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



αProteoCell membrane

Genome

Genome


Host membrane

Endosymbiosis

Endosymbiosis: when an organism (the host) bring another organism (the symbiont) inside of its cell.


αProteoCell membrane

Genome

Genome


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


Origin of the nucleus

22

N

αProteo

Host membrane

Nucleus

Cell membrane

Genome

Genome



Mitochondria

23

N

Mitochondrion

Genome

MNucleus

Cell membrane

Genome


Different histories within one genome

24

Bacteria Archaea Eukaryotes

Nucleus

MitochondrionA model of a eukaryotic cell

Nuclear Tree

Mitochondrial Tree

Eukaryotes Bacteria ArchaeaB


Chimeras

25


Nucleus


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


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


N M

N M

N M

N M

N M

N M

N M

N M

N

++

++-+

+++




N M

N M

N M

N M

N M

N M


N M

N M

N M

N M

N M

N M

N M

N M

N

++

++-+

+++




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


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


MNucleus

Cell membrane

Nuclear Genome

Cyanobacterial Cell envelope

Cyanobacterial Genome Cyano


Engulfment

43

N

Mitochondrion


MNucleus

Cell membrane

Nuclear Genome


Cyanobacterial Genome Cyano


Endosymbiosis

44

N

Mitochondrion


MNucleus

Cell membrane

Nuclear Genome


Cyanobacterial Genome

Cyano

Is a “Primary symbiosis” because the symbiont has not experienced a prior symbiosis.


Chloroplast

45

N

Mitochondrion


MNucleus

Cell membrane

Nuclear Genome

Chloroplast Cell envelope

Chloroplast Genome

Chloroplast


Membrane lost in some

46

N

Mitochondrion


MNucleus

Cell membrane

Nuclear Genome

Outer cell membrane lost in some

Chloroplast Genome

Chloroplast


Cell wall lost in some

47

N

Mitochondrion


MNucleus

Cell membrane

Nuclear Genome


Chloroplast Genome

Chloroplast


N

Mitochondrion


MNucleus

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



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

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



6868


N MC

N MC

N MC

N MC

N MC

N MC


69

Hypothesis 1: Ancestral AND Loss


N MC

N MC

N MC

N MC

N MC

N MC


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

72

Some organisms have complicated membranes around their chloroplasts.


N MC

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 MC


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


NM

N M

C

Symbiont

Host

EndosymbiosisEndosymbiosis: when an organism (the host) bring another organism (the symbiont) inside of its cell.


NM

N M

C

Symbiont

Host

This is a “secondary” symbioses because the symbiont itself already was a host of other symbionts.

Endosymbiosis


NM

N

C

Symbiont

Host

Second mitochondria often lost


NM

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 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

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 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


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


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 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

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 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


101


Secondary Symbioses of Others

102


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


•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/full109

http://onlinelibrary.wiley.com/doi/10.1111/j.1550-7408.2007.00245.x/full


•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 MN M

C

Tertiary Symbioses?


Euglenoid


N M

Engulfment

113

N MN M

C


N M

114

N MN 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 MC NMC

NMC NMC N MC

N MC

N MC

N MC

N MC

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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