Download Lesson08Phylogenetics

Doug Raiford
Lesson 8
5/23/2017
Phylogenetics
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
Definition
 study of evolutionary relatedness
among various groups of organisms

All life evolved from a
single-celled organism
 Cenancestor

Traditional techniques:
 Relied upon phenotypical (observable
characteristic or trait of an organism)
differences
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
Understanding of the origins of life
 Who we are? From whence did we come?

If can understand biological systems and
how they came to be…
Why study phylogenetics?
 Perhaps can predict
▪ Reaction to changing environments
▪ Reaction to drugs (similar organisms will probably
react similarly)

What our future holds
 How we will evolve
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DNA similar in related
organisms
How would we go
about measuring DNA
similarity?
 Must align first
 Must use homologous
genes/proteins
 Just count
thedo
locations
Where
genes and proteins
where different
come into the picture?
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Different rates of evolutionary change
 Organisms: different environmental factors
 Proteins: under different selective pressures
 Regions of proteins:
▪ Interiors, tightly packed,
hydrophobic
▪ External loops, less important for
structural integrity
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Gap of virtually any length could happen in
single event
Buchnera/1-356
Lactobacillus/1-363
Geobacter/1-338
Actinobacillus/1-376
Salmonella/1-353
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MENL----------------DKKKALDRVIMEIEKAYGKGAIMKLG-EMA
MAKD----------------EKKAALDAALKKIEKNFGKGAVMRMG-EKA
MTQ-----------------EREKAIELALSQIEKQFGKGAIMRLGADEA
MAADNKKAQKNTVTKQIDPEQKEKALAAALAQIEKQFGKGSIMRLG-DTQ
MAID---------------ENKQKALAAALGQIEKQFGKGSIMRLG-EDR
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
DNA material
doesn’t stay put
Bacteria reproduce
asexually
 But plasmids…
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

Also, viruses…
Finally, take-up…
Not surprising…
 Meiosis, mitosis,
translocating genes
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Horizontal gene transfer (HGT)
More of a bush (especially at the base)
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Need a gene that is in all organisms (ubiquitous)
The gene should be evolutionarily stable (very
similar in all organisms)
Should compare regions of the gene that are
highly conserved
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Circular DNA found in
organelles outside the
nucleus
 No crossover:
passed down
in the egg
 Exact copy from
female parent
 Mitochondria are the powerhouse of the cell

 Break-down food, release energy
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


Dominant molecule in
microbial ribosomes
(translation)
Ubiquitous, same role in
every organism
Highly conserved
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Multiple sequence alignments
 ClustalW
 Sound
Easily familiar?
identifyWhat
regions
that
arealready
highlyhave?
tools
do we
conserved

atgccgca-actgccgcaggagatcaggactttcatgaatatcatcatgcgtggga-ttcag
acctccatacgtgccccaggagatctggactttcacc---tggatcatgcgaccgtacctac
t-atgg-t-cgtgccgcaggagatcaggactttca-gt--g-aatcatctgg-cgc--c-aa
t--tcgt-ac-tgccccaggagatctggactttcaaa---ca-atcatgcgcc-g-tc-tat
aattccgtacgtgccgcaggagatcaggactttcag-t--a-tatcatctgtc-ggc--tag
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Used 16S to investigate tree of life
Discovered three domains (not two)
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Build cladogram or phylogram:
 A tree diagram used to illustrate phylogenetic
relationships

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Length of each branch = number of sequence
changes that occurred (except in cladogram
where length not used)
The amount of time usually not known
Sometimes utilize
a dendrogram
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Each sequence taxon (plural: taxa)
Each subtree = clade (long “a”)
Tree length
 Sum of all the branch lengths
Sometimes utilize
a dendrogram
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Assumption of a uniform rate of mutation in
the tree branches
Is this reasonable?
Allows some conclusions to be drawn
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Distance
Maximum parsimony
Maximum likelihood
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Main packages
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 PAUP
 PHYLIP
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Unweighted pair group
method with arithmetic
mean (UPGMA)
 One of the first and simplest
distance methods

Basically hierarchical
clustering
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Need all pair-wise distances
Count
up the
number of columns
How
measure
distance?
where
there are
and
Want
to measure
thedifferences
number of mutations
divide by
thethe
length
of the
that occurred
since
species
split
sequences: the probability of a
mutation at a given location
Distance between
organism A and B is 4
2
Organism A
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Organism B
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A
A
B
C
D
0
6
6
6
0
4
4
0
2
B
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All pair-wise distances
C
D
0
1
1
3
2
A
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B
C
1
D
20
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Find closest
Place next to each other in
tree
Find average distance
to rest
A
A
B
C
D
0
6
6
6
0
4
4
0
2
B
C
D
0
1
A
B
CD
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A
B
CD
0
6
6
0
4
1
3
2
A
1
B
C
1
D
0
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
Find the next closest
Place next to each other in
tree
A
A
B
CD
0
6
6
0
4
B
CD
0
1
A
BCD
A
BCD
0
6
2
0
A
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3
1
B
C
1
D
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A
A
B
C
D
0
6
6
7
0
4
5
0
3
B
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New distance matrix
C
D
A
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B
C
D
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C and D still closest
So start tree with these two
Find average distance
to rest
A
B
CD
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A
B
CD
0
6
6.5
0
4.5
A
A
B
C
D
0
6
6
7
0
4
5
0
3
B
C
D
A
0
B
C
D
0
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(A,(B,(C,D)))
A

B
D
((A,B),(C,D))
A

C
B
C
D
Binary trees
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Find the next closest
Place next to each other in
tree (collapse B with CD)
A
BCD
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A
BCD
0
6.25
A
B
A
B
CD
0
6
6.5
0
4.5
CD
A
B
0
C
D
0
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