JYC: CSM17 BioinformaticsCSM17 Week2: Biological Classification Fundamental concepts Traditional methods Nomenclature (naming) Taxonomy & systematics Overview.

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Presentation transcript:

JYC: CSM17 BioinformaticsCSM17 Week2: Biological Classification Fundamental concepts Traditional methods Nomenclature (naming) Taxonomy & systematics Overview of main ‘systems’ Cluster analysis / Numerical Taxonomy

JYC: CSM17 Fundamental concepts the species concept classification has its roots in biology homology

JYC: CSM17 Traditional/classical methods Floras & monographs New species Herbaria & museums Mostly phenotypic characters

JYC: CSM17 Herbarium of the Royal Botanic Gardens, Kew (London, UK)

JYC: CSM17 Nomenclature (Naming) the type concept the binomial system –Carolus Linnaeus, Species Plantarum (1753) type descriptions (Latin) and authorities Index Kewensis IPNI (International Plant Names Index) ‘version control’ ICBN & ICZN

JYC: CSM17 How to interpret IPNI search Aizoaceae Lithops karasmontana subsp. bella (N.E.Br.) D.T.Cole -- Lithops Flowering Stones: 217 (1988):. (IK)Aizoaceae Lithops karasmontana subsp. bella (N.E.Br.) D.T.Cole Aizoaceae is the FAMILY Lithops is the GENUS karasmontana is the SPECIES bella is the SUBSPECIES (subsp.) N.E. Brown is the AUTHOR of Lithops bella N.E.Brown D.T. Cole decided that L. bella was a subsp. of L. karasmontana

JYC: CSM17 Lithops karasmontana subsp. bella (N.E.Br.) D.T.Cole

JYC: CSM17 Taxonomy and systematics Taxonomy –putting things into classes... –a ‘taxonomy’ is a classification system –‘taxonomy’ is the theory, principles & practice of classification Systematics –the scientific study of the variation of living organisms and the relationships between them

JYC: CSM17 Overview of Life viruses bacteria algae protista - e.g. Amoeba, Paramecium mosses & liverworts higher plants animals

JYC: CSM17 What is a species? the biological species concept the ‘practical’ species concept about 1.7 million known –about 300K green plants –about 1.05M animals approximately million yet to be discovered

JYC: CSM17 Biological variation helps ensure survival phenotypic plasticity –environmental conditions genotypic variation –the ‘real’ (encoded) variation

JYC: CSM17 Rosa canina var. lutetiana f. lasiostylus KingdomPlantae Division (Phylum) Tracheophyta Class Angiospermopsida Order Rosales Family Rosaceae Genus Rosa Species canina Subspecies Variety (var.) lutetiana Form (f.) lasiostylis

JYC: CSM17 Numerical taxonomy Multivariate analysis Cluster analysis / clustering using a computer… Sneath & Sokal 1960s, 1970s

JYC: CSM17 Distance Measures (Metrics) Similarity / Dissimilarity... Euclidean distance –Standardisation & Normalisation Sneath’s simple matching coefficient Gower’s similarity coefficient

JYC: CSM17 Dendrograms Tree diagrams Phenograms

JYC: CSM17 Linkage methods Nearest Neighbour (single link) Furthest Neighbour Group Average Link (complete link e.g. UPGMA)

JYC: CSM17 DELTA DEscriptive Language for TAxonomy a suite of programs and tools a database format uses text-based files

JYC: CSM17 PCLASS a cluster analysis tool bundled with DELTA an example treefile... (((((((DAS3: ,AME1: ): ,(AME3: ,AME2: ): ): ,(HET2: ,HET1: ): ): ,(TUA2: ,TUA1: )

JYC: CSM17 TREEVIEW a dendrogram (tree diagram) generator

JYC: CSM17 Useful Websites & Journals Taxon - the journal for botanical taxonomists IPNI: Kew Gardens: TREEVIEW: eeview.html eeview.html DELTA:

JYC: CSM17 References & Bibliography Dallwitz, M.J., Paine, T.A. & Zurcher, E.J. (1997). User’s guide to the DELTA system -a general system for processing taxonomic descriptions, Edition 4.07, CSIRO Division of Entomology: Canberra, Australia. Dunn, G. & Everitt, B.S. (1982). An introduction to mathematical taxonomy. Cambridge University Press, UK. Everitt, B.S. (1993). Cluster Analysis. John Wiley & Sons, New York, USA. Page, R. D. M. (1996). TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12: Pankhurst, R.J. (1991). Practical Taxonomic Computing. University of Cambridge Press: UK. Sneath, P.H.A. & Sokal, R.R. (1973). Numerical Taxonomy. W.H.Freeman, San Francisco, USA. Stace, C.A. (1980). Plant Taxonomy & Biosystematics. Edward Arnold, London