Constructing phylogenetic trees by FIg19vk

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									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
       Triosephosphate Isomerase

Spinach     CNGTKESITKLVSDLNSATLEAD

Rice        CNGTTDQVDKIVKILNEGQIAST

Monkey      MNGRKQNLGELIGTLNAAKVPAD

Human       MNGRKQSLGELIGTLNAAKVPAD

Mosquito    MNGDKASIADLCKVLTTGPLNAD
        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
       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
          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)
       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
Second subtree:
  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
The Final tree…
 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!
 A common human ancestor…
 Can the scenario on the right happen?
 Can the scenario on the left happen?
 M1 must be smaller than H!
… must exist! But when and
         where?
         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
    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
           “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
    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
                 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
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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