and the Cyclical Nature of Oscillations between
Vicariance and Geodispersal. Areas and Biotas. "Area" as It Relates to
Phylogenetic Biogeographic Analysis. The Boundaries of Biotic Areas and
Comparing the Geographic Ranges of Taxa. Conclusions. Analytical Methods in
Phylogenetic Biogeography. Historical Biogeography Using Modifi ed Brooks
Parsimony Analysis. Overview of MBPA. Steps 1 and 2: Fitch Optimization of
Area States on a Phylogeny. Area Distributions. Step 3.1: The Vicariance
Matrix. Step 3.2: The Dispersal Matrix. Steps 4 and 5: MBPA Analyses and
Comparison. Alternative Biogeographic Methods. How Extinction Affects Our
Ability to Study Biogeographic Patterns in the Extant Biota. Statistical
Approaches to Biogeographic Analysis. Tracking Biogeographic Change within
a Single Clade. Phylogeography: Within Species Biogeography. The
Biogeography of Biodiversity Crises. A Brief History of the Events
Influencing Our Present Concepts of Historical Biogeography. Fundamental
Divisions in Biogeography, a Pre-Evolutionary Context, or What Causes
Biogeographic Patterns, Vicariance or Dispersal? The Growing Evolutionary
Perspective and the Continued Debate About Vicariance and Dispersal.
Chapter Summary. Chapter 10. Specimens and Curation. Specimens, Vouchers,
and Samples. The Need for Voucher Specimens. Access to Specimens. Previous
Literature. Systematic Collections. Access to Specimens in the Age of the
Internet. Collecting and Collection Information. Field Data. The
Systematics Collection. Loans and Exchanges. Curation. Receipt of
Specimens, Accessing the Collections, and Initial Sorting. Sorting and
Identifying. Cataloging. Storage. Arrangements of Collections. Type
Specimens. Catalogs. What Is in a Catalog? The Responsibility of Curators.
The Importance of Museum Collections. Integrating Biodiversity and
Ecological Data. A Simple Example: Range Predictions. Predicting Species
Invasions. Global Climate Change. Chapter Summary. Chapter 11. Publication
and Rules of Nomenclature. Kinds of Systematic Literature. Descriptions of
New Species. Revisionary Studies. Keys. Faunistic and Floristic Works.
Atlases. Catalogs. Checklists. Handbooks and Field Guides. Taxonomic
Scholarship. Phylogenetic Analyses. Access to the Literature. Literature in
Zoology. Literature in Botany. Publication of Systematic Studies. Major
Features of the Formal Taxonomic Work. Name Presentation. Synonomies.
Material Examined. The Diagnosis. The Description. Illustrations and
Graphics. Comparisons and Discussion. Distributional Data. Etymology. Keys.
Indented Key. Bracket Key. The Rules of Nomenclature. Basic Nomenclatural
Concepts. Priority. Correct Name and Valid Name. Synonyms. Homonyms.
Conserved Names (Nomen conservadum). Limits of Priority. Names and Name
Endings. Types. Chapter Summary. Literature Cited. Index.
Introduction. Phylogenetic Propositions. Topics Covered. Terms and
Concepts. Disciplines. Organisms and Grouping of Organisms. Phylogenetic
History and Evolution. Attributes of Organisms. Classification. Philosophy
and Systematics. The Form of Phylogenetic Hypotheses. Chapter Summary.
Chapter 2. Species and Speciation. What Is It to Be a Species? Species as
Kinds. Species as Sets. Species as Individuals. Species Concepts.
Process-Based Concepts. The Evolutionary Species Concept. Justifications
for the ESC. Variations on the ESC. Process-Based Concepts Emphasizing
Reproductive Isolation. Phylogenetic Species Concepts. Some Additional
Species Concepts. Sorting through Species Concepts. Speciation: Modes and
Patterns. Allopartic Speciation. Allopartic Mode I: Vicariance. Allopatric
Speciation, Mode II Peripatric Speciation. Distinguishing between
Allopatric Modes of Speciation. Parapatric Speciation. Sympatric
Speciation. Identifying Modes of Speciation in the Fossil Record. The
Evolutionary Species Concept, Speciation, and Ecology. Empirical Methods
for Determining Species Limits. Nontree-Based Methods. Tree-Based Methods.
Chapter Summary. Chapter 3. Supraspecific Taxa. Concepts of Naturalness and
Supraspecific Taxa. The Natural Taxon. Monophyly, Paraphyly and Polyphyly.
Hennig's Concepts Placed in History. Natural Higher Taxa as Monophyletic
Groups sensu Hennig (1966). Logical Consistency: The Hallmark of Proposed
Natural Classifi cations. Paraphyletic Groups Misrepresent Character
Evolution. Paraphyly and Polyphyly: Two Forms of Nonmonophyly. Node-Based
and Stem-Based Monophyly: Same Concept Different Graphs. Chapter Summary.
Chapter 4. Tree Graphs. Phylogenetic Trees. Stem-Based Phylogenetic Trees.
Node-Based Phylogenetic Trees. Cyclic Graphs. Cladograms. Nelson Trees in
Phylogenetics. From Nelson Trees to Phylogenetic Trees. Gene Trees.
Individuals versus Sets of Individuals Used in an Analysis. Representing
Character Evolution on Trees. Unrooted Trees and Their Relationship to
Phylogenetic Trees. Node Rotation. Other Kinds of Tree Terminology.
Concepts of Monophyly and Trees. Chapter Summary. Chapter 5. Characters and
Homology. A Concept of Character. Character States as Properties. Shared
Character States. Historical Character States as Properties. Ahistorical
Kind Properties. Historical Groups and Natural Kinds. Homology.
Haszprunar's Homology Synthesis. Concepts of Homology in Systematics.
Phylogenetic Characters and Phylogenetic Homology: An Overview. Taxic
Homologies as Properties of Monophyletic Groups. Transformational Homology:
Linking Different Hypotheses of Qualitative Identity in a Transformation
Series. Discovering and Testing Homology. Patterson's Tests. Similarity and
Remane's Criteria. Similarity in Position: Morphology. Similarity in
Position: Molecular Characters. Special or Intrinsic Similarity. Stacking
Transformations: Intermediate Forms. Conjunction. Phylogenetic Homology
(Forging Congruence between Hennig's and Patterson's Views). Avoiding
Circularity: How Congruence Works. Working with Characters. Qualitative
versus Quantitative Characters: Avoiding Vague Characters. Morphometrics
and Phylogenetics. Characters, Transformation Series, and Coding. Complex
Characters or Separate Characters? Missing Data. Homology and
"Presence-Absence" Coding. Chapter Summary. Chapter 6. Parsimony and
Parsimony Analysis. Parsimony. Parsimony: Basic Principles. Kinds of
Parsimony. Classic Hennigian Argumentation. Polarization. Example 1. The
Phylogenetic Relationships of Leysera. A Posteriori Character
Argumentation. Algorithmic versus Optimality Approaches. Optimality-Driven
Parsimony. Determining Tree Length. Finding Trees. Random Addition
Searches. Rearranging Tree Topologies. The Parsimony Ratchet. Simulated
Annealing. Optimizing Characters on Trees. ACCTRAN Optimization. DELTRAN
Optimization. Summary Tree Measures. Example 2: Olenelloid Trilobites.
Evaluating Support. Using Consensus Techniques to Compare Trees.
Statistical Comparisons of Trees. Weighting Characters in Parsimony. A
Priori Weighting. Weighting by Performance. Weighting by Character
Elimination. Weighting: Concluding Remarks. Phylogenetics Without
Transformation? Chapter Summary. Chapter 7. Parametric Phylogenetics.
Maximum Likelihood Techniques. Simplicity. Likelihood in Phylogenetics: An
Intuitive Introduction. Likelihood in Phylogenetics: A More Formal
Introduction. Selecting Models. Bayesian Analysis. Interpreting Models in a
Phylogenetic Context. Chapter Summary. Chapter 8. Phylogenetic Classifi
cation. Classifications: Some General Types. Classification of Natural
Kinds. Historical Classifications (Systematizations). Convenience
Classifications. Biological Classifications. Constituents and Grouping in
Phylogenetic Classifications. The Linnean Hierarchy. Definition of Linnean
Higher Categories. Conventions for Annotated Linnean Classifications.
Ancestors in Phylogenetic Classification. Species and Higher Taxa of Hybrid
Origin. Alternative Methods of Classifying in the Phylogenetics Community.
The PhyloCode. PhyloCode Controversies. Stability of Names Relative to
Clade Content. Proper Names of Taxa. The Future of Linnean Nomenclature.
Alternative "Schools" and Logical Consistency. Chapter Summary. Chapter 9.
Historical Biogeography. The Distinction between Ecological and
Phylogenetic Biogeography and the Importance of Congruence. Hierarchies of
Climate and Geological Change and Their Relationship to Phylogenetic
Biogeographic Patterns and Processes. The Importance of Vicariance in the
Context of Evolutionary Theory. The Importance of "Dispersal" in
Phylogenetic Biogeography. Geodispersal: Not Dispersal. Historical
Perspective on Geodispersal and the Cyclical Nature of Oscillations between
Vicariance and Geodispersal. Areas and Biotas. "Area" as It Relates to
Phylogenetic Biogeographic Analysis. The Boundaries of Biotic Areas and
Comparing the Geographic Ranges of Taxa. Conclusions. Analytical Methods in
Phylogenetic Biogeography. Historical Biogeography Using Modifi ed Brooks
Parsimony Analysis. Overview of MBPA. Steps 1 and 2: Fitch Optimization of
Area States on a Phylogeny. Area Distributions. Step 3.1: The Vicariance
Matrix. Step 3.2: The Dispersal Matrix. Steps 4 and 5: MBPA Analyses and
Comparison. Alternative Biogeographic Methods. How Extinction Affects Our
Ability to Study Biogeographic Patterns in the Extant Biota. Statistical
Approaches to Biogeographic Analysis. Tracking Biogeographic Change within
a Single Clade. Phylogeography: Within Species Biogeography. The
Biogeography of Biodiversity Crises. A Brief History of the Events
Influencing Our Present Concepts of Historical Biogeography. Fundamental
Divisions in Biogeography, a Pre-Evolutionary Context, or What Causes
Biogeographic Patterns, Vicariance or Dispersal? The Growing Evolutionary
Perspective and the Continued Debate About Vicariance and Dispersal.
Chapter Summary. Chapter 10. Specimens and Curation. Specimens, Vouchers,
and Samples. The Need for Voucher Specimens. Access to Specimens. Previous
Literature. Systematic Collections. Access to Specimens in the Age of the
Internet. Collecting and Collection Information. Field Data. The
Systematics Collection. Loans and Exchanges. Curation. Receipt of
Specimens, Accessing the Collections, and Initial Sorting. Sorting and
Identifying. Cataloging. Storage. Arrangements of Collections. Type
Specimens. Catalogs. What Is in a Catalog? The Responsibility of Curators.
The Importance of Museum Collections. Integrating Biodiversity and
Ecological Data. A Simple Example: Range Predictions. Predicting Species
Invasions. Global Climate Change. Chapter Summary. Chapter 11. Publication
and Rules of Nomenclature. Kinds of Systematic Literature. Descriptions of
New Species. Revisionary Studies. Keys. Faunistic and Floristic Works.
Atlases. Catalogs. Checklists. Handbooks and Field Guides. Taxonomic
Scholarship. Phylogenetic Analyses. Access to the Literature. Literature in
Zoology. Literature in Botany. Publication of Systematic Studies. Major
Features of the Formal Taxonomic Work. Name Presentation. Synonomies.
Material Examined. The Diagnosis. The Description. Illustrations and
Graphics. Comparisons and Discussion. Distributional Data. Etymology. Keys.
Indented Key. Bracket Key. The Rules of Nomenclature. Basic Nomenclatural
Concepts. Priority. Correct Name and Valid Name. Synonyms. Homonyms.
Conserved Names (Nomen conservadum). Limits of Priority. Names and Name
Endings. Types. Chapter Summary. Literature Cited. Index.