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

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

Microbe Launch Today to ISS at 1:48 PST
3
see http://spacemicrobes.org
Follow live via
#SpaceMicrobes

Outline
• Endosymbioses
!Mitochondria
!Chloroplast
!Secondary endosymbioses
!Tertiary endosymbiosis
• Lateral gene transfer
4

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
5

Case 1: Mitochondrial Evolution
6

One Theory of Mitochondrial Evolution
7

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

Engulfment
10
αProteo
Cell
membrane
Genome
Genome

αProteo
Cell
membrane
Genome
Genome
Host
membrane
Endosymbiosis
Endosymbiosis: when an organism
(the host) bring another organism (the
symbiont) inside of its cell.

αProteo
Cell
membrane
Genome
Genome
Host
membrane
Endosymbiosis
Endosymbiosis: when an organism
(the host) bring another organism (the
Is a “Primary symbiosis” because symbiont
has not experienced a prior symbiosis

Origin of the nucleus
13
N
αProteo
Host
membrane
Nucleus
Cell
membrane
Genome
Genome

Mitochondria
14
N
Mitochondrion
Genome
M
Nucleus
Cell
membrane
Genome

The ancestor of all eukaryotes
N M
N M
N M
N M
N M
N M
Archaea
Eukarya
Bacteria
LUCA
NM
NM
NM
NM
NM
NM

Model prediction 1
Predicted tree for the nuclear genome

Bacteria Archaea Eukaryotes
Model prediction 1

Predicted tree for the mitochondrial genome
Model prediction 2

Bacteria ArchaeaEukaryotes
Predicted tree for the mitochondrial genome
Bacteria
Model prediction 2

What if mitochondria had many separate origins?
20

Bacteria ArchEuks
Alternative model: multiple origins of mitochondria
Possible tree for alternative model
Bact Euks Euks

Testing the models
22

Many
similarities
to bacteria /
archaea
Testing the models: morphology not informative

Many
similarities
to bacteria /
archaea
DNA
Testing the models: use DNA

rRNA (and other) sequencing
25

25
rRNA rRNArRNA

25
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG

25
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters!
S ACUGCACCUAUCGUUCG!
!
E ACUCCAGCUAUCGAUCG!
!
C ACCCCAGCUCUCGCUCG

25
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters!
R ACUCCACCUAUCGUUCG!
F ACUCCAGGUAUCGAUCG!
C ACCCCAGCUCUCGCUCG!
W ACCCCAGCUCUGGCUCG
Taxa Characters!
!
!
C ACCCCAGCUCUCGCUCG

25
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters!
R ACUCCACCUAUCGUUCG!
F ACUCCAGGUAUCGAUCG!
C ACCCCAGCUCUCGCUCG!
W ACCCCAGCUCUGGCUCG
Taxa Characters!
!
!
C ACCCCAGCUCUCGCUCG
B AMito B

Evidence
26
Phylogenetic analysis indicates that all mitochondria are derived from a
single endosymbiosis involving a Proteobacterium.

Evidence
27
Phylogenetic analysis indicates that all mitochondria are derived from a
single endosymbiosis involving a Proteobacterium.

Different histories within one genome
28
Bacteria ArchaeaEukaryotes Bacteria
Nucleus
Mitochondrion
A model
of a
eukaryotic
cell
Nuclear
Tree
Mitochondrial
Tree

Other Predictions of this Model
N M
N M
N M
N M
N M
N M
Archaea
Eukarya
Bacteria
LUCA
NM
NM
NM
NM
NM
NM

N M
N M
N M
N M
N M
N M
Archaea
Eukarya
Bacteria
LUCA
NM
NM
NM
NM
NM
NM
To think about at home:
!
What does this model
imply about the
evolution of eukaryotes
that do not have
mitochondria?

N M
N M
N M
N M
N M
N M
Archaea
Eukarya
Bacteria
LUCA
NM
NM
NM
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 …

Case 2: Chloroplast Evolution
32

One Theory of Chloroplast Evolution
33

Eukaryotic Cell
34
N
M
Mitochondrion
Mitochondrial
Genome
Nucleus
Cell membrane
Nuclear Genome

Symbiosis with Free Living Cyanobacterium
35
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Cyanobacterial
Cell envelope
Cyanobacterial
Genome Cyano

Engulfment
36
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Cyanobacterial
Cell envelope
Cyanobacterial
Genome Cyano

Endosymbiosis
37
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.

Chloroplast
38
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Chloroplast
Cell envelope
Chloroplast
Genome
Chloroplast

Membrane lost in some
39
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Outer cell membrane lost in some
Chloroplast
Genome
Chloroplast

Cell wall lost in some
40
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Chloroplast
Genome
Chloroplast

N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Chloroplast
Genome
Chloroplast
If this model is correct, what should phylogenetic trees of genes
from the chloroplast look like?

If single origin what should trees look like?
42

Model prediction 1

Bacteria ArchaeaEukaryotes
Predicted tree for the chloroplast genome
Bacteria
Model prediction 2

What if chloroplast had many separate origins?
45

Bacteria ArchEuks
Alternative model: multiple origins of chloroplasts
Possible tree for alternative model
Bact Euks Euks

Testing the models
47

Testing the models: morphology not informative
Many
similarities
to bacteria /
archaea

DNA
Testing the models: use DNA

Chloroplast Phylogeny
50

Chloroplast Phylogeny
51

Different histories within one genome
52
Nuclear
Tree
Mitochondrial
Tree
Nucleus
CPST
MITO
Chloroplast
Tree

But ….
53

Model Has Limitations
N M
N M
N M
N M
N M
N M
Archaea
Eukarya
Bacteria
LUCA
NM
NM
NM
NM
NM
NM
Model like this is
inconsistent with much
of the data
C
C
C
C
C
C
54

Scattered distribution of chloroplasts
5555

N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
56
Hypothesis 1:
Ancestral AND Loss

Cryptomonad

N M
C
N M
N M
N M
N M
N M
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

N M
C
60
Hypothesis 2:
Diversification of Major
Lineages
!
Symbiosis in Plantae
Ancestor
“Secondary Symbiosis” in
other lineages

Model for “Secondary” Symbiosis
61

Symbiosis between two eukaryotic cells
62
N
M
“Normal” eukaryote
Plantae representative with chloroplast
N M
C

N
M
N M
C
Engulfment

N
M
N
M
C
Symbiont
Host
Endosymbiosis
Endosymbiosis: when an organism (the host) bring another organism (the

N
M
N
M
C
Symbiont
Host
This is a “secondary” symbioses because the symbiont itself already was a
host of other symbionts.
Endosymbiosis

N
M
N
C
Symbiont
Host
Second mitochondria often lost

N
M
C
Symbiont
Host
Second nucleus often lost

Secondary Symbioses of Euglenas
68

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 M
C
NM
C
NM
C NM
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
70

Euglena plastid
DNA says its
plastid is related to
those of
chlorophytes
71

A lonely excavate ...
N
M
72

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

N
M
N M
C
74
Engulfment of Chlorophyte

N
M
N M
C
75
Endosymbiosis

N M
N M
N M
N M
N M
N M
C
NM
C
NM
C NM
C N M
C
N M
C
N M
C
N M
C
N M
C
Phylogenetic analysis of
plastid DNA reveals that the
eukaryote engulfed by
euglena was a Chlorophyte
backbone is
76

N M
N M
N M
N M
N M
N M
C
NM
C
NM
C NM
C N M
C
N M
C
N M
C
N M
C
N M
C
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
backbone is
77

Secondary Symbioses of Diatoms
78

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 M
C
NM
C
NM
C NM
C N M
C
N M
C
N M
C
N M
C
N M
C
Diatom nuclear DNA tells
backbone is
80

Diatom plastid
DNA says its
plastid is related to
those of red algae
81

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

N
M
N M
C
84

N
M
N M
C
85

N M
N M
N M
N M
N M
N M
C
NM
C
NM
C NM
C N M
C
N M
C
N M
C
N M
C
N M
C
diatoms was a red algae
backbone is
86

Secondary Symbioses of Others
87

N M
N M
N M
N M
N M
N M
C
NM
C
NM
C NM
C N M
C
N M
C
N M
C
N M
C
N M
C
Many other secondary endosymbioses
Apicomplexans
Dinoflagellates
Amoebozoans
88

Still Can’t Fit Model to Some Eukaryotes
89

Dinoflagellate Kryptoperidinium foliaceum
http://onlinelibrary.wiley.com/doi/10.1111/j.1550-7408.2007.00245.x/full
90

•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

N
M
92
Tertiary Symbioses?

N
M
93
N
M
N M
C
Tertiary Symbioses?
Euglenoid

N
M
Engulfment
94
N
M
N M
C

N
M
95
N
M
N M
C
Host
Symbiont
Endosymbsiosis
This is a “tertiary” symbiosis because the symbiont itself already underwent a
secondary symbiosis.

N M
N M
N M
N M
N M
N M
C
NM
C
NM
C NM
C N M
C
N M
C
N M
C
N M
C
N M
C
96
Brown Algae
Tertiary Endosymbsiosis

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

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