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

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Phylogenetic trees Computer models of evolution
Dr Dan EverettCSCI 1210
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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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Triosephosphate Isomerase
Spinach CNGTKESITKLVSDLNSATLEAD
Rice CNGTTDQVDKIVKILNEGQIAST
Monkey MNGRKQNLGELIGTLNAAKVPAD
Human MNGRKQSLGELIGTLNAAKVPAD
Mosquito MNGDKASIADLCKVLTTGPLNAD

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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

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Sequence distance matrix
Spinach Rice Mosquito Monkey Human
Spinach 0.0 84.9 105.6 90.8 86.3
Rice 84.9 0.0 117.8 122.4 122.6
Mosquito 105.6 117.8 0.0 84.7 80.8
Monkey 90.8 122.4 84.7 0.0 3.3
Human 86.3 122.6 80.8 3.3 0.0
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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)

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Revised distance matrix
Spinach Rice Mosquito Primate
Spinach 0.0 84.9 105.6 88.55
Rice 84.9 0.0 117.8 122.5
Mosquito 105.6 117.8 0.0 82.75
Primate 88.55 122.5 82.75 0.0
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Second subtree
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Revised distance matrix, again
Spinach Rice Animal
Spinach 0.0 84.9 97.1
Rice 84.9 0.0 120.2
Animal 97.1 120.2 0.0
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The Final tree
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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!

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A common human ancestor

• Can the scenario on the right happen?
• Can the scenario on the left happen?
• M1 must be smaller than H!

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must exist! But when and where?
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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

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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

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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

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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

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Acknowledgements

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