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Studying Evolution Through Computational Phylogeny

Studying Evolution Through Computational Phylogeny. Yulia Newton University of California Santa Cruz ynewton@soe.ucsc.edu http://users.soe.ucsc.edu/~ynewton /. Types of Evolution. Types of Evolution. Different Ways to Draw an Evolutionary Tree. and many more …. Tree Anatomy. clade.

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Studying Evolution Through Computational Phylogeny

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  1. Studying Evolution Through Computational Phylogeny Yulia Newton University of California Santa Cruz ynewton@soe.ucsc.edu http://users.soe.ucsc.edu/~ynewton/

  2. Types of Evolution

  3. Types of Evolution

  4. Different Ways to Draw an Evolutionary Tree and many more …

  5. Tree Anatomy clade edge nodes root

  6. Roots Common ancestor http://www.snowballearth.org/

  7. Root Placement

  8. Outgroup Use http://www.cscs.umich.edu/

  9. Outgroup Use (Cont’d) Da-FeiFeng, Glen Cho, and Russell F. Doolittle. Determining divergence times with a protein clock: Update and reevaluation, PNAS, 1997.

  10. Cladogram • Cladogram – all taxa are at the same level • Tells us how long ago speciation for each taxa happened http://evolution.berkeley.edu/

  11. Phylogram • Phylogram – the length of the edge indicates how much evolution happened since the last common ancestor • Tells us how closely two species are related

  12. Phylogram (cont’d) http://scientopia.org/

  13. Cladogram vs. Phylogram http://www.mrent.org/

  14. Cladogram vs. Phylogram

  15. Steps for Building Phylogenetic Trees

  16. Newick Format output Text format representation of the tree: (((A,C), (B,D)), (E,F)) input

  17. Drawing Tree From Newick Format (((A,C), (B,D)), (E,F))

  18. Drawing Tree From Newick Format (((A,C), (B,D)), (E,F))

  19. Drawing Tree From Newick Format (((A,C), (B,D)), (E,F))

  20. Drawing Tree From Newick Format (((A,C), (B,D)), (E,F))

  21. Drawing Tree From Newick Format (((A,C), (B,D)), (E,F))

  22. Drawing Tree From Newick Format (((A,C), (B,D)), (E,F))

  23. Which two are the closest relatives?

  24. Which two are the closest relatives?

  25. Which two are the closest relatives?

  26. Which two are the closest relatives?

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