The document is a set of slides for a lecture on the Tree of Life. It discusses evidence that all life on Earth is related, including universal traits like the genetic code and cell structure. It covers historical models of the Tree of Life from Darwin to the modern understanding based on Carl Woese's work comparing rRNA sequences. Woese's RNA-based tree supported the division of life into Bacteria, Archaea, and Eukarya domains, reflecting a more complex early evolution than previously thought.

1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Lecture 7:
The Tree of Life: I
BIS 002C
Biodiversity & the Tree of Life
Spring 2016
Prof. Jonathan Eisen
1

2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
About Me
• At UC Davis since 2005
! UC Davis Genome Center
! Dept. of Evolution and Ecology
! Dept. of Medical Microbiology and Immunology
• Research: Evolution, ecology and function of
communities of microbes
• Open Science
• More info
! Tree of Life blog: phylogenomics.blogspot.com
! Lab page: phylogenomics.wordpress.com
! Twitter: @phylogenomics
2

3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Where we are going and where we have been
• Previous Lecture:
!6: Inferring Trees
• Current Lecture:
!7: The Tree of Life I
• Next Lecture:
!8: The Tree of Life II
3

4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
• Brad Pitt movie
• Natural food remedies
• Art by the arboretum
• Name of my blog
!4
Tree of Life Imagery is Everywhere
4

5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Thought Questions & Main Topics
• If you found life on another planet, how
could you determine if it was related to life
on Earth?
• What is the evidence that all life on Earth is
related by a common descent and thus is
on a single “Tree of Life”?
• What is the structure of the Tree of Life?
5

6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Key Concepts from Previous Lectures
• Groupings in trees: monophyly, sister taxa,
outgroup, ingroup
• Phylogeny inference
• Trees: polytomies, rooted, unrooted
• Trait evolution: ancestral & derived,
homology
• Traits: data matrices, alignments
6

7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Thought Questions & Main Topics
• If you found life on another planet, how
could you determine if it was related to life
on Earth?
• What is the evidence that all life on Earth is
related by a common descent and thus is
on a single “Tree of Life”?
• What is the structure of the Tree of Life?
7

8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Life on Mars
8

9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Life on Mars
8

10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Life on Mars
8

11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
• How would one determine if the Martian
organisms are related to the Earth ones?
9
Life on Mars

12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
10
Life on EarthLife on Mars

13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
11
Life on EarthLife on Mars

14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
12
Life on EarthLife on Mars

15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Evidence?
• How could one determine if organisms on
Mars were related to organisms on Earth?
• (Assuming of course that Donald Trump is
alive)
13

16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Not Just A Thought Experiment
14

17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Dawn Sumner - UC Davis Geology Professor
15
http://geology.ucdavis.edu/people/faculty/sumner.php

18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Thought Questions & Main Topics
• If you found life on another planet, how
could you determine if it was related to life
on Earth?
• What is the evidence that all life on Earth is
related by a common descent and thus is
on a single “Tree of Life”?
• What is the structure of the Tree of Life?
16

19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Diversity of Life
17

20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Darwin - Tree or maybe Trees of Life
18
“There is grandeur in this
view of life, with its several
powers, having been
originally breathed into a
few forms or into one; and
that, whilst this planet has
gone cycling on according
to the fixed law of gravity,
from so simple a
beginning endless forms
most beautiful and
wonderful have been, and
are being, evolved.”

21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 19
“There is grandeur in this
view of life, with its several
powers, having been
originally breathed into a
few forms or into one; and
that, whilst this planet has
gone cycling on according
to the fixed law of gravity,
from so simple a
beginning endless forms
most beautiful and
wonderful have been, and
are being, evolved.”
Darwin - Tree or maybe Trees of Life

22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
20
Life on EarthLife on Earth
Multiple Origins
of Life on Earth

23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
21
Life on EarthLife on Earth
Single Origin of
Life on Earth

24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
22
Life on EarthLife on Earth
Single Origin of
Life on Earth
EVIDENCE????

25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Diversity of Life
23

26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Universal Traits: Examples
24

27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Universal Traits: Examples
! Made up of cells
! Use of DNA as a genetic material
! Use of ACTG in DNA
! Use of ACUG in RNA
! Three letter genetic code
! Central dogma (DNA -> RNA -> protein)
! Use water as a solvent
! Lipoprotein cell envelope
! 20 core amino acids in proteins
! Live on Earth
! Ribosome for translation
! RNA polymerase proteins
! Store energy in chemicals
! Pump compounds in and out of cells
25

28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Homology vs. Homoplasy
• Homology: similarity that is due to
inheritance from a common ancestor
• Homoplasy: similarity that has evolved
independently
• For a trait to be evidence that all organisms
are related it must be universal AND
homologous
26

29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
! Made up of cells
! Use of DNA as a genetic material
! Use of ACTG in DNA
! Use of ACUG in RNA
! Three letter genetic code
! Central dogma (DNA -> RNA -> protein)
! Use water as a solvent
! Lipoprotein cell envelope
! 20 core amino acids in proteins
! Live on Earth
! Ribosome for translation
! RNA polymerase proteins
! Store energy in chemicals
! Pump compounds in and out of cells
27
Universal Homologies
The existence
of Universal
Homologies
means all life on
Earth is related.

30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Central Dogma in All Organisms
28
DNA, double stranded, w/ ACTG
RNA w/ ACUG
Transcription
Translated into Proteins
using tRNA
using ribosomes
using 3 letter code
using 20 core amino acids
Lipoprotein Cell Envelope
Translation

31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Figure 14.6 The Genetic Code
29

32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Figure 14.14 Ribosome Structure
30

33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Thought Questions & Main Topics
• If you found life on another planet, how
could you determine if it was related to life
on Earth?
• What is the evidence that all life on Earth is
related by a common descent and thus is
on a single “Tree of Life”?
• What is the structure of the Tree of Life?
31

34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Thought Questions & Main Topics
• If you found life on another planet, how
could you determine if it was related to life
on Earth?
• What is the evidence that all life on Earth is
related by a common descent and thus is
on a single “Tree of Life”?
• What is the structure of the Tree of Life?
• Historical Trees of Life
32

35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
The Tree of Life
33

36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Ernst Haeckel 1866
34www.mblwhoilibrary.org
Plantae AnimaliaProtista

37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Whittaker – Five Kingdoms 1969
35
Plantae Animalia
Protista
Fungi
Monera

38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Prokaryotes vs. Eukaryotes
36
EukaryotesProkaryotes

39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Prokaryotes vs. Eukaryotes
37
EukaryotesProkaryotes

40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Limitations of This?
• Are all prokaryotes the same?
• Should we define organisms by the
absence of a trait?
38

41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Prokaryotes vs. Eukaryotes
39

42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Possible Trees
40
Tree 1
Prok Euk

43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 41
Tree 2
Alternative Trees
Prok Euk

44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 42
Tree 3
Alternative Trees
Prok Euk

45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 43
Tree 4
Alternative Trees
Prok Euk

46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
44

47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Which Tree is Most Parsimonious (character: nucleus)?
45
Tree 1 Tree 2
Tree 3 Tree 4
A)Tree 1
B)Tree 2
C)Tree 1&2
D)Tree 1&3
E)Tree 1,2,&3
P E

48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 46
Tree 1 Tree 2
Tree 3 Tree 4
P E
Which Tree is Most Parsimonious (character: nucleus)?
A)Tree 1
B)Tree 2
C)Tree 1&2
D)Tree 1&3
E)Tree 1,2,&3

49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
21
1
Which Tree is Most Parsimonious?
47
Tree 1 Tree 2
Tree 3 Tree 4
P E
1

50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
How many character state changes needed?
48
EukaryotesProkaryotes
Tree 1

51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 49
Eukaryotes
Ancestral
Derived
Prokaryotes
Tree 1 Possible Ancestry #1
How many character state changes needed?

52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 50
Eukaryotes
Given this tree … can we infer ancestral state?
Ancestral
Derived
Prokaryotes
Tree 1 Possible Ancestry #1

53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 51
Eukaryotes
Given this tree … can we infer ancestral state?
Derived
Ancestral
Prokaryotes
Tree 1 Possible Ancestry #2

54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 52
Eukaryotes
Derived
Ancestral
Given this tree … can we infer ancestral state?
Prokaryotes
Tree 1 Possible Ancestry #2

55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
53

56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
In Which Tree are Prokaryotes Monophyletic
54
Tree 1 Tree 2
Tree 3 Tree 4
P E
A) Tree 1
B) Tree 2
C) Trees 1 & 3
D) Trees 1 & 2
E) Trees 1,2,3

57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
In Which Tree are Prokaryotes Monophyletic?
55
Tree 1 Tree 2
Tree 3 Tree 4
P E
A) Tree 1
B) Tree 2
C) Trees 1 & 3
D) Trees 1 & 2
E) Trees 1,2,3

58. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
In Which Tree are Prokaryotes Monophyletic?
56
Tree 1 Tree 2
P E
Monophyletic Group = Clade
A monophyletic group includes all of the
descendant species of a given common
ancestor

59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
In Which Tree are Eukaryotes Monophyletic
57
Tree 1 Tree 2
Tree 3 Tree 4
P E

60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Conclusion
• Prokaryote vs eukaryote distinction does
not tell us the topology of the tree
58

61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Thought Questions & Main Topics
• If you found life on another planet, how
could you determine if it was related to life
on Earth?
• What is the evidence that all life on Earth is
related by a common descent and thus is
on a single “Tree of Life”?
• What is the structure of the Tree of Life?
• Historical Trees of Life
• The Modern Tree of Life
59

62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Diversity of Life
60

63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Carl Woese
http://mcb.illinois.edu/faculty/profile/1204
61

64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62

65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62

66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62

67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62

68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62

69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA

70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA

71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG

72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG

73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG

74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG

75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG

76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG

77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG

78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG

79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
Eukaryotes

80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
Eukaryotes
Eubacteria

81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
Eukaryotes
Eubacteria

82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
Eukaryotes
Eubacteria
????

83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
Eukaryotes
Eubacteria

84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
Eukaryotes
Eubacteria
Archaebacteria

85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Unrooted Tree of Life from Woese
63

86. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
64
Eukaryotes
Archaebacteria
Eubacteria

87. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Archaea Dominate Extremely Hot Environments
65

88. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Archaea Dominate Extremely Salty Environments
66

89. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Table 26.1 The Three Domains of Life on Earth
67

90. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
68
Eukaryotes
Archaebacteria
Eubacteria

91. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
69
Eukaryotes
Archaea
Eubacteria

92. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
70
Eukaryotes
Archaea
Bacteria

93. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
71
Eukaryotes
Archaea Bacteria

94. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
72
Eukaryotes
Archaea Bacteria
Can You Tell Which Groups are Sister Taxa from this?

95. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
73
Eukaryotes
Archaea Bacteria
What is Missing?

96. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
74

97. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
How many different ways are there to root this tree?
A: 0
B: 1
C: 2
D: 3
E: Not possible to determine
75
Eukaryotes
Archaea Bacteria

98. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
How many different ways are there to root this tree?
A: 0
B: 1
C: 2
D: 3
E: Not possible to determine
76
Eukaryotes
Archaea Bacteria

99. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
77
Eukaryotes
Archaea Bacteria

100. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
BacteriaArchaea

101. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
BacteriaArchaea

102. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
BacteriaArchaea

103. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
BacteriaArchaea

104. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
BacteriaArchaea

105. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria

106. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
Archaea

107. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
Archaea

108. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
Archaea

109. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
Archaea

110. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
Archaea

111. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Bacteria
Archaea

112. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Bacteria
Archaea Eukaryotes

113. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Bacteria
Archaea Eukaryotes

114. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Bacteria
Archaea Eukaryotes

115. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Archaea Eukaryotes

116. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Archaea BacteriaEukaryotes

117. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
79
Eukaryotes
Archaea Bacteria

118. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
80
Eukaryotes
Archaea Bacteria

119. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
81
Eukaryotes
Archaea Bacteria

120. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
A Polytomous Three Domain Tree of Life
82
Bacteria Archaea Eukaryotes
Polytomy

121. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker Question
83

122. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
84
How Many Distinct Ways To
Resolve this Polytomy?
A: 1
B: 2
C: 3
D: 4
E: Can’t tell
Bacteria EukaryotesArchaea

123. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
85
How Many Distinct Ways To
Resolve this Polytomy?
A: 1
B: 2
C: 3
D: 4
E: Can’t tell
Bacteria Archaea Eukaryotes

124. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 86
Bacteria Eukaryotes
Archaea and Bacteria as Sister Groups
Archaea

125. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 87
Archaea
Eukaryotes and Archaea as Sister Groups
EukaryotesBacteria

126. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 88
Bacteria
Eukaryotes and Bacteria as Sister Groups
EukaryotesArchaea

127. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Resolving the Tree of Life Polytomy
89

128. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 90
Bacteria EukaryotesArchaea

129. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 91
Phylogenetic Inference
polytomy

130. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 92
polytomy
outgroup
Phylogenetic Inference

131. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 93
outgroup
Phylogenetic Inference

132. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 94
Outgroup
Bacteria Archaea Eukaryotes
Outgroup for the Tree of Life?

133. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 95
Bacteria Archaea Eukaryotes
Outgroup for the Tree of Life?