Example of checking alignment
ClustalW alignment
Fixed alignment
PHYLOGENETIC TREES
What is a phylogeny?
Phylogeny is the history of a group of
taxa described as an evolutionary tree
with a common ancestor at the base
and descendent taxa as branch tips
descendent
taxa
common
ancestor
Terms to describe phylogenetic trees
Remember ClustalW midpoint rooting.
Unrooted tree
Birds
Rooted tree
Crocodiles
Birds
Crocodiles
Snakes
Snakes
Lizards
Turtles
Lizards
Turtles
Mammals
Amphibians
Mammals
Amphibians
1
Taxa can rotate around interior nodes
without changing relationships
Terms to describe phylogenetic trees
Amphibians
Interior branches
Ancestral states can be reconstructed
Turtles
Lizards
Birds
Snakes
Crocodiles
Mammals
Terms to describe phylogenetic trees
Crocodiles
Lizards
Snakes
Turtles
Mammals
Amphibians
Mammals
Turtles
Lizards
Snakes
Crocodiles
Birds
Amphibians
Turtles
Taxa can rotate around interior nodes
without changing relationships
Mammals
Crocodiles
Birds
Lizards
Snakes
Mammals
Amphibians
Turtles
Snakes
Lizards
Crocodiles
Birds
Taxa can rotate around interior nodes
without changing relationships
Amphibians
Mammals
Amphibians
Amphibians
Mammals
Birds
Turtles
Mammals
Lizards
Turtles
Amphibians
Snakes
Lizards
Turtles
Crocodiles
Snakes
Snakes
Birds
Crocodiles
Lizards
Birds
Crocodiles
Interior nodes
Birds
Terminal nodes
ItIt is
is incorrect
incorrect to
to say
say
“high
“high or
or low
low homology”
homology”
or
or “percent
“percent homology.”
homology.”
Peripheral branches
Birds
Crocodiles
Snakes
Homology
Homology is
is aa hypothesis
hypothesis that
that similarity
similarity
of
of aa trait
trait in
in two
two or
or more
more species
species indicates
indicates
descent
descent from
from aa common
common ancestor.
ancestor.
Lizards
Turtles
Mammals
aa trait
trait could
could be
be aa
morphological,
morphological,
behavioral,
behavioral, or
or
molecular
molecular character
character
Amphibians
2
Homologous features are derived
from common ancestors.
Two common reasons for deceptive appearances
Homoplasy
Divergence
It seems reasonable to assume that
things that look similar are related.
But, appearances can be misleading.
Example of Homoplasy
Two common reasons for deceptive appearances
Homoplasy
flippers
Divergence
flippers
Example of Divergence
Terms to describe character states
Boa
Synapomorphy
Derived homologous
character
trunk
big ears
flippers
reduced hindlimbs
Plesiomorphy
Primitive character
state.
four limbs
no limbs
Cobra
Lizards
Birds
Crocodiles
Turtles
Mammals
Amphibians
3
Terms to describe character states
How
How are
are phylogenies
phylogenies constructed?
constructed?
Three commonly used methods
Plesiomorphy, synapomorphy, and homoplasy
are relative terms and may change depending
on the taxonomic problem.
Parsimony
Distance
Maximum Likelihood
Parsimony Methods
The basic idea of
parsimony is to minimize
the number of changes
occurring on a phylogeny.
Check all possible tree
topologies and choose the
shortest.
Few
Few assumptions:
assumptions:
1.
1. Simpler
Simpler hypotheses
hypotheses are
are preferred
preferred
to
to complicated
complicated ones.
ones.
2.
2. Only
Only synapomorphies
synapomorphies are
are informative
informative
about
about relationships.
relationships.
Morphology
HUMAN
GORILLA
DOG
FROG
SHARK
123456
111111
011111
001110
000011
000000
Morphology
1
2 6
3 4
GORILLA
5
6
1.
2.
3.
4.
5.
6.
Bipedal
Position of orbits
Warm-blooded
Hair
Bony skeleton
Short tail
HUMAN
DOG
FROG
SHARK
7 steps
HUMAN
GORILLA
DOG
FROG
SHARK
1.
2.
3.
4.
5.
6.
123456
111111
011111
001110
000011
000000
Bipedal
Position of orbits
Warm-blooded
Hair
Bony skeleton
Short tail
4
Which tree is more parsimonious?
Morphology
1
234
6
HUMAN
HUMAN
GORILLA
DOG
FROG
SHARK
GORILLA
5
34
FROG
123456
111111
011111
001110
000011
000000
1
1
26
3 4
1.
2.
3.
4.
5.
6.
SHARK
8 steps
HUMAN
GORILLA
5
DOG
Bipedal
Position of orbits
Warm-blooded
Hair
Bony skeleton
Short tail
34
6
FROG
DOG
FROG
SHARK
SHARK
8 steps
7 steps
Morphology
Molecular (DNA)
1 2 3 1
42
5 36 475869 10 11
HUMAN
1A
1 1C1T1C1A T T
HUMAN
CACT
GORILLA
0A
1 1C1T1C1G T T
GORILLA
CACT
0A
0 1T 1T 1C0A T C
DOG DOG C A C T
00
FROGFROG C A T T0 A
T 0A 1C1G T T
SHARK
00
SHARK
C A T T0 A
T 0A 0C0A T T
6
GORILLA
5
DOG
234
HUMAN
Molecular (DNA)
6
HUMAN
9
37
GORILLA
11
DOG
1 2 3 4 5 6 7 8 9 10 11
HUMAN
GORILLA
DOG
FROG
SHARK
CACTACTCATT
CACTACTCGTT
CACTATTCATC
CATTATACGTT
CATTATACATT
9
1.
2.
3.
4.
5.
6.
Aligned position 1
Bipedal
Positionposition
Aligned
of orbits2
Warm-blooded
Aligned
position 3
Hair
Aligned
position 4
Bony skeleton
Aligned
position 5
Short
(andtail
so on)
How
How are
are phylogenies
phylogenies constructed?
constructed?
Three commonly used methods
Parsimony
Distance
Maximum Likelihood
FROG
SHARK
6 steps
1.
2.
3.
4.
5.
Aligned position 1
Aligned position 2
Aligned position 3
Aligned position 4
Aligned position 5
(and so on)
Distance Methods
Overall similarity indicates
evolutionary relationships.
Taxa are grouped by the number
of differences in character states.
No distinction is made between
synapomorphies and plesiomorphies.
5
Distance methods start by calculating the
distances between pairs of species.
Morphology
HUMAN
GORILLA
DOG
FROG
SHARK
111111
011111
001110
000011
000000
Human
Molecular (DNA)
CACTACTCATT
CACTACTCGTT
CACTATTCATC
CATTATACGTT
CATTATACATT
Gorilla
Dog
Frog
Human
Gorilla
2
Dog
5
5
Frog
8
6
7
Shark
9
9
6
3
Maximum Likelihood Methods
How
How are
are phylogenies
phylogenies constructed?
constructed?
Three commonly used methods
ML methods find the tree most
likely to produce the data observed
given a specific model of how
character states change.
Parsimony
Distance
ML methods are almost always
used with only molecular data.
Maximum Likelihood
Which method should I use?
• Depends on the data being analyzed.
• Try all methods to determine if results are
robust to model assumptions.
• My preference is for ML.
Some things we ignored
•
•
•
•
•
•
Base composition
Transition/transversion bias
DNA substitution models
Multiple substitutions
Character weighting
Choice of taxa
6
Does a tree generated from a
gene sequence always give the
species tree?
Representation of tree using nested parentheses
Is the branching order
significant?
•
•
•
•
•
ORIGINAL DATA
Bootstrap test for significance.
Resample data with replacement
Reconstruct phylogeneny
Redo 100s of times
Build consensus tree, bootstrap values are
percent on times that branch was recovered.
AAATCTGCTAGCATGCA
AAATCTGCTACCATGCA
BOOTSTRAPPED DATA SETS
AAAAACCCGGCTCAGCA
AAAAACCCGGCTCAGCA
AATTGGAAGCCAAGGCA
AATTGGAACCCAAGGCA
AATTTTTCCCCATTGCC
AATTTTTCCCCATTGCC
AAAATCCCCCATGGGAA
AAAATCCGCCATGGGAA
AATTTCCAAACCCCTCA
AATTTCCAAACCCCTCA
AATTGGCACCCCAAAAC
AATTGGCAGGCCAAAAC
AATTTGCCCCCCCCAAA
AATTTGCCCCCCCCAAA
AAATTCTTCCTGGCAAA
AAATTCTTCCTGGCAAA
AAATCCCGGTACTTGCA
AAATCCCGGTACTTGCA
AAAATTTCCACCATTCA
AAAATTTCCAGGATTCA
7