bis2c: lecture 10: not trees
TRANSCRIPT
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 9
DNA
Mitochondria have their own genomes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 12
Phylogenetic Tree of Mitochondrial Genes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Phylogenetic Tree of Mitochondrial Genes
13
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Phylogenetic Tree of Mitochondrial Genes
15
Conclusion: All Mitochondria Have a Common Ancestry
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
A common ancestor of eukaryotes
17
Cell membrane
Genome
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 18
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
19
αProteo
Cell membrane
Genome
Genome
Bacterial cell envelope
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 20
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 21
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
22
N
αProteo
Host membrane
Nucleus
Cell membrane
Genome
Genome
Bacterial cell envelope
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Mitochondria
23
N
Mitochondrion
Genome
MNucleus
Cell membrane
Genome
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Different histories within one genome
24
Bacteria Archaea Eukaryotes
Nucleus
MitochondrionA model of a eukaryotic cell
Nuclear Tree
Mitochondrial Tree
Eukaryotes Bacteria ArchaeaB
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Chimeras
25
Bacteria Archaea Eukaryotes
Nucleus
MitochondrionA model of a eukaryotic cell
Nuclear Tree
Mitochondrial Tree
Eukaryotes Bacteria ArchaeaB
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?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Mitochondria found throughout eukaryotic diversity in almost all taxa
N M
N M
N M
N M
N M
N M
N M
N M
N
++
++-+
+++
Phylogeny of mitochondria suggest all have a common origin
Phylogeny of mitochondria is congruent to phylogeny of nucleus from same taxa
Can infer then that mitochondria were likely present in the common ancestor of all eukaryotes.
N M
Mitochondria found throughout eukaryotic diversity in almost all taxa
N M
N M
N M
N M
N M
N M
N M
N M
N
++
++-+
+++
Phylogeny of mitochondria suggest all have a common origin
Phylogeny of mitochondria is congruent to phylogeny of nucleus from same taxa
Can infer then that mitochondria were likely present in the common ancestor of all eukaryotes.
N M
N M
N M
N M
N M
N M
Mitochondria found throughout eukaryotic diversity in almost all taxa
N M
N M
N M
N M
N M
N M
N M
N M
N
++
++-+
+++
Phylogeny of mitochondria suggest all have a common origin
Phylogeny of mitochondria is congruent to phylogeny of nucleus from same taxa
Can infer then that mitochondria were likely present in the common ancestor of all eukaryotes.
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Phylogenetic Tree of Mitochondrial Genes
36
Some species have mitochondrially related genes even though they do not have mitochondria
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Different histories within one genome
37
Bacteria Archaea Eukaryotes
Nucleus
MitochondrionA model of a eukaryotic cell
Nuclear Tree
Mitochondrial Tree
Eukaryotes Bacteria ArchaeaB
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Scattered distribution of chloroplasts
3939
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Eukaryotic Cell
41
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
42
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
43
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
44
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
45
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
46
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
47
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 48
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?
49
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 50
Bacteria Archaea Eukaryotes
Model prediction 1
Predicted tree for the nuclear genome
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 51
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?
52
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 53
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 55
Testing the models: morphology not informative
Many similarities to bacteria / archaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Chloroplast Phylogeny
59
Conclusion: All Chloroplasts Have a Common Ancestry
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Different histories within one genome
Nucleus
CPST
MITO
Chloroplast Tree
Bacteria Archaea Eukaryotes
Nuclear Tree
Mitochondrial Tree
Eukaryotes Bacteria ArchaeaB
Bacteria BEukaryotes Archaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Different histories within one genome
Nucleus
CPST
MITO
Chloroplast Tree
Bacteria Archaea Eukaryotes
Nuclear Tree
Mitochondrial Tree
Eukaryotes Bacteria ArchaeaB
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
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
BacteriaLUCAN M
N MN M
N M
N M
N M
Model like this is inconsistent with much of the data
C
C
C
C
C
C
67
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Scattered distribution of chloroplasts
6868
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
69
Hypothesis 1: Ancestral AND Loss
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
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.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Cryptomonad
72
Some organisms have complicated membranes around their chloroplasts.
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
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N MC
Scattered distribution of chloroplasts
75
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
Symbiosis between two eukaryotic cells
77
N M
“Normal” eukaryote
Plantae representative with chloroplast
N M
C
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 79
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 80
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 81
NM
N
C
Symbiont
Host
Second mitochondria often lost
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 82
NM
C
Symbiont
Host
Second nucleus often lost
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.
84
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
85
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
88
Engulfment of Chlorophyte
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
91
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
92
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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 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
95
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
101
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N M
N M
N M
N M
N M
N MC NM
C NMC NM
C NMC
NMC
NMC
NMC
NMC
Many other secondary endosymbioses
Apicomplexans
Dinoflagellates
Amoebozoans
103
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•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
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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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
• Not colonial; live as single cells
• Some secrete shells or glue sand grains together to form a casing.
• Many pathogens
106
Amoebozoans: Loboseans
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Still Can’t Fit Model to Some Eukaryotes
108
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/full109
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
110
A community of brown algae: The marine kelp forest
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
111
Tertiary Symbioses?
“Normal” eukaryote
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
112
N MN M
C
Tertiary Symbioses?
“Normal” eukaryote
Euglenoid
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
N M
114
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 NMC
NMC NMC N MC
N MC
N MC
N MC
N MC
115
Tertiary endosymbioses?
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 116
• 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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 123
Bacteria Archaea Eukaryotes
Virus Evolution Model 1: The Fourth Domain
Viruses
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 124
Bacteria Archaea Eukaryotes
Virus Evolution Model 2: Separate Origin
Viruses
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 125
Bacteria Archaea EukaryotesViruses Viruses
Virus Evolution Model 3: From Within Other Groups