"in silico DNA, RNA, Protein Sequence,
and Structure Analysis:
Theory and Practice"

9:30 AM Phylogenetic Trees II: Cladistics and Character Based trees; Evolutionary Genetics; Tree Statistics.

How do molecular and morphological characteristics differ in their use and methodologies for developing phylogenetic trees? Cladistics is a contemporary form of evolutionary taxonomy that is based on "a system of derivation from a single originating group based on the number of shared derived characteristics. A clade is a lineage of descent from a single branching point in the cladogram. The ideal cladogram will not only show [inferred] evolutionary relationships between groups, but will also accurately reflect how long they have been separated. Derived characteristics are synapomorphies, whereas shared ancestral characteristics are symplesiomorphies. The presence of shared ancestral characters simply [allows us to infer something] about overall relatedness but nothing about degrees of relatedness In its most pared-down form, molecular cladistics looks at the number of similarities between molecules performing similar functions in different groups.... To decipher the very complicated patterns that can arise from the vast amount of data, taxonomists are increasingly turning to computer models that will attempt to derive the most parsimonious cladograms possible: that is those that best agree with the available data. However, even this approach can lead to disagreements over fine details -- most recently in the argument over "African Eve" - the concept that all modern humans derive from a small precursor group emerging from Africa around 200,000 years ago"Quote from James Michael Cummins Associate Professor in Anatomy, Murdoch University. (http://numbat.murdoch.edu.au/Anatomy/fmhv/lecture3.html).

How does all that chromosomal DNA fit into a 1 micron cubed space of a bacterial cell without being a knotted tangle? What is a coiled coiled coiled coil structure of DNA in an eucaryotic chromosome? How do topisomerases, helicases, and recombinases work? Links, writhes, twists, and concatenanes will be introduced in such a fashion that will help you look at electron micrographs of DNA or electrophoretograms of supercoiled DNA with understanding. Hence, we can appreciate the theoretician's ironic maxim: "I wouldn't have seen it, if I had not believed it."

Supercomputing for molecular cladistics (D. Sankoff, Y. Abel, R.J. Cedergren & M.W. Gray) Classification and Related Methods of Data Analysis (H.H. Bock, ed.) Amsterdam: North-Holland, 385-394 (1988). FROM: http://www.ucmp.berkeley.edu/clad/clad4.html

Daniel R. Brooks and Deborah A. McLennan. 1991. Phylogeny, Ecology, and Behavior. University of Chicago Press, Chicago, USA. 434 pages.

Niles Eldridge and Joel Cracraft. 1980. Phylogenetic Patterns and the Evolutionary Process. Columbia University Press, New York, USA. 348 pages.

Paul H. Harvey and Mark D. Pagel. 1991. The Comparative Method in Evolutionary Biology. Oxford University Press, Oxford & New York. 239 pages.

Wayne P. Maddison and David R. Maddison. 1992. MacClade: Analysis of phylogeny and character evolution. Version 3.0. Sinauer Associates, Sunderland, Massachusets, USA.

D. L. Swofford. 1991. Phylogenetic Analysis Using Parsimony (PAUP), version 3.0s. Illinois Natural History Survey, Champaign, Illinois, USA.

E. O. Wiley, D. Siegel-Causey, D. R. Brooks, & V. A. Funk. 1991. The Compleat Cladist: a primer of phylogenetic procedures. Univ. of Kansas Museum of Natural History, Spec. Pub. No. 19.

The empirical discovery of phylogenetic invariants (V. Ferretti & D. Sankoff) Advances in Applied Probability 25, 290-302(1993).

Probability models for genome rearrangement and linear invariants for phylogenetic inference (D.Sankoff & M. Blanchette) Proceeedings of the Third Annual International Conference on Computational Molecular Biology (RECOMB 99) (S.Istrail, P.Pevzner M.Waterman, eds.) New York:ACM Press, 302-309 (1999).

Reconstructing the pre-doubling genome (N. El-Mabrouk, D. Bryant, and D. Sankoff) Proceeedings of the Third Annual International Conference on Computational Molecular Biology (RECOMB 99) (S.Istrail, P.Pevzner M.Waterman, eds.) New York:ACM Press, 154-163 (1999).

Simmons, Henry. 198. "DNA Topology: Knots No Sailor Ever Knew." Mosaic 2(1):2-10 (January/February).

Scovell, William M. 1986. "Supercoiled DNA." J. Chemical Education 63(7):562-565.

Dazey, Isabel K., Spengler, Sylvia J. and Sumners, De Witt. Department of Mathematics, Florida State University, Tallahassee, FL USA.

V½zquez, Ma. Elena, Dazey, Isabel, and Sumners, De Witt. "Tangle Analysis of Processive Gin Recombination." Department of Mathematics, Florida State University, Tallahassee, FL USA