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Bioinformatics CSM17 Week 4: Evolutionary systems

Delve into the fascinating world of evolutionary systems, covering the historical roots with figures like Charles Darwin and Cronquist, modern methods including cladistics and tools like HENNIG86 and PAUP. Learn the principles of phylogeny, evolution, and cladistics while exploring the evolution of species and the use of tools and software for phylogenetic analysis. Discover the importance of character congruence, homology, and parsimony in understanding evolutionary relationships. With references and useful websites provided for further exploration.

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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 • now at version 3.6 (beta) • 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 • 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) • Forey, P.L. et al. (1993) Cladistics - a practical course in systematics. Systematics Association Publication No. 10. Clarendon Press, Oxford, UK. ISBN 0-19-857766-4 (paperback) [superceded by Kitching et al!] • 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) • 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) JYC: CSM17

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