bis2c: lecture 7: the tree of life
TRANSCRIPT
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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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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
• Brad Pitt movie
• Natural food remedies
• Art by the arboretum
• Name of my blog
!4
Tree of Life Imagery is Everywhere
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Life on Mars
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Life on Mars
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Life on Mars
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
• How would one determine if the Martian organisms are related to the Earth ones?
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Life on Mars
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
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Life on EarthLife on Mars
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
11
Life on EarthLife on Mars
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
12
Life on EarthLife on Mars
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Not Just A Thought Experiment
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Dawn Sumner - UC Davis Geology Professor
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http://geology.ucdavis.edu/people/faculty/sumner.php
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Diversity of Life
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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.”
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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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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
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Life on EarthLife on Earth
Multiple Origins of Life on Earth
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
21
Life on EarthLife on Earth
Single Origin of Life on Earth
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
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Life on EarthLife on Earth
Single Origin of Life on Earth EVIDENCE????
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Diversity of Life
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Universal Traits: Examples
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
! 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.
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Figure 14.6 The Genetic Code
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Figure 14.14 Ribosome Structure
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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?
• Historical Trees of Life
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
The Tree of Life
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Ernst Haeckel 1866
34www.mblwhoilibrary.org
Plantae AnimaliaProtista
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Whittaker – Five Kingdoms 1969
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Plantae Animalia
Protista
Fungi
Monera
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Prokaryotes vs. Eukaryotes
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EukaryotesProkaryotes
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Prokaryotes vs. Eukaryotes
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EukaryotesProkaryotes
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Limitations of This?
• Are all prokaryotes the same?
• Should we define organisms by the absence of a trait?
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Prokaryotes vs. Eukaryotes
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Possible Trees
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Tree 1
Prok Euk
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Tree 2
Alternative Trees
Prok Euk
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Tree 3
Alternative Trees
Prok Euk
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Tree 4
Alternative Trees
Prok Euk
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 46
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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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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1
Which Tree is Most Parsimonious?
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Tree 1 Tree 2
Tree 3 Tree 4
P E
1
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
How many character state changes needed?
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EukaryotesProkaryotes
Tree 1
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 49
Eukaryotes
AncestralDerived
Prokaryotes
Tree 1 Possible Ancestry #1
How many character state changes needed?
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Eukaryotes
Given this tree … can we infer ancestral state?
AncestralDerived
Prokaryotes
Tree 1 Possible Ancestry #1
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Eukaryotes
Given this tree … can we infer ancestral state?
DerivedAncestral
Prokaryotes
Tree 1 Possible Ancestry #2
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Eukaryotes
DerivedAncestral
Given this tree … can we infer ancestral state?
Prokaryotes
Tree 1 Possible Ancestry #2
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
In Which Tree are Eukaryotes Monophyletic
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Tree 1 Tree 2
Tree 3 Tree 4
P E
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Conclusion
• Prokaryote vs eukaryote distinction does not tell us the topology of the tree
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
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?
• Historical Trees of Life
• The Modern Tree of Life
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Diversity of Life
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Carl Woese
http://mcb.illinois.edu/faculty/profile/1204
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
ACUGC ACCUAU CGUUCG
ACUCC AGCUAU CGAUCG
ACCCC AGCUCU CGCUCG
Taxa Characters S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
![Page 74: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/74.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
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
![Page 75: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/75.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
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
![Page 76: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/76.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
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
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
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
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
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
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
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
Eukaryotes
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
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
EukaryotesEubacteria
![Page 81: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/81.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
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
EukaryotesEubacteria
![Page 82: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/82.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
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
EukaryotesEubacteria
????
![Page 83: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/83.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
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
EukaryotesEubacteria
![Page 84: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/84.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
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
EukaryotesEubacteria
Archaebacteria
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Unrooted Tree of Life from Woese
63
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
64
Eukaryotes
Archaebacteria Eubacteria
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Archaea Dominate Extremely Hot Environments
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Archaea Dominate Extremely Salty Environments
66
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Table 26.1 The Three Domains of Life on Earth
67
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
68
Eukaryotes
Archaebacteria Eubacteria
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
69
Eukaryotes
Archaea Eubacteria
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
70
Eukaryotes
Archaea Bacteria
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
71
Eukaryotes
Archaea Bacteria
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
72
Eukaryotes
Archaea Bacteria
Can You Tell Which Groups are Sister Taxa from this?
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
73
Eukaryotes
Archaea Bacteria
What is Missing?
![Page 96: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/96.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
74
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
How many different ways are there to root this tree? A: 0
B: 1 C: 2 D: 3
E: Not possible to determine
75
Eukaryotes
Archaea Bacteria
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
How many different ways are there to root this tree? A: 0
B: 1 C: 2 D: 3
E: Not possible to determine
76
Eukaryotes
Archaea Bacteria
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
77
Eukaryotes
Archaea Bacteria
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
BacteriaArchaea
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
BacteriaArchaea
![Page 102: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/102.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
BacteriaArchaea
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
BacteriaArchaea
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
BacteriaArchaea
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
Archaea
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
Archaea
![Page 108: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/108.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
Archaea
![Page 109: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/109.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
Archaea
![Page 110: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/110.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
Archaea
![Page 111: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/111.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Bacteria
Archaea
![Page 112: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/112.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Bacteria
Archaea Eukaryotes
![Page 113: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/113.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Bacteria
Archaea Eukaryotes
![Page 114: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/114.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Bacteria
Archaea Eukaryotes
![Page 115: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/115.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Archaea Eukaryotes
![Page 116: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/116.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Archaea BacteriaEukaryotes
![Page 117: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/117.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
79
Eukaryotes
Archaea Bacteria
![Page 118: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/118.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
80
Eukaryotes
Archaea Bacteria
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
81
Eukaryotes
Archaea Bacteria
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
A Polytomous Three Domain Tree of Life
82
Bacteria Archaea Eukaryotes
Polytomy
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker Question
83
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
84
How Many Distinct Ways To Resolve this Polytomy? A: 1 B: 2 C: 3 D: 4 E: Can’t tell
Bacteria EukaryotesArchaea
![Page 123: BiS2C: Lecture 7: The Tree of Life](https://reader034.vdocuments.mx/reader034/viewer/2022042517/587c46091a28ab5a1d8b79d7/html5/thumbnails/123.jpg)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
85
How Many Distinct Ways To Resolve this Polytomy? A: 1 B: 2 C: 3 D: 4 E: Can’t tell
Bacteria Archaea Eukaryotes
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Bacteria Eukaryotes
Archaea and Bacteria as Sister Groups
Archaea
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Archaea
Eukaryotes and Archaea as Sister Groups
EukaryotesBacteria
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Bacteria
Eukaryotes and Bacteria as Sister Groups
EukaryotesArchaea
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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Resolving the Tree of Life Polytomy
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Bacteria EukaryotesArchaea
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Phylogenetic Inference
polytomy
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polytomy
outgroup
Phylogenetic Inference
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outgroup
Phylogenetic Inference
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Outgroup
Bacteria Archaea Eukaryotes
Outgroup for the Tree of Life?
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Bacteria Archaea Eukaryotes
Outgroup for the Tree of Life?