Igor Ya. Pavlinov. Introduction to the contemporary phylogenetics (a cladogenetic aspect). M.: KMK Sci. Press Ltd., 2005. — 391 p. 51 ill. Bibl. 132.

 

The book contains a review of theoretical fundamentals, principles, notions, methods, and applications of the contemporary phylogenetics (with emphasis on its cladogenetic aspect). Certain elementary ideas of scientific epistemology are overviewed which constitute the basis of cognitive activity in phylogenetics: the interdependence of ontology and epistemology, cognitive situations, principal argumentation schemes, general principles (cognizability, rationality, parsimony, common cause, etc.). A short sketch of history of the phylogenetic science is provided, and its modern schools are characterized. The ontological and epistemological prerequisites of the phylogenetics proper are considered: the background evolutionary models are outlined, the structure of both phylogenesis and phylogenetic pattern is described, and the essential phylogenetic metaphors (phylogenetic tree, phylogenetic signal, etc.) are characterized. Its basic principles are expounded: correspondence, uncertainty, phylogenetic unity, etc. The key concepts and notions of phylogenetics are discussed in more detail, such as similarity, kinship, homology, character, weighting, etc. The structure and contents of phylogenetic hypothesis are analyzed. Certain methodological problems of the factological foundations of phylogenetics are also under consideration. A general scheme of cladogenetic investigation is presented, starting from the formulation of the initial condition to testing of the resulting cladistic hypothesis. Principal algorithms and methods of numerical phyletics are briefly outlined, including numerical estimates of phylogenetic relationship and recent methods of constructing phylogenetic trees (compatibility, parsimony, maximum likelihood, etc.). Basic rules of turning cladistic hypothesis into more content wise phylogenetic one are discussed. Impact of the “new” phylogenetics is shown onto recent studies in taxonomy, historical biogeography, ecology, and co-evolution. The vocabulary of notions and terms used in the contemporary phylogenetics (cca 360 items) is provided.

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