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.
Recombinant DNA technology (Immunological screening)
Jonathan Eisen Tree of Life Lecture Slides
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
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
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?
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?