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Exploring Phylogenetic Trees in Evolutionary Models

Dive into the world of phylogenetic trees and evolutionary models with Dr. Dan Everett. Understand gene sequences, active sites, and the significance of DNA tools in constructing accurate trees. Explore the "Out of Africa" hypothesis and the concept of "Mitochondrial Eve."

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Exploring Phylogenetic Trees in Evolutionary Models

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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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