Fundamentals of Plant-Parasitic Nematode Diagnostics, Systematics, and Classification

1. Introduction

1.1 General body organization

1.2 The human and animal parasites

1.3 The plant parasites

1.4 Paleontological evidence of parasitism

1.5 Types of parasitism

1.6 The free-living nematodes

1.7 Abundance and survival

1.8 Nematodes in nature – agriculture continuum

1.9 Relevance of biosystematic knowledge for a nematologist


2. General principles for nematode taxonomy and systematics

2.1 Concept and definition of taxonomy

2.2 Levels of taxonomy

2.2.1 Alpha-taxonomy

2.2.2 Beta-taxonomy

2.2.3 Gamma-taxonomy

2.3 Taxonomic attempts towards classification

2.3.1 Morphotaxonomy

2.3.2 Numerical taxonomy

2.3.3 Cytotaxonomy

2.3.4 Chemotaxonomy

2.3.5 Molecular taxonomy

2.3.6 Other types of taxonomy concepts

2.4 Concept and definition of systematics

2.5 Systematics and taxonomy: which holds what?

2.6 From systematics to classification

2.7 Biological classification and hierarchy

2.8 Theories of classification

2.8.1 Essentialism

2.8.2 Nominalism

2.8.3 Empiricism

2.8.4 Cladism

2.8.5 Evolutionary classification

2.9 Brief classification of life forms

2.10 Definition of species and species concept

2.10.1 Morphological species concept

2.10.2 Non-dimensional species concept

2.10.3 Phenetic species concept

2.10.4 Biological species concept

2.10.5 Genetic species concept

2.10.6 Hennigian species concept

2.10.7 Agamospecies concept

2.10.8 Evolutionary species concept

2.10.9 Taxonomic species concept

2.10.10 Reproductive competition concept

2.10.11 Ecological species concept

2.10.12 Phylogenetic species concept

2.10.13 Autapomorphic species concept

2.10.14 Recognition species concept

2.10.15 Cladistic species concept

2.10.16 Cohesion species concept

2.10.17 Genealogical concordance concept

2.10.18 Evolutionary significant unit concept

2.10.19 Internodal species concept

2.10.20 Composite species concept

2.10.21 Genotypic cluster concept

2.10.22 Genic species concept

2.10.23 Differential fitness species concept

2.10.24 Successional species concept

2.10.25 Quasispecies concept

2.11 Speciation and extinction

2.11.1 Species complex, species flock and taxonomic inflation

2.12 Below-species ranks

2.13 Concept of genus

2.14 System of nomenclature


3. Character and character types

3.1 Definition of character

3.1.1 Character state

3.1.2 Character weighing

3.1.3 Character complexity

3.1.4 Character polarity

3.2 Types of character

3.2.1 General characters

3.2.2 Phenetic characters

3.2.3 Phylogenetic characters

3.2.4 Cladistic characters

3.3 Character data and selection of characters


4. Identification of nematodes

4.1 Approaches of identification

4.2 Taxonomic key

4.2.1 Types of taxonomic key

4.2.1.1 Single-access keys

4.2.1.2 Multi-access keys

4.2.1.3 Interactive keys

4.2.2 Use, construction, merits and demerits of taxonomic keys

4.3 Tools and techniques of identification

4.3.1 Morphological tools

4.3.2 Biochemical tools

4.3.3 Molecular tools

4.4 Identification of common plant-parasitic nematode genera


5. Note on molecular phylogeny and evolutionary history

5.1 Why to know phylogeny?

5.2 Phylogenetic tree or evolutionary tree

5.2.1 Construction of tree using molecular data

5.2.1.1 Selection of target molecular marker

5.2.1.2 Retrieval of sequences

5.2.1.3 Multiple sequence alignment

5.2.1.4 Selection of appropriate model

5.2.1.5 Making of tree

5.2.1.6 Assessment of tree reliability

5.2.2 Rooting of tree


6. Classification of plant-parasitic nematodes

6.1 Higher classification of nematodes

6.2 Nematodes and their allies

6.3 Classification of nematodes with special reference to plant-parasites


7. Representation and management of taxonomic data

7.1 Types of taxonomic literatures

7.2 Management of taxonomic data for a publication