Porella : features, morphology, anatomy, reproduction etc.
BIS2C_2020. Lecture 13 Organelles and Endosymbiosis
1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
BIS2C
Biodiversity & the Tree of Life
Spring 2020
Lecture 13:
Organelles and Endosymbiosis
Prof. Jonathan Eisen
2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Black necked stilt
3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Yellow headed blackbird
20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Learning Goals
• Understand the models and the evidence that
supports those models, that explain the origin of
the nucleus, mitochondria and chloroplasts
• Understand the differences between primary,
secondary and tertiary endosymbioses
• Understand how to track the multiple
evolutionary histories within eukaryotic genomes
that result from endosymbioses
21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
!12: Mutualisms and Microbiomes
!13: Endosymbiosis and Organelles
!14: Plants
Lecture 13 Context
22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 13 Outline
• Background and Context
• Endosymbiosis and Organelles
!Origin and evolution of the nucleus
!Origin and evolution of mitochondria
!Origin and evolution of chloroplasts
23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 13 Outline
• Background and Context
• Endosymbiosis and Organelles
!Origin and evolution of the nucleus
!Origin and evolution of mitochondria
!Origin and evolution of chloroplasts
24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Background: Lab
• Many parts of Lab 3
25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Background: Lecture 12 Review
26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 12 Outline
• Background and Context
• Mutualisms
• The Human Microbiome
27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 12 Outline
• Background and Context
• Mutualisms
• The Human Microbiome
28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Classes of symbiosis
Organism
Class of symbiosis A B
Mutualism + +
29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Mutualistic Symbioses of Bacteria w/ Eukaryotes
• Digestive
! Ruminants
! Cellulolytic insects
• Defensive
• Behavioral
! Squid light organs
• Autotrophic
! Photosynthetic (many)
! Chemosynthetic in deep sea
• Nutritional
! Aphids
! Nitrogen fixation in legumes
30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
These worms with their symbionts function as
chemolithoautotrophs. This is weird because
“normal" worms and most other animals are
A: Chemolithoheterotrophs
B: Chemoorganoautotrophs
C: Chemoorganoheterotrophs
D: Photolithoautotrophs
Thought Question
31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 12 Outline
• Background and Context
• Mutualisms
• The Human Microbiome
32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Classes of symbiosis
Organism
Class of symbiosis A B
Mutualism + +
Commensalism + 0
Microbes in human microbiome likely benefit.
Many interactions with human microbiome likely
“commensalism” because we do not know effect on humans
33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Classes of symbiosis
Organism
Class of symbiosis A B
Mutualism + +
Some associations in the human microbiome
appear to be mutualistic
34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Story 1: The Obese Mouse
35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Story 2: Disturbing the Microbiome
Antibiotics
Diet Changes
Hygiene
C-sections
Story 2: Disturbing the Microbiome (vs expected)
36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Story 3: Restoring the Microbiome
• C-section story is an example of attempting
to restore a disturbed microbiome
• Many other examples
37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 13 Outline
• Background and Context
• Endosymbiosis and Organelles
!Origin and evolution of the nucleus
!Origin and evolution of mitochondria
!Origin and evolution of chloroplasts
38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 13 Outline
• Background and Context
• Endosymbiosis and Organelles
!Origin and evolution of the nucleus
!Origin and evolution of mitochondria
!Origin and evolution of chloroplasts
39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Nucleus: An organelle found in all eukaryotes
40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Common Features of Eukaryotic Cells
41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Additional Traits Common To Eukaryotes
• Cell Structure
!Cytoskeleton
!Phagocytosis
!Diverse organelles and compartments
• Molecular Processes
!Mitosis (vs. binary fission)
!Sexual reproduction (vs. gene transfer)
" Meiosis
" Haploidy vs. Diploidy
" Fertilization
!Linear chromosomes & telomeres
!Chromosomes packaged into chromatin
!Decoupling of transcription and translation
!Introns and splicing
42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
An ancestor of all eukaryotes
Cell
membrane
Genome
43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Cell
membrane
Genome
Nucleus
An ancestor of all eukaryotes
44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Cell
membrane
Genome
Other Eukaryotic Features
Nucleus
An ancestor of all eukaryotes
45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
1
46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Traits Shared by Eukaryotes and Asgard Archaea
• Cell Structure
!Cytoskeleton
!Phagocytosis
!Diverse organelles and compartments
• Molecular Processes
!Mitosis (vs. binary fission)
!Sexual reproduction (vs. gene transfer)
" Meiosis
" Haploidy vs. Diploidy
" Fertilization
!Linear chromosomes & telomeres
!Chromosomes packaged into chromatin
!Decoupling of transcription and translation
!Introns and splicing
47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
1
Some key
traits may
have
originated
here
48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 13 Outline
• Introduction
• Origin and evolution of the nucleus
• Origin and evolution of mitochondria
• Origin and evolution of chloroplasts
49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Mitochondrion: Organelle in (Almost) All Eukaryotes
Respiration and
production of
ATP for
eukaryotes
50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Many
similarities to
bacteria /
prokaryotic
archaea
But morphology
not useful for
phylogeny of
bacteria &
prokaryotic
archaea
Origin and evolution of mitochondria
51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
DNA
Origin and evolution of mitochondria
52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Thought Question
• T/F
• The fact that mitochondria have DNA
genomes shows that they are derived from
bacteria
53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Thought Question
• T/F
• The fact that mitochondria have DNA
genomes shows that they are derived from
bacteria
54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Thought Question
• T/F
• The fact that mitochondria have DNA
genomes shows that they are derived from
bacteria
• Prokaryotic Archaea have DNA genomes too
and some look a lot like mitochondria
55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Origin and evolution of mitochondria
56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
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
PB AMito B
Origin and evolution of mitochondria
57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
PB AMito B
All mitochondrial trace
a common ancestry to a
single lineage within the
alpha subgroup of the
Proteobacteria phylum
of Bacteria
Origin and evolution of mitochondria
58. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lynn Margulis
Konstantin Mereschkowski
Origin and evolution of mitochondria
Endosymbiotic Theory
59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
A common ancestor of eukaryotes
Cell
membrane
Genome
Nucleus
60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
A Proteobacterium
αProteo
Genome
Bacterial cell envelope
61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Proteobacteria are Gram negative
• Two major ways it is
used in bacteria
• Gram-positive bacteria -
thick peptidoglycan layer
outside 1 cell membrane
• Gram-negative bacteria
- thin peptidoglycan
layer outside between
two cell membranes
• This has many impacts
on biology, including
sensitivity to antibiotics
62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
A Proteobacterium
αProteo
Genome
Bacterial cell envelope
63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
A Symbiosis Between Eukaryote and a Proteobacterium
Genome
Bacterial cell envelope
Cell
membrane
Genome
Nucleus
αProteo
64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Engulfment
Nucleus
Cell
membrane
Genome
Genome
Bacterial cell envelope
αProteo
65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
Cell
membrane
Genome
Genome
Bacterial cell envelope
Host
membrane
αProteo
Endosymbiosis: when an organism
(the host) bring another organism (the
symbiont) inside of its cell.
Nucleus
66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
Cell
membrane
Genome
Genome
Bacterial cell envelope
Host
membrane
Endosymbiosis: when an organism
(the host) bring another organism (the
symbiont) inside of its cell.
Is a “Primary symbiosis” because symbiont
has not experienced a prior symbiosis
Nucleus
αProteo
67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
Cell
membrane
Genome
Genome
Bacterial cell envelope
Host
membrane
αProteo
Endosymbiosis: when an organism
(the host) bring another organism (the
symbiont) inside of its cell.
Lost a membrane
Nucleus
68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
Cell
membrane
Genome
Genome
Bacterial cell envelope
Host
membrane
αProteo
Endosymbiosis: when an organism
(the host) bring another organism (the
symbiont) inside of its cell.
Lost cell wall
Nucleus
69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Eukaryote with a Mitochondrion
N
Mitochondrion
Genome
M
Nucleus
Cell
membrane
Genome
70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
1
71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
Endosymbiosis with a
Proteobacterium that
became the mitochondrion
2
2
1
Note - Proteobacteria
were already diverse
at this point even
though this tree does
not show this
72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Eukaryotic Parts Have Different Histories
Nucleus
A model
of a
eukaryotic
cell
Bacteria Eukaryotes“Prok. Archaea”
Nuclear
Tree
Mitochondrial
Tree
Eukaryotes Bacteria “Prok. Archaea”PB
Mitochondrion
73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Eukaryotic Parts Have Different Histories
Nucleus
MitochondrionA model
of a
eukaryotic
cell
Bacteria Eukaryotes“Prok. Archaea”
Nuclear
Tree
Mitochondrial
Tree
Eukaryotes Bacteria “Prok. Archaea”PB
74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Eukaryotic Parts Have Different Histories
Nucleus
MitochondrionA model
of a
eukaryotic
cell
Bacteria Eukaryotes“Prok. Archaea”
Nuclear
Tree
Mitochondrial
Tree
Eukaryotes Bacteria “Prok. Archaea”PB
75. More Detailed Phylogeny of Eukaryotes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Phylogeny of Eukaryotic
Groups
The exact phylogeny here
does not matter and you do
not need to know this full
phylogeny.
76. N M
N M
N M
N M
N M
N M
N M
N M
N
+
+
+
+
-
+
+
+
+
Presence/Absence of Mitochondria
Some eukaryotes
do not have
mitochondria
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Giardia = Diplomonad
Trichomonas = Parabisalid
Best explanation is
that they lost their
mitochondria
77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 13 Outline
• Introduction
• Origin and evolution of the nucleus
• Origin and evolution of mitochondria
• Origin and evolution of chloroplasts
78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Chloroplast: Organelle Found in Photosynthetic Eukarya
79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Many
similarities to
bacteria /
prokaryotic
archaea
But morphology
not useful for
phylogeny of
bacteria &
prokaryotic
archaea
Origin and evolution of chloroplasts
80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
DNA
Origin and evolution of chloroplasts
81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
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
Cyano “pA”CPST B
Origin and evolution of chloroplasts
82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Chloroplast Phylogeny
Conclusion: All Chloroplasts Have a Common Ancestry and Are Derived from A
Single Cyanobacterial Lineage
83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Extending the Endosymbiosis Model …
84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Eukaryotic Cell
N
M
Mitochondrion
Mitochondrial
Genome
Nucleus
Cell membrane
Nuclear Genome
85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Cyanobacterium
Cyano
86. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Cyanobacteria are Gram negative
• Two major ways it is
used in bacteria
• Gram-positive bacteria -
thick peptidoglycan layer
outside 1 cell membrane
• Gram-negative bacteria
- thin peptidoglycan
layer outside between
two cell membranes
• This has many impacts
on biology, including
sensitivity to antibiotics
87. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Symbiosis with Free Living Cyanobacterium
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Cyanobacterial
Cell envelope
Cyanobacterial
Genome Cyano
88. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Engulfment
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Cyanobacterial
Cell envelope
Cyanobacterial
Genome Cyano
89. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Cyanobacterial
Cell envelope
Cyanobacterial
Genome
Cyano
Is a “Primary symbiosis” because the symbiont has not
experienced a prior symbiosis.
90. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Chloroplast
Cell envelope
Chloroplast
Genome
Chloroplast
Becomes the Chloroplast
91. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Chloroplast
Cell envelope
Chloroplast
Genome
Chloroplast
Outer chloroplast membrane lost in some
92. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Chloroplast
Cell envelope
Chloroplast
Genome
Chloroplast
Outer chloroplast membrane lost in some
93. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Chloroplast
Cell envelope
Chloroplast
Genome
Chloroplast
Chloroplast cell wall lost in some
94. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Chloroplast
Cell envelope
Chloroplast
Genome
Chloroplast
Chloroplast cell wall lost in some
95. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
1
96. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
Endosymbiosis with a
Proteobacterium that
became the mitochondrion
2
2
1
97. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
Endosymbiosis with a
Proteobacterium that
became the mitochondrion
2
Endosymbiosis with a
Cyanobacterium that became
the chloroplast
3
3
2
1
98. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Eukaryotes with Chloroplasts: Three Histories
Nucleus
MITO
CPST
Bacteria “Pr. Archaea” Eukaryotes
Nuclear
Tree
Mitochondrial
Tree
Eukaryotes Bacteria “Pr. Archaea”PB
Chloroplast
Tree
Bacteria CBEukaryotes “Pr. Archaea”
99. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Eukaryotes with Chloroplasts: Three Histories
Nucleus
MITO
CPST
Bacteria “Pr. Archaea” Eukaryotes
Nuclear
Tree
Mitochondrial
Tree
Eukaryotes Bacteria “Pr. Archaea”PB
Chloroplast
Tree
Bacteria CBEukaryotes “Pr. Archaea”
100. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Scattered distribution of chloroplasts
101. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
Scattered distribution of chloroplasts
Hypothesis 1:
Ancestral AND Loss
102. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
Scattered distribution of chloroplasts
Hypothesis 1:
Ancestral AND Loss
Not supported by analysis
of phylogeny of
chloroplasts.
X
103. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N M
C
N M
N M
N M
N M
N M
Scattered distribution of chloroplasts
Hypothesis 2:
Diversification of Major
Lineages
Symbiosis in Plantae
Ancestor
And then other organisms
with chloroplasts got them
later …
104. The Plantae consist of
several clades; all
chloroplasts trace back
to a single incidence of
endosymbiosis.
Plantae group w/in Eukaryotes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
105. Plantae group only
have “simple”
membrane around their
chloroplasts
Plantae group w/in Eukaryotes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
106. N M
C
N M
C
N M
C
N M
C
Each lineage accumulates
some unique properties,
such as sequences of some
of their genes (N, M or C
genes).
N M
C
N M
C
N M
C
N M
C
N M
C
Plantae group w/in Eukaryotes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
107. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N M
C
Scattered distribution of chloroplasts
Hypothesis 2:
Diversification of Major
Lineages
Symbiosis in Plantae
Ancestor
And then “Secondary
Symbiosis” in other
lineages
108. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Models and Examples
• For the following topic you need to know the
general models for additional symbioses in
the history of chloroplasts and how to infer
history of symbioses
• You should also know which taxa are
involved in the main examples covered
109. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Model for “Secondary” Symbiosis
110. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Symbiosis between two eukaryotic cells
N
M
“Normal” eukaryote
Blue
membranes
to help track
111. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Symbiosis between two eukaryotic cells
Plantae representative with chloroplast
Black
Membranes to
Help Track
N M
C
112. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Symbiosis between two eukaryotic cells
N
M
“Normal” eukaryote
Plantae representative with chloroplast
N M
C
113. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Engulfment
N
M
N M
C
114. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
N
M
N
M
C
Symbiont
Host
Endosymbiosis: when an organism (the host) bring another organism (the
symbiont) inside of its cell.
115. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
N
M
N
M
C
Symbiont
Host
This is a “secondary” symbioses because the symbiont itself already was a
host of other symbionts.
116. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Thought Question
N
M
N
M
C
Symbiont
Host
This is a “secondary” symbioses because the symbiont itself already was a
host of other symbionts.
How many different histories could there be after a secondary endosymbiosis?
117. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N
M
N
M
C
Symbiont
Host
This is a “secondary” symbioses because the symbiont itself already was a
host of other symbionts.
How many different histories could there be after a secondary endosymbiosis?
Thought Question
118. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N
M
N
M
C
Symbiont
Host
Loss of components
Second mitochondria often lost
119. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
N
M
N
C
Symbiont
Host
Second mitochondria often lost
120. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
N
M
N
C
Symbiont
Host
Second nucleus often lost
121. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
N
M
C
Symbiont
Host
Second nucleus often lost
122. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
N
M
C
Symbiont
Host
Symbiont membrane sometimes lost
123. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
N
M
C
Symbiont
Host
Symbiont membrane sometimes lost
125. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Excavates: Euglenids
• Have flagella.
• Some are
photosynthetic,
some always
heterotrophic, and
some can switch.
Movement in the euglenoid Eutreptia
126. N M
N M
N M
N M
N M
N M
C
N M
C
N M
C N M
C N M
C
N M
C
N M
C
N M
C
N M
C
Euglena Nuclear DNA tells
us what its phylogenetic
backbone is
Excavates: Euglenid Chloroplast Origins
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
127. Euglena plastid
DNA says its plastid
is related to those of
chlorophytes
Excavates: Euglenid Chloroplast Origins
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
128. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Model to explain this …
130
129. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
A lonely Excavate ...
131
N
M
130. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N M
C
Chlorophyte
131. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
Chlorophyte
132. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N M
C
Chlorophyte
133. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Symbiosis
N
M
N M
C
134. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Engulfment
N
M
N M
C
135. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
N
M
N M
C
136. N M
N M
N M
N M
N M
N M
C
N M
C
N M
C N M
C N M
C
N M
C
N M
C
N M
C
N M
C
Excavates: Euglenid Chloroplast Origins
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
137. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Stramenopiles: Diatoms
A colony of the diatom,
Bacillaria paradoxa
•Unicellular, but many associate in
filaments.
•Have carotenoids and appear yellow or
brown.
•Excellent fossil record
•Most are photoautotrophic
•Responsible for 20% of all carbon fixation.
•Oil, gas source
138. N M
N M
N M
N M
N M
Many lines of evidence indicate that it occurred in the
common ancestor of the “Plantae” lineage.
One line of evidence for this is that all organisms on this
branch have chloroplasts and the cells of these organisms
resemble the “primary” symbiotic cell.
N M
C
N M
C
N M
C N M
C N M
C
N M
C
N M
C
N M
C
N M
C
Diatom nuclear DNA tells us
what its phylogenetic
backbone is
Diatom Chloroplast Origins
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
139. Diatom plastid DNA
says its plastid is
related to those of
red algae
Diatom Chloroplast Origins
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
140. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
A lonely Stramenopile ...
142
N
M
141. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
A lonely red algae ...
143
N M
C
142. Red algae
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
143. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
A lonely red algae ...
145
N M
C
144. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Symbiosis
N
M
N M
C
145. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Engulfment
N
M
N M
C
146. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Endosymbiosis
N
M
N M
C
147. N M
N M
N M
N M
N M
N M
C
N M
C
N M
C N M
C N M
C
N M
C
N M
C
N M
C
N M
C
Diatom Chloroplast Origins
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
148. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N M
N M
N M
N M
N M
N M
C
N M
C
N M
C N M
C N M
C
N M
C
N M
C
N M
C
N M
C
Many other secondary endosymbioses
Apicomplexans
Dinoflagellates
Amoebozoans
149. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N M
N M
N M
N M
N M
N M
C
N M
C
N M
C N M
C N M
C
N M
C
N M
C
N M
C
N M
C
Many other secondary endosymbioses
Apicomplexans
Dinoflagellates
Amoebozoans
150. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
•Most are marine and are important
photoautotrophic primary producers
•Mixture of pigments give them a golden brown
color.
•Have two flagella, one in an equatorial groove,
the other in a longitudinal groove.
Alveolates: Dinoflagellates
Certium
tenue
Coral symbiont
Tour - Don’t Need to
Know These Details
151. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Alveolates: Apicomplexans
• All parasitic
• Have a mass of organelles at one tip
—the apical complex that help the
parasite enter the host’s cells.
Apical complex • Plasmodium falciparum-
Malaria kills 700,000-2,000,000
people per year—75% of them
are African children
152
Tour - Don’t Need to
Know These Details
152. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
• Not colonial; live as single cells
• Some secrete shells or glue sand
grains together to form a casing.
• Many pathogens
Amoebozoans: Loboseans Tour - Don’t Need to
Know These Details
153. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Rhizaria: Cercozoans
Some cercozoans are aquatic, others
live in soil.
They have diverse forms and habitats.
One group has chloroplasts derived
from a green alga by secondary
endosymbiosis.
Euglyphid
Chlorarachnion reptans
Tour - Don’t Need to
Know These Details
154. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
155. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
1
156. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
Endosymbiosis with a
Proteobacterium that
became the mitochondrion
2
2
1
157. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
Endosymbiosis with a
Proteobacterium that
became the mitochondrion
2
Endosymbiosis with a
Cyanobacterium that became
the chloroplast
3
3
2
1
158. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
Endosymbiosis with a
Proteobacterium that
became the mitochondrion
2
Endosymbiosis with a
Cyanobacterium that became
the chloroplast
3
3
2
1
Secondary
159. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Still Can’t Fit Model to Some Eukaryotes
160. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Dinoflagellate Kryptoperidinium foliaceum
http://onlinelibrary.wiley.com/doi/10.1111/j.1550-7408.2007.00245.x/full
161. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
•All are multicellular; some get very large (e.g.,
giant kelp).
•The carotenoid fucoxanthin imparts the brown
color.
•Almost exclusively marine.
Stramenopiles: Brown Algae
A community of brown algae: The marine kelp forest
162. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Model to Explain These
163. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Diatom Doing It’s Thing
N
M
N M
C
Diatom
164. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N
M
A Lonely Stramenopile
Stramenopile
165. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N
M
Symbiosis
N
M
N M
C
Stramenopile
Diatom
166. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N
M
Engulfment
N
M
N M
C
167. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N
M
Endosymbsiosis
Host
Symbiont
This is a “tertiary” symbiosis because the symbiont itself already underwent a
secondary symbiosis.
N
M
N M
C
168. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N
M
Endosymbsiosis
Host
Symbiont
Note - many of these organelles and genomes will have been lost sometime in
the history of such tertiary symbioses. I am showing all of them here so that
you can track where they would go IF everything was kept
N
M
N M
C
169. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N
M
Thought Question
Host
Symbiont
How many different histories could thereby after a tertiary symbiosis?
N
M
N M
C
170. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N
M
Thought Question
Host
Symbiont
How many different histories could thereby after a tertiary symbiosis?
N
M
N M
C
171. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N
M
Many of the genomes and components frequently lost
Host
Symbiont
Can end up like this
C
172. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
N M
N M
N M
N M
N M
N M
C
N M
C
N M
C N M
C N M
C
N M
C
N M
C
N M
C
N M
C
Tertiary endosymbioses?
Brown Algae
Tertiary Endosymbsiosis
173. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
174. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
1
175. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
Endosymbiosis with a
Proteobacterium that
became the mitochondrion
2
2
1
176. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
Endosymbiosis with a
Proteobacterium that
became the mitochondrion
2
Endosymbiosis with a
Cyanobacterium that became
the chloroplast
3
3
2
1
177. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
Endosymbiosis with a
Proteobacterium that
became the mitochondrion
2
Endosymbiosis with a
Cyanobacterium that became
the chloroplast
3
3
2
1
Secondary
178. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
Endosymbiosis with a
Proteobacterium that
became the mitochondrion
2
Endosymbiosis with a
Cyanobacterium that became
the chloroplast
3
3
2
1
Secondary
Tertiary
179. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Past, Present and Future
!12: Mutualisms and Microbiomes
!13: Endosymbiosis and Organelles
!14: Plants