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

3. 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

4. Triosephosphate Isomerase Spinach CNGTKESITKLVSDLNSATLEAD Rice CNGTTDQVDKIVKILNEGQIAST Monkey MNGRKQNLGELIGTLNAAKVPAD Human MNGRKQSLGELIGTLNAAKVPAD MosquitoMNGDKASIADLCKVLTTGPLNAD

5. 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

6. Sequence distance matrix SpinachRiceMosquitoMonkeyHuman Spinach0.084.9105.690.886.3 Rice84.90.0117.8122.4122.6 Mosquito105.6117.80.084.780.8 Monkey90.8122.484.70.03.3 Human86.3122.680.83.30.0

7. 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)

8. Revised distance matrix: SpinachRiceMosquitoPrimate Spinach0.084.9105.688.55 Rice84.90.0117.8122.5 Mosquito105.6117.80.082.75 Primate88.55122.582.750.0

9. Second subtree:

10. Revised distance matrix, again SpinachRiceAnimal Spinach0.084.997.1 Rice84.90.0120.2 Animal97.1120.20.0

11. The Final tree…

12. 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!

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

14. … must exist! But when and where?

15. 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

16. 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

17. “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

18. 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

19. Acknowledgements Human family tree: Dr Curtis Strobeck, University of Alberta  http://www.biology.ualberta.ca/courses/biol380/uplo ads/winter03/lecture/b1/curt_strobeck/public/lectures /Lecture_26_Tree_of_Individuals.pdf http://www.biology.ualberta.ca/courses/biol380/uplo ads/winter03/lecture/b1/curt_strobeck/public/lectures /Lecture_26_Tree_of_Individuals.pdf http://www.biology.ualberta.ca/courses/biol380/uplo ads/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