bis2c: lecture 7: the tree of life

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016

Lecture 7: The Tree of Life: I

BIS 002C Biodiversity & the Tree of Life

Spring 2016

Prof. Jonathan Eisen

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About Me

• At UC Davis since 2005 !UC Davis Genome Center !Dept. of Evolution and Ecology !Dept. of Medical Microbiology and Immunology

• Research: Evolution, ecology and function of communities of microbes

• Open Science • More info

!Tree of Life blog: phylogenomics.blogspot.com !Lab page: phylogenomics.wordpress.com !Twitter: @phylogenomics

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http://phylogenomics.blogspot.com

http://phylogenomics.wordpress.com

http://twitter.com/phylogenomics


Where we are going and where we have been

• Previous Lecture: !6: Inferring Trees

• Current Lecture: !7: The Tree of Life I

• Next Lecture: !8: The Tree of Life II

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• Brad Pitt movie

• Natural food remedies

• Art by the arboretum

• Name of my blog

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Tree of Life Imagery is Everywhere

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Thought Questions & Main Topics

• If you found life on another planet, how could you determine if it was related to life on Earth?

• What is the evidence that all life on Earth is related by a common descent and thus is on a single “Tree of Life”?

• What is the structure of the Tree of Life?

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Key Concepts from Previous Lectures

• Groupings in trees: monophyly, sister taxa, outgroup, ingroup

• Phylogeny inference

• Trees: polytomies, rooted, unrooted

• Trait evolution: ancestral & derived, homology

• Traits: data matrices, alignments

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Life on Mars

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• How would one determine if the Martian organisms are related to the Earth ones?

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Life on Mars


Are These Separate Trees or Connected?

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Life on EarthLife on Mars



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Evidence?

• How could one determine if organisms on Mars were related to organisms on Earth?

• (Assuming of course that Donald Trump is alive)

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Not Just A Thought Experiment

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Dawn Sumner - UC Davis Geology Professor

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http://geology.ucdavis.edu/people/faculty/sumner.php






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Diversity of Life

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Darwin - Tree or maybe Trees of Life

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“There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and wonderful have been, and are being, evolved.”

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 19

“There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and wonderful have been, and are being, evolved.”

Darwin - Tree or maybe Trees of Life



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Life on EarthLife on Earth

Multiple Origins of Life on Earth



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Single Origin of Life on Earth



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Single Origin of Life on Earth EVIDENCE????


Diversity of Life

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Universal Traits: Examples

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Universal Traits: Examples

! Made up of cells ! Use of DNA as a genetic material ! Use of ACTG in DNA ! Use of ACUG in RNA ! Three letter genetic code ! Central dogma (DNA -> RNA -> protein) ! Use water as a solvent ! Lipoprotein cell envelope ! 20 core amino acids in proteins ! Live on Earth ! Ribosome for translation ! RNA polymerase proteins ! Store energy in chemicals ! Pump compounds in and out of cells

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Homology vs. Homoplasy

• Homology: similarity that is due to inheritance from a common ancestor

• Homoplasy: similarity that has evolved independently

• For a trait to be evidence that all organisms are related it must be universal AND homologous

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! Made up of cells ! Use of DNA as a genetic material ! Use of ACTG in DNA ! Use of ACUG in RNA ! Three letter genetic code ! Central dogma (DNA -> RNA -> protein) ! Use water as a solvent ! Lipoprotein cell envelope ! 20 core amino acids in proteins ! Live on Earth ! Ribosome for translation ! RNA polymerase proteins ! Store energy in chemicals ! Pump compounds in and out of cells

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Universal Homologies

The existence of Universal Homologies means all life on Earth is related.


Central Dogma in All Organisms

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DNA, double stranded, w/ ACTG

RNA w/ ACUG

Transcription

Translated into Proteins

using tRNA using ribosomes using 3 letter code using 20 core amino acids

Lipoprotein Cell Envelope

Translation


Figure 14.6 The Genetic Code

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Figure 14.14 Ribosome Structure

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• Historical Trees of Life

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The Tree of Life

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Ernst Haeckel 1866

34www.mblwhoilibrary.org

Plantae AnimaliaProtista


Whittaker – Five Kingdoms 1969

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Plantae Animalia

Protista

Fungi

Monera


Prokaryotes vs. Eukaryotes

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EukaryotesProkaryotes



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Limitations of This?

• Are all prokaryotes the same?

• Should we define organisms by the absence of a trait?

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Possible Trees

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Tree 1

Prok Euk


Tree 2

Alternative Trees

Prok Euk


Tree 3

Alternative Trees

Prok Euk


Tree 4

Alternative Trees

Prok Euk


Clicker

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Which Tree is Most Parsimonious (character: nucleus)?

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Tree 1 Tree 2

Tree 3 Tree 4

A)Tree 1B)Tree 2C)Tree 1&2D)Tree 1&3E)Tree 1,2,&3

P E


Tree 1 Tree 2

Tree 3 Tree 4

P E

Which Tree is Most Parsimonious (character: nucleus)?

A)Tree 1B)Tree 2C)Tree 1&2D)Tree 1&3E)Tree 1,2,&3


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1

Which Tree is Most Parsimonious?

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Tree 1 Tree 2

Tree 3 Tree 4

P E

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How many character state changes needed?

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Tree 1


Eukaryotes

AncestralDerived

Prokaryotes

Tree 1 Possible Ancestry #1

How many character state changes needed?


Eukaryotes

Given this tree … can we infer ancestral state?

AncestralDerived

Prokaryotes



Eukaryotes


DerivedAncestral

Prokaryotes



Eukaryotes

DerivedAncestral


Prokaryotes



Clicker

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In Which Tree are Prokaryotes Monophyletic

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Tree 1 Tree 2

Tree 3 Tree 4

P E

A) Tree 1B) Tree 2C) Trees 1 & 3D) Trees 1 & 2E) Trees 1,2,3


In Which Tree are Prokaryotes Monophyletic?

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Tree 1 Tree 2

Tree 3 Tree 4

P E

A) Tree 1B) Tree 2C) Trees 1 & 3D) Trees 1 & 2E) Trees 1,2,3


In Which Tree are Prokaryotes Monophyletic?

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Tree 1 Tree 2

P E

Monophyletic Group = Clade

A monophyletic group includes all of the descendant species of a given common ancestor


In Which Tree are Eukaryotes Monophyletic

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Tree 1 Tree 2

Tree 3 Tree 4

P E


Conclusion

• Prokaryote vs eukaryote distinction does not tell us the topology of the tree

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• Historical Trees of Life

• The Modern Tree of Life

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Diversity of Life

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Carl Woese

http://mcb.illinois.edu/faculty/profile/1204

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Woese Tree of Life

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Woese Tree of Life

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rRNA rRNArRNA


Woese Tree of Life

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rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG


Woese Tree of Life

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rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

Taxa Characters S ACUGCACCUAUCGUUCG

E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG


Woese Tree of Life

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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


E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG


Woese Tree of Life

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rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG



E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG

Eukaryotes


Woese Tree of Life

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rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG



E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG

EukaryotesEubacteria


Woese Tree of Life

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rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG



E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG


????


Woese Tree of Life

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rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG



E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG



Woese Tree of Life

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rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG



E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG


Archaebacteria


Unrooted Tree of Life from Woese

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Simplified Three Domain Unrooted Tree of Life

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Eukaryotes

Archaebacteria Eubacteria


Archaea Dominate Extremely Hot Environments

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Archaea Dominate Extremely Salty Environments

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Table 26.1 The Three Domains of Life on Earth

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Eukaryotes

Archaebacteria Eubacteria



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Eukaryotes

Archaea Eubacteria



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Eukaryotes

Archaea Bacteria



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Eukaryotes

Archaea Bacteria



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Eukaryotes

Archaea Bacteria

Can You Tell Which Groups are Sister Taxa from this?



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Eukaryotes

Archaea Bacteria

What is Missing?


Clicker

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Clicker

How many different ways are there to root this tree? A: 0

B: 1 C: 2 D: 3

E: Not possible to determine

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Eukaryotes

Archaea Bacteria


Clicker

How many different ways are there to root this tree? A: 0

B: 1 C: 2 D: 3

E: Not possible to determine

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Eukaryotes

Archaea Bacteria



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Eukaryotes

Archaea Bacteria



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Eukaryotes

BacteriaArchaea



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Eukaryotes

Bacteria



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Eukaryotes

Bacteria

Archaea



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Bacteria

Archaea



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Bacteria

Archaea Eukaryotes



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Archaea Eukaryotes



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Archaea BacteriaEukaryotes



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Eukaryotes

Archaea Bacteria



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Eukaryotes

Archaea Bacteria



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Eukaryotes

Archaea Bacteria


A Polytomous Three Domain Tree of Life

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Bacteria Archaea Eukaryotes

Polytomy


Clicker Question

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Clicker

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How Many Distinct Ways To Resolve this Polytomy? A: 1 B: 2 C: 3 D: 4 E: Can’t tell

Bacteria EukaryotesArchaea


Clicker

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How Many Distinct Ways To Resolve this Polytomy? A: 1 B: 2 C: 3 D: 4 E: Can’t tell



Bacteria Eukaryotes

Archaea and Bacteria as Sister Groups

Archaea


Archaea

Eukaryotes and Archaea as Sister Groups

EukaryotesBacteria


Bacteria

Eukaryotes and Bacteria as Sister Groups

EukaryotesArchaea


Resolving the Tree of Life Polytomy

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Bacteria EukaryotesArchaea


Phylogenetic Inference

polytomy


polytomy

outgroup



outgroup



Outgroup


Outgroup for the Tree of Life?



Outgroup for the Tree of Life?