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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 3
!
Lecture 3:
!
Characters, Traits and States
!
!
!
BIS 002C
Biodiversity & the Tree of Life
Spring 2014
!
Prof. Jonathan Eisen
1
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Where we are going and where we have been
• Previous Lecture:
!Trees, Taxa and Groups.
• Current Lecture:
!Characters, Traits and States
• Next Lecture:
!Inferring trees.
2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 2 Outline
3
• Groupings in trees
! Monophyletic groups
! Non monophyletic groups
! Relatedness
! Ingroups and outgroups
! “Sisters”
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
Sister groups: two clades or species that are each other’s
closest relatives (the two descendants of a single node)
Key Concept: Sister groups
44
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
g and h are “sisters” or “sister taxa”
55
Key Concept: Sister groups
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
6
The group “g and h” is sister to f
f is sister to the group “g and h” 6
Key Concept: Sister groups
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 3: Key Concept
Using a phylogenetic tree to trace and infer
the history of traits.
7
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 3: Outline
• Knowing history
• Character traits and states
• State changes
• Synapomorphies
• Homoplasy
• Character state reconstruction
8
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 3: Outline
• Knowing history
• Character traits and states
• State changes
• Synapomorphies
• Homoplasy
• Character state reconstruction
9
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Computer Simulation http://www.life10e.com/at22.02.html
10
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Computer Simulation http://www.life10e.com/at22.02.html
10
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lab Simulation
11
In the laboratory, researchers produced an unambiguous phylogeny of nine viral lineages,
enhancing the mutation rate to increase variation among the lineages.
Outgroup
lineage
A lineage
D lineage
C lineage
E lineage
F lineage
H lineage
B lineage
G lineage
Growth in
presence
of mutagen
400 400 400
Generations
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Thought Simulation
12
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Dog Breed Geneology (imperfect record)
13
http://www.macwebguru.com/2010/09/11/the-dog/
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lenski Long Term E. coli evolution 1988 ——
14
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lenski Long Term E. coli evolution 1988 ——
15
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 16
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 3: Outline
• Knowing history
• Character traits and states
• State changes
• Synapomorphies
• Homoplasy
• Character state reconstruction
17
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept: Character Traits and States
• Character:
!A heritable feature of an organism.
!Also known as a character trait or trait.
• Character state:
!The particular form that a character takes.
• Example:
!Character = heart
!Character state = present/absent
!Character state = # of chambers
18
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Character trait = fur; Character state = different colors
19
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
20
Model Tree
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
21
Character Evolution Example 1
Character Trait: Face
Character State: Happy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
22
Character Evolution Example 1
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
23
Character Evolution Example 1
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
24
Character Evolution Example 1
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
25
Character Evolution Example 1
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
26
Character Evolution Example 1
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
27
Character Evolution Example 1
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
28
Character Evolution Example 1
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
29
Character Evolution Example 1
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 30
Character Evolution from Tree of Life video
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept: Homologous characters
Characters (e.g., a face) that are inherited
from a common ancestor are homologous.
31
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 3: Outline
• Knowing history
• Character traits and states
• State changes
• Synapomorphies
• Homoplasy
• Character state reconstruction
32
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept: Divergence
• Species change over time
• Known (generally) as divergence, or
divergent evolution.
33
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Character trait = fur; Character state = different colors
34
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
35
Character Evolution Example 2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
36
Character Evolution Example 2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
37
Character Evolution Example 2
Character State:
Frowny
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
38
Character Evolution Example 2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
39
Character Evolution Example 2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
40
Character Evolution Example 2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
41
Character Evolution Example 2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
42
Character Evolution Example 2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
43
Character Evolution Example 2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
44
Character Evolution Example 2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
45
Character Evolution Example 2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
46
Character Evolution Example 2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept: Ancestral and Derived States
• A character with the same form as in the
ancestor of a group has an ancestral
state.
!
• A character with a different form as in the
ancestor of a group has a derived state.
47
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
48
Which state is ancestral?
!
a) Smiley Face
b) Frowny Face
c) Both
d) Neither
Clicker Question
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept: Ancestral & Derived Status is Relative
• A trait may be ancestral or derived,
depending on the point of reference.
• Example: feathers are an ancestral trait for
any group of modern birds.
• But in a phylogeny of all vertebrates,
feathers would be a derived trait, showing
the relationship between birds and their
theropod dinosaur relatives.
49
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
50
Character Evolution Example 2
Character Trait: Face
Ancestral State: Happy
Derived State: Frowny
For This Clade
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 3: Outline
• Knowing history
• Character traits and states
• State changes
• Synapomorphies
• Homoplasy
• Character state reconstruction
51
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept: Synapomorphy
• Derived traits that are shared among a
group and are viewed as evidence of the
common ancestry of the group are known
as synapomorphies.
• The vertebral column is a synapomorphy of
all vertebrates.
52
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
53
Synapomorphy Example
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Synapomorphy
54
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept: Synapomorphy
• Synapomorphy = a shared derived trait
!
• Derivation: Greek
! Syn ~ with (a.k.a. shared)
! Apo ~ away from (a.k.a. derived)
! Morphy ~ shape (a.k.a. character trait or state
55
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
1
2
3 4
5
Which traits are synapomorphies for fgh?
56
6
7
8 9
A: 7,8,9
B: 4,5,6,7
C: 6
D: 6,7,8,9
E: 7
Clicker Question
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e Birds Dinos f
Synapomorphy Example
57
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e Birds Dinos f
1
2
3
4
58
Synapomorphy Example
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e Birds Dinos f
1
2
3
hair
milk
mammary glands
four-chambered heart 4
59
Synapomorphy Example
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e Birds Dinos f
1
2
3
hair
milk
mammary glands
four-chambered heart 4
60
Synapomorphy Example
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e Birds Dinos f
1
2
3
4
5
6
61
Synapomorphy Example
Mammals Reptiles
hair
milk
mammary glands
four-chambered heart
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 3: Outline
• Knowing history
• Character traits and states
• State changes
• Synapomorphies
• Homoplasy
• Character state reconstruction
62
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept: Homoplasy
Traits that are similar for reasons other than
inheritance from a common ancestor are
called homoplastic traits or homoplasies.
63
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
Homoplasy Example
64
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
65
Homoplasy Example
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
66
Homoplasy Example
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
67
Homoplasy Example
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
68
Homoplasy Example
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
69
Homoplasy Example
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
70
Homoplasy Example
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
71
Homoplasy Example
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
72
Homoplasy Example
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
73
Homoplasy Example
Frowny face is homoplasious
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept: Convergence
Similar traits can develop in unrelated
groups of organisms:
Convergent evolution—independently
evolved traits subjected to similar
selection pressures may become
superficially similar.
!
Example: the wings of bats and birds
74
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Figure 22.4 The Bones Are Homologous, the Wings Are Not
75
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Convergence
a Bats c d e Birds g f
+
76
can fly
can’t fly
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 3 Outline
• Knowing history
• Character traits and states
• State changes
• Synapomorphies
• Homoplasy
• Character state reconstruction
77
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept: Character State Reconstruction
Character state reconstruction methods
allow one to infer history of states and state
changes
78
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a Bats c d e Birds g f
+
Character State Reconstruction
can fly
can’t fly
79
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a Bats c d e Birds g f
+
Character State Reconstruction
In theory, each node could have either of the two states
can fly
can’t fly
80
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a Bats c d e Birds g f
+
Character State Reconstruction
can fly
can’t fly
81
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a Bats c d e Birds g f
+
Character State Reconstruction
can fly
can’t fly
82
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a Bats c d e Birds g f
+
Character State Reconstruction
can fly
can’t fly
83
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a Bats c d e Birds g f
+
Character State Reconstruction
can fly
can’t fly
84
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Character State Reconstruction
Which pattern is the most plausible?
+++
85
Pattern 1 Pattern 2 Pattern 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept: Principle of parsimony
The Principle of Parsimony: the simplest of two
(or more) competing theories is to be preferred
(assuming all else is equal).
86
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concept: Principle of parsimony
The Principle of Parsimony: the simplest of two
(or more) competing theories is to be preferred
(assuming all else is equal).
!
Which character state pattern requires the fewest
changes in states?
87
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Principle of parsimony
How many “steps” (state changes) required for each?
88
+++
Pattern 1 Pattern 2 Pattern 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a Bats c d e Birds g f
+
Principle of parsimony
can fly
can’t fly
89
Pattern 1: How many steps?
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a Bats c d e Birds g f
+
Principle of parsimony
can fly
can’t fly
90
Pattern 1: How many steps?
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a Bats c d e Birds g f
Mammals Reptiles
+
Principle of parsimony
Note you could
have more
changes but
seven is the
minimum needed.
We focus on the
minimum needed.
Pattern 1: Seven Steps is the minimum needed.
can fly
can’t fly
91
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a Bats c d e Birds g f
+
Principle of parsimony
Pattern 2: How many steps?
can fly
can’t fly
92
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a Bats c d e Birds g f
+
Principle of parsimony
Pattern 2: Two steps
can fly
can’t fly
93
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a Bats c d e Birds g f
+
Principle of parsimony
Pattern 3: How many steps?
can fly
can’t fly
94
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a Bats c d e Birds g f
+
Principle of parsimony
Pattern 3: Six steps
can fly
can’t fly
95
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Principle of parsimony
+++
Which pattern is the most plausible?
96
Pattern 1 Pattern 2 Pattern 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Principle of parsimony
Which pattern is the most plausible?
+++
Pattern1: 7 Steps Pattern2: 2 Steps Pattern3: 6 Steps
97
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Principle of parsimony
+++
98
Which pattern is the most plausible?
Pattern1: 7 Steps Pattern2: 2 Steps Pattern3: 6 Steps
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a Bats c d e Birds g f
+
Principle of parsimony
Pattern 2: Flight in birds and bats arose separately and is
homoplasious.
can fly
can’t fly
99
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a Bats c d e Birds g f
+
Principle of parsimony
ASSUMPTIONS …
can fly
can’t fly
100
Mammals Reptiles
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Figure 22.4 The Bones Are Homologous, the Wings Are Not
101
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Figure 22.10 The Origin of a Sexually Selected Trait
102102
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Figure 22.10 The Origin of a Sexually Selected Trait
103
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Figure 22.10 The Origin of a Sexually Selected Trait
104104
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 105
SIVsyk
(Sykes monkeys)
HIV-1 (humans)
SIVcpz
(chimpanzees)
SIVhoest
(L’Hoest monkeys)
SIVsun
(sun-tailed monkeys)
SIVmnd (mandrills)
SIVagm (African
green monkeys)
SIVsm (sooty
mangabeys)
HIV-2 (humans)
Common
ancestor
Where did HIV Come From?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 106
Common
ancestor
Where did HIV Come From?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 107
Common
ancestor
Where did HIV Come From?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 108
Common
ancestor
Where did HIV Come From?
Virus transferred from simian host to humans
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Which Came First Red or Green Fluorescent Protein
109
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Kinds of Phylogenetic Trees
110
A B C D
A
B
C
D
A B C D
Units of
character
divergence
Units of
time
Cladogram Phylogram Chronogram
Different kinds of trees
Only the relative
branching order
is depicted. No
meaning to
branch lengths.
Branch length is
proportional to
the amount of
character change
Branch length is
proportional to
time
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Next Lecture: Phylogenetic Tree Inference
What if you did not know the phylogeny and
only knew the traits and the organisms?
How would you infer homology,
convergence, homoplasy, etc?
111
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Table 22.1
112
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
22.2 How Are Phylogenetic Trees Constructed?
The root of the tree is located between the
ingroup and the outgroup.
A trait present in both ingroup and outgroup
must have evolved before the ingroup and
thus must be ancestral for the ingroup.
Lampreys (jawless fishes) arose before the
lineage leading to other vertebrates—they
are the outgroup.
113
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
22.2 How Are Phylogenetic Trees Constructed?
Chimpanzees and mice share two derived
traits—fur and mammary glands. They are
synapomorphies for this group.
Keratinous scales are a synapomorphy of
the crocodile, pigeon, and lizard.
Information about the synapomorphies
allows construction of the tree.
114
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Figure 22.5 Constructing a Phylogenetic Tree
115
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Figure 22.5 Constructing a Phylogenetic Tree
116

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BIS2C. Biodiversity and the Tree of Life. 2014. L3. Characters, Traits and States.

  • 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 3 ! Lecture 3: ! Characters, Traits and States ! ! ! BIS 002C Biodiversity & the Tree of Life Spring 2014 ! Prof. Jonathan Eisen 1
  • 2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Where we are going and where we have been • Previous Lecture: !Trees, Taxa and Groups. • Current Lecture: !Characters, Traits and States • Next Lecture: !Inferring trees. 2
  • 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 2 Outline 3 • Groupings in trees ! Monophyletic groups ! Non monophyletic groups ! Relatedness ! Ingroups and outgroups ! “Sisters”
  • 4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f Sister groups: two clades or species that are each other’s closest relatives (the two descendants of a single node) Key Concept: Sister groups 44
  • 5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f g and h are “sisters” or “sister taxa” 55 Key Concept: Sister groups
  • 6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 6 The group “g and h” is sister to f f is sister to the group “g and h” 6 Key Concept: Sister groups
  • 7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 3: Key Concept Using a phylogenetic tree to trace and infer the history of traits. 7
  • 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 3: Outline • Knowing history • Character traits and states • State changes • Synapomorphies • Homoplasy • Character state reconstruction 8
  • 9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 3: Outline • Knowing history • Character traits and states • State changes • Synapomorphies • Homoplasy • Character state reconstruction 9
  • 10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Computer Simulation http://www.life10e.com/at22.02.html 10
  • 11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Computer Simulation http://www.life10e.com/at22.02.html 10
  • 12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lab Simulation 11 In the laboratory, researchers produced an unambiguous phylogeny of nine viral lineages, enhancing the mutation rate to increase variation among the lineages. Outgroup lineage A lineage D lineage C lineage E lineage F lineage H lineage B lineage G lineage Growth in presence of mutagen 400 400 400 Generations
  • 13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Thought Simulation 12
  • 14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Dog Breed Geneology (imperfect record) 13 http://www.macwebguru.com/2010/09/11/the-dog/
  • 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lenski Long Term E. coli evolution 1988 —— 14
  • 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lenski Long Term E. coli evolution 1988 —— 15
  • 17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 16
  • 18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 3: Outline • Knowing history • Character traits and states • State changes • Synapomorphies • Homoplasy • Character state reconstruction 17
  • 19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: Character Traits and States • Character: !A heritable feature of an organism. !Also known as a character trait or trait. • Character state: !The particular form that a character takes. • Example: !Character = heart !Character state = present/absent !Character state = # of chambers 18
  • 20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Character trait = fur; Character state = different colors 19
  • 21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 20 Model Tree
  • 22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 21 Character Evolution Example 1 Character Trait: Face Character State: Happy
  • 23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 22 Character Evolution Example 1
  • 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 23 Character Evolution Example 1
  • 25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 24 Character Evolution Example 1
  • 26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 25 Character Evolution Example 1
  • 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 26 Character Evolution Example 1
  • 28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 27 Character Evolution Example 1
  • 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 28 Character Evolution Example 1
  • 30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 29 Character Evolution Example 1
  • 31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 30 Character Evolution from Tree of Life video
  • 32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: Homologous characters Characters (e.g., a face) that are inherited from a common ancestor are homologous. 31
  • 33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 3: Outline • Knowing history • Character traits and states • State changes • Synapomorphies • Homoplasy • Character state reconstruction 32
  • 34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: Divergence • Species change over time • Known (generally) as divergence, or divergent evolution. 33
  • 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Character trait = fur; Character state = different colors 34
  • 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 35 Character Evolution Example 2
  • 37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 36 Character Evolution Example 2
  • 38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 37 Character Evolution Example 2 Character State: Frowny
  • 39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 38 Character Evolution Example 2
  • 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 39 Character Evolution Example 2
  • 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 40 Character Evolution Example 2
  • 42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 41 Character Evolution Example 2
  • 43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 42 Character Evolution Example 2
  • 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 43 Character Evolution Example 2
  • 45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 44 Character Evolution Example 2
  • 46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 45 Character Evolution Example 2
  • 47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 46 Character Evolution Example 2
  • 48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: Ancestral and Derived States • A character with the same form as in the ancestor of a group has an ancestral state. ! • A character with a different form as in the ancestor of a group has a derived state. 47
  • 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 48 Which state is ancestral? ! a) Smiley Face b) Frowny Face c) Both d) Neither Clicker Question
  • 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: Ancestral & Derived Status is Relative • A trait may be ancestral or derived, depending on the point of reference. • Example: feathers are an ancestral trait for any group of modern birds. • But in a phylogeny of all vertebrates, feathers would be a derived trait, showing the relationship between birds and their theropod dinosaur relatives. 49
  • 51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 50 Character Evolution Example 2 Character Trait: Face Ancestral State: Happy Derived State: Frowny For This Clade
  • 52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 3: Outline • Knowing history • Character traits and states • State changes • Synapomorphies • Homoplasy • Character state reconstruction 51
  • 53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: Synapomorphy • Derived traits that are shared among a group and are viewed as evidence of the common ancestry of the group are known as synapomorphies. • The vertebral column is a synapomorphy of all vertebrates. 52
  • 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 53 Synapomorphy Example
  • 55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Synapomorphy 54
  • 56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: Synapomorphy • Synapomorphy = a shared derived trait ! • Derivation: Greek ! Syn ~ with (a.k.a. shared) ! Apo ~ away from (a.k.a. derived) ! Morphy ~ shape (a.k.a. character trait or state 55
  • 57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 1 2 3 4 5 Which traits are synapomorphies for fgh? 56 6 7 8 9 A: 7,8,9 B: 4,5,6,7 C: 6 D: 6,7,8,9 E: 7 Clicker Question
  • 58. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e Birds Dinos f Synapomorphy Example 57 Mammals Reptiles
  • 59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e Birds Dinos f 1 2 3 4 58 Synapomorphy Example Mammals Reptiles
  • 60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e Birds Dinos f 1 2 3 hair milk mammary glands four-chambered heart 4 59 Synapomorphy Example Mammals Reptiles
  • 61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e Birds Dinos f 1 2 3 hair milk mammary glands four-chambered heart 4 60 Synapomorphy Example Mammals Reptiles
  • 62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e Birds Dinos f 1 2 3 4 5 6 61 Synapomorphy Example Mammals Reptiles hair milk mammary glands four-chambered heart
  • 63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 3: Outline • Knowing history • Character traits and states • State changes • Synapomorphies • Homoplasy • Character state reconstruction 62
  • 64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: Homoplasy Traits that are similar for reasons other than inheritance from a common ancestor are called homoplastic traits or homoplasies. 63
  • 65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f Homoplasy Example 64
  • 66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 65 Homoplasy Example
  • 67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 66 Homoplasy Example
  • 68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 67 Homoplasy Example
  • 69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 68 Homoplasy Example
  • 70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 69 Homoplasy Example
  • 71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 70 Homoplasy Example
  • 72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 71 Homoplasy Example
  • 73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 72 Homoplasy Example
  • 74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 73 Homoplasy Example Frowny face is homoplasious
  • 75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: Convergence Similar traits can develop in unrelated groups of organisms: Convergent evolution—independently evolved traits subjected to similar selection pressures may become superficially similar. ! Example: the wings of bats and birds 74
  • 76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Figure 22.4 The Bones Are Homologous, the Wings Are Not 75
  • 77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Convergence a Bats c d e Birds g f + 76 can fly can’t fly Mammals Reptiles
  • 78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 3 Outline • Knowing history • Character traits and states • State changes • Synapomorphies • Homoplasy • Character state reconstruction 77
  • 79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: Character State Reconstruction Character state reconstruction methods allow one to infer history of states and state changes 78
  • 80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a Bats c d e Birds g f + Character State Reconstruction can fly can’t fly 79 Mammals Reptiles
  • 81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a Bats c d e Birds g f + Character State Reconstruction In theory, each node could have either of the two states can fly can’t fly 80 Mammals Reptiles
  • 82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a Bats c d e Birds g f + Character State Reconstruction can fly can’t fly 81 Mammals Reptiles
  • 83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a Bats c d e Birds g f + Character State Reconstruction can fly can’t fly 82 Mammals Reptiles
  • 84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a Bats c d e Birds g f + Character State Reconstruction can fly can’t fly 83 Mammals Reptiles
  • 85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a Bats c d e Birds g f + Character State Reconstruction can fly can’t fly 84 Mammals Reptiles
  • 86. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Character State Reconstruction Which pattern is the most plausible? +++ 85 Pattern 1 Pattern 2 Pattern 3
  • 87. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: Principle of parsimony The Principle of Parsimony: the simplest of two (or more) competing theories is to be preferred (assuming all else is equal). 86
  • 88. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: Principle of parsimony The Principle of Parsimony: the simplest of two (or more) competing theories is to be preferred (assuming all else is equal). ! Which character state pattern requires the fewest changes in states? 87
  • 89. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Principle of parsimony How many “steps” (state changes) required for each? 88 +++ Pattern 1 Pattern 2 Pattern 3
  • 90. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a Bats c d e Birds g f + Principle of parsimony can fly can’t fly 89 Pattern 1: How many steps? Mammals Reptiles
  • 91. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a Bats c d e Birds g f + Principle of parsimony can fly can’t fly 90 Pattern 1: How many steps? Mammals Reptiles
  • 92. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a Bats c d e Birds g f Mammals Reptiles + Principle of parsimony Note you could have more changes but seven is the minimum needed. We focus on the minimum needed. Pattern 1: Seven Steps is the minimum needed. can fly can’t fly 91
  • 93. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a Bats c d e Birds g f + Principle of parsimony Pattern 2: How many steps? can fly can’t fly 92 Mammals Reptiles
  • 94. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a Bats c d e Birds g f + Principle of parsimony Pattern 2: Two steps can fly can’t fly 93 Mammals Reptiles
  • 95. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a Bats c d e Birds g f + Principle of parsimony Pattern 3: How many steps? can fly can’t fly 94 Mammals Reptiles
  • 96. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a Bats c d e Birds g f + Principle of parsimony Pattern 3: Six steps can fly can’t fly 95 Mammals Reptiles
  • 97. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Principle of parsimony +++ Which pattern is the most plausible? 96 Pattern 1 Pattern 2 Pattern 3
  • 98. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Principle of parsimony Which pattern is the most plausible? +++ Pattern1: 7 Steps Pattern2: 2 Steps Pattern3: 6 Steps 97
  • 99. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Principle of parsimony +++ 98 Which pattern is the most plausible? Pattern1: 7 Steps Pattern2: 2 Steps Pattern3: 6 Steps
  • 100. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a Bats c d e Birds g f + Principle of parsimony Pattern 2: Flight in birds and bats arose separately and is homoplasious. can fly can’t fly 99 Mammals Reptiles
  • 101. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a Bats c d e Birds g f + Principle of parsimony ASSUMPTIONS … can fly can’t fly 100 Mammals Reptiles
  • 102. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Figure 22.4 The Bones Are Homologous, the Wings Are Not 101
  • 103. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Figure 22.10 The Origin of a Sexually Selected Trait 102102
  • 104. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Figure 22.10 The Origin of a Sexually Selected Trait 103
  • 105. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Figure 22.10 The Origin of a Sexually Selected Trait 104104
  • 106. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 105 SIVsyk (Sykes monkeys) HIV-1 (humans) SIVcpz (chimpanzees) SIVhoest (L’Hoest monkeys) SIVsun (sun-tailed monkeys) SIVmnd (mandrills) SIVagm (African green monkeys) SIVsm (sooty mangabeys) HIV-2 (humans) Common ancestor Where did HIV Come From?
  • 107. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 106 Common ancestor Where did HIV Come From?
  • 108. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 107 Common ancestor Where did HIV Come From?
  • 109. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 108 Common ancestor Where did HIV Come From? Virus transferred from simian host to humans
  • 110. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Which Came First Red or Green Fluorescent Protein 109
  • 111. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Kinds of Phylogenetic Trees 110 A B C D A B C D A B C D Units of character divergence Units of time Cladogram Phylogram Chronogram Different kinds of trees Only the relative branching order is depicted. No meaning to branch lengths. Branch length is proportional to the amount of character change Branch length is proportional to time
  • 112. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Next Lecture: Phylogenetic Tree Inference What if you did not know the phylogeny and only knew the traits and the organisms? How would you infer homology, convergence, homoplasy, etc? 111
  • 113. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Table 22.1 112
  • 114. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 22.2 How Are Phylogenetic Trees Constructed? The root of the tree is located between the ingroup and the outgroup. A trait present in both ingroup and outgroup must have evolved before the ingroup and thus must be ancestral for the ingroup. Lampreys (jawless fishes) arose before the lineage leading to other vertebrates—they are the outgroup. 113
  • 115. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 22.2 How Are Phylogenetic Trees Constructed? Chimpanzees and mice share two derived traits—fur and mammary glands. They are synapomorphies for this group. Keratinous scales are a synapomorphy of the crocodile, pigeon, and lizard. Information about the synapomorphies allows construction of the tree. 114
  • 116. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Figure 22.5 Constructing a Phylogenetic Tree 115
  • 117. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Figure 22.5 Constructing a Phylogenetic Tree 116