BIS2C. Biodiversity and the Tree of Life. 2014. L9. Acquisitions and Mergers
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Transcript of BIS2C. Biodiversity and the Tree of Life. 2014. L9. Acquisitions and Mergers
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 9
!
Lecture 9 !
Acquisitions and Mergers !!
BIS 002C Biodiversity & the Tree of Life
Spring 2014 !
Prof. Jonathan Eisen
1
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Where we are going and where we have been
• Previous Lecture: !8: Microbial Diversity part 2
• Current Lecture: !9: Acquisitions and Mergers
• Next Lecture: !10: Extremophiles
2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Microbe Launch Today to ISS at 1:48 PST
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see http://spacemicrobes.org
Follow live via #SpaceMicrobes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Outline
• Endosymbioses !Mitochondria !Chloroplast !Secondary endosymbioses !Tertiary endosymbiosis
• Lateral gene transfer
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Key Concepts
• Different parts of a cell or genome can have different histories
• The history of eukaryotes is littered with endosymbioses
• The history of bacteria and archaea is littered with acquisition of foreign DNA
• Theories about evolutionary history can be tested via analysis of data
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Case 1: Mitochondrial Evolution
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
One Theory of Mitochondrial Evolution
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
An ancestor of eukaryotes
8
Cell membrane
Genome
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 9
αProteo
Genome
Bacterial cell envelope
Cell membrane
Genome
A Symbiosis with a Proteobacterium
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Engulfment
10
αProteo
Cell membrane
Genome
Genome
Bacterial cell envelope
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 11
αProteoCell membrane
Genome
Genome
Bacterial cell envelope
Host membrane
Endosymbiosis
Endosymbiosis: when an organism (the host) bring another organism (the symbiont) inside of its cell.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 12
αProteoCell membrane
Genome
Genome
Bacterial cell envelope
Host membrane
Endosymbiosis
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Origin of the nucleus
13
N
αProteo
Host membrane
Nucleus
Cell membrane
Genome
Genome
Bacterial cell envelope
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Mitochondria
14
N
Mitochondrion
Genome
MNucleus
Cell membrane
Genome
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
The ancestor of all eukaryotes
15
N M
N M
N M
N M
N M
N M
Archaea
Eukarya
BacteriaLUCANM
NMNM
NM
NM
NM
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 16
Model prediction 1
Predicted tree for the nuclear genome
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 17
Bacteria Archaea Eukaryotes
Model prediction 1
Predicted tree for the nuclear genome
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 18
Predicted tree for the mitochondrial genome
Model prediction 2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 19
Bacteria ArchaeaEukaryotes
Predicted tree for the mitochondrial genome
Bacteria
Model prediction 2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
What if mitochondria had many separate origins?
20
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 21
Bacteria ArchEuks
Alternative model: multiple origins of mitochondria
Possible tree for alternative model
Bact Euks Euks
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Testing the models
22
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 23
Many similarities to bacteria / archaea
Testing the models: morphology not informative
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 24
Many similarities to bacteria / archaeaDNA
Testing the models: use DNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
rRNA (and other) sequencing
25
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
rRNA (and other) sequencing
25
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
rRNA (and other) sequencing
25
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
rRNA (and other) sequencing
25
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
rRNA (and other) sequencing
25
rRNA rRNArRNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
rRNA (and other) sequencing
25
rRNA rRNArRNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
rRNA (and other) sequencing
25
rRNA rRNArRNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
rRNA (and other) sequencing
25
rRNA rRNArRNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
rRNA (and other) sequencing
25
rRNA rRNArRNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters! S ACUGCACCUAUCGUUCG!! E ACUCCAGCUAUCGAUCG!! C ACCCCAGCUCUCGCUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
rRNA (and other) sequencing
25
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
rRNA (and other) sequencing
25
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
rRNA (and other) sequencing
25
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
B AMito B
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Evidence
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Phylogenetic analysis indicates that all mitochondria are derived from a single endosymbiosis involving a Proteobacterium.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Evidence
27
Phylogenetic analysis indicates that all mitochondria are derived from a single endosymbiosis involving a Proteobacterium.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Different histories within one genome
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Bacteria Archaea EukaryotesBacteria ArchaeaEukaryotes Bacteria
Nucleus
MitochondrionA model of a eukaryotic cell
Nuclear Tree
Mitochondrial Tree
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Other Predictions of this Model
29
N M
N M
N M
N M
N M
N M
Archaea
Eukarya
BacteriaLUCANM
NMNM
NM
NM
NM
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Other Predictions of this Model
30
N M
N M
N M
N M
N M
N M
Archaea
Eukarya
BacteriaLUCANM
NMNM
NM
NM
NM
To think about at home: !What does this model imply about the evolution of eukaryotes that do not have mitochondria?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Other Predictions of this Model
31
N M
N M
N M
N M
N M
N M
Archaea
Eukarya
BacteriaLUCANM
NMNM
NM
NM
NM
To think about at home: !What does this model imply about what phylogenetic trees of mitochondrial and nuclear genes should look like for the eukaryotic part of the tree …
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Case 2: Chloroplast Evolution
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
One Theory of Chloroplast Evolution
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Eukaryotic Cell
34
N
M
Mitochondrion
Mitochondrial Genome
Nucleus
Cell membrane
Nuclear Genome
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Symbiosis with Free Living Cyanobacterium
35
N
Mitochondrion
Mitochondrial Genome
MNucleus
Cell membrane
Nuclear Genome
Cyanobacterial Cell envelope
Cyanobacterial Genome Cyano
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Engulfment
36
N
Mitochondrion
Mitochondrial Genome
MNucleus
Cell membrane
Nuclear Genome
Cyanobacterial Cell envelope
Cyanobacterial Genome Cyano
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Endosymbiosis
37
N
Mitochondrion
Mitochondrial Genome
MNucleus
Cell membrane
Nuclear Genome
Cyanobacterial Cell envelope
Cyanobacterial Genome
Cyano
Is a “Primary symbiosis” because the symbiont has not experienced a prior symbiosis.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Chloroplast
38
N
Mitochondrion
Mitochondrial Genome
MNucleus
Cell membrane
Nuclear Genome
Chloroplast Cell envelope
Chloroplast Genome
Chloroplast
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Membrane lost in some
39
N
Mitochondrion
Mitochondrial Genome
MNucleus
Cell membrane
Nuclear Genome
Outer cell membrane lost in some
Chloroplast Genome
Chloroplast
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Cell wall lost in some
40
N
Mitochondrion
Mitochondrial Genome
MNucleus
Cell membrane
Nuclear Genome
Cell wall lost in some
Chloroplast Genome
Chloroplast
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 41
N
Mitochondrion
Mitochondrial Genome
MNucleus
Cell membrane
Nuclear Genome
Cell wall lost in some
Chloroplast Genome
Chloroplast
If this model is correct, what should phylogenetic trees of genes from the chloroplast look like?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
If single origin what should trees look like?
42
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 43
Bacteria Archaea Eukaryotes
Model prediction 1
Predicted tree for the nuclear genome
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 44
Bacteria ArchaeaEukaryotes
Predicted tree for the chloroplast genome
Bacteria
Model prediction 2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
What if chloroplast had many separate origins?
45
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 46
Bacteria ArchEuks
Alternative model: multiple origins of chloroplasts
Possible tree for alternative model
Bact Euks Euks
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Testing the models
47
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 48
Testing the models: morphology not informative
Many similarities to bacteria / archaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 49
DNA
Testing the models: use DNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Chloroplast Phylogeny
50
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Chloroplast Phylogeny
51
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Different histories within one genome
52
Bacteria Archaea EukaryotesBacteria ArchaeaEukaryotes Bacteria
Nuclear Tree
Mitochondrial Tree
Nucleus
CPST
Bacteria ArchaeaEukaryotes BacteriaMITO
Chloroplast Tree
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
But ….
53
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Model Has Limitations
N M
N M
N M
N M
N M
N M
Archaea
Eukarya
BacteriaLUCANM
NMNM
NM
NM
NM
Model like this is inconsistent with much of the data
C
C
C
C
C
C
54
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Scattered distribution of chloroplasts
5555
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N MC
N MC
N MC
N MC
N MC
N MC
Scattered distribution of chloroplasts
56
Hypothesis 1: Ancestral AND Loss
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Cryptomonad
57
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N MC
N M
N M
N M
N M
N M
Scattered distribution of chloroplasts
58
Hypothesis 2: Diversification of Major Lineages !Symbiosis in Plantae Ancestor
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N MC
Scattered distribution of chloroplasts
60
Hypothesis 2: Diversification of Major Lineages !Symbiosis in Plantae Ancestor
“Secondary Symbiosis” in other lineages
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Model for “Secondary” Symbiosis
61
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Symbiosis between two eukaryotic cells
62
N M
“Normal” eukaryote
Plantae representative with chloroplast
N M
C
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 63
N M
N M
C
Engulfment
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 64
NM
N M
C
Symbiont
Host
EndosymbiosisEndosymbiosis: when an organism (the host) bring another organism (the symbiont) inside of its cell.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 65
NM
N M
C
Symbiont
Host
This is a “secondary” symbioses because the symbiont itself already was a host of other symbionts.
Endosymbiosis
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 66
NM
N
C
Symbiont
Host
Second mitochondria often lost
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 67
NM
C
Symbiont
Host
Second nucleus often lost
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Secondary Symbioses of Euglenas
68
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Excavates: Euglenids
• Have flagella. • Some are
photosynthetic, some always heterotrophic, and some can switch.
69
Movement in the euglenoid Eutreptia
N M
N M
N M
N M
N M
N MC NM
C NMC NM
C N MC
N MC
N MC
N MC
N MC
Euglena Nuclear DNA tells us what its phylogenetic backbone is
70
Euglena plastid DNA says its plastid is related to those of chlorophytes
71
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
A lonely excavate ...
N M
72
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
N M
73
Engulfment of Chlorophyte
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
N M
C
74
Engulfment of Chlorophyte
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
N M
C
75
Endosymbiosis
N M
N M
N M
N M
N M
N MC NM
C NMC NM
C N MC
N MC
N MC
N MC
N MC
Phylogenetic analysis of plastid DNA reveals that the eukaryote engulfed by euglena was a Chlorophyte
Euglena Nuclear DNA tells us what its phylogenetic backbone is
76
N M
N M
N M
N M
N M
N MC NM
C NMC NM
C N MC
N MC
N MC
N MC
N MC
Phylogenetic analysis of plastid DNA reveals that the eukaryote engulfed by euglena was a Chlorophyte
Note - in some cases a “relic” nuclear genome of the symbiont is also still present and this can also be used to determine what type of organism the symbiont was
Euglena Nuclear DNA tells us what its phylogenetic backbone is
77
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Secondary Symbioses of Diatoms
78
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Stramenopiles: Diatoms
79
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
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 MC NM
C NMC NM
C N MC
N MC
N MC
N MC
N MC
Diatom nuclear DNA tells us what its phylogenetic backbone is
80
Diatom plastid DNA says its plastid is related to those of red algae
81
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
A lonely stramenophile ...
N M
82
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
N M
Engulfment of a red algae
83
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
N M
C
84
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
N M
C
85
N M
N M
N M
N M
N M
N MC NM
C NMC NM
C N MC
N MC
N MC
N MC
N MC
Phylogenetic analysis of plastid DNA reveals that the eukaryote engulfed by diatoms was a red algae
Euglena Nuclear DNA tells us what its phylogenetic backbone is
86
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Secondary Symbioses of Others
87
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
N M
N M
N M
N M
N MC NM
C NMC NM
C N MC
N MC
N MC
N MC
N MC
Many other secondary endosymbioses
Apicomplexans
Dinoflagellates
Amoebozoans
88
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Still Can’t Fit Model to Some Eukaryotes
89
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Dinoflagellate Kryptoperidinium foliaceum
http://onlinelibrary.wiley.com/doi/10.1111/j.1550-7408.2007.00245.x/full90
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
•All are multicellular; some get very large (e.g., giant kelp). •The carotenoid fucoxanthin imparts the brown color. •Almost exclusively marine.
Stramenopiles: Brown Algae
91
A community of brown algae: The marine kelp forest
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
92
Tertiary Symbioses?
“Normal” eukaryote
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
93
N MN M
C
Tertiary Symbioses?
“Normal” eukaryote
Euglenoid
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
Engulfment
94
N MN M
C
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
95
N MN M
C
Host
Symbiont
Endosymbsiosis
This is a “tertiary” symbiosis because the symbiont itself already underwent a secondary symbiosis.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
N M
N M
N M
N M
N MC NM
C NMC NM
C N MC
N MC
N MC
N MC
N MC
96
Brown Algae
Tertiary Endosymbsiosis
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Plants and Animals Get Many Functions from Symbionts
• Endosymbioses (only really work with eukaryotic cells as hosts) !Legumes with nitrogen fixing bacteria !Aphids with amino acid synthesizing
bacteria !Tubeworms with chemosynthetic bacteria !Lichens - fungi with algae or cyanobacteria !100s more
• Other symbioses !Cellulose digestion in the guts of termintes,
ruminants 97