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Bioinformatics CSM17 Week 4: Evolutionary systems

Bioinformatics CSM17 Week 4: Evolutionary systems. Evolution and phylogeny Historical systems Modern methods Tools and software. Evolution and phylogeny. definition of terms what is phylogeny? what is evolution?. Historical systems. Charles Darwin Cronquist (plants)

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Bioinformatics CSM17 Week 4: Evolutionary systems

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  1. Bioinformatics CSM17 Week 4: Evolutionary systems • Evolution and phylogeny • Historical systems • Modern methods • Tools and software JYC: CSM17

  2. Evolution and phylogeny • definition of terms • what is phylogeny? • what is evolution? JYC: CSM17

  3. Historical systems • Charles Darwin • Cronquist (plants) • Mostly phenotypic characters JYC: CSM17

  4. Historical systems • Charles Darwin • The voyage of the Beagle • The Galapagos Islands • The Origin of Species (1859) JYC: CSM17

  5. Modern methods • Cladistics • Willi Hennig (1950, 1966) • Phylogenetic systematics JYC: CSM17

  6. Cladistics principles • clades • convergence (homoplasy) • parallelism • apomorphy and synapomorphy • plesiomorphy and symplesiomorphy • has 4 main Axioms (assumptions, premises) JYC: CSM17

  7. Cladistics axiom #1 • Nature’s hierarchy can be represented by a branching diagram • Cladograms • Monophyly JYC: CSM17

  8. Cladistics axiom #2 • Characters change status at different hierachical levels. Those present in all members of the group, or have a wider distribution than the group cannot indicate relationships within the group • Outgroup(s) JYC: CSM17

  9. Cladistics axiom #3 • Character congruence is the decisive criterion for distinguishing homology from non-homology JYC: CSM17

  10. Cladistics axiom #4 • The principle of parsimony maximises character congruence • Occam’s Razor - the simplest is best JYC: CSM17

  11. Cladistics terms • apomorphy (advanced, derived) • synapomorphy (shared and advanced) • plesiomorphy (primitive, ancestral) • symplesiomorphy (shared and ancestral) JYC: CSM17

  12. Tools and software • HENNIG86 (Farris, 1988) • PAUP (Swofford, 1983) • PHYLIP (Felsenstein, 1985) • MacClade (Maddison & Maddison, 1987) JYC: CSM17

  13. HENNIG86 • The first! • Willi Hennig • Characters polarised before cladogram construction JYC: CSM17

  14. PAUP • Swofford (1983) • widely used on Mac • recently available for PC • costs money... JYC: CSM17

  15. PHYLIP • by Joe Felsenstein (Univ. Washington) • produced in 1985 • for a number of platforms (incl. PC) • FREE! (by download) JYC: CSM17

  16. PARS • A Parsimony method • Wagner parsimony JYC: CSM17

  17. Useful Websites • PHYLIP http://evolution.genetics.washington.edu/phylip.html • HENNIG Society: http://www.cladistics.org/education.html • TREE OF LIFE http://tolweb.org/tree/phylogeny.html JYC: CSM17

  18. References & Bibliography • Krane, D.E. & Raymer, M.L. (2003) Fundamental concepts of bioinformatics. Benjamin Cummings Publishers, San Francisco, USA. ISBN 0-8053-4633-3 (paperback) Chapter 5. • Kitching, I. J. et al. (1998) Cladistics - the theory and practice of parsimony analysis. Systematics Association Publication No. 11. Oxford University Press, UK. ISBN 0-19-850138 (paperback) • Skelton, P. & Smith, A (2002). Cladistics – a practical primer on CD-ROM. Cambridge University Press, UK. ISBN 0-521-52341 (hardback + CD-ROM) • Pankhurst, R. J. (1991) Practical Taxonomic Computing. Cambridge University Press, UK. pp. 68-87. ISBN 0-521-41760-0 (hardback) • Lewin, R. (1999). Patterns in Evolution. Scientific American Library, New York • Gee, H. (2000) Deep Time - cladistics, the revolution in evolution. Fourth Estate Ltd., London, UK. • Gibas, C. & Jambeck, P. (2001). Developing bioinformatics computer skills. O’Reilly, USA. pp. 199-205. ISBN 1-56592-664-1 (paperback) JYC: CSM17

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