Principles of

Animal Taxonomy

AshokVerma

Alpha Science International Ltd.

Oxford, U.K.
 CONTENTS

1. Historical Resume of Taxonomy 1.1

The Vedic Period; Aristotle's Contribution; The Pre-Linnaean Period;
Linnaeus' Contribution; The Post Linnaean Period; Darwin's Contribution;
Population Systematics; Phylogenetic Systematics

2. Basic Concepts of Animal Taxonomy 2.1

Systematics; Why Classify Organisms; Features of Classification;
Hierarchical Classification; Categories; Taxa; Rank; Species; Genus;
Family; Order; Class; Phylum; Kingdom; Taxonomic Characters; Attributes
for Classifying Organisms; Fossils; The Task of Systematise Taxonomy-
Myths and Conception; Importance of Taxonomic Study

3. Types of Classification 3.1

Principle of Zoological Classification; Differences; Accident; Property;
Features of Classification; Types of Classification; Ecological
Classification; Teleological Classification; Artificial Classification; Merits
of Artificial Classification; Demerits of Artificial Classification; Natural
Classification; Morphology; Homology; Population; Cladistics; Phenetics;
Phyletics; Merits of Natural Classification; Biological Classification;
Evolutionary Classification; Phylogenetic Classification; Genetic Basis of
Classification

4. Zoological Nomenclature 4.1

Early System of Naming; Binomial Nomenclature; Salient Features of
Biological Nomenclature; Linnaean Hierarchy; Trinomial Nomenclature;
Types of Nomenclature; Rank Based; Circumscription Based; Description
Based; Phylogeny Based; Hierarchy Based; Necessity for Rules of
Nomenclature; Nomenclature Code; The General Principles of
Nomenclature; Principle of Binomial Nomenclature; Principles of Name
Bearing Types; Principle of Priority; Limitations of Rules of Priority;
Authorship; Principles of Co-ordination; Availability and validity of
Names; Publication of Names; First Reviser Principle; Describing New
Species; Derivation of Name; Termination of Name; Spellings; Gender
Agreement; Principles of Typification; Kinds of Type Specimens; Primary
Type; Holotype; Syntype; Lectotype; Neotype; Secondary Type; Allotype;
Paratype; Paralectotype; Topotype; Monotype; Indication; Significance of
Type Specimens; Voucher Specimens; Status of Names; Valid Name;
Invalid Names; Principles of Homonymy; Senior Homonyms; Junior
Homonyms; Primary Homonym; Secondary Homonym; Junior Secondary
Homonym; Hemi-homonym; Double Homonymy; Synonyms; Subjective
Synonyms; Subjective Invalid Synonyms; Junior Subjective Synonyms;
Nominotypical subspecies and subspecies Autonyms; Emendation;
Justified; Unjustifed; Unavailable; Misspelling; Incorrectly formed name;
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Doubtful cases, Other

Unnecessary replacement; Suppressed by ruling;
of Names; Misapplied Names; Unnamed; Temporary Name; Nomen
Types
Nomen Nomen protectum; Nomen
nudum; Nomen dubium; novum;

oblitum; Nomen hybridum; Nomen trivial; Vernacular Name; Parenthesis;

Use of latin
Brackets; Asterisk; Abbreviation; Punctuation Marks;
and 'ex '; Numerical in Compound Names; Sensu strict;
proposition 'in'
Sensu lato; Partim or pro parte; Use of certain suffix; Use
of suffix 'ensis' or
Preamble to
'iensis'; Historical Background of Zoological Nomenclature;
the International Code of Zoological Nomenclature; Features of Zoological
Nomenclature; Uniqueness; Universality; Stability; Explanatory Note to the
Code; Range and Authority of Code; Freedom of Taxonomic Thought;
Catalogues of Zoological Names; International Commission of Zoological
Nomenclature; Universal Rules and Powers of Commission; ICZN
Amendment on Electronic Publication; International Trust for Zoological
Nomenclature; Nomenclature vis-a-vis Taxonomy; Taxonomic Inflation;
Modern Developments

5. Microtaxonomy and Macrotaxonomy 5.1

Micro taxonomy; Phenon; Taxon; Category; Species and Classification;
Macrotaxonomy

6. Phylogenetic Systematics 6.1

Recapitulation Theory; Cladistics Analysis; Apomorphy; Plesiomorphy;
Symplesiomorphy; Synapomorphy; Hypothesis of Cladistic Analysis; First
hypothesis; Second hypothesis; Third hypothesis; Basics of Cladistic
Analysis; Organisms are descended from common ancestor; Bifurcating
Pattern of Cladogenesis; Changes in Characteristics; Methodology of
Cladistic Analysis; Construction of Cladogram; Selection of Taxa;
Determination of Characters; Polarity of Characters is determined;
Grouping of Taxa by synapomorphies; Parsimony; Outgroup Camparison;
Interpretation of Cladogram; Characteristic Features of Cladistics;
Monophyletic Grouping; Paraphyletic Grouping; Polyphyletic Grouping;
Holophyletic Grouping; Evolutionary tree, Phylogenetic Tree and
Cladogram; Pattern Cladism; Biosynthetic Phylogeny; Significance of
Phylogenetic Systematics

7. Phylogenetic Trees 7.1

Understanding Phylogenetic Trees; Node; Branch; Topology; Branch
Length; Root; Distance Scale; Clade; Operational Taxonomic Units;
Hypothetical Taxonomic Units; Out Group; Features of Phylogenetic Tree;
Kinds of Phylogenetic Tree; Cladogram; Phenogram; Phylogram;
Dendrogram; Curvogram; Eurogram; Swoopogram; Chronogram;
Understanding Phylogeny; Construction of Phylogenetic Trees; Distance
Based Methods; Maximum Parsimony; Maximum Likelyhood; Bayesian
Phylogenetic Interference; Distance Methods; Limitations in Construction
of Phylogenetic Tree; Statistical Tests; Phylogenetic Analysis Tool;
Common Genes and New Family Tree; Gene Tree versus Species Tree;
Significance of Phylogenetic Trees

8. Molecular Phylogeny 8.1

Essentials of MolecularPhylogenetic Analysis; Database for Phylogenetic
Analysis; Tree Building; Orthologs; Paralogs; Xenologs; HomoloGene;
Entrej Genome; Measurement of Immunological Distance; Protein
Sequences; Hemoglobin; Cytochrome; Genetic Complement; Nucleic Acid
 Contents xvii

Phylogeny; DNA Hybridization Technique; Comparison of DNA Sequence;

Chromosome Painting; Molecular Clock; Importance of Molecular
Phylogeny

9. Evolutionary Taxonomy 9.1

Features of Evolutionary Taxonomy; Distinctness; Degree of Differences;
Ecology and Evolution; Grade Characteristics; Equivalence; Stability; Size
of Taxon; Splitters and Lumpers; Sister Groups; Mosaic Evolution; Concept
of Evolutionary Taxonomy; Evolutionary Taxonomy versus Cladistics;
Evolutionary Taxonomy versus Phylogenetics; Limitations of Evolutionary
Taxonomy; Significance of Evolutionary Taxonomy and its Decline

10. Numerical Taxonomy 10.1

Features of NumericalTaxonomy; Basis of Numerical Taxonomy;
Phenetics; The Adansonian Principle; Procedures in Numerical Taxonomy;
Distance Methods; Character Data Method; Operational Taxonomic Units;
Binary Characters; Qualitative Multistate Characters; Quantitative
Multistate Characters; Measurement of Quantitative Characters; Structure
of Taxonomic System; Essentials of Taxonomic System; Monothetic
Method; NaturalMethods; Nested Hierarchy; Establishment of
Resemblance and Description of Taxa; Frequency Distribution of Similarity
Coefficient; Euclidean Distance; Differential Shading of Similarity Matrix;
Data Analysis; Distance Analysis; Cluster Analysis; Factor Analysis;
Representation of Clustering; Limitations of Numerical Taxonomy;
Significance of Numerical Taxonomy

11. Population Taxonomy 11.1

Characteristics of Population; Population Density; Population Dynamics;
Biotic Potential; Carrying Capacity; Interaction and Variability in
Populations; Positive Interaction; Mutualism; Commensalism; Proto-
cooperation; Negative Interaction; Exploitation; Shelter; Food; Parasitism;
Predation; Defence Mechanism; Source of Variation in Populations;
Developmental Variations; Non-genetic Variations; Age Variation;
Seasonal Variation; Cyclomorphosis; Social Variation; Genetic Variation;
Discontinuous Variation; Continuous Variation; Environmental Variability
due to Phenotypic Plasticity; Genetic Variability in Populations;
Differentiation of Populations; Genetic Drift and Gene Pool; Population
Genetics; Mutation, Natural Selection and Adaptation in Population

12. Taxonomic Characters 12.1

Characters andSystematics; Diagnostic Significance; Evolutionary
Significance; Phylogenetic Significance; Kinds of Taxonomic Characters;
Diagnostic Characters; Key Characters; Measurement of Characters;
Coding of Characters; List of Characters; Distribution of Character States;
Missing Characters; Inapplicable Characters; Qualitative Characters; Binary
Characters; Multiseriate Characters; Quantitative Characters; Meristic
Characters; Continuous Quantitative; Ordered Characters; Unordered
Characters; Homology; Test for Homology; Similarity; Conjunction;
Congruence with other Homologies; Serial Homology; Homoplasy;
Convergence; Parallelism; Weighting of Characters; Character Analysis;
Morphological Characters; Body Parts and Coloration; Developmental
Characters; Genetic Characters; Cytological Characters; Physiological
Characters; Molecular Characters; Behavioural Characters; Effect of
Ecological Factors; Parasites and Symbionts; Geographical Characters;
xviii Contents

Source of
Unrelated Characters; Character Displacement; Classification and
Assessment
Data; Significance of Characters in Biodiversity

13.1
13. The Species Concept
of Species
The Species Taxon; The Species Category; Different Types
Concept; Typological Species; Nominalistic Species; Biological Species;
Disadvantage of Biological Species; Asexual Apomictic Species; Sibling
and Cryptic Species; Gradual Speciation; Rings of Races; Hybrid Complex;
Evolutionary Species; Phylogenetic Species; Recognition Species; Other
Kinds of Species; Taxonomic Species; Morphospecies; Palaeospecies;
Agamospecies; Phenetic Species; Chronospecies; Cohesion Species; Ring
Species; Umbrella Species; Keystone Species; Indicator Species;
Biospecies; Flagship Species; Subspecies; Demerits of Subspecies Concept;
Temporal Subspecies; Other Interspecies Group; Deme; Race; Cline;
Variety; Morphotype; Super Species; How Do New Species Occur?;
Process of Speciation; Anagenesis; Cladogenesis; Premating Isolating
Mechanism; Post Mating Isolating Mechanism; Hybrid Inviability; Hybrid
Sterility; Behavioural Sterility; Role of Reproductive Isolation in
Speciation; Pattern of Speciation; Allopatric Speciation; Parapatric
Speciation; Alloparapatric Speciation; Sympatric Speciation; Mechanism of
Isolation; Natural Selection, Environment and Speciation; Establishment of
New Species; Speciation versus Biodiversity

14.1
14. Zoological Types
Type Species; Type Genus; Features of Type Specimen; Principles of
Typification; Correcting Misidentification of Types; Designation of Type
Specimen; Kinds of Type Specimen; Primary Type; Holotype; Neotype;
Secondary Type; Syntype; Isotype; Lectotype; Paralectotype; Hapantotype;
Tertiary Type; Paratype; Specimens of Special Origin; Significance of Type
Specimens

15. Taxonomic Categories 15.1

Hierarchy; Types of Category; The Lower Category; The Infraspecies

Category; Polytypic Species; Variety; Subspecies; Super Species; Race;
The Higher Category; Genus; Features of Genus; Family; Features of
Family; Subfamily; Superfamily; Order; Class; Phylum; Sub Phylum/Super
phylum; Kingdom; Origin of Categories; Demerits of Higher Categories
Groupings

16. Meristic and Non-Meristic Data Analysis 16.1

Morphological Variability in Natural Population; Meristic Characters; Fish
Meristic Characters; Standard Length; Total Length; Length of the Head;
Snout Length; Upper Jaw Length; Lower Jaw Length; Eye Diameter; Girth
Length; Height or depth of the Body; Length of the Caudal Peduncle; Fin
Formula; Scale Counts; Insect Meristic Characters; Non-Meristic
Characters; Other Characters; Chemical Marks in Otolith; Thermal Marks;
Elastomeres; Biological Marks; Significance of Character Study

17. Biodiversity Assessment 17.1

Genetic Diversity; Diversity between Species; Diversity of Ecosystem;
Distribution of Biodiversity; Assessment of Biodiversity; Types of
Biodiversity; Alpha Diversity; Beta Diversity; Gamma Diversity;
Biodiversity Indices; Species Richness; Factors Affecting Species Richness;
 Contents xix

Simpson Diversity Index; Shanon -Weiner Index; Sorenson's Similarity

Index; Association Index; Dominance Index; Dissimilarity Index; Quadratic
Entropy Index; Measures of Biodiversity; Phylogenetic Measurement of
Biodiversity; Taxonomic Surrogacy; Biodiversity Hotspots; Genetic
Pollution; Biodiversity and Ecosystem; Biodiversity and Climate Change;
Biodiversity & Genetic Resources; Loss of Biodiversity vis-a-vis Food
Security; Biodiversity, Agriculture and Sustainable Development;
Biodiversity and Human Health; Biodiversity, Trade and Commerce;
Biodiversity -The Refreshing Asset; Biodiversity Informatics; Biodiversity
vis-a-vis Evolution; Threats to Biodiversity; Laws for Conservation of
Nature and Natural Resources

18. Taxonomic Keys 18.1

Construction of Taxonomic Key; Features of Taxonomic Keys; Types of
Taxonomic Key; Dichotomous Key; Diagnostic Keys; Synoptic Key;
Diagnostic versus Synoptic Key; Variation in Single Access Key;
Presentation of Taxonomic Keys; Nested Style; Linked Style; Bracket Key;
Indented Key; Simple Non-bracket Key; Simple Bracket Key; Serial Key;
Pictorial Key; Branching Key; Box Type Key; Circular Key; Computer
Aided Keys; Description of Genera; Merits and Demerits of Taxonomic
keys

19. Taxonomic Publications 19.1

Taxonomic Literature; Atlas; Catalog; Checklist; Fauna; Field Guide; Field
Book; Hand Book; Manual; Monographs; Synopsis and Reviews; Revision;
Treatise; Features of Taxonomic Publications; Diagnosis; Original
Description; Report; Style of Description; Sequence of Characters; Contents
of Description; Illustrations; Reference and Bibliography; Keys; Form and
Style of Taxonomic Publications; Index to Organism Names; Journals on
Systematics; Registration of New Name in Zoology; Electronic Publications
of New Animal Names; Significance of Taxonomic Publications

20. Collections and Preservation of Natural History Specimens 20.1

Collection Procedures; Time of Collection; Place of Collection; Terrestrial
Collection; Aquatic Collection; Fresh Water Collection; Marine Collection;
Recording of Data; Collecting Equipments; Aquatic Collection; Dip Net;
Seine; Dredge Net; Terrestrial Collection; Aerial Net; Sweep Net; Beat
Sheet; Aspirator; Traps; Pitfall Traps; Light Traps; Bait Traps; Berlese
Funnel; Paper Bags; Narcotizing Agents; Killing Bottle; Use of Killing
Bottle; Preservation of Collected Specimens; Preservation in Liquid 20.9
Emptying of Killing Bottle; Preservation of Insects; Relaxing the Collected
Specimens; Mounting of Insects; Spreading Board; Pinning of Insects;
Pinning Dowel; Labeling; Stuffing of Insects; Display of Small Insects;
Carding; Mounting Minute Insects on Slides; Storage of Insects; Protection
of Insect Collections; Identification of Insects; Dispatching Insects for
Identification; Collection and Preservation of Fish; Useful Tips for
Collection and Curation; Significance of Natural History Specimens;
Environmental Studies; Conservation of Nature; Applications of
Biochemical Knowledge; Archaeology and Ethnology; Evolution and
Behaviour; Historical Studies; Service to the Society; Trade and Commerce;
Recreation; Agriculture; Natural History Collections as National Resource
 Contents
XX

21. Information Retrieval Z1'\

Working of Information Retrieval System; Biological Names and
TaxMeOn-Meta-Ontology; Name Collections; Species List;
Taxonomies;
Research Result; Information Retrieval Models and Gadgets;
Biological
Informational Retrieval Models; Vertica
Informational Retrieval Objects;
Taxonomy; The Representation; The Reasoning; Keyword-base; Horizontal
Tasks; Ad Hoc Retrieval; Known Item Search, Interactive
Taxonomy;
Retrieval; Filtering; Browsing; Mining; Gathering; Crawling; Managing
Animal Diversity; Object Oriented Taxonomic Biodiversity Databases,
Universal Register, Zoological
Computer Programs and Internet Resources;
Record* Animal Diversity Web; The Electronic Zoo; Description Language
for Taxonomy; Global Index Names; Global Names Architecture; Index to
Information System,
Organism Names; The Global Biodiversity
Database
TaxonTree; Expert Center for Taxonomic Identification; SysTax
and Evolution, Mantis,
System; Bayesian Analysis to Molecular Biology
U Bio
Tree BASE; Pandora; BioNet International; Diana; Platypus; Taxis;
Taxonomicon; The Index of Life;
Portal' OCEAN; Systema Naturae 2000;
The Tree of Life; The Web of Life; The Facts of Life;
Tree of Life Web
of Life
Project; Species 2000; IT IS; ZooBank; The Catalogue
22«!
22. Recent Trends in Taxonomy .

Morphological Characters; Embryological Study; Ecological Approach;

Behavioural Pattern; Cytotaxonomy; Molecular Phylogeny;
Chemotaxonomy; Histochemical Methods; Comparative Serology;
Numerical Taxonomy; Molecular Taxonomy; Barcoding Life; Basics of
of Birds;
Barcoding; Applications of DNA Barcode; Identification
Species; Molecular Operational Taxonomic Units;
Delimiting Cryptic
Integrated Operational Taxonomic Units; Cataloguing Ancient Life;
Constraints of DNA Taxonomy; Convention on Biodiversity; The Global
Taxonomic Initiative; Parataxonomy; Integrative Taxonomy

of Taxonomy andBiosystematics 23.1

23. Significance
Systematics Biology; Systematics and Applied Biology;
and Theoretical
Green Revolution; Biological Control; Economic Entomology; Quarantine;
Management of Wild Life; Trade and Commerce; Ecological Problems;
Taxonomy and Systematics; Natural History Collections; Taxonomy vis-a-
vis Biodiversity Conservation; Taxonomic Minimalism; Taxonomy: The
Present Scenario

Bibliography
A uthor Index AI.l
Genus Index G1.1
SI. 1
Subject Index