Principles and Techniques of Contemporary Taxonomy

ISBN-13: 9789401049450 / Angielski / Miękka / 2013 / 311 str.

Donald L.J. Quicke

Opis

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.

Spis treści

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.- 2.2.1 Discrete coding of continuous characters and ratios.- 2.2.2 Identifying primitive and advanced character states.- 2.2.3 Homoplasy: convergence, parallelisms and reversals.- 2.2.4 Homology versus analogy.- 2.2.5 Character state transitions.- 2.2.6 Dealing with missing data and polymorphic characters.- 2.3 Classes of characters requiring special consideration.- 2.3.1 Characters subject to strong selection pressures.- 2.3.2 Environmental effects.- 2.3.3 Molecular sequence characters.- 2.3.4 Electron microscopy and the use of microcharacters.- 2.3.5 Colour as a taxonomic character.- 2.3.6 Cryptic and internal characters.- 2.3.7 Animal artefacts.- 2.3.8 Behavioural characters.- 2.4 Taxa and species concepts.- 2.4.1 Phylogenetic groups: monophyly, polyphyly and paraphyly.- 2.5 What is a species?.- 2.5.1 Biological species concept.- 2.5.2 Phvlogenetic species concept.- 2.5.3 Evolutionary species concept.- 2.5.4 Problems with parthenogenetic species and asexual clones — some further considerations.- 3 Phylogenetic Reconstruction — Cladistics and Related Methods.- 3.1 Cladistics and cladograms.- 3.1.1 Parsimony.- 3.1.2 Compatibility analysis.- 3.1.3 Maximum likelihood and related methods.- 3.2 Parsimony and finding the shortest trees.- 3.2.1 Finding the shortest trees and the impact of computerization.- 3.2.2 Tree facts and figures.- 3.2.3 Building trees from distance data.- 3.2.4 Rooting trees.- 3.2.5 Consistency and other indices.- 3.2.6 Weighting characters.- 3.2.7 Coping with multiple trees.- 3.2.8 Consensus trees.- 3.2.9 Comparing trees.- 3.3 Which method? — an overview.- 3.3.1 How well does parsimony analysis estimate trees?.- 3.3.2 Compatibility versus parsimony.- 3.3.3 Congruence between data sets (or how do we know when to believe a phylogeny?).- 3.3.4 Reticulate evolution, hybrids and intraspecific evolution.- 3.4 Cladistics and classification.- 4 Phenetic Methods in Taxonomy.- 4.1 Introduction.- 4.1.1 Similarity and distance measures.- 4.1.2 Measures using binary characters.- 4.1.3 Distance and similarity measures using continuous data.- 4.2 Analysing similarity and distance data.- 4.3 Hierarchic clustering procedures.- 4.3.1 Nearest neighbour clustering.- 4.3.2 Furthest neighbour (complete linkage).- 4.3.3 Unweighted pair-group method using arithmetic averages (UPGMA).- 4.3.4 Weighted pair-group method using arithmetic averages (WPGMA).- 4.3.5 Centroid clustering.- 4.4 Ordination methods.- 4.4.1 Principal components analysis.- 4.4.2 Principal coordinate analysis.- 4.4.3 Canonical variate analysis.- 4.4.4 Non-metric multidimensional scaling.- 5 Keys and Identification.- 5.1 Introduction.- 5.1.1 Purpose of keys.- 5.1.2 Good practice in writing keys.- 5.2 Types of keys.- 5.2.1 Dichotomous keys.- 5.2.2 Multiple-entry keys.- 5.3 Efficiency.- 5.3.1 Length of dichotomous keys.- 5.3.2 Reliability.- 5.3.3 Choice of characters.- 5.3.4 Likelihood of encountering taxon.- 5.4 Computerized key construction.- 5.4.1 Interactive identification.- 5.4.2 Matching.- 5.4.3 Automated taxon descriptions.- 5.4.4 Databases.- 6 Nomenclature and Classification.- 6.1 Introduction.- 6.2 The binomial system and the hierarchy of taxa.- 6.3 The International Commissions.- 6.3.1 Codes of nomenclature.- 6.3.2 Independence of the Codes.- 6.4 Basic principles of nomenclature.- 6.4.1 Priority.- 6.4.2 Synonymy.- 6.4.3 Homonymy.- 6.4.4 The type concept.- 6.5 Miscellaneous group-related factors.- 6.5.1 Animals and animal-like Protista.- 6.5.2 Plants and plant-like Protista.- 6.5.3 Fungi.- 6.5.4 Lichens.- 6.5.5 ‘Blue-green algae’ (Cyanophyta versus Cyanobacteria).- 6.5.6 Bacteria and other prokaryotes.- 6.5.7 Viruses.- 6.5.8 Organisms showing extreme polymorphisms.- 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.- 8.2.1 Sex pheromones.- 8.2.2 Lipids and hydrocarbons.- 8.2.3 Secondary plant metabolites.- 8.2.4 Neurotransmitters.- 8.2.5 Pigments.- 8.2.6 Animal toxins.- 8.2.7 Pyrolysis products.- 8.3 Fermentation properties and drug resistance in microorganisms.- 8.4 The 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.- 10.2.1 SDS polyacrylamide electrophoresis.- 10.2.2 Gradient gel electrophoresis.- 10.2.3 Isoelectric focusing.- 10.2.4 Two-dimensional electrophoresis.- 10.3 Systematic aspects of electrophoresis.- 10.3.1 Isozymes and allozymes.- 10.3.2 Interpreting allozyme banding.- 10,3.3 Analysis of allozyme data.- 10.3.4 Isozymes at subspecies, species and genus level.- 10.4 Chemical protein analysis procedures.- 10.4. I Selective cutting of protein chains.- 10.4.2 Chromatography of digests.- 10.4.3 Amino acid sequencing.- 10.5 Analysis of amino acid sequence data.- 10.5.1 Minimum nucleotide replacement.- 10.5.2 Merits of minimum nucleotide replacement analysis.- 11 Nucleic Acid Methods.- 11.1 Nucleic acids in taxonomy.- 11.2 Nucleic acids in cells.- 11.2.1 Nuclear DNA.- 11.2.2 Repetitive DNA.- 11.2.3 Mitochondrial DNA.- 11.2.4 Chloroplast DNA.- 11.2.5 Ribosomal RNA and ribosomal genes.- 11.2.6 Transfer RNAs and the genetic code.- 11.2.7 Prokaryote and viral genomes.- 11.3 Amplifying DNA and dealing with small samples.- 11.3.1 Cloning.- 11.3.2 Polymerase chain reaction.- 11.4 G+C content.- 11.5 Restriction fragment analysis.- 11.6 DNA hybridization.- 11.6.1 Interpretation of DNA hybridization data.- 11.7 Sequencing and associated methods.- 11.8 Conservation versus variability.- 11.9 Analysing sequence data.- 11.9.1 Sequence alignment.- 11.9.2 Transition and transversion rates.- 11.9.3 Insertions and deletions.- 11.9.4 Paired and unpaired nucleotides in tRNAs and rRNAs.- 11.9.5 A brief overview of the phylogenetic analysis of sequence data.- 11.10 Pros and cons of hybridization and sequencing.- 11.11 Fossil DNA.- 12 Palaeotaxonomy, Biogeography, Evolution and Extinction.- 12.1 Palaeotaxonomy.- 12.1.1 Completeness of the fossil record.- 12.1.2 Interpretation of evidence.- 12.1.3 The palaeo-species concept.- 12.1.4 Phylogenetic analysis and classification of fossil taxa.- 12.1.5 Phylogenetic aspects of fossil taxa.- 12.1.6 Inclusion in classification of extant organisms.- 12.1.7 Stratigraphy, evolutionary rates and molecular clocks.- 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.- 13.1.1 Management of museum collections.- 13.1.2 Museum funding.- 13.1.3 Specimens and data.- 13.1.4 Living culture collections.- 13.1.5 Voucher specimens.- 13.2 The future of taxonomy.- 13.2.1 Biodiversity and conservation priorities.- 13.2.2 Taxonomy, zoos and captive breeding.- 13.2.3 Taxonomy and legislation.