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Empirical Approaches to Introducing Phylogenetic Trees

Empirical Approaches to Introducing Phylogenetic Trees. Introduction: Students often find it difficult to understand the concept of phylogeny . Our goal was to develop classroom exercises to introduce how evolutionary changes alter the genetic tree. Climbing a Tree. Finding a tree

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Empirical Approaches to Introducing Phylogenetic Trees

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  1. Empirical Approaches to Introducing Phylogenetic Trees

  2. Introduction: Students often find it difficult to understand the concept of phylogeny . Our goal was to develop classroom exercises to introduce how evolutionary changes alter the genetic tree

  3. Climbing a Tree

  4. Finding a tree Order the oligonucleotides with respect to their position in the cladogram below. P0 CCCGGGGGCCCCAACCCCCCCCCCCCCCCCCCGGGGGCCC 40 P1 CCCGGGGGCCCCAACCCCCCCCCCCCCAACCCGGGGGCCC 40 P2 CCCGGGGGCCCCAACCCCCAACCCCCCCCCCCGGGGGCCC 40 P3 CCCGGGGGCCCCCCCCCCCAACCCCCCAACCCGGGGGCCC 40 P4 CCCGGGGGCCCCAACCCCCCCCCCCCCAACCCGGGGGCCC 40 P5 CCCGGGGGCCCCCCCCCCCCCCCCCCCAACCCGGGGGCCC 40

  5. Preparing to climb P0 CCCGGGGGCCCCAACCCCCCCCCCCCCCCCCCGGGGGCCC 40 P2 CCCGGGGGCCCCAACCCCCAACCCCCCCCCCCGGGGGCCC 40 P3 CCCGGGGGCCCCCCCCCCCAACCCCCCAACCCGGGGGCCC 40 P5 CCCGGGGGCCCCCCCCCCCCCCCCCCCAACCCGGGGGCCC 40 P1 CCCGGGGGCCCCAACCCCCCCCCCCCCAACCCGGGGGCCC 40 P4 CCCGGGGGCCCCAACCCCCCCCCCCCCAACCCGGGGGCCC 40

  6. Sizing up the branches P0 CCCGGGGGCCCCAACCCCCACCCCCCCCCCCCGGGGGCCC 40 P2 CCCGGGGGCCCCAACCCCCAACCCCCCCCCCCGGGGGCCC 40 P3 CCCGGGGGCCCCCCCCCCCAACCCCCCAACCCGGGGGCCC 40 P5 CCCGGGGGCCCCCCCCCCCCCCCCCCCAACCCGGGGGCCC 40 P1 CCCGGGGGCCCCAACCCCCCCCCCCCCAACCCGGGGGCCC 40 P4 CCCGGGGGCCCCAACCCCCCCCCCCCCAACCCGGGGGCCC 40

  7. Let’s Climb! P0 CCCGGGGGCCCCAACCCCCACCCCCCCCCCCCGGGGGCCC 40 P2 CCCGGGGGCCCCAACCCCCAACCCCCCCCCCCGGGGGCCC 40 P3 CCCGGGGGCCCCCCCCCCCAACCCCCCAACCCGGGGGCCC 40 P5 CCCGGGGGCCCCCCCCCCCCCCCCCCCAACCCGGGGGCCC 40 P1 CCCGGGGGCCCCAACCCCCCCCCCCCCAACCCGGGGGCCC 40 P4 CCCGGGGGCCCCAACCCCCCCCCCCCCAACCCGGGGGCCC 40

  8. Awesome View!

  9. Going back down . . . P0 CCCGGGGGCCCCAACCCCCCCCCCCCCCCCCCGGGGGCCC 40 P1 CCCGGGGGCCCCAACCCCCCCCCCCCCAACCCGGGGGCCC 40 P2 CCCGGGGGCCCCAACCCCCAACCCCCCCCCCCGGGGGCCC 40 P3 CCCGGGGGCCCCCCCCCCCAACCCCCCAACCCGGGGGCCC 40 P4 CCCGGGGGCCCCAACCCCCCCCCCCCCAACCCGGGGGCCC 40 P5 CCCGGGGGCCCCCCCCCCCCCCCCCCCAACCCGGGGGCCC 40 P6 CCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCC 40

  10. Back on land . . . Substitute one A residue for one C residue in two of the oligonucleotides below to convert the upper cladogram to the lower. Check your answer using Clustalw andsubmit a correct answer to your instructor. Thanks! P0 CCCGGGGGCCCCAACCCCCCCCCCCCCCCCCCGGGGGCCC 40 P2 CCCGGGGGCCCCAACCCCCAACCCCCCCCCCCGGGGGCCC 40 P3 CCCGGGGGCCCCCCCCCCCAACCCCCCAACCCGGGGGCCC 40 P5 CCCGGGGGCCCCCCCCCCCCCCCCCCCAACCCGGGGGCCC 40 P1 CCCGGGGGCCCCAACCCCCCCCCCCCCAACCCGGGGGCCC 40 P4 CCCGGGGGCCCCAACCCCCCCCCCCCCAACCCGGGGGCCC 40

  11. Exercise 2:

  12. WARISHELL • WARISHALL • WARISBALL • WARISABALL • WARISAMALL • WARISAMALT • WARISAMALE • MAREISAMALE • MATEISAMALE • MYMATEISAMALE • MYMATEISAFEMALE

  13. WARISHELL • WARISHALL • WARISBALL • WARISABALL • WARISAMALL • WARISAMALT • WARISAMALE • MAREISAMALE • MATEISAMALE • MYMATEISAMALE • MYMATEISAFEMALE

  14. WARISHELL • WARISHALL • WARISBALL • WARISABALL • WARISAMALL • WARISAMALT • WARISAMALE • MAREISAMALE • MATEISAMALE • MYMATEISAMALE • MYMATEISAFEMALE

  15. WARISHELL • WARISHALL • WARISBALL • WARISABALL • WARISAMALL • WARISAMALT • WARISAMALE • MAREISAMALE • MATEISAMALE • MYMATEISAMALE • MYMATEISAFEMALE

  16. WARISHELL • WARISHALL • WARISBALL • WARISABALL • WARISAMALL • WARISAMALT • WARISAMALE • MAREISAMALE • MATEISAMALE • MYMATEISAMALE • MYMATEISAFEMALE

  17. WARISHELL • WARISHALL • WARISBALL • WARISABALL • WARISAMALL • WARISAMALT • WARISAMALE • MAREISAMALE • MATEISAMALE • MYMATEISAMALE • MYMATEISAFEMALE

  18. WARISHELL • WARISHALL • WARISBALL • WARISABALL • WARISAMALL • WARISAMALT • WARISAMALE • MAREISAMALE • MATEISAMALE • MYMATEISAMALE • MYMATEISAFEMALE

  19. WARISHELL • WARISHALL • WARISBALL • WARISABALL • WARISAMALL • WARISAMALT • WARISAMALE • MAREISAMALE • MATEISAMALE • MYMATEISAMALE • MYMATEISAFEMALE

  20. WARISHELL • WARISHALL • WARISBALL • WARISABALL • WARISAMALL • WARISAMALT • WARISAMALE • MAREISAMALE • MATEISAMALE • MYMATEISAMALE • MYMATEISAFEMALE

  21. WARISHELL • WARISHALL • WARISBALL • WARISABALL • WARISAMALL • WARISAMALT • WARISAMALE • MAREISAMALE • MATEISAMALE • MYMATEISAMALE • MYMATEISAFEMALE

  22. WARISHELL • WARISHALL • WARISBALL • WARISABALL • WARISAMALL • WARISAMALT • WARISAMALE • MAREISAMALE • MATEISAMALE • MYMATEISAMALE • MYMATEISAFEMALE

  23. Unrooted tree (generated by Phylip's Drawtree)

  24. Unrooted tree (generated by Phylip's Drawtree)

  25. Real World Example: Below are amino acid sequences for insulin Which ones would you predict to be similar? Which ones would you predict to be different?

  26. Questions? Comments?

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