Principles and Techniques of Contemporary Taxonomy

Taxonomy is an ever-changing, controversial and exCitmg field of biology. It has not remained motionless since the days of its founding fathers in the last century, but, just as with other fields of endeavour, it continues to advance in leaps and bounds, both in procedure and in philosophy. These changes are not only of interest to other taxonomists, but have far reaching implications for much of the rest of biology, and they have the potential to reshape a great deal of current biological thought, because taxonomy underpins much of biological methodology. It is not only important that an ethologist. physiologist. biochemist or ecologist can obtain information about the identities of the species which they are investigating; biology is also uniquely dependent on the comparative method and on the need to generalize. Both of these necessitate knowledge of the evolutionary relationships between organisms. and it is the science of taxonomy that can develop testable phylogenetic hypotheses and ultimately provide the best estimates of evolutionary history and relationships.

1 Introduction.- 1.1 The compass of taxonomy and systematics.- 1.2 The 1960s and the emergence of new ideas.- 1.3 Cladistics and numerical taxonomy: the conflict.- 1.4 Assumptions and philosophy of cladistics and the use of parsimony criteria.- 1.5 Taxonomy and the comparative method in biology.- 2 Characters, Taxa and Species.- 2.1 Nature and handling of data.- 2.2 Characters.- 2.3 Classes of characters requiring special consideration.- 2.4 Taxa and species concepts.- 2.5 What is a species?.- 3 Phylogenetic Reconstruction — Cladistics and Related Methods.- 3.1 Cladistics and cladograms.- 3.2 Parsimony and finding the shortest trees.- 3.3 Which method? — an overview.- 3.4 Cladistics and classification.- 4 Phenetic Methods in Taxonomy.- 4.1 Introduction.- 4.2 Analysing similarity and distance data.- 4.3 Hierarchic clustering procedures.- 4.4 Ordination methods.- 5 Keys and Identification.- 5.1 Introduction.- 5.2 Types of keys.- 5.3 Efficiency.- 5.4 Computerized key construction.- 6 Nomenclature and Classification.- 6.1 Introduction.- 6.2 The binomial system and the hierarchy of taxa.- 6.3 The International Commissions.- 6.4 Basic principles of nomenclature.- 6.5 Miscellaneous group-related factors.- 6.6 Names of higher groups.- 6.7 Starting dates for nomenclature.- 6.8 Citation of authors.- 6.9 Publication.- 6.10 Type depositories.- 6.11 Good practice.- 6.12 Major taxonomic publications.- 7 Cytotaxonomy.- 7.1 Introduction.- 7.2 Karyotypes.- 7.3 Chromosome banding.- 7.4 Chiasma frequency.- 7.5 Inversions. translocations and their significance.- 7.6In situhybridization.- 8 Chemotaxonomy and Related Topics.- 8.1 Origins of chemotaxonomy.- 8.2 Classes of compounds and their biological significance.- 8.3 Fermentation properties and drug resistance in microorganisms.- 8.4The use of chemical data.- 9 Immunotaxonomy.- 9.1 History.- 9.2 Precipitin reaction.- 9.3 Immunodiffusion.- 9.4 Immunoelectrophoresis.- 9.5 Microcomplement fixation (MC’F).- 9.6 Use of monoclonal antibodies.- 9.7 Radioimmunoassay.- 9.8 Analysis of immunological data.- 10 Proteins and Taxonomy.- 10.1 Introduction.- 10.2 Techniques of protein electrophoresis.- 10.3 Systematic aspects of electrophoresis.- 10.4 Chemical protein analysis procedures.- 10.5 Analysis of amino acid sequence data.- 11 Nucleic Acid Methods.- 11.1 Nucleic acids in taxonomy.- 11.2 Nucleic acids in cells.- 11.3 Amplifying DNA and dealing with small samples.- 11.4 G+C content.- 11.5 Restriction fragment analysis.- 11.6 DNA hybridization.- 11.7 Sequencing and associated methods.- 11.8 Conservation versus variability.- 11.9 Analysing sequence data.- 11.10 Pros and cons of hybridization and sequencing.- 11.11 Fossil DNA.- 12 Palaeotaxonomy, Biogeography, Evolution and Extinction.- 12.1 Palaeotaxonomy.- 12.2 Biogeography.- 12.3 Coevolution.- 12.4 Phylogenetic trees and the pattern of evolution.- 13 Museums, Herbaria, Biodiversity, Conservation and the Future of Taxonomy.- 13.1 Museums and their roles.- 13.2 The future of taxonomy.