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Phylogenetic trees: Computer models of evolution Dr Dan Everett CSCI 1210

Phylogenetic trees: Computer models of evolution Dr Dan Everett CSCI 1210. Gene sequence and active sites. This diagram represents the amino acid sequence of the gene for Yeast Ubiquitin Activating Enzyme , UBA-1 Colored regions are conserved – no random mutations observed.

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Phylogenetic trees: Computer models of evolution Dr Dan Everett CSCI 1210

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  1. Phylogenetic trees: Computer models of evolution Dr Dan EverettCSCI 1210

  2. Gene sequence and active sites • This diagram represents the amino acid sequence of the gene for Yeast Ubiquitin Activating Enzyme, UBA-1 • Colored regions are conserved – no random mutations observed

  3. Triosephosphate Isomerase

  4. Sequence differences • The sequences are peptides, not DNA codons • The sequences must be aligned to correct for insertions and deletions (hard problem) • Monkey vs. human proteins show fewer differences than spinach vs. rice

  5. Sequence distance matrix

  6. First step in the tree construction • Humans and monkeys are most closely related of all pairs of species in the table. • Create an initial subtree. (Hypothetical common ancestors in green)

  7. Revised distance matrix:

  8. Second subtree:

  9. Revised distance matrix, again

  10. The Final tree…

  11. Why this result is significant… • Before DNA techniques, biologists constructed phylogenetic trees using traditional tools (fossils, anatomy, etc) • DNA tools provide an independent method for constructing phylogenetic trees • Trees constructed with different methods match quite well!

  12. A common human ancestor… • Can the scenario on the right happen? • Can the scenario on the left happen? • M1 must be smaller than H!

  13. … must exist! But when and where?

  14. Mitochondrial DNA • Mitochondria are the “energy factories” of the cell • Mitochondria float in the cytoplasm • They have their own DNA and reproduce independently of the cell nucleus • Passed by mother to child in the egg • Not subject to sexual recombination, so simpler to track

  15. The “Out of Africa” Hypothesis • This phylogenetic tree constructed using mitochondrial DNA from 145 humans • Consistent with migration of original humans from Africa • Numbers represent thousands of years since common ancestor

  16. “Mitochondrial Eve” • Existed about 200,000 years ago in Africa • Was the common female ancestor of all living humans • Was NOT the only living female at the time! • Use mitochondrial DNA because we inherit it from our mothers only Rebecca Cann et al, Nature 1987

  17. Critique of “Mitochondrial Eve” • Rates of ‘neutral’ mutation are not constant • In some cases mitochondrial DNA has combined with nuclear DNA from the father • Do these problems invalidate the theory? http://www.apologeticspress.org/docsdis/2003/dc-03-01.htm

  18. Acknowledgements Human family tree: Dr Curtis Strobeck, University of Alberta • http://www.biology.ualberta.ca/courses/biol380/uploads/winter03/lecture/b1/curt_strobeck/public/lectures/Lecture_26_Tree_of_Individuals.pdf • UAB-1 gene sequence:http://www.nottingham.ac.uk/biochemcourses/students/ub/e1.html • Phylogentic tree computation example: Gaston Gonnet, • Institute for Scientific Computing • Zurich, Switzerland

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