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

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Microbe Launch Today to ISS at 1:48 PST

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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



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

13

N

αProteo

Host membrane

Nucleus

Cell membrane

Genome

Genome



Mitochondria

14

N

Mitochondrion

Genome

MNucleus

Cell membrane

Genome


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


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 / archaeaDNA

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! S ACUGCACCUAUCGUUCG! R ACUCCACCUAUCGUUCG! E ACUCCAGCUAUCGAUCG! F ACUCCAGGUAUCGAUCG! C ACCCCAGCUCUCGCUCG! W ACCCCAGCUCUGGCUCG




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


B AMito B


Evidence

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


Evidence

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


Different histories within one genome

28

Bacteria Archaea EukaryotesBacteria ArchaeaEukaryotes Bacteria

Nucleus

MitochondrionA model of a eukaryotic cell

Nuclear Tree

Mitochondrial Tree


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



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?



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 …


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


MNucleus

Cell membrane

Nuclear Genome

Cyanobacterial Cell envelope

Cyanobacterial Genome Cyano


Engulfment

36

N

Mitochondrion


MNucleus

Cell membrane

Nuclear Genome


Cyanobacterial Genome Cyano


Endosymbiosis

37

N

Mitochondrion


MNucleus

Cell membrane

Nuclear Genome


Cyanobacterial Genome

Cyano

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


Chloroplast

38

N

Mitochondrion


MNucleus

Cell membrane

Nuclear Genome

Chloroplast Cell envelope

Chloroplast Genome

Chloroplast


Membrane lost in some

39

N

Mitochondrion


MNucleus

Cell membrane

Nuclear Genome

Outer cell membrane lost in some

Chloroplast Genome

Chloroplast


Cell wall lost in some

40

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?

42


Bacteria Archaea Eukaryotes

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

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Bacteria Archaea EukaryotesBacteria ArchaeaEukaryotes Bacteria

Nuclear Tree

Mitochondrial Tree

Nucleus

CPST

Bacteria ArchaeaEukaryotes BacteriaMITO

Chloroplast Tree


But ….

53


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

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Scattered distribution of chloroplasts

5555


N MC

N MC

N MC

N MC

N MC

N MC


56

Hypothesis 1: Ancestral AND Loss


Cryptomonad

57


N MC

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 MC


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


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

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 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

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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 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


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


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Secondary Symbioses of Diatoms

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Stramenopiles: Diatoms

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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


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 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


86


Secondary Symbioses of Others

87


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


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/full90

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

91

A community of brown algae: The marine kelp forest


N M

92

Tertiary Symbioses?



N M

93

N MN M

C

Tertiary Symbioses?


Euglenoid


N M

Engulfment

94

N MN M

C


N M

95

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 NM

C NMC NM

C N MC

N MC

N MC

N MC

N MC

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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