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
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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.
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3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 2 Outline
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• 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
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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”
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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.
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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
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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
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10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Computer Simulation http://www.life10e.com/at22.02.html
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11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Computer Simulation http://www.life10e.com/at22.02.html
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12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lab Simulation
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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
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14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Dog Breed Geneology (imperfect record)
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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 ——
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16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lenski Long Term E. coli evolution 1988 ——
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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
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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
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20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Character trait = fur; Character state = different colors
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21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Model Tree
22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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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
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Character Evolution Example 1
24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Character Evolution Example 1
25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Character Evolution Example 1
26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Character Evolution Example 1
27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Character Evolution Example 1
28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Character Evolution Example 1
29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Character Evolution Example 1
30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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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.
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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.
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35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Character trait = fur; Character state = different colors
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36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Character Evolution Example 2
37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Character Evolution Example 2
38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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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
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Character Evolution Example 2
40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Character Evolution Example 2
41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Character Evolution Example 2
42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Character Evolution Example 2
43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Character Evolution Example 2
44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Character Evolution Example 2
45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Character Evolution Example 2
46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Character Evolution Example 2
47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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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.
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49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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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.
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51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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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.
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54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Synapomorphy Example
55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Synapomorphy
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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
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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?
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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
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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
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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
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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
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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.
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65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
Homoplasy Example
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66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Homoplasy Example
67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Homoplasy Example
68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Homoplasy Example
69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Homoplasy Example
70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Homoplasy Example
71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Homoplasy Example
72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Homoplasy Example
73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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Homoplasy Example
74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
a b c d e h g f
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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
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76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Figure 22.4 The Bones Are Homologous, the Wings Are Not
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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
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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
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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
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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
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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
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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
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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
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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).
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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?
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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111. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Kinds of Phylogenetic Trees
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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?
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113. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Table 22.1
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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.
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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.
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116. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Figure 22.5 Constructing a Phylogenetic Tree
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117. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Figure 22.5 Constructing a Phylogenetic Tree
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