BiS2C: Lecture 7: The Tree of Life
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Transcript of 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
1
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?
5
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
6
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?
7
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Life on Mars
8
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Life on Mars
8
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Life on Mars
8
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?
9
Life on Mars
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
10
Life on EarthLife on Mars
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
11
Life on EarthLife on Mars
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
12
Life on EarthLife on Mars
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)
13
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
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?
16
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Diversity of Life
17
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Darwin - Tree or maybe Trees of Life
18
“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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
20
Life on EarthLife on Earth
Multiple Origins of Life on Earth
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Are These Separate Trees or Connected?
22
Life on EarthLife on Earth
Single Origin of Life on Earth EVIDENCE????
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Diversity of Life
23
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Universal Traits: Examples
24
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
26
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
27
Universal Homologies
The existence of Universal Homologies means all life on Earth is related.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Central Dogma in All Organisms
28
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Figure 14.6 The Genetic Code
29
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Figure 14.14 Ribosome Structure
30
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?
31
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
32
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
The Tree of Life
33
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Ernst Haeckel 1866
34www.mblwhoilibrary.org
Plantae AnimaliaProtista
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Whittaker – Five Kingdoms 1969
35
Plantae Animalia
Protista
Fungi
Monera
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Prokaryotes vs. Eukaryotes
36
EukaryotesProkaryotes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Prokaryotes vs. Eukaryotes
37
EukaryotesProkaryotes
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?
38
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Prokaryotes vs. Eukaryotes
39
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Possible Trees
40
Tree 1
Prok Euk
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 41
Tree 2
Alternative Trees
Prok Euk
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 42
Tree 3
Alternative Trees
Prok Euk
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 43
Tree 4
Alternative Trees
Prok Euk
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
44
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Which Tree is Most Parsimonious (character: nucleus)?
45
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
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
21
1
Which Tree is Most Parsimonious?
47
Tree 1 Tree 2
Tree 3 Tree 4
P E
1
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
How many character state changes needed?
48
EukaryotesProkaryotes
Tree 1
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?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 50
Eukaryotes
Given this tree … can we infer ancestral state?
AncestralDerived
Prokaryotes
Tree 1 Possible Ancestry #1
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 51
Eukaryotes
Given this tree … can we infer ancestral state?
DerivedAncestral
Prokaryotes
Tree 1 Possible Ancestry #2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 52
Eukaryotes
DerivedAncestral
Given this tree … can we infer ancestral state?
Prokaryotes
Tree 1 Possible Ancestry #2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
53
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
In Which Tree are Prokaryotes Monophyletic
54
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
In Which Tree are Prokaryotes Monophyletic?
55
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
In Which Tree are Prokaryotes Monophyletic?
56
Tree 1 Tree 2
P E
Monophyletic Group = Clade
A monophyletic group includes all of the descendant species of a given common ancestor
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
In Which Tree are Eukaryotes Monophyletic
57
Tree 1 Tree 2
Tree 3 Tree 4
P E
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
58
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
59
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Diversity of Life
60
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Carl Woese
http://mcb.illinois.edu/faculty/profile/1204
61
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Woese Tree of Life
62
rRNA rRNArRNA
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
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
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
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
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
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
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
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
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
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
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
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
????
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
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Unrooted Tree of Life from Woese
63
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
64
Eukaryotes
Archaebacteria Eubacteria
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Archaea Dominate Extremely Hot Environments
65
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Archaea Dominate Extremely Salty Environments
66
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Table 26.1 The Three Domains of Life on Earth
67
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
68
Eukaryotes
Archaebacteria Eubacteria
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
69
Eukaryotes
Archaea Eubacteria
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
70
Eukaryotes
Archaea Bacteria
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
71
Eukaryotes
Archaea Bacteria
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?
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?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker
74
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
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
77
Eukaryotes
Archaea Bacteria
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
BacteriaArchaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
BacteriaArchaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
BacteriaArchaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
BacteriaArchaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
BacteriaArchaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
Archaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
Archaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
Archaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
Archaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Eukaryotes
Bacteria
Archaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Bacteria
Archaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Bacteria
Archaea Eukaryotes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Bacteria
Archaea Eukaryotes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Bacteria
Archaea Eukaryotes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Archaea Eukaryotes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
78
Archaea BacteriaEukaryotes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
79
Eukaryotes
Archaea Bacteria
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
80
Eukaryotes
Archaea Bacteria
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Simplified Three Domain Unrooted Tree of Life
81
Eukaryotes
Archaea Bacteria
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
A Polytomous Three Domain Tree of Life
82
Bacteria Archaea Eukaryotes
Polytomy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Clicker Question
83
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
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 86
Bacteria Eukaryotes
Archaea and Bacteria as Sister Groups
Archaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 87
Archaea
Eukaryotes and Archaea as Sister Groups
EukaryotesBacteria
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 88
Bacteria
Eukaryotes and Bacteria as Sister Groups
EukaryotesArchaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Resolving the Tree of Life Polytomy
89
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 90
Bacteria EukaryotesArchaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 91
Phylogenetic Inference
polytomy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 92
polytomy
outgroup
Phylogenetic Inference
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 93
outgroup
Phylogenetic Inference
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 94
Outgroup
Bacteria Archaea Eukaryotes
Outgroup for the Tree of Life?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 95
Bacteria Archaea Eukaryotes
Outgroup for the Tree of Life?