JYC: CSM17 BioinformaticsCSM17 Week2: Biological Classification Fundamental concepts Traditional...
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JYC: CSM17
Bioinformatics CSM17 Week2: Biological Classification• Fundamental concepts
• Traditional methods
• Nomenclature (naming)
• Taxonomy & systematics
• Overview of main ‘systems’
• Cluster analysis / Numerical Taxonomy
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JYC: CSM17
Fundamental concepts
• the species concept• classification has its roots in biology• homology
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JYC: CSM17
Traditional/classical methods
• Floras & monographs• New species• Herbaria & museums• Mostly phenotypic characters
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JYC: CSM17
Herbarium of the Royal Botanic Gardens, Kew (London, UK)
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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
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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 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
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JYC: CSM17
Lithops karasmontana subsp. bella (N.E.Br.) D.T.Cole
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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
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JYC: CSM17
Overview of Life
• viruses
• bacteria
• algae
• protista - e.g. Amoeba, Paramecium
• mosses & liverworts
• higher plants
• animals
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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 5-100 million yet to be discovered
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JYC: CSM17
Biological variation• helps ensure survival• phenotypic plasticity
– environmental conditions
• genotypic variation– the ‘real’ (encoded) variation
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JYC: CSM17
Rosa canina var. lutetiana f. lasiostylus• Kingdom Plantae• Division (Phylum) Tracheophyta• Class Angiospermopsida• Order Rosales• Family Rosaceae• Genus Rosa• Species canina• Subspecies• Variety (var.) lutetiana• Form (f.) lasiostylis
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JYC: CSM17
Numerical taxonomy
• Multivariate analysis
• Cluster analysis / clustering
• using a computer…
• Sneath & Sokal 1960s, 1970s
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JYC: CSM17
Distance Measures (Metrics)
• Similarity / Dissimilarity...• Euclidean distance
– Standardisation & Normalisation
• Sneath’s simple matching coefficient
• Gower’s similarity coefficient
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JYC: CSM17
Dendrograms
• Tree diagrams
• Phenograms
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JYC: CSM17
Linkage methods
• Nearest Neighbour (single link)
• Furthest Neighbour
• Group Average Link (complete link e.g. UPGMA)
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JYC: CSM17
DELTA
• DEscriptive Language for TAxonomy
• a suite of programs and tools
• a database format
• uses text-based files
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JYC: CSM17
PCLASS• a cluster analysis tool bundled with
DELTA
• an example treefile...(((((((DAS3:0.07322,AME1:0.07322):0.02505,(AME3:0.06559,AME2:0.06559):0.03269):0.02093,(HET2:0.08696,HET1:0.08696):0.03225):0.01429,(TUA2:0.06325,TUA1:0.06325)
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JYC: CSM17
TREEVIEW
• a dendrogram (tree diagram) generator
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JYC: CSM17
Useful Websites & Journals• Taxon - the journal for botanical taxonomists
www.botanik.univie.ac.at/iapt/• IPNI: www.ipni.org• Kew Gardens: www.kew.org• TREEVIEW:
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
• DELTA: http://delta-intkey.com/
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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: 357-358.
• 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