Slides for BIS2C "Biodiversity and the Tree of Life" Class at UC Davis Spring 2020. Lecture 6. The Tree of Life.

1. BIS2C
Biodiversity & the Tree of Life
Spring 2020
Lecture 6:
The Tree of Life
Prof. Jonathan Eisen

2. !5: Inferring Trees
!6: The Tree of Life
!7: The Domains of Life
Lecture 6 Context

3. 1.Give examples of universal traits shared by all
organisms
2.Understand how to determine which of these are
evidence for common ancestry of life
3.Understand what “universal homologies” are
4.Understand why the existence of universal
homologies means all life on earth has a
common origin
5.Understand how to determine if life on another
planet has common origin to life on Earth
Lecture 6 Learning Goals

4. Lecture 6 Outline
• Background and Context
• Tree of Life vs. Trees of Life
- Concept
- Universal traits
- Homology vs. Homoplasy
- Universal homologies

5. Lecture 6 Outline
• Background and Context
• Tree of Life vs. Trees of Life
- Concept
- Universal traits
- Homology vs. Homoplasy
- Universal homologies

6. Background: About Me

7. Background: About Me
• Jonathan Eisen
• At UC Davis since 2005
• Evolution & Ecology
• Medical Microbiology and
Immunology
• Genome Center
• Center for Population Biology
• Web site: phylogenomics.me
• Tree of Life Blog:
phylogenomics.blogspot.com
• Twitter: @phylogenomics
• Ted: tinyurl.com/EisenTed

8. • Lab 1: Introduction to Phylogeny
!Phylogenetic methods
!Phylogenetic trees
!Homology, homoplasy
!Characters, character states
Background: Lab Connections

9. Lecture 6 Outline
• Background and Context
• Tree of Life vs. Trees of Life
- Concept
- Universal traits
- Homology vs. Homoplasy
- Universal homologies

10. Lecture 6 Outline
• Background and Context
• Tree of Life vs. Trees of Life
- Concept
- Universal traits
- Homology vs. Homoplasy
- Universal homologies

11. Diversity of Life of Earth

12. Diversity of Life of Earth
Ignoring viruses for now

13. Tree of Life vs. Trees of Life
“As buds give rise by growth
to fresh buds, and these, if
vigorous, branch out and
overtop on all sides many a
feebler branch, so by
generation I believe it has
been with the great Tree of
Life, which fills with its dead
and broken branches the
crust of the earth, and covers
the surface with its ever-
branching and beautiful
ramifications.”
Darwin, 1872

14. “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.”
Tree of Life vs. Trees of Life

15. Key Questions for Today:
• Is there a single tree of life or are there
multiple trees of life?
• Is there a single origin for all of life, or
are there multiple origins?
Tree of Life vs. Trees of Life

16. Tree of Life vs. Trees of Life
Connect
These on a
Single Tree
of Life

17. Connect
These on a
Single Tree
of Life
Tree of Life vs. Trees of Life

18. Branch Order Does
Not Matter As Long
As There Is A Single
Common Ancestor
Tree of Life vs. Trees of Life
Connect
These on a
Single Tree
of Life

19. Tree of Life vs. Trees of Life
Connect
These on a
Single Tree
of Life
Branch Order Does
Not Matter As Long
As There Is A Single
Common Ancestor

20. Tree of Life vs. Trees of Life
Connect These
on a Multiple
Trees of Life

21. Tree of Life vs. Trees of Life
Connect These
on a Multiple
Trees of Life

22. Tree of Life vs. Trees of Life
Connect These
on a Multiple
Trees of Life
Branch Order Does
Not Matter As Long
As There Is A Single
Common Ancestor

23. Tree of Life vs. Trees of Life
Connect These
on a Multiple
Trees of Life
Branch Order Does
Not Matter As Long
As There Is A Single
Common Ancestor

24. Tree of Life vs. Trees of Life
Connect These
on a Multiple
Trees of Life
Branch Order Does
Not Matter As Long
As There Is A Single
Common Ancestor

25. Tree of Life vs. Trees of Life
Connect These
on a Multiple
Trees of Life
Branch Order Does
Not Matter As Long
As There Is A Single
Common Ancestor

26. Thought Question
In theory, how many separate Origins of Life could
we have for these five taxa?
A: 1
B: 2
C: 3
D: 4
E: 5

27. In theory, how many separate Origins of Life could
we have for these five taxa?
A: 1
B: 2
C: 3
D: 4
E: 5
Thought Question

28. Hypothesis 1:
Separate Origins
Hypothesis 2:
Common Origin
Two Hypotheses
Tree of Life vs. Trees of Life
How Can We Choose Which
Hypothesis is Best?

29. • Recreate conditions of early Earth
• Model and theory
• Study Earth history
• Inferences from comparing organisms
How Do We Study The Origin(s) of Life?

30. • Recreate conditions of early Earth
• Model and theory
• Study Earth history
• Inferences from comparing organisms
How Do We Study The Origin(s) of Life?

31. Lecture 6 Outline
• Background and Context
• Tree of Life vs. Trees of Life
- Concept
- Universal traits
- Homology vs. Homoplasy
- Universal homologies

32. Universal Traits
Universal Traits?

33. Which of the following is NOT a universal
trait of all of life?
A: Made up of cells
B: Carry out transcription and translation
C: Extract energy from the environment
D: Universal molecular code to make
proteins
E: Contain genomes inside a nucleus
Thought Question

34. Which of the following is NOT a universal
trait of all of life?
A: Made up of cells
B: Carry out transcription and translation
C: Extract energy from the environment
D: Universal molecular code to make
proteins
E: Contain genomes inside a nucleus
Thought Question

35. The basic structural and physiological
unit of most living organisms is the
A: Organelle
B: Aggregate
C: Genome
D: Cell
E: Membrane
Thought Question

36. The basic structural and physiological
unit of most living organisms is the
A: Organelle
B: Aggregate
C: Genome
D: Cell
E: Membrane
Thought Question

37. List traits found in all organisms.
Universal Traits

38. List traits found in all organisms.
Universal Traits
Pause to Think

39. List traits found in all organisms.
• 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
• Acquires energy from environment
• Store energy in chemicals
Existence of
universal traits
does not prove all
life has a common
origin
Universal Traits

40. Lecture 6 Outline
• Background and Context
• Tree of Life vs. Trees of Life
- Concept
- Universal traits
- Homology vs. Homoplasy
- Universal homologies
• Martians

41. Homology
Similarity that is due to inheritance from a
common ancestor
Homoplasy
Similarity that has evolved independently
Homology vs. Homoplasy

42. Slide by Brian Moore for BIS2C at UC Davis Spring 2018

43. Slide by Brian Moore for BIS2C at UC Davis Spring 2018

44. List traits found in all organisms.
• 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
• Acquires energy from environment
• Store energy in chemicals
Universal Traits
Yes: not evidence
for common
ancestry.
No: evidence for
common ancestry.
Could trait have
evolved with a
reasonable
probability in
separate origins of
life?

45. Homology vs. Homoplasy Assessment

46. Uses Water as Solvent
Homology vs. Homoplasy: Water
Could “uses water as a solvent" have evolved with a
reasonable probability in separate origins of life?

47. Uses Water as Solvent
Homology vs. Homoplasy: Water
If YES: “uses water as a solvent" could have evolved with a
reasonable probability in separate origins of life
Thus this trait does not require a single tree of life. In other
words, multiple trees are possible.

48. Uses Water as Solvent
Homology vs. Homoplasy: Water
If NO: “uses water as a solvent" could not have evolved with a
reasonable probability in separate origins of life.
Then only possibility is a single tree.

49. • Recreate conditions of early Earth
• Model and theory
• Study Earth history
• Inferences from comparing organisms
How Do We Study The Origin(s) of Life?
Water abundant and likely only major
available solvent for life.

50. Uses Water as Solvent
Homology vs. Homoplasy: Water
YES: “uses water as a solvent" could have evolved with a
reasonable probability in separate origins of life.
Thus this trait does not require a single tree of life. In other
words, multiple trees are possible.

51. Uses Cells
Homology vs. Homoplasy: Cells

52. Homology vs. Homoplasy: Cells
Cells: Membrane bound compartments that are the
fundamental building blocks of all organisms

53. Uses Cells
Homology vs. Homoplasy: Cells
Could “uses cells” have evolved with a reasonable
probability in separate origins of life?

54. Homology vs. Homoplasy: Cells
If YES: “uses cells" could have evolved with a reasonable
probability in separate origins of life
Thus this trait does not require a single tree of life. In other
words, multiple trees are possible.
Uses Cells

55. Homology vs. Homoplasy: Cells
If NO: “uses cells” could not have evolved with a reasonable
probability in separate origins of life.
Then only possibility is a single tree.
Uses Cells

56. • Recreate conditions of early Earth
• Model and theory
• Study Earth history
• Inferences from comparing organisms
How Do We Study The Origin(s) of Life?
Cell-like structures can
form from very simple
components under early
life conditions

57. Homology vs. Homoplasy: Cells
YES: “uses cells” could have evolved with a reasonable
probability in separate origins of life.
Thus this trait does not require a single tree of life. In other
words, multiple trees are possible.
Uses Cells

58. Uses DNA as Genetic Material
Homology vs. Homoplasy: DNA

59. Homology vs. Homoplasy: DNA
Nucleic acids are made up of
chains of nucleotides.
Nucleotides are made up of a
sugar, a base, and and a
phosphate
DNA = deoxyribonucleic acid
RNA = ribonucleic acid

60. Uses DNA as Genetic Material
Homology vs. Homoplasy: DNA
Could “uses DNA” have evolved with a reasonable
probability in separate origins of life?

61. Homology vs. Homoplasy: DNA
If YES: “uses DNA” could have evolved with a reasonable
probability in separate origins of life
Thus this trait does not require a single tree of life. In other
words, multiple trees are possible.
Uses DNA as Genetic Material

62. Homology vs. Homoplasy: DNA
If NO: “uses DNA” could not have evolved with a reasonable
probability in separate origins of life.
Then only possibility is a single tree.
Uses DNA as Genetic Material

63. • Recreate conditions of early Earth
• Model and theory
• Study Earth history
• Inferences from comparing organisms
How Do We Study The Origin(s) of Life?
Nucleotides form in early Earth
conditions. DNA might form too and thus
could readily be used by different origins
of life.

64. Homology vs. Homoplasy: DNA
MAYBE: “uses DNA” could have evolved with a reasonable
probability in separate origins of life.
Thus it is unclear if this trait requires a single tree of life or if
multiple trees are possible.
Uses DNA as Genetic Material

65. Homology vs. Homoplasy: DNA
Might be evidence that there is one tree.
Uses DNA as Genetic Material

66. Homology vs. Homoplasy: Central Dogma
Central Dogma
CD CD CD CD CD

67. CD CD CD CD CD
DNA»RNA»Protein
Homology vs. Homoplasy: Central Dogma

68. Homology vs. Homoplasy: Central Dogma

69. Could “the central dogma” have evolved with a reasonable
probability in separate origins of life?
Central Dogma
Homology vs. Homoplasy: Central Dogma
CD CD CD CD CD

70. • Recreate conditions of early Earth
• Model and theory
• Study Earth history
• Inferences from comparing organisms
How Do We Study The Origin(s) of Life?
No clear reason why or how a separate
origin of life could or would end up with
DNA»RNA»protein

71. Central Dogma
CD CD CD CD CD
CD
CD
CD
CD
Homology vs. Homoplasy: Central Dogma
NO: “uses central dogma” likely could not have evolved with a
reasonable probability in separate origins of life.
Then only likely possibility is a single tree.

72. Thus multiple origins of life is not likely
Central Dogma
Homology vs. Homoplasy: Central Dogma
CD CD CD CD CD
CD
CD
CD

73. Homology vs. Homoplasy Assessment

74. Ribosome For Translation
Homology vs. Homoplasy: Ribosome for Translation

75. Homology vs. Homoplasy: Ribosome for Translation

76. • Recreate conditions of early Earth
• Model and theory
• Study Earth history
• Inferences from comparing organisms
How Do We Study The Origin(s) of Life?
Absolutely no way a separate origin of
life would use the same ribosomes,
with 50+ proteins, multiple rRNAs, and
similar 3D structures and mechanisms

77. NO WAY: “uses ribosome for translation” could have evolved in
separate origins of life.
Then only possibility is a single tree.
Homology vs. Homoplasy: Ribosome for Translation
Ribosome For Translation

78. List common traits of all organisms.
Homology vs. Homoplasy Overview

79. List common traits of all organisms.
• 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
• Acquires energy from environment
• Store energy in chemicals
Homology vs. Homoplasy

80. Easily could be
homoplasious
List common traits of all organisms.
• 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
• Acquires energy from environment
• Store energy in chemicals
Homology vs. Homoplasy

81. Might be
homoplasious
List common traits of all organisms.
• 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
• Acquires energy from environment
• Store energy in chemicals
Homology vs. Homoplasy

82. Likely
Homologous
List common traits of all organisms.
• 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
• Acquires energy from environment
• Store energy in chemicals
Homology vs. Homoplasy

83. List common traits of all organisms.
• 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
• Acquires energy from environment
• Store energy in chemicals
Definitely
Homologous
Homology vs. Homoplasy

84. Lecture 6 Outline
• Background and Context
• Tree of Life vs. Trees of Life
- Concept
- Universal traits
- Homology vs. Homoplasy
- Universal homologies
• Martians

85. Universal Trait
Trait shared by all organisms.
Universal Homology

86. Universal Homology
Trait shared by all organisms that could not
have arisen in separate origins of life and
thus is evidence for common ancestry.
Universal Homology

87. Hypothesis 1:
Separate Origins
Hypothesis 2:
Common Origin
Two Hypotheses
Tree of Life vs. Trees of Life
How Can We Choose Which
Hypothesis is Best?

88. Hypothesis 2:
Common Origin
Hypothesis 1:
Separate Origins
Two Hypotheses
Tree of Life vs. Trees of Life
The existence of Universal
Homologies means all life on
Earth is related.

89. “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.”
Tree of Life vs. Trees of Life

90. “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.”
Tree of Life vs. Trees of Life

91. !5: Inferring Trees
!6: The Tree of Life
!7: The Domains of Life
Lecture 6 Context