BiS2C: Lecture 10: Not Trees

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Lecture 10:
Not Trees
BIS 002C
Biodiversity & the Tree of Life
Spring 2016
Prof. Jonathan Eisen
1

Where we are going and where we have been
• Previous Lecture:
!9: Microbial Diversity
• Current Lecture:
!10: Not trees
• Next Lecture:
!11: Functional Diversity
2

Not Trees
3

Key Concepts
• Different parts of a cell or genome can have different
histories
• Many cases and causes of this including
• Viral insertion of DNA and movement between hosts
• Lateral gene transfer (unidirectional movement of DNA
from one cell to another)
• Endosymbiosis (one cell bringing another cell inside of
it)
• Detecting such events can be done via phylogenetic
analysis
4

Diverse Organelles
5
Mitochondrion Chloroplast
Nucleus

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 8
Many
similarities to
bacteria /
archaea
Mitochondria look like bacteria
But
morphology
not useful for
phylogeny of
bacteria &
archaea

DNA
Mitochondria have their own genomes

Woese Tree of Life
10
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

Phylogenetic Tree of Mitochondrial Genes

13

Eukaryote Groups - More Detail
1414

15
Conclusion: All Mitochondria Have a Common Ancestry

One Theory of Mitochondrial Evolution
16

A common ancestor of eukaryotes
17
Cell
membrane
Genome

αProteo
Genome
Bacterial cell envelope
Cell
membrane
Genome
A Symbiosis with a Proteobacterium

Engulfment
19
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
22
N
αProteo
Host
membrane
Nucleus
Cell
membrane
Genome
Genome

Mitochondria
23
N
Mitochondrion
Genome
M
Nucleus
Cell
membrane
Genome

Different histories within one genome
24
Bacteria Archaea Eukaryotes
Nucleus
Mitochondrion
A model
of a
eukaryotic
cell
Nuclear
Tree
Mitochondrial
Tree
Eukaryotes Bacteria ArchaeaB

Chimeras
25
Nucleus
Mitochondrion
A model
of a
eukaryotic
cell
Nuclear
Tree
Mitochondrial
Tree

N M
N M
N M
N M
N M
N M
N M
N M
N
+
+
+
+
-
+
+
+
+
Presence/Absence of Mitochondria
• How Explain
Pattern of
Presence /
Absence?

Excavates: Diplomonads and Parabisalids
• Unicellular
• Lack mitochondria and most are
anaerobic. This is a derived condition
• Giardia lamblia - a diplomonad - is a
human parasite
• Trichomonas vaginalis - parabasalid - STD
27

N M
N M
N M
N M
N M
N M
N M
N M
N
+
+
+
+
-
+
+
+
+
Mitochondria found throughout
eukaryotic diversity in almost all
taxa
Phylogeny of mitochondria
suggest all have a common origin
Phylogeny of mitochondria is
congruent to phylogeny of
nucleus from same taxa

taxa
N M
N M
N M
N M
N M
N M
N M
N M
N
+
+
+
+
-
+
+
+
+
Can infer then that
mitochondria were likely
present in the common
ancestor of all eukaryotes.
N M

taxa
N M
N M
N M
N M
N M
N M
N M
N M
N
+
+
+
+
-
+
+
+
+
Can infer then that
N M
N M
N M
N M
N M
N M

taxa
N M
N M
N M
N M
N M
N M
N M
N M
N
+
+
+
+
-
+
+
+
+
Can infer then that
N M
N M
N M
N M
N M
N M
Then can infer that
lineages w/o
mitochondria lost them
sometime in their
history

36
Some species have
mitochondrially
related genes even
though they do not
have mitochondria

37
Nucleus
Mitochondrion
A model
of a
eukaryotic
cell
Nuclear
Tree
Mitochondrial
Tree

Case 2: Chloroplast Evolution
38

Scattered distribution of chloroplasts
3939

Copying the Mitochondrial Model …
40

Eukaryotic Cell
41
N
M
Mitochondrion
Mitochondrial
Genome
Nucleus
Cell membrane
Nuclear Genome

Symbiosis with Free Living Cyanobacterium
42
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Cyanobacterial
Cell envelope
Cyanobacterial
Genome Cyano

Engulfment
43
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Cyanobacterial
Cell envelope
Cyanobacterial
Genome Cyano

Endosymbiosis
44
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
45
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Chloroplast
Cell envelope
Chloroplast
Genome
Chloroplast

Membrane lost in some
46
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Outer cell membrane lost in some
Chloroplast
Genome
Chloroplast

Cell wall lost in some
47
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?
49

Model prediction 1
Predicted tree for the nuclear genome

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

What if chloroplast had many separate origins?
52

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

Testing the models
54

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

DNA
Testing the models: use DNA

Chloroplast Phylogeny
57

58

59
Conclusion: All Chloroplasts Have a Common Ancestry

Nucleus
CPST
MITO
Chloroplast
Tree
Nuclear
Tree
Mitochondrial
Tree
Bacteria BEukaryotes Archaea

Why does it matter which
lineage they came from?
Many photosynthetic
bacteria
Chloroplast biology is
more similar to that of
cyanobacteria than to
other photosynthetic
bacteria

But ….
66

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
67

6868

N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
69
Hypothesis 1:
Ancestral AND Loss

N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
70
Hypothesis 1:
Ancestral AND Loss
If correct, then tree of
chloroplasts should still
parallel tree of nuclear
genome (with some
organisms missing).
But it does not.

Plantae group only
have “simple”
membrane around their
chloroplasts

Cryptomonad
Some organisms have
complicated
membranes around
their chloroplasts.

N M
C
N M
N M
N M
N M
N M
73
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
75
Hypothesis 2:
Diversification of Major
Lineages
Symbiosis in Plantae
Ancestor
“Secondary Symbiosis” in
other lineages

Model for “Secondary” Symbiosis
76

Symbiosis between two eukaryotic cells
77
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
83

Excavates: Euglenids
• Have flagella.
• Some are
photosynthetic,
some always
heterotrophic, and
some can switch.
84
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
85

Euglena plastid
DNA says its
plastid is related to
those of
chlorophytes
86

A lonely excavate ...
N
M
87

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
88
Engulfment of Chlorophyte

N
M
N M
C
89
Engulfment of Chlorophyte

N
M
N M
C
90
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
91

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
92

Secondary Symbioses of Diatoms
93

Stramenopiles: Diatoms
94
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
95

Diatom plastid
DNA says its
plastid is related to
those of red algae
96

A lonely stramenophile ...
N
M
97

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
98

N
M
N M
C
99

N
M
N M
C
100

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
101

Secondary Symbioses of Others
102

N M
N M
N M
N M
N M
N M
C
NM
C
NM
C NM
C NM
C
NM
C
NM
C
NM
C
NM
C
Many other secondary endosymbioses
Apicomplexans
Dinoflagellates
Amoebozoans
10

•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
104

Alveolates: Apicomplexans
• All parasitic
• Have a mass of organelles at one tip
—the apical complex that help the
parasite enter the host’s cells.
105
Apical complex • Plasmodium falciparum-
Malaria kills 700,000-2,000,000
people per year—75% of them
are African children
105

• Not colonial; live as single cells
• Some secrete shells or glue sand
grains together to form a casing.
• Many pathogens
106
Amoebozoans: Loboseans

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
107
Chlorarachnion reptans

Still Can’t Fit Model to Some Eukaryotes
108

Dinoflagellate Kryptoperidinium foliaceum
http://onlinelibrary.wiley.com/doi/10.1111/j.1550-7408.2007.00245.x/full
109

•All are multicellular; some get very large
(e.g., giant kelp).
•The carotenoid fucoxanthin imparts the
brown color.
•Almost exclusively marine.
Stramenopiles: Brown Algae
110
A community of brown algae: The marine kelp forest

N
M
111
Tertiary Symbioses?

N
M
112
N
M
N M
C
Tertiary Symbioses?
Euglenoid

N
M
Engulfment
113
N
M
N M
C

N
M
114
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
115
Tertiary endosymbioses?
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
116

Viruses
117

Figure 26.25 Viruses Are Diverse
!118

Figure 26.25 Viruses Are Diverse (Part 1)
!119

!120

!121

• Where do viruses sit on the tree of life?
• Viruses are obligate parasites of other organisms and
cannot live on their own
• Three main theories about viruses and where they sit on
the tree of life
• 1. Viruses are relics from a pre-cellular world
• 2. Viruses are escaped portions of cellular organisms
• 3. Viruses are extremely derived and reduced cellular
organisms
!122

Virus Evolution Model 1: The Fourth Domain
Viruses

Virus Evolution Model 2: Separate Origin
Viruses

Bacteria Archaea EukaryotesViruses Viruses
Virus Evolution Model 3: From Within Other Groups

Probably a Little of Each
126

BiS2C: Lecture 10: Not Trees

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