The BEDROCK Project
    EOT-PACI
National Science Foundation
Howard Hughes Medical Institute
Thammasat University


"Phylogenetic Trees: Reclassifying Life, Retelling Time; Topo-, Chrono-, and Patrocladistics"

Abstract: Bioinformatics is the science of deriving evolutionary inferences from molecular data. Many powerful computer tools exist for conducting bioinformatic analyses, but proper interpretation of these tools' output requires a solid grasp of evolutionary principles. Particularly crucial is the ability to understand the graphs that represent the genealogy of relationships called phylogenetic trees. In this talk, we will introduce some basic phylogenetic concepts using simple tree-building exercises: ultrametric trees, additive trees, enumerating trees. A discussion of split decomposition will highlight the nature of trees as testable evolutionary hypotheses rather than as definitive answers. Several technical concepts that are extraordinary helpful in constructing and evaluating trees include the use of outgroups, to root trees, resolution of homoplasies, measurements of tree improvement, three aspects of homology: Orthology, Paralogy, Xenology , and triangulation of inference based on on trees, multiple sequence alignments, and either representation of relationships on a map, a timeline, or a three-dimensional view of a molecule. Finally, we will present two HIV data sets that allow students to conduct bioinformatic analyses and explore evolutionary issues in a research-like environment. Most of the data and tools covered in this presentation are available online at no charge.

  • Phylogenetic trees and tools
    • Ultrametric trees
    • Additive trees
    • Enumerating tree topologies
    • Distance-based versus character-based trees
    • Multiple sequence alignment
    • Cladistics
    • Tree length and consistency index
    • Split decomposition
  • Phylogeography and Topocladistics
    • Multiple sequence alignment
    • Phylogenetic tree with terminal leaves distributed to particular location on a Map
  • Molecular Clocks and Chronocladistics
    • Multiple sequence alignment
    • Phylogenetic tree with terminal leaves distributed to particular location on a Chronometer (e.g., geological time scale of eras, stratigraphic column, molecular clock)
  • Molecular Genealogy and Patrocladistics
    • Multiple sequence alignment
    • Phylogenetic tree with terminal leaves distributed in relationship to a Pedigree, Fate map, or known phylogenetic record (tree)
  • Homology
    • Orthology
    • Paralogy
    • Xenology
  • Deep Phylogenies
    • Long branch attraction problem (rooting your tree)
    • Biases of composition (mutation models)
    • Molecular clocks don't run on time (ultrametric trees again)

Books:

Avise J.C. 2000. Phylogeography: The History and Formation of Species. Harvard University Press: Cambridge, MA.

Eggleton P. and Vane-Wright R.I., eds. 1994. Phylogenetics and Ecology. Academic Press: San Diego, CA.

Felsenstein Joseph. 2003. Inferring Phylogenies. Sinauer Associates: Sunderland, MA.

Humphries C.J. and Parenti L.R. 1999. Cladistic Biogeography 2nd Edition: Interpreting Patterns of Plant and Animal Distributions. Oxford University Press: Oxford, U.K.

Maddison David R. and Maddison Wayne P. 2000. MacClade 4: Analysis of Phylogeny and Character Evolution. Sinauer Associates: Sunderland, MA.

Miyamoto, Micheal M. and Joel Craycraft, editors. 1991. Phylogenetic Analysis of DNA Sequences. Oxford University Press: New York, NY.

Page, Roderic D. M., editor. 2003. Tangled Trees: Phylogeny, Cospeciation, and Coevolution . University of Chicago Press: Chicago, IL.

Semple, Charles and Michael Steel. 2003. Phylogenetics Oxford University Press : New York, NY.

Web sites:

Tutorial:      http://www.science.uts.edu.au/sasb/WestonCrisp.html

 

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