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The book is intended for the biologists and
other researchers interested in the general problems of contemporary
evolutionary biology and phylogenetics, as well as for the students and
lecturers in the evolutionary biology and taxonomy.
Contents
Foreword
Chapter 1. Introduction:
subject, aims and structure of phylogenetics
Part
I. Phylogenetics as a science
Chapter 2. The elements of
scientific epistemology
2.1. Nomothetics and idiographics
2.1.1. Cognitive situations
2.1.2. Research programs and thinking styles
2.1.3. Principal argumentation schemes
2.1.4. Scientific pluralism
2.1.5. Between a fact and a theory
2.2. General principles
2.2.1. Cognizability principle
2.2.2. Rationality principle
2.2.3. Parsimony principle
2.2.4. Modeling principle
2.2.5. Common cause principle
2.2.6. Systemity principle
Chapter 3. Historical
pathways of phylogenetics
3.1. Prehistory: in search of the Natural System
3.2. Transformism, evolutionism, phylogenetics
3.3. Classical phylogenetics
3.4. Phylistics
3.5. The 'new' phylogenetics
3.5.1. Cladistics
3.5.2. Genophyletics
3.5.3. Numerical phyletics
3.5.4. Schools of the 'new' phylogenetics
Chapter 4. Backgrounds of
phylogenetics
4.1. Ontological backgrounds
4.1.1. Evolutionary models
4.1.2. The structure of phylogenesis
4.1.2.1. Temporal constituent
4.1.2.2. Cladogenesis, semogenesis, anagenesis
4.1.3. Phylogenetic pattern
4.2. Metaphors of phylogenetics
4.2.1. Phylogenetic tree
4.2.1.1. Some formalizations
4.2.2. Developmental spiral
4.2.3. Phylogenetic signal
4.2.4. Evolutionary cone
4.3. Particular principles of phylogenetics
4.3.1. Correspondence principles
4.3.2. Uncertainty principles
4.3.3. Principle of phylogenetic unity
4.3.3.1. Monophyly principle
4.3.3.2. Inherited similarity principle
4.3.4. Substitution principle
4.3.5. Principle of dichotomy
Chapter 5. Principal
concepts and notions of phylogenetics
5.1. The basic model of cladogenetics
5.2. The kinship and related notions
5.2.1. Kinship interpretations
5.2.2. Concept of ancestor
5.2.3. 'N-phyly'. Phylogenetic
groups
5.2.4. The bases for judgment about kinship
5.3. The homology
5.3.1. Concepts of homology
5.3.2. Criteria of homology
5.4. The character
5.4.1. Initial formalizations
5.4.2. The cladistic character
5.5. The similarity
5.5.1. Some properties of similarity
5.5.2. Categories of similarity
5.5.3. Synapomorphy and symplesiomorphy
5.6. The weighting
5.6.1. Basic principles
5.6.2. Character weighting
5.6.3. Similarity weighting
5.7. Phylogenetic hypothesis
PART
I I. CLadOGENy RECONSTRUCTINGs
Chapter 6. Factology of
cladogenetics
6.1. Comparative data
6.1.1. Morphology
6.1.2. Paleontology
6.1.3. Embryology
6.1.4. Molecular biology
6.1.5. Other comparative data
6.2. Experimental data
6.3. Combining different kinds of data
6.4. Systematic collections
Chapter 7. Methodologies and
methods
7.1. Criteria of method consistency
7.2. Classification of phylogenetic methods
7.3. Comparative-historical method
Chapter 8. General scheme of
cladogenetic investigation
8.1. Initial conditions
8.2. Sample organization
8.3. Character analysis
8.4. Reconstructing phylogenetic trees
8.5. Testing of cladistic hypothesis
Chapter 9. Modern methods of
reconstructing phylogenetic trees
9.1. Qualitative and quantitative methods
9.2. Quantitative measures of phylogenetic closeness
9.3. Optimality criteria of trees
9.4. Principal algorithms
9.4.1. Distance-based methods
9.4.2. Compatibility analysis methods
9.4.3. Parsimony methods
9.4.4. Maximum likelihood methods
9.4.5. Generalized trees
9.4.6. Probabilistic estimation of trees
9.4.7. Computer modeling
9.5. Principal computer programs
Part
I I I. Applications of cladogenetics
Chapter 10. From
cladogenesis to phylogenesis
Chapter 11. Cladogenetics
and semogenetics
11.1. Reconstructing semogeneses
11.1.1. Direct scheme
11.1.2. Indirect scheme
11.2. Revealing cladogenetic signal
Chapter 12. Cladogenetics
and systematics
Chapter 13. Cladogenetics
and historical biogeography
13.1. Principal models
13.2. Principal methods
Chapter 14. Cladogenetics
and co-evolution
Conclusion
Glossary
References