Download Constructing phylogenetic trees

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/s
tudents/ub/e1.html
Phylogentic
tree
computation example: Gaston
Gonnet,
Institute for Scientific Computing
Zurich, Switzerland